U.S. Department of the Interior 

Interagency Land Retirement Team 

1243 N Street 

Fresno, California September 2005 

Land Retirement 

Demonstration Project 

Five-Year Report 
Cover photos: The imprinter used to plant native seed, restored native perennial shrub habitat, 

and an alkali scrub annual flower called Monolopia stricta or Crum's monolopia. 
Prepared for 

U.S. Department of the Interior 

Interagency Land Retirement Team 

1243 N Street 

Fresno, California September 2005 

Land Retirement 

Demonstration Project 

Five-Year Report 

Prepared by 

U.S. Department of the Interior 

Bureau of Reclamation 

Interagency Land Retirement Team 

1243 N Street 

Fresno, CA 93721-1813 

Siran Erysian 

Stephen L. Lee 

Robert May 

Bureau of Reclamation 

Technical Service Center 

PO Box 25007 

Denver, CO 80225-0007 

Joseph Brummer 

Jim Yahnke 

U.S. Fish & Wildlife Service 

Interagency Land Retirement Team 

1243 N Street 

Fresno, CA 93721-1813 

Beatrice A. Olsen 

Bureau of Land Management 

Fresno, CA 93721-1813 

Stephen Laymon 

Tracy Rowland 

California State University, Stanislaus 

Endangered Species Recovery Program 

1900 N Gateway Boulevard, Suite 101 

Fresno, CA 93727

Georgia Basso 

Krista R. Garcia 

Adrian J. Howard 

Patrick A. Kelly 

Amy J. Kokx 

Darren P. Newman 

Scott E. Phillips 

Nur P. Ritter 

Curtis E. Uptain 

Daniel F. Williams 

San Diego State University 

San Diego, CA 92182 

Stuart H. Hurlbert 

Acknowledgments 

iii 

Acknowledgments 

The Land Retirement Demonstration Project has been implemented with 

considerable team effort. Bob May (Bureau of Reclamation), Stephen Lee 

(Reclamation), Bea Olsen (U.S. Fish and Wildlife Service [FWS]), Tracy 

Rowland (Bureau of Land Management [BLM]), and Stephen Laymon (BLM) 

have had the daunting role of administration, land acquisition, agency 

coordination, and management of the Atwell Island land retirement site. Siran 

Erysian (Reclamation) provided Geographic Information System (GIS) support 

and maps for the physical impacts chapter and Scott Phillips (California State 

University [CSU], Stanislaus, Endangered Species Recovery Program [ESRP]) 

provided GIS support and maps for the remainder of the chapters. 

ESRP field staff (in addition to the authors) that contributed immense effort to 

this project include Howard Clark, Ellen Cypher, Scott Deal, Patrick Morrison, 

Richard Gebhardt, Emily Magill, Steve Messer, Laurie Williams, Kimberly 

Kreitinger, Jenn Haas, Michelle Selmon, Karen Dulik, Gene “Woody” Moise, 

Paul Brandy, Tamra Sandoval, Rachel Zwerdling-Morales, Geoff Gray, Rhianna 

Lee, Roberta Fargo, and Foung Vang. They, along with many of the authors, 

have spent many late nights, early mornings, and hot afternoons in the field. They 

have spent much time and effort organizing equipment, implementing research 

trials, maintaining an on-site nursery, sampling, entering and analyzing data, and 

writing progress reports and annual reports. Administrative support was provided 

by Cecilia Lopez, Cristina Lopez, Alicia Villegas, Jacqueline Furr, Daniela 

Giovannetti, and Heather Williams. 

Dr. Fred Schreiber (CSU Fresno) and Rain Healer (CSU Fresno) assisted with 

invertebrate identifications, and Dr. Norman Smith (Fresno County Agricultural 

Commission) assisted in invertebrate ecological classifications. Mr. Robert Jones 

and Billy Costello, our neighboring farmers, assisted in site maintenance, planted 

barley in the buffer areas surrounding the study plots, assisted with nursery 

maintenance and installing a variety of experimental trials. Staff from Richard F 

and F Contracting Inc., including Jeronimo Diaz, Valentina Diaz, Maria Diaz, 

Reyna Diaz, Francisco Rodriquez, and others spent a great deal of time and effort 

helping to plant, weed, and harvest the nursery. Richard Lopez at Westlands 

Water District (WWD) has been a tremendous help in guiding us through the 

convoluted web of water allocations, orders, and transfers. Without his help, we 

may well have needlessly spent a great deal of money on unused water. Battalion 

Chief Gary Karle, Captain Doug Johnson, and Fire Captain Specialist Josh 

Chrisman collaborated with us in writing a pre-fire management plan and 

provided methods to reduce fire hazard. 

We would like to thank Ray Laclergue and Bonnie Bladen of Intermountain 

Nursery for providing native plant materials and for giving invaluable advice for 
Land Retirement Demonstration Project 

Five Year Report 

iv 

growing native plants in our nursery. We purchased seed from Jody Miller at 

S and S seeds, David Gilpin at Pacific Coast Seeds, and Scott Stewart at 

ConservaSeed. They provided invaluable advice for our various restoration trials, 

as did John Anderson at Hedgerow Farms. David Dyer, at the Natural Resource 

Conservation Service’s Plant Materials Center in Lockeford, California, donated 

some plant materials and provided advice during the installation of our own seed 

processing facility. 

Willard Schaff and William House provided native seed collecting services. 

Andy Pon, at Westside Transplants, allowed us to use his seed cleaning 

equipment and advised us on nursery practices. John Stebbins at California State 

University, Fresno, provided space in a lathe house for growing seedlings. The 

California Department of Fish and Game, Fresno West Golf and Country Club, 

Westlands Water District, and Paul Lanfranco granted us permission to collect 

native seed from various locations in Fresno County. Richard Kochevar at New 

Mexico Department of Agriculture, State Seed Laboratory, performed seed testing 

on our native seed collections. Robert J. Huddleston and Richard Knoernschild of 

the Mendota Wildlife Area provided storage space for our tractor and implements, 

seed, and other materials. Dr. Ted St. John provided information that enabled us 

to build a seed imprinter. Sherrill Campbell at HCL Machineworks assisted in 

developing and constructing modifications to the imprinter to improve seed 

imprinting. 
Contents 

v 

Contents 

Page 

Acknowledgments ................................................................................................iii

Acronyms and Abbreviations .......................................................................... xvii

Executive Summary........................................................................................... xix

Chapter 1. Introduction........................................................................................ 1

1.1. Background................................................................................................ 1 

1.2. Development, Implementation, and Scope of the Land Retirement 

Demonstration Project ............................................................................. 3 

1.3. Tranquillity Project Site Location and Description ................................... 5 

1.4. Literature Cited .......................................................................................... 7 

Chapter 2. Physical Impacts of Agricultural Land Retirement in the 

San Joaquin Valley ...................................................................................... 9

2.1. Introduction................................................................................................ 9 

2.2. Tranquillity Site ....................................................................................... 10 

2.2.1. Geology ......................................................................................... 10 

2.2.2. Soils ............................................................................................... 10 

2.2.3. Groundwater .................................................................................. 13 

2.2.4. Climate and Weather ..................................................................... 14 

2.2.5. Irrigation ........................................................................................ 16 

2.2.6. Monitoring of Selenium Levels..................................................... 16 

2.2.6.1. Surface Water Monitoring ............................................... 16 

2.2.6.2. Soil Monitoring................................................................ 17 

2.2.6.3. Soil Chemical Analyses ................................................... 19 

2.2.6.4. Groundwater Level Monitoring ....................................... 19 

2.2.6.5. Groundwater Quality Monitoring .................................... 21 

2.2.7. Groundwater Response to Land Retirement.................................. 22 

2.2.8. Groundwater Quality ..................................................................... 32 

2.2.8.1. Groundwater Salinity....................................................... 32 

2.2.8.2. Groundwater Major Ion Chemistry.................................. 32 

2.2.8.3. Trace Elements in Groundwater ...................................... 35 

2.2.8.4. Selenium Trend in Groundwater...................................... 38 

2.2.8.5. Boron in Groundwater ..................................................... 44 

2.2.8.6. Origin and Isotopic Composition of Groundwater .......... 44 

2.2.8.7. Groundwater Age............................................................. 45 

2.2.9. Evaporative Concentration of Shallow Groundwater.................... 46 

2.2.10. Trend Analysis for Soils.............................................................. 48 

2.2.11. Change Detection Analyses......................................................... 51

2.2.12. Soil Interpretive Summary........................................................... 52 

2.2.13. Conclusions ................................................................................. 59 
Land Retirement Demonstration Project 

Five Year Report 

vi 

2.3. Atwell Island Site..................................................................................... 60 

2.3.1. Geology ......................................................................................... 60 

2.3.2. Soils ............................................................................................... 60 

2.3.3. Weather.......................................................................................... 67 

2.3.4. Irrigation ........................................................................................ 67 

2.3.5. Hydrology and Surface Water Monitoring.................................... 68 

2.3.6. Groundwater Level Monitoring..................................................... 69 

2.3.7. Groundwater Quality Monitoring.................................................. 69 

2.3.7.1. Groundwater Response to Land Retirement.................... 71 

2.3.7.2. Groundwater Salinity....................................................... 71 

2.3.7.3. Groundwater Major Ion Chemistry.................................. 72 

2.3.7.4. Selenium in Groundwater ................................................ 73 

2.3.8. Conclusions ................................................................................... 73 

2.4. Literature Cited ........................................................................................ 74 

Chapter 3. Selenium Levels of Biota from Retired Agricultural Lands 

in the San Joaquin Valley, California ...................................................... 79

3.1. Introduction.............................................................................................. 79 

3.2. Methods.................................................................................................... 81 

3.3. Results...................................................................................................... 83 

3.3.1. Plants ............................................................................................. 83 

3.3.2. Invertebrates .................................................................................. 90 

3.3.3. Small Mammals............................................................................. 96 

3.4. Discussion and Conclusions .................................................................. 101 

3.5. Literature Cited ...................................................................................... 103 

Chapter 4. Results of a Habitat Restoration Study on Retired 

Agricultural Lands in the San Joaquin Valley, California .................. 107

4.1. Introduction............................................................................................ 107 

4.2. Methods.................................................................................................. 108 

4.2.1. Study Design ............................................................................... 108 

4.2.2. Restoration Methods.................................................................... 108 

4.2.3. Plot-Level Monitoring ................................................................. 111 

4.2.3.1. Vegetation Survey Methods........................................... 111 

4.2.3.2. Invertebrates................................................................... 112 

4.2.3.3. Amphibians and Reptiles ............................................... 114 

4.2.3.4. Birds............................................................................... 114 

4.2.3.5. Small Mammals ............................................................. 115 

4.2.4. Site-Wide Surveys ....................................................................... 115 

4.2.4.1. Spotlighting Surveys...................................................... 115 

4.2.4.2. Track Station Surveys.................................................... 116 

4.2.4.3. Winter Raptor Surveys................................................... 117 

4.2.4.4. Statistical Analysis of Vegetation Data ......................... 118 

4.2.4.5. Analysis of Data for the Other Biotic Groups ............... 119 
Contents 

vii 

4.3. Results.................................................................................................... 120 

4.3.1. Plot-Level Monitoring ................................................................. 120 

4.3.1.1. Vegetation...................................................................... 120 

4.3.1.2. Invertebrates................................................................... 129 

4.3.1.3. Amphibians and Reptiles ............................................... 134 

4.3.1.4. Birds............................................................................... 135 

4.3.1.5. Small Mammals ............................................................. 144 

4.3.2. Site-Wide Surveys ....................................................................... 146 

4.3.2.1. Spotlighting Surveys...................................................... 146 

4.3.2.2. Track Station Surveys.................................................... 151 

4.3.2.3. Winter Raptor Surveys................................................... 155 

4.4. Discussion.............................................................................................. 156 

4.4.1. Vegetation.................................................................................... 156 

4.4.2. Invertebrates ................................................................................ 158 

4.4.3. Amphibians and Reptiles............................................................. 160 

4.4.4. Birds............................................................................................. 161 

4.4.5. Small Mammals........................................................................... 163 

4.4.6. Site-Wide Surveys ....................................................................... 163 

4.4.6.1. Spotlighting Surveys...................................................... 163 

4.4.6.2. Track Station Surveys.................................................... 164 

4.4.6.3. Winter Raptor Surveys................................................... 164 

4.5. Conclusions and Recommendations ...................................................... 165 

4.5.1. Conclusions ................................................................................. 165 

4.5.2 Recommendations......................................................................168 

4.6. Literature Cited ...................................................................................... 170 

Chapter 5. Overview of the Implications and Concerns of Agricultural 

Land Retirement in the San Joaquin Valley, California..................... 177

5.1. Declining Groundwater.......................................................................... 178 

5.2. Selenium in Groundwater ...................................................................... 178 

5.3. Selenium in Soil..................................................................................... 178 

5.4. Selenium Concentrations in Biota ......................................................... 179 

5.5. Surface Water Ponding .......................................................................... 179 

5.6. Wildlife Abundance, Diversity, and Recovery of Sensitive Species..... 179 

5.7. Restoration Challenges and Techniques ................................................ 180 

5.8. Agricultural Pests................................................................................... 183 

5.9. Recommendation ................................................................................... 183

Appendix 1. CVPIA Land Retirement Program Chronology

Appendix 2. Compliance with Biological Opinion 

Appendix 3. Research and Restoration 
Land Retirement Demonstration Project 

Five Year Report 

viii 

Tables 

Table 2-1. Estimates of Natural drainage rates and vertical permeability at 

the Tranquillity site. ...................................................................................... 29 

Table 2-2. Groundwater level decline observed in fifteen wells at the 

Tranquillity site for the time period from October 1999 

to October 2004............................................................................................. 30 

Table 2-3. Baseline year groundwater quality data for shallow wells at the 

Tranquillity site — major ions and field parameters. ................................... 33 

Table 2--4. Baseline year groundwater quality data for deep wells at the 

Tranquillity site — major ions and field parameters. ................................... 33 

Table 2--5. Baseline groundwater quality data for shallow wells at the 

Tranquillity site — trace elements and tritium. ............................................ 34 

Table 2-6. Baseline groundwater quality data for deep wells at the 

Tranquillity site— trace elements and tritium. ............................................. 34 

Table 2-7. Summary statistics for selenium concentrations measured in 

groundwater samples taken from Coast Range deposits for the 5 years 

of groundwater monitoring at the Tranquillity Site. .................................... 38 

Table 2-8. Analysis of seasonality of selenium data based on KruskalWallis 1-way ANOVA................................................................................. 39 

Table 2-9. Parametric and nonparametric correlations of selenium 

concentration in the Tranquillity wells on time ............................................ 40 

Table 2-10. Summary of results of linear and nonlinear trends without and 

with adjustment for outliers. ......................................................................... 41 

Table 2-11. Change detection analyses for COCs in soil at the 

Tranquillity site............................................................................................. 52 

Table 2-12. Comparison of total selenium concentrations at the 

Tranquillity site to Western U.S. and San Joaquin Valley soils. .................. 52 

Table 2-13. Average soluble to total selenium percentages all sites 

at Tranquillity................................................................................................ 53 

Table 2-14. Total selenium (mg/kg dry soil) ....................................................... 63 

Table 2-15. Soluble selenium 1-5 extract (mg/kg dry soil) ................................. 63 

Table 2-16. A comparison of total selenium concentrations with soluble 

selenium concentrations................................................................................ 64 

Table 2-17. Soil salinity (ECe dS/m) at the Atwell Island site ............................ 65 

Table 2-18. Soluble boron 1-5 extract (mg/kg dry soil) at the 

Atwell Island site. ......................................................................................... 66 

Table 2-19. Estimated 2002 net crop water requirement and deep 

percolation losses at the Atwell Island site. .................................................. 68 
Contents 

ix 

Table 2-20. Baseline groundwater quality data for shallow wells at the 

Atwell Island site - major ions, field parameters, and selenium. ................ 72 

Table 3-1. List of biotic groups monitored, corresponding performance 

standards (USFWS 1999), and an indication whether performance 

standards were met. ..................................................................................... 80 

Table 3-2. Geometric means (Mean), sample size (N), number of nondetects (ND), minimum (Min), maximum (Max), and standard 

deviation factor (SD factor) of selenium concentrations (mg/kg dry 

weight) in plant species collected from Tranquillity, 1999 to 2003. ............ 85 

Table 3-3. Geometric means (Mean), sample size (N), number of nondetects (ND), minimum (Min), maximum (Max), and standard 

deviation factor (SD factor) of selenium concentrations (mg/kg dry 

weight) in plant species collected from Atwell Island, 2000 to 2002........... 86 

Table 3-4. Results of analysis of variance tests of selenium concentrations 

(mg/kg dry weight) between sample years in plant species collected 

from Tranquillity, 1999 to 2003. ................................................................. 87 

Table 3-5. Results of Analysis of Variance tests of selenium concentrations 

(mg/kg dry weight) between sample years in plant species collected 

from Atwell Island, 2000 to 2002. .............................................................. 87 

Table 3-6. List of plant samples from Tranquillity that exceeded the 

population-level performance standard (2.0 mg/kg). .................................. 88 

Table 3-7. Results of Analysis of Variance tests of selenium concentrations 

(mg/kg dry weight) between landform types in plant species collected 

from Tranquillity, 1999 to 2003. ................................................................. 88 

Table 3-8. Results of Analysis of Variance tests of selenium concentrations 

(mg/kg) between landform types in plant species collected from Atwell 

Island, 2000 to 2002. ................................................................................... 89 

Table 3-9. Results of Analysis of Variance tests of selenium concentrations 

(mg/kg) between plant parts in plant species collected from 

Tranquillity, 1999 to 2003. . ........................................................................ 90 

Table 3-10. Results of Analysis of Variance tests of selenium 

concentrations (mg/kg) between plant parts in plant species collected 

from Atwell Island, 2000 to 2002. . ............................................................. 90 

Table 4-1. Overview of shrub island planting, Tranquillity HRS. Figures in 

the Initial Planting columns indicate the number of individuals that 

were initially transplanted to each island.................................................... 110 

Table 4-2. Plot-level survey dates for the various biotic groups, 1999 to 

2003. .......................................................................................................... 112 

Table 4-3. Dates of spotlighting surveys, track station surveys, and winter 

raptor surveys conducted from 1999 to 2003. ............................................ 116 
Land Retirement Demonstration Project 

Five Year Report 

x 

Table 4-4. Overall vegetation species richness in the Tranquillity HRS 

study plots. . ............................................................................................... 120 

Table 4-5. Species imprinted in the Tranquillity HRS Plots (1999), and an 

overview of those imprinted species noted in the quadrats during 

spring vegetation monitoring, 2000-2003................................................... 121 

Table 4-6. Non-imprinted, native species (excluding Atriplex argentea) 

noted in the quadrats during spring vegetation monitoring in the 

Tranquillity HRS, 1999-2003. .................................................................... 122 

Table 4-7. All species noted in the quadrats during spring vegetation 

monitoring in the Tranquillity HRS, 2003, including species code, 

common name, life-form, origin, mean percent cover, and relative 

abundance. ................................................................................................ 123 

Table 4-8. Invertebrate families collected on the Tranquillity study 

plots that contain agriculturally beneficial species, 1999 to 2003. ............. 133 

Table 4-9. Invertebrate families collected on the Tranquillity study plots 

that contain agricultural pest species, 1999 to 2003. .................................. 134 

Table 4-10. Diversity of amphibians and reptiles observed at Tranquillity 

1999-2003. .................................................................................................. 135 

Table 4-11. Special status bird species observed on the Tranquillity study 

plots, 1999 to 2003. ................................................................................... 135 

Table 4-12. Blocks with the highest mean richness of birds, season and 

year of occurrence, and the magnitude of difference from other blocks. ... 136 

Table 4-13. Blocks with the highest mean abundance of birds, season and 

year of occurrence, and the magnitude of difference from other blocks. ... 138 

Table 4-14. Blocks with the highest mean abundance of grassland obligate 

birds, grassland facultative birds, and other birds, season and year of 

occurrence, and the magnitude of difference from other blocks................. 139 

Table 4-15. Nest abundance and species richness, 2002 and 2003. 

Parentheses indicate nest numbers off study plot areas and asterisks 

indicate nests not monitored. ...................................................................... 140 

Table 4-16. Mean nest initiation dates, mean fledging dates, mean clutch 

size, and nesting success rates of bird species nesting on the 

Tranquillity study site, 2002 and 2003. ...................................................... 142 

Table 4-17. Vegetative composition and ground cover at mallard and 

red-winged blackbird nests. ........................................................................ 143 

Table 4-18. The number of small mammals captured in live traps and 

pitfall traps on the Habitat Restoration Study plots, Tranquillity site, 

1999 to 2003. .............................................................................................. 144 

Table 4-19. The number of ornate shrews (Sorex ornatus), California voles 

(Microtus californicus), and Botta’s pocket gophers captured in the 

pitfall traps at the Tranquillity study site, 1999 to 2003. ............................ 145 
Contents 

xi 

Table 4-20. Rates of observation (mean number per kilometer) of wildlife 

species observed during spotlight surveys conducted near Tranquillity, 

California, 1999 to 2003. Asterisks denote zero observations................... 148 

Table 4-21. Annual numbers and mean rates of visitation of wildlife at 

track stations established at the Tranquillity site, 1999 to 2003. 

Asterisks denote zero observations............................................................. 152 

Table 4-22. Seasonal mean rates of visitation of wildlife at track stations 

established at the Tranquillity site, 1999 to 2003. . ................................... 153 

Table 4-23. Frequency and rate of bird species encountered at the 

Tranquillity site, 1999 to 2003 during winter raptor surveys. .................... 156 

Table A3-1. Annual monitoring activities on the Habitat Restoration Study 

plots (Tranquillity site), 1999-2003, with the number of times each 

survey was conducted per year. ...................................................................... 4 

Table A3-2. Annual site-wide monitoring activities at the Tranquillity site, 

1999-2003, with the number of times each survey was conducted per 

year.................................................................................................................. 4 

Table A3-3. Annual monitoring activities on the Habitat Restoration Study 

plots (Atwell Island site) 2001-02, with the number of times each 

survey was conducted per year. ...................................................................... 5 

Figures 

Figure 1-1. Drainage-impaired lands in the San Joaquin Valley........................... 2 

Figure 1-2. Location of the Tranquillity site including the 178 ha (440 ac) 

North Avenue parcel and the 16 ha (40 ac) Manning Avenue parcel............. 6 

Figure 2-1. U.S. Department of Agriculture soil mapping units, 

Tranquillity site............................................................................................. 12 

Figure 2-2. Conceptual site model for groundwater conditions at the 

Tranquillity site............................................................................................. 14 

Figure 2-3. Monthly precipitation at CIMIS Station 105, Westlands Water 

District, near the Tranquillity site (1993-2003). ........................................... 15 

Figure 2-4. Annual precipitation at CIMIS Station 105, Westlands Water 

District, near the Tranquillity site (1993-2003). ........................................... 15 

Figure 2-5. Soil sample locations at the Tranquillity site. ................................... 18 

Figure 2-6. Monitor well and sump location map, Tranquillity site.................... 20 

Figure 2-7. Hydrographs for three agricultural drain sumps at the 

Tranquillity site showing a declining shallow groundwater trend................ 23 

Figure 2-8. Hydrographs for the monitor well cluster site 325 and 326 at 

the Tranquillity site showing a declining shallow groundwater trend 

and vertical (downward) hydraulic gradient. ................................................ 24 
Land Retirement Demonstration Project 

Five Year Report 

xii 

Figure 2-9. Hydrographs for monitor wells 15M1 and 16A1 at the 

Tranquillity site showing a declining shallow groundwater trend................ 24 

Figure 2-10. Depth to shallow groundwater, October 1999. The project 

area underlain by shallow groundwater within 2.1 m (7 feet) of the 

land surface is approximately 243 ha (600 acres)......................................... 25 

Figure 2-11. Depth to shallow groundwater, October 2000. The project 

area underlain by shallow groundwater within 2.1 m (7 feet) of the 

land surface is approximately 22 ha (55 acres)............................................. 26 

Figure 2-12. Depth to shallow groundwater, October 2001. The project 

area underlain by shallow groundwater within 2.1 m (7 feet) of the 

land surface is approximately 14 ha (34 acres)............................................. 27 

Figure 2-13. Contour map showing spatial distribution of net water table 

declines at the Tranquillity site from October 1999 to October 2004. ......... 31 

Figure 2-14. Comparison of dominant major ion concentrations and 

electrical conductivity for groundwater samples from shallow and deep 

wells. ............................................................................................................. 35 

Figure 2-15. Ratio of selenium to manganese (Se/Mn) concentration in 

groundwater samples plotted verses well depth. The Se/Mn ratio 

shows a decreasing trend with depth indicating oxidizing geochemical 

conditions in the shallow wells and reducing conditions in the deep 

wells. ............................................................................................................. 37 

Figure 2-16. Boxplots of selenium concentrations in Coast Range deposits 

for the 5 years of groundwater sampling at the Tranquillity site. The 

inner black boxes represent the 95 percent confidence interval of the 

median concentration. ................................................................................... 38 

Figure 2-17. Selenium data and trend in well 16B1 along with “best fit” 

nonlinear regression [Sinusoidal Fit: y=a+b*cos(cx+d)]............................. 42 

Figure 2-18. Selenium data and trend in well 16B1 without outlier datum 

along with “best fit” nonlinear regression - [Sinusoidal Fit: 

y=a+b*cos(cx+d)]......................................................................................... 42 

Figure 2-19. Selenium data and trend in well 16B1 along with “best fit” 

nonlinear regression - [Harris Model: y=1/(a+bxc

)]. .................................... 43 

Figure 2-20. Selenium data and trend in well 16Q1 along with ‘best fit” 

nonlinear regression - [Rational Function: y=(a+bx)/(1+cx+dx2

)]............... 43 

Figure 2-21. Plot of stable isotope data for groundwater samples from the 

Tranquillity site indicating the shallow groundwater has undergone 

significant evaporation.................................................................................. 45 

Figure 2-22. Photos of open surface cracks in Tranquillity clay soils at the 

Tranquillity site (Jan 2005)........................................................................... 47 

Figure 2-23. ECe Trends in top foot of soil from 1999 to 2004........................... 48 

Figure 2-24. ECe Trends in 2 to 3 foot depth of soil from 1999 to 2004............. 49 

Figure 2-25. ECe Trends in 4 to 5 foot depth of soil from 1999 to 2004............. 49 
Contents 

xiii 

Figure 2-26. Soluble selenium trends in top foot of soil from 1999 to 2004....... 49 

Figure 2-27. Soluble selenium trends in 2 to 3-foot depths of soil from 

1999 to 2004. ................................................................................................ 50 

Figure 2-28. Soluble selenium trends in 4 to 5 foot depths of soil from 1999 

to 2004. ......................................................................................................... 50 

Figure 2-29. Total selenium trends in top foot of soil from 1999 to 2004. ......... 50 

Figure 2-30. Total selenium trends in 2 to 3 foot depth from 1999 to 2004........ 51 

Figure 2-31. Total selenium trends in 4 to 5 foot depth from 1999 to 2004........ 51 

Figure 2-32. Total selenium concentrations in surface soils 0-30 cm (0-1 

foot) at the Tranquillity site from the 2004 sampling event. ........................ 55 

Figure 2-33. Soluble selenium in surface soils 0-30 cm (0-1 foot) at the 

Tranquillity site from the 2004 sampling event............................................ 56 

Figure 2-34. Soluble boron concentrations in the surface soils 0-30 cm (0-1 

foot) at the Tranquillity site from the 2004 sampling event. ........................ 57 

Figure 2-35. Soil salinity (ECe) concentrations (dS/m) in the surface soils 

0-30 cm (0-1 foot) at the Tranquillity site from the 2004 sampling 

event.............................................................................................................. 58 

Figure 2-36. U.S. Department of Agriculture soil mapping units and soil 

sample locations at the Atwell Island site..................................................... 62 

Figure 2-37. Monitor well locations at the Atwell Island site. ............................ 70 

Figure 2-38. Hydrographs of groundwater levels observed in Wells 5B3 

and 5B4 showing pre-project and post-project groundwater levels.............. 71 

Figure 3-1. Geometric means (solid circles) and error bars (mean 

multiplied by and divided by one standard deviation factor) of 

selenium concentrations in crickets collected from the Tranquillity and 

Atwell Island study sites. ............................................................................ 92 

Figure 3-2. Geometric means (solid circles) and error bars (mean 

multiplied by and divided by one standard deviation factor) of 

selenium concentrations in beetles collected from the Tranquillity and 

Atwell Island study sites. ............................................................................ 93 

Figure 3-3. Geometric means (solid circles) and error bars (mean 

multiplied by and divided by one standard deviation factor) of 

selenium concentrations in spiders collected from the Tranquillity and 

Atwell Island study sites. ............................................................................ 94 

Figure 3-4. Geometric means (solid circles) and error bars (mean 

multiplied by and divided by one standard deviation factor) of 

selenium concentrations in isopods collected from the Tranquillity and 

Atwell Island study sites. ............................................................................ 95 

Figure 3-5. Geometric means (solid circles) and error bars (mean 

multiplied by and divided by one standard deviation factor) of 

selenium concentrations in deer mouse (PEMA) bodies collected from 

Tranquillity and Atwell Island. ................................................................... 97 
Land Retirement Demonstration Project 

Five Year Report 

xiv 

Figure 3-6. Geometric means (solid circles) and error bars (geometric mean 

multiplied by and divided by one standard deviation factor) of 

selenium concentrations in deer mouse (PEMA) livers collected from 

Tranquillity and Atwell Island. ................................................................... 98 

Figure 3-7. Geometric means of selenium concentrations in deer mouse 

(PEMA) bodies and livers collected from irrigated and non-irrigated 

lands at Tranquillity, 1999 to 2003. .............................................................. 99 

Figure 3-8. Geometric means (solid circles) and error bars (geometric mean 

multiplied by and divided by one standard deviation factor) of 

selenium concentrations in shrew (SOOR) bodies collected from 

Tranquillity. .............................................................................................. 100 

Figure 3-9. Geometric means (solid circles) and standard deviations of 

selenium concentrations in shrew (SOOR) livers collected from the 

Tranquillity study site. .............................................................................. 101 

Figure 4-1. Map of the Tranquillity HRS plots showing treatments and 

blocks. ....................................................................................................... 109 

Figure 4-2. Locations of pitfall arrays, amphibian and reptile coverboards, 

avian transects and point-count locations, and small mammal trapping 

lines on a study plot at the Tranquillity site................................................ 113 

Figure 4-3. Locations of the spotlight survey route, track stations, and 

winter raptor survey route, 1999 to 2003.................................................... 117 

Figure 4-4. Distribution of Bromus madritensis (red brome) at the 

Tranquillity HRS, 2003. Each small rectangle represents a ‘sextant’; 

i.e., the portion of the plot in which a particular group of four sampling 

quadrats was located. ................................................................................ 124 

Figure 4-5. Distribution of Sisymbrium irio (London rocket) at the 

Tranquillity HRS. Each small rectangle represents a ‘sextant’, i.e., the 

portion of the plot in which a particular group of four sampling 

quadrats was located. ................................................................................ 125 

Figure 4-6. Species rank-abundance by treatment, Tranquillity HRS Plots 

2003. Species letter codes correspond to those presented in Table 4-7. ... 127 

Figure 4-7. Species rank-abundance by treatment, Tranquillity HRS Plots 

2003. ......................................................................................................... 128 

Figure 4-8. Ordinal richness of invertebrates for all treatments in 1999 to 

2003. .......................................................................................................... 130 

Figure 4-9. Mean invertebrate abundance for all treatments in 1999 to 

2003. .......................................................................................................... 131 

Figure 4-10. Mean abundance of Coleoptera and Araneae for all treatments 

in 1999 to 2003. ........................................................................................ 132 

Figure 4-11. Mean richness of birds by treatment in winter, spring, 

summer, and fall 1999 to 2003. . ............................................................... 136 
Contents 

xv 

Figure 4-12. Mean abundance of birds by treatment in winter, spring, 

summer, and fall 1999 to 2003. ................................................................ 137 

Figure 4-13. Mean abundance (mean number of birds observed per plot per 

day, all seasons combined) of obligate grassland birds, facultative 

grassland birds, and other birds, 1999 to 2003. .......................................... 138 

Figure 4-14. Mean abundance of grassland obligates and facultative birds 

by treatment, 1999 to 2003. ........................................................................ 139 

Figure 4-15. Locations of bird nests found in 2002 at the Tranquillity 

study site. .................................................................................................... 141 

Figure 4-16. Locations of bird nests found in 2003 at the Tranquillity 

study site. .................................................................................................... 141 

Figure 4-17. Mean abundance of small mammals per 120 trap nights in 

winter, spring, summer, and fall at the Tranquillity study site, 1999 to 

2003. .......................................................................................................... 146 

Figure 4-18. Annual wildlife abundance observed during spotlight surveys 

conducted near Tranquillity, California, 1999 to 2003............................... 147 

Figure 4-19. Seasonal abundance of wildlife observed during spotlight 

surveys conducted near Tranquillity, California, 1999 to 2003.................. 149 

Figure 4-20. Abundance of barn owls (Tyto alba) and western burrowing 

owls (Athene cunicularia hypugea) observed during spotlight surveys 

conducted near Tranquillity, California, 1999 to 2003............................... 150 

Figure 4-21. Abundance of desert cottontails (Sylvilagus auduboni) and 

black-tailed hares (Lepus californicus) observed during summer 

spotlight surveys conducted near Tranquillity, California, 1999 

to 2003. ....................................................................................................... 150 

Figure 4-22. Seasonal abundance of coyotes (Canis latrans) and domestic 

dogs (Canis familiaris) observed during spotlight surveys conducted 

near Tranquillity, California, 1999 to 2003. ............................................... 151 

Figure 4-23. The yearly abundance (mean rate of visitation) of wildlife 

during track station surveys conducted at the Tranquillity site, 

1999 to 2003. .............................................................................................. 154 

Figure 4-24. The seasonal abundance (mean rate of visitation) of wildlife at 

track stations established at the Tranquillity site, 1999 to 2003. ................ 154 

Acronyms and Abbreviations 

xvii 

Acronyms and Abbreviations 

ac Acres 

AIWD Atwell Island Water District 

ANOVA Analysis of variance 

BLM Bureau of Land Management 

BO Biological Opinion 

CDFG California Department of Fish and Game 

CDWR California Department of Water Resources 

CIMIS California Irrigation Management Information System 

cm Centimeters 

CNDDB California Natural Diversity Database 

COC Constituents of concern 

CVP Central Valley Project 

CVPIA Central Valley Project Improvement Act 

DOI Department of the Interior 

dS/m DeciSiemens per meter 

EA Environmental Assessment 

EC Electrical conductivity 

EPA Environmental Protection Agency 

ER Ecological Reserve 

ESRI Environmental Systems Research Institute 

ESRP Endangered Species Recovery Program 

EUP Experimental Use Permit 

ft Foot or feet 

FWS U.S. Fish and Wildlife Service 

GIS Geographic Information System 

GPS Global Positioning System 

ha Hectares 

HRS Habitat Restoration Study 

IPM Integrated pest management 

km Kilometer 

LRDP Land Retirement Demonstration Project 

LRP Land Retirement Program 

LRT Land Retirement Team 

m Meter 

mg/kg Milligrams per kilogram 

mi Miles 

μg/L Micrograms per liter 

μS/cm MicroSiemens/centimeter 

mg/L Milligrams per liter 

mm Millimeter 

MOU Memorandum of Understanding 

msl Mean sea level 

NRCS Natural Resources Conservation Service 
Land Retirement Demonstration Project 

xviii 

NWR National Wildlife Refuge 

PEMA Deer mouse 

pH Symbol for logarithm of the reciprocal of hydrogen 

ion concentration in gram atoms per liter 

ppb Parts per billion 

ppm Parts per million 

PVC Polyvinyl Choride 

QAPP Quality Assurance Project Plan 

REC Recognized environmental condition 

Reclamation Bureau of Reclamation 

SJVDP San Joaquin Valley Drainage Program 

TU Tritium units 

USDA U.S. Department of Agriculture 

USDI U.S. Department of the Interior 

USGS U.S. Geological Survey 

WWD Westlands Water District 
Executive Summary 

xix 

Executive Summary 

Irrigated agriculture in areas with shallow groundwater tables and little or no 

drainage outlet, as practiced in the center and western side of the San Joaquin 

Valley, has resulted in high salt concentrations that inhibit plant growth. More 

than 708,200 hectares (ha) (1,750,000 acres) of agricultural land in the San 

Joaquin Valley are considered drainage-impaired. Adverse effects to plants, fish, 

and wildlife can occur from this saline drain water, especially with its high 

concentrations of the trace elements, selenium, and boron. Selenium is of a 

primary concern because it is widely distributed throughout the valley and has 

proven to be toxic to certain vertebrate species, especially in aquatic habitats. 

Decades of irrigation have transferred soluble selenium from the upper soils to the 

shallow groundwater. 

The Central Valley Project (CVP) provides water deliveries to San Joaquin Valley 

farms on more than 404,700 ha (1,000,000 acres). As the majority of the 

watershed was urbanized or converted to agricultural production, less than 

5 percent of the lands remained uncultivated. This change in land use resulted in 

the loss of native wetland, saltbush scrub, alkali sink, and California prairie 

habitats, which contributed to the listing of numerous endemic species of plants 

and wildlife (FWS 1998). 

The selective retirement of irrigated lands characterized by low productivity, poor 

drainage and high selenium concentrations in the shallow groundwater was 

recommended. The Central Valley Project Improvement Act (CVPIA), enacted in 

1992 as Public Law 102-575 Title 34, Section 3408(h), authorized the purchase of 

land, water and other property interests from willing sellers who received CVP 

water. The program goals were to reduce drainage, enhance fish and wildlife 

resources, and make water available for other CVPIA purposes. The Land 

Retirement Program (LRP) was developed cooperatively by an interagency 

Department of the Interior team with representatives from the Bureau of 

Reclamation (Reclamation), the U.S. Fish and Wildlife Service (FWS), and the 

Bureau of Land Management (BLM). 

Because concerns were raised about the magnitude of the project and the lack of 

knowledge about its effects on listed species, the Land Retirement Demonstration 

Project (LRDP) was implemented to provide site-specific scientific data. The 

FWS Biological Opinion (BO) for the LRDP in 1999 raised specific concerns 

about the scope and degree of land retirement impacts on groundwater levels, 

groundwater and surface water quality, soil chemistry, and biota. There was a 

need to monitor selenium loads at different trophic levels for corresponding 

groundwater levels and quality. 
Land Retirement Demonstration Project 

Five Year Report 

xx 

The LRDP was designed as a 5-year project to provide site-specific scientific data 

to determine the effects of land retirement on drain water volume, groundwater 

depth and quality, soils, and biota. Contaminants analysis was regularly 

performed on surface and groundwater, soils, vegetation, invertebrates, and 

vertebrates. Techniques were tested to determine effective, safe, and economical 

upland habitat restoration. Various efforts were taken to educate stakeholders 

about the effects of land retirement and habitat restoration techniques. The need 

for continued use of acquired water on LRDP lands was evaluated. 

A resource monitoring plan (Selmon et al. 1999) that outlined the focus of habitat 

restoration research and established wildlife monitoring protocols was prepared 

and implemented by the California State University, Stanislaus, Endangered 

Species Recovery Program (ESRP). The plan included a Habitat Restoration 

Study (HRS) to monitor four restoration treatments and the vegetative and 

wildlife response to those treatments. Twenty study plots were established and a 

wide-range of data were collected over the 5 years. Selenium levels in a variety 

of trophic levels were monitored. Results of the LRDP are reported in this 

document and represent the culmination of the 5-year research and monitoring 

efforts implemented in 1999 and concluded in 2004. Although habitat restoration 

research and active site restoration efforts were included in the plan, results of 

those tasks will be given in a later report. 

The Land Retirement Demonstration Project has two study sites located in two 

drainage-impaired basins. The Tranquillity site is located in western Fresno 

County and the Atwell Island site is located in Kings and Tulare Counties. The 

lands purchased were previously in agricultural production—primarily cotton, 

tomatoes, grain, and sugar beets. 

The full 5-year study was completed at the Tranquillity site. Accordingly, this 

report primarily focuses on data from that site, but does include information from 

Atwell Island on the physical impacts and on selenium. Only at the Tranquillity 

site were 5 years of data collected for the Habitat Restoration Study. Activities at 

Atwell Island included baseline sampling prior to installation of treatments in 

2001 and 1 year of post-treatment sampling conducted in early 2002. Physical 

impacts monitoring is discussed for the Atwell Island site. Due to reductions in 

CVPIA funding, all responsibilities for restoration research, site management, and 

monitoring of biota and selenium levels were reassigned from ESRP to BLM in 

2002. BLM reports accomplishments and survey results for Atwell Island 

annually. The 5 year report for the site activities and research will be produced in 

2007. 

Appropriate habitat restoration must accompany land retirement to maximize 

benefits for wildlife and endangered species. Land retirement without habitat 

restoration often leads to large fields infested with weeds and pests that impact 

neighboring agriculture and require extensive and continuous management. 

Although land retirement has the potential to enhance wildlife values and improve 

ecological systems in the San Joaquin Valley, it is recognized that land uses other 
Executive Summary 

xxi 

than wildlife habitat may take precedence on some lands. Some land uses, 

particularly grazing and dryland farming can be compatible with and may even 

contribute to habitat values for wildlife. 

Restoration activities were expanded to include the collection of more than 100 

native upland plant species from Ecological Reserves and isolated, small 

remnants of native habitat within an 80 kilometer (km) or (50 mile [mi]) radius of 

the Tranquillity site. Native plant research continues at an on-site nursery and is 

yielding large quantities of seed for use in replicated restoration trials and other 

restoration efforts. The results of these efforts will be reported at a later date. 

Tranquillity Site Physical Impacts Monitoring Results 

Five years of groundwater monitoring at the Tranquillity site supports conceptual 

and numerical models that predicted a declining shallow water table in response 

to land retirement. The performance objective established by FWS regarding 

water table response to land retirement stated that the depth to groundwater shall 

not show a net increasing trend (i.e. not rise to the land surface) over the life of 

the project. The FWS performance objective at the Tranquillity site was clearly 

met. Groundwater levels in all the wells monitoring the shallow water table at the 

site showed a declining trend (increasing depth to groundwater from land surface) 

during the study. Percolation of applied irrigation water prior to land retirement 

was the primary source of groundwater recharge that sustained the high water 

table. In the absence of irrigation recharge, the shallow water table has steadily 

receded from the land surface over the 5-year study. Large downward hydraulic 

gradients measured at the site confirm the presence of perched water table 

conditions in the fine-grained Coast Range deposits at the site. Discharge of the 

shallow groundwater occurs primarily through slow downward percolation 

through the thick, low-permeability, surficial clay deposits at the site. Some 

shallow groundwater was also undoubtedly discharged by evaporation from the 

water table when it was in proximity to the land surface at the beginning of the 

study. The water table response observed at the Tranquillity site is representative 

of conditions that would be present at a high percentage of lands that are targeted 

for retirement on the lower alluvial fan and basin rim settings in the western San 

Joaquin Valley. 

The declining shallow water table is a very important aspect of land retirement 

due to the poor quality of the shallow groundwater observed beneath the 

Tranquillity site. The high salinity and selenium concentrations in the shallow 

groundwater found in the Coast Range deposits at the site are a result of leaching 

from soils under irrigated conditions and evaporation from the shallow water 

table. Evaporation from the shallow water table has concentrated salts and trace 

elements in the shallow groundwater. The performance objective for selenium in 

groundwater at the Tranquillity site established by FWS stated that the selenium 

concentration in groundwater shall not show a net increasing trend over the life of 

the project. The FWS performance objective was clearly not met. Rising levels 
Land Retirement Demonstration Project 

Five Year Report 

xxii 

of selenium observed in the shallow groundwater in the Coast Range deposits are 

likely a result of oxidation and advective transport of mobile selenium species in 

the alkaline conditions near the falling shallow water table. As long as the water 

table continues to decline, as expected in response to land retirement, the high 

concentrations of selenium in the groundwater should have no consequences to 

biota at the site. In contrast, selenium is present at very low concentrations in the 

groundwater found in the coarse-textured Sierran deposits at the Tranquillity site. 

In the reducing geochemical environment observed in the Sierran groundwater, 

selenium is relatively insoluble and immobile. 

The Tranquillity site is underlain by flood basin and basin rim deposits that 

consist primarily of moderately to densely compacted clays that range in 

thickness from 1.5 to 10.7 meters (m) (5 to 35 feet) thick. The clay soils have 

low-permeability and provide poor drainage conditions for irrigated agricultural 

production. The predominant soil type at the Tranquillity site is Tranquillity clay. 

This is the most extensive soil type mapped by the U.S. Department of 

Agriculture on the lower alluvial fans and basin rim landforms in the areas 

targeted for land retirement. Soils at the Tranquillity site contain moderately 

elevated concentrations of selenium (average 1.0 milligrams per kilogram 

[mg/kg]) when compared to the common range (0.1-1.4 mg/kg) for western U.S. 

and San Joaquin Valley soils; however, they are still well within the range 

commonly found in western soils. 

Total selenium concentrations, soluble selenium concentrations, and salinity 

(ECe) in the surface soil (depth 0- 30 cm—centimeters [1 foot]) showed a 

decreasing trend over the 5 years of monitoring at the Tranquillity site. The 

decreasing selenium and salinity trends in the surface soil indicate that upward 

flux of salt and selenium from capillary rise and evaporation of shallow 

groundwater at the soil surface is minimal, and that some leaching of soluble 

selenium and salt from surface soils occurred during the 5-year study despite 

dryer than average climatic conditions. 

About 10-20 percent of the selenium present in the subsoils (depth 0.6 to 0.9 m 

and 1.2 to 1.5 m [2-3 and 4-5 feet]) is soluble and mobile in the alkaline, 

oxidizing chemical conditions found in the soil. Soluble selenium concentrations 

(average 4.6 parts per billion [ppb] in saturation extracts) and percentages are 

much lower in the surface soils (depth 0-1 foot). Even if surface water ponding 

should occur during very wet periods, it is probable that selenium concentrations 

in the ponded water would be below the aquatic life criteria of 5 ppb based on the 

soil selenium saturation extract data. No performance objectives were established 

for soil selenium levels for the demonstration project; however, the maximum 

surface soil concentration (1.7 mg/kg) observed during the 5 years of monitoring 

at the Tranquillity site was well below typical soil toxicity thresholds for selenium 

in sediment (4 mg/kg). 

FWS established performance standards for selenium and mercury in ponded 

surface water that lasts for more than 30 days. Due to dry climatic and soil 
Executive Summary 

xxiii 

conditions during the study, no surface water ponding was observed at the site 

that lasted for more than 30 days. Monitoring of precipitation during the course 

of the study suggests that the precipitation threshold to cause ponding of surface 

water at the site is well in excess of 5 centimeters (cm) (2 inches) of rainfall per 

month. The extensive network of dessication cracks in the clay soils at the 

Tranquillity site greatly inhibits the formation of surface water ponds. 

Atwell Island Site Physical Impacts Monitoring Results 

The Atwell Island site lies on the southwestern margin of the Tulare Lake bed. 

The site is underlain by lakebed and marsh deposits consisting primarily of clay 

and silt with some sand. Soils in the Atwell Island study area consist of silt and 

sand loams that are formed from alluvium derived from igneous and sedimentary 

rocks. The U.S. Department of Agriculture soil mapping units found at the site in 

order of abundance include the Posochanet silt loam, Nahrumb silt loam, 

Westcamp silt loam, Excelsior fine sandy loam, and Lethent fine sandy loam. 

Baseline soil chemistry data from three research areas at the site were collected 

during 2002. The surface soils (0 to 30 cm [0-12 inch] depth) at the research sites 

are moderately to highly saline (mean ECe 3.85-9.25 deciSiemens/meter [dS/m]) 

and contain low selenium concentrations (mean total selenium 0.097-0.114 

milligrams per kilogram [mg/kg]). By comparison, the mean selenium 

concentration in western U.S. soil is about 0.34 mg/kg. 

Soils at the Atwell Island site are relatively low in both soluble and total 

selenium. Boron concentrations were moderate in surface soils and are elevated 

in subsoils. Both boron and soil salinity are plant growth limiting factors at the 

Atwell Island sites. Study Area 1 appeared to be using moisture from the water 

table. While this has benefitted plant growth in the short term, it may indicate soil 

salinity problems in the future. The medium textured soils at the Study Area 1 

site exhibited capillary fringe zones approaching 1.5 m (5 feet) thick. A declining 

shallow water table in response to land retirement will lessen the likelihood of 

salinization of surface soils. 

Monitoring wells were installed at the site in the fall of 2001 to establish baseline 

groundwater conditions. Initial groundwater level measurements indicate the 

presence of a perched water table beneath much of the site. Groundwater levels 

observed to date in the shallow groundwater system range from approximately 1.2 

to 4.6 m (4 – 15 feet) below land surface. The water table is generally shallowest 

(nearest to the land surface) in the northwest portion of the site and becomes 

deeper to the southeast. A declining shallow water table in response to land 

retirement has been observed on portions of the site where irrigation has ceased or 

been greatly reduced. 

The shallow groundwater underlying the Atwell Island site is moderately saline in 

nature. Salinity in the shallow groundwater samples, expressed as electrical 

conductivity (EC), ranged from 575 to 52,925 microSiemens/centimeter (μS/cm), 
Land Retirement Demonstration Project 

Five Year Report 

xxiv 

with a median value of 13,740 μS/cm. By comparison, drinking water typically is 

less than 750 μS/cm, irrigation water is less than 1,250 μS/cm, and seawater is 

about 50,000 μS/cm. The shallow groundwater at the site is best described as a 

sodium sulfate type of water. Sodium is the dominant major cation found in the 

shallow groundwater samples, with sodium concentrations ranging from 469 to 

15,100 milligrams/liter (mg/L), and a median concentration of 4,500 mg/L. 

Sulfate is the dominant major anion found in the shallow groundwater, with 

sulfate concentrations ranging from 261 to 22,200 mg/L, and a median 

concentration of 5,700 mg/L. Selenium concentrations measured in the shallow 

groundwater wells at the site during the baseline year of monitoring range from 

less than the detection limit of 0.4 to 208 micrograms per liter (μg/L), with a 

median concentration of 8.56 μg/L. The Environmental Protection Agency (EPA) 

water-quality criterion for long-term exposure to selenium in aquatic 

environments is 5 μg/L (EPA 1988). Approximately 50 percent of the 

groundwater samples (35 of 72 samples) collected during the baseline year of 

sampling had selenium concentrations that were less than the EPA aquatic life 

criteria. 

No ephemeral surface water pools resulting from rainfall were observed at the site 

to date. Selenium concentrations in three surface water samples taken from the 

artificial wetland at the site are below the EPA aquatic life criteria, and ranged 

from below the detection limit (less than 0.4 μg/L) to 0.6 μg/L. 

Selenium Monitoring in Biota 

As required by the LRDP Biological Opinion (FWS 1999), we monitored 

selenium levels in plants, invertebrates, and small mammals on retired agricultural 

lands over a 5-year period at the Tranquillity site and over a 3-year period at the 

Atwell Island site. Results are compared to performance standards established by 

FWS for the project (FWS 1999) and to selenium levels in biota from seleniumnormal situations in the western United States (USDI 1998). We compare the 

concentrations of selenium in biota from our study sites to concentrations of 

selenium in biota found at Kesterson National Wildlife Refuge (NWR). 

The mean concentration of selenium in plants, invertebrates, and small mammals 

at both the Atwell Island and Tranquillity sites was below the established 

performance standards, within the range for biota typically found in seleniumnormal situations in the western United States, and usually about an order of 

magnitude less than selenium levels found at Kesterson NWR. Selenium levels in 

biota from Atwell Island tended to be lower than at Tranquillity. Generally, no 

clear differences in selenium levels were found between years. At the 

Tranquillity site, selenium levels in plants and small mammals tended to be 

greater on cultivated (irrigated) lands than on uncultivated (non-irrigated lands). 

Approximately 6 percent of all samples were considered unusually high in 

selenium (exceeding one standard deviation of the data set). The outliers suggest 
Executive Summary 

xxv 

the need for selenium monitoring on newly acquired lands and continued 

monitoring on existing retired lands. 

Results of the Habitat Restoration Study 

The Biological Opinion for the Land Retirement Demonstration Project required 

that a 5-year Habitat Restoration Study be conducted to determine the responses 

of wildlife to land retirement and restoration efforts. We designed a study with 

four levels of restoration treatments (seeding with native plants, installing 

topographic contours, a combination of seeding and contouring, and control) and 

applied these treatments to twenty 4 ha (10-acre [ac]) study plots in a randomized 

block design. On the plots, we monitored vegetation, invertebrates, and 

amphibians and reptiles once each year, and we monitored birds and small 

mammals four times each year. Other monitoring at the site included track station 

surveys, spotlighting, winter raptor surveys, and monitoring of bird nesting 

success. 

We successfully established plant cover to stabilize soils, established plant cover 

to provide wildlife habitat, and established native wildlife. Some of the 

restoration approaches used on the HRS plots showed promise. Microtopographic 

contouring appeared to have both positive effects in promoting establishment of 

native vegetation, and providing habitat heterogeneity for small mammals and 

other biota. Shrub establishment—particularly of Atriplex polycarpa—was very 

successful and approached densities that would be considered appropriate habitat 

for some species of concern. Nevertheless, restoration response was generally 

less than optimal. Factors contributing to the limited success of native plant 

restoration are thought to include inadequate seed delivery methods (imprinting 

may not be appropriate for use on the HRS soil types and for many of the 

species), competition from invasive species (primarily black mustard, London 

rocket, and tumbling saltweed), inappropriate seed source (most of the seed was 

purchased commercially and was not obtained from the proximity of the project 

site), and drought conditions experienced throughout the term of the project. 

Because there were few notable differences among the restoration treatments, 

there were also few observable trends in wildlife diversity and abundance 

associated with the treatments. However, the information on wildlife diversity 

and abundance that was obtained shows that retired agricultural lands are valuable 

to wildlife. Over a 5-year period, we identified 101 families within 21 orders of 

invertebrates, 1 species of amphibian, 4 species of reptiles, 48 species of birds, 

and 8 species of small mammals, 1 species of canid (coyote), 2 species of 

mustelids (skunk and long-tailed weasel), and 2 domesticated species (cat and 

dog) that utilize the Tranquillity site. Nine species of birds utilized the study area 

as breeding habitat and 12 species of sensitive birds were using the study area. 

One factor that may have limited the abundance and diversity of native wildlife 

on the study plots is the lack of nearby lands that support wildlife which could 
Land Retirement Demonstration Project 

Five Year Report 

xxvi 

disperse onto the study plots. Only small, remnant parcels of native habitat exist 

in the vicinity. 

There were no indications the HRS lands supported greater agricultural pest 

densities than did surrounding retired and fallowed lands. Rather, agriculturally 

beneficial species were common and widespread on the site, especially in restored 

areas. 

Although this pilot project did not necessarily emphasize the establishment of 

threatened and endangered wildlife on the study plots, we were successful in 

providing suitable habitat for a number of rare species of birds. With the 

incorporation of appropriate management actions, the habitat that has been 

established should be suitable for various other rare species. 

The wildlife information generated by this project is immensely valuable as a 

description of baseline conditions that, if compared to data collected from retired 

lands that are restored to prime native habitats, would provide insight into the 

value of restoration to wildlife. There have been no other wildlife studies or 

monitoring efforts in the central San Joaquin Valley of this duration or scope, 

making this a unique data set that describes the wildlife community existing on 

lands dominated by non-native plant species. Within the San Joaquin Valley, 

similar conditions are common and widespread among scattered, remnant patches 

of land that are not intensively farmed. 

Recommendations 

A number of tasks remain to be accomplished to fulfill the intent of this pilot 

project and to ensure that land retirement and the restoration of retired lands can 

proceed. Some of these include: 

• Publish findings of completed and ongoing research in open scientific 

literature. 

• Develop a long-term management and monitoring plan for the Tranquillity 

site. 

• Continue maintenance and expansion of the native plant nursery and seed 

collecting activities. 

• Continue research on development of restoration technologies, including 

seed delivery techniques, weed control methods, harvesting techniques, 

and seed cleaning techniques, which are promising and have begun to bear 

fruit. 
Executive Summary 

xxvii 

• Document and protect localities of known populations of native plants and 

animals in the project vicinity to ensure the survival and persistence of 

existing populations. 

• Develop criteria and methods for the propagation and translocation of 

threatened and endangered species to restored lands. 

• Provide public awareness of the positive effects and benefits of land 

retirement, such as increased depth to groundwater and establishment of 

native shrub species using various habitat restoration techniques. 

Based upon the findings presented in this report and experiences gained during 

this 5-year project, the Land Retirement Team and the Endangered Species 

Recovery Program fully support land retirement. We believe that land retirement 

has the potential to solve a variety of drainage issues while concurrently providing 

habitat for wildlife. Restoration can improve the overall ecosystem function by 

improving air quality, reducing weed loads, creating wildlife habitat, and assisting 

with recovery of sensitive species. Land retirement is expected to be beneficial to 

adjacent farming operations by improving water quality, improving air quality 

through dust abatement, and increasing abundance and diversity of invertebrate 

pollinators and predators. These benefits are justification for continuation and 

expansion of retiring drainage impacted lands, continued research of restoration 

techniques, and restoration of selected parcels of retired lands in the San Joaquin 

Valley. 

Chapter 1. Introduction 

1 

Chapter 1. Introduction 

by Curtis E. Uptain and Beatrice A. Olsen 

1.1. Background 

“Land Retirement,” defined here as the removal of land from irrigated agricultural 

production, is a means by which drain water accumulation can be substantially 

reduced. Drain water reduction can be imperative because irrigated agriculture in 

areas with shallow groundwater and no drainage outlet can sustain drainage water 

with high salt concentrations that can, in turn, inhibit plant growth. These 

conditions are characteristic of large portions of the center and western side of the 

San Joaquin Valley, as evidenced by the more than 708,200 hectares (ha) or 

(1,750,000 acres [ac]) of agricultural land in the valley that are considered to be 

drainage-impaired (Figure 1-1). 

The salt content of irrigation water increases as water evaporates, passes over 

saline soils, or occurs through plant uptake. Where drainage is adequate, salts can 

be flushed from the root zones by sufficient rainfall or irrigation. However, this 

seldom eliminates the long-term accumulation of salinity. Short-term flushing of 

salts from soils results in excess drain water with high salt concentrations. 

Adverse effects to plants, fish, and wildlife can occur from saline drain water 

when present at the surface or in downstream tributaries. In areas lacking good 

drainage, repeated irrigation may raise the water table. When the water table 

reaches the root zone of plants, capillary action often carries water close to the 

soil surface, where it evaporates and leaves a surface salt residue. 

Additionally, high concentrations of trace elements that occur naturally in 

westside San Joaquin Valley soils, including selenium, boron, molybdenum, and 

arsenic, are problematic. Selenium is of a primary concern because it is widely 

distributed throughout the valley and has proven to be toxic to certain vertebrate 

species, especially in aquatic habitats. Decades of irrigation have transferred 

soluble selenium from the upper soils to the shallow groundwater. 

The Central Valley Project (CVP), with its massive system of dams, reservoirs, 

canals, power plants and other facilities, began providing irrigation water for San 

Joaquin Valley agriculture in 1951. The San Luis Unit and the State Water 

Project of the CVP, which were authorized in 1960, expanded water deliveries to 

approximately 404,700 ha (1,000,000 acres) by1968. By 1979, fewer than 

61,500 ha (151,750 acres), or about 2 percent, remained uncultivated. The 

majority of the watershed was converted to agricultural production or urbanized. 

Most of the remaining undeveloped land is located in the foothills of the Coast 
Land Retirement Demonstration Project 

Five Year Report 

2 

Figure 1-1. Drainage-impaired lands in the San Joaquin Valley. 
Chapter 1. Introduction 

3 

Range and in the extreme southern portion of the valley. This change in land use 

resulted in the loss of native wetland, saltbush scrub, alkali sink, and California 

prairie habitats and contributed to the listing of numerous endemic species of 

plants and wildlife (FWS 1998). 

The San Joaquin Valley Drainage Program (SJVDP), established in 1984, 

combined federal and state efforts to investigate drainage issues and identify 

possible solutions. The program estimated that 161,800 to 225,000 ha (400,000 to 

554,000 acres) would become unsuitable for irrigated agriculture by 2040 if no 

actions were taken to remedy drainage problems. One recommended action to 

reduce drainage-related problems was the selective retirement of irrigated lands 

characterized by low productivity, poor drainage and high selenium 

concentrations in the shallow groundwater. 

The Central Valley Project Improvement Act (CVPIA), enacted in 1992 as Public 

Law 102-575 Title 34, Section 3408(h), authorized the purchase of land, water, 

and other property interests from willing sellers who received CVP water. Such 

lands would achieve the program goals to reduce drainage, enhance fish and 

wildlife resources, and make water available for other CVPIA purposes. CVPIA 

did not authorize a recommended quantity of acres for permanent land retirement. 

The Land Retirement Program (LRP) was developed cooperatively by an 

interagency Department of the Interior team with representatives from the Bureau 

of Reclamation (Reclamation), the U.S. Fish and Wildlife Service (FWS), and the 

Bureau of Land Management (BLM) (See Appendix 1). Additional background 

information on the CVPIA Land Retirement Program can be found in a variety of 

reports (USDI 1997, USDI 1999, Selmon et al. 2000, Uptain et al. 2001, 2002, 

and 2004) and web sites (see http://usbr.gov/mp/cvpia). 

1.2. Development, Implementation, and Scope of the 

Land Retirement Demonstration Project 

During the comment period for the Land Retirement Program Draft 

Environmental Assessment (EA), concerns were raised about the magnitude of 

the project and the lack of knowledge about the positive and negative effects of 

retiring agricultural land on a large scale (USDI 1999). Although land retirement 

was featured in the FWS Recovery Plan for Upland Species of the San Joaquin 

Valley (FWS 1998), FWS had concerns that the high selenium levels would be 

unsafe for listed species. The Land Retirement Demonstration Project (LRDP) 

was implemented to provide site-specific scientific data to guide the 

implementation of the LRP and develop tools to predict potential benefits and 

impacts of retiring land from irrigated agriculture. The FWS Biological Opinion 

(BO) for the LRDP raised specific concerns about the scope and degree of land 

retirement impacts on groundwater levels, groundwater and surface water quality, 

soil chemistry, and biota. There was a need to monitor selenium loads at different 

trophic levels for corresponding groundwater levels and quality (FWS 1999). 
Land Retirement Demonstration Project 

Five Year Report 

4 

The Land Retirement Demonstration Project was designed and implemented as a 

5-year project to address the concerns expressed in the Biological Opinion by 

accomplishing five goals: 

• Provide site-specific scientific data to determine the effects of land 

retirement on drain water volume, groundwater depth and quality, soils, 

and biota. 

• Perform contaminants analysis regularly on surface and groundwater, 

soils, vegetation, invertebrates, and vertebrates. 

• Evaluate techniques to determine effective, safe, and economical means 

for upland habitat restoration that contain self-sustaining native upland 

communities, using adaptive management principles (Holling 1978, 

Walters and Holling 1990) to maximize efficiency of the restoration 

research program. 

• Educate stakeholders about the Land Retirement Program effects of land 

retirement and habitat restoration techniques. 

• Evaluate the need for continued use of acquired water on Demonstration 

Project lands. 

Other requirements of the Biological Opinion were met and are addressed in 

Appendix 2. 

In this report, the physical setting for the LRDP sites, monitoring methods 

employed for physical parameters, and a conceptual model of the groundwater 

system are presented in Chapter 2. Reclamation implemented a monitoring plan 

that utilized approved sampling protocols and analysis of physical factors, 

including surface water, groundwater, and soils (CH2M Hill 1999). Groundwater 

monitoring data are compared against performance criteria set forth in the 

Biological Opinion (FWS 1999). 

A resource monitoring plan (Selmon et al. 1999) that outlined the focus of habitat 

restoration research and established wildlife monitoring protocols was prepared 

by the California State University, Stanislaus, Endangered Species Recovery 

Program (ESRP). The plan included a Habitat Restoration Study (HRS) to 

monitor four restoration treatments and the vegetative and wildlife response to 

those treatments. Twenty study plots were established and a wide-range of data 

were collected over the 5 years (See Section 4.2.1 for experimental design 

description). Selenium levels in a variety of trophic levels were monitored. 

Results of the LRDP are reported here that represent the culmination of the 5-year 

research and monitoring efforts implemented in 1999 and concluded in 2003. 

Although habitat restoration research and active site restoration efforts were 

accomplished, the results of those tasks will be presented in other reports. 
Chapter 1. Introduction 

5 

The Land Retirement Demonstration Project has two project sites, the Tranquillity 

and the Atwell Island sites (Figure 1-1, shown earlier). The full 5-year study was 

completed only at the Tranquillity site. Accordingly, this report primarily focuses 

on data obtained at the Tranquillity site, but does include information from Atwell 

Island on the physical impacts of land retirement (Chapter 2) and on selenium 

levels in biota (Chapter 3). Only at the Tranquillity site were 5 years of data 

collected for the Habitat Restoration Study (Chapter 4). Activities at Atwell 

Island included baseline sampling prior to installation of treatments in 2001 and 

1 year of post-treatment sampling conducted in early 2002. Due to reductions in 

CVPIA funding, all responsibilities for restoration research, site management, and 

monitoring of biota and selenium levels were reassigned from ESRP to BLM in 

2002. BLM will report Atwell Island site activities and research in 2007. 

Appropriate habitat restoration must accompany land retirement to maximize 

benefits for wildlife and endangered species. Land retirement without habitat 

restoration often leads to large fields infested with weeds and pests that impact 

neighboring agriculture and require extensive and continuous management. 

Although land retirement has the potential to enhance wildlife values and improve 

ecological systems in the San Joaquin Valley, it is recognized that land uses other 

than wildlife habitat may take precedence on some lands. Some land uses, 

particularly grazing and dryland farming, can be compatible with and may even 

contribute to habitat values for wildlife. 

Although the goals of the LRDP focus primarily on requirements described in the 

Biological Opinion, restoration activities were expanded to include the collection 

of more than 100 native upland plant species from Ecological Reserves and 

isolated, small remnants of native habitat within an 80 km (50 mile) radius of the 

Tranquillity site. Seed collected from local plant genotypes have been planted in 

an on-site nursery and are yielding large quantities of seed for use in restoration 

research and other restoration efforts. Seed is cleaned, processed, and stored in 

our mechanized seed-cleaning facility. Research continues to be conducted on 

planting, propagation, weed control, and harvesting techniques. The replicated 

research trials that we are conducting are directly applicable to large-scale 

restoration efforts. A list of current research activities are provided in 

Appendix 3. The results of these efforts will be reported at a later date. 

1.3. Tranquillity Project Site Location and Description 

The LRDP study sites are located in two geographically and physiographically 

different drainage-impaired basins. The Tranquillity site is located in western 

Fresno County (Figure 1-2) and the Atwell Island site is located in Kings and 

Tulare Counties (see Figure 1-1). In the fall of 1998, the Land Retirement Team 

(LRT) purchased 666 ha (1,646 acres) in western Fresno County. By late 2001, a 

total of 845 ha (2090 acres) had been acquired, of which 239 ha (591 acres) were 

purchased with water. 
Land Retirement Demonstration Project 

Five Year Report 

6 

Figure 1-2. Location of the Tranquillity site including the 178 ha (440 ac) North 

Avenue parcel and the 16 ha (40 ac) Manning Avenue parcel. 

The 178 ha (440 acre) North Avenue Parcel was obtained in late 2001 and was 

previously fallowed and grazed by sheep. The land initially purchased in 1998 

had previously been in agricultural production, primarily cotton, tomatoes, grain, 

and sugar beets. The remaining acreage had been idled for longer than 5 years 

and contained sufficient plant cover. For weed and erosion control, and to 

provide as homogeneous a plant cover as possible for the research plots, barley 

was planted on approximately 486 ha (1,200 acres) in 1999. 

The site is immediately surrounded by agricultural fields, although in the last few 

years more of these fields have been idled under the land retirement program 

initiated by Westlands Water District (WWD). The San Luis Canal, which 
Chapter 1. Introduction 

7 

previously transported drainage water to Kesterson National Wildlife Refuge 

(NWR), traverses the site. 

The 3,468 ha (8,570 acre) Mendota Wildlife Area is located adjacent to the 

eastern boundary of the North Avenue Parcel and within 4.8 kilometers (km) 

(3 miles) north of the HRS site. The 377 ha (932 acre) Alkali Sink Ecological 

Reserve (ER) and the 718 ha (1,775 acre) Kerman ER are located within 16 km 

(10 mile [mi]) of the HRS site. These areas contain remnants of the once 

widespread alkali sink, saltbush scrub, and annual grassland habitats. 

1.4. Literature Cited 

CH2M Hill. 1999. Quality assurance project plan, Land Retirement 

Demonstration Project, soil, groundwater, and surface water monitoring. 41 

pp. 

Holling, C.S., ed. 1978. Adaptive environmental assessment and management. 

Wiley, New York. 377 pp. 

San Joaquin Valley Drainage Program. 1990. Fish and Wildlife Resources and 

Agricultural Drainage in the San Joaquin Valley, California. Vols. I, II. 

707pp. +appendices. 

Selmon, M., P. Kelly, and C. Uptain. 1999. Resource monitoring plan for the 

Land Retirement Demonstration Project in western Fresno County. 36 pp. 

Selmon, M., P. Kelly, C. Uptain, and S. Lee. 2000. Land Retirement 

Demonstration Project, 1999 annual report. Unpubl. report prepared for the 

Interagency Land Retirement Team, Fresno, California. 84 pp. 

Uptain, C., K. Dulik, P. Brandy, M. Selmon, P. Kelly, D. Williams, S. Lee, and J. 

Brummer. 2001. Land Retirement Demonstration Project, 2000 annual 

Report. Unpubl. report to the Interagency Land Retirement Team, Fresno, 

California. 113 pp. 

Uptain, C., N. Ritter, S. Lee, S. Laymon, K. Kreitinger, S. Phillips, A. Harpster, J. 

Smith, A. Howard, S. Messer, D. Newman, P. Kelly, and D. Williams. 2002. 

Land Retirement Demonstration Project, year three, 2001 annual report. 

Unpubl. report to the Interagency Land Retirement Team, Fresno, California. 

138 pp. 
Land Retirement Demonstration Project 

Five Year Report 

8 

Uptain, C.E., N.P. Ritter, S.L. Lee, J. Brummer, S.A. Laymon, K.R. Garcia, A.J. 

Howard, G. Basso, K.E. Kreitinger, S. E. Phillips, S.R Messer, D.P. 

Newman, E.M. Magill, L.L. Williams, P.A. Kelly, and D.F. Williams. 2004. 

Land Retirement Demonstration Project: Year four 2002 annual report. 

Unpubl. Report to the United States Dept. of the Interior, Land Retirement 

Team, Fresno, California. 274 pp. 

U.S. Department of the Interior. 1997. Central Valley Project Improvement Act 

Section 3408(h): Land Retirement Program guidelines. Unpubl. report by 

the Interagency Land Retirement Team, Fresno, California. 19 pp. 

U.S. Department of the Interior. 1999. Final Environmental Assessment: Central 

Valley Project Improvement Act Land Retirement Program Demonstration 

Project. Unpubl. report by the Interagency Land Retirement Team, Fresno, 

California. 127 pp. 

U.S. Fish and Wildlife Service. 1998. Recovery plan for upland species of the 

San Joaquin Valley, California. Portland, Oregon. 319 pp. 

U.S. Fish and Wildlife Service. 1999. Biological Opinion formal section 7 

consultation for the Central Valley Project Improvement Act Land 

Retirement Program Demonstration Project. Reference No. 1-1-99-0125. 

Sacramento, California. 64 pp. 

Walters, C.J. and C.S. Holling. 1990. Large scale management experiments and 

learning by doing. Ecology 71:2060-2068. 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

9 

Chapter 2. Physical Impacts of 

Agricultural Land Retirement in the 

San Joaquin Valley 

by Stephen L. Lee, Joseph Brummer, and Jim Yahnke 

2.1. Introduction 

This chapter describes the physical setting at the Tranquillity and Atwell Island 

Project sites including soil, groundwater, and surface water conditions. The 

methods utilized for monitoring soil, groundwater, and surface water during the 

study are discussed. A conceptual model of the groundwater system at the 

Tranquillity site is presented with a discussion of soil and groundwater response 

to land retirement. Monitoring data from the Tranquillity Site are compared 

against performance criteria established by the U.S. Fish and Wildlife Service 

(FWS) and summarized in the table below. 

FWS Performance Standard Performance Standard Met? 

Depth to groundwater will not show a 

net increasing trend (decreasing depth 

to soil surface) over 5 years of 

monitoring. 

YES 

Selenium concentration in 

groundwater will not show a net 

increasing trend over 5 years of 

monitoring. 

NO 

Standing water that persists more than 

30 days in duration shall not exceed 

2 μg/L (parts per billion) selenium and 

2 ng/L (parts per trillion) mercury. 

NOT MEASURED 
Land Retirement Demonstration Project 

Five Year Report 

10 

2.2. Tranquillity Site 

2.2.1. Geology 

The Tranquillity Demonstration Project site is located in the western San Joaquin 

Valley, an asymmetrical basin bounded by the Coast Ranges on the west, the 

Tehachapi Mountains on the south, the Sierra Nevada on the east and the delta of 

the San Joaquin and Sacramento Rivers on the north. The axis of the valley 

trough is closer to the Coast Ranges than to the Sierra Nevada. The basin is filled 

with alluvium overlying older Mesozoic and Cenozoic marine and continental 

sediments. Alluvial deposits underlying the central San Joaquin Valley were shed 

from the adjacent Coastal and Sierra Nevada ranges and vary in thickness from 

274 to 1,006 meters (m) (900 to 3,300 feet [ft]) (Miller et al. 1971). The Sierra 

Nevada consists mainly of granitic and metamorphic rocks of pre-Tertiary age. 

The Coast Ranges are composed primarily of folded and faulted beds of 

Cretaceous age marine shale and sandstone in the north and Cenozoic age 

sandstone and shale in the south (Prokopovich 1987). Bull (1964a and b) 

identified a series of alluvial fans derived from sediments from the coastal ranges 

that form the western margin of the San Joaquin Valley in the study area. 

The Tranquillity demonstration project site is located in the trough of the 

San Joaquin valley in western Fresno County. The site is underlain directly by 

flood basin deposits derived from overbank deposition from the San Joaquin 

River and Fresno Slough. The flood basin deposits consist of fine textured, 

moderately to densely compacted clays that range in thickness from 1.5 to 10.7 m 

(5 to 35 feet) (Belitz and Heimes 1990). The flood basin clays have lowpermeability and greatly impede the downward movement of water. On the 

northern part of the site (Section 10, Figure 2-1), the flood basin deposits rest 

upon well sorted micaceous sand derived from the Sierra Nevada. The Sierran 

sands are highly permeable, reduced in oxidation state, and vary in thickness 

between 122 and 152 m (400 and 500 feet) in the project vicinity. On the 

southern part of the site (Sections 15 and 16, Figure 2-1), the flood basin deposits 

overlie sediments derived from the coastal ranges. The coastal range sediments 

inter-finger with Sierran sands in the project vicinity, and are oxidized and 

primarily fine grained. The Corcoran clay is a regionally extensive fine grained 

lakebed deposit that underlies the site at a depth of approximately 152 m (500 

feet). 

2.2.2. Soils 

Soils in the Tranquillity Demonstration Project area primarily consist of clays, 

silty clays, and silty clay loams, which formed in alluvium, derived from igneous 

and sedimentary rock. Individual soil mapping units at the project site include (in 

order of abundance) Tranquillity clay, Lillis clay, and Lethent silt loam. These 

soil series cover more than 56,658 hectares (ha) (140,000 acres) in western Fresno 

County, and are representative of soil conditions found in the drainage impacted 

lands in Western Fresno County. The Tranquillity mapping unit is the 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

11 

predominant soil type in the study area and covers approximately 80 percent of 

the site, while the Lillis and Lethent mapping units occur exclusively in 

Section 10 and cover the remainder of the site (Figure 2-1). The Tranquillity clay 

is a very deep, poorly to moderately drained saline-sodic soil found on low-lying 

alluvial fans and flood plains with slopes between 0 and 1 percent. The 

permeability of this soil is slow and the unit is suited to growing irrigated, salttolerant crops, or for wildlife habitat (USDA 1996). Runoff is low, and the 

hazard of water erosion is slight. The depth to the water table varies and is 

commonly highest during irrigation applications in the winter and early spring. 

These soils generally require intensive management to reduce salinity and 

maintain agricultural productivity. 

The U.S. Department of Agriculture (USDA) took soil samples from the major 

soil horizons in a test pit located in the NW 1/4 of Section 16 (Figure 2-1) at the 

site in 1992. The samples were analyzed in the laboratory for particle size, 

chemistry, and mineralogy. These soils consist predominantly of clay-sized 

particles less than 0.002 millimeters (mm) in diameter. The USDA reported that 

the clay fraction from six samples taken from the test pit ranged from 48 to 52 

percent of the total samples. Silt size particles (0.002-0.05 mm in diameter) 

ranged from 36-37 percent of the total samples, and sand-size particles made up 

from 11-16 percent of the total samples (USDA 1992). Total selenium 

concentrations ranged from 0.5 to 1.1 parts per million (ppm), and the 
Land Retirement Demonstration Project 

Five Year Report 

12 

Figure 2-1. U.S. Department of Agriculture soil mapping units, Tranquillity site. 

Electrical Conductivity (EC) of saturation extracts ranged from 3.7 to 10.9 

deciSiemens/meter (dS/m). These soils are highly plastic with Plasticity Indices 

ranging from 23-52 percent. The predominant clay mineral is Montmorillonite, 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

13 

which can take on water in the crystal lattice, resulting in high shrink-swell 

potential and development of deep cracks at the soil surface upon drying. 

The Lillis clay mapping unit covers about 10 percent of the study area in the 

eastern half of Section 10 (Figure 2-1). These soils are very deep, poorly drained, 

saline-sodic soils found typically on floodplains and basins. Permeability of the 

Lillis soil is extremely slow, water infiltration rate is high, and when the soil is 

dry, the surface cracks open. As the soil becomes wet and the cracks close, the 

infiltration rate greatly decreases. Surface water runoff is low and the hazard of 

water erosion is slight. The unit is used mainly for wildlife habitat and recreation. 

The USDA took soil samples from the major soil horizons in a test pit located in 

the SW 1/4 of Section 10 at the site in 1992. The samples were analyzed in the 

laboratory for particle size, chemistry, and mineralogy. These soils consist 

predominantly of clay-sized particles less than 0.002 mm in diameter. The USDA 

reported that the clay fraction from nine samples taken from the test pit ranged 

from 59 to 66 percent of the total samples. Silt-size particles (0.002-0.05 mm in 

diameter) ranged from 29-36 percent of the total samples, and sand-sized particles 

made up from 2-7 percent of the total samples (USDA 1992). Total selenium 

concentrations ranged from 0.3 to 0.7 ppm, and the EC of saturation extracts 

ranged from 9.6 to 38.6 dS/m. These soils are highly plastic with Plasticity 

Indices ranging from 33-61 percent. The predominant clay mineral is 

Montmorillonite, which can take on water in the crystal lattice, resulting in high 

shrink, swell potential. 

The Lethent silt loam mapping unit covers about 10 percent of the site in the north 

half of Section 10, Figure 2-1). These soils are deep, moderately well drained, 

saline-sodic soil found on low-lying alluvial fans and basin rims. Permeability of 

this soil is very slow; runoff is slow; and the hazard of water erosion is slight 

(USDA 1996). 

2.2.3. Groundwater 

A conceptual site model for current groundwater conditions at the Tranquillity 

site is shown in Figure 2-2. Prior to agricultural development, the site was a 

discharge point for groundwater. Recharge to the semi-confined aquifer occurred 

along the Coast Range and intermittent stream channels to the west of the site and 

groundwater generally flowed toward the axis of the valley, where it rose close to 

the land surface and was discharged by evapotranspiration and also contributed to 

streamflow along the valley trough (Belitz and Heimes 1990). Evaporation of 

groundwater from a shallow water table resulted in high concentrations of salt and 

trace elements in the soil near the land surface. Heavy groundwater pumping that 

occurred concurrently with agricultural development lowered the regional water 

table and created large downward hydraulic gradients in the semi-confined 

aquifer. Irrigation with imported surface water and pumped groundwater in the 

absence of artificial drains flushed the salts from the surface soils into the shallow 
Land Retirement Demonstration Project 

Five Year Report 

14 

Figure 2-2. Conceptual site model for groundwater conditions at the Tranquillity 

site. 

groundwater and created a perched water table condition in the heavy clay soils 

underlying the site. Evaporation from the shallow water table under irrigated 

conditions further concentrated high levels of salts and trace elements in the 

shallow groundwater. Retirement of the land from irrigated agriculture has 

resulted in a decline in the shallow water table as recharge has been essentially 

eliminated and perched groundwater is discharged by downward percolation from 

the bottom of the clay layer and evaporation from the near surface water table. 

Selenium is expected to be mobile in the oxidized geochemical conditions found 

in the Coast Range deposits at the site and immobile in the reduced conditions 

found in the Sierra Nevada deposits. 

2.2.4. Climate and Weather 

The Mediterranean climate in central California is characterized by cool, wet 

winters and hot, dry summers. The project site receives an average of about 

7 inches of rainfall annually, with most of the rain occurring between the months 

of November through April. Hourly precipitation, temperature, wind, and relative 

humidity data are collected at the California Irrigation Management Information 

System (CIMIS) weather station No. 105, located 2.4 kilometers (km) (1.5 miles) 

west of the demonstration project site at the Westlands Water District (WWD) 

Tranquillity Field Office. The CIMIS station is operated and maintained by the 

California Department of Water Resources (CDWR), and is the best source of 

weather data for the Tranquillity site. As shown in Figure 2-3 and Figure 2-4, 4 

of the 6 years (1993, 1995, 1996 and 1998) preceding the land retirement 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

15 

0

0.5

1

1.5

2

2.5

3

3.5

4

4.5

Jan-93

Jul-93

Jan-94

Jul-94

Jan-95

Jul-95

Jan-96

Jul-96

Jan-97

Jul-97

Jan-98

Jul-98

Jan-99

Jul-99

Jan-00

Jul-00

Jan-01

Jul-01

Jan-02

Jul-02

Jan-03

Jul-03

Date

Precip. (inches)

Figure 2-3. Monthly precipitation at CIMIS Station 105, Westlands Water District, 

near the Tranquillity site (1993-2003). 

,

0

2

4

6

8

10

12

14

16

1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Year

Rainfall (inches)

Figure 2-4. Annual precipitation at CIMIS Station 105, Westlands Water District, 

near the Tranquillity site (1993-2003). 
Land Retirement Demonstration Project 

Five Year Report 

16 

demonstration project had above average rainfall, while the 5 years of monitoring 

during the demonstration project have been dry, with below average rainfall 

(1999-2003). 

2.2.5. Irrigation 

The demonstration project lands south of Adams Avenue were actively farmed 

and irrigated up to the time they were retired from irrigated agriculture in 1998 for 

the study. The crops consisted primarily of cotton, sugar beets, and alfalfa, which 

were irrigated by furrow or sprinkler irrigation systems. The land north of Adams 

Avenue has not been irrigated since 1989, except for a 24.3 ha (60 acre) field of 

safflower located in the northwest corner of section 10. Approximately 

15.2 centimeters (cm) (6 inches) of water have been applied annually to the 

safflower field by the California Department of Fish and Game (CDFG). The 

safflower is left in the field to attract upland game birds for hunting. During the 

first 3 years of the demonstration project, a small quantity of irrigation water was 

applied to the barley crop planted in the habitat restoration study area. The barley 

covers an area of about 389 ha (960 acres) and serves as a cover crop to provide 

weed and dust control, as well as to isolate the experimental restoration plots from 

each other. Approximately 7.6, 12.4, and 11.7 cm (3.0, 4.9, and 4.6 inches) of 

water were applied to the barley during 1999, 2000 and 2001, respectively, using 

a hand moved sprinkler irrigation system. The barley buffer area has not been 

irrigated since 2001. 

2.2.6. Monitoring of Selenium Levels 

The monitoring of selenium levels in groundwater and biota followed a tiered 

sampling approach that was cooperatively developed with FWS specifically for 

this project (FWS 1999). The monitoring of selenium and salinity in soils was not 

a requirement in the FWS Biological Opinion for the project; however, the soil 

monitoring program was implemented to address concerns raised by the scientific 

community over potential impacts to soils that may result from land retirement 

2.2.6.1. Surface Water Monitoring 

In the Biological Opinion for the Land Retirement Demonstration Project, the 

FWS established performance standards for selenium and mercury concentrations 

in surface water. The performance standard specified that standing water that 

persists for more than 30 days shall not exceed 2 micrograms/liter (μg/L) 

selenium, and 2 nanograms/liter mercury (FWS 1999). Precipitation at the site 

was monitored by viewing the CIMIS website during the rainy season. The site 

was also visited during the wet season to document any standing water that 

persisted for more than 30 days in duration. 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

17 

2.2.6.2. Soil Monitoring 

The objective of the soil monitoring program for the demonstration project is to 

detect changes in levels of constituents of concern (COCs) including selenium, 

boron, and salinity that may result from land retirement over the 5-year life of the 

study. The soil sampling program was accomplished by members of the 

Interagency Land Retirement Team and Reclamation’s Technical Service Center. 

Baseline soil samples were collected at the Tranquillity site during September and 

October 1999. The Tranquillity sites were re-sampled in November 2002 and 

August 2004 for the purpose of change detection. A rectangular sampling grid 

was chosen for monitoring soil chemistry at the demonstration project site 

(Figure 2-5). The sampling protocol used at the Tranquillity site is as follows. 

Baseline soil samples were taken at the land surface at 124 locations. Surface soil 

samples were taken at the corners of the 4 ha (10 acre) study plots from a depth of 

0-30 cm (0-1 foot) using a shovel. The samples were homogenized in the field at 

field moist conditions using a putty knife and stainless steel mixing bowls. The 

samples were collected at each site within a radius of about 1 meter of the staked 

locations. The coordinates of the sample locations were recorded in the field with 

a Global Positioning System (GPS) receiver. Discrete soil samples were taken at 

depths of 0-30 cm (0-1 foot), 60.9 - 91.4 cm (2-3 feet), and 121.9-152.4 cm 

(4-5 feet) at the centers of the 4 ha (10-acre) experimental plots to assess baseline 

soil chemistry with depth from the land surface (Figure 2-5). The baseline 60.9 to 

91.4 cm and 121.9 to 152.4 cm (2-3 and 4-5 foot) depth samples were taken with 

a 10.1 cm (4-inch) inside diameter split barrel core sampler to a depth of 152.4 cm 

(5 feet). A continuous core was obtained at each site by pushing the core barrel 

with the hydraulic system of a Mobile Drill Model B-90 drill rig. Discrete depth 

samples were taken at a total of 26 locations at the site during the baseline 

sampling event. The discrete depth samples were homogenized in the field at 

field moist conditions using a putty knife and stainless steel mixing bowls. The 

coordinates of the sample locations were recorded in the field with a GPS 

receiver. 

During the re-sampling events in 2002 and 2004, a slightly different sampling 

strategy was employed. Eight-increment composite soil samples were collected 

in a stratified random manner from the 0-30 cm (0-1 foot) depth within a 6.1 m 

(20-foot) radius of the original baseline sampling site. The 60.9 to 91.4 cm and 

121.9 to 152.4 cm (2-3 and 4-5 foot) depth discrete soil samples were collected 

from a single core located approximately 152.4 cm (5 feet) south of the original 

site for the 2002 sampling event, and 152.4 cm (5 feet) west of the original site in 

the 2004 sampling event. The 152.4 cm (5 feet) offset was used to ensure that 

backfill from the original sampling site was not incorporated into the later sample. 

Identical sampling depths of 0-30, 60.9 to 91.4 and 121.9 to 152.4 cm (0-1, 2-3 

and 4-5 feet) were used for all the surveys. The 0 to 30 cm (0-1 foot) depth 

samples were collected with a tile spade. A hand auger was used to collect all the 

60.9 to 91.4 and 121.9 to 152.4 cm (2-3 and 4-5 feet) depth samples in the 2002 

and 2004 sampling events. A total of 110 sites were re-sampled in 2004. A 
Land Retirement Demonstration Project 

Five Year Report 

18 

Figure 2-5. Soil sample locations at the Tranquillity site. 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

19 

subset of 57 sites, including nearly all of the 1.5 m (5 feet) deep (24 of 26) boring 

sites, were re-sampled in the 2002 sampling event. 

2.2.6.3. Soil Chemical Analyses 

The soil samples were tested for total selenium, soluble boron, soluble selenium, 

and soil salinity. Soil salinity analysis included the electrical conductivity of one 

part soil, five-part water extracts (ECe), and the electrical conductivity of 

saturation extracts (ECe). The ECe test was used to be consistent with the baseline 

sampling event while the saturation extracts were run to evaluate soil salinity in 

relation to plant growth response. 

The Quality Assurance Project Plan (QAPP) for the Land Retirement 

Demonstration Project describes in detail the analytical procedures and quality 

assurance measures taken to ensure soil and water data quality (CH2MHill 1999). 

Data quality analysis and data validation were conducted by Reclamation’s MidPacific Regional Office, Environmental Monitoring Branch. Soil samples were 

sent to Reclamation’s Technical Service Center in Denver (D-8570), Soil and 

Sediment Laboratory to be dried, ground, mixed, and split for chemical analysis. 

The D-8570 laboratory determined pH5, pH paste, ECe, percent field soil 

moisture by weight, and saturation percentage. The soil preparation lab also 

inserted about 15 percent certified reference materials and water samples in the 

sample batches that were sent to the analytical laboratory. These samples were 

double blind to the analytical laboratory. Samples were sent to the U.S. 

Geological Survey (USGS) Rock and Mineral Analysis Laboratory for selenium 

and boron analysis. Selenium was run by hydride generation (Method A011), 

while boron was determined by ICAP (Method E011) analysis. Total selenium 

was determined on a multi-acid digest. All USGS testing procedures used in this 

investigation are listed in their analytical methods manual (USGS 1996). 

2.2.6.4. Groundwater Level Monitoring 

One of the primary objectives of the Demonstration Project is to measure the 

response of the shallow water table to land retirement. Various conceptual and 

numerical models (SJVDP 1990a, Fio 1999, and Belitz and Phillips 1992) 

predicted a decline in the shallow water table in response to land retirement. 

FWS established a performance objective for the project that the depth to 

groundwater will not show a net increasing trend (decreasing depth to the soil 

surface) over a 5-year monitoring period (FWS 1999). There are approximately 

50 monitor wells and 3 drain sumps in the project vicinity that are used to 

measure groundwater levels beneath the site on a quarterly basis. Water levels are 

measured to the nearest 3 millimeter (mm) (0.01 foot) using an electric well 

sounding device. The water level data are recorded in a field book and is on file 

at the Reclamation office in Fresno, California. The locations of the monitoring 

wells and sumps are shown on Figure 2-6. Existing wells constructed prior to the 

1998 purchase of the demonstration project lands were installed by Westlands 

Water District and Reclamation for the primary purpose of measuring depths to 
Land Retirement Demonstration Project 

Five Year Report 

20 

Figure 2-6. Monitor well and sump location map, Tranquillity site. 

groundwater beneath drainage impacted lands in WWD. The previously existing 

wells are constructed of polyvinyl chloride (PVC) casing ranging in diameter 

from 1.9 to 10.1 cm (0.75 to 4 inches) and vary in depth from 0.9 to 26 m (3 to 86 

feet) below the ground surface. These wells were installed using various 

construction techniques that range from jetting a short length of pipe into the 

ground to standard rotary drilling with hydraulic drill rigs. A complete set of 

water level data are available from 20 monitoring wells at the project site for the 

entire period of record from October 1999 to October 2004. 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

21 

During summer 1999, Reclamation installed 15 additional wells to measure 

groundwater levels and to obtain representative groundwater samples for water 

quality analyses for this study. The new wells were installed using a hollow stemauger drill rig and are constructed of 5 cm (2-inch) PVC casing and 3 m (10 feet) 

sections of 0.5 mm (0.020 inch) slotted PVC wellscreen. A commercial filter 

pack was placed around the wellscreen with a tremie pipe. Screened intervals 

were chosen after reviewing the soil cores during drilling. Typical screened 

intervals for the shallow wells are 4.3 to 7.3 m (14 to 24 feet) below land surface. 

The wellscreens for the deeper wells were placed in the more permeable materials 

encountered during drilling and range in depth (to bottom of wellscreen) from 15 

to 24 m (50 to 78 feet) from land surface. Well construction diagrams for the new 

wells are on file at the Reclamation office in Fresno, California. Well 

construction diagrams for the previously existing wells are unavailable. 

There are 18 subsurface drain water collection sumps located in a north-to-south 

alignment bisecting the northern half of Section 15 at the site. The sumps are part 

of an experimental drainage system that was installed at the site in 1966. 

Subsurface tile drains lines were installed beneath the northwest quarter of 

Section 15 at a depth of approximately 1.8 m (6 feet), with a drain spacing of 

approximately 46 m (150 feet) and a length of approximately 366 m (1,200 feet). 

The drain lines are 5 to 10 cm (2 to 4 inches) in diameter and discharge to 

91.4 cm (3 feet) diameter concrete outlet stands that are open to the atmosphere. 

The outlet stands are connected to a master sump by a 39 cm (12 inch) collector 

pipe. Water levels have been measured quarterly using an electric sounding 

device in the three outlet stands shown in Figure 2-6. No drain water was 

discharged by pumping the master drain sump during this study. 

2.2.6.5. Groundwater Quality Monitoring 

A groundwater quality monitoring program was implemented to assess project 

performance against standards set by FWS (FWS 1999). The groundwater quality 

performance standard states that the selenium concentration in the groundwater 

will not show a net increasing trend over 5 years of monitoring. Groundwater 

samples were taken on a quarterly basis during year 1 and year 5 of monitoring at 

the Tranquillity site. The baseline year groundwater quality samples were taken 

in October 1999 and February, May, and July 2000. The 5-five groundwater 

samples were taken in October 2003 and February, May, and July 2004. Annual 

groundwater samples were taken in May 2001, 2002, and 2003. Unfiltered 

groundwater samples were taken from 12 wells and 2 drain sumps to assess 

baseline groundwater quality at the site. Shallow wells were sampled with a 

peristaltic pump or bailer while the deep wells were sampled with a submersible 

pump (Grundfos Redi Flo 2). Standard operating procedures for groundwater 

sampling used by the Mid-Pacific Region of Reclamation and those outlined in 

the Quality Assurance Project Plan for the Land Retirement Demonstration 

Project (CH2M Hill 1999) were employed to obtain, preserve, and analyze 

groundwater samples. 
Land Retirement Demonstration Project 

Five Year Report 

22 

Unfiltered groundwater samples were analyzed for major ions (calcium, 

magnesium, potassium, sodium, chloride, sulfate, total alkalinity), trace elements 

(selenium, boron, iron, manganese), and isotopes (H2

, O18 and H3). Specific 

conductance (electrical conductivity), pH, and temperature of groundwater 

samples were measured in the field at the time of sampling. Fluorometric 

analyses of groundwater samples for selenium were performed by Olsen 

Biochemistry Laboratories, South Dakota State University. Analyses for isotopes 

(H2, O18) were performed by the USGS Water Resources Division Laboratory in 

Reston, Virginia. Analyses for tritium (H3

) were performed by the USGS Water 

Resources Division laboratory in Menlo Park, California. All other analyses were 

performed by various contract laboratories with oversight from the environmental 

monitoring branch of Reclamation in Sacramento, California. 

The selenium data in groundwater were evaluated for seasonal bias using the 

SYSTAT (SPSS 2000) nonparametric Kruskal-Wallis one way analysis of 

variance procedure. The selenium trends for individual monitor wells were 

analyzed with SYSTAT using both parametric and non-parametric regression 

techniques. The Wilcoxon sign rank test was used to analyze the selenium data 

for soil. 

2.2.7. Groundwater Response to Land Retirement 

Groundwater level data were analyzed by plotting hydrographs for individual 

monitoring wells—hydrographs are time series plots of groundwater levels 

measured in monitor wells. Synoptic groundwater maps depicting the depth to 

shallow water table on a site-wide basis on specific dates were also used to 

examine water table response over time. The synoptic maps were produced using 

the Spatial Analyst module of the Environmental Systems Research Institute 

(ESRI) ArcView software. A contour map showing net water table declines over 

the 5-year monitoring period was produced using version 8 of Surfer (Golden 

Software 2004) to show the spatial distribution of the water table response. 

Groundwater level data from the demonstration site support the conceptual model 

of a declining shallow groundwater table in response to land retirement. All of 

the wells monitored at the Tranquillity site have shown a declining water level 

trend over the 5-year period of record. The hydrographs for the drain sumps and 

wells shown in Figure 2-7 are representative of the declining groundwater level 

trend observed at the site during the 5 years of monitoring. The hydrographs 

shown in Figure 2-7 represent water levels measured in three drain sumps (15C1, 

15F2, 15K1) during the time period from July 1998 to July 2000. The drain 

sumps are connected to tile drain lines that underlie the northwest quarter of 

Section 15, and are useful for measuring shallow groundwater trends in that 

portion of the site. The drain sump locations are shown in Figure 2-6. No water 

was pumped from the sumps during the demonstration project. All three of these 

sumps show an overall declining trend in groundwater levels for the period of 

record. Total water-level declines observed in sumps 15C1, 15F2, and 15K1 are 

1.4, 0.9, and 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

23 

Figure 2-7. Hydrographs for three agricultural drain sumps at the Tranquillity site 

showing a declining shallow groundwater trend. 

0.7 m (4.5, 3.0, and 2.4 feet), respectively. Sumps 15C1 and 15 F2 were observed 

to be completely dry starting in January 2000, while sump 15C1 was observed to 

be completely dry starting in October 2000. The drain sumps have remained dry 

as of October 2004. 

The hydrographs for wells 325 and 326 are shown in Figure 2-8. These 

hydrographs are representative of the declining water level trends observed at the 

site during the 5 years of monitoring. The total water-level declines observed in 

wells 325 and 326 for the period of record are 3.08 and 3.14 m (10.1 and 

10.3 feet), respectively. These wells constitute a nested pair of wells that were 

drilled in the same location but are completed at different depths. All of the 

nested well pairs at the site have significant vertical (downward) groundwater 

gradients, indicating perched water table conditions at the site. A declining 

groundwater level trend was observed in wells 15M1 and 16A1 (Figure 2-9). The 

total water-level declines observed in wells 15M1 and 16A1 were 2.7 and 3 m 

(8.8 and 9.8 feet), respectively. 

Synoptic depth to groundwater maps are another way to portray the decline of the 

shallow water table at the Tranquillity site. Figure 2-10 through Figure 2-12 show 

the depth to groundwater from the land surface as measured in monitor wells at 

the site in October 1999, 2000, and 2001. The measured depth to groundwater 

data was contoured using ESRI ArcView Spatial Analyst software. During 

October 1999, approximately 30 percent 243 ha (600 acres) of the site was 

underlain by a water table within 2.1 m (7 feet) of the land surface. During 
Land Retirement Demonstration Project 

Five Year Report 

24 

Figure 2-8. Hydrographs for the monitor well cluster site 325 and 326 at the 

Tranquillity site showing a declining shallow groundwater trend and vertical 

(downward) hydraulic gradient. 

-18

-16

-14

-12

-10

-8

-6

-4

-2

0

Aug-99Nov-99Feb-00May-00Aug-00Nov-00Feb-01May-01Aug-01Nov-01Feb-02May-02Aug-02Nov-02Feb-03May-03Aug-03Nov-03Feb-04May-04Aug-04

Date

Depth to Groundwater from Land Surface (ft)

 Well 15M1

Well 16A1

Figure 2-9. Hydrographs for monitor wells 15M1 and 16A1 at the Tranquillity site 

showing a declining shallow groundwater trend. 

-25

-20

-15

-10

-5

0

May-98Aug-98Nov-98Feb-99May-99Aug-99Nov-99Feb-00May-00Aug-00Nov-00Feb-01May-01Aug-01Nov-01Feb-02May-02Aug-02Nov-02Feb-03May-03Aug-03Nov-03Feb-04May-04Aug-04

Date

Depth to Groundwater from Land Surface (Ft)

 Well 325 (24 ft)

Well 326 (47 ft)
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

25 

Figure 2-10. Depth to shallow groundwater, October 1999. The project area 

underlain by shallow groundwater within 2.1 m (7 feet) of the land surface is 

approximately 243 ha (600 acres). 
Land Retirement Demonstration Project 

Five Year Report 

26 

Figure 2-11. Depth to shallow groundwater, October 2000. The project area 

underlain by shallow groundwater within 2.1 m (7 feet) of the land surface is 

approximately 22 ha (55 acres). 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

27 

Figure 2-12. Depth to shallow groundwater, October 2001. The project area 

underlain by shallow groundwater within 2.1 m (7 feet) of the land surface is 

approximately 14 ha (34 acres). 
Land Retirement Demonstration Project 

Five Year Report 

28 

October 2000, approximately 3 percent of the site (22 ha or 55 acres) was 

underlain by a water table within 2.1 m (7 feet) of the land surface. In October 

2001 the area of the site underlain by a water table within 2.1 m (7 feet) of the 

land surface decreased to less than 2 percent of the site (14 ha or 34 acres). As of 

October 2002, no part of the site had a shallow water table within 2.1 m (7 feet) of 

the land surface. 

The site can be divided into two distinct areas based on the depth to groundwater 

observations. The depth to the water table north of Adams Avenue (Section 10) 

was significantly greater than that observed south of Adams Avenue. The 

differences can be attributed to two factors. This northern part of the site 

(Section 10) has been retired from irrigated agriculture since 1994, and has not 

received significant application of irrigation water (groundwater recharge) since 

that time. Section 10 is also underlain by more permeable Sierran sand deposits, 

which allow more rapid percolation of applied irrigation water. 

Analyses of the groundwater data at the Tranquillity site indicate a decreasing rate 

of water table decline over time. The slopes of the hydrographs shown in 

Figure 2-8 and Figure 2-9 show a flattening trend over time. Examination of 

individual wells suggests that the extinction depth for groundwater evaporative 

discharge may be about 3 m (10 feet). The volume and flow of upflux is so small 

between a depth of 2.1 and 3 m (7 and 10 feet) that evaporative discharge in the 

soil cracking system at the 60.9 to 121.9 cm (2-4 feet) depth may be sufficient to 

maintain a very small amount of unsaturated upward flow. Once the water table 

receded below 3 m (10 feet), all discharge is believed to be vertical deep 

percolation through the first barrier layer. Deep percolation rates are controlled by 

the permeability of the first barrier layer and the hydraulic head on the barrier. 

Examination of well logs, cone penetrometer data, and nested well water levels 

indicates the first barrier layer is present at depths ranging from 4.0 to 9.1 m (13- 

30 feet) below the ground surface (average 6.1 m or 20 feet) and that unsaturated 

conditions are present below the first barrier layer. The average annual rate of 

decline was about 44 cm (1.2 feet) per year which equates to a water volume of 

about 1.8 cm (.06 feet) per year. This rate is expected to decrease as less head is 

available to push water through the barrier layer. 

2.2.7.1. Natural Drainage Rates 

The Tranquillity site is currently isolated from actively irrigated lands; however, 

during the first few years of the study irrigation of lands near site 16Q1 may have 

contributed some lateral flows to that site. No commercial irrigation was 

conducted near well 15M1 and lateral gradients (.0008) have remained nearly flat 

in that area. The natural drainage at the demonstration site is controlled by the 

permeability of the first barrier layer, the depth of saturation above the barrier, 

and the thickness of the barrier layer. All nested wells in the area indicate 

unsaturated conditions below the first barrier layer and perched water table 

conditions. 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

29 

Based on observations of soil substrata at drill sites, examination of 12 cone 

penetrometer logs, as well as hydraulic conductivity testing in the area, the 

specific yield of the substrata in the 1.8 to 3.7 m (6-12 feet) zone is estimated at 

about 5 percent and the average depth to barrier is about 6.1 m (20 feet). 

Substrata soil textures at site 16Q1 were somewhat coarser in the deep substrata 

and a specific yield of 10 percent was estimated for that boring. Hydraulic 

barriers were also noted in the two drill holes. The barrier was at 6.2 m 

(20.5 feet) in well 15M1 and about 4.2 m (13.8 feet) in well 16Q1. Based on the 

water table decline over the 5-year period, the depth of the head on the hydraulic 

barriers and the assumption that lateral water movement and evaporative 

discharge is negligible, a vertical permeability and natural drainage rate could be 

estimated. Vertical permeability and natural drainage estimates are shown in 

Table 2-1. Soil data for site 15 M1 was used to estimate the natural drainage rates 

for the min, max, and average water table declines. 

Table 2-1. Estimates of Natural drainage rates and vertical permeability at the 

Tranquillity site. 

Site Water table decline (feet) Natural drainage rate 

(feet/year) 

Vertical permeability of 

barrier (feet/day) 

15M1 6.01 0.060 5.48 x 10-5 

15M1* 2.38 0.040 4.38 x 10-5 

16Q1 6.38 0.128 2.06 x 10-4 

Min 0.51 0.005 nd 

Max 9.54 0.095 nd 

Ave 5.79 0.058 nd 

* last 3 years after water receded below 10 feet. 

nd = not determined 

The FWS performance objective regarding declining groundwater levels in 

response to land retirement was clearly met. The combination of dry climatic 

conditions and greatly reduced application of irrigation water associated with land 

retirement have resulted in significant declines of the shallow water table at the 

Tranquillity demonstration site. Every monitor well at the site showed a declining 

water level trend over time. The average decline in the water table measured in 

15 wells at the site during the 5-year period of record is approximately 1.8 m 

(6 feet). The average rate of decline in the water table measured in these wells 

over the 5-year period of record was approximately 0.4 m (1.2 feet) per year. The 

maximum decline of the water table was 2.9 m (9.54 feet) (Well 16G1), while the 

minimum decline of the water table was 0.15 m (0.51 feet) (Well 10M1) 

(Table 2-2 and Figure 2-13) The largest drop in the water table occurred on the 

westernmost part of the site in section 16, while the smallest drop observed was in 

the northern part of the site in Section 10 (Figure 2-13). 
Land Retirement Demonstration Project 

Five Year Report 

30 

 Table 2-2. Groundwater level decline observed in fifteen 

 wells at the Tranquillity site for the time period from 

 October 1999 to October 2004. 

Well Water Level Decline (Feet) 

10M1 0.51 

15A1 5.94 

15A2 5.99 

15C2 5.65 

15M1 6.38 

15N2 6.90 

325 7.23 

15P1 6.78 

15F1 4.44 

16A1 7.69 

16B1 8.10 

16G1 9.54 

16J1 4.44 

16Q1 6.01 

23D4 4.27 

MAX 9.54 

MIN 0.51 

AVG 5.99 

RATE 1.20 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

31 

Figure 2-13. Contour map showing spatial distribution of net water table declines 

at the Tranquillity site from October 1999 to October 2004. 

5.02

0.51

5.94 5.65

6.38

7.23

6.78

4.44 7.69

8.1

9.54

4.44

6.01

4.27

2.05

3.03

0

1

2

3

4

5

6

7

8

9

10

23D4

15L1 15P1

325

16J1

16Q1

16G1 15M1

16A1

10M1

10P1

15C2 15A1

5.94

10G3

15F1

Decline in Feet

Well Number

Section 

Corner

10

16 15

8.1

16B1
Land Retirement Demonstration Project 

Five Year Report 

32 

2.2.8. Groundwater Quality 

2.2.8.1. Groundwater Salinity 

A general indication of the total dissolved ionic constituents in the groundwater 

can be obtained by determining the capability of a groundwater sample to conduct 

an applied electrical current. This property is reported as specific conductance 

(also electrical conductivity, EC), and is expressed in terms of the conductivity of 

a cube of water 1 square centimeter on a side. EC is expressed in units of 

microSiemens/cm (μS/cm). 

Baseline EC data for the groundwater samples collected during the first year of 

monitoring are presented in Table 2-3 and Table 2-4. The shallow, perched 

groundwater is extremely saline in nature. Salinity in the shallow groundwater 

and drain sump samples, expressed as EC, ranged from 11,500 to 76,980 μS/cm, 

with a median value of 43,925 μS/cm. By comparison, drinking water typically is 

less than 750 μS/cm, irrigation water is less than 1,250 μS/cm, and seawater is 

about 50,000 μS/cm. The groundwater samples obtained from the underlying 

semi-confined aquifer are much less saline. Salinity in the groundwater samples 

obtained from the deep wells (> 50 feet deep), expressed as EC, ranged from 

5,630 to 18,580 μS/cm, with a median value of 7,675 μS/cm. 

The extreme salinity of the shallow groundwater at the site is a result of the 

irrigation of saline soils. Naturally occurring salts have been leached from the 

soil profile under irrigated conditions. Salts also have been transported to the site 

in the applied irrigation water. Direct evaporation from the shallow water table 

and transpiration of applied water by crops has concentrated salts in the shallow 

groundwater, resulting in the high EC values observed in the shallow groundwater 

samples. 

2.2.8.2. Groundwater Major Ion Chemistry 

Baseline major ion chemistry for the groundwater samples collected during 

year 1 of monitoring at the Tranquillity site are presented in Table 2-5 and Table 

2-6. The groundwater found in the perched zone and in the underlying semiconfined aquifer is best described as a sodium-sulfate type of water. Sodium is 

the dominant major cation found in the shallow groundwater samples, with 

sodium concentrations ranging from 2,300 to 25,000 milligrams per liter (mg/L), 

and a median concentration of 13,000 mg/L. Sodium is also the dominant major 

cation found in groundwater samples taken from the deep wells, with 

concentrations ranging from 760 to 3,800 mg/L, and a median concentration of 

1,100 mg/L. Sulfate is the dominant major anion found in both the shallow, 

perched groundwater and in the underlying semi-confined groundwater at the site. 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

33 

Table 2-3. Baseline year groundwater quality data for shallow wells at the 

Tranquillity site — major ions and field parameters. 

Statistic Min. 

25th 

percentile Median 

75th 

percentile Max. Mean 

Number of Samples 44 44 44 44 44 44 

EC(field) (μS/cm) 11,500 32,620 43,260 52,350 76,980 41,987 

pH (field) 6.74 7.54 7.78 7.9 8.37 7.73 

Calcium (mg/L) 250 400 420 450 500 417 

Magnesium (mg/L) 42 250 525 663 1300 515 

Sodium (mg/L) 2,300 8,725 13,000 16,500 25,000 13,009 

Potassium (mg/L) 7 20 30 42 94 32 

Total Alkalinity 

(mg/L) 150 260 330 423 610 351 

Chloride (mg/L) 380 1,150 2,700 3200 4,100 2,332 

Sulfate (mg/L) 4,300 24,500 31,000 62,000 26,330 

Table 2--4. Baseline year groundwater quality data for deep wells at the 

Tranquillity site — major ions and field parameters. 

Statistic Min. 

25th 

percentile Median 

75th 

percentile Max. Mean 

Number of Samples 12 12 12 12 12 12 

EC(field) (μS/cm) 5,630 6,763 7,675 17,315 18,580 10,633 

pH (field) 6.82 7.13 7.21 7.28 7.46 7.21 

Calcium (mg/L) 280 300 320 360 390 327 

Magnesium (mg/L) 280 300 310 328 350 315 

Sodium (mg/L) 760 823 1,100 2,425 3,800 1,714 

Potassium (mg/L) 6 9 13 14 20 12 

Total Alkalinity 

(mg/L) 200 250 270 329 340 277 

Chloride (mg/L) 300 410 540 1,700 1,900 924 

Sulfate (mg/L) 2,100 2,750 3,100 5,525 7,300 4,067 
Land Retirement Demonstration Project 

Five Year Report 

34 

Table 2--5. Baseline groundwater quality data for shallow wells at the Tranquillity 

site — trace elements and tritium. 

Statistic Min. 25th 

percentile Median 75th percentile Max. Mean 

Number of Samples 44 44 44 44 44 44 

Boron (mg/L) 10 26 46 55 81 42 

Iron (mg/L) 0.1 0.8 2.1 15 160 19.4 

Manganese (mg/L) 0.008 0.11 0.23 1.1 3.9 0.757 

Selenium (mg/L) 0.005 0.195 1.28 3.812 5.39 2.095 

Tritium (TU) 0 0.9 2.4 3.7 6 2.3 

Table 2-6. Baseline groundwater quality data for deep wells at the Tranquillity 

site— trace elements and tritium. 

Statistic Min. 25th 

percentile Median 75th percentile Max. Mean 

Number of Samples 12 12 12 12 12 12 

Boron (mg/L) 2.5 2.8 3.2 6.6 8.3 4.4 

Iron (mg/L) 0.3 0.6 1.2 1.3 1.6 1 

Manganese (mg/L) 0.25 0.318 1.75 2.5 4.3 1.718 

Selenium (mg/L) < 0.0004 0.0005 1.84 1.91 1.95 1.0873 

Tritium (TU) 0 0.4 10.1 11.6 14 7.5 

TU = tritium units 

Sulfate concentrations found in groundwater samples from the shallow wells 

(< 15 m or 50 feet deep) ranged from 4,300 to 62,000 mg/L, with a median 

concentration of 24,500 mg/L. Sulfate concentrations in groundwater samples 

from the deep wells (> 15 m or 50 feet deep) completed in the semi-confined 

aquifer ranged from 2,100 to 7,300 mg/L, with a median concentration of 3,100 

mg/L (Figure 2-14). 

High sodium and sulfate concentrations in the groundwater on the west side of the 

San Joaquin Valley result from weathering of sulfate rich rocks in the adjacent 

Coast Ranges. Davis (1961) hypothesized that the sulfate in groundwater in the 

study region originates from the oxidation of organic marine shales containing 

reduced iron sulfide minerals. Presser et al. (1990) reported oxidation of iron 

sulfide minerals for west-side streams in the study vicinity. Another probable 

source of sulfate in the shallow groundwater is from gypsum (calcium sulfate) 

that has historically been applied to soils by farmers in the region as a method of 

soil salinity (sodium) management. 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

35 

Figure 2-14. Comparison of dominant major ion concentrations and electrical 

conductivity for groundwater samples from shallow and deep wells. 

2.2.8.3. Trace Elements in Groundwater 

The trace elements of concern monitored for this study include selenium and 

boron. High concentrations of selenium and boron in the shallow groundwater 

are of concern due to potential toxicity to wildlife and plants. Iron and 

manganese concentrations were also monitored because they provide insight into 

geochemical conditions in the groundwater system. A summary of baseline trace 

element data for the first year of groundwater monitoring is presented earlier in 

Table 2-5 and Table 2-6. 

Selenium concentrations measured in the shallow groundwater system 

(wells < 15 m or 50 feet deep) during the first year of monitoring were high, 

ranging from 5 to 5,390 μg/L (0.005 to 5.390 mg/L), with a median concentration 

of 1,280 μg/L (1.280 mg/L). By comparison, the Environmental Protection 

Agency (EPA) water-quality criterion for long-term exposure in aquatic 

environments is 5 μg/L (EPA 1988). It becomes clear why the conceptual model 

of a declining shallow water table is an essential element of land retirement in 

light of the extremely high concentrations of selenium observed in the shallow 

groundwater. Deverel and Millard (1988) concluded that the main factors 

affecting selenium concentrations in the shallow groundwater of the western San 

Joaquin Valley are the degree of groundwater salinity and the geologic source of 

the alluvial soils. 
Land Retirement Demonstration Project 

Five Year Report 

36 

Selenium concentrations measured in the deep wells (> 15 m or 50 feet deep) at 

the site showed considerable spatial variation (Table 2-6). Selenium 

concentrations found in well 15M3 (21 m or 69 feet deep), ranged from 1,840 to 

1,950 μg/L during the first year of monitoring, while selenium concentrations 

found in wells 15C3 and 10G3 (25 and 23 m or 83 and 75 feet deep, respectively) 

ranged from the analytical limit of detection (< 0.0004 mg/L) to 0.0005 mg/L. 

The large variation in selenium concentration seen in the deep wells may be 

explained due to differing geochemical conditions found in Coast Range deposits 

and the Sierran sands underlying the site. Well 15M3 is perforated in Coast 

Range sediments, while wells 15C3 and 10G3 are perforated in sediments derived 

from the Sierra Nevada Range. 

Dubrovsky et al. (1993) noted high concentrations of selenium in shallow 

groundwater in Coast Range sediments and low concentrations in underlying 

Sierra Nevada sediments in previous groundwater quality investigations in the 

western San Joaquin Valley. The authors hypothesized that the absence of 

selenium in groundwater from wells screened in the Sierra Nevada deposits may 

be due to a redox (chemical reduction or oxidation) process. Selenium can exist 

in four valence states; -2, 0, +4, and +6. The +6 and +4 valences occur as the 

oxyanions selenate (SeO42) and selenite (SeO32) under alkaline, oxidizing 

conditions. Selenate is the most oxidized form of selenium, is relatively mobile in 

aqueous environments, and does not associate with solid phase materials (Leckie 

et al. 1980, Frost and Griffin 1977, and Hingston et al. 1974). Deverel and Fujii 

(1988) reported that the selenium in soil solutions and shallow groundwater in the 

western San Joaquin Valley is in the selenate form, and a very small percentage of 

soil selenium is in the absorbed phase. Although no attempt has been made to 

speciate selenium in groundwater samples from the Land Retirement 

Demonstration Project, the selenium found in the shallow groundwater at the site 

probably occurs predominantly as selenate. 

Under more reduced conditions, such as those found in the underlying Sierra 

Nevada deposits in the northern part of the site, selenium can exist as elemental 

selenium (zero valence) and selenide (Se2

). The solubility of selenate minerals 

generally is high (Elrashadi et al. 1987), and there are no apparent solubility 

constraints on selenate in shallow groundwater in the western San Joaquin Valley, 

even in groundwater saturated with respect to sulfate minerals (Deverel and 

Gallanthine 1989). Consequently, selenate tends to behave conservatively in 

oxidizing groundwater. The mobility of selenite in groundwater is severely 

constrained by adsorption onto a variety of mineral surfaces (Balistrieri and Chao 

1987, Neal et al.1987, Goldberg and Glanbig 1988). The solubilities of the 

reduced forms of selenium (elemental selenium and selenide) are extremely low 

(Elrashadi et al. 1987). Field and laboratory studies of selenium contamination at 

Kesterson Reservoir demonstrated selenium removal by reduction of selenate to 

less mobile forms (Lawrence Berkeley Laboratory 1987, White et al. 1988, Weres 

et al. 1989). Similar geochemical processes may be responsible for the extremely 

low selenium concentrations observed in Wells 15C3 and 10G3 at the Tranquillity 

site. 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

37 

Dubrovsky et al. (1993) noted that selenium concentrations in groundwater 

decreased rapidly at the same depth at which manganese concentrations increase 

at a research site located in the vicinity of the Tranquillity site in the western San 

Joaquin Valley. The authors concluded that the decrease in selenium is due to a 

process that occurs under reducing conditions. High concentrations of dissolved 

iron and manganese in groundwater can indicate geochemically reducing 

conditions. A similar trend is observed at the land retirement study site when 

ratios of selenium to manganese concentrations are plotted verses well depth. The 

selenium/manganese ratios are generally high in the shallow wells and extremely 

low in the deep wells, especially those perforated in the Sierran deposits 

(Figure 2-15). This supports the conceptual model that oxidizing conditions are 

prevalent in the shallow groundwater, and that reducing conditions are prevalent 

in the deep groundwater found in the Sierran deposits. The presence of reducing 

geochemical conditions in the Sierran deposits probably play a significant role in 

the extremely low selenium concentrations observed in wells 15C3 and 10G3. 

Figure 2-15. Ratio of selenium to manganese (Se/Mn) concentration in 

groundwater samples plotted verses well depth. The Se/Mn ratio shows a 

decreasing trend with depth indicating oxidizing geochemical conditions in the 

shallow wells and reducing conditions in the deep wells. 
Land Retirement Demonstration Project 

Five Year Report 

38 

2.2.8.4. Selenium Trend in Groundwater 

The Fish and Wildlife Service established performance standards for selenium in 

groundwater in the Biological Opinion for the Land Retirement Demonstration 

Project (FWS 1999). The performance standard for selenium in groundwater 

specifies that the selenium concentration in groundwater will not show a net 

increasing trend over the 5-year monitoring period. The summary statistics for 

the annual selenium data for the wells monitoring Coast Range deposits at the 

Tranquillity site are shown in Figure 2-16 and Table 2-7. The annual selenium 

data for the Coast Range wells show a relatively high degree of spatial variability. 

The coefficients of variation (standard deviation/mean) for the annual data ranged 

from 0.79-0.89 mg/L. The 95 percent confidence intervals calculated for the 

median annual selenium data were also large, indicating high spatial variability. 

Figure 2-16. Boxplots of selenium concentrations in Coast Range deposits for the 

5 years of groundwater sampling at the Tranquillity site. The inner black boxes 

represent the 95 percent confidence interval of the median concentration. 

Table 2-7. Summary statistics for selenium concentrations measured in 

groundwater samples taken from Coast Range deposits for the 5 years of 

groundwater monitoring at the Tranquillity Site. All selenium concentrations are 

reported in milligrams/liter (mg/L). 

Year Number 

samples Min 25th 

percentile Median Mean 75th 

percentile Max Std. Dev. Coeff. of 

variation 

1 45 0.095 0.237 1.910 2.237 3.975 5.39 1.782 0.79 

2 10 0.104 0.212 1.785 2.111 3.820 5.14 1.795 0.85 

3 10 0.110 0.222 1.595 2.367 4.468 5.70 2.107 0.89 

4 11 0.119 0.262 1.710 2.403 4.450 6.08 2.125 0.88 

5 44 0.110 0.272 1.610 2.441 4.345 6.72 2.089 0.85 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

39 

Regression analyses of selenium concentrations over time for individual wells 

were performed as a way to evaluate observed trends against the FWS 

performance standard for selenium in groundwater. 

A problem often encountered in time series analysis of groundwater quality data 

is the inherent seasonality sometimes present in the data. The seasonal variation 

in time series data may overwhelm any longer term trend. This is particularly true 

in a small data set. The Tranquillity well data consist of 11 samples collected 

from 10 wells and 8 samples from 1 other well between October 1999 and July 

2004. The samples are not consistent within the years. Of the 11 samples, 5 were 

collected during May and the remainder were collected during February, July, and 

October (2 in each month). The data were evaluated for seasonal bias using the 

SYSTAT (SPSS 2000) nonparametric Kruskal-Wallis one way analysis of 

variance procedure. The results are shown in Table 2-8. The seasons were 

represented by the 4 months in which the samples were collected. None of the 

well data sets showed any significant degree of seasonality (α < 0.05). It should 

be noted that there were only 8 samples from well 10M1 and that none of those 

samples were collected during October. The lack of seasonality helps to validate 

the use of linear regressions of selenium on time as a way to evaluate project 

performance. 

Table 2-8. Analysis of seasonality of selenium data based on Kruskal-Wallis 

1-way analysis of variance (ANOVA). 

Well K-W Stat. Prob. > K-W Stat 

10M1 1.409 0.4945 

15F1 1.618 0.6553 

15M1 0.955 0.8122 

15M3 3.711 0.2944 

15P1 4.950 0.1755 

16A1 0.589 0.8989 

16B1 1.372 0.7122 

16B3 0.354 0.9496 

16G1 0.275 0.9646 

16J1 2.653 0.4483 

16Q1 2.954 0.3988 

Parametric and non-parametric regression analyses were performed to analyze the 

selenium trends in eleven of the wells at the Tranquillity site using the SYSTAT 

statistical software (SPSS 2000). All of the wells with the exception of well 

10M1 monitor groundwater in the Coast Range deposits at the site. A way of 

eliminating the influence of large values early or late in the series is to run nonparametric (rank-order) correlations, rather than parametric correlation/ 

regressions. It should be noted that influence by large values also affects the 

distribution of residuals. Parametric correlation/regression analysis assumes that 
Land Retirement Demonstration Project 

Five Year Report 

40 

the residuals are normally distributed. The SYSTAT regression routine generates 

a number of statistics associated with the regression, including a list of outliers, 

identification of samples that exert undue influence on the result, and test 

statistics (F and t) for evaluating the significance of the relationship. None of the 

results showed observations that exerted undue influence on the results, but most 

included outliers. The effect of outliers is discussed later in this document. 

Table 2-9 shows a comparison of the results of the nonparametric correlations 

with those of parametric correlation/regression analysis, including tests of 

significance based on the F-value of the regression. In addition to the r2

-value, 

the parametric regression generates an r-value (correlation coefficient), which is 

the same as if only a correlation was calculated. The nonparametric (Spearman) 

correlations generate a statistic known as ρ. The probability distribution 

associated with the significance of r and ρ is slightly different when the number of 

pairs is 10 or less, but is the same when the number of pairs is 11 or greater. 

The parametric correlations show a significant increasing trend in selenium in 8 of 

the 11 wells (Table 2-9). The remaining three wells shown generated 

nonsignificant regressions and consequently showed no trend. There were also 

three wells that did not show a significant trend based on the nonparametric 

Spearman correlations. However, one of the nonsignificant parametric 

correlations shows a significant decreasing trend based on its Spearman 

correlation and one of the highly significant parametric trends (well 16J1 – r = 

0.787, probability < 0.01) becomes non-significant based on the non-parametric 

correlation. The correlations for the remaining wells indicate the same trend 

based on either of the correlations, although the trend for well 16B3 is less 

definitive (compare r and ρ) based on the nonparametric correlation. 

Table 2-9. Parametric and nonparametric correlations of selenium concentration in 

the Tranquillity wells on time 

Well r2 Pearson r Prob. > r1 Spearman ρ Prob. > ρ1

10M1 0.4465 -0.6682 N.S.2 -0.8193 < 0.05 

15F1 0.6931 0.8325 < 0.01 0.8091 < 0.01 

15M1 0.5133 0.7164 < 0.05 0.8364 < 0.01 

15M3 0.1099 0.3315 N.S. 0.5023 N.S. 

15P1 0.0639 -0.2527 N.S. 0.1142 N.S. 

16A1 0.8099 0.8999 < 0.01 0.8246 < 0.01 

16B1 0.9049 0.9513 < 0.01 0.9589 < 0.01 

16B3 0.7874 0.8874 < 0.01 0.7608 < 0.05 

16G1 0.6621 0.8137 < 0.01 0.8585 < 0.01 

16J1 0.6195 0.7871 < 0.01 0.5695 N.S. 

16Q1 0.5291 0.7274 < 0.05 0.6865 < 0.05 1

 Prob.: probability of a Pearson’s r or Spearman’s ρ of the magnitude shown occurring by 

chance alone. 

2

 N.S. - not significant, i.e. prob. > 0.05. 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

41 

After a preliminary review of the regressions of the selenium data, it appeared that 

the outliers all occurred in the early part of the monitoring period. Because the 

data were not evenly distributed over time; i.e., four samples were collected 

during each of water years 2000 and 2004, with only one each in 2001, 2002, and 

2003, there could be a biasing effect. Because of the possible bias, the 

regressions were recalculated after deleting the outliers. The review also 

indicated that rather than being outliers, the samples that appeared to be outliers 

were showing that a nonlinear, rather than a linear, regression might be more 

appropriate. To evaluate this, nonlinear regressions were calculated both with and 

without the outliers. The results are summarized in Table 2-10 and some of the 

regressions are shown in Figure 2-17, Figure 2-18, Figure 2-19, and Figure 2-20. 

Where Table 2-10 indicates that there is no trend, either there was no significant 

regression or the regression was significant, but no trend could be discerned. 

Significant regressions showing no trend were confined to nonlinear regressions. 

Table 2-10. Summary of results of linear and nonlinear trends without and with 

adjustment for outliers. 

Trend without adjustment Trend with outliers deleted Well Outlier (Date) Linear Nonlinear Linear Nonlinear 

15M1 May-01 Increase Increase(?) Increase N/A1

15P1 Jul-00 None None None None 

15M3 May-02 None None2

 Increase Increase 

16B3 None Increase Increase —— —— 

16J1 None Increase Decrease3 —— —— 

16A1 May-01 Increase Increase Increase Increase 

15F1 None Increase Increase —— —— 

16Q1 Oct-99 Increase Decrease3 Increase Decrease3 

16G1 Oct-99 Increase Increase Increase Increase4

16B1 May-02 Increase Increase Increase Increase 

10M1 May-00 None None2

 Decrease None2

1

 Linear trend is more significant 

2

 Regression shows no current trend, but is statistically significant 3

 Following an initial increase, Se has been decreasing in more recent data 

4

 Increase initially, but eventually forms an asymptote 
Land Retirement Demonstration Project 

Five Year Report 

42 

16B1

r

2

 = 0.9049

0

0.02

0.04

0.06

0.08

0.1

0.12

0.14

0.16

0.18

0 10 20 30 40 50 60

Months

Selenium (mg/L)

Obs. NL Reg. Trend

r

2 = 0.9567

Figure 2-17. Selenium data and trend in well 16B1 along with “best fit” nonlinear 

regression [Sinusoidal Fit: y=a+b*cos(cx+d)]. 

16B1

r

2

 = 0.9533

0

0.02

0.04

0.06

0.08

0.1

0.12

0.14

0.16

0.18

0 10 20 30 40 50 60

Months

Selenium (mg/L)

Obs. Nonlinear Trend

r

2 = 0.9716

Figure 2-18. Selenium data and trend in well 16B1 without outlier datum along with 

“best fit” nonlinear regression - [Sinusoidal Fit: y=a+b*cos(cx+d)]. 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

43 

16B3

r

2

 = 0.7874

3.8

3.9

4

4.1

4.2

4.3

4.4

4.5

0 10 20 30 40 50 60

Months

Selenium (mg/L)

Obs. NL Reg. Trend

r

2

 = 0.8698

Figure 2-19. Selenium data and trend in well 16B1 along with “best fit” nonlinear 

regression - [Harris Model: y=1/(a+bxc

)]. 

16Q1

r

2

 = 0.5291

3.3

3.4

3.5

3.6

3.7

3.8

3.9

0 10 20 30 40 50 60

Months

Selenium (mg/L)

Obs. NL Reg. Trend

r

2

 = 0.8693

Figure 2-20. Selenium data and trend in well 16Q1 along with ‘best fit” nonlinear 

regression - [Rational Function: y=(a+bx)/(1+cx+dx2

)]. 
Land Retirement Demonstration Project 

Five Year Report 

44 

The performance objective for selenium in groundwater at the Tranquillity site 

established by FWS stated that the selenium concentration in groundwater shall 

not show a net increasing trend over the life of the project. The FWS 

performance objective was clearly not met. Rising levels of selenium observed in 

the shallow groundwater in the Coast Range deposits are likely a result of 

oxidation and advective transport of mobile selenium species in the alkaline 

conditions near the falling shallow water table. As long as the water table 

continues to decline as expected in response to land retirement, the high 

concentrations of selenium in the groundwater should have no consequences to 

biota at the site. In contrast, selenium is present at very low concentrations in the 

groundwater found in the coarse-textured Sierran deposits at the Tranquillity site. 

In the reducing geochemical environment observed in the Sierran groundwater, 

selenium is relatively insoluble and immobile. 

2.2.8.5. Boron in Groundwater 

The presence of high concentrations of boron in the shallow groundwater is of 

concern due to potential toxicity to plants and wildlife. Boron concentrations in 

the shallow groundwater at the site are very high. The boron concentrations 

measured in the shallow wells during the first year range from 10 to 81 mg/L, 

with a median value of 45.5 mg/L (Table 2-5). No water-quality criteria for boron 

exist for aquatic life or human health. No more than 750 μg/L of boron should be 

applied to sensitive crops (EPA 1986). Perry et al. (1994) proposed a toxicity 

threshold in water for crops and aquatic plants of 10 mg/L. Deverel and Millard 

(1988) noted that boron is geochemically mobile and present as oxyanions in 

oxidized, alkaline environments such as the western San Joaquin Valley shallow 

groundwater. 

The authors also reported high correlation between log transformed boron and 

specific conductance data for shallow groundwater in the western San Joaquin 

Valley. Boron concentrations observed in the deep wells at the site are an order 

of magnitude lower than those in the shallow wells. Boron concentrations 

measured in the deep wells during year 1 of monitoring range from 2.5 to 8.3 

mg/L, with a median concentration of 3.2 mg/L (Table 2-6). The large difference 

in boron concentration between the shallow and deep groundwater at the site may 

be due to adsorption onto soil surfaces or differing geochemical conditions 

between the shallow and deep groundwater systems. Adsorption of boron on soil 

particles can affect and limit its solubility (Keren and Bingham 1985). Fujii and 

Swain (1995) concluded that the relatively conservative behavior of boron 

observed in shallow groundwater in the San Joaquin Valley probably reflects the 

presence of high concentrations of competing constituents for adsorption sites. 

2.2.8.6. Origin and Isotopic Composition of Groundwater 

Groundwater samples were analyzed for tritium and stable isotope ratios of 

oxygen and hydrogen during the first 3 years of monitoring. A summary of the 

tritium data are presented in Table 2-5 and Table 2-6. The oxygen and hydrogen 

isotope data shown in Figure 2-21 can provide insight into the evaporation history 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

45 

of the water, while the tritium data can be used to develop an understanding of the 

age and origin of the groundwater at the site. 

2.2.8.7. Groundwater Age 

The levels of tritium, a radioactive isotope of hydrogen with a half-life of 12.43 

years, rose in the environment during the 1950s and 1960s because of 

atmospheric detonation of nuclear weapons. Tritium concentrations can be used 

to develop an understanding of the origin and history of water samples. Tritium 

concentrations in water samples are reported in tritium units (TU). Prior to 1952, 

precipitation contained < 5 TU. Due to radioactive decay, groundwater derived 

from precipitation before 1952 now has < 0.5 TU. Groundwater derived from 

precipitation recharged since 1952, including canal water used as irrigation since 

1968, commonly has a tritium concentration exceeding 10 TU. Groundwater with 

Figure 2-21. Plot of stable isotope data for groundwater samples from the 

Tranquillity site indicating the shallow groundwater has undergone significant 

evaporation. 

a tritium concentration of < 1.6 TU either has recharged prior to 1952 or may 

have originated as post-1952 irrigation water from deep wells. This large contrast 

in tritium concentration allows comparison of older groundwater, much of which 

was recharged prior to agricultural development, to young water recharged since 

1952 and derived from irrigation (Dubrovsky et al. 1993). 
Land Retirement Demonstration Project 

Five Year Report 

46 

The tritium data from the shallow wells indicate that the shallow, perched 

groundwater consist of a mixture of water recharged before and after 1952. 

Tritium concentrations of the shallow groundwater samples range from 0 to 6 TU, 

with a median concentration of 2.4 TU. Low tritium concentrations (< 1 TU) 

observed in wells 16Q1 and 16F1 may indicate recharge from irrigation water that 

was pumped from deep production wells completed in the sub-Corcoran aquifer. 

The tritium data from the deep wells (well 15M3 and 16B3) completed in coastal 

range deposits indicate that the groundwater was recharged before 1952. Tritium 

concentrations observed in these two wells ranged from 0 to 0.5 TU, with a 

median concentration of 0.1 TU. The tritium data from the deep wells completed 

in Sierra Nevada sediments indicate that the groundwater has been recharged 

since 1952. Tritium concentrations found in wells 15C3 and 10G3 range from 9.6 

to 14.0 TU, with a median concentration of 10.5 TU. 

2.2.9. Evaporative Concentration of Shallow Groundwater 

In areas where the water table is shallow in the western San Joaquin Valley, 

particularly at depths less than 1.5 m (5 feet) below land surface, evaporative 

concentration of dissolved solids in groundwater can increase salinity and 

selenium concentrations far above the levels resulting from leaching of soil salts 

by irrigation (Deverel and Fujii 1988). Under irrigated conditions, loss of water 

by evapotranspiration tends to concentrate salts in groundwater rather than soil 

because the salts are regularly flushed downward by percolating irrigation water 

and net groundwater movement is generally downward (Dubrovsky et al. 1993). 

Hydrogen and oxygen isotope concentrations from shallow groundwater samples 

at the Tranquillity site show that groundwater salinity is primarily a result of 

evaporation and evapotranspiration of the shallow groundwater. The evaporation 

process adds kinetic separation to the hydrogen2

 (deuterium) and oxygen18 species 

causing increased enrichment in the O18 species (Gat and Gonfiantini 1981). This 

results in a plot of the delta deuterium (D) verses delta O18 that has a smaller 

slope than the meteoric water line. The comparison of delta D and delta O18

shown in Figure 2-21 illustrates the evaporation that has taken place in the 

shallow groundwater at the site. Similar evaporative trend lines have been 

reported by Deverel and Fujii (1988) and Presser and Barnes (1984) for shallow 

groundwater in the western San Joaquin Valley. 

2.2.9.1. Surface Water 

In the Biological Opinion for the Land Retirement Demonstration Project, the 

FWS established performance standards for selenium and mercury concentrations 

in surface water. The performance standard specified that standing water that 

persists for more than 30 days shall not exceed 2 micrograms/liter (μg/L) 

selenium, and 2 nanograms/liter mercury (FWS 1999). Standing water at the site 

was monitored by examining precipitation data on the CIMIS website and 

periodically visiting the site during the wet season to document any standing 

water that persisted for more than 30 days in duration. Since groundwater levels 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

47 

beneath the site have steadily declined over the 5-year study, the only source of 

standing water would presumably come from precipitation that does not infiltrate, 

run off the site or evaporate within 30 days of a winter or spring storm event. 

No vernal pools that persisted for more than 30 days were observed at the 

Tranquillity site during the 5-year study. Precipitation during the study has been 

below average (Figure 2-4), and the maximum monthly rainfall observed during 

the study was just below 5 cm (2 inches) (Figure 2-3). The precipitation threshold 

for formation of vernal pools at the site is unknown, but is certainly in excess of 

5 cm (2 inches) per month. An important factor governing the formation of 

vernal pools at the site is the clay content of the soils. These basin rim clay soils 

have high plasticity indices (33-61 percent), and thus have a tendency to shrink 

upon drying and swell upon wetting as water enters and leaves the crystal lattice 

of the clay mineral structure. The shrink-swell behavior of the soil has resulted in 

a large network of surface cracks during the extended period of below-average 

rainfall (Figure 2-22). Before vernal pools can form on the surface, enough 

moisture must be absorbed by the clay soil to cause swelling sufficient to seal the 

surface cracks. Several unsuccessful attempts were made in 2004 to artificially 

simulate vernal pool formation by excavating small “ponds” and filling them with 

irrigation water. In all cases, the water seeped into the surface cracks after several 

days. 

Figure 2-22. Photos of open surface cracks in Tranquillity clay soils at the 

Tranquillity site (Jan 2005). 

The crack was open to a depth of approximately 42 inches on this date. Soil 

moisture from fall and winter storms had penetrated to a depth of about 12 inches. 

The extensive network of surface cracks in the soil at the site inhibits the 

formation of surface water ponds (vernal pools). 
Land Retirement Demonstration Project 

Five Year Report 

48 

2.2.10. Trend Analysis for Soils 

One of the objectives of the demonstration project was to evaluate the effect that 

land retirement would have on soils. Concerns were raised that upflux of shallow, 

saline groundwater with high selenium content on retired lands would salinize the 

surface soil and create potentially toxic conditions for wildlife. No performance 

objectives for soil salinity or soil selenium concentrations were established for the 

demonstration project. Constituents of concern for soil monitoring include soil 

salinity (ECe), selenium and boron. Soil salinity and selenium data collected at 24 

paired sites in 1999, 2002 and 2004 are presented in Figure 2-23 through Figure 

2-31. This data are from the central sampling location in each 10-acre 

demonstration plot at the Tranquillity site as well as four sites located on retired 

lands east of the plots in sections 10 and 15. The bar graphs indicate that most of 

the changes in constituents of concern (COC) concentrations occurred during the 

first 3 years of the demonstration project. 

Figure 2-23. ECe Trends in top foot of soil from 1999 to 2004. 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

49 

Figure 2-24. ECe Trends in 2 to 3 foot depth of soil from 1999 to 2004. 

Figure 2-25. ECe Trends in 4 to 5 foot depth of soil from 1999 to 2004. 

Figure 2-26. Soluble selenium trends in top foot of soil from 1999 to 2004. 
Land Retirement Demonstration Project 

Five Year Report 

50 

Figure 2-27. Soluble selenium trends in 2 to 3-foot depths of soil from 1999 to 

2004. 

Figure 2-28. Soluble selenium trends in 4 to 5 foot depths of soil from 1999 to 

2004. 

Figure 2-29. Total selenium trends in top foot of soil from 1999 to 2004. 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

51 

Figure 2-30. Total selenium trends in 2 to 3 foot depth from 1999 to 2004. 

Figure 2-31. Total selenium trends in 4 to 5 foot depth from 1999 to 2004. 

2.2.11. Change Detection Analyses 

The Wilcoxon sign rank test was used to determine if the concentration changes at 

the paired soil sampling sites were statistically significant at the 95 percent 

confidence level. All data presented in the following statistical summaries are on 

a dry soil weight basis except for the soil salinity data, which are the 

concentration of the extract. Table 2-11 summarizes statistical analysis of the 

1999 and 2004 data using the Wilcoxon sign-rank tests for each constituent of 

concern. 
Land Retirement Demonstration Project 

Five Year Report 

52 

Table 2-11. Change detection analyses for COCs in soil at the Tranquillity site. 

Constituents of 

Concern 

Depth 

(feet) 

Median 

1999 

ug/kg 

Median 

2004 

ug/kg 

Sites 

decreasing

Sites 

increasing 

Z change 

direction Prob>Z Significant 

(95% CI) 

Soluble 

Selenium 0-1 18 11 96 12 -8.03 down <0.00001 Yes 

Soluble 

Selenium 2-3 47 65 7 17 2.357 up 0.0184 Yes 

Soluble 

Selenium 4-5 82.5 125 4 22 3.823 up 0.000132 Yes 

Total 

Selenium 0-1 1000 990 66 19 -4.14 down 0.000035 Yes 

Total 

Selenium 2-3 940 1075 7 17 2.959 up 0.0031 Yes 

Total 

Selenium 4-5 920 910 11 10 0.400 up 0.6892 No 

Salinity 

(ECe) dS/m 0-1 3.66 1.53 102 8 -8.74 down <0.000001 Yes 

Salinity 

(ECe) dS/m 2-3 6.67 4.99 24 2 -3.54 

down 0.00396 Yes 

 Salinity 

(ECe) dS/m 4-5 7.35 5.88 22 4 -4.00 

down 0.000063 Yes 

2.2.12. Soil Interpretive Summary 

Total selenium concentrations, soluble selenium concentrations, and salinity 

(ECe) in the surface soil (depth 0-30 cm or 0-1 foot) at the Tranquillity site 

showed a decreasing trend over the 5-year study. Soils at the Tranquillity site 

contain moderately elevated concentrations of selenium (mean selenium 1.0 

milligrams per kilogram [mg/kg]) when compared to values reported for western 

U.S. and San Joaquin Valley soils (Table 2-12). 

Table 2-12. Comparison of total selenium concentrations at the Tranquillity site to 

Western U.S. and San Joaquin Valley soils. 

Mean selenium western states soils (Shacklette and Boerngen 1984) 0.34 mg/kg 

Mean selenium San Joaquin Valley soils (Tidball et. al. 1986) 0.14 mg/kg 

Mean selenium Tranquillity site (1999) 1.05 mg/kg 

Max selenium Tranquillity site (2004) 1.7 mg/kg 

Uncommonly high selenium western soils (Shacklette and Boerngen 1984) 1.4 mg/kg 

Typical sediment toxicity threshold 4 mg/kg 

Kesterson Reservoir sediment criteria (Benson et. al. 1993) 4 mg/kg 

The spatial variability for total selenium in the Tranquillity soil series is low 

(Figure 2-23). The coefficient of variation for total selenium in the Tranquillity 

soils was about 18 percent during the baseline sampling event in 1999. Total 

selenium concentrations appear to be slowly decreasing in surface soils at the site. 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

53 

This is an important trend because this represents the total inventory of selenium 

in the soil and is not subject to seasonal or temporary concentration changes due 

to climatic factors or soil reaction changes. Soluble selenium concentrations in 

surface soils (depth 0-30 cm or 0-1 foot) also decreased which is considered a 

positive change since most biologic activity takes place in surface soils. The 

soluble selenium concentrations in the substrata and the percent of soluble/ total 

selenium increased during the first 3 years but tended to decline during the 3-5-

year demonstration period. A summary of soluble selenium percentages is 

presented in Table 2-13. 

Table 2-13. Average soluble to total selenium percentages all sites at Tranquillity. 

Depth zone 1999 (57 sites) 2002 (57 sites) 1999 (all sites) 2004 (all sites) 

1 foot 3.2 2.5 2.9 1.5 

2-3 feet 8.1 13.2 8.1 10.1 

4-5 feet 15.3 28.7 15.2 19.1 

* 2002 data are for about 50 percent of the shallow sites but include 22 of 26 substrata sites. 

The surface soils appear to have been leached of selenium while the soluble 

selenium content of the substrata zones (60.9-91.4 cm and 121.9-152.4 cm or 

2-3 and 4-5 foot depth) appears to have been enriched somewhat by leaching from 

surface layers. The principal reason for soluble selenium increases in substrata 

appears to be the slight increase in soil reaction (pH) and the increased oxidized 

conditions present as the water table elevation and associated capillary fringe 

zone declined during the study period. 

Surface soil (0-30 cm or 0-1 foot depth) salinity (ECe) at the Tranquillity site 

decreased over the 5 years of monitoring for this study. Soil salinity decreased at 

102 out of 110 sites sampled from the 0-30 cm (0-1 foot) depth from 1999 to 

2004. Decreases in soil salinity based on 1-5 extract concentrations were 

statistically significant. Salinity declines were surprisingly large in soil surface 

samples. Decreases in soil salinity were also observed in the substrata (depths 

60.9-91.4 and 121.9-152.4 cm or 2-3 and 4-5 feet). Some of the soil salinity 

reduction in surface layers may be due to the beneficial leaching effects of 

rainfall. The predominant salt at the site is sodium sulfate which is very soluble 

in water. The magnitude of the soil salinity reduction may also be related to the 

soils tendency to form deep and wide cracks upon drying. Before the land was 

retired from irrigation, bare soil surface evaporation may have formed a salt 

concentration in the upper few inches of soil. Upon extended drying, the soil 

cracked deeply while the saline surface layers developed a loose crumb structure. 

Much of the loose surface material dropped into the deep cracks and was 

deposited in the substrata. Some of the cracks observed at the Tranquillity Site 

were more than 1.5 m (5 feet) deep and 30 cm (1 foot) wide. These soils are 

commonly termed vertisols since they have the ability to invert over many wetting 

and drying cycles. 
Land Retirement Demonstration Project 

Five Year Report 

54 

2.2.12.1. Saturation Extract Testing 

Saturation extract testing was also conducted to determine plant adaptability, 

relative growth potential, and other agronomic factors. Soluble selenium 

concentrations are not limiting for plant growth at the site. The average 

concentration found in saturation extracts from samples collected in the top foot 

of soil was 4.6 μg/liter. The element most limiting plant growth and adaptability 

in the site surface soils probably is boron. Soil salinity was decreasing and 

average ECe values in the 2004 surveys were 3.3 dS/m in the top foot of soil. 

Soil salinity levels and boron levels sharply increased with depth in substrata. 

Boron and soil salinity are both elevated at the site and would limit plant 

selections as well as plant growth of many plants. Figures 2-32 through 2-35 

show the ECe, SEe and the soluble boron concentration of surface soils 0-30 cm 

(0-1 foot) at the site during the 2004 soil surveys in September 2004. Soil boron 

phytotoxicity threshold levels are about 2 mg/L in a saturation extract and about 

4 mg/kg on a soil dry weight basis. ECe thresholds are about 4 ds/m. About 

40 percent of the survey area surface soils exceed soil salinity thresholds and 

about 95 percent exceed the boron threshold. Limited data collected during the 

survey indicate that soil salinity is lowest in the seedbed 0-10.1 cm (0-4 inch) inch 

zone. Seedbed soil salinity levels should permit germination, emergence, and 

growth of most climatically adapted native plants. 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

55 

Figure 2-32. Total selenium concentrations in surface soils 0-30 cm (0-1 foot) at 

the Tranquillity site from the 2004 sampling event. 

Land Retirement Demo Project - Tranquility Site

2004 Soil Sampling Event

Total Selenium in mg/kg at the 0-12" Depth

+ Sample Points

0 1000 2000 3000 4000 5000 6000 7000

Easting in Feet

0

1000

2000

3000

4000

5000

6000

7000

8000

9000

10000

Northing in Feet

0.64 0.39 0.19

0.58

0.45

0.66 0.74

0.68

0.66 0.91

0.95 0.76

0.83

0.82 0.78

0.83 0.84

0.84

0.87 1.1

0.67 0.85

0.75

0.86 0.81

0.61

1.2 0.71

0.89

0.93 0.79

1.1 1.7

1.5

1.2 1.5

1.25 1.1

1.4

1.3 1.4

0.89 0.81

1

1 0.79

0.87 1.1

1 0.95

0.93

1 1.1

1 1.2

0.99

0.99 1.1

0.98 1.1

1.1

1.1 1.2

1.2 1.1

1.2

1.1 1

1.1 1.6

1.1 1.1

1.1

1.1 1.2

0.99 0.94

0.89

0.84 0.99

1.1 0.96

0.99

1 1.05

1.1 1.2

1.1

1.1 1.3

1 0.95

0.84

0.85 0.93

1 1.1

1.1

0.98 1

1.1 0.91

0.94

0.99 0.83

0.92 0.84

0.92

0.93 1.1

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

1.1

1.2

1.3

1.4

1.5

1.6

1.7
Land Retirement Demonstration Project 

Five Year Report 

56 

Figure 2-33. Soluble selenium in surface soils 0-30 cm (0-1 foot) at the Tranquillity 

site from the 2004 sampling event. 

Land Retirement Demo Project - Tranquillity Site

2004 Soil Sampling Event

Soluble Selenium Saturation Extract

In ppb at the 0-12" Depth

+ Sample Points

0 1000 2000 3000 4000 5000 6000 7000

Easting in Feet

0

1000

2000

3000

4000

5000

6000

7000

8000

9000

10000

Northing in Feet

2.4 12.3 1.9

2.6

3.8

2.5 4.5

4.3

3.7 4.2

3.4 8.8

4.8

2.6 3

2.5 4.1

3.3

4 6.3

4.1 3.9

4.7

5.7 5.3

2.8

7.6 5.5

3

4 3.2

4.8 22

9.6

4.3 8.7

4.6 4.5

11

5.6 6.8

3.3 2.7

5.4

3.8 3.1

2.4 4.4

4 3.1

3.5

3.3 3.7

5.1 8.2

4

4.8 3.6

5.2 5.2

4.6

5.6 5.3

4.5 3.6

4.5

3.9 3.4

4.3 4.9

4.4 4.1

4.5

4.3 4.5

3.2 5.3

4.9

4.4 4.4

4.3 4.5

4.2

3.3 5.1

3.9 4

3.6

4.3 4

4 3.1

4.4

3.8 3.9

4.2 5.8

5.2

4.5 5.2

4.5 5.2

4.9

4.3 4.1

3.9 3.5

3.4

4.25 4

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

57 

Figure 2-34. Soluble boron concentrations in the surface soils 0-30 cm (0-1 foot) at 

the Tranquillity site from the 2004 sampling event. 

Land Retirement Demo Area - Tranquility Site

2004 Soil Sampling Event

Soluble Boron in mg/kg

 at the 0-12" Depth

+ Sample Points

0 1000 2000 3000 4000 5000 6000 7000

Easting in Feet

0

1000

2000

3000

4000

5000

6000

7000

8000

9000

10000

Northing in Feet

19.6 21.5 14.1

17.4

19.1

17.4 25.0

16.3

12.9 15.0

17.9 22.9

13.2

9.9 9.5

6.5 9.7

6.8

6.5 11.7

12.2 12.4

11.8

11.6 11.5

29.4

11.1 15.8

8.2

7.7 9.9

8.3 17.9

12.5

7.9 13.0

7.3 8.1

7.9

7.0 9.8

7.6 9.2

9.7

7.1 10.2

8.4 16.2

13.2 7.7

9.0

11.8 7.2

8.3 17.2

6.5

4.7 9.9

4.6 6.5

7.7

4.9 5.5

9.5 5.7

8.2

7.0 10.0

13.9 17.2

8.7 7.2

5.5

6.2 10.5

3.7 4.3

4.9

6.0 4.9

3.4 4.4

3.8

4.5 3.3

5.4 8.7

4.7

3.7 3.7

6.0 7.0

4.2

3.5 5.8

2.6 4.0

3.3

4.1 4.8

4.0 3.8

3.4

4.5 4.1

5.4 5.5

4.5

3.6 5.2

2

4

6

8

10

12

14

16

18

20

22

24

26

28

30
Land Retirement Demonstration Project 

Five Year Report 

58 

Figure 2-35. Soil salinity (ECe) concentrations (dS/m) in the surface soils 0-30 cm 

(0-1 foot) at the Tranquillity site from the 2004 sampling event. 

Land Retirement Demonstation Area

Tranquility Site

2004 Soil Sampling Event

ECe of Saturation Extract in dS/m

 at the 0-12" Depth

+ Sample Points

0 1000 2000 3000 4000 5000 6000 7000

Easting in Feet

0

1000

2000

3000

4000

5000

6000

7000

8000

9000

10000

Northing in Feet

5 6.12 3.42

3.38

6.2

4.71 5.61

4.51

3.38 5

5.24 4.54

4.81

3.66 3.41

3.14 3.97

3.04

1.56 4.55

4.3 3.72

5.56

5.22 4.37

5.84

6.14 4.62

3.49

3.73 4.65

3.24 8.5

6.45

4.45 6.27

3.74 4

5.01

3.18 4.69

3.91 3.72

4.31

3.43 4.06

3.62 4

3.98 3.21

3.28

3.58 4.22

2.85 5.44

2.91

1.94 3.12

2.71 2.9

3.07

2.54 2.95

4.09 3.07

3.59

3.51 4.14

5.65 3.48

3.58 2.51

2.57

3.36 4.22

1.7 1.77

1.22

2.5 1.39

1.22 1.67

1.52

1.39 1.34

2.82 3.94

2.72

1.36 1.53

2.43 3.15

1.16

1.09 2.41

1.01 1.43

1.3

1.77 1.522

1.24 1.4

0.79

1.7 1.28

1.84 1.46

2.29

2.1 2.68

0

1

2

3

4

5

6

7

8
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

59 

2.2.13. Conclusions 

Five years of groundwater monitoring at the Tranquillity site support conceptual 

and numerical models that predicted a declining shallow water table in response 

to land retirement. FWS performance objective regarding water table response to 

land retirement at the Tranquillity site was clearly met. Percolation of applied 

irrigation water prior to land retirement was the primary source of groundwater 

recharge that sustained the high water table. In the absence of irrigation recharge 

the shallow water table has steadily receded from the land surface over the 5-year 

study. Large downward hydraulic gradients measured at the site confirm the 

presence of perched water table conditions in the fine-grained Coast Range 

deposits. Discharge of the shallow groundwater occurs primarily through slow 

downward percolation through surficial clay deposits at the site. Some shallow 

groundwater was also discharged by evaporation from the water table when it was 

in close proximity to the land surface at the beginning of the study. The water 

table response observed at the Tranquillity site is representative of conditions that 

would be present at a high percentage of lands that are targeted for retirement on 

the lower alluvial fan and basin rim settings in the western San Joaquin Valley. 

The declining shallow water table is an important aspect of land retirement due to 

poor quality of the shallow groundwater observed beneath the Tranquillity Site. 

The high salinity and selenium concentrations in the shallow groundwater found 

in the Coast Range deposits at the site are a result of leaching under irrigated 

conditions and evaporation from the shallow water table. Evaporation from the 

shallow water table has concentrated salts and trace elements in the shallow 

groundwater. The FWS performance objective for selenium in groundwater at the 

Tranquillity site was clearly not met. Rising levels of selenium observed in the 

shallow groundwater of the Coast Range deposits are likely a result of oxidation 

and advective transport of mobile selenium species in the groundwater near the 

falling shallow water table. As long as the water table continues to decline as 

expected in response to land retirement, the high concentrations of selenium 

in groundwater should have no consequences to biota at the site. In contrast, 

selenium is present at very low concentrations in the groundwater of the coarse 

textured Sierran deposits at the Tranquillity site. In the reducing geochemical 

environment observed in the Sierran groundwater, selenium is relatively insoluble 

and immobile. 

The predominant soil type at the Tranquillity site is Tranquillity clay. This is the 

most extensive soil type mapped by the Natural Resources Conservation Service 

on the lower alluvial fans and basin rim landforms in the areas targeted for land 

retirement by district and federal programs. Soils at the Tranquillity site contain 

moderately elevated concentrations of selenium (average 1.0 mg/kg) when 

compared to the common range (0.1-1.4 mg/kg) for western U.S. and San Joaquin 

Valley soils; however, they are still well within the range commonly found in 

western soils. Total selenium concentrations, soluble selenium concentrations, 

and salinity in the surface soil (depth 0-1 foot) showed a decreasing trend over the 

5 years of monitoring at the Tranquillity site. The decreasing selenium and 

salinity trends in the surface soil indicate that upflux of salt and selenium from 
Land Retirement Demonstration Project 

Five Year Report 

60 

capillary rise and evaporation of shallow groundwater at the soil surface is 

minimal, and that some leaching of soluble selenium and salt from surface soils 

occurred during the 5-year study despite dryer-than-average climatic conditions. 

About 10-20 per cent of the selenium present in the subsoils is soluble and mobile 

in the alkaline, oxidizing chemical conditions found in the soil. Soluble selenium 

concentrations and percentages are much lower in the surface soils (average 4.6 

parts per billion [ppb] in saturation extracts). Even if surface water ponding 

should occur during very wet periods, it is probable that selenium concentrations 

in the ponded water would be below the aquatic life criteria of 5 ppb. No 

performance objectives were established for soil selenium levels for the 

demonstration project; however, the maximum surface soil concentration 

observed during the 5 years of monitoring at the Tranquillity site was well below 

typical soil toxicity thresholds for sediment (4 mg/kg). 

FWS established performance standards for selenium and mercury in ponded 

surface water that lasts for more than 30 days. Due to dry climatic and soil 

conditions during the study, no surface water ponding was observed at the site 

that lasted for more than 30 days. Monitoring of precipitation during the course 

of the study suggests that the precipitation threshold to cause ponding of surface 

water at the site is well in excess of 5 cm (2 inches) of rainfall per month. The 

extensive network of desiccation cracks in the clay soils at the Tranquillity site 

greatly inhibits the formation of surface water ponds. 

2.3. Atwell Island Site 

2.3.1. Geology 

The Atwell Island demonstration site lies on the southwestern margin of the 

Tulare Lake bed, which is the dominant geologic feature in the study area. The 

site is underlain by lakebed and marsh deposits consisting primarily of clay and 

silt with some sand with a thickness in excess of 1,097 m (3,600 feet) (Page 

1986). The Corcoran Clay member of the Tulare Formation is a regionally 

extensive, fine-grained lake-bed deposit that underlies the Atwell Island site at a 

depth of approximately 274 m (900 feet) below the land surface. A relict sand 

dune deposit consisting of fine-grained wind-blown sand from the former 

shoreline of the Tulare Lake bed traverses the western boundary of the site from 

southwest to northeast. 

2.3.2. Soils 

Soils in the Atwell Island study area consist of silt loam and fine sandy loams that 

are formed in alluvium derived from igneous and sedimentary rocks. Silty clay 

loam soils are also present in the southeast portion of the site. Individual soil 

mapping units found in the study area, in the order of abundance, include the 

Posochanet silt loam, Nahrub silt loam, the Westcamp silt loam, Excelsior fine 

sandy loam, and Lethent fine sandy loam. The Posochanet soils occur primarily 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

61 

in the central portion of the site and cover about 30 percent of the total study area. 

These soils are saline, alkaline, very deep, and moderately well-drained with slow 

permeability. Subsoil and substrata textures are commonly silty clay loam and 

silty clay. Salinity ranges from 4 to 8 dS/m in the upper portion and 4 to 30 dS/m 

in the lower portion. Surface runoff is generally slow, with a low hazard of water 

erosion. 

Nahrub silt loam occurs on basin rims and consists of mixed alluvium from 

granitic rocks. Nahrub soils cover about 30 percent of the total surface area in the 

southeast part of the site. These soils are very deep, somewhat poorly drained, 

with very slow permeability. Salinity ranges from 1-16 dS/m in the upper part to 

8-30 dS/m in the lower part. Surface runoff is very slow with low surface erosion 

hazard. 

Westcamp silt loam soils cover the northwest corner of the study area. The 

Westcamp soils are saline, alkaline soils that have a perched water table. These 

soils are very deep, somewhat poorly drained, with very slow permeability. A 

transient perched water table occurs at a depth of 1.2-1.8 m (4-6 foot). Salinity 

ranges from about 2-16 dS/m. 

Excelsior fine sandy loam soils are found on the sand ridge that traverses the site 

from northeast to southwest. The sand ridge covers about 15 percent of the total 

study area. The Excelsior soils are very deep, somewhat excessively drained, 

alkaline soils. Permeability of the sand ridge soil is moderately rapid, runoff is 

very slow and hazard of water erosion is slight; however, the potential for wind 

erosion is high under sparsely vegetated conditions. Salinity ranges from 0-8 

dS/m in the upper part and 2-16 dS/m in the lower part. 

The Lethent fine sandy loam occurs in a small area in the southwest part of the 

study area. This soil is saline, alkaline, very deep, and moderately well drained. 

Permeability is very slow and the hazard of water erosion is slight. 

2.3.2.1. Soil Monitoring 

Soil Sampling Baseline soil sampling was conducted at the Atwell Island site 

during spring 2002. Sixteen sites were sampled within each experimental study 

area. Each site was located at the approximate center of the 0.8 ha (2-acre) 

research plots (Figure 2-36). Three soil samples were collected from each site. A 

0-30 cm (0-12 inch), four increment composite soil sample was collected within 

3 m (10 feet) of the central boring. A single soil sample was collected from the 

30-76 cm (12-30-inch) depth interval. This sample represents the active root zone 

of irrigated soils. A single soil sample was also collected from the 76-152 cm 

(30-60-inch) substrata zone. This zone represents the lower root zone just above 

the vadose zone. All soil material was sampled in the 30-76 cm and 76-152 cm 

(12-30 and 30-60-inch) samples. Sampling in this manner resulted in 48 soil 

samples collected on each 65 ha (160-acre) study area (Figure 2-36). Two field 

replicate (QC) samples were collected from each quarter section. Field replicate 
Land Retirement Demonstration Project 

Five Year Report 

62 

Figure 2-36. U.S. Department of Agriculture soil mapping units and soil sample 

locations at the Atwell Island site. 

samples were obtained using the fractional shoveling method (Gerlach 2002). All 

sample sites were located and mapped using a global positioning system receiver. 

Soil samples were analyzed for total and water-soluble selenium, sulfate, chloride, 

electrical conductivity, and moisture. All surface soil samples were analyzed for 

boron, magnesium, potassium, sodium, carbonate, and nitrate. The Quality 

Assurance Project Plan (QAPP) for the Land Retirement Demonstration Project 

described in detail the analytical procedures and quality assurance measures taken 

to ensure soil data quality (CH2M Hill 1999). The soils analyses were performed 

by the USGS and Reclamation analytical laboratories in Denver, Colorado. 

The baseline soil-sampling event was completed during March of 2002. Surface 

0-30 cm (0-12 inch) four increment soil samples where collected within 3 m 

(10 feet) of central deep boring sites. Deeper (30-76 cm and 76-152 cm or 

12-30 inch and 30-60 inch) samples where collected from a single hand auger 

boring. All soil layers where included in the sampling. The soil samples have 

been analyzed and the data collected has been validated. A statistical summary of 

the baseline data are presented in the next section. 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

63 

Statistical summary of the baseline data Statistical summaries of data 

collected during the 2002 baseline soil sampling event are presented in Table 2-14 

through Table 2-18. All data are on a dry soil weight basis except for the soil 

salinity data, which are the concentration of the extract. 

Table 2-14. Total selenium (mg/kg dry soil) 

Study area Depth (inches) Median Average 95 % CI 

Study Area 1 0-12 0.100 0.097 0.076 - 0.118 

 12-30 0.050 0.087 0.062 - 0.112 

 30-60 0.050 0.076 0.061 - 0.091 

 0-60 Weighted average 0.080 0.084 0.069 - 0.099 

Study Area 2 0-12 0.115 0.144 0.092 - 0.196 

 12-30 0.120 0.118 0.090 - 0.146 

 30-60 0.120 0.139 0.100 - 0.178 

 0-60 Weighted average 0.120 0.132 0.110 - 0.154 

Study Area 3 0-12 0.100 0.104 0.083 - 0.125 

 12-30 0.100 0.086 0.071 - 0.101 

 30-60 0.145 0.141 0.110 - 0.172 

 0-60 Weighted average 0.120 0.120 0.104 - 0.136 

Total selenium A statistical summary of total selenium concentrations is 

presented in Table 2-15. In Study Area 1, there appears to be a slightly inverted 

selenium distribution, possibly from upflux and evaporative processes; however, 

this trend is not significant at the 95 percent confidence level. In Study Area 2, no 

trends with depth are apparent. In Study Area 3, the 76-152 cm (30-60 inch) 

substrata zone is significantly higher in total selenium than the 30-76 cm (12-

30 inch) zone. 

Table 2-15. Soluble selenium 1-5 extract (mg/kg dry soil) 

Study area Depth (inches) Median Geo Mean Average 95% CI 

Study Area 1 0-12 2.50 4.31 5.63 3.23 - 8.03 

 12-30 2.50 3.46 4.5 2.23 - 6.73 

 30-60 2.50 3.26 4.06 2.27 - 5.85 

 0-60 Weighted average 3.35 3.92 4.53 3.22 - 5.84 

Study Area 2 0-12 7.00 9.90 15.22 7.43 - 23.01 

 12-30 12.00 16.48 24.22 11.89 – 36.54 

 30-60 26.75 29.93 44.59 22.76 – 66.42 

 0-60 Weighted average 19.55 24.52 32.63 18.44 – 46.82 

Study Area 3 0-12 3.75 4.07 4.69 3.35 - 6.03 

 12-30 13.75 16.64 18.03 13.97 – 22.09 

 30-60 33.50 31.74 34.59 27.84 – 41.34 

 0-60 Weighted average 21.10 22.18 23.67 19.45 – 27.89 
Land Retirement Demonstration Project 

Five Year Report 

64 

Soluble selenium 1-5 extract A statistical summary of soluble selenium 

concentrations is presented in Table 2-15. The data are for 1 part soil to 5 parts 

DI water extracts. The concentrations found in the extracts were multiplied by a 

factor of 5 to determine the micrograms per kilogram (μg/kg) dry weight 

concentration in the soil. 

In Study Area 1, no significant differences in soluble selenium occurred with 

depth. Study Area 2 showed no significant differences in soluble selenium 

concentrations due to the high selenium concentration variability. There appeared 

to be an increasing selenium concentration with depth in Study Area 2. However, 

the trend is not significant at the 95 percent confidence level. In Study Area 3, 

there was a significant increase in soluble selenium concentration with depth at 

this site (Table 2-15). 

Soluble selenium commonly exhibits high, random spatial variability. The soils 

of the Atwell Island site were no exception, as coefficients of variation values 

were quite high (Table 2-15). The three study areas all had low total selenium 

values, yet it appears that a significant portion of the selenium at many of the 

sampled sites is in soluble form (Table 2-16). The alkaline soil reaction at the 

sites and the oxidized nature of the soils tend to favor the selenate selenium 

species, which is very soluble. 

Table 2-16. A comparison of total selenium concentrations with soluble selenium 

concentrations 

Study area Weighted average of 

total selenium (mg/kg) 

Weighted average of 

soluble selenium 

(mg/kg) 

Percent soluble 

1 0.084 0.0045 5.4 

2 0.132 0.0326 24.7 

3 0.120 0.0237 19.8 

Study Area 1 was much lower in soluble selenium than the other two study areas. 

The distribution in the profile also was more uniform, probably indicative of 

upflux from shallow groundwater and the medium textured soils in Study Area 1 

that are more conducive to capillary rise of water from the water table. 

Concentrations in surface soils were not elevated enough to warrant concern 

about terrestrial wildlife poisoning or accumulation in plants. The low total 

selenium concentrations at the site might cause selenium deficiencies for some 

organisms. However, a relatively large portion of the selenium probably is 

present in soluble and biologically available forms due to the oxidized, alkaline 

conditions prevailing in Atwell Island site soils. 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

65 

The data summarized in Table 2-15 contains many values below the reporting 

limit. In all cases, the value used for statistical purposes was one-half of the 

lower reporting limit value. 

Soil salinity A statistical summary of soil salinity concentrations is presented in 

Table 2-17. Although the variation in soil salinity with depth is not significant at 

the 95 percent confidence level in Study Area 1, the data indicate an inverted 

salinity profile. Study Area 1 contains medium textured soils that can conduct 

large amount of groundwater and salt into the root zone. Because of this soil 

texture, it will be important to lower the water table to at least 3.7 m (12 feet) on 

this study area in order to avoid salt accumulation in the active root zone. Winter 

rains should gradually leach out excess salts in the 0-76 cm (0-30-inch) active 

root zone if the water table is lowered to 3.7 m (12 feet) or greater. 

Table 2-17. Soil salinity (ECe dS/m) at the Atwell Island site 

Study area Depth (inches) Median Average 95% CI 

Study Area 1 0-12 8.71 9.25 7.75 - 10.75 

 12-30 7.53 7.59 6.42 - 8.75 

 30-60 5.56 5.66 4.75 - 6.55 

 0-60 Weighted average 6.85 6.92 5.95 - 7.89 

Study Area 2 0-12 2.50 3.85 1.54 -6.16 

 12-30 4.95 7.34 4.71 - 9.97 

 30-60 12.13 12.61 9.98 - 15.24 

 0-60 Weighted average 8.24 9.28 7.18 - 11.38 

Study Area 3 0-12 4.85 4.29 3.46 - 5.12 

 12-30 8.80 9.21 8.19 - 10.24 

 30-60 13.66 13.52 11.62 - 15.44 

 0-60 Weighted average 10.30 10.39 9.16 - 11.61 

The 76-152 cm (30-60 inch) substrata zone in Study Area 2 was significantly 

higher in salinity than the 0-30 cm and 30-76 cm (0-12 and 12-30 inch) zone. The 

soil profile exhibited what is termed a regular soil salinity pattern with salinity 

increasing with depth. Variability was very high in this study area; it appears we 

should evaluate dividing the study area into two areas for the purpose of trend 

analysis. 

The profile for Study Area 3 shows a favorable regular salinity distribution. The 

salinity increase with depth is significant at the 95 percent level. The clay soils at 

this site tend to discourage upflux from the groundwater table. As long as the 

water table remains below 2.7 m (9 feet), this site should be slowly leached of 

salts in the 0-76 cm (0-30 inch) active root zone. Variation of soil salinity was 

low on this study area. 

The weighted average soil salinity is higher in Study Area 3 than in Study Area 1 

but this is somewhat misleading. Surface soil salinity is significantly higher on 
Land Retirement Demonstration Project 

Five Year Report 

66 

Study Area 1 than on the other two study areas. The elevated surface soil salinity 

could inhibit germination and emergence of seeds of salt sensitive plants; 

however, most weedy plants can germinate and emerge from moderately saline 

surface soils. 

Soluble boron A statistical summary of the data is presented Table 2-18. The 

data are from 1 part soil to 5 parts DI water extracts prepared on a weight basis. 

The data were converted to mg/kg dry soil by multiplying the 1/5 extract 

concentration by a factor of 5. 

Table 2-18. Soluble boron 1-5 extract (mg/kg dry soil) at the Atwell Island site. 

Study area Depth (inches) Median Average 95% CI 

Study Area 1 0-12 4.05 4.10 3.72 - 4.48 

 12-30 2.98 2.99 2.67 - 3.30 

 30-60 8.50 8.45 7.1 - 9.8 

 Weighted average 5.75 5.93 5.23 - 6.64 

Study Area 2 0-12 1.95 2.32 1.81 - 2.83 

 12-30 13.00 14.13 10.80 - 17.4 

 30-60 22.75 22.5 21.05 - 23.95 

 Weighted average 15.55 15.94 14.47 - 17.41 

Study Area 3 0-12 3.10 2.99 2.47 - 3.51 

 12-30 13.75 14.91 12.56 - 17.24 

 30-60 22.00 20.56 18.32 - 22.80 

 Weighted average 16.35 15.34 13.68 - 17.00 

The concentrations at all depths in Study Area 1 were significantly different from 

one another. In Study Areas 2 and 3, boron concentrations increased sharply with 

depth with each depth increment significantly higher than the shallower sample 

zone. The surface 0-30 cm (0-12 inch) concentration is suited for all plants but 

deeper concentrations could be phytotoxic to most plants (Table 2-18). 

Spatial trends between study areas Study Area 2 had the highest weightedaverage total selenium values, while Study Area 3 is intermediate, and Study Area 

1 has the lowest values (Table 2-14). At the 95 percent confidence level Study 

Areas 2 and 3 are significantly higher than Study Area 1 but are not significantly 

different from one another. 

The 76-152 cm (30-60 inch) substrata zone in Study Areas 2 and 3 are 

significantly higher than the substrata zone in Study Area 1 (95 percent 

confidence level). 

Soil selenium values are low at the Atwell Island site. USGS reports that the 

average total selenium value of a large random sample of western states soils is 

about 0.34 mg/kg. The geometric mean (median) value from the western states 

suite of soils was 0.23 mg/kg. 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

67 

The selenium values at all three Atwell Island study areas are below toxic levels 

and may be deficient for some organisms. Soluble selenium data from the site 

will be examined to gain a better understanding of the selenium readily available 

for plant uptake and animal nutrition. 

Boron concentrations in Study Area 1 were much lower than in the other two 

study areas. Study Area 2 and Study Area 3 had similar elevated concentrations 

of soluble boron in substrata. Only boron-tolerant plants are recommended for 

Study Areas 2 and 3. Shallow rooted annual grasses may also tolerate the high 

boron concentrations at these sites. Plants moderately tolerant to boron should be 

successful at Study Area 1. 

Soil interpretive summary The Atwell Island site was relatively low in both 

soluble and total selenium. Boron concentrations were moderate in surface soils 

and are elevated in subsoils. Both boron and soil salinity are plant-growthlimiting factors at the Atwell Island sites. Study Area 1 appeared to be using 

moisture from the water table. While this has benefitted plant growth in the short 

term, it may indicate soil salinity problems in the future. The medium-textured 

soils at the Study Area 1 site exhibited capillary fringe zones approaching 1.5 m 

(5 feet) thick. A declining shallow water table in response to land retirement will 

lessen the likelihood of salinization of surface soils. 

2.3.3. Weather 

Precipitation, temperature, and wind data are collected at the National Weather 

Service weather station #42, which is located approximately 32 km (20 miles) 

southeast of the Atwell Island site in Wasco. The data from the Wasco station are 

available on the Western Region Climate Information website at 

http://www.wrcc.dri.edu. Precipitation has been below average during the first 3 

years of hydrologic monitoring at the Atwell Island site. The average annual 

rainfall for the 51-year period of record at Wasco is approximately 17.5 cm 

(6.9 inches). Rainfall totals measured at the Wasco station for 2002, 2003, and 

2004 were 10.8, 13.5, and 11.4 cm (4.27, 5.33 and 4.50 inches), respectively. 

Most of the rainfall has occurred from November through April. 

2.3.4. Irrigation 

The largest volume of irrigation water applied at the site during the baseline year 

of monitoring (2002) was from ongoing farming operations. Farming operations 

continued on approximately 951 ha (2,350 acres) of the Atwell Island site. 

Irrigation applications on these lands are currently scheduled based on a calendar 

or rotational approach. Metered pumping volumes for applied irrigation water are 

not available. Typical irrigation applications consist of gravity flow (flood 

irrigation) of about 15.2 cm (6 inches) per acre. An estimate of applied water and 

deep percolation (groundwater recharge) for irrigated lands within the 

demonstration project boundary at the Atwell Island site during 2002 is shown in 

Table 2-19. Estimated deep percolation losses in 2002 are about 15 percent less 
Land Retirement Demonstration Project 

Five Year Report 

68 

than those in 2001. Irrigation of high water use crops such as alfalfa will be 

phased out as restoration of the site to native upland progresses. Fifty seven 

hectares (140 acres) of barley were planted on the habitat restoration study blocks 

to provide weed and dust control and to isolate the individual study plots. The 

barley crop was not irrigated in 2002. 

Table 2-19. Estimated 2002 net crop water requirement and deep percolation 

losses at the Atwell Island site. 

Crop Acreage 

Total crop water 

requirement1 

CWR (acre-feet) 

Irrigation water 

application 

requirement2 

IWAR (acre-feet) 

Estimated deep 

percolation3 DP 

(acre-feet) 

Alfalfa 1,179 4,710 7,246 2,536 

Oats 1,137 932 1,433 502 

Safflower 37 96 148 52 

Total 2,353 5,738 8,827 3,090 

1

 CWR = Crop ET - Effective Precip. + Leaching Requirement (after Smith 2001) 2

 Assumes an Irrigation Efficiency of 65 percent 

3

 IWAR - CWR = DP 

2.3.5. Hydrology and Surface Water Monitoring 

The natural drainage in the study area is to the north-northwest with ground 

surface elevations ranging from about 62.5 m (205 feet) above mean sea level 

(msl) in the southeast portion of the site to about 65.5 m (215 feet) above msl in 

the northeastern portion of the site. A pronounced sand ridge traverses the 

northern boundary of the site in a northeasterly direction. The sand ridge was 

formed from windblown sand deposited along the southern shore of the Tulare 

Lake bed. Surface water courses within the study area consist primarily of 

irrigation supply canals and irrigation return flow ditches. The site has an 

artificially constructed 8 ha (20 acres) wetland that is filled from surface irrigation 

water supplies. Shallow ephemeral surface water ponds may form on low-lying 

portions of the site due to localized sheet flow run-off during prolonged winter 

storm events. The surrounding areas near the Atwell Island site receive periodic 

unregulated winter storm flows from Deer Creek, Poso Creek, and the White 

River. The central portion of the Atwell Island site is generally not subject to 

long term flooding, due to its higher topographic position with respect to the 

adjacent lower lying lands. Although no flooding has been observed on the 

eastern portion of the Atwell Island site during this study to date, these lands are 

subject to periodic flooding due to topography and proximity to Poso and Deer 

Creeks. 

The biological opinion for the demonstration project requires water quality 

monitoring for ephemeral surface water pools that form as a result of rainfall. No 

surface-water ponding that lasted more than 30 days was observed at the site 

during the first 3 years of monitoring due to dry climatic conditions. However, 

ponded water from the artificial wetland at the site was sampled and analyzed for 

selenium in January, July, and October 2002. Selenium concentrations were 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

69 

below detection limits (<0.4 μg/L) in the January and July samples. A selenium 

concentration of 0.6 μg/L was observed in the October sample, which is below the 

5 μg/L EPA water-quality criteria for long term exposure in aquatic environments 

(EPA 1988). 

2.3.6. Groundwater Level Monitoring 

Approximately 20 monitor wells in the project vicinity are used to measure 

groundwater levels beneath the site on a quarterly basis. The well locations are 

shown on Figure 2-37. Existing wells constructed prior to the purchase of the 

demonstration project lands were installed by the USGS, the California 

Department of Water Resources (CDWR) and Reclamation to assess groundwater 

conditions in the Tulare basin. 

These existing wells are constructed of PVC casing ranging in diameter from 1.9 

to 7.6 cm (0.75 to 3 inches) and vary in depth from 6.1 to 58 m (20 to 190 feet) 

below the ground surface. The wells were installed using various construction 

techniques that range from jetting a short length of pipe into the ground to 

standard rotary drilling with hydraulic drill rigs. During fall 1999, Reclamation 

installed 17 new monitoring wells to measure groundwater levels and obtain 

representative groundwater samples for water quality analyses for the Land 

Retirement Demonstration Project. The new wells range in depth from 4.6 to 

18.3 m (15 to 60 feet) below land surface and were installed using a hollow stem 

auger drill rig and are constructed of 5 cm (2-inch) PVC casing. Well 

construction diagrams for the new wells are on file in Reclamation offices in 

Fresno and Sacramento. Well construction information for the USGS wells are 

published by Beard et al. (1994), Fujii and Swain (1995) and Swain and Duell 

(1993). 

2.3.7. Groundwater Quality Monitoring 

The purposes of groundwater-quality monitoring at the site are to observe 

selenium concentrations over time and to evaluate selenium exposure risk to 

wildlife via the groundwater pathway. Baseline groundwater samples were taken 

on a quarterly basis during 2002 at the Atwell Island site. The baseline 

groundwater quality samples were taken in January, May, July, and October 2002. 

Annual groundwater sampling began at Atwell Island in May 2003, and will 

continue for 5 years. Sampling was conducted in spring to coincide with the 

seasonal high water table in the region. Annual and baseline groundwater quality 

data will be compared to evaluate changes in groundwater quality. Unfiltered 

groundwater samples were taken from 16 wells to assess baseline groundwater 

quality at the site. Standard operating procedures for groundwater sampling used 

by the Mid-Pacific Region of Reclamation and those outlined in the Quality 

Assurance Project Plan for the Land Retirement Demonstration Project (CH2M 

Hill 1999) were employed to obtain groundwater samples. 
Land Retirement Demonstration Project 

Five Year Report 

70 

Figure 2-37. Monitor well locations at the Atwell Island site. 

Unfiltered groundwater samples were analyzed for major ions (calcium, 

magnesium, potassium, sodium, chloride, sulfate, total alkalinity), trace elements 

(selenium, boron, iron, manganese) and isotopes (H-2, O-18 and H-3). Specific 

conductance (electrical conductivity [EC]), pH, and temperature of groundwater 

samples were measured in the field at the time of sampling. Fluorometric 

analyses of groundwater samples for selenium were performed by Olsen 

Biochemistry Laboratories, South Dakota State University. Analyses for isotopes 

(H-2, O-18) were performed by the USGS Water Resources Division laboratory in 

Reston, Virginia. Analyses for tritium (H-3) were performed by the USGS Water 

Resources Division laboratory in Menlo Park, California. All other analyses were 

performed by commercial laboratories under contract to Reclamation. The 

Quality Assurance Project Plan for the Land Retirement Demonstration Project 

describes in detail the analytical procedures and quality assurance measures taken 

to ensure groundwater data quality (CH2M Hill 1999). 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

71 

2.3.7.1. Groundwater Response to Land Retirement 

Calendar year 2002 was the baseline year for monitoring groundwater levels and 

groundwater quality at the Atwell Island site. Groundwater levels measured in 

20 wells confirm the presence of shallow, perched water table conditions at the 

Atwell Island site. Groundwater levels observed during the baseline year of 

monitoring (2002) in the shallow groundwater system range from 4.3 to 14.8 feet 

below land surface. In general, the water table is highest (nearest the land 

surface) in the northwest corner of the site and becomes deeper in the southeast 

portion of the site. These observations are consistent with those of Beard et al. 

(1994) and Reclamation (1982). 

A declining shallow water table in response to land retirement has been observed 

on parts of the site where irrigation has ceased or been greatly reduced (Figure 

2-38). Pre-project water level data reported by the USGS (Beard et al. 1994) 

show seasonal high groundwater levels around 5 feet below land surface. Postproject, seasonal high water levels measured in well 5B3 during 2002 have 

dropped to a depth ranging from approximately 7 to 8 feet below land surface (a 

decline of 2-3 feet). Groundwater level monitoring will continue at the site to 

evaluate shallow water table response to land retirement. 

-12

-10

-8

-6

-4

-2

0

Jan-90Jan-91Jan-92Jan-93Jan-94Jan-95Jan-96Jan-97Jan-98Jan-99Jan-00Jan-01Jan-02Jan-03Jan-04Jan-05

DATE

Depth to Groundwater Below 

Land Surface (ft.)

Well 5B3 (20 ft.)

Well 5B4(63 ft.)

Pre-Project Post Project

Figure 2-38. Hydrographs of groundwater levels observed in Wells 5B3 and 5B4 

showing pre-project and post-project groundwater levels. 

2.3.7.2. Groundwater Salinity 

Baseline electrical conductivity data for the groundwater samples collected during 

the first year of monitoring are presented in Table 2-20. The shallow groundwater 
Land Retirement Demonstration Project 

Five Year Report 

72 

is moderately saline in nature. Salinity in the shallow groundwater samples, 

expressed as EC, ranged from 575 to 52,925 μS/cm, with a median value of 

13,740 μS/cm. By comparison, drinking water typically is less than 750 μS/cm, 

irrigation water is less than 1,250 μS/cm, and seawater is about 50,000 μS/cm. 

The elevated salinity of the shallow groundwater at the site is a result of the 

irrigation of saline soils. Naturally occurring salts have been leached from the 

soil profile under irrigated conditions. Salts also have been transported to the site 

in the applied irrigation water. Direct evaporation from the shallow water table 

and transpiration of applied water by crops has concentrated salts in the shallow 

groundwater, resulting in the high EC values observed in the shallow groundwater 

samples. 

2.3.7.3. Groundwater Major Ion Chemistry 

Baseline major ion chemistry data for the groundwater samples collected during 

2002 at the Atwell Island site are presented in Table 2-20. The shallow 

groundwater at the site is best described as a sodium sulfate type of water. 

Sodium is the dominant major cation found in the shallow groundwater samples, 

with sodium concentrations ranging from 469 to 15,100 mg/L, and a median 

concentration of 4,500 mg/L. Sulfate is the dominant major anion found in the 

shallow groundwater with sulfate concentrations ranging from 261 to 

22,200 mg/L, and a median concentration of 5,700 mg/L. By comparison, Fujii 

and Swain (1995) reported median shallow groundwater concentrations of 8,400 

and 13,000 mg/L for sodium and sulfate, respectively, in nine samples taken from 

the southwestern margin of the Tulare Lake bed. 

Table 2-20. Baseline groundwater quality data for shallow wells at the Atwell 

Island site - major ions, field parameters, and selenium. Note: selenium 

concentrations are expressed in micrograms/liter (μg/L). 72 samples were used to 

calculate the selenium statistics. 

Statistic Minimum 25th 

percentile Median 75th 

percentile Maximum Mean 

Number of 

Samples 64 64 64 64 64 64 

EC(field) (μS/cm) 575 4,615 13,740 26,095 52,925 18,059 

pH (field) 6.24 7.21 7.49 7.93 9.12 7.60 

Calcium (mg/L) 3 40 320 438 850 282 

Magnesium (mg/L) 1 21 148 590 1800 390 

Sodium (mg/L) 469 1,290 4,500 11,350 15,100 6,180 

Potassium (mg/L) 1 4 9 30 152 23 

Total Alkalinity 

(mg/L) 366 429 580 881 2,050 736 

Chloride (mg/L) 216 549 3,400 7,385 12,800 4,312 

Sulfate (mg/L) 261 1,225 5,700 17,325 22,200 8,382 

Selenium (mg/L) <0.4 0.54 8.56 68.25 208 34.2 
Chapter 2. Physical Impacts of Agricultural 

Land Retirement in the San Joaquin Valley 

73 

2.3.7.4. Selenium in Groundwater 

Selenium concentrations measured in the shallow groundwater wells at the site 

during the baseline year of monitoring range from less than the detection limit of 

0.4 to 208 micrograms per liter (μg/L), with a median concentration of 8.56 μg/L 

(Table 2-20). The EPA water-quality criteria for long-term exposure to selenium 

in aquatic environments are 5 μg/L (EPA 1988). Approximately 50 percent of the 

groundwater samples (35 of 72 samples) collected during the baseline year of 

sampling were less than the EPA aquatic life criteria. Selenium concentrations in 

the shallow groundwater show considerable spatial variation throughout the site. 

In general, the highest selenium concentrations in groundwater range from 

approximately 60 to more than 200 μg/L, and are found in the central portion of 

the site in sections 5, 6, 7, and 8 (Figure 2-37). These high selenium areas are 

associated with the Excelsior and Posochanet soil series (Figure 2-36). The 

Posochanet soils found within Study Area 1 also contained the highest selenium 

concentrations observed in the baseline soil investigation. The groundwater 

underlying the eastern and western portions of the site contain much lower levels 

of selenium (<0.4 to 17 μg/L). Fujii and Swain (1995) noted that the distribution 

of selenium in shallow groundwater in the Tulare basin is strongly influenced by 

sources of selenium, selenium concentrations in soil, evaporation of shallow 

groundwater, and redox conditions. 

2.3.8. Conclusions 

The soils at the Atwell Island site have relatively low concentrations of both 

soluble and total selenium. Boron concentrations were moderate in surface soils 

and are elevated in subsoils. Both boron and soil salinity are plant growth 

limiting factors at the Atwell Island sites. Study Area 1 appeared to be using 

moisture from the water table. While this has benefitted plant growth in the short 

term, it may indicate soil salinity problems in the future. The medium textured 

soils at the Study Area 1 site exhibited capillary fringe zones approaching 1.5 m 

(5 feet) thick. A declining shallow water table in response to land retirement will 

lessen the likelihood of salinization of surface soils. 

No surface-water ponding that lasted more than 30 days was observed at the site 

during the first 3 years of monitoring due to dry climatic conditions. However, 

ponded water from the artificial wetland at the site was sampled and analyzed for 

selenium in January, July, and October 2002. Selenium concentrations were 

below detection limits (<0.4 μg/L) in the January and July samples. A selenium 

concentration of 0.6 μg/L was observed in the October sample, which is below the 

5 μg/L EPA water-quality criterion for long term exposure in aquatic 

environments (EPA 1988). 

A declining shallow water table in response to land retirement has been observed 

on parts of the Atwell Island site where irrigation has ceased or been greatly 

reduced. The seasonal pattern shown by some of the monitor well hydrographs is 

a result of periodic recharge to the shallow groundwater from irrigation that 

continues in the central portion of the project site. Sodium and sulfate are the 
Land Retirement Demonstration Project 

Five Year Report 

74 

dominant ions found in the shallow groundwater at the site. The elevated salinity 

and moderately high concentrations of selenium in the shallow groundwater are a 

result of leaching during irrigation and evaporation from the shallow water table. 

Selenium concentrations in groundwater at Atwell Island show considerable 

spatial variability, with the highest concentrations associated with Excelsior and 

Posochanet soils in the central part of the site. Groundwater, surface water and 

soils will continued to be monitored for five years as required in the FWS 

Biological Opinion for the Land Retirement Demonstration Project. 

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California. 

U.S. Environmental Protection Agency. 1986. Quality criteria for water. U.S. 

Environmental Protection Agency report 440/5-86-001. 453 pp. 

U.S. Environmental Protection Agency. 1988. Water quality criteria documents. 

Federal Register 53 (2): 177-179. 
Land Retirement Demonstration Project 

Five Year Report 

78 

Weres, O., A.R. Jaoni, and L. Tsao. 1989. The distribution, speciation, and 

geochemical cycling of selenium in a sedimentary environment, Kesterson 

Reservoir, California, U.S.A. Applied Geochemistry 4: 543-563. 

White, A.F., S.M. Benson, A.W. Yee, H.A. Wollenberg, Jr., and S. Flexser. 

1988. Groundwater contamination at the Kesterson Reservoir, California: 

geochemical parameters influencing selenium mobility. Water Resources 

Research 27(6): 1085-1098. 
Chapter 3. Selenium Levels of Biota from 

Retired Agricultural Lands in the San Joaquin Valley 

79 

Chapter 3. Selenium Levels of Biota 

from Retired Agricultural Lands in 

the San Joaquin Valley, California 

by Curtis E. Uptain and Stuart H. Hurlbert

3.1. Introduction 

The high concentrations of selenium in the groundwater and soils of the Land 

Retirement Demonstration Project (LRDP) study sites have the potential to be 

detrimental to wildlife. Alkaline soils and high selenium levels, conditions that 

are present on retired lands, are favorable to selenium bio-availability (USDI 

1998). High concentrations of selenium are known to cause a variety of adverse 

effects to wildlife including embryonic malformation and death, reduced 

longevity, reduced reproductive success, reduced growth and survival rates, 

winter stress syndrome, food aversion, anemia and mass wasting, alopecia (loss of 

feathers) and loss of hair and nails, depressed immune system function, altered 

enzyme function, skin lesions, respiratory failure, and paralysis (Ghosh et al. 

1993, Hedland 1993, Heinz and Fitzgerald 1993, Johnston 1987, Koller and Exon 

1986, Lemly 1993a and b, Ohlendorf et al. 1993, Saiki and Ogle 1995). Although 

the groundwater and soils in the region contain high amounts of selenium, the 

degree that selenium is available to and accumulates in biota from agricultural 

lands and upland habitats is not well understood. The effects of land retirement 

and of habitat restoration of retired lands on the bio-availability of selenium are 

not known. 

We monitored selenium levels in plants, invertebrates, and small mammals 

collected from retired agricultural lands over a 5-year period at the Tranquillity 

study site and over a 3-year period at the Atwell Island study site (see Figure 1-1 

for site locations) following protocols established by the project’s Biological 

Opinion (FWS 1999). Table 3-1 provides a list of the biotic groups monitored, 

the corresponding population-level performance standard established by FWS 

(1999) for each group, and an indication whether performance standards were 

met. 

Results are compared to selenium levels found in similar biotic groups collected 

from selenium-normal situations in the western United States (USDI 1998). We 

also compare our results to the concentrations of selenium in corresponding biota 

that were previously collected from Kesterson National Wildlife Refuge 

(Kesterson NWR, see Figure 1-1), a site where high levels of selenium resulting 
Land Retirement Demonstration Project 

Five Year Report 

80 

from the deposition of agricultural drain water caused a variety of toxic effects to 

wildlife (USDI 1992). When comparative data are not available from Kesterson 

NWR, Reclamation relates its findings to other local and regional information. 

Table 3-1. List of biotic groups monitored, corresponding performance standards 

(USFWS 1999), and an indication whether performance standards were met. ATWL 

= Atwell Island site, TRNQ = Tranquillity site. All selenium values are on a dry 

weight basis except rodent blood and coyote or kit fox blood, which is on a wet 

weight basis. 

Biotic 

group 

Performance 

standard 

Met Not met Not 

monitored 

Vegetation Not to exceed 2ppm (2 mg/kg) Se X 

Invertebrates Not to exceed 2.5ppm (2.5 mg/kg) Se 

Crickets X 

Beetles X 

Spiders X 

Isopods X (ATWL) X1

 (TRNQ) 

Reptiles 

Whole body Not to exceed 3ppm (3mg/kg) Se X2

Feces Not to exceed 2ppm (2mg/kg) Se X2

Eggs/ovaries Not to exceed 5ppm (5 mg/kg) Se X2

Blood Not to exceed 1 ppm (1 mg/kg) Se X2

Birds 

Blood Not to exceed 1 ppm (1 mg/kg) Se X3

Eggs Not to exceed 5ppm (5 mg/kg) Se X3

Feathers Not to exceed 4ppm (4 mg/kg) Se X3

Rodents 

Hair Not to exceed 5ppm (5 mg/kg) Se X4

 

Blood Not to exceed 0.5ppm (0.5 mg/kg) Se X4

 

Coyote or kit 

fox blood 

Not to exceed 1 ppm (1 mg/kg) Se X5

X1 – Isopods from TRNQ slightly exceeded the performance standard for invertebrates. 

This is not unexpected since Isopods are known to be detritus feeders and accumulate 

Se in greater quantities than other invertebrate groups. 

X2

 – Se levels in reptiles were not monitored because they were not available for 

sampling (see Chapter 4). 

X3

 – Monitoring of birds was only required if standing water was present for more than 30 

days. Standing water did not occur on either site. 

X4

 – Although performance standards were set for rodent hair and blood, it was 

cooperatively determined that it would be preferable to sample rodent bodies and livers. 

No subsequent performance standards were established for rodent bodies and livers, but 

the Se values obtained for rodent bodies and livers appear to meet performance 

objectives. 

X5

 – Se levels in coyote or kit fox were not monitored because they were not available for 

sampling. 
Chapter 3. Selenium Levels of Biota from 

Retired Agricultural Lands in the San Joaquin Valley 

81 

3.2. Methods 

The monitoring of selenium concentrations in groundwater (see Chapter 2) and 

biota followed a tiered sampling approach that was cooperatively developed with 

the FWS specifically for this project (FWS 1999). The monitoring of selenium in 

soils (see Chapter 2) was not included in those protocols. The intensity of 

sampling was based upon the depth to groundwater and concentration of selenium 

in groundwater. Although the depth to groundwater under the retired lands 

increased after irrigation ceased (see Chapter 2), the level of monitoring remained 

at the highest intensity (Tier IV) because of the high selenium concentration 

present in the groundwater. 

At Tranquillity, samples of vegetative and reproductive parts of plants were 

collected in July and October 1999, June 2000, May 2001, April and May 2002, 

and in April, May, June, and August 2003. At Atwell Island, plant samples were 

collected in April and May 2000, May 2001, and April and May 2002. Samples 

were collected from areas that were widely scattered over the project sites and 

from a variety of cultivated, uncultivated, and experimental areas when possible. 

Cultivated areas are those where barley or some other irrigated crop was present; 

uncultivated areas are those that were fallowed or idled and have not recently 

received irrigation water. Experimental areas are those where restoration 

treatments (contouring, planting of native seed, or no treatment) were applied. 

We collected samples of native and non-native vegetation that were dominant on 

the landscape. Hence, the number of species and number of samples collected 

varied from year to year depending upon the distribution and abundance of each 

species and the availability of funding (e.g., when sampling at both Atwell Island 

and Tranquillity concurrently, fewer samples were taken at Tranquillity because 

of the need to support work at Atwell Island). Despite the yearly changes in 

vegetation dominance and the variability in sampling, we attempted to collect a 

standardized set of samples that included a suite of species that were expected to 

occur in each of the collection areas throughout the study period. Some of these 

species are Sisymbrium irio, Brassica nigra, Atriplex argentea, Hordeum 

murinum, Melilotus indica, and Hordeum vulgare. 

The plants were collected when green and not showing signs of advanced water 

stress. Samples were placed in plastic bags, labeled, and stored on ice. Upon 

returning to the lab, the samples were washed, dried, separated into “part” (e.g., 

fruits, vegetative structures, etc.), transferred to a whirl-pack bag, and frozen. 

Invertebrate samples consisting of crickets, spiders, isopods, and beetles were 

collected from Tranquillity in July 1999, June 2000 and 2001, and May 2002 and 

2003. At Atwell Island, samples were collected in July 2000, June 2001, and May 

2002. Invertebrates were collected from pitfall traps located within the 

experimental areas of the project sites. At Tranquillity, invertebrates were 

collected from five pitfall arrays on each of 20, 4 ha (10 ac) study plots. Each 

pitfall array consisted of four, 13 liter (3 gal) pitfall buckets connected by a 6.1 m 
Land Retirement Demonstration Project 

Five Year Report 

82 

(20 ft) long by 30 cm (1 ft) high galvanized steel flashing. One composite sample 

of each invertebrate type was collected from each study block (a set of four plots, 

one of each restoration treatment configured in a randomized block design). At 

Atwell Island, one composite sample of each invertebrate type was collected from 

each of three study areas. Each study area consisted of 16, 0.8 ha (2 ac) plots with 

each plot containing a single pitfall array. We attempted to collect a composite 

sample of at least 2 grams (g) of each invertebrate type from a pitfall bucket, 

pitfall array, multiple arrays on a plot, or sometimes multiple plots within a study 

block or study area. The spatial distribution of each sample depended upon the 

abundance and availability of the invertebrate type being collected. All samples 

were individually bagged and labeled, immediately stored on ice, then transferred 

to a freezer upon returning to the lab. 

Small mammals were collected from the two project sites by a combination of 

live-trapping using Sherman traps and by collecting mammals from pitfall traps. 

We attempted to collect five deer mice (Peromyscus maniculatus) from each 

landform (cultivated, uncultivated, and experimental) and five shrews (Sorex 

ornatus) from experimental areas. Trapped animals were sacrificed by cervical 

dislocation, individually bagged and labeled, and placed on ice. Once the samples 

arrived at the lab, the livers were extracted from the animals and all samples were 

frozen. Small mammal liver tissues were analyzed for selenium concentration 

separately from the remaining body tissues. Small mammal body and liver tissues 

were collected and analyzed, instead of hair and blood, to ensure that an adequate 

amount of tissue for analysis could be collected. 

All biotic samples were analyzed to determine selenium concentrations by 

Laboratory and Environmental Testing (L.E.T.), Inc., Columbia, Missouri. Data 

provided include selenium concentration by dry weight, selenium concentration 

by wet weight, sample dry weight, sample percent moisture, and sample detection 

limit. The laboratory also provided reports on duplicates, spikes, and reference 

samples for quality control. Selenium concentration by dry weight was used for 

analysis. The reported selenium concentrations of some samples were adjusted 

upwards: when the amount of selenium in a sample was less than the detection 

limit (e.g., selenium was at non-detectable levels), then the selenium value for that 

sample was increased to the detection limit. These increases are slight because 

the detection limits are at the lower range of the data sets. This allows each 

sample to be included in the analyses and it ensures that the mean selenium 

concentration for a sample group is not underestimated. The number of nondetects in each sample group is reported in figures and tables so that the bias 

introduced by this manipulation and the corresponding analysis can be 

appropriately interpreted. 

Selenium data of the biotic samples were log transformed and statistically 

analyzed by performing single factor (e.g., years) or multifactor (e.g., years and 

landform types) analysis of variances (ANOVAs) using Statistica 6 (StatSoft, Inc. 

2002). In most cases, post-hoc analyses were performed using the Fisher’s PLSD 

test. Student’s t-tests were used to compare mean selenium concentrations 
Chapter 3. Selenium Levels of Biota from 

Retired Agricultural Lands in the San Joaquin Valley 

83 

between the two study sites. SigmaPlot 8.0 (SPSS, Inc. 2002) was used for 

graphics generation. The geometric mean (hereinafter also referred to as mean) 

and standard deviation factor of each data group are presented in the data tables. 

The standard deviation factor is the standard deviation of the log-transformed data 

that has been back-transformed. The geometric mean and error bars (the 

geometric mean multiplied by and divided by one standard deviation factor) are 

shown in the figures. Data points that had selenium levels that exceeded the 

population-level performance standards are plotted on the figures to show the 

distribution of the highest and most problematic values within each data set. 

When a performance standard was not established (e.g., small mammal livers), 

then those values that exceeded the geometric mean multiplied by one standard 

deviation factor were plotted. 

In addition to comparing mean selenium concentrations to the performance 

standards established for this project, the team also compared the values to typical 

population-level background concentrations of selenium in the western United 

States (USDI 1998) and to selenium concentrations reported in biota from 

Kesterson NWR (USDI 1992). Kesterson NWR is a site where drainage water 

was deposited, adverse affects to wildlife occurred, and remedial actions were 

implemented. Selenium values collected from 1988 to 1992 in the grassland 

habitat at Kesterson NWR were used because the grassland habitat type most 

closely resembles the conditions present at the project sites. Whenever 

comparative data from Kesterson NWR does not exist, Reclamation data are 

compared to other local and regional information when possible. 

3.3. Results 

3.3.1. Plants 

The mean selenium concentration in 31 species of plants collected from 

Tranquillity varied from 0.11 to 1.10 mg/kg (Table 3-2). Many of these species 

are represented by only a single composite sample; hence, they have minor 

statistical value. Of the 14 species where 5 or more samples were obtained, the 

mean selenium concentrations were from 0.21 (Bromus madritensis) to 0.93 

(Suaeda moquinii) mg/kg. The mean selenium concentration in 20 species 

collected from Atwell Island varied from less than 0.17 to 0.5 mg/kg. Ten species 

from Atwell Island were represented with five or more samples. These varied in 

selenium from less than 0.17 (Hemizonia pungens) to less than 0.25 (Distichlis 

spicata) mg/kg (Table 3-3). Seven species were common to both sites and were 

represented by five or more composite samples (A. argentea, B. madritensis, B. 

nigra, H. murinum, H. vulgare, M. indica, and S. irio). All of these species were 

lower in selenium levels at Atwell Island than at Tranquillity (p <0.01 in all 

cases), except B. madritensis (p = 0.71). 

Twelve species at Tranquillity and 8 species at Atwell Island were collected over 

multiple years (Tables 3-4 and 3-5). Only one species from Tranquillity, B. nigra, 

clearly showed a temporal increase in selenium; the mean selenium level was 
Land Retirement Demonstration Project 

Five Year Report 

84 

greater in 2003 (0.74 mg/kg) than in 2000 (0.47 mg/kg) and 2001 (0.30 mg/kg). 

There also is some evidence of a temporal increase in selenium in Avena sp. and 

A. argentea at Tranquillity. The mean concentration of selenium in plants from 

Atwell Island contained at least 32 to 49 percent less selenium than corresponding 

plant species from Tranquillity during the 3 years of concurrent sampling 

(p < 0.01 each year). 

The mean selenium concentrations in plants at both sites were below the 

performance standards set for the project by the FWS (2.0 mg/kg). No plant 

samples of any species were collected from Atwell Island exceeded the 

performance standard; however, 11 samples (3.4%) of 5 species collected from 

Tranquillity exceeded the performance standard (Table 3-6). Although the mean 

selenium concentrations in vegetation collected from both Atwell Island and 

Tranquillity were approximately an order of magnitude less than the mean 

selenium concentration in plants collected from Kesterson NWR from 1988 to 

1992 (2.3 to 6.7 mg/kg), 10 samples collected from Tranquillity were within this 

range (Table 3-6). The mean selenium concentrations in plants collected from 

both Tranquillity and Atwell Island are within the range typically found on nonseleniferous soils in the western United States. 
Chapter 3. Selenium Levels of Biota from 

Retired Agricultural Lands in the San Joaquin Valley 

85 

Table 3-2. Geometric means (Mean), sample size (N), number of non-detects (ND), 

minimum (Min), maximum (Max), and standard deviation factor (SD factor) of 

selenium concentrations (mg/kg dry weight) in plant species collected from 

Tranquillity, 1999 to 2003. 

Species N (ND) Mean Min Max SD factor 

Acroptilon repens 1 (0) 0.39 0.39 0.39 - 

Allenrolfea occidentalis 1 (0) 0.11 0.11 0.11 - 

Atriplex argentea 44 (13) <0.37 <0.20 1.90 1.88 

Atriplex polycarpa 13 (3) <0.39 <0.20 2.10 2.13 

Atriplex spinifera 2 (1) <0.22 <0.10 0.50 3.12 

Avena sp. 17 (1) <0.27 <0.10 0.50 1.55 

Bassia hyssopifolia 2 (0) 1.10 0.71 1.70 1.85 

Beta vulgaris 6 (1) <0.46 <0.20 0.73 1.61 

Bromus madritensis 13 (11) <0.21 <0.20 0.43 1.24 

Brassica nigra 54 (9) <0.49 <0.20 3.50 2.16 

Capsella bursa-pastoris 1 (0) 0.77 0.77 0.77 - 

Chenopodium album 1 (0) 0.78 0.78 0.78 - 

Chenopodium murale 1 (0) 0.20 0.20 0.20 - 

Grindelia camporum 1 (0) 0.71 0.71 0.71 - 

Helianthus annuus 1 (0) 0.36 0.36 0.36 - 

Heliotropium curassavicum 8 (3) <0.68 <0.20 3.90 3.77 

Hordeum murinum 12 (4) <0.31 <0.10 0.83 1.86 

Hordeum vulgare 74 (19) <0.30 <0.10 1.30 1.66 

Isocoma acradenia 1 (0) 0.40 0.40 0.40 - 

Lasthenia californica 2 (0) 0.61 0.31 1.20 2.60 

Lactuca serriola 1 (0) 0.50 0.50 0.50 - 

Malvella leprosa 1 (0) 0.41 0.41 0.41 - 

Malva parviflora 1 (0) 0.20 0.20 0.20 - 

Melilotus indica 11 (5) <0.28 <0.20 0.40 1.33 

Phacelia distans 7 (4) <0.25 <0.20 0.40 1.33 

Phalaris minor 2 (0) 0.20 0.20 0.20 1.00 

Sesuvium verrucosum 3 (0) 0.65 0.20 1.70 2.96 

Senecio vulgaris 1 (0) 0.74 0.74 0.74 - 

Sisymbrium irio 25 (3) <0.61 <0.20 2.40 2.04 

Sonchus sp. 5 (0) 0.55 0.31 1.00 1.70 

Suaeda moquinii 12 (1) <0.93 <0.20 5.00 3.09 
Land Retirement Demonstration Project 

Five Year Report 

86 

Table 3-3. Geometric means (Mean), sample size (N), number of non-detects (ND), 

minimum (Min), maximum (Max), and standard deviation factor (SD factor) of 

selenium concentrations (mg/kg dry weight) in plant species collected from Atwell 

Island, 2000 to 2002. 

Species N (ND) Mean Min Max SD factor 

Atriplex argentea 16 (14) <0.21 <0.20 0.40 1.22 

Atriplex polycarpa 2 (2) <0.20 <0.20 0.20 1.00 

Avena sp. 4 (4) <0.20 <0.20 0.20 1.00 

Bromus madritensis 7 (6) <0.22 <0.20 0.40 1.30 

Brassica nigra 10 (6) <0.23 <0.20 0.50 1.41 

Cressa truxillensis 12 (10) <0.21 <0.20 0.30 1.17 

Distichlis spicata 6 (4) <0.25 <0.10 1.40 2.45 

Heliotropium 

curassavicum 4 (4) <0.20 <0.20 <0.20 1.00 

Hemizonia pungens 13 (11) <0.17 <0.10 0.20 1.36 

Hordeum murinum 18 (17) <0.20 <0.10 0.30 1.21 

Hordeum vulgare 20 (19) <0.20 <0.20 0.30 1.09 

Isocoma acradenia 1 (1) <0.20 <0.20 <0.20 - 

Lasthenia californica 3 (2) <0.20 <0.20 0.20 1.00 

Lactuca serriola 1 (0) 0.50 0.50 0.50 - 

Melilotus indica 14 (14) <0.19 <0.10 <0.30 1.33 

Medicago sativa 1 (1) <0.20 <0.20 <0.20 - 

Sesuvium verrucosum 2 (1) <0.20 <0.20 0.20 1.00 

Sisymbrium irio 12 (10) <0.21 <0.10 0.73 1.55 

Spergularia macrotheca 1 (1) <0.20 <0.20 <0.20 - 

Suaeda moquinii 2 (1) <0.20 <0.20 0.20 1.00 
Chapter 3. Selenium Levels of Biota from 

Retired Agricultural Lands in the San Joaquin Valley 

87 

Table 3-4. Results of analysis of variance tests of selenium concentrations (mg/kg 

dry weight) between sample years in plant species collected from Tranquillity, 1999 

to 2003. GM = geometric mean, N = sample size, ND = number of non-detects. p

values marked with an asterisk must be interpreted with caution because of the 

high number of non-detects in one or more data sets. 

GM by sample year(N:ND) Species 1999 2000 2001 2002 2003 

F p value

Atriplex argentea <0.49 

(12:3) <0.31 (15:6) <0.29 

(9:4) - 0.48 (8:0) 2.33 0.09 

Atriplex polycarpa - - <0.33 

(4:1) 

<0.29 

(4:2) 0.57 (5:0) 1.05 0.38* 

Avena sp. - <0.30 (10:1) - - 0.23 (7:0) 4.11 0.06 

Beta vulgaris - <0.39 (4:1) - - 0.62 (2:0) 1.35 0.31 

Bromus 

madritensis - <0.20 (5:4) <0.20 

(6:6) - - No variance* 

Brassica nigra - <0.47 (26:5) <0.30 

(12:4) - 0.74 (16:0) 5.55 0.01 

Heliotropium 

curassavicum - <1.41 (3:1) - - 0.98 (2:0) 0.96 0.49 

Hordeum 

murinum - <0.22 (4:3) - - <0.41 

(7:1) 1.72 0.23* 

Hordeum vulgare <0.25 

(10:3) 

<0.28 

(20:8) 

<0.40 

(16:2) 

<0.26 

(12:6) 

<0.33 

(16:0) 1.44 0.23* 

Melilotus indica - - <0.25 

(8:5) - 0.34 (2:0) 2.22 0.17* 

Sisymbrium irio - - - <0.51 

(14:3) 

0.77 

(11:0) 2.01 0.17 

Suaeda moquinii - - 0.51 

(5:0) 

<1.19 

(4:1) 1.82 (3:0) 1.45 0.29 

Table 3-5. Results of Analysis of Variance tests of selenium concentrations (mg/kg 

dry weight) between sample years in plant species collected from Atwell Island, 

2000 to 2002. GM = geometric mean, N = sample size, ND = number of non-detects. 

p values marked with an asterisk must be interpreted with caution because of the 

high number of non-detects in one or more data sets. 

GM by sample year (N:ND) 

Species 2000 2001 2002 F p value

Atriplex argentea <0.21 (10:9) <0.21 (6:5) - 0.00 0.99* 

Bromus madritensis - <0.20 (3:2) <0.25 (3:3) 0.57 0.60* 

Cressa truxillensis <0.22 (9:7) - <0.20 (3:3) 0.71 0.42* 

Hemizonia pungens <0.15 (8:7) <0.20 (3:2) <0.20 (2:2) 1.15 0.35* 

Hordeum murinum <0.19 (10:10) <0.21 (6:5) <0.20 (2:2) 0.93 0.41* 

Hordeum vulgare - <0.20 (6:6) <0.21 (14:13) 0.42 0.53* 

Melilotus indica <0.18 (10:10) <0.20 (4:4) - 0.32 0.58* 

Sisymbrium irio <0.17 (4:4) - <0.24 (8:8) 1.64 0.23* 
Land Retirement Demonstration Project 

Five Year Report 

88 

Table 3-6. List of plant samples from Tranquillity that exceeded the populationlevel performance standard (2.0 mg/kg). Those marked with an asterisk had selenium 

levels that fell within the range of geometric means of vegetation collected from Kesterson 

NWR between 1988 and 1992 (2.3 to 6.7 mg/kg).

Collection Year Species Se concentration (mg/kg) 

2000 Heliotropium curassavicum 3.9* 

2000 Heliotropium curassavicum 3.6* 

2001 Suaeda moquinii 2.6* 

2002 Suaeda moquinii 4.4* 

2002 Sisymbrium irio 2.4* 

2002 Suaeda moquinii 2.3* 

2003 Atriplex polycarpa 2.1 

2003 Suaeda moquinii 5.0* 

2003 Brassica nigra 3.5* 

2003 Brassica nigra 3.2* 

2003 Heliotropium curassavicum 2.3* 

Seven plant species from Tranquillity and five plant species from Atwell Island were 

collected in sufficient numbers on various landforms (cultivated, uncultivated, and 

experimental lands) to allow an analysis of the affects of landform type on selenium 

levels (Tables 3-7 and 3-8). There were no clear differences in selenium levels 

between landform types for any species at Atwell Island, but this could be because of 

the generally low selenium levels and the high percentage of non-detects in the data 

sets. At Tranquillity, mean selenium levels in A. argentea were at least 40 percent 

lower on uncultivated lands than on cultivated or experimental lands (p < 0.01 and 

p = 0.02, respectively) and mean selenium levels in B. nigra were at least 50 to 70 

percent lower on uncultivated lands than on experimental or cultivated lands 

(p < 0.01 and p < 0.01, respectively). 

Table 3-7. Results of analysis of variance tests of selenium concentrations (mg/kg 

dry weight) between landform types in plant species collected from Tranquillity, 

1999 to 2003. GM = geometric mean, N = sample size, ND = number of non-detects, 

Uncult = uncultivated lands, Cult = cultivated lands, Exp = experimental lands. p values 

marked with an asterisk must be interpreted with caution because of the high number of 

non-detects in one or more data sets.

GM by landform(N:ND) 

Species Uncult Cult Exp F p value

Atriplex argentea <0.24 (16:9) <0.39 (10:1) <0.41 (12:3) 10.02 < 0.01* 

Avena sp. - 0.26 (7:0) <0.28 (10:1) 0.15 0.70 

Brassica nigra <0.28 (22:8) 0.87 (16:0) <0.58 (16:1) 17.04 < 0.01 

Hordeum murinum <0.23 (3:2) 0.57 (1:0) <0.33 (8:2) 0.85 0.46* 

Hordeum vulgare 0.20 (2:0) <0.32 (48:8) <0.27 (22:3) 1.49 0.22 

Melilotus indica 0.27 (6:3) 0.28 (4:2) 0.36 (1:0) 0.43 0.66* 

Sisymbrium irio 0.78 (3:0) <0.47 (10:2) <0.71 (12:1) 1.08 0.36 
Chapter 3. Selenium Levels of Biota from 

Retired Agricultural Lands in the San Joaquin Valley 

89 

Table 3-8. Results of Analysis of Variance tests of selenium concentrations 

(mg/kg) between landform types in plant species collected from Atwell Island, 2000 

to 2002. GM = geometric mean, N = sample size, ND = number of non-detects, 

Uncult = uncultivated lands, Cult = cultivated lands, Exp = experimental lands. p

values marked with an asterisk must be interpreted with caution because of the 

high number of non-detects in one or more data sets. 

GM by landform (N:ND) 

Species Uncult Cult Exp F p value

Atriplex 

argentea <0.22 (13:11) <0.20 (3:3) - 0.44 0.52* 

Hordeum 

murinum <0.20 (15:14) <0.20 (3:3) - 0.02 0.88* 

Hordeum 

vulgare - <0.21 (14:13) <0.20 (6:6) 0.41 0.53* 

Melilotus indica <0.18 (11:11) <0.20 (3:3) - 0.22 0.65* 

Sisymbrium irio <0.22 (8:6) - <0.20 (4:4) 0.07 0.79* 

There were no discernable differences in the selenium concentration between 

plant parts (whole plant, vegetation, and fruits) from plants collected from Atwell 

Island, but there were clear differences in the selenium concentration between 

plants parts in two species collected from Tranquillity (Tables 3-7 and 3-9). In H. 

murinum the whole plant had 61 percent less selenium than the fruits (p < 0.01) 

yet in H. vulgare the fruits had 24 percent less selenium than the vegetative 

structures. There is some evidence that the fruits of Phacelia distans had about 

40 percent less selenium than the vegetative structures and that the fruits of 

Sonchus sp. had about 60 percent less selenium than the vegetative structures. 

The small sample sizes (and high numbers of non-detects in the P. distans data) 

are reason to interpret the findings for these two species with caution. There also 

is some evidence that the fruits of A. argentea were higher in selenium than other 

parts of the plant and that the vegetative structures of M. indica were lower in 

selenium than the whole plant. 
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Table 3-9. Results of Analysis of Variance tests of selenium concentrations 

(mg/kg) between plant parts in plant species collected from Tranquillity, 1999 to 

2003. GM = geometric mean, N = sample size, ND = number of non-detects, 

Whole = whole plant, Veg = vegetation. p values marked with an asterisk must be 

interpreted with caution because of the high number of non-detects in one or more 

data sets. 

GM by plant part (N:ND) 

Species Whole Veg Fruits F p value 

Atriplex argentea <0.35 (19:5) <0.35 (22:8) 0.84 (3:0) 2.87 0.07 

Avena sp. <0.30 (10:1) 0.22 (3:0) 0.24 (4:0) 0.86 0.44 

Bromus madritensis <0.20 (6:5) - <0.22 (7:6) 0.85 0.38* 

Brassica nigra - <0.55 (27:4) <0.43 (27:5) 1.26 0.27 

Hordeum murinum <0.22 (5:4) 0.26 (3:0) 0.57 (4:0) 4.73 0.04* 

Hordeum vulgare - <0.34 (40:8) <0.26 (34:11) 6.04 < 0.01 

Melilotus indica 0.36 (3:0) <0.25 (8:5) - 4.62 0.06* 

Phacelia distans <0.20 (1:1) <0.33 (3:2) <0.20 (3:1) 15.62 < 0.01* 

Sisymbrium irio - <0.79 (12:1) <0.49 (13:2) 3.12 0.09 

Sonchus sp. - 0.71 (2:0) 0.31 (2:0) 806.35 < 0.01 

Table 3-10. Results of Analysis of Variance tests of selenium concentrations 

(mg/kg) between plant parts in plant species collected from Atwell Island, 2000 to 

2002. GM = geometric mean, N = sample size, ND = number of non-detects, 

Whole = whole plant, Veg = vegetation. p values marked with an asterisk must be 

interpreted with caution because of the high number of non-detects in one or more 

data sets. 

GM by plant part (N:ND) 

Species Whole Veg Fruits F p value 

Atriplex argentea <0.21 (10:9) <0.21 (6:5) - 0.00 0.99* 

Avena sp. - <0.20 (2:2) <0.20 (2:2) No variance* 

Bromus 

madritensis <0.25 (3:3) - <0.20 (3:2) 0.57 0.60* 

Brassica nigra <0.28 (5:1) <0.20 (5:5) 2.58 0.15* 

Hemizonia 

pungens <0.16 (10:9) <0.20 (3:2) - 1.09 0.32* 

Hordeum murinum <0.19 (12:12) - <0.21 (6:5) 1.74 0.21* 

Hordeum vulgare - <0.18 (10:10) <0.20 (10:7) 1.00 0.33* 

Melilotus indica <0.18 (10:10) <0.20 (4:4) - 0.32 0.58* 

Sisymbrium irio <0.17 (4:4) <0.28 (4:4) <0.20 (4:3) 1.42 0.29* 

3.3.2. Invertebrates 

The mean selenium concentrations in crickets (Figure 3-1) collected from 

Tranquillity (0.40 to 0.81 mg/kg) were higher than those collected from Atwell 

Island (0.13 to 0.49 mg/kg; p <0.01). Selenium levels in crickets did not appear 

to vary between years at Atwell Island, but did at Tranquillity. The mean 
Chapter 3. Selenium Levels of Biota from 

Retired Agricultural Lands in the San Joaquin Valley 

91 

selenium concentration in crickets collected in 1999 was 44 percent lower than in 

those collected in 2000, 51 percent lower than in those collected in 2001, and 47 

percent lower than in those collected in 2003 (p = 0.2, p < 0.01, and p = 0.01, 

respectively). 

The mean selenium concentrations in beetles (Figure 3-2) collected from 

Tranquillity (0.65 to 1.35 mg/kg) were higher than those collected from Atwell 

Island (0.14 to 0.85 mg/kg, p <0.01). The mean concentration of selenium in 

beetles varied between years at both sites. At the Tranquillity site, beetles were 

approximately 50 percent lower in selenium in 2002 than in 2000 and 2001 

(p = 0.02 and p = 0.01, respectively) and at Atwell Island the selenium 

concentration in beetles was more than four times higher in 2000 than in 2001 and 

2002 (p < 0.01 and p = 0.02). However, the high number of non-detects in the 

Atwell Island 2000 data set (8 of 10 samples) coupled with a high detection limit 

for some samples (4 samples had a detection limit of 2.0 mg/kg) makes this 

apparent relationship uncertain. 

The mean selenium concentrations in spiders (Figure 3-3) were higher at 

Tranquillity (1.27 to 2.24 mg/kg) than at Atwell Island (0.25 to 1.04 mg/kg, p

<0.01). The mean concentration of selenium in spiders did not appear to vary 

between years at Tranquillity. At Atwell Island, selenium in spiders was almost 

twice as high in 2000 as in 2001 (p = 0.03) and more than four times higher than 

in 2002 (p < 0.01). These apparent relationships are uncertain because of the nondetects in the 2000 data set. 

The mean selenium concentrations in isopods (Figure 3-4) were much higher at 

Tranquillity (1.04 to 3.47 mg/kg) than at Atwell Island (0.13 to 0.48 mg/kg, 

p < 0.01). The mean concentration of selenium in isopods appeared to vary 

between years at both sites. The mean concentration of selenium in isopods 

collected from Tranquillity in 2002 was approximately 70 percent less than those 

collected in 2000, 2001, and 2003 (p < 0.01 in all cases). At Atwell Island, the 

mean concentration of selenium in isopods was approximately 4 times greater in 

2000 than in 2002 (p < 0.01), but this relationship is uncertain because of the 

number of non-detects in the 2000 and 2002 data sets. 

The mean concentration of selenium in all invertebrate groups (crickets, beetles, 

spiders, and isopods) collected from Atwell Island remained below the 

performance standard of 2.0 mg/kg established for project lands (Figures 3-1, 3-2, 

3-3, and 3-4; FWS 1999). Furthermore, only one spider sample and one isopod 

sample exceeded the performance standard. At Tranquillity, the mean 

concentration of selenium in invertebrates also remained below the performance 

standard, except for the spiders that were collected in 1999 and isopods that were 

collected in every year except 2002. Twelve isopod samples, 8 spider samples, 3 

beetle samples and 0 cricket samples collected from Tranquillity exceeded the 

performance standard. It is not unexpected that spiders and isopods exceeded the 

performance standard. The performance standard established was for terrestrial 

invertebrates as a group. Spiders are predators and isopods are detritus feeders; 
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Figure 3-1. Geometric means (solid circles) and error bars (mean multiplied by and 

divided by one standard deviation factor) of selenium concentrations in crickets 

collected from the Tranquillity and Atwell Island study sites. Data points that 

exceed the performance standard are represented by open circles. The ↓ signifies 

a mean lower than that reported because of the occurrence of non-detects in the 

data set. A = the range of geometric means of selenium concentrations in crickets 

(5.9 to 7.6 mg/kg) collected from 1988 to 1992 in grassland habitat at Kesterson 

NWR (USDI 1992). B = background level of selenium in terrestrial invertebrates (2.5 

mg/kg) collected from non-seleniferous soils in the western United States (USDI 

1998). C = the performance standard set by the U.S. Fish and Wildlife Service for 

selenium concentrations in terrestrial invertebrates (2.0 mg/kg) for Land 

Retirement Demonstration Project lands (FWS 1999). 
Chapter 3. Selenium Levels of Biota from 

Retired Agricultural Lands in the San Joaquin Valley 

93 

Figure 3-2. Geometric means (solid circles) and error bars (mean multiplied by and 

divided by one standard deviation factor) of selenium concentrations in beetles 

collected from the Tranquillity and Atwell Island study sites. Data points that 

exceed the performance standard are represented by open circles. The ↓ signifies 

a mean lower than that reported because of the occurrence of non-detects in the 

data set. A = the range of geometric means of selenium concentrations in beetles 

(8.7 to 21.0 mg/kg) collected from 1988 to 1992 in grassland habitat at Kesterson 

NWR (USDI 1992). B = background level of selenium in terrestrial invertebrates (2.5 

mg/kg) collected from non-seleniferous soils in the western United States (USDI 

1998). C = the performance standard set by the FWS for selenium concentrations 

in terrestrial invertebrates (2.0 mg/kg) for LRDP lands (FWS 1999). 
Land Retirement Demonstration Project 

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94 

Figure 3-3. Geometric means (solid circles) and error bars (mean multiplied by and 

divided by one standard deviation factor) of selenium concentrations in spiders 

collected from the Tranquillity and Atwell Island study sites. Data points that 

exceed the performance standard are represented by open circles. The ↓ signifies 

a mean lower than that reported because of the occurrence of non-detects in the 

data set. A = the range of geometric means of selenium concentrations in spiders 

(8.8 to 15.0 mg/kg) collected from 1988 to 1992 in grassland habitat at Kesterson 

NWR (USDI 1992). B = background level of selenium in terrestrial invertebrates (2.5 

mg/kg) collected from non-seleniferous soils in the western United States (USDI 

1998). C = the performance standard set by FWS for selenium concentrations in 

terrestrial invertebrates (2.0 mg/kg) for LRDP lands (FWS 1999). 
Chapter 3. Selenium Levels of Biota from 

Retired Agricultural Lands in the San Joaquin Valley 

95 

Figure 3-4. Geometric means (solid circles) and error bars (mean multiplied by and 

divided by one standard deviation factor) of selenium concentrations in isopods 

collected from the Tranquillity and Atwell Island study sites. Data points that 

exceed the performance standard are represented by open circles. The ↓ signifies 

a mean lower than that reported because of the occurrence of non-detects in the 

data set. A = the range of geometric means of selenium concentrations in isopods 

(53.0 to 60.0 mg/kg) collected from 1988 to 1992 in grassland habitat at Kesterson 

NWR (USDI 1992). B = background level of selenium in terrestrial invertebrates (2.5 

mg/kg) collected from non-seleniferous soils in the western United States (USDI 

1998). C = the performance standard set by FWS for selenium concentrations in 

terrestrial invertebrates (2.0 mg/kg) for LRDP lands (FWS 1999). 
Land Retirement Demonstration Project 

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both would be expected to accumulate more selenium than herbivorous or 

granivorous terrestrial invertebrates and, indeed, isopods are known to accumulate 

high amounts of selenium (USDI 1992). 

The mean selenium concentrations in terrestrial invertebrates collected from both 

sites generally remained within the range for terrestrial invertebrates occurring on 

non-seleniferous soils in the western United States (2.5 mg/kg, USDI 1998). The 

only exception to this was at Tranquillity where isopods exceeded this range in all 

years but 2002. The selenium levels in all invertebrate groups collected from the 

Tranquillity and Atwell Island sites are approximately an order of magnitude less 

than corresponding invertebrate groups collected between 1988 and 1992 in 

grassland habitat at Kesterson NWR. 

3.3.3. Small Mammals 

The mean selenium concentrations in deer mouse (Peromyscus maniculatus) 

bodies (Figure 3-5) were higher at Tranquillity (0.89 to 1.34 mg/kg) than at 

Atwell Island (0.62 and 0.68 mg/kg, p < 0.01). The mean concentration of 

selenium in deer mouse bodies did not appear to vary between years at Atwell 

Island site, but at Tranquillity, deer mouse bodies had approximately 34 percent 

less selenium in 2001 than in 2003 (p < 0.01). Similarly, the mean selenium 

concentrations in deer mouse livers (Figure 3-6) were higher at Tranquillity (2.27 

to 3.90 mg/kg) than at Atwell Island (2.21 to 2.37 mg/kg, p < 0.01). The 

concentration of selenium in deer mouse livers did not appear to vary between 

years at Atwell Island site, but at Tranquillity, deer mouse livers had 

approximately 30 to 42 percent less selenium in 2001 than in other years (p ≤ 0.01 

for all years). The concentrations of selenium in deer mice clearly differed 

between irrigated and nonirrigated landforms (Figure 3-7). The greatest 

difference was in 2001 when deer mouse body tissues from non-irrigated sites had 

47 percent less selenium than those from irrigated sites and deer mouse liver 

tissues from nonirrigated sites had 50 percent less selenium than those from 

irrigated sites. 

Selenium levels in deer mouse bodies collected from both Tranquillity and Atwell 

Island (Figure 3-7) were within the range that is typically found in small 

mammals occurring on non-seleniferous soils in the western United States (2.0 

mg/kg, USDI 1998). Selenium levels in deer mouse bodies collected from both 

Tranquillity and Atwell Island were an order of magnitude less than selenium 

levels found in deer mouse bodies collected from grassland habitats at Kesterson 

NWR from 1988 to 1992. Selenium levels in deer mouse livers collected from 

Tranquillity and Atwell Island (Figure 3-7) were within the range of selenium 

levels found in small mammal livers collected near a selenium-normal wetland 

(between 1 and 10 mg/kg, USDI 1998) located in the San Joaquin Valley. 

Selenium levels in deer mouse livers from both sites also were within or slightly 

above the range of selenium concentrations in small mammal livers (< 3 mg/kg) 

collected from an agroforestry plantation located in the San Joaquin Valley (Clark 

1987). No performance standards were set by FWS for small mammal body or 
Chapter 3. Selenium Levels of Biota from 

Retired Agricultural Lands in the San Joaquin Valley 

97 

Figure 3-5. Geometric means (solid circles) and error bars (mean multiplied by and 

divided by one standard deviation factor) of selenium concentrations in deer 

mouse (PEMA) bodies collected from Tranquillity and Atwell Island. Data points 

that exceed the mean multiplied by one standard deviation factor are represented 

by open circles. A = the range of geometric means of selenium concentrations in 

deer mouse bodies (4.8 to 11.0 mg/kg) collected at Kesterson NWR from 1988 to 

1992 (USDI 1992). B = the performance standard established for rodent hair for 

this project (5.0 mg/kg). C = background level of selenium in small mammal bodies 

(2.0 mg/kg) collected from non-seleniferous soils in the western United States 

(USDI 1998). . D = the performance standard established for rodent blood for this 

project (0.5 mg/kg). 
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Figure 3-6. Geometric means (solid circles) and error bars (geometric mean 

multiplied by and divided by one standard deviation factor) of selenium 

concentrations in deer mouse (PEMA) livers collected from Tranquillity and Atwell 

Island. Data points that exceed the mean multiplied by one standard deviation 

factor are represented by open circles. A = the upper range of selenium in small 

mammal livers collected from near a selenium-normal wetland (between 1 and 10 

mg/kg, Clark 1987). B = the performance standard established for rodent hair for 

this project (5.0 mg/kg). C = the upper range of selenium concentrations in small 

mammal livers collected from an agroforestry plantation (< 3 mg/kg, CDFG 1993). 

D = the performance standard established for rodent blood for this project (0.5 

mg/kg). 
Chapter 3. Selenium Levels of Biota from 

Retired Agricultural Lands in the San Joaquin Valley 

99 

Figure 3-7. Geometric means of selenium concentrations in deer mouse (PEMA) 

bodies and livers collected from irrigated and non-irrigated lands at Tranquillity, 

1999 to 2003. 

liver tissues. Instead, performance standards were set for small mammal blood 

(0.5 mg/kg) and hair (5.0 mg/kg). The selenium values obtained from deer mouse 

bodies exceeded the values established for blood and the selenium levels obtained 

for livers were less than the performance standards set for hair. Nevertheless, the 

selenium levels present in the bodies and livers of deer mice appear to be within 

acceptable limits. 

The mean selenium concentrations in shrew (Sorex ornatus) bodies collected from 

Tranquillity varied from 1.95 to 2.51 mg/kg (Figure 3-8). There were no 

discernable differences in selenium concentrations between years. Livers were 

not extracted from the bodies of shrews in 1999, so no data from that year are 

available for analysis. However, the mean selenium concentrations in shrew 

livers varied from 2.00 to 4.18 mg/kg (Figure 3-9) from 2000 to 2002 and there 

were clear differences between years. The selenium concentration in shrew liver 

tissue was 63 percent lower in 2002 than in 2000 (p < 0.01) and 45 percent lower 

than in 2001 (p = 0.03). This may be misleading, however, because of the small 

sample size (n = 1) of shrew livers analyzed in 2002. 

The mean selenium concentrations in shrew bodies collected from Tranquillity 

(Figure 3-9) were near the upper level of the range of selenium in small mammal 

body tissues collected from non-seleniferous soils in the western United States 

(generally < 2.0 mg/kg, USDI 1998). This is not unexpected because shrews are 
Land Retirement Demonstration Project 

Five Year Report 

100 

Figure 3-8. Geometric means (solid circles) and error bars (geometric mean 

multiplied by and divided by one standard deviation factor) of selenium 

concentrations in shrew (SOOR) bodies collected from Tranquillity. Data points 

that exceed the geometric mean multiplied by one standard deviation factor are 

represented by open circles. A = the range of geometric means of selenium 

concentrations in shrew bodies (15.0 to 27.0 mg/kg) collected at Kesterson NWR 

from 1988 to 1992 (USDI 1992). B = the performance standard established for 

rodent hair for this project (5.0 mg/kg). C = background level of selenium in small 

mammal bodies (2.0 mg/kg) collected from non-seleniferous soils in the western 

United States (USDI 1998). D = the performance standard established for rodent 

blood for this project (0.5 mg/kg). 

insectivores and bio-accumulation of selenium in shrews is expected to be greater 

than in most other small mammals. The mean selenium levels in shrews collected 

from Tranquillity were approximately an order of magnitude less than selenium 

levels found in shrews collected between 1988 and 1992 from grassland habitats 

at Kesterson NWR (15.0 to 27.0 mg/kg). No performance standards were set for 

small mammal body tissues by the FWS. Instead, performance standards were set 

for small mammal blood (0.5 mg/kg) and hair (5.0 mg/kg). The selenium in 

shrew bodies collected from the Tranquillity site exceeded those established for 

blood, but were lower than the standard established for hair. Selenium levels in 

the livers of shrews collected from Tranquillity (Figure 3-9) were within the range 

of selenium levels found in the livers of small mammals (between 1 and 10 

mg/kg) collected from near a selenium-normal wetland located in the San Joaquin 

Valley. Selenium levels in the livers of shrews collected from Tranquillity were 

also near the upper range of selenium levels found in small mammal livers (< 3 

mg/kg) collected from an agroforestry plantation in the San Joaquin Valley (Clark 
Chapter 3. Selenium Levels of Biota from 

Retired Agricultural Lands in the San Joaquin Valley 

101 

1988). Accordingly, the selenium levels present in the bodies and livers of deer 

mice appear to be within acceptable limits. 

Figure 3-9. Geometric means (solid circles) and standard deviations of selenium 

concentrations in shrew (SOOR) livers collected from the Tranquillity study site. 

Data points that exceed the standard deviation are represented by open circles. 

A = the upper range of selenium in small mammal livers collected from near a 

selenium-normal wetland (between 1 and 10 mg/kg, Clark 1987). B = the 

performance standard established for rodent hair for this project (5.0 mg/kg). 

C = the upper range of selenium in small mammal livers collected from an 

agroforestry plantation (< 3 mg/kg, CDFG 1993). D = the performance standard 

established for rodent blood for this project (0.5 mg/kg). 

3.4. Discussion and Conclusions 

The concentrations of selenium observed in biota at both project sites are 

generally considered to be within acceptable limits and, although a risk 

assessment model was not generated, there is evidence of low risk to wildlife. 

Whereas high selenium levels in groundwater could result in a potential risk to 

biota, the exposure pathway is limited because the depth to groundwater has 

increased. Similarly, although selenium levels in the soils remain elevated (but 

show evidence of decline), the extremely dry conditions that prevail at both 

Atwell Island and Tranquillity may limit the exposure pathway. The physical 

conditions present on these sites are thought to be representative of other drainage 
Land Retirement Demonstration Project 

Five Year Report 

102 

impacted areas of the San Joaquin Valley and it is reasonable to assume that the 

bio-accumulation of selenium and risk to wildlife would be similar to that found 

on our study sites. 

There is less risk of exposure to selenium at Atwell Island than at Tranquillity 

because of lower levels of selenium in the soils and groundwater. Mean selenium 

levels in biota on both project sites tend to be within the range typically found in 

biota occurring on non-seleniferous soils in the western United States and are 

generally below the population-level performance standards set for the project by 

the FWS (FWS 1999). Furthermore, selenium levels in biota from both sites are 

generally an order of magnitude less than found at Kesterson NWR. 

The generally low levels of selenium in biota may be a result of very low water 

availability during the study period. Precipitation was below normal or nearnormal; ephemeral pools (pools of water lasting 30 days or more) were never 

present, and the team suspects that soil moisture was too low to allow a high 

degree of selenium uptake. There were no wetlands on the Tranquillity site. Both 

project sites were primarily dry, upland environments rather than aquatic or 

wetland environments, which likely reduces the potential for the bio-availability 

and bio-accumulation of selenium. 

The assumption that reduced water availability results in lowered selenium 

accumulation also is supported by the higher selenium levels observed in some 

biota from irrigated lands compared with selenium levels present in biota from 

non-irrigated lands. This trend was evident in some of the most common and 

widespread species present on the Tranquillity site: A. argentea, B. nigra, and in 

the bodies and livers of deer mice. These observations suggest that retiring lands 

from irrigated agriculture may reduce the potential for selenium bio-accumulation 

at the population level. 

Although the mean selenium concentrations in biota were generally below the 

performance standards, some samples within specific groups exceeded those 

standards. Eleven of 325 (3.4 %) plant samples and 22 of 115 (19.1 %) 

invertebrate samples (mostly isopods and spiders) collected from Tranquillity 

exceeded performance standards and 2 of 83 (2.4%) invertebrate samples 

collected from Atwell Island exceeded performance standards (see Table 3-6 and 

Figures 3-1 through 3-4). Although performance standards were not set for small 

mammal bodies and livers, some samples collected from both Tranquillity and 

Atwell Island appeared to be somewhat high in selenium (see Figures 3-5, 3-6, 

3-8, and 3-9). In many cases, these samples were collected from areas known to 

be rich in selenium (e.g., areas with high selenium levels in the soil or sediments 

within the San Luis Drain). These samples are reason for caution. 

The Tranquillity site is reasonably representative of conditions found on other 

drainage impacted lands within the region (i.e., those lands that could potentially 

be retired from irrigated agriculture). Tranquillity clay—the predominant soil 

type at the site—is the most extensive soil type mapped by the Natural Resources 
Chapter 3. Selenium Levels of Biota from 

Retired Agricultural Lands in the San Joaquin Valley 

103 

Conservation Service on the lower alluvial fan and basin rim landforms in the 

western San Joaquin Valley. Selenium levels in the soil and groundwater (prior to 

retirement) were similar to other drainage impacted lands in the region (see 

Chapter 2) and the vegetation and habitat characteristics that developed on the site 

(exclusive of successfully restored areas) appear to be similar to that occurring on 

fallowed lands within the region. We expect that our results are regionally 

applicable and would be indicative of conditions on other retired lands. 

We contend that land retirement and the restoration of retired lands, if properly 

implemented, monitored, and managed, would be beneficial to wildlife, including 

threatened and endangered species, and would generally not pose a severe risk of 

selenium exposure. However, we urge that land retirement be integrated with a 

comprehensive selenium monitoring program to monitor exposure of wildlife to 

selenium on a site by site basis. Furthermore, a suite of remedial actions should 

be developed in the event that selenium exposure on a site is or becomes 

problematic. 

3.5. Literature Cited 

California Department of Fish and Game. 1993. Selenium in wildlife from 

agroforestry plantations in the San Joaquin Valley. Final report to the Calif. 

Dept. of Water Resources, Stockton, California. In U.S. Department of the 

Interior. 1998. Guidelines for interpretation of the biological effects of 

selected constituents in biota, water, and sediment. 198 pp. 

Clark, D. R., Jr. 1987. Selenium accumulation in mammals exposed to 

contaminated California irrigation drainwater. Sci. Total Environ. 66:147-

168. In U.S. Department of the Interior. 1998. Guidelines for interpretation 

of the biological effects of selected constituents in biota, water, and sediment. 

198 pp. 

Central Valley Project Improvement Act. 1992. Federal Register: March 9, 1998. 

Vol. 63, No. 45. p 11453. 

Ghosh, A., S. Sarkar, A.K. Pramanik, S. Gosh, and S. Palchowdhury. 1993. 

Selenium toxicosis in grazing buffaloes and its relationship with soils and 

plants of West Bengal. Indian J. Anim. Sci. 63:57-560. 

Hedland, J.D. 1993. Conservation planning for water quality concerns; toxic 

element – Selenium. U.S. Soil Conservation Service, West National 

Technical Center, Portland Oregon. Technical Note, Water Quality Series 

No. W1. 

Heinz, G.H., and M.A. Fitzgerald. 1993. Reproduction in mallards following 

overwinter exposure to selenium. Environ. Pollut. 81:117-122. 
Land Retirement Demonstration Project 

Five Year Report 

104 

Johnston, P.A., 1987. Acute toxicity of inorganic selenium to Daphnia magna 

(Straus) and the effect of sub-acute exposure upon growth and reproduction. 

Aquat. Toxicol. 10:335-352. 

Koller, L.D. and J.H. Exon. 1986. The two faces of selenium – deficiency and 

toxicity – are similar in animals and man. Ca. J. Vet. Res. 50:297-306. 

Lemly, A.D. 1985. Toxicology of selenium in a freshwater reservoir: 

implications for environmental hazard evaluation and safety. Ecotoxicol. 

Environ. Safety 10:314-338. 

Lemly, A.D. 1993a. Teratogenic effects of selenium in natural populations of 

freshwater fish. Ecotoxicol. Environ. Safety 26:181-204. 

Lemly, A.D. 1993b. Metabolic stress during winter increases the toxicity of 

selenium to fish. Aquatic. Toxicol. 27:138-158. 

Ohlendorf, H.M. 1989. Bioaccumulation and effects of selenium in wildlife. In

L.W. Jacobs, ed., Selenium in agriculture and the environment. American 

Society of Agronomy and Soil Science Society of America, Madison, 

Wisconsin. Special publication 23. pp. 133-177. 

Ohlendorf, H.M., J.P. Skorupa, M.K. Saiki, and D.A Barnum. 1993. Food-chain 

transfer of trace elements to wildlife. In R.G. Allen and C.M.U. Neale, eds. 

Management of irrigation and drainage systems: integrated perspectives. 

American Society of Civil Engineers, New York. p. 596-603. 

Saiki, M.K. and R.S. Ogle. 1995. Evidence of impaired reproduction by western 

mosquitofish inhabiting seleniferous agricultural drainwater. Trans. Am. 

Fish Soc. 12:578-587. 

SPSS, Inc. 2002. SigmaPlot 2002 for windows version 8.02. 

StatSoft, Inc. 2002. STATISTICA (data analysis software system), version 6. 

www.statsoft.com. 

U.S. Department of the Interior. 1998. Guidelines for interpretation of the 

biological effects of selected constituents in biota, water, and sediment. 198 

pp. 

U.S. Department of the Interior. 1992. Kesterson Reservoir biological 

monitoring report and 1993 biological monitoring plan. U.S. Bureau of 

Reclamation, Mid-Pacific Regional Office, Sacramento, California. 79 pp. 

U.S. Fish and Wildlife Service. 1998. Recovery plan for upland species of the 

San Joaquin Valley, California. Region 1, Portland, Oregon. 319 pp. 
Chapter 3. Selenium Levels of Biota from 

Retired Agricultural Lands in the San Joaquin Valley 

105 

U.S. Fish and Wildlife Service. 1999. Formal section 7 consultation for the 

Central Valley Project Improvement Act Land Retirement Program 

Demonstration Project. Sacramento Fish and Wildlife Office, Sacramento, 

California. 64 pp. 

Chapter 4. Results of a Habitat Restoration Study on 

Retired Agricultural Lands in the San Joaquin Valley 

107 

Chapter 4. Results of a Habitat 

Restoration Study on Retired 

Agricultural Lands in the San 

Joaquin Valley, California 

by Curtis E. Uptain, Krista R. Garcia, Nur P. Ritter, Georgia Basso, Darren P. 

Newman, and Stuart H. Hurlbert 

4.1. Introduction 

Land retirement without habitat restoration would likely lead to large fields 

infested with weeds and pests which would affect neighboring agriculture and 

require extensive and continuous management. Appropriate habitat restoration 

must accompany land retirement to minimize weeds and pests and to maximize 

benefits for wildlife. Although land retirement has the potential to enhance 

wildlife values and improve ecological systems in the San Joaquin Valley, it is 

recognized that land uses other than wildlife habitat may take precedence on some 

lands. Some land uses, particularly grazing and, in some cases, dryland farming 

can be compatible with and may even contribute to habitat values for wildlife. 

Land retirement could provide wildlife habitat and contribute to the recovery of 

endangered and threatened plant and animal species (FWS 1998). Retired 

agricultural lands could provide connecting linkages and corridors between 

existing habitat areas or large areas of contiguous blocks of land that would 

provide habitat for new core populations of sensitive species. 

The Biological Opinion for the Land Retirement Demonstration Project (LRDP) 

(FWS 1999) required that a 5-year Habitat Restoration Study (HRS) be conducted 

focusing on determining the responses of wildlife to land retirement and 

restoration efforts. Specific objectives of the HRS were to: 

• Determine the efficacy of revegetation with native plants as a means to 

facilitate upland habitat restoration. 

• Determine the efficacy of microtopographic contouring as a means to 

facilitate upland habitat restoration. 

• Examine the responses of plants and wildlife to land retirement and 

restoration. 

To accomplish these goals, a large-scale (323.75 ha; 800 ac) study was initiated at 

the Tranquillity site in 1999. Twenty long-term study plots were established and 
Land Retirement Demonstration Project 

Five Year Report 

108 

a broad range of data were collected over a 5-year period (see Section 4.2.1 for a 

description of the experimental design). At the plot-scale, vegetation, 

invertebrates, amphibians, reptiles, birds, and small mammals were all monitored 

throughout the duration of the project. Avian nesting success on the study plots 

also was studied in 2002 and 2003. Site-wide monitoring included track station 

surveys, windshield surveys, and spotlighting. The results of these monitoring 

efforts provide information on wildlife use of retired agricultural lands over a 5-

year period. The results also allowed an evaluation of the effectiveness of the 

restoration efforts and the relative value of those restoration efforts to wildlife. 

4.2. Methods 

4.2.1. Study Design 

A 323.75 ha (800 ac) Habitat Restoration Study (HRS) was established on retired 

agricultural lands in 1999 to examine the responses of wildlife to restoration 

efforts. The study incorporated a complete randomized block design and 

consisted of twenty, 4.05 ha (10 ac) study plots arrayed in 5 blocks (Figure 4-1). 

The size of the HRS was determined by that which could be reasonably 

manipulated and monitored with a high degree of experimental rigor, but which 

was sufficient to yield significant results in a relatively short amount of time 

(5 years or less). Two restoration factors were studied: (1) the introduction of 

native plants through seeding (imprinting) and transplanting; and (2) the reestablishment of surface contouring (i.e., microtography). Four combinations of 

these treatment factors were applied (Figure 4-1). 

4.2.2. Restoration Methods 

Plots were arranged in a randomized block design to control variation caused by 

the heterogeneous physical characteristics of the site. Four treatments were 

randomly assigned to plots within each block; plots were established in April of 

1999. Plot corners were permanently marked with 0.91 m (3 ft) sections of 

reinforcing bar (rebar) and pin flags were added to help locate plot corners. Plot 

corners were located with a Global Positioning System (GPS) receiver, and data 

points were archived. 

To minimize interactions between plots and to reduce weeds and soil erosion, 

each plot was surrounded by a 12.14 ha (30 ac) buffer that was maintained with a 

barley cover crop. During the first year of the Demonstration Project (1999), all 

HRS experimental plots and associated buffer regions were planted in barley. To 

grow a healthy cover crop the soil was disked and leveled and the soil was 

prepared until it was of uniform texture. Barley was drilled at approximately 

77.11 kg per 0.40 ha (170 lbs per ac). 
Chapter 4. Results of a Habitat Restoration Study on 

Retired Agricultural Lands in the San Joaquin Valley 

109 

Figure 4-1. Map of the Tranquillity HRS plots showing treatments and blocks. Key 

to Treatments: CR = contouring and seeding; NR = seeding and no contouring; 

CN = contouring and no seeding, and NN = no contouring and no seeding. 

Due to the effectiveness of the 1999 crop at controlling weeds and providing 

vegetative cover on retired lands, barley was used as the cover crop for all 

subsequent years. The seed was inexpensive ($0.10-$0.15 per .45 kilo) and was 

planted without extensive ground preparation. Irrigation was applied to give the 

barley a competitive advantage over weeds and with the hopes of obtaining a 

profitable crop. The barley was irrigated with approximately 7.6 cm (3 in) of 

water (an amount which would not contribute to deep percolation) in spring of 

1999, 2000, and 2001. The barley was not irrigated in subsequent years to reduce 

costs and, although this precluded production of a harvestable crop, the barley 

was flailed and replanted to reduce the need to purchase seed. 

Imprinting is an experimental seeding method that creates small impressions in 

the soil and deposits seed directly in the indentation (Dixon 1988). This method 

of seeding promotes seed-soil contact while protecting the seed from wind and 
Land Retirement Demonstration Project 

Five Year Report 

110 

predators. Native seed was imprinted evenly across the plots receiving the 

reintroduction prescription in March 2000. Plant species were selected based on 

representative species from nearby ecological reserves and known species 

composition of the desired plant communities. Further information on rates of 

applications, costs and mix preparation can be found in Selmon et al. (2000). 

Microtopographic contours (berms) were created to reintroduce minor vertical 

variation across the landscape. Such heterogeneity may create microhabitat 

suitable for plant germination and animal burrows. Berms were established on 

experimental plots in January 2000 using a modified agricultural implement 

commonly used to create “checks” in flood-irrigated agricultural fields. The 240, 

12 m (39.3 ft) long berms were installed on each plot. Prior to installation of the 

HRS plots, it was found that berms were compacted by imprinting. Accordingly, 

the berms in the seeded plots were initially installed at about twice standard 

height. The resulting berms on all plots after seeding were consistent in height. 

Native plants also were introduced onto the experimental plots via direct 

transplanting in March and April of 2000. Seedlings were grown from seed in 

local nurseries from commercial and local seed sources. Transplanted seedlings 

were closely grouped in “shrub islands” (i.e., closely-grouped planting) to 

maximize the potential for “nurse plant” effects. Two types of shrub islands were 

created (Table 4-1). Twenty-five islands (13 Type A and 12 Type B) were 

installed on each plot. In fall 2000, all shrub islands were inventoried. Wherever 

necessary, additional seedlings were transplanted into the existing shrub islands 

such that each island had the minimum number of species as shown in Table 4-1. 

Transplanting in the Type B islands was augmented by broadcast seed of Isocoma 

acradenia. 

Table 4-1. Overview of shrub island planting, Tranquillity HRS. Figures in the 

Initial Planting columns indicate the number of individuals that were initially 

transplanted to each island. Figures in the Fall Replanting columns indicate the 

target number (i.e., minimum number of living individuals) for each species 

following replanting in fall 2000. 

“Type A” “Type B” 

Initial Planting Fall Replanting Initial Planting Fall Replanting

Allenrolfea occidentalis 14 4 - - 

Atriplex polycarpa - - 12 8 

Isocoma acradenia - - 2 seeding 

Leymus triticoides 4 0 - - 

Sporobolus airoides 22 8 - - 

Nursery stock generally needs ample rain or irrigation after planting for 

establishment in native soils. The Tranquillity study site rarely receives sufficient 

rainfall to support transplanted nursery stock, so DriWaterTM, a time-release water 

product, was installed adjacent to seedlings when planting the shrub islands. To 
Chapter 4. Results of a Habitat Restoration Study on 

Retired Agricultural Lands in the San Joaquin Valley 

111 

facilitate establishment, additional water was applied 2-3 times with a backpack 

sprayer within 2 weeks of planting. 

4.2.3. Plot-Level Monitoring 

4.2.3.1. Vegetation Survey Methods 

Vegetation monitoring was timed (as much as possible) to coincide with the 

period when the majority of the annual species had begun to senesce. Monitoring 

dates for all years are presented in Table 4-2. Sampling methodologies were 

consistent throughout the 4 years of monitoring on the plots. Data were collected 

from 24 quadrats (35 x 70 cm) on each plot. A stratified random sampling 

approach was employed, with plots divided into sixth-sections and four sampling 

points randomly selected within each section. All species were noted and the 

percent cover for each species estimated using a modified Daubenmire cover 

scale (0-1 percent; 1-5 percent; 5-25 percent; 25-50 percent; 50-75 percent; 75-95 

percent; 95-100 percent; Bonham 1989). The total percent cover of all species 

within the quadrat was also estimated using the same scale. Whenever possible, 

species were identified completely; failing this, species were assigned morphospecies names (e.g., “Unknown Compositae”). 

In addition to cover data, qualitative data were entered for each quadrat (e.g., 

whether or not the percent cover of vegetation in the quadrat was representative of 

the general area), and for individual species (e.g., flowering condition). 

Qualitative assessments were also made at the plot-wide scale. To document that 

portion of the flora that was not represented in the quadrats, a running list was 

compiled of all species noted on the plot. However, estimates of species richness 

were based solely on the species that occurred in the quadrats. 

In fall of 2002, a census of shrubs and shrub-like annuals was conducted on the 

HRS plots; however, this survey was not repeated in 2003. A complete account 

of the 2002 survey was presented in Uptain et al. (2004). 

Photographic vouchers were taken on the HRS plots to document post-treatment 

conditions and to provide a permanent record of changes in vegetation structure 

and composition. Photographs (one 35 millimeter [mm] and one digital) were 

taken from each of two standard locations along the southern boundary of each 

plot (43 meters [m] from each of the corners), with the cameras oriented 

northwards. Copies of the photos are archived at Endangered Species Recovery 

Program (ESRP) and Reclamation offices in Fresno, with the 35 mm photos 

stored in binders and the digital photos archived on compact disk. Photographs 

were taken quarterly, except in 2003 when three photographic surveys were made 

(March 21; June 18, 24-25; September 16-18). 
Land Retirement Demonstration Project 

Five Year Report 

112 

Table 4-2. Plot-level survey dates for the various biotic groups, 1999 to 2003. 

Monitoring in 1999 (baseline monitoring) preceded the installation of the HRS plots 

but was conducted on the 323.75 ha (800 ac) area on which the plots were 

subsequently cited. 

Biotic group Year Survey Dates 

1999 23, 26, 27, 29 Apr 

2000 25-27 Apr; 1 May 

2001 7-9 May 

2002 11, 12, 15, 20 Mar 

Vegetation 

2003 8-11, 15-16, 21-22 Apr 

1999 8-10 June 

2000 6-7, 13-14 June 

2001 19-22 June 

2002 16-19 April 

Invertebrates 

2003 20-23 May 

1999 8-10 June 

2000 6-7, 13-14 June 

2001 11-13 July 

2002 8-10 June, 29 April, 2-3 May, 9-11 July, 8-10 Jan(pitfall) 

Amphibians 

and Reptiles 

2003 14-16 Jan, 7-9 May, 8-10 July, 21-23 Oct, 3-4 Dec (just amphib) 

1999 12-14 May, 21-23 July, 20-22 Oct 

2000 12-14 Jan, 8-10 May, 26-28 July, 17-19 Oct 

2001 17-19 Jan, 18-20 April, 18-20 July, 2-4 Oct 

2002 16-18 Jan, 2-4 April, 22-24 July, 8-10 Oct 

Birds 

2003 14-16 Jan, 7-9 May, 8-10 July, 21-23 Oct 

1999 11-14 Oct 

2000 15-18 May, 8-11Aug, 6-9 Nov 

2001 27 Feb-2 Mar, 30 April-3 May, 6-9 Aug, 5-8 Nov 

2002 29 Jan-1 Feb, 6-9 May, 15-18 July, 28-31 Oct 

Small 

Mammals 

2003 4-7March, 28-30 April-1 May, 21-24 July, 6-9 Oct 

4.2.3.2. Invertebrates 

Invertebrates were collected over a 5-year period (Table 4-2) from five pitfall 

arrays (Figure 4-2) that were established on each of the 20 study plots. Each array 

consisted of four, 11.36 liters (3 gal) buckets sunk into the ground to the rim. The 

buckets were connected by 6.1 m by 30 cm (20 ft by 1 ft) sections of galvanized 

steel flashing used to guide invertebrates into the buckets. During the four 

consecutive survey days, bucket lids were removed and supported approximately 

2.5 cm (1 in) above the rim by wooden stakes. Buckets were opened for 

approximately 24 hours between each survey day. 
Chapter 4. Results of a Habitat Restoration Study on 

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113 

Figure 4-2. Locations of pitfall arrays, amphibian and reptile coverboards, avian 

transects and point-count locations, and small mammal trapping lines on a study 

plot at the Tranquillity site. 

All invertebrates found within the pitfalls were identified to order and counted. A 

voucher specimen was collected of each invertebrate type that was present on 

each plot. These were later identified to the family level whenever possible. The 

numbers of orders found on each plot over the 4-day survey period were tallied to 

obtain richness. The abundance of invertebrates present on each plot was 

determined by tallying the numbers of invertebrates found in each bucket over the 

4-day sampling period, then adding the tallies of all buckets on a plot, then 

dividing the total by four to obtain an average number per day. Richness and 

abundance values are based upon the ordinal level because consistent and 

accurate invertebrate field identification beyond that level was not possible. 

Once the identification process was complete, invertebrate orders and families 

were classified into one of four functional groups; herbivores, predators, 

pollinators, and parasites. Although this process is not complete, the 

classification has enabled us to identify agriculturally beneficial and harmful 
Land Retirement Demonstration Project 

Five Year Report 

114 

invertebrates which occur on the study plots and assess the potential impacts of 

land retirement in promoting populations of these invertebrates. 

4.2.3.3. Amphibians and Reptiles 

Reptile and amphibian surveys were typically conducted concurrently with avian 

surveys (Table 4-2). On occasion, asynchronous surveys were conducted because 

of time constraints imposed by the avian surveys and the need to conduct 

amphibian surveys during periods of rain. Visual encounter surveys (Heyer et al. 

1994) were conducted along the small mammal trapping transects, and four 0.37 

m by 0.37 m (4 ft by 4 ft) coverboards per plot (Figure 4-2) were inspected for the 

presence and/or sign of amphibians and reptiles. Additionally, incidental 

sightings of amphibians and reptiles were recorded during other surveys and other 

site visits. 

4.2.3.4. Birds 

Bird diversity and abundance surveys Avian surveys were conducted 

quarterly over a 5-year period (Table 4-2) on the study plots. Four point counts 

on variable circular plots (Verner 1985) and two parallel north-south transects 

(Figure 4-2) were censused for four consecutive mornings. Surveys began within 

30 minutes of sunrise (Ralph et al. 1993). All five blocks were concurrently 

sampled by 5 biologists synchronizing starting times between blocks to within 

5 minutes of each other. Each circular-plot was censused for 5 minutes and each 

transect was censused for 5 minutes, resulting in 30 minutes of observations per 

plot. The direction of the survey route was alternated on each subsequent survey 

day. All species recorded on experimental plots were included in data analyses; 

fly-over and species not on experimental plots were incidentally noted but 

excluded from analyses. Avian species observed on experimental plots were 

identified to species and all detected birds were documented as either a visual or a 

vocal account. Location, activity, and distances from observer also were 

recorded. 

Nest survey We searched for nests from the first week of March through the 

first week of April in 2002 and 2003 to identify nests, determine nesting success, 

and the causes of nest failure. Rope dragging, the standard method used to search 

for ground nesting birds and their nests (Labisky 1957), was conducted using a 

60 m (200 ft) long, 0.95 cm (0.38 inch) thick nylon rope. Each plot was surveyed 

once each week for 4 consecutive weeks. Three sweeps of the rope were 

necessary to completely cover each plot. When a bird flushed, the surrounding 

area was searched for active nests. Nest locations were mapped on a site map, 

their positions were recorded using a hand-held global positioning system unit, 

and they were marked in the field using a pin-flag placed 5 m (16.5 ft) south of 

the nest. Active nests were checked at 3- to 4-day intervals until nesting ended. 

Precautions described by Ralph et al. (1993) were used to minimize nest 

disturbance and the risk of predation. Data recorded included nest height, nest 

dimensions, nest orientation, the presence or absence of adults, the number of 
Chapter 4. Results of a Habitat Restoration Study on 

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115 

eggs or nestlings present, and a brief description of nestlings (e.g., number, size, 

presence of pin feathers, etc.). Clutch initiation was estimated by backdating 

(Alisauskas and Ankney 1992) and mean clutch size and median fledge date were 

calculated for all monitored nests. Photographs of nests and nestlings were taken. 

Vegetation at each nest site was characterized once nests were vacated. Each site 

was characterized using four 35 cm by 70 cm (14 - 28 inch) sampling quadrats 

placed immediately adjacent to the nest in each cardinal direction. Within each 

quadrat, we estimated percent cover (total vegetative cover, cover of shrubs, 

grasses, forbs, litter, and bare ground), the total cover of each plant species 

present, and the average height of plants. 

4.2.3.5. Small Mammals 

Small mammal trapping was conducted quarterly over a 5-year period 

(Table 4-2). On each study plot, 30 Sherman live-traps were placed in three lines 

of 10 traps each with an inter-trap spacing of 15m (50 ft) (Jones 1996, Figure 

4-2). Traps were baited with a small handful of millet, opened approximately an 

hour before sunset, and checked and closed starting 2 hours after dark. All five 

blocks were checked simultaneously by one biologist per block. Each night, the 

starting point was moved to the ending point of the previous night so that the traps 

were open for approximately the same amount of time over the survey period. 

Captured mammals were identified, sexed, weighed, and reproductive status and 

trap location noted. Kangaroo rats (Dipodomys heermanni) were marked with 

passive integrated transponders (PIT tags) and other species were marked by 

clipping a patch of fur from the rump or hindquarters. 

Pitfall traps also were used to capture small mammals. Data from the pitfall traps 

were used to augment the assessment of species richness and some small 

mammals captured in the pitfalls were sacrificed for selenium analysis. The 

4-day pitfall survey was conducted concurrently with the invertebrate surveys 

(Table 4-2). Pitfall traps were checked after sunrise for small mammals and 

closed, prior to processing invertebrates. The tip of the tail was removed from 

shrews (Sorex ornatus) and pocket mice (Perognathus inornatus) to be used in a 

genetics study. 

4.2.4. Site-Wide Surveys 

4.2.4.1. Spotlighting Surveys 

Spotlight surveys were conducted quarterly from fall 1999 to fall 2003 

(Table 4-3) to evaluate the site-wide richness and abundance of wildlife at the 

Tranquillity site. In spring 2001, heavy rains and flooding of the site precluded a 

survey. Two biologists illuminated the landscape along a 25.07 km (15.58 mi.) 

route (Figure 4-3) using 1,000,000 candlepower spotlights. Surveys were 

conducted for 3 consecutive days, except in spring of 2002 when flooding of the 

site required the survey to be conducted during two, 2-day periods. Each survey 

began at sunset and was completed in approximately 2 hours. The vehicle was 
Land Retirement Demonstration Project 

Five Year Report 

116 

driven at 15 to 25 kph (10 to 15 mph), and species observed were identified with 

the aid of 10 x 50 power binoculars. Data recorded included species, number of 

individuals, location (odometer reading and/or GPS waypoint) and additional 

notes. The start and end times, temperature, mileage, environmental conditions 

(wind speed and direction, cloud cover and moon phase), and additional notes 

(e.g., flooded areas, unusual activity etc.) were recorded. The richness and 

abundance of amphibians, reptiles, avian, and mammals were generated for each 

survey period. 

Table 4-3. Dates of spotlighting surveys, track station surveys, and winter raptor 

surveys conducted from 1999 to 2003. 

Survey Year Dates 

1999 14-16 Sep; 20-22 Dec 

2000 27-29 March; 19-21 June; 11-13 Sep; 27-29 Nov 

2001 29-31 May; 17-19 Sep; 17-19 Dec 

2002 4-5, 11-12 March; 24-26 June; 9-11 Sep; 9-11 Dec 

Spotlighting 

2003 24-26 March; 16-18 June; 15-17 Sep 

1999 15-17 Sep; 21-23 Dec 

2000 28-30 March; 20-22 June; 12-14 Sep; 28-30 Nov 

2001 14-16 March; 30-31May, 1 June; 11-13 Sep; 18-20 Dec 

2002 5, 12-13 March; 25-27 June; 11-13 Sep; 10-12 Dec 

Track stations 

2003 25-27 March; 17-19 June; 16-18 Sep 

1999 21-23 Dec 

2000 3-5 Jan (2001) 

2001 18-20 Dec 

2002 10-12 Dec 

Winter raptor 

2003 6-8 Jan (2004) 

4.2.4.2. Track Station Surveys 

Seventeen track stations (Figure 4-3) were checked for 3 consecutive days each 

quarter from 1999 to 2003 (Table 4-3). Surveys were not conducted in spring or 

summer 1999 because the project had not yet been initiated. Each station 

consisted of a 1 m (3.3 ft) square galvanized steel plate covered with a 5 to 8 cm 

(2 to 3 in) layer of equal parts of dolomite and fine sand. A can of wet cat food 

was set in the center of the plate as an attractant. The substrate and cat food were 

replaced as needed. Each track station was checked for tracks between 0600 and 

1000 hours. We attempted to identify tracks to the species level, but sometimes 

only identifications to family or order were possible. Data are reported as 

richness and rate of visitation. 
Chapter 4. Results of a Habitat Restoration Study on 

Retired Agricultural Lands in the San Joaquin Valley 

117 

Figure 4-3. Locations of the spotlight survey route, track stations, and winter 

raptor survey route, 1999 to 2003. 

4.2.4.3. Winter Raptor Surveys 

Windshield surveys were conducted in December or January from 1999 to 2003 

(Table 4-3) to determine raptor abundance and distribution. Surveys generally 

began 1 hour after sunrise, but start times were delayed if fog hindered visual 

observations. The 25.07 km (15 mi) survey route was located adjacent to the 
Land Retirement Demonstration Project 

Five Year Report 

118 

demonstration site (Figure 4-3). The route was surveyed for 3 consecutive days 

each survey period by driving the route slowly (approximately 5 to 10 miles per 

hour or 8 to16 kilometers per hour). Raptors were identified using binoculars and 

a spotting scope. Data recorded included species, sex, age (when possible), 

activity at time of first observation, and location. The start location, weather 

conditions (cloud cover, wind, moon phase, and temperature), start and end times, 

and start and end odometer readings were recorded. Loggerhead shrikes (Lanius 

ludovicianus), mountain plovers (Charadrius montanus), and other sensitive bird 

species also were recorded and reported to the California Natural Diversity 

Database (CNDDB). Raptor abundance was calculated as the average number 

observed per day over each 3-day census. 

4.2.4.4. Statistical Analysis of Vegetation Data 

Species were grouped by “origin” (e.g., introduced, native, etc.) for some 

analyses. One category, the “tumbling saltweeds” is a modification of what had 

been referred to in previous annual reports as the “Native–Undesirable” category. 

The tumbling saltweeds are composed of two species, Atriplex argentea

(silverscale saltbush) an undesirable native species, and the non-native Atriplex 

rosea (tumbling oracle). These annual herbs, which possess a shrub-like form, 

have demonstrated the capacity to quickly become established and to dominate 

large areas of the study plots. 

The remaining categories are self-explanatory (e.g., “Native”); however, the 

“Imprinted and Introduced” category merits a brief explanation. This category 

was created to integrate the contribution of species that could be ascribed to 

genera that were represented in both the “Native - Imprinted” and “Introduced” 

categories, but which were frequently not identifiable to the level of species. In 

the 2003-04 growing season, the “Imprinted and Introduced” category was 

represented at the Tranquillity HRS by a single pair of species: the grasses Vulpia 

microstachys (imprinted) and V. myuros (introduced). Fertile individuals of both 

species were frequently encountered; nevertheless, quadrats would often contain 

only infertile material, and it was not possible to confidently ascribe this material 

to a particular species. It was assumed that both species were present on any plot 

in which Vulpia was noted; hence, the Imprinted and Introduced category 

contributed two species to estimates of species richness. For analyses of 

abundance, one-half of the percent cover value from the Imprinted and Introduced 

species was applied to the Native – Imprinted category and one-half to the 

Introduced category. 

Descriptive statistics, t-tests, and Analysis of Variance (ANOVA) procedures 

were conducted using the software package STATISTICA (StatSoft, Inc. 2002). 

To simultaneously express floristic relationships among the Tranquillity Study 

Plots and to examine the relationship between site vegetation and block effect, 

data were organized into a binary matrix of plots versus species (recorded as 

percent cover values) and were analyzed by Detrended Correspondence Analysis 
Chapter 4. Results of a Habitat Restoration Study on 

Retired Agricultural Lands in the San Joaquin Valley 

119 

(DCA, Hill and Gauch Jr. 1980). Ordinations were conducted using the software 

package PC-Ord (McCune and Mefford 1999). 

4.2.4.5. Analysis of Data for the Other Biotic Groups 

The effects of restoration treatments on the richness and abundance of 

invertebrates, amphibians and reptiles, birds, and small mammals were analyzed 

using Analysis of Variance applied to log-transformed data. If warranted, posthoc analyses using Fisher LSD tests were performed. Statistical analyses were 

accomplished using Statistica 6 (Statsoft, Inc. 2002). The geometric means 

(hereafter referred to as means) of the data sets were graphed using Sigma Plot 

(SPSS Inc. 2002). 

In addition to evaluating the affects of restoration on richness and abundance of 

invertebrates as a group, we separately evaluated the abundance of the beetles 

(Coleoptera) and spiders (Araneae). These two orders are commonly used as 

indicators of restoration effects because they are sensitive to environmental 

change, taxonomically well known, and biologically diverse (Perner and Malt 

2003, Rykken et al. 1997). Additionally, we separated invertebrate orders into 

three groups—herbivores, pollinators, and predators—to evaluate the abundance 

of these groups in response to restoration treatments. Similarly, we grouped birds 

into one of three categories—obligate grassland species (those birds that require 

grassland habitats), facultative grassland species (those birds that benefit from 

grassland habitats), and other species—to evaluate the abundance of birds based 

upon ecological roles. 

Nesting data were analyzed using the Mayfield method (Mayfield 1961, 1975) to 

calculate various parameters associated with nesting survival. The relationship 

between the presence of plants and nest success was statistically evaluated. Chisquare tests were used to determine if nest success or failure was influenced by 

the presence of individual plant species and student’s t-tests were used to evaluate 

nest success relative to nest height and the mean number of plant species present. 

Spearman rank correlation was used to evaluate the correlation between the 

number of successful nests and the number of plant species present at the nest 

site. All statistical tests were performed in Statistica 6 (Statsoft, Inc. 2002). 

Data from spotlight and track station surveys were log transformed and analyzed 

using single-factor or multifactor Analysis of Variance in Statistica 6 (StatSoft, 

Inc. 2002). Data from winter raptor surveys were log transformed and analyzed 

using repeated measures Analysis of Variance and Spearman rank correlation. 
Land Retirement Demonstration Project 

Five Year Report 

120 

4.3. Results 

4.3.1. Plot-Level Monitoring 

4.3.1.1. Vegetation 

Results are initially considered with reference to site-wide patterns. 

Subsequently, patterns among treatments and blocks (i.e., replicates) are 

considered. 

Site-level At the site level, species richness initially increased after imprinting 

(i.e., from 1999 to 2000; Table 4-4). Nevertheless, site-level richness decreased 

during the following 2 years, reaching levels that were approximately equivalent 

to that of the baseline year (i.e., 1999). 

Table 4-4. Overall vegetation species richness in the Tranquillity HRS study plots. 

Included data are solely those species which occurred within the quadrats. 

Species Category 1999 2000 2001 2002 2003 

Native - Imprinted 0 5 5 4 3 

Native 3 5 2 2 2 

‘Tumbling 

Saltweeds’ 

1 1 1 1 1 

Imprinted & 

Introduced 

0 2 2 2 0 

Barley 1 1 1 1 1 

Introduced 15 16 15 12 17 

Not Known 6 5 1 4 0 

Total 26 35 27 26 24 

Thirteen native species were imprinted into the plots in 2000 (Table 4-5); see 

Selmon 2000 for an overview of the experimental design and plot installation). 

Of these imprinted species, only six (46.2 percent) were noted during vegetation 

monitoring in 2000 and 2001, and only five (38.5 percent) in 2002. By 2003, 

only three of the imprinted species occurred in the spring monitoring quadrats 

(Table 4-5). Less than half of the species that were imprinted were observed 

during any particular year’s monitoring; however, approximately two-thirds (9) of 

the imprinted species have been observed at some point during monitoring (i.e., 

during at least 1 year’s monitoring). 
Chapter 4. Results of a Habitat Restoration Study on 

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121 

Table 4-5. Species imprinted in the Tranquillity HRS Plots (1999), and an overview 

of those imprinted species noted in the quadrats during spring vegetation 

monitoring, 2000-2003. 

Species Family Common Name 2000 2001 2002 2003 

Allenrolfea occidentalisA Chenopodiaceae iodinebush - - - - 

Atriplex polycarpa Chenopodiaceae allscale saltbush - - + + 

Atriplex spinifera Chenopodiaceae spinescale saltbush - - - - 

Bromus carinatus Poaceae California brome + + + - 

Frankenia salina Frankeniaceae alkali heath + - +B

 - 

Heliotropium curassavicum Boraginaceae seaside heliotrope - - - - 

Hemizonia pungens Asteraceae common spikeweed - + - - 

Isocoma acradenia Asteraceae goldenbush + - - - 

Lasthenia californica Asteraceae California goldfields + + + + 

Leymus triticoides Poaceae creeping wild-rye - + - - 

Sporobolus airoides Poaceae alkali sacaton - - - - 

Suaeda moquinii Chenopodiaceae bush seepweed + + - - 

Vulpia microstachys Poaceae small fescue + + + + 

A. A few, transplanted individuals are still alive on Block 1; however, none of these occurred within the 

quadrats. 

B. Noted in a single, non-imprinted plot. 

In addition to species that are actively introduced to restoration sites through 

imprinting and direct planting, it is hoped that native species would become 

established on retired lands without human intervention. It is expected that these 

species would become established either through existing seed banks or through 

colonization from other areas and, indeed, at the Tranquillity HRS, a number of 

non-imprinted natives have been noted on the plots (Table 4-6). As discussed in 

the Methods section, the native Atriplex argentea (the native component of the 

‘tumbling saltweeds’) is considered to have an overall negative impact on 

restoration and, hence, is non-desirable. Therefore, that species is not included in 

the tally of “naturally established” native species. Discounting A. argentea, eight 

non-imprinted native species have been noted on the HRS plots (Table 4-6). 

Non-imprinted native species were best represented during the first year of 

restoration (i.e., 2000), with five species noted during monitoring (Table 4-6). 

However, only two such species were noted during each of the subsequent year’s 

monitoring. As will be discussed later, none of these species were wellrepresented on the HRS plots. 
Land Retirement Demonstration Project 

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Table 4-6. Non-imprinted, native species (excluding Atriplex argentea) noted in the 

quadrats during spring vegetation monitoring in the Tranquillity HRS, 1999-2003. 

Species 1999 2000 2001 2002 2003 

Amsinckia menziesii - - + + - 

Eremalche parryi + - - - - 

Hordeum depressum + + - - + 

Malacothrix coulteri - - - + - 

Malvella leprosa - + - - - 

Monolepis nuttalliana - + - - - 

Phacelia ciliata + + + - + 

Solanum americanum - + - - - 

Total: 3 5 2 2 2 

The dominance by non-native species that was suggested by the site-level 

richness patterns was even more evident when species’ abundances were 

considered (Table 4-7). The eleven most abundant species were non-native, with 

three species (Sisymbrium irio, Bromus madritensis, and Capsella bursa-pastoris) 

providing more than three-quarters (77.0 percent) of the vegetative cover. 

In general, vegetation on the HRS plots tended towards dominance by one or the 

other of two most abundant species: Sisymbrium irio (London rocket) and Bromus 

madritensis (red brome). To examine the spatial partitioning of these two species, 

we developed a spatial analysis in which the plots were divided into sixths and the 

mean abundances of selected species represented graphically (Figure 4-4 and 

Figure 4-5). 

As was noted, vegetation monitoring employed stratified random sampling, with 

the plots divided into sixth-sections (sextants) and four quadrats situated within 

each section. For this analysis, the mean percent cover for each ‘sextant’ was 

calculated from the cover values from the four quadrats. Although this type of 

representation does not allow for statistical analyses, it is well-suited to show 

spatial variations in species abundances. 

This approach was employed, because there was an evident partitioning of the 

two dominant weeds, with Bromus madritensis dominant on the northernmost 

plots (Block 1) and Sisymbrium irio the more abundant species on most areas of 

the remaining 16 plots (Blocks 2-4). This partitioning is clearly represented in the 

graphs (Figure 4-4 and Figure 4-5). Although not included here, a graph of the 

sextant abundance data for Capsella bursa-pastoris (the third most abundant 

species) showed a similar pattern to that of S. irio. 
Chapter 4. Results of a Habitat Restoration Study on 

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123 

Table 4-7. All species noted in the quadrats during spring vegetation monitoring in 

the Tranquillity HRS, 2003, including species code, common name, life-form, 

origin, mean percent cover, and relative abundance. Species codes are used to 

identify species in subsequent figures. Relative abundance represents the percent 

contribution of a particular species to the total cover. Key to Origins: C = Cultivar; 

I = Introduced, N = Native (non-imprinted): N-I = Imprinted Native; T = Tumbling 

Saltweeds; U = Unknown. 

Taxon Code Common Name Life-form ‘Origin’ % Cov. Rel. Abd. 

Sisymbrium irio A London rocket annual herb I 42.048 47.889

Bromus madritensis B red brome annual herb I 15.190 17.299

Capsella bursa-pastoris C shepherd's purse annual herb I 10.335 11.771

Melilotus indica D sourclover annual herb I 5.962 6.791

Brassica nigra E black mustard annual herb I 3.329 3.792

Senecio vulgaris F old-man-in-the-Spring annual herb I 3.184 3.627

Erodium cicutarium G redstem filaree annual herb I 2.775 3.160

Hordeum murinum H foxtail barley annual herb I 2.690 3.063

Sonchus sp. I prickly lettuce annual herb I 0.341 0.388

Vulpia myuros J rattail fescue annual herb I 0.311 0.355

Avena sp. K oats annual herb I 0.289 0.329

Atriplex polycarpa L allscale saltbush shrub N-I 0.286 0.326

Lactuca serriola M prickly lettuce annual herb I 0.272 0.310

Beta vulgaris N beet annual herb I 0.194 0.221

Hordeum vulgare O barley annual herb C 0.158 0.180

Vulpia microstachys P small fescue annual herb N-I 0.149 0.170

Atriplex argentea Q silverscale saltbush annual herb T 0.079 0.090

Hordeum depressum R alkali barley annual herb N 0.040 0.045

Bromus diandrus S ripgut brome annual herb I 0.031 0.036

Bromus sp. T brome annual herb I 0.031 0.036

Malacothrix coulteri U snake's head annual herb N 0.031 0.036

Lasthenia californica V California goldfields annual herb N-I 0.030 0.034

Malva parviflora W cheeseweed annual herb I 0.023 0.026

Phacelia ciliata X Great Valley phacelia annual herb N 0.009 0.011

Bromus carinatus Y California brome perennial herb N-I 0.006 0.007

Lolium perenne Z perennial ryegrass perennial herb I 0.006 0.007

Bromus hordeaceus a soft brome annual herb I 0.001 0.001

Chenopodium sp. b N.A. not known U 0.001 0.001

Phalaris minor c littleseed canarygrass annual herb I 0.001 0.001
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Figure 4-4. Distribution of Bromus madritensis (red brome) at the Tranquillity HRS, 

2003. Each small rectangle represents a ‘sextant’; i.e., the portion of the plot in 

which a particular group of four sampling quadrats was located. The shading 

represents the mean percent cover of red brome in that particular sextant. 
Chapter 4. Results of a Habitat Restoration Study on 

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125 

Figure 4-5. Distribution of Sisymbrium irio (London rocket) at the Tranquillity HRS. 

Each small rectangle represents a ‘sextant’, i.e., the portion of the plot in which a 

particular group of four sampling quadrats was located. The shading represents 

the mean percent cover of London Rocket in that particular sextant. 
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Generally, the areas dominated by Bromus madritensis were those with soils 

characterized by high electrical conductivity readings and high levels of soluble 

boron. These areas were the only part of the HRS in which the salt-tolerant

Allenrolfea occidentalis survived. The buffers of the red brome-dominated plots 

also tended to have a large component of brome. This pattern was increasingly 

evident in the later years of the project, and was apparent throughout Block 1 and 

in the northern half of Block 4. Although Sisymbrium irio was an obvious 

component in buffers of the London rocket-dominated plots, it was not nearly as 

abundant as was red brome in the northernmost buffers. 

A few additional, site-wide patterns should be noted. First, the relative absence of 

non-imprinted, native species was particularly troubling. With the exception of 

the tumbling saltweed Atriplex argentea, few non-imprinted native species have 

been observed on the study Plots. To date, only two ‘desirable’ native species, 

Malacothrix coulteri (snakes head) and Phacelia ciliata (valley Phacelia), have 

shown any sign of becoming established on the study site. Throughout the course 

of the project, abundances of both these species have been low (Table 4-7; 

Figure 4-6; Figure 4-7). 

Also of note was the difference in appearance between the herbaceous vegetation 

on the plots and in the buffer areas (excluding those buffers dominated by red 

brome). Generally, species (both introduced and adventitious natives) in the 

buffer were more robust and showed less stress with the onset of the dry season 

than did the same species on the plots. In part, this pattern may be attributable to 

the barley ameliorating conditions to some degree (i.e., by functioning as a nurse 

crop). This difference in vegetation may also be a function of the different 

delivery techniques, as the plots were imprinted and the buffers drilled. 

Specifically, the depressions created by the imprinter appear to facilitate erosion 

of the clay soils at the Tranquillity site. 

Treatments and blocks The predominance of non-native species that was 

evidenced in the site-wide abundance data (Table 4-7) was also clear when 

considering treatment-level vegetation patterns. To graphically represent the 

contribution of the various species and species classes to the site’s vegetation, a 

series of rank-abundance curves were plotted (Figure 4-6; Figure 4-7). 

Plots were ordered sequentially by Block number within each graph; hence, the 

leftmost curve represents the Plot from Block 1, the second to the left, Block 2, 

etc. Rank-abundance curves were plotted along the x-axis in such a way as to 

minimize overlap. Thus, no ordinal scale is presented along the x-axis; rather, the 

curves are interpreted such that the leftmost data point represents the highest 

(first) ranked species, with subsequent data points representing the second highest 

ranked species, etc. 
Chapter 4. Results of a Habitat Restoration Study on 

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127 

Figure 4-6. Species rank-abundance by treatment, Tranquillity HRS Plots 2003. 

Species letter codes correspond to those presented in Table 4-7. The five most 

abundant species in each plot and all native species are identified by letter code. 
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Figure 4-7. Species rank-abundance by treatment, Tranquillity HRS Plots 2003. 

Species letter codes correspond to those presented in Table 4-7. The five most 

abundant species in each plot and all native species are identified by letter code. 
Chapter 4. Results of a Habitat Restoration Study on 

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129 

Regardless of treatment, the most abundant species on all plots were introduced. 

Sisymbrium irio (A) was the most abundant species on 15 plots. Bromus 

madritensis (B) was the most abundant species on 4 plots, and Capsella bursapastoris (C), the most abundant on a single plot. In no instances were imprinted 

native species highly ranked. 

No strong differences were apparent in the slopes of the curves generated for the 

restored plots (Figure 4-6) versus those of the non-restored plots (Figure 4-7). 

This pattern differs from that observed in the preceding year (see Uptain et al. 

2004), when the curves for the restored plots were noticeably less steep than those 

of the non-restored plots. This difference suggests that vegetation on the restored 

plots was becoming more homogenous, more dominated by a few species, over 

time. 

Atriplex polycarpa (L) is seen to have been more abundant on the imprinted and 

contoured plots (Figure 4-6) than on the imprinted but not contoured plots. This 

pattern was not surprising, as it was obvious during monitoring that A. 

polycarpa—as well as the other seeded perennial species—were most often 

located on the berms and associated trenches. In contrast, the most abundant 

imprinted annual species, Vulpia microstachys (P), was somewhat better 

represented on the non-contoured plots. Although the aforementioned patterns 

are noteworthy, the strongest pattern evidenced in the rank-abundance curves is 

the relatively low overall percent contribution of the native species. 

The diminished presence of the cultivated barley (Hordeum vulgare) and of the 

tumbling saltweeds (Atriplex rosea and A. argentea) is of interest. In the first 

years following imprinting, there was concern that the barley that had persisted on 

the plots would out-compete the seeded species. While this may have occurred to 

some extent, the low abundance of barley relative to that of the dominant weed 

species suggests that this exclusion was not a major limiting factor in the 

establishment of native species. The low abundance of tumbling saltweeds is 

noteworthy because these species had dominated much of the site during the first 

summer after imprinting, and had facilitated the establishment of Sisymbrium irio

(Uptain et al. 2004). Although Atriplex rosea and A. argentea were still abundant 

in re-seeded areas of the buffers in 2003, they had become scarce on the plots by 

this time. It seems likely that the diminished abundance of the tumbling 

saltweeds can be attributed to the low levels of soil disturbance on the plots. To 

elaborate, these species were readily able to colonize the plots in the summer 

following imprinting, as these areas had been recently disked. 

4.3.1.2. Invertebrates 

From 1999 to 2003 the richness (number of orders) of invertebrates on each 

treatment ranged from 11 to 17 (Figure 4-8). When data from all years are 

combined, the mean richness of invertebrates on each treatment varied only 

slightly (from 7.9 on contoured and unseeded plots to 8.5 on not contoured and 

seeded plots). Similarly, when data from all treatments are combined, the mean 
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130 

richness of invertebrates in each year varied only slightly (from 7.5 in 2002 to 8.6 

in 2003). An analysis of the treatment factors (seeding and contouring) shows 

that there were differences between seeded and contoured plots versus not-seeded 

and not-contoured plots in both 2001 and 2002 (Figure 4-8). However, the mean 

richness of invertebrates is nearly identical (9.3 vs. 9.1 in 2001 and 7.1 vs. 7.1 in 

2002) which indicates that there are no real differences. 

There were large differences in invertebrate abundances between years (p < 0.01) 

with the fewest invertebrates present in 2002 (mean = 184.6 invertebrates per 

plot) and the most invertebrates present in 2000 and 2001 (mean = 1,207.7 

invertebrates per plot; Figure 4-9). There were no clear effects of seeding (S) or 

contouring (C) in any year. There were clear differences in the abundance of 

invertebrates between the study blocks in 2001, 2002, and 2003. 

Figure 4-8. Ordinal richness of invertebrates for all treatments in 1999 to 2003. 

Treatment codes are CR = contoured and seeded, NR = not contoured but seeded, 

CN = contoured but not seeded, and NN = not contoured and not seeded. 

Treatment factor codes are S = seeded, C = contoured, S*C = seeded and 

contoured interactions, B = block, and SSE = sum of squares error. 
Chapter 4. Results of a Habitat Restoration Study on 

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131 

Figure 4-9. Mean invertebrate abundance for all treatments in 1999 to 2003. 

Treatment codes are CR = contoured and seeded, NR = not contoured but seeded, 

CN = contoured but not seeded, and NN = not contoured and not seeded. 

Treatment factor codes are S = seeded, C = contoured, S*C = seeded and 

contoured interactions, B = block, and SSE = sum of squares error. 

Neither beetles (Coleopteran) nor spiders (Araneae) showed a consistent response 

to contouring or seeding (Figure 4-10). However, in 2001 the abundance of 

beetles was greater on non-contoured plots (mean = 25.3) than on contoured plots 

(mean = 20.0) and in 2003 beetles were greater on non-seeded plots 

(mean = 75.7) than on seeded plots (mean = 40.0, Figure 4-10). In 2001 the plots 

that were seeded and contoured had a lower abundance of beetles (mean = 17.38) 

than plots that had no treatment applied (mean = 20.89; Figure 4-10), which is 

attributed to the influence of contouring. 

Predators, pollinators, and parasites are beneficial to Central Valley agriculture 

and several herbivorous invertebrate families contain agricultural pests (N. Smith 

pers. comm. 2004). There were 12 orders containing at least 57 agriculturallybeneficial families identified on the HRS plots and 8 orders containing 17 families 

of agricultural pest species (Table 4-8 and Table 4-9Table 4-9). 
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Figure 4-10. Mean abundance of Coleoptera and Araneae for all treatments in 1999 

to 2003. Treatment codes are CR = contoured and seeded, NR = not contoured but 

seeded, CN = contoured but not seeded, and NN = not contoured and not seeded. 

Treatment factor codes are S = seeded, C = contoured, S*C = seeded and 

contoured interactions, B = block, and SSE = sum of squares error. 
Chapter 4. Results of a Habitat Restoration Study on 

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133 

 Table 4-8. Invertebrate families collected on the Tranquillity study 

 plots that contain agriculturally beneficial species, 1999 to 2003. 

Order Family Functional group(s) 

Acarina Anystidae Predator 

Araneae Araneidae Predator 

 Clubionidae Predator 

 Gnaphosidae Predator 

 Lycosidae Predator 

 Oxyopidae Predator 

 Pholcidae Predator 

 Salticidae Predator 

 Theridiosomatidae Predator 

 Thomisidae Predator 

Coleoptera Carabidae Predator 

 Cleridae Predator 

 Coccinellidae Predator 

 Histeridae Predator 

 Melyridae Predator 

 Staphylinidae Predator 

Diptera Chironomidae Pollinator 

 Dolichopodidae Predator 

 Muscidae Pollinator 

 Sciomyzidae Parasite/sitiod 

 Stratiomyidae Predator 

 Syrphidae Predator, Pollinator 

 Tachinidae Pollinator, Parasite/sitiod 

Hemiptera Anthocoridae Predator 

 Lygaeidae Predator 

 Nabidae Predator 

 Reduviidae Predator 

Hymenoptera Andrenidae Pollinator 

 Apidae Pollinator 

 Bethylidae Pollinator, Parasite/sitiod 

 Braconidae Pollinator, Parasite/sitiod 

 Ceraphronidae Pollinator, Parasite/sitiod 

 Chalcididae Pollinator, Parasite/sitiod 

 Chalcidoidea Pollinator, Parasite/sitiod 

 Chrysididae Pollinator, Parasite/sitiod 

 Cynipidae Pollinator, Herbivore 

 Diapriidae Pollinator 

 Encyrtidae Pollinator, Parasite/sitiod 

 Eulophidae Pollinator, Parasite/sitiod 

 Formicidae Predator, Pollinator 

 Halictidae Pollinator 

 Ichneumonidae Pollinator, Parasite/sitiod 

 Megaspilidae Pollinator 

 Mutillidae Pollinator, Parasite/sitiod 

 Platygastridae Pollinator, Parasite/sitiod 

 Pompilidae Predator, Pollinator 

 Pteromalidae* Parasite/sitiod 

 Scelionidae Pollinator, Parasite/sitiod 

 Torymidae Pollinator, Parasite/sitiod 

Mantodea Mantidae Predator 

Neuroptera Chrysopidae Predator 

 Hemerobiidae Predator 

Odonata Coenagrionidae Predator 

 Unknown Odonata Predator 

Opiliones Unknown Opiliones Predator 

Scorpiones Unknown Scorp. Predator 

Scolopendromorpha Unknown Scolo. Predator 
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Table 4-9. Invertebrate families collected on the Tranquillity study plots that 

contain agricultural pest species, 1999 to 2003. 

Order Family Genus/Species Common name 

Functional 

group 

Acarina (Astigmata) Rhizoglyphus sp. Rhizoglyphid mites Scavenger 

Coleoptera Chrysomelidae Chaetocnema repens Dichondra Flea Beetle Herbivore 

 Chrysomelidae Epitrix hirtipennis Tobacco Flea Beetle Herbivore 

 Curculionidae Hypera postica Alfalfa weevil Herbivore 

 Elateridae Aeolus sp. Click Beetle Herbivore 

 Elateridae Anchastus sp. Click Beetle Herbivore 

Diptera Opomyzidae Opomyzidae Fly Herbivore 

Hemiptera Lygaeidae Nysius raphanus False Chinch Bug Herbivore 

 Miridae Lygus hesperus Lygus bug Herbivore 

 Pentatomidae Chlorochroa sp. Green Stink Bug Herbivore 

 Chlorochroa uhleri Uhler's Stink Bug Herbivore 

 Chlorochroa sayi Say Stink Bug Herbivore 

 Thyanta punctiventris Stink Bug Herbivore 

Homoptera Aphididae Macrosiphum 

euphorbiae 

Potato Aphid Herbivore 

 Cicadellidae Circulifer tenellus Beet Leafhopper Herbivore 

Lepidoptera Noctuidae Peridroma saucia Variegated Cutworm Herbivore 

 Plutellidae Plutella maculipennis Diamondback Moth Herbivore 

Orthoptera Acrididae grasshopper Herbivore 

Thysanoptera Thripidae Frankliniella 

occidentalis 

Western Flower 

Thrips 

Herbivore 

 Thripidae Caliothrips fasciatus bean Thrips Herbivore 

4.3.1.3. Amphibians and Reptiles 

Diversity of amphibians and reptiles increased from a low of one species observed 

in 1999, to three species observed since 2001 (Table 4-10). Western toads (Bufo 

boreas) were the only amphibian observed and were seen during a variety of 

surveys and seasons. Two species of reptiles, the western whiptail 

(Cnemidophorus tigris) and the gopher snake (Pituophis catenifer), were seen in 

1999 and 2000, but were not observed in the following years. They are likely still 

present in low numbers. California king snakes (Lampropeltis getulus 

californiae) and western fence lizards (Sceloporus occidentalis) were observed 3 

of the 5 years. 
Chapter 4. Results of a Habitat Restoration Study on 

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135 

Table 4-10. Diversity of amphibians and reptiles observed at Tranquillity 1999-

2003. 

Year Species observed Richness 

1999 western whiptail 1 

2000 western toad, gopher snake 2 

2001 western toad, western fence lizard, California king snake 3 

2002 western toad, western fence lizard, California king snake 3 

2003 western toad, western fence lizard, California king snake 3 

4.3.1.4. Birds 

Bird diversity and abundance surveys Forty-four species of birds were 

observed using the study plots over the 5-year study period. In addition to these, 

numerous other species had been documented using neighboring areas including 

the buffer, roadsides, adjacent lands, and airways. Of the 44 species observed 

using the study plots, ten are of special status (Table 4-11). 

Table 4-11. Special status bird species observed on the Tranquillity study plots, 

1999 to 2003. CSC = California special concern species, FSC = federal special 

concern species, FP = fully protected in California. 

Species Status 

western burrowing owl (Athene cunicularia hypugaea) CSC, FSC 

California horned lark (Eremophila alpestris actica) CSC 

loggerhead shrike (Lanius ludovicianus) CSC, FSC 

long-billed curlew (Numenius americanus) CSC 

mountain plover (Charadrius montanus) CSC 

northern harrier (Circus cyaneus) CSC 

prairie falcon (Falco mexicanus) CSC 

short-eared owl (Asio flammeus) CSC 

white-tailed kite (Elanus leucurus) FP 

Vaux's swift (Chaetura vauxi) CSC 

The richness (number of bird species present) per year on all plots combined 

ranged from 13 to 19 and richness per season ranged from 7 to 19. The lowest 

richness for a restoration treatment was in the summer of 1999 when there was a 

mean of 0.40 bird species per plot on the control plots (Figure 4-11). 

Surprisingly, the highest richness was also on control plots in the winter of 2001, 

when there was a mean of 6.40 bird species per plot. The greatest variation in 

mean richness among treatments was during the summer surveys, but summer 

also accounted for the lowest richness in all years. Neither seeding nor 

contouring, nor their interaction, had a detectable effect on avian richness, except 

in the summer of 1999 when seeding resulted in a 127 percent greater mean 
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Figure 4-11. Mean richness of birds by treatment in winter, spring, summer, and 

fall 1999 to 2003. Treatment codes are CR = contoured and seeded, NR = not 

contoured but seeded, CN = contoured but not seeded, and NN = not contoured 

and not seeded. Treatment factor codes are S = seeded, C = contoured, 

S*C = seeded and contoured interactions, B = block, and SSE = sum of squares 

error. 

richness than other treatment factors. There were discernable differences in 

richness between study blocks in all seasons but not in all years. In those 

instances, blocks 1, 2, and 4 had richness values from 106 to 284 percent greater 

than on other blocks (Table 4-12). 

Table 4-12. Blocks with the highest mean richness of birds, season and year of 

occurrence, and the magnitude of difference from other blocks (percent greater 

than the lowest and highest values from other blocks). 

Block Season Year Magnitude of difference p-value 

2 and 4 winter 2001 107 to 242% < 0.01 

1 spring 1999 147 to 284% 0.03 

2 summer 2000 156 to 280% 0.03 

4 fall 1999 106 to 284% 0.01 
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The seasonal abundances of birds on all plots combined ranged from a low of 

35 birds in summer of 2002 to a high of 3,283 birds in winter 2001. The greatest 

variation in the mean abundance of birds between the various restoration 

treatments was during the summer survey periods (Figure 4-12). Neither seeding 

or contouring, or their interaction affected the abundance of birds. However, 

there were clear differences in avian abundance among blocks in some seasons 

and years. In those instances, blocks 2, 4, and 5 had from 102 to 835 percent 

greater abundance of birds than other blocks (Table 4-13). Obligate grassland 

birds and facultative grassland birds were more numerous than other birds 

(p < 0.01 and p < 0.01) by approximately 394 and 325 percent, respectively 

(Figure 4-13). Obligate grassland birds were more numerous than facultative 

grassland birds, except in 2001, but these differences were not statistically 

supported (p = 0.56). Neither seeding nor contouring, or the interaction of these 

factors, influenced the abundance of obligate grassland birds or facultative 

grassland birds (Figure 4-14). The only exception to this was in 2003 when 

obligate grassland birds were less common on the contoured plots than on the 

seeded, seeded and contoured, or control plots. 

Figure 4-12. Mean abundance of birds by treatment in winter, spring, summer, and 

fall 1999 to 2003. Treatment codes are CR = contoured and seeded, NR = not 

contoured but seeded, CN = contoured but not seeded, and NN = not contoured 

and not seeded. Treatment factor codes are S = seeded, C = contoured, 

S*C = seeded and contoured interactions, B = block, and SSE = sum of squares 

error. 
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Table 4-13. Blocks with the highest mean abundance of birds, season and year of 

occurrence, and the magnitude of difference from other blocks (percent greater 

than the lowest and highest values from other blocks). 

Block Season Year Magnitude of difference p-value 

2 Winter 2001 116 to 440% 0.02 

5 Spring 2000 104 to 214% 0.02 

5 Spring 2001 102 to 136% 0.04 

2 Fall 1999 135 to 835% 0.03 

4 Fall 2001 112 to 167% 0.03 

4 Fall 2002 105 to 277% 0.04 

Figure 4-13. Mean abundance (mean number of birds observed per plot per day, all 

seasons combined) of obligate grassland birds, facultative grassland birds, and 

other birds, 1999 to 2003. 

There were clear differences in the abundance of obligate and facultative 

grassland birds and other birds between study blocks. When differences occurred, 

blocks 2 and 4 had a greater abundance of obligate grassland species, Block 2 had 

a greater abundance of facultative species and Block 1 had a greater abundance of 

other birds (Table 4-14). 
Chapter 4. Results of a Habitat Restoration Study on 

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139 

Figure 4-14. Mean abundance of grassland obligates and facultative birds by 

treatment, 1999 to 2003. 

Table 4-14. Blocks with the highest mean abundance of grassland obligate birds, 

grassland facultative birds, and other birds, season and year of occurrence, and 

the magnitude of difference from other blocks (percent greater than the lowest and 

highest values from other blocks). 

Grassland niche Block Year Magnitude of difference p-value 

Obligate 2 1999 160 to 623% 0.02 

 4 2001 110 to 204% 0.02 

Facultative 2 2000 113 to 245% 0.02 

Other 1 2000 91 to 292% 0.01 
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Bird nesting on the Habitat Restoration Study plots Seventeen nests of three 

species were located on the study plots in 2002 (Table 4-15). Six nests of two 

additional species were found outside of the study plots, five of which were 

monitored. In 2003, 21 nests of three species were located on the study plots. A 

single western meadowlark (Sturnella neglecta) nest was located in a buffer and it 

was not monitored. A northern harrier (Circus cyaneus) nest that was found on 

Plot 13 also was not monitored because of the sensitive status of this species and 

the potential for monitoring to interrupt nesting success. Mallard (Anas 

platyrhynchos) nests declined from 14 in 2002 to 4 in 2003 while red-winged 

blackbirds (Agelaius phoeniceus) did not nest on the site in 2002 but were the 

most common nesting bird with 16 nests present in 2003. 

Table 4-15. Nest abundance and species richness, 2002 and 2003. Parentheses 

indicate nest numbers off study plot areas and asterisks indicate nests not 

monitored. 

Numbers of nests located 

Species 2002 2003 

horned lark (Eremophila alpestris) (1)* 0 

loggerhead shrike (Lanius ludovicianus) (2) 0 

mallard (Anas platyrhynchos) 14 4 

northern harrier (Circus cyaneus) 0 1* 

red-winged blackbird (Agelaius phoeniceus) 0 16 

short-eared owl (Asio flammeus) 2 (1) 0 

western meadowlark (Sturnella neglecta) 1 (2) (1)* 

Total nests 17 (6) 21 (1) 

Species richness 5 4 

Approximately equal numbers of nests were found on plots with contours and on 

plots without contours in both 2002 and 2003 (Figure 4-15 and Figure 4-16). In 

2002 nests were approximately 352 percent more abundant on non-seeded plots 

(13) than on seeded plots (4), but in 2003 nests were approximately equal in 

number on non-seeded (11) and seeded plots (10). The greatest concentration of 

nests found in 2002 (41 percent) was on plot 6; a plot that was contoured, but not 

seeded. In contrast, the greatest concentration of nests found in 2003 (33 percent) 

was on plot 20; a plot that was seeded, but not contoured. In 2002 the distribution 

of nests was concentrated in Block 2 (48 percent) and in 2003 nests were 

concentrated in Block 5 (59 percent). 
Chapter 4. Results of a Habitat Restoration Study on 

Retired Agricultural Lands in the San Joaquin Valley 

141 

Figure 4-15. Locations of bird nests found in 2002 at the Tranquillity study site. 

Figure 4-16. Locations of bird nests found in 2003 at the Tranquillity study site. 
Land Retirement Demonstration Project 

Five Year Report 

142 

All nesting bird species initiated clutches in mid-March, except loggerhead 

shrikes, which initiated clutching in late February (Table 4-16). Mean fledging 

dates for all species occurred in April. Mean clutch size varied by species from 

3.7 to 10.2 eggs. These clutch sizes are within the expected range for each 

species (Baicich and Harrison 1997). Nesting success rates varied by species 

from 33 percent in western meadowlarks to 100 percent in loggerhead shrikes 

(Lanius ludovicianus). The clutch size and nest success rate of mallards declined 

from 2002 to 2003. 

Table 4-16. Mean nest initiation dates, mean fledging dates, mean clutch size, and 

nesting success rates of bird species nesting on the Tranquillity study site, 2002 

and 2003. 

Year Species Initiation 

date 

Fledge 

date 

Clutch 

size 

Success 

rate 

Sample 

size (n)

mallard (Anas platyrhynchos) 16-Mar 17-Apr 10.2 0.57 14 

short-eared owl (Asio flammeus) 18-Mar 25-Apr 7.7 0.67 3 

western meadowlark (Sturnella neglecta) 19-Mar 09-Apr 3.7 0.33 3 

2002 

loggerhead shrike (Lanius ludovicianus) 28-Feb 06-Apr 5.5 1.00 2 

2003 mallard (Anas platyrhynchos) 15-Mar 21.5-Apr 8.7 0.50 4 

red-winged blackbird (Agelaius phoeniceus) 11.5-Mar 26.5-Apr 3.4 0.62 16 

Two of the three short-eared owl nests found in 2002 were successful, producing 

five and six fledglings, respectively. Both nests were oriented toward the north 

and they were approximately 50 cm (20 inches) in diameter. Nests consisted of a 

ground scrape sparsely lined with dead barley stems. The nests of western 

meadowlarks were domed structures concealed by a canopy of fine grass with a 

small tunnel at the entrance of each nest. One loggerhead shrike nest was located 

in a quailbush (Atriplex lentiformis)-hedgerow in the northern section of the 

project site, approximately 0.4 km (0.25 mi) north of the study plots. Another 

was located in an A. polycarpa shrub growing in the bottom of the Lateral 7 Inlet 

Canal. Both nests were approximately 1.5 m (5 ft) above the ground. One nest 

was a cup of small twigs lined with fine grass and no information was obtained on 

the second nest due to a fire, which occurred post-fledging. One nest produced 

six fledglings and the other produced five. 

The 14 mallard nests present on the site in 2002 and the 16 red-winged blackbird 

nest present on the site in 2003 were sufficient to calculate various parameters 

associated with nesting survival. The Mayfield method (Mayfield 1961, 1975) 

was only applied to these two data sets. 

Nesting parameters of mallards Eight of the 14 mallard nests successfully 

yielded fledglings. The survival rate of nests (nests surviving per day during 

incubation) was 0.98 resulting in a 55 percent probability of a nest surviving 

through the 27.5 day incubation period. There was a 95 percent probability that 

eggs would survive the incubation period within a surviving nest. However, since 
Chapter 4. Results of a Habitat Restoration Study on 

Retired Agricultural Lands in the San Joaquin Valley 

143 

the success rate of nests is only 55 percent, the actual rate of egg survival is 52 

percent. Some surviving eggs did not hatch and produce surviving young. When 

this is taken into account, there was a 51 percent probability that an egg would 

produce a hatchling. Due to the precocial behavior of mallard ducklings, 

determining the exact survival of nestlings and fledglings is difficult without 

constant nest monitoring following hatching. We have assumed that those eggs 

that successfully produced a hatchling also produced a successful fledgling 

(unless there was compelling evidence to the contrary obtained during nest 

inspections). Accordingly, the fledgling survival rate of 51 percent may be 

somewhat elevated. 

Mallard nests typically were constructed of dead barley (Hordeum vulgare) and 

silver scale (Atriplex argentea) stems, contained down lining, and were 

constructed flush with the ground level. Approximately 80 percent of the nests 

were partially or completely concealed by shrubs, primarily dead A. argentea. 

One nest was found underneath a live Atriplex polycarpa. The vegetative 

composition surrounding the nest sites was approximately 27 percent forbs, 

26 percent shrubs, and 9 percent grasses (Table 4-17). There was an average 3.14 

plant species associated with mallard nests and there were no differences between 

the number of plant species associated with successful nests and unsuccessful 

nests (p = 0.95). There was no positive correlation between nest success and the 

number of plant species present at the nest sites (p = 0.48) and the presence of 

individual plant species did not affect nest success (p > 0.34 for all 6 species 

tested). 

 Table 4-17. Vegetative composition and ground cover at mallard and 

 red-winged blackbird nests. 

Average estimated percentages for 

ground cover categories 

2002 

mallard n = 14 

2003 

red-winged blackbird = 16 

Litter 25% 47% 

Bare ground 11% 18% 

Grass 9% 35% 

Shrub 26% 0 

Forb 27% 0 

Total green 62% 35% 

Nesting parameters of red-winged blackbirds Ten of the 16 red-winged 

blackbird nests yielded at least one fledgling. The survival rate of nests was 0.96 

resulting in a 50 percent probability of a nest surviving through the 14-day 

incubation period. There was a 96 percent probability that eggs would survive the 

incubation period within a surviving nest. However, since the success rate of 

nests was only 50 percent, the actual rate of egg survival was 48 percent. Because 

some surviving eggs did not produce surviving young, there was a 56 percent 

probability that a surviving egg would produce a hatchling. 
Land Retirement Demonstration Project 

Five Year Report 

144 

Red-winged blackbird nests were constructed at an average height of 28.57 cm 

(11.2 inches) on a stand of London rocket (Sisymbrium irio). Dead grasses and 

forbs, primarily barley stems and black mustard (Brassica nigra), were woven 

into a deep cup to form each nest. There was no difference in the height of 

successful and unsuccessful nests (p = 0.63) and there was an average of 3.75 

plant species associated with the nest sites. There were no differences in the 

number of plant species present at successful and unsuccessful nest sites 

(p = 0.09), but there was a positive correlation between nest success and the 

number of plant species present at the nest sites (R = 0.02). The presence of 

individual plant species did not affect nest success (p > 0.25 for all 11 species 

tested). 

4.3.1.5. Small Mammals 

Seven species of small mammals were captured (Table 4-18): deer mice 

(Peromyscus maniculatus), Heermann’s kangaroo rats (Dipodomys heermanni), 

house mouse (Mus musculus), California vole (Microtus californicus), western 

harvest mouse (Reithrodontomys megalotis), ornate shrew (Sorex ornatus), and 

Botta’s pocket gopher (Thomomys botta). The majority of captures (97 percent) 

were deer mice. Ornate shrews, California voles, deer mice, and Botta’s pocket 

gophers were captured in pitfalls. Shrews were primarily captured from 

contoured plots in 1999 and from seeded plots in 2000, 2001, and 2002 

(Table 4-19). In 2003 shrews were captured in equal numbers on treated plots but 

were captured in greater numbers on the control plots. 

Table 4-18. The number of small mammals captured in live traps and pitfall traps 

on the Habitat Restoration Study plots, Tranquillity site, 1999 to 2003. 

 Species 1999 2000 2001 2002 2003 

Dipodomys heermanni 0 0 0 12 5 

Microtus californicus 0 0 1 0 0 

Mus musculus 2 14 47 1 0 

Peromyscus maniculatus 24 592 2,310 1,830 1,849 

Live-traps 

Reithrodontomys megalotis 0 0 0 1 0 

Microtus californicus 3 0 37 2 1 

Peromyscus maniculatus 0 0 0 40 14 

Sorex ornatus 14 18 25 20 26 

Thomomys botta 0 0 0 2 0 

Pitfall traps 

species richness 4 3 4 7 4 
Chapter 4. Results of a Habitat Restoration Study on 

Retired Agricultural Lands in the San Joaquin Valley 

145 

Table 4-19. The number of ornate shrews (Sorex ornatus), California voles 

(Microtus californicus), and Botta’s pocket gophers captured in the pitfall traps at 

the Tranquillity study site, 1999 to 2003. 

Treatment code1

Year Species CR CN NR NN Total 

1999 Sorex ornatus 1 10 2 1 14 

Microtus californicus 1 1 1 0 3 

2000 Sorex ornatus 7 3 5 3 18 

Microtus californicus 0 0 0 0 0 

2001 Sorex ornatus 11 0 11 3 25 

Microtus californicus 4 19 10 4 37 

Sorex ornatus 6 2 8 4 20 

Microtus californicus 1 0 1 0 2 

2002 

Thomomys botta 0 1 0 1 2 

2003 Sorex ornatus 6 6 6 8 26 

Microtus californicus 0 1 0 0 1 

1 Treatment codes: CR = contoured and seeded, NR = not contoured but seeded, 

 CN = contoured but not seeded, and NN = not contoured and not seeded. 

There was no clear evidence that restoration treatment (p = 0.28) or treatment 

factor (p = 0.18 for the seeded factor and p = 0.56 for the contoured factor) 

consistently affected the abundance of small mammals. However, in some years 

and seasons, treatment factor did seem to affect the abundance of small mammals 

(Figure 4-17). In spring 2001, seeding appeared to result in a 108 percent greater 

abundance of small mammals than non-seeding, and in fall 2002, the combination 

of seeding and contouring appeared to result in a 125 percent greater abundance 

of small mammals than not seeding and not contouring. The abundance of small 

mammals fluctuated yearly (p < 0.01), seasonally (p < 0.01), and by block 

(p < 0.01). The lowest total abundance was in fall 1999 when there were 27 

captures and the greatest abundances were in summer 2001 and spring 2002 when 

we captured 996 and 995 animals, respectively. 
Land Retirement Demonstration Project 

Five Year Report 

146 

Figure 4-17. Mean abundance of small mammals per 120 trap nights in winter, 

spring, summer, and fall at the Tranquillity study site, 1999 to 2003. Treatment 

codes: CR = contoured and seeded, NR = not contoured but seeded, 

CN = contoured but not seeded, and NN = not contoured and not seeded. 

Treatment factor codes are S = seeded, C = contoured, S*C = seeded and 

contoured interactions, B = block, and SSE = sum of squares error. 

4.3.2. Site-Wide Surveys 

4.3.2.1. Spotlighting Surveys 

The only amphibians and reptiles that were observed during the spotlight surveys 

were western toads (Bufo boreas) and California king snakes (Lampropeltis 

getulus californiae). These species were observed infrequently, with the greatest 

rate of observation occurring in 2000 when 0.13 western toads per km (0.6 mi) 

were observed (Figure 4-18). During the entire survey period, only two 

California king snakes were observed, one in summer of 2000 and one in fall of 

2001 (Table 4-20). Birds and mammals were more common, but the rate of 

observations of these species never exceeded 0.6 observations per km (0.6 mi). 
Chapter 4. Results of a Habitat Restoration Study on 

Retired Agricultural Lands in the San Joaquin Valley 

147 

Figure 4-18. Annual wildlife abundance observed during spotlight surveys 

conducted near Tranquillity, California, 1999 to 2003. 

The abundance of western toads did not vary between years, but did vary between 

seasons (p < 0.01, Figure 4-18 and Figure 4-19). They were more common in the 

summer than in any other season (p < 0.01 in all cases) and they were more 

common in the spring than in the winter or fall (p < 0.01 in both cases). The 

greatest abundance of western toads occurred in summer of 2000 (0.4 per km or 

0.6 mile), but they declined by approximately 97 percent by the fall of 2000 

(p < 0.01). 
Land Retirement Demonstration Project 

Five Year Report 

148 

Table 4-20. Rates of observation (mean number per kilometer) of wildlife species 

observed during spotlight surveys conducted near Tranquillity, California, 1999 to 

2003. Asterisks denote zero observations. 

Taxa Code 1999 2000 2001 2002 2003 

FA WI SP SU FA WI SU FA WI SP SU FA WI SP SU FA

Mean 

rate

BUBO 0.04 * 0.09 0.40 0.01 * 0.09 0.08 * 0.07 0.03 0.05 0.01 0.03 0.15 0.03 0.07 

LAGE * * * 0.01 * * * 0.01 * * * * * * * * < 0.01

Sub-totals 0.04 * 0.09 0.41 0.01 * 0.09 0.09 * 0.07 0.03 0.05 0.01 0.03 0.15 0.03 

Amphibians 

and Reptiles 

Yearly mean 0.02 0.13 0.06 0.04 0.07 0.06 

BCNH * * * * * * 0.30 * * * 0.04 * 0.01 * * 0.01 0.02 

KILL * * 0.04 0.01 0.03 0.19 * * 0.03 0.08 * * * * * * 0.02 

NOHA * * * * * * * * * * * * 0.01 * * * < .01

RTHA * 0.27 * * 0.12 0.19 0.01 0.13 0.15 0.01 * * 0.24 0.04 0.03 0.08 0.08 

AMKE * * * * * * * * * 0.01 * * * * * * < .01

BAOW 0.56 0.19 * 0.39 0.21 0.11 0.05 0.31 0.15 0.04 0.40 0.23 0.11 0.01 0.23 0.28 0.20 

SEOW 0.01 * 0.05 0.01 0.01 0.01 0.01 0.01 * * * * 0.01 * * * 0.01 

BUOW 0.04 0.04 0.16 0.07 * * * * * * 0.12 0.03 0.03 0.17 0.09 0.09 0.05 

LENI * * * * * * * 0.01 * * * * * * * * <0.01

WEME * * * * * * * 0.04 * * * * * * * * <0.01

SAVS * * * * * * * * * 0.03 * * * * * * <0.01

Sub-totals 0.61 0.50 0.25 0.48 0.37 0.50 0.37 0.50 0.33 0.17 0.56 0.26 0.41 0.22 0.35 0.46 

Yearly 

mean 

0.56 0.40 0.40 0.35 0.34 0.41 

Unid avian 0.08 0.07 0.15 0.05 0.09 0.04 0.07 0.09 * 0.02 * * * * * * 0.04 

Unid duck * * * * * * 0.01 * * * * * * * * * <0.01

Unid egret * * * * * * 0.01 * * * * * * * * * < 0.01

Unid raptor * * * * * * * * * * * * 0.01 * * * < 0.01

Birds 

Unid owl * * * * * * 0.01 * * 0.01 * * * * * * <0.01

SYAU 0.04 * 0.17 0.11 0.03 0.04 0.05 0.16 0.11 0.17 0.52 0.35 0.17 0.15 0.05 0.12 0.14 

LECA 0.05 0.09 0.11 0.15 0.05 0.01 0.08 0.12 * 0.01 0.13 0.09 0.07 0.08 0.05 0.23 0.08 

SPBE * * * * * 0.01 * * * * * * * * * * <0.01

THBO * * * * * * * * * 0.01 * * * * * * <0.01

DIHE * * 0.01 0.11 * * * 0.08 * 0.03 0.04 0.04 * 0.12 * 0.20 0.04 

PEMA * * * * 0.01 * 0.13 0.09 * 0.01 0.07 0.01 * * * 0.04 0.02 

MICA 0.01 * * * * * 0.03 0.03 * * 0.01 * * * * * <0.01

CAFA * * * * * 0.01 * * * * * 0.04 0.01 * * * <0.01

CALA * * 0.03 * * 0.04 0.03 * * * * * 0.01 * * * 0.01 

FESY * * * * * * * * * 0.01 * * * * * 0.03 <0.01

Sub-totals 0.10 0.09 0.32 0.37 0.09 0.11 0.32 0.48 0.11 0.24 0.77 0.53 0.26 0.35 0.10 0.62 

Yearly 

mean 

0.10 0.22 0.30 0.45 0.36 0.29 

Unid bat 0.01 * * * * * * 0.01 * 0.09 * * * * * * 0.01 

Unid 

leporid 

0.01 0.03 * * * 0.01 * * * * * * 0.01 * * * <0.01

Unid 

rodent 

* 0.01 0.01 0.01 * * 0.03 0.01 * 0.01 * 0.01 * * * 0.01 0.01 

Mammals 

Unid canid * 0.01 * * * * 0.01 * * 0.01 * * * * * 0.01 <0.01

Totals 0.75 0.59 0.66 1.26 0.47 0.61 0.78 1.07 0.44 0.48 1.36 0.84 0.68 0.60 0.60 1.11 0.77 

Species richness 7 4 7 8 8 9 10 11 4 11 8 7 11 6 6 9 7.88 

Species codes: BUBO = western toad, LAGE = California king snake, BCNH = black-crowned night heron, 

KILL = killdeer, NOHA = northern harrier, RTHA = red-tailed hawk, AMKE = American kestrel, BAOW = barn owl, 

SEOW = short-eared owl, BUOW = burrowing owl, LENI = lesser nighthawk, WEME = western meadowlark, 

SAVS = savannah sparrow, SYAU = desert cottontail, LECA = black-tailed hare, SPBE = California ground squirrel, 

THBO = valley pocket gopher, DIHE = Heermann's kangaroo rat, PEMA = deer mouse, MICA = California vole, 

CAFA = domestic dog, CALA = coyote, FESY = domestic cat
Chapter 4. Results of a Habitat Restoration Study on 

Retired Agricultural Lands in the San Joaquin Valley 

149 

The abundance of birds was approximately 40 percent higher in 1999 than in 

2002 (p = 0.01) and 2003 (p = 0.04, Figure 4-18). The greatest decline in 

abundance (63 percent) occurred between fall 1999 and spring 2002 (p < 0.01, 

Figure 4-19). The abundance of birds also varied between seasons (p < 0.01); 

spring abundances were up to 72 percent lower than all other seasons (p < 0.01 in 

all cases). Barn owls (Tyto alba) or western burrowing owls (Athene cunicularia 

hypugea), a California species of special concern, were the most common birds 

observed in most years and in most seasons (Table 4-20). Although there was a 

decline in barn owls of approximately 36 percent between 1999 and 2000, this 

decline is not statistically meaningful. Barn owls remained more abundant than 

burrowing owls during all survey years (Figure 4-20). Short-eared owls (Asio 

flammeus), also a California species of special concern, were observed in fall 

1999, winter 2002, and during each survey period from spring 2000 to fall 2001 

(Table 4-20). 

The abundance of mammals increased nearly five-fold from 1999 to 2002 

(p < 0.01, Figure 4-18). There was an 87 percent decline in mammals from 

summer 2002 to summer 2003 (p < 0.01, Figure 4-19). The high numbers of 

mammals observed in 2002 was primarily due to an irruption of desert cottontails 

(Sylvilagus auduboni) during the summer and fall (Figure 4-21, Table 4-20). 

Figure 4-19. Seasonal abundance of wildlife observed during spotlight surveys 

conducted near Tranquillity, California, 1999 to 2003. 
Land Retirement Demonstration Project 

Five Year Report 

150 

Figure 4-20. Abundance of barn owls (Tyto alba) and western burrowing owls 

(Athene cunicularia hypugea) observed during spotlight surveys conducted near 

Tranquillity, California, 1999 to 2003. 

Figure 4-21. Abundance of desert cottontails (Sylvilagus auduboni) and blacktailed hares (Lepus californicus) observed during summer spotlight surveys 

conducted near Tranquillity, California, 1999 to 2003. 
Chapter 4. Results of a Habitat Restoration Study on 

Retired Agricultural Lands in the San Joaquin Valley 

151 

The mean abundance of mammals varied between seasons (p = 0.01). The mean 

abundance of mammals in winter was 80 percent lower than in summer, 

78 percent lower than in fall, and 73 percent lower than in spring (p < 0.01, 

p = 0.01, and p = 0.04, respectively). The abundance of mammals increased more 

than six-fold from fall of 2000 to fall of 2003 (Figure 4-19, p < 0.01) due 

primarily to increases in desert cottontails, black-tailed hares (Lepus californicus), 

and Heermann’s kangaroo rats (Dipodomys heermanni, Table 4-20). Domestic 

dogs and coyotes (Canis latrans) were the only species of canids observed and 

were infrequently encountered (Table 4-20). Both species were observed in the 

winter, only coyotes were seen in the spring and summer, and only domestic dogs 

were observed in the fall (Figure 4-22). 

Figure 4-22. Seasonal abundance of coyotes (Canis latrans) and domestic dogs 

(Canis familiaris) observed during spotlight surveys conducted near Tranquillity, 

California, 1999 to 2003. n = number of spotlight surveys conducted for each 

season over the five-year study period. 

4.3.2.2. Track Station Surveys 

Nine orders of invertebrates, including seven families within six orders, visited 

track plates. The most frequent visitors were beetles (25 percent) and isopods 

(7 percent, Table 4-21). The number of track stations visited by invertebrates 

varied from 0 to 35 per three-day survey period. The highest rate of visitation 

was in 2000 (0.41), which was approximately 1.5 to 4.5 times the rate of visitation 

during other years (Table 4-21). The abundance (mean number of track stations 

visited) of invertebrates did not vary statistically between years or seasons 

(Table 4-21, Table 4-22, Figure 4-23, Figure 4-24). 
Land Retirement Demonstration Project 

Five Year Report 

152 

Table 4-21. Annual numbers and mean rates of visitation of wildlife at track stations 

established at the Tranquillity site, 1999 to 2003. Asterisks denote zero observations. 

Taxon Code 1999 2000 2001 2002 2003 Total Mean rate

Invertebrate LYCOSIDAE * 1 * * 1 <0.01 

 ISOPODA * 10 5 * * 15 0.02 

 LITHOBIIDAE * 1 1 * * 2 <0.01 

 ACRIDIDAE 1 * * * * 1 <0.01 

 GRYLLIDAE * 2 * 1 1 4 <0.01 

 PHLAEOTHRIPIDAE * 4 * * * 4 <0.01 

 CHRYSOPIDAE 1 * * * 1 <0.01 

 COLEOPTERA 2 31 10 * 11 54 0.06 

 DIPTERA * * * * 14 14 0.02 

 APIDAE 1 1 * * * 2 <0.01 

 UNKNOWN 4 33 7 52 22 118 0.14 

Invertebrate total 9 83 24 53 48 217 0.25 

Invertebrate mean rate 0.09 0.41 0.12 0.26 0.31 0.25 

Amphibia BUBO * 15 5 7 5 32 

Amphibia total 0 15 5 7 5 32 0.04 

Amphibia mean rate 0.00 0.07 0.02 0.03 0.03 0.04 

Reptilia OPHIDIA * * 1 * * 1 <0.01 

 SAURIA * * 2 * * 2 <0.01 

Reptilia total 0 0 3 0 0 3 <0.01 

Reptilia mean rate 0.00 0.00 0.01 0.00 0.00 <0.01 

Aves BUOW * 1 * * * 1 <0.01 

 CORA * 2 2 * * 4 <0.01 

 AMCR * 1 2 1 3 7 0.01 

 RWBL * 7 7 * * 14 0.02 

 UNKNOWN * 12 7 14 30 63 0.07 

Aves total 0 23 18 15 33 89 0.10 

Aves mean rate 0.00 0.11 0.09 0.07 0.22 0.10 

Mammalia SYAU 2 * * 1 21 24 0.03 

 LECA 1 * * * 1 2 <0.01 

 LEPORIDAE 3 2 8 14 3 30 0.03 

 SPBE * 5 4 14 22 45 0.05 

 DIHE 1 3 * 5 19 28 0.03 

 PEMA * * * 6 * 6 0.01 

 MICA 1 2 2 * * 5 0.01 

 RODENTIA 10 57 143 88 83 381 0.44 

 CAFA 2 1 7 5 9 24 0.03 

 CALA 1 * * * * 1 <0.01 

 CANIDAE * * * 1 * 1 <0.01 

 MEME * * 2 * * 2 <0.01 

 MUFR * * * * 1 1 <0.01 

 MUSTELIDAE * * * 4 * 4 <0.01 

 FESY * 1 * 1 * 2 <0.01 

 UNKNOWN * * 3 * 1 4 <0.01 

Mammalia total 21 71 169 139 160 560 0.65 

Mammalia mean rate 0.21 0.35 0.83 0.68 1.05 0.65 

Unknown * * 6 5 3 14 

Unknown total * * 6 5 3 14 0.02 

Unknown mean rate 0.00 0.00 0.03 0.02 0.02 0.02 

Year Total 30 192 225 219 249 915 1.06 

Year Mean Rate 0.29 0.94 1.10 1.07 1.63 1.06 

Key to codes: LYCOSIDAE = wolf spider, ISOPODA = isopod, LITHOBIIDAE = centipede, 

ACRIDIDAE = grasshopper, GRYLLIDAE = cricket, PHLAEOTHRIPIDAE = thrips, CHRYSOPIDAE = lacewing, 

COLEOPTERA = beetles, DIPTERA = flies, APIDAE = bees, BUBO = western toad, OPHIDIA = unidentified snake, 

SAURIA = unidentified lizard, BUOW = burrowing owl, CORA = common raven, AMCR = American crow, 

RWBL = red-winged blackbird, SYAU = desert cottontail, LECA = black-tailed hare, LEPORIDAE = unidentified 

leporid, SPBE = California ground squirrel, DIHE = Heermann's kangaroo rat, PEMA = deer mouse, 

MICA = California vole, RODENTIA = unidentified rodent, CAFA = domestic dog, CALA = coyote, 

CANIDAE = unidentified canid, MEME = striped skunk, MUFR = long-tailed weasel, MUSTELIDAE = unidentified 

mustelid, FESY = domestic cat. 
Chapter 4. Results of a Habitat Restoration Study on 

Retired Agricultural Lands in the San Joaquin Valley 

153 

Table 4-22. Seasonal mean rates of visitation of wildlife at track stations established at the 

Tranquillity site, 1999 to 2003. Asterisks denote zero observations. 

1999 2000 2001 2002 2003 

Taxon/Code 

FA WI SP SU FA WI SP SU FA WI SP SU FA WI SP SU FA 

Mea

n 

Invert rate 0.18 * 0.08 0.98 0.29 0.27 0.16 0.08 0.22 0.02 0.37 0.67 * * 0.47 0.20 0.27 0.25 

Amphib rate * * * 0.18 0.10 0.02 0.04 0.02 0.04 * * 0.10 0.04 * 0.04 0.06 * 0.04 

Reptilia rate * * * * * * * 0.02 0.04 * * * * * * * * <0.01

Aves 

BUOW * * * 0.02 * * * * * * * * * * * * * <0.01

AMCR * * * 0.02 * * * * 0.04 * 0.02 * * * * 0.06 * 0.01 

CORA * * * 0.02 0.02 * 0.04 * * * * * * * * * * <0.01

RWBL * * * * * 0.14 0.14 * * * * * * * * * * 0.02 

Unid avian * * 0.06 0.10 0.02 0.06 0.06 0.04 0.02 0.02 0.04 0.16 0.06 0.02 0.18 0.12 0.29 0.07 

Aves rate * * 0.06 0.16 0.04 0.20 0.24 0.04 0.06 0.02 0.06 0.16 0.06 0.02 0.18 0.18 0.29 

Mammals 

SYAU * * * * * * 0.02 * 0.04 * * * * * * * 0.02 <0.01

LECA * 0.02 * * * * * * * * * * * * * * 0.02 <0.01

SPBE * 0.04 * * * * * * * * 0.02 * * * 0.06 * 0.35 0.03 

DIHE 0.02 * * 0.02 0.04 * * * * * * * 0.10 * 0.12 0.18 0.08 0.03 

PEMA 0.08 0.12 0.25 0.37 0.25 0.24 0.75 0.80 0.76 0.49 0.71 0.27 0.59 0.16 0.43 0.69 0.51 0.44 

MICA * * * * * * * * * * * * * * * * 0.02 <0.01

Rodentia * * * 0.02 0.06 0.02 0.02 * * 0.06 0.04 0.20 0.02 0.02 0.10 0.08 0.25 0.05 

CAFA 0.02 0.02 * * * 0.02 * 0.02 0.10 0.02 0.02 * 0.02 0.06 0.02 0.12 0.04 0.03 

CALA 0.02 * * * * * * * * * * * * * * * * <0.01

MEME 0.02 * * 0.04 * * * 0.02 0.02 * * * * * * * * 0.01 

MUFR * * * * * * * * * * * 0.02 0.06 * * * * <0.01

Mustelidae * * * * * * * * * * * 0.12 * * * * * 0.01 

FESY * * * * * 0.02 * * * * 0.02 * * * * * * <0.01

Unid leporid * * * * * * * * 0.04 * * * * * * * * 0.00 

Unid canid * * * * * * * * * * * * 0.02 * * * * 0.00 

Unid mammal 0.06 * * * 0.02 0.02 * 0.10 0.06 * * 0.24 0.04 * * 0.06 * 0.04 

Mammal rate 0.22 0.20 0.25 0.45 0.37 0.32 0.79 0.94 1.02 0.57 0.81 0.85 0.85 0.24 0.73 1.13 1.29 

Totals 0.40 0.20 0.39 1.77 0.80 0.81 1.23 1.10 1.38 0.61 1.24 1.78 0.95 0.26 1.42 1.57 1.85 1.04 

Rate of visitation = number track stations visited / number of survey nights 

Species codes: BUOW = burrowing owl, AMCR = American crow, CORA = common raven, RWBL = red-winged 

blackbird, SYAU = desert cottontail, LECA = black-tailed hare, SPBE = California ground squirrel, DIHE = Heermann's 

kangaroo rat, PEMA = deer mouse, MICA = California vole, Rodentia = unidentified rodents, CAFA = domestic dog, 

CALA = coyote, MEME = striped skunk, MUFR = long-tailed weasel, FESY = domestic cat
Land Retirement Demonstration Project 

Five Year Report 

154 

Figure 4-23. The yearly abundance (mean rate of visitation) of wildlife during track 

station surveys conducted at the Tranquillity site, 1999 to 2003. 

Figure 4-24. The seasonal abundance (mean rate of visitation) of wildlife at track 

stations established at the Tranquillity site, 1999 to 2003. 
Chapter 4. Results of a Habitat Restoration Study on 

Retired Agricultural Lands in the San Joaquin Valley 

155 

Western toads were the only amphibian that visited the track plates. Their 

abundance varied between years and seasons, but these variances were not 

statistically meaningful (Figure 4-23 and Figure 4-24). Western toads did not 

visit the track plates in 1999 but did in all other years (Table 4-21). The highest 

rate of visitation was 0.18 in summer of 2000 (Table 4-22). 

Both lizard and snake tracks were observed. It is likely that these tracks were 

from western fence lizards and either gopher snakes or California king snakes 

because these were the only reptiles observed at the site. Reptiles were detected 

only in the summer and fall of 2001 (Table 4-22); the annual mean rate of 

visitation was 0.01 (Table 4-21). 

At least four species of birds visited the track plates (Table 4-21 and Table 4-22). 

Approximately 11 percent of all tracks noted were from birds. Tracks of a 

western burrowing owl (a California species of special concern) were seen on a 

single track plate in 2000 (Table 4-21). The abundance of birds varied between 

years (p < 0.02, Figure 4-23) but did not vary between seasons (Figure 4-24). No 

avian tracks were noted in 1999 (Table 4-21). The rate of visitation of birds 

increased from 0.00 in 1999 to 0.22 in 2003 (p < 0.01, Figure 4-23). The greatest 

increases in the abundance of bird visits were from 1999 to 2000, and from 2002 

to 2003. The rate of visitation increased from 0.00 in 1999 to 0.11 in 2000, and 

from 0.07 in 2002 to 0.22 in 2003. 

At least 11 species of mammals visited the track plates over the five-year study 

period (Table 4-21 and Table 4-22). Mammals were less common in 1999 than 

2001, 2002, and 2003 (p < 0.01, p = 0.05 and p < 0.01 respectively; Figure 4-23, 

Table 4-21). The rate of visitation of mammals increased nearly five-fold from 

1999 to 2003. This increase was predominantly due to California ground 

squirrels (Spermophilus beechyi), desert cottontails (Sylvilagus auduboni) and 

Heermann’s kangaroo rats (Dipodomys heermanni, Figure 4-23, Table 4-21). The 

yearly rates of visitation of unidentified rodents were and order of magnitude 

higher than any other taxonomic group and accounted for nearly 42 percent of all 

observations (Table 4-21). 

4.3.2.3. Winter Raptor Surveys 

American kestrels (Falco sparverius), northern harriers (Circus cyaneus), and 

red-tailed hawks (Buteo jamaicensis) were the most frequently observed raptors 

during the winter raptor surveys (Table 4-23). Although these species were 

observed during every day of every survey; their abundance was variable. 

Species richness increased annually (except in 2002) and reached a maximum of 

seven species in 2001 and 2003. Total raptor abundance ranged from 94 to 144 

per survey. The abundance of raptors and additional wintering species increased 

each year except in 2003, but these increases were not statistically supported 

(p = 0.99). Approximate increases varied between years and differed by 20 

percent from 1999 to 2000, 12 percent from 2000 to 2001, 14 percent from 2001 

to 2002 and decreased approximately 35 percent from 2002 to 2003. 
Land Retirement Demonstration Project 

Five Year Report 

156 

Table 4-23. Frequency and rate of bird species encountered at the Tranquillity site, 

1999 to 2003 during winter raptor surveys. 

Species 1999 2000 2001 2002 2003 

code1

Total Freq2 Rate3 Total Freq2 Rate3 Total Freq2 Rate3 Total Freq2 Rate3 Total Freq2 Rate3

AMKE 34 100% 1.02 31 100% 0.93 33 100% 0.99 36 100% 1.08 23 100% 0.69

BAOW 0 0% 0.00 0 0% 0.00 0 0% 0.00 0 0% 0.00 1 33% 0.03

FEHA 0 0% 0.00 0 0% 0.00 3 100% 0.09 0 0% 0.00 5 67% 0.15

NOHA 24 100% 0.72 32 100% 0.96 37 100% 1.11 13 100% 0.39 12 100% 0.36

PEFA 0 0% 0.00 0 0% 0.00 1 33% 0.03 2 67% 0.06 0 0% 0.00

PRFA 1 33% 0.03 2 67% 0.06 0 0% 0.00 0 0% 0.00 3 67% 0.09

RLHA 3 100% 0.09 1 33% 0.03 1 33% 0.03 0 0% 0.00 0 0% 0.00

RTHA 21 100% 0.63 22 100% 0.66 24 100% 0.72 30 100% 0.90 28 100% 0.84

Raptors 

WTKI 6 67% 0.18 14 100% 0.42 7 100% 0.21 1 33% 0.03 1 33% 0.03

Total raptor richness 6 6 7 5 7 

LOSH 0 0% 0.00 11 100% 0.33 14 100% 0.42 22 100% 0.66 14 100 0.42

MOPL 0 0% 0.00 0 0% 0.00 6 33% 0.18 40 33% 1.20 0 0 0.00

Buteo 

sp. 

4 67% 0.12 0 0% 0.00 1 33% 0.03 0 0% 0.00 0 0 0.00

Additional 

wintering 

species 

unidenti

fied 

1 33% 0.03 0 0% 0.00 0 0% 0.00 0 0% 0.00 0 0 0.00

Total abundance 94 113 127 144 87 

1

 Species codes: AMKE = American kestrel, BAOW = barn owl, FEHA = ferruginous hawk, LOSH = loggerhead 

shrike, MOPL = mountain plover, NOHA = northern harrier, PEFA = peregrine falcon, PRFA = Prairie falcon, 

RLHA = rough-legged hawk, RTHA = red-tailed hawk, and WTKI = white-tailed kite. 

2 Frequency: Percent of survey with positive observations.3 Rate: Mean number observed per mile of survey.

4.4. Discussion 

4.4.1. Vegetation 

Although it may appear that restoration efforts on the study plots were not as 

successful as initially hoped, a number of restoration goals were met. We 

successfully established plant cover to stabilize soils, established plant cover to 

provide wildlife habitat, and established native wildlife. Native shrub species 

were successfully established on many plots and in various research trials and 

hedgerows, but the long-term establishment of most native annual plant species 

has proven to be more problematic. Soil conditions that historically existed on the 

site were seasonally dynamic, with successive periods of flooding and drying. 

Decades of intensive agricultural use greatly affected soil characteristics, depleted 

the native plant seed bank, and promoted the dominance of introduced weeds. 

These historic conditions greatly increased the challenge in establishing native 

upland plant communities on the study site. 

Although slightly more than two-thirds of the 13 imprinted species have been 

encountered during vegetation monitoring, establishment of the majority of these 

species has been quite limited. Additionally, the number of imprinted species 
Chapter 4. Results of a Habitat Restoration Study on 

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157 

encountered during each of the final 2 years of monitoring was less than the 

number encountered during the initial two post-imprinting surveys. 

Some imprinted annual species persisted on the plots, but these species were 

characterized by low abundances and patchy distributions. Likewise, few 

additional native annual species were able to become established on the plots. 

And, although it had been hoped that the vegetation on the plots would be 

augmented by native seed from the existing seed bank and from adjacent lands, 

few additional native annual species were able to become established. As with 

the imprinted annuals, these adventitious natives were patchily distributed and of 

low abundance. 

Generally, the establishment of perennial species was much more successful than 

that of annual species. Nevertheless, the perennial vegetation declined after 

attacks by agricultural pests (particularly, false chinch bugs; Nysius sp.). 

Additional decline in the perennial vegetation appeared to be linked to soil 

motility and extensive soil cracking. 

While numerous fertile individuals of Atriplex polycarpa, Suaeda moquinii and 

Isocoma acradenia became established on the plots, we saw little evidence of 

successful second generation from these (potential) progenitors. This lack of 

successful establishment appears to be primarily attributable to competition from 

the annual invasive species on the plots. Seedling establishment from the parent 

native perennials was generally limited to the areas beneath and directly around 

the parent plants (i.e., areas where there was sufficient open soil). However, these 

seedlings rarely survived beyond seedling stage—probably due to competition 

with the parent plants. As noted, precipitation during the course of the 

Demonstration Project was substantially lower than the 30-year average. This 

scarcity of rainfall undoubtedly limited these species “expansion.” 

Non-native species dominated large portions of the HRS plots. By the final year 

of monitoring, three non-native species, Sisymbrium irio, Bromus madritensis, 

and Capsella bursa-pastoris, accounted for more than three-fourths of the 

vegetative cover. The “tumbling saltweeds,” Atriplex rosea and A. argentea were 

readily established on the disturbed (i.e., tilled) soils of the HRS plots. By the end 

of the first growing season following imprinting, these species were dominant on 

many of the plots. Although the abundance of these species was greatly 

diminished in subsequent years, many of their “skeletons” (i.e., senescent stems 

and leaves) remained onsite for the following growing season and served to 

facilitate the establishment of other weeds, as only a few, invasive species were 

able to become established beneath the skeletons. The mustards, Sisymbrium irio

and Brassica nigra, in particular, benefited in this way. 

Bromus madritensis appeared to be particularly effective in limiting the 

establishment of imprinted species. This pattern is readily seen in the rankabundance curves (previously shown in Figure 4-6 and Figure 4-7). All plots on 

Block 1 (represented by the leftmost curves in these figures) were steeper, and 
Land Retirement Demonstration Project 

Five Year Report 

158 

were generally poorer in species than plots in the other blocks. As noted, Bromus 

madritensis tended to dominate the northern HRS plots; the buffers of the red 

brome-dominated plots also tended to have a large component of brome. The 

northern portion of the HRS area had soils characterized by high electrical 

conductivity readings and high levels of soluble boron (Figure 2-34; Figure 2-35). 

However, it should also be noted that Section 10 (i.e., the area with the densest 

brome component) had a different land-use history than the areas on which the 

other four blocks were sited. Section 10 had been fallowed for a number of years 

prior to restoration, and it may be that vegetation on this portion of the site 

represented a later stage of post-agricultural succession. 

Clearly, weed management is essential to ensure the long-term persistence of 

native species on restored lands. To date, only intensive and repeated weed 

suppression has successfully reduced weed loads and allowed natives to persist, 

but this has been costly and labor intensive. Numerous experimental 

techniques—including herbicide use, establishing cover crops, flaming, mowing, 

discing, pre-irrigating, solarization, and manual weeding—have been explored for 

weed-eradication techniques; however, none have yet provided effective longterm results. We are continuing research in an attempt to develop cost-effective 

and efficient techniques for weed control that would be applicable for large-scale 

land retirement (see Appendix 1). 

The microtopographic contours (berms) persisted throughout the study period, 

although their height decreased over the course of the study due to compaction 

and disturbance, and as the shallow furrows along the edges of the berms became 

partially filled with soil and litter. Still, these contours successfully provided 

structural and vegetative heterogeneity to what had previously been a 

homogenous landscape. Topographic contouring clearly facilitated establishment 

of the perennial vegetation. The majority of the imprinted perennials became 

established either on the berms, or in the furrows. No clear pattern between 

establishment of imprinted annual species and contouring was discernable. 

No strong statistical support was found for a positive correlation between the 

diversity and abundance of small mammals and contouring. Nevertheless, we 

suspect that contours would ultimately enhance the landscape for burrowing 

animals, and would become an increasingly important component of restored 

habitats as the wildlife community continues to diversify. The design of the 

contours could be improved to increase their benefit to wildlife. In restoration 

efforts that are not strictly controlled by a statistically rigorous study design and 

other limiting factors, heterogeneity could be greatly increased by fashioning 

meandering contours of variable height and width. 

4.4.2. Invertebrates 

The invertebrate community showed little notable response to the treatments, 

which was expected because of the similarity among the treatments. The overall 

richness of invertebrates and the abundance of coleopterans showed some limited 
Chapter 4. Results of a Habitat Restoration Study on 

Retired Agricultural Lands in the San Joaquin Valley 

159 

responses to the treatments, but there were no prevailing trends. The richness and 

abundance of invertebrates tended to be more influenced by location (study block) 

than by the application of any particular treatment. 

Because of the limited long-term success of our restoration treatments, all of the 

HRS study plots more closely resemble fallowed lands than restored habitat. Gelt 

(1993) noted that homogenous plant communities dominated by invasive species 

often characterize fallowed lands. Reduced grassland plant species richness, 

characteristic of fallowed lands and monocultures, results in altered invertebrate 

community structure (Knopps 1999). Because there is a positive correlation 

between increased habitat diversity and increased invertebrate richness and/or 

abundance (Dodero 2003, Kremen et al. 2002, Knopps 1999, Speight et al.1999, 

Erhardt 1985), we would expect that the successful restoration of retired 

agricultural lands would lead to a more stable and complex invertebrate 

community. 

On the Habitat Restoration Study site, the diversity of agriculturally beneficial 

invertebrates was greater than the diversity of agricultural pests. Beneficial 

invertebrates, including predators, parasitoids, and pollinators, provide valuable 

pest regulation and pollination services to agricultural land (Samu 2003, Kremen 

et al. 2002, Schowaltzer 2000, Allen-Wardell et al. 1988). In structurally diverse 

agro-ecosystems, agriculturally beneficial insects tend to be more abundant 

(Kremen et al. 2002, Thomas et al.1992), and pest populations are typically 

reduced (Samu 2003, Schowalter 1996). Kremen et al.’s (2002, 2004) work in the 

Central Valley of California demonstrates the economic and production benefits 

of incorporating natural habitat into the agricultural landscape. Several studies 

have demonstrated that monocultures, typical of agricultural expanses, invite 

sudden, dramatic, and widespread outbreaks of invertebrate pests (Turchin 1988, 

Root 1973, Irving 1970). Reducing landscape homogeneity through the 

reestablishment of a diverse native plant community could provide a barrier to the 

movement of agricultural pests and reduce the severity of outbreak (Schowalter 

1996, Piemeisel and Lawson 1937). These benefits could be achieved through the 

successful restoration of retired lands. 

The native plant nursery that has been established on the Tranquillity site houses 

the greatest diversity of native plant species in the San Joaquin Valley. We have 

observed heightened invertebrate diversity, particularly with agriculturally 

beneficial species, in the nursery as compared to the study plots and other 

surrounding lands. This observation is supported by the competitive exclusion 

principle (Hardin 1960) and by Speight et al. (1999) who asserted that habitats 

having greater plant species richness should support greater insect species 

richness. The HRS study was designed to test for a correlation between the level 

of native plant diversity and the richness of invertebrates. However, the relatively 

low success of the restoration treatments precludes a meaningful analysis. 

An analysis of invertebrate richness and abundance at the ordinal level, as was 

conducted in this study, is limiting. We have found that the data are too coarse to 
Land Retirement Demonstration Project 

Five Year Report 

160 

provide meaningful information on invertebrate community structure and 

dynamics. Furthermore, an analysis at the ordinal level is primarily relevant to 

short-term abiotic factors (Hemerik and Brussaard 2002) rather than long-term 

biotic factors. There is an opportunity to evaluate the invertebrate community 

structure, dynamics, and the correlation of invertebrate richness to native plant 

diversity at the family or species level. These studies could be implemented on 

lands where research trials or restoration have proven successful. An analysis of 

specific sensitive indicator orders (Coleoptera, Lepidoptera, and Araneae) has 

been used to measure restoration success at the ecosystem level (Waltz and 

Covington 2004, Perner and Malt 2003, Hemerik and Brussaard 2002) and could 

be incorporated into the design of future monitoring and evaluation efforts. 

4.4.3. Amphibians and Reptiles 

Amphibian diversity and abundance was low throughout the 5-year survey period. 

Fisher and Schaffer (1996) note a large-scale decline in native amphibian species 

in the San Joaquin Valley and suggest lack of suitable habitat as a major factor. 

The only amphibian species observed at the Tranquillity site, the western toad, is 

typically associated with lakes, rivers, and streams, but is also found in grassland 

habitats (Stebbins 1985). Western toads likely emigrated to the study area from 

canals and ditches that occur on surrounding farmland. These water sources are 

needed for breeding. Western toad abundance was especially high in the summer 

of 2001. The potential for the study site to provide a diverse assemblage of 

amphibians is fairly low in the near term. However, if suitable breeding sites 

become available, other species of amphibians could become established on the 

site. Species that could become established include: pacific treefrog (Pseudacris 

regilla), western spadefoot toad (Spea (=Scaphiopus) hammondi; a California 

species of special concern), and California tiger salamander (Ambystoma 

californiense, federally listed threatened species, USFWS 2004). 

California king snake was the only species of reptile observed during spotlighting 

surveys although a gopher snake and western whiptail have also been observed on 

the site. A northern pacific rattlesnake (Crotulus viridus oreganus) was observed 

within 8 km (5 mi) of the site. In addition, a local farmer (Robert Jones, pers. 

comm.) reported seeing coast horned lizards (Phrynosoma coronatum; a 

California species of special concern, CDFG 2003) in the area until approximately 

1990. There is one 2002 record of a coast horned lizard from Alkali Sink 

Ecological Reserve approximately 11 km (7 mi) to the north-northeast of the site 

(CDFG 2003). 

Lack of suitable habitat likely precludes a greater diversity and abundance of 

reptiles. As native vegetation becomes established and microtopographic features 

are created due to rain and wind, it is expected that reptiles will colonize the site 

to a greater degree. Reptile species that may inhabit the site in the future include 

those listed above that have been seen in proximity to the site and the sideblotched lizard (Uta stansburiana), western skink (Eumeces skiltonianus), Gilbert 

skink (E. gilberti), southern alligator lizard (Gerrhonotus multicarinautus), 
Chapter 4. Results of a Habitat Restoration Study on 

Retired Agricultural Lands in the San Joaquin Valley 

161 

western yellow-bellied racer (Coluber constrictor), San Joaquin Coachwhip 

(Masticophis flagellum), California glossy snake (Arizona elegans occidentalis), 

Valley garter snake (Thamnophis sirtalis fitchii), California black-headed snake 

(Tantilla planiceps), and southwestern black-headed snake (Tantilla 

hobartsmithi). Currently, the prey base appears adequate for most colubrid 

snakes (see Section 4.3.5). In addition, invertebrate abundance and diversity 

appears to be satisfactory to sustain species that prey upon insects. 

4.4.4. Birds 

There were no substantial differences in the richness or abundance of birds 

between treatments or treatment factors, but there were differences between 

blocks in all seasons. These results are not unexpected because of the similarity 

of the vegetation on all plots and inherent spatial differences between blocks. The 

abundance, richness, and composition of birds varied annually and seasonally, but 

this is expected because of the typical cyclic patterns of birds (circadian rhythms 

and circannual cycles, Gill 1999). Although the study plots were primarily 

composed of non-native weedy species, the landscape characteristics closely 

resembles a grassland and it is not surprising that the greatest abundance of birds 

were obligate grassland species, followed by facultative grassland species. 

Eleven short-eared owlets (Asio flammeus) were successfully reared in plots 8 and 

10 in 2002. During various surveys conducted in 2003 we observed 14 shorteared owls communally roosting on Block 1, and 10 roosting on Block 5. The 

only other known short-eared owl nesting locations in the San Joaquin Valley are 

Mendota Wildlife Area approximately 5 mi (8 km) from the Tranquillity site 

where one nest was documented in 1987 (CDFG 1987), and Kern NWR, 

approximately 72 mi (115 km) south of the Tranquillity site (Cooper 2004). 

There are also numerous western burrowing owls nesting under sections of the 

displaced concrete lining of the San Luis Drain, which traverses a portion of the 

Tranquillity site. They have been observed roosting, foraging, and burrowing on 

the site. The short-eared owl and the western burrowing owl are species of 

special concern in California (CDFG 1999) and the short-eared owl is a rare 

species in Fresno and Madera Counties according to Fresno Audubon Society 

(2001). The widespread use of the Tranquillity site by these species demonstrates 

the potential of retired agricultural lands to contribute to the recovery of a variety 

of sensitive species. The reproductive success and population dynamics of the 

short-eared owl are closely tied to the abundance of its prey (Holt and Leasure 

1993), and the high density of deer mice and California voles on the study plots 

likely contributes to the success of these species at the Tranquillity site. 

All of the successful mallard nests were associated with relatively high shrub 

cover, primarily dead A. argentea skeletons. The placement of nests in vegetation 

has been found to be beneficial (Gloutney and Clark 1997) and it is likely that 

shrubs contributed to nest success by providing nest cover and concealment. 

Approximately 57 percent of the nests on Plot 6 were successful, which may have 

led to high nest-site fidelity. It is not clear why mallards preferentially selected 
Land Retirement Demonstration Project 

Five Year Report 

162 

Plot 6 for nesting when other plots had structural heterogeneity similar to Plot 6. 

Mallards typically nest within 1.6 km (1 mile) of a water source (Kaufman 1996, 

Baichich and Harrison 1997) but this was not observed on the Tranquillity site. 

There are a number of agricultural canals, ditches, and drains on and near the site, 

but they are dry during the breeding and nesting season and did not provide a 

source of water. 

The most abundant nests in 2003 were of red-winged blackbirds. Male redwinged blackbirds were often observed actively defending nesting territories by 

mobbing and vocalizing to deter predators. Brown-headed cowbirds (Molothrus 

ater) were observed in the vicinity of blackbird nests, but we did not observe nest 

parasitism. It is well known that red-winged blackbirds are often parasitized by 

brown-headed cowbirds (Freeman et al. 1990), but the high degree of territory 

defense that we observed may have effectively eliminated parasitism. Past studies 

have shown that group defense against cowbirds may be an important deterrent to 

nest parasitism (Freeman et al. 1990). Berger (1951), Payne (1973), and Norman 

and Robertson (1975) found that female cowbirds would use perches to locate and 

monitor potential nests for subsequent parasitism. Adequate perch sites are 

extremely limited at the Tranquillity site, which may have contributed to a lack of 

parasitism. Parasite pressure on red-winged blackbirds may be reduced by an 

increased availability of other, more preferred hosts (Friedman 1963, Friedman et 

al. 1977). This is not likely to be the case at the Tranquillity site because there are 

few alternate hosts nesting on the site. The degree of cowbird parasitism also has 

been found to be lower in localities where cowbirds are recent arrivals (Friedman 

1963, Friedman et al. 1977). It is likely that the lack of parasitism by cowbirds at 

the Tranquillity site is partially due to the recent conversion of agricultural crops 

to habitat, the recent nesting efforts by red-winged blackbirds, and the recent 

arrival of brown-headed cowbirds at the site. 

The number of nests and the species of birds that successfully nested on the 

Tranquillity site changed dramatically from 2002 to 2003. The primary difference 

was that mallards were the most successful nesting bird in 2002 while red-winged 

blackbirds were the most successful nesting bird in 2003. We suspect that the 

principal reason for this shift was a change in vegetative structure and subsequent 

loss of potential cover. Atriplex argentea, which had been associated with all 

mallard nests, is an annual sub-shrub that was present on the study plots in large 

numbers in 2002, but was much less common in 2003. London rocket was a 

dominant component of the landscape in 2003. London rocket was used as 

nesting supports and nesting material for red-winged blackbird nests. Although 

both of these plant species have contributed to the nesting success of these two 

bird species, they are considered weedy, invasive plants and are undesirable. For 

habitat restoration to be beneficial to nesting birds, these plant species must be 

replaced by native species that would provide the same or better quality 

conditions for nesting birds. Furthermore, an increase in the abundance and 

diversity of native plants would likely provide nesting opportunities for a wider 

variety of bird species. 
Chapter 4. Results of a Habitat Restoration Study on 

Retired Agricultural Lands in the San Joaquin Valley 

163 

4.4.5. Small Mammals 

In 1999, when the study plots were planted in barley, deer mice and ornate shrews 

were the most abundant small mammal species, but they were present in low 

numbers. Once the barley was replaced by restoration treatments and discing was 

halted, there was an increase in the abundance and diversity of small mammals. 

The abundance of deer mice and the diversity of small mammals in general did 

not differ between treatment or treatment factor. It is not surprising that seeding 

did not influence small mammal abundance or diversity because of the similarity 

between seeded and non-seeded plots. However, we are somewhat surprised that 

contouring did not enhance the small mammal community. Contours are thought 

to provide a suitable site in which to construct burrow systems and provide 

topographical relief to act as refugia during periods of high rainfall. The soils on 

the Tranquillity site exhibit a tremendous potential for shrinking and swelling. 

Large cracks in the soil are widespread, especially during the dry summer months. 

We suspect that these soil characteristics provide adequate opportunities for 

burrow construction and relief from the effects of flooding, and lessen the 

potential benefits of contouring to small mammals. Currently, the Tranquillity 

site supports a viable, self-sustaining small mammal community that contributes 

to the success of predatory birds and mammals. However, this small mammal 

community is not typical of native habitats in the San Joaquin Valley. Rather, the 

community is typical of disturbed, ruderal habitats. We would expect that 

effective restoration would ultimately enhance and naturalize the small mammal 

community. 

4.4.6. Site-Wide Surveys 

4.4.6.1. Spotlighting Surveys 

Most of the 11 species of birds observed during spotlighting surveys were owls 

and grassland associated raptors. Barn owls and short-eared owls are associated 

with open grassland habitats and agricultural fields and small mammals constitute 

a majority of their diet (Marti 1992, Holt 1993). Because abundance of deer mice 

was typically very high during the study, we would expect that barn owls preyed 

significantly upon this species. While barn owls made up a majority of the 

observations, red-tailed hawks were also well represented throughout the survey 

period. Black-crowned night herons (Nycticorax nycticorax) were observed 

during four of the 16 survey periods but abundance was especially high in the 

summer of 2001. Black-crowned night herons are known to feed on fish and 

frogs (Kaufman 1996) and the relatively high abundance of herons during 

summer of 2001 may have been related to the high abundance of western toads 

seen during that same survey period. 

There was a dramatic increase in abundance of mammals at the Tranquillity site 

over the 5-year study period. This increase is likely tied to the continued 

maturation of the vegetative community and reduced farming disturbance at the 

site. Leporid abundance fluctuated but was always the dominant mammalian taxa 
Land Retirement Demonstration Project 

Five Year Report 

164 

observed throughout the survey although Heermann’s kangaroo rats were also 

highly abundant during the summer of 2000 and fall of 2003. Kangaroo rats are 

especially adapted to arid conditions (Jameson and Peeters 1988) in the valley 

grassland and foothill woodland communities of California to southwestern 

Oregon (Ingles 1965). As fossorial animals, kangaroo rats will provide 

aestivation and hibernation habitat for a variety of species, including invertebrates 

and small reptiles. Although coyotes have been observed infrequently during 

spotlighting surveys, they are known to den on the plots and forage in the area. 

Because coyotes feed extensively on leporids and small mammals (Jameson and 

Peeters 1988), we expect that abundance of coyotes will increase in the future. It 

is interesting that dogs and coyotes appeared to coexist in winter, yet seemed to 

exclude each other in spring, summer, and fall. 

4.4.6.2. Track Station Surveys 

Twenty-eight taxa were recorded visiting the trackplates over the 5-year study 

period. Approximately 75 percent of tracks observed were invertebrates (mostly 

beetles) or mammals (mostly rodents). Felids and mustelids were recorded in 

extremely low numbers suggesting that abundance of these taxa are especially 

low. While coyote and/or dog tracks were recorded during 12 of the 17 surveys, 

they were recorded infrequently during each survey period, which also suggests 

that these animals were relatively low in abundance. This is particularly evident 

given that the target species for track station surveys are typically mesocarnivores including canids, felids and mustelids. 

4.4.6.3. Winter Raptor Surveys 

There was an increase in the diversity and abundance of raptors on the 

Tranquillity site over the 5-year study period. The highest diversity was in 2001 

and 2003 and the highest abundance was in 2002. The diversity and abundance of 

raptors present on the Tranquillity site is very similar to the abundance and 

diversity of raptors at Kern National Wildlife Refuge, (Cooper 2004). California 

special concern species (CDFG 1999) that were present at the Tranquillity site 

included ferruginous hawks (Buteo regalis), northern harriers, prairie falcons 

(Falco mexicanus), mountain plovers, and loggerhead shrikes. The abundance of 

northern harrier and the loggerhead shrikes remained relatively constant, but the 

abundance of the other sensitive species fluctuated. Red-tailed hawks at the 

Tranquillity site exhibited both light and dark morphologies (in 2003 

approximately 25 percent of all red-tailed hawks observed exhibited a darkmorphology). However, the majority of the ground roosting red-tailed hawks 

were of the dark morphology. Ground roosting is relatively uncommon in this 

species, especially in light-morphed birds (Preston 1980). 

Red-tailed hawks, white-tailed kites, northern harriers, kestrels, loggerhead 

shrikes, barn owls, western burrowing owls, and short-eared owls have all been 

observed nesting on and near the Tranquillity site. The presence of a viable, selfsustaining small mammal population likely contributes to the abundance, 
Chapter 4. Results of a Habitat Restoration Study on 

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165 

diversity, and successful breeding of these raptors. Although the Tranquillity site 

represents relatively high quality raptor habitat, it could be improved by 

successful restoration. Land retirement and the implementation of effective 

habitat restoration have the potential to greatly benefit raptors within the San 

Joaquin Valley. 

4.5. Conclusions and Recommendations 

4.5.1. Conclusions 

The Land Retirement Demonstration Project proved to be a valuable learning 

experience regarding restoration of retired lands. This pilot project emphasized 

standard restoration techniques, which we have shown to be generally ineffective 

and not well suited to retired farmlands on heavy clay soils. By testing these 

standard methods on a small scale, we avoided the expense and inefficiency that 

likely would have occurred had these techniques been implemented on a larger 

scale. Based upon those initial results, we have implemented a wide array of 

research trials (see Appendix 3) that focus on the limiting factors that we 

identified. Some of those limiting factors have been overcome, but a number of 

issues remain to be resolved before restoration can be effectively conducted. 

Some of the restoration approaches used on the HRS plots showed promise. 

Microtopographic contouring appeared to have positive effects in promoting 

establishment of native vegetation, and potentially providing habitat heterogeneity 

for small mammals and other biota. Shrub establishment—particularly of 

Atriplex polycarpa—approached densities that would be considered appropriate 

habitat for some species of concern. Nevertheless, in general, restoration 

response was less than optimal. 

Factors contributing to the limited success of native plant restoration are thought 

to include inadequate seed delivery methods (imprinting may not be appropriate 

for use on the HRS soil types and for many of the species), competition from 

invasive species, inappropriate seed source (most of the seed was purchased 

commercially and was not obtained from the proximity of the project site), and 

drought conditions experienced throughout the term of the project. 

The Habitat Restoration Study represents a significant expenditure of resources, 

and has required a concentrated effort by all involved parties. Given the immense 

challenges associated with the Tranquillity site (e.g., substantial weed loads, 

difficult soils, deficient rainfall, site history, etc.), it was not surprising that the 

restoration response was not as pronounced as was originally envisioned. 

Nevertheless, the HRS can be considered a valuable foundation in developing 

practical restoration strategies. 

We are currently involved in an extensive research program that is advancing the 

state of knowledge of appropriate restoration technologies and recommendations 

for large-scale restoration efforts in the San Joaquin Valley (see Appendix 1). 
Land Retirement Demonstration Project 

Five Year Report 

166 

The greatest obstacle to date has been weed control, so current research is 

primarily focused on that topic, but considerable time and expense is also being 

spent researching other restoration issues. Among these are: collecting seed from 

remnant populations of native plants, propagating and increasing the seed supply 

of locally collected plants, determining germination and propagation requirements 

of various plant species, and developing appropriate mechanical seed harvesting, 

planting, and ground preparation procedures. Continuation of this research is 

essential if land retirement and the restoration of retired lands are expected to 

proceed. 

Because there were few notable differences among the restoration treatments, 

there were also few observable trends in wildlife diversity and abundance 

associated with the treatments. However, the information on wildlife diversity 

and abundance obtained shows that retired agricultural lands are valuable to 

wildlife. Even in the absence of widespread and successful restoration, retired 

agricultural lands are important to wildlife. Unquestionably, removing active 

agriculture and associated recurring disking and irrigating removes threats to 

wildlife. Over a 5-year period, the following were identified—101 families 

within 21 orders of invertebrates, 1 species of amphibian, 4 species of reptiles, 

48 species of birds, 8 species of small mammals, 1 species of canid (coyote), 

2 species of mustelids (skunk and long-tailed weasel), and 2 domesticated species 

(cat and dog) that utilize the Tranquillity study site. Nine species of birds utilized 

the study area as breeding habitat and 12 species of sensitive birds were using the 

study area. 

Although there have been some instances of agricultural pest outbreaks and weeds 

which required control measures, there were no indications that the HRS lands 

supported greater pest densities than did surrounding retired and fallowed lands. 

Rather, agriculturally beneficial species were common and widespread on the site, 

especially in restored areas. 

One factor that may have limited the abundance and diversity of native wildlife 

on the study plots is the lack of nearby lands that support wildlife which could 

disperse onto the study plots. Only small, remnant parcels of native habitat exist 

in the vicinity. Within 80 km (50 mi) of the site, fewer than 100 locations 

containing native plants have been located. The largest and most ecologically 

diverse areas are the Alkali Sink Ecological Reserve, the Kerman Ecological 

Reserve, and the Mendota Wildlife Area, all located within 16 km (10 mi) of the 

project site (see Chapter 1). A few sites in the immediate vicinity of the project 

site do provide opportunities for some wildlife dispersal. These are primarily 

limited to the San Luis Drain right-of-way, the Lateral 7 Inlet Canal right-of-way, 

various dirt roads that cross the site, and land directly north of the site which has 

been fallowed. The diversity of wildlife on these lands is not great and dispersal 

of wildlife onto the plots from these areas is expected to be minimal. The barley 

buffers, which are approximately 101 m (330 ft) wide, may also have contributed 

to lower abundance and diversity of some taxonomic groups than might otherwise 

be expected. The width of the buffers, however, was a compromise between the 
Chapter 4. Results of a Habitat Restoration Study on 

Retired Agricultural Lands in the San Joaquin Valley 

167 

need to allow wildlife to invade the plots, yet at the same time isolate the plots to 

minimize interactions between restoration treatments. 

Although this project did not necessarily emphasize the establishment of 

threatened and endangered wildlife on the study plots, that is one long-term goal 

of the land retirement program. We increased the suitability of habitat for a 

number of rare species of birds and, as restoration techniques are designed and 

applied, the benefits to wildlife including sensitive species would be expected to 

increase. With the incorporation of appropriate management actions, the habitat 

that has been established could become increasingly suitable for various other rare 

species (e.g., San Joaquin kit fox, blunt-nosed leopard lizard, and San Joaquin 

kangaroo rats). Many rare upland species seem to be dependent upon an open 

vegetative structure, independent of native plant diversity or the presence of a 

fully functional native plant community. Accordingly, habitat for rare species 

may be more easily established and managed than a diverse, native upland plant 

community. 

The data presented in this report are immensely valuable as a description of 

baseline conditions that, if compared to data collected from retired lands that are 

successfully restored to native habitats, would provide insight into the value of 

restoration to wildlife. There have been no other wildlife studies or monitoring 

efforts in the central San Joaquin Valley of this duration or scope, making this a 

unique data set that describes the wildlife community existing on lands dominated 

by non-native species. Within the San Joaquin Valley, similar conditions are 

common and widespread among scattered, remnant patches of land that are not 

intensively farmed. 

The three primary objectives of the Habitat Restoration Study have been 

accomplished. Below is a summary of findings related to each objective. 

1. Determine the efficacy of revegetation with native plants as a means to 

facilitate upland habitat restoration. 

Standard native plant revegetation techniques as applied to the study plots 

(planting commercially purchased seed of an appropriate species mix on prepared 

ground using a seed imprinter) facilitated upland habitat restoration, but to a 

degree that was less than optimal. Some species persisted for a short time, some 

species became established but diminished over time, and others (e.g., Atriplex

polycarpa and Suaeda moquinii) became established on some plots. Competition 

with weeds appeared to be the primary factor limiting restoration success, 

although other factors (e.g., low seed viability, seed delivery methods, and insect 

damage) were problematic. Revegetation research, which became an increasingly 

important component of the project, led to the development of promising and 

innovative techniques to combat these issues. A combination of selective 

herbicide use, application of activated charcoal (to protect native seed from 

herbicide exposure), and planting seed using a modified seed drill seems 
Land Retirement Demonstration Project 

Five Year Report 

168 

particularly promising. These techniques will be applied and tested under field 

conditions in 2005 and 2006. 

2. Determine the efficacy of microtopographic contouring as a means to facilitate 

upland habitat restoration. 

Microtopographic contouring as applied to the study plots (i.e., straight, uniform 

size, uniform orientation), showed some value in facilitating the establishment of 

native plant species (particularly shrubs) but appeared to be of limited value to 

wildlife, at least in the short term. We suspect that with time, their importance to 

wildlife would increase (as burrowing species such as kangaroo rats become 

residents). A more complex system of microtopographic contouring would add 

additional heterogeneity and likely result in increased benefits to plants and 

wildlife. 

3. Examine the responses of plants and wildlife to land retirement and 

restoration. 

A multitude of plants and wildlife responded well to land retirement. The 

cessation of active agriculture and associated irrigation and disking allowed for 

the incursion and establishment of many native and non-native species on retired 

lands. The implementation of improved revegetation techniques and appropriate 

land management actions would be expected to enhance benefits for desirable 

species. 

4.5.2 Recommendations 

A number of tasks remain to fulfill the intent of this project and to ensure that 

land retirement and the restoration of retired lands can proceed. Continuation of 

current restoration research, the implementation of new restoration research 

topics, and other high priority tasks are needed. Specific tasks that should be 

accomplished include: 

• Publish findings of completed and on-going research in the open scientific 

literature, which is subjected to world-wide scientific scrutiny. It is 

important to have this information widely available, especially to those 

attempting restoration in the San Joaquin Valley. Unfortunately, 

information contained in unpublished, gray literature is often overlooked 

or unavailable to scientists and managers. Government agencies should 

always provide their personnel and consultants with strong incentives and 

the time and resources to publish their work. 

• Develop a long-term management and monitoring plan for the Tranquillity 

site. This management plan should include long-term wildlife monitoring 

on the HRS plots (or a subset) every 3 to 5 years to document changes in 

biota over time, monitoring of selenium levels to ensure safe conditions 

for wildlife, and developing and implementing a restoration strategy for 

Tranquillity site lands. 
Chapter 4. Results of a Habitat Restoration Study on 

Retired Agricultural Lands in the San Joaquin Valley 

169 

• Continue maintenance and expansion of the native plant nursery and seed 

collecting activities. The native plant nursery has proven to be an 

essential component of restoration. It facilitates research on seed delivery 

methods, propagation techniques, and harvesting techniques, and it also 

functions to increase the stock of locally collected native plant seed. The 

nursery has proved itself invaluable in outreach activities by providing a 

visually appealing representation of native landscapes. The continuation 

of seed collecting activities is necessary to increase the number of species 

of native plants and to improve the genetic diversity of local genotypes of 

plants that would be available for restoration. 

• Continue research on development of restoration technologies, including 

seed delivery techniques, weed control methods, harvesting techniques, 

and seed cleaning techniques. Currently, there is an insufficient seed 

source and a severe lack of restoration technologies that are appropriate 

for the implementation of large-scale restoration in the San Joaquin 

Valley. Continuation of these activities is vital to a successful large-scale 

land retirement project and other large-scale restoration efforts in the 

region. 

• Document and protect localities of known populations of native plants and 

animals in the project vicinity to ensure the survival and persistence of 

existing populations. Native populations of plants and wildlife in the 

San Joaquin Valley are exceedingly small in size and rare in occurrence. 

These fragmented populations are vital stockpiles of resources that would 

be needed for restoration. 

• Develop criteria and methods for the propagation and translocation of 

threatened and endangered species to restored lands. Because there is a 

paucity of existing native lands (and those that do exist are isolated by 

large expanses of agricultural lands that act as barriers to the movement of 

wildlife) occurring in the western San Joaquin Valley, it is not likely that 

many threatened and endangered wildlife species would emigrate to 

retired lands. Accordingly, to ensure maximum benefits to threatened and 

endangered wildlife, techniques must be developed for the safe and 

successful translocation of these species. 

• Provide public awareness of the positive effects and benefits of land 

retirement. An ongoing outreach program is essential to generate public 

interest and acceptance of land retirement and native lands restoration. 

Appropriate outreach can also be instrumental in developing and securing 

additional funding. 
Land Retirement Demonstration Project 

Five Year Report 

170 

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Chapter 5. Overview of the Implications and Concerns of 

Agricultural Land Retirement in the San Joaquin Valley 

177 

Chapter 5. Overview of the 

Implications and Concerns of 

Agricultural Land Retirement in the 

San Joaquin Valley, California 

by Beatrice A. Olsen and Curtis E. Uptain 

This chapter is a synopsis of the results acquired from work at the Land 

Retirement Demonstration Project (LRDP) study sites over a 5-year period. The 

key points of the results of the various studies are summarized. The knowledge 

acquired will be used to address concerns associated with land retirement that 

were not a focus of the studies. 

The LRDP Tranquillity site is representative of conditions encountered on most 

drainage impacted areas of the San Joaquin Valley, including a high percentage of 

those lands targeted for retirement by district and federal programs. The 

predominant soil type at the site is Tranquillity clay which is the most extensive 

soil type mapped by the Natural Resources Conservation Service (NRCS) on the 

lower alluvial fan and basin rim landforms in the western San Joaquin Valley. 

Accordingly, the information presented in this report is applicable to the entire 

region. 

The 5-year studies clearly show that retiring land from irrigated agriculture results 

in numerous physical and biological benefits. Some of these include declining 

groundwater and a declining salinity and selenium in surface soils. Land 

retirement provides important habitat for a wide variety of wildlife and has the 

potential to contribute to the recovery of sensitive species. Selenium levels in 

biota from retired lands indicate that there is a low risk of contamination in this 

terrestrial environment, despite the relatively high (but declining) level of 

selenium in the system. Surface ponding of water did not occur and would not 

likely contribute to the bio-accumulation of selenium. A high number of 

agriculturally beneficial insects were found on retired lands, whereas the 

predicted increase in the abundance and diversity of agricultural pests has not 

occurred. Land retirement did not result in a decrease of selenium concentrations 

in groundwater. 

Standard restoration techniques applied to the study plots were somewhat 

successful in establishing native shrubs and a limited variety of native annual 

plants. However, in general those techniques were relatively ineffective at 

establishing a diverse community of native flora. Appropriate restoration 
Land Retirement Demonstration Project 

Five Year Report 

178 

techniques are currently being developed and recommendations will be made in 

the near future. 

The data set obtained from these studies is unique in that it describes the wildlife 

community existing on lands dominated by non-native species. No other wildlife 

studies or monitoring efforts in the central San Joaquin Valley of this duration or 

scope exist. The data provide insights into the value of land retirement and of 

habitat restoration to wildlife. The results obtained and the restoration techniques 

being developed can be applied to meet a variety of management objectives on 

large blocks of retired lands, including the recovery of threatened and endangered 

species. 

5.1. Declining Groundwater 

The water table response observed during groundwater monitoring supports the 

conceptual and numerical models that predicted a declining shallow water table in 

response to land retirement. Prior to land retirement, percolation of applied 

irrigation water was the primary source of groundwater recharge that sustained 

the high water table. Without irrigation, groundwater recharge has been greatly 

reduced and the shallow water table has steadily receded from the land surface. 

5.2. Selenium in Groundwater 

The high concentrations of salinity and selenium in the shallow groundwater 

found in Coast Range deposits at the site are a result of leaching under irrigated 

conditions and evaporation from the shallow water. Land retirement resulted in 

an increase in depth to groundwater, but did not substantially change the selenium 

concentrations in groundwater. Critical to the well being of biota is that the 

access to this contaminated groundwater is very limited because of the declining 

water table after cessation of irrigation. 

5.3. Selenium in Soil 

Soils of the predominant type at the site contain moderately elevated 

concentrations of selenium (average 1.0 mg/kg) when compared to the common 

range (0.1-1.4 mg/kg) for Western U.S. and San Joaquin Valley soils. Total 

selenium concentrations, soluble selenium concentrations, and salinity in the top 

30 cm (1 foot) of surface soil showed a decreasing trend over the 5 years of 

monitoring. The decreasing selenium and salinity trends in the surface soil 

indicate that an upflux of salt and selenium from capillary rise and evaporation of 

shallow groundwater at the soil surface is minimal. 
Chapter 5. Overview of the Implications and Concerns of 

Agricultural Land Retirement in the San Joaquin Valley 

179 

5.4. Selenium Concentrations in Biota 

A risk assessment for the biota in this terrestrial system was not an objective of 

the LRDP. However, the levels of selenium concentrations observed in extensive 

monitoring of soil, groundwater, and biota indicate a low risk to wildlife. 

Whereas high selenium levels in groundwater could present a potential risk to 

biota, the exposure pathway is limited because the depth to groundwater increased 

to greater than 2.1 m (7 feet). Mean selenium levels in biota are within the range 

typically found in biota occurring on non-seleniferous soils in the western United 

States and are generally below performance standards set for the project by the 

U.S. Fish and Wildlife Service (FWS 1999). Furthermore, selenium levels in 

biota are generally an order of magnitude less than found at Kesterson National 

Wildlife Refuge. Although the risk to wildlife from selenium exposure is limited, 

a few samples contained relatively high levels of selenium and we recommend 

that land retirement be integrated with a comprehensive selenium monitoring 

program. 

The generally low levels of selenium in biota may be a result of very little 

available water during the study period. The potential bio-availability and bioaccumulation of selenium is reduced because dry, upland environments, rather 

than aquatic or wetland environments, dominate the system. This is supported by 

the higher selenium levels that were found in common and widespread species 

collected from irrigated lands compared to those collected from non-irrigated 

lands. 

5.5. Surface Water Ponding 

Due to dry climatic and soil conditions during the study, surface water ponding 

did not last for more than 30 days at the site. Monitoring of precipitation during 

the study period suggests that the precipitation threshold to cause ponding of 

surface water is in excess of 5 cm (2 inches) of rainfall per month. The extensive 

network of dessication cracks in the Tranquillity clay soils greatly inhibits the 

formation of surface water ponds. Should surface water ponding occur during 

very wet periods, it is likely that selenium concentrations in the ponded water 

would remain below 5 parts per billion (ppb) (the aquatic life criteria) given the 

surface soil selenium concentrations. 

5.6. Wildlife Abundance, Diversity, and Recovery of 

Sensitive Species 

Results of the Habitat Restoration Study (HRS) demonstrate that retired lands 

provide habitat for a wide variety of wildlife, even in the absence of highly 

successful restoration. Over a 5-year period, we identified 101 families within 21 

orders of invertebrates, 1 species of amphibian, 4 species of reptiles, 48 species of 
Land Retirement Demonstration Project 

Five Year Report 

180 

birds, and 8 species of small mammals, 1 species of canid (coyote), 2 species of 

mustelids (skunk and long-tailed weasel), and 2 domesticated species (cat and 

dog) that utilize the Tranquillity study site. Nine species of birds used the study 

area as breeding habitat and 12 species of sensitive birds were using the study 

area. Although this is an impressive list of species, we would have expected a 

greater diversity of wildlife and a greater degree of emigration had there been 

suitable wildlife habitat in the immediate vicinity. 

The successful restoration of retired lands would provide increased vegetative 

diversity and result in an even greater diversity and abundance of wildlife. To 

maximize benefits for wildlife and to preclude retired lands from becoming 

infested with weeds and pests, appropriate habitat restoration must be conducted. 

Land uses, such as grazing and dryland farming, can be compatible with this 

effort. Creating topography, or berms, in the retired agricultural, laser-leveled 

landscape has benefits for plants and animals. 

Land retirement and restoration, if properly implemented, monitored, and 

managed, would contribute to listed plant and animal species recovery. These 

lands could provide connecting linkages and corridors between existing habitat 

areas or large areas of contiguous blocks of land that would provide habitat for 

new core populations. The recovery of threatened and endangered animal species 

does not necessarily require a fully restored San Joaquin Valley ecosystem. Many 

rare upland species seem to be dependent upon an appropriate vegetative 

structure, rather than a highly diverse, fully functional native plant community. 

Habitat for rare species may be simplified and more easily established and 

managed than a diverse, native upland plant community. A diverse, native 

ecosystem, however, will provide the numerous benefits inherent in a totally 

functional ecosystem. 

Providing the appropriate habitat for these species will require phases of 

implementation and successive management. Open spaces with low vegetation 

densities and heights are required for many listed species, while others require 

dense shrub cover. Phased restoration may or may not be immediately 

compatible with some sensitive species. Similarly, neither a single restoration 

prescription nor a single plant community would meet all species needs. 

Accordingly, a matrix of land uses, restoration strategies, plant communities, and 

management techniques is preferred. The LRDP data collected and the ongoing 

trials provide the basis for an implementation plan for the listed species recovery 

on retired agricultural lands. 

5.7. Restoration Challenges and Techniques 

Appropriate restoration must accompany land retirement or lands will largely 

become weed- and pest-infested fields. Without restoration, retired lands would 

require extensive and continuous management to reduce negative impacts to 

active agricultural practices on neighboring lands. Soil conditions that 
Chapter 5. Overview of the Implications and Concerns of 

Agricultural Land Retirement in the San Joaquin Valley 

181 

historically existed on the site were seasonally dynamic, with successive periods 

of flooding and drying. Decades of intensive agricultural use greatly affected soil 

characteristics, depleted the native plant seed bank, reduced topographic relief, 

and promoted the dominance of introduced weeds. These historic conditions 

greatly increased the challenges associated with establishing native upland plant 

communities on the study site. 

Specific challenges to successful restoration include competition from invasive 

species, lack of sufficient quantities and varieties of local native plant seed, 

inadequate seed delivery methods, and insufficient knowledge of germination, 

propagation, harvesting, and seed cleaning techniques. Inconsistent and 

inadequate precipitation affected plant survivorship and decreased restoration 

success. 

Despite the immense challenges associated with restoration of retired farmlands, 

we successfully established plant cover to stabilize soils, to provide for wildlife 

habitat, and to establish native wildlife. The establishment of native plant species 

on the site was more difficult than originally envisioned. As a result of the 

significant expenditure of effort and resources for this demonstration project, the 

information obtained provides a valuable foundation to develop practical 

restoration strategies. 

Weed suppression is the primary challenge in the restoration of these lands. 

Initially, a barley crop was planted on many portions of the demonstration project 

to control weeds and prevent soil erosion. Barley persisted for several years 

without the need to replant, but insufficient rainfall and seed production required 

some reseeding in subsequent years. Barley was excellent at controlling weeds 

and is an excellent cover crop or nurse crop, but it must be maintained. Despite 

the use of barley to help control weeds, only intensive and repeated weed 

suppression has successfully reduced weed loads and allowed natives to persist. 

These efforts have been costly and labor intensive. Numerous experimental 

techniques including herbicide use, establishing cover crops, flaming, mowing, 

discing, pre-irrigating, solarization, and manual weeding have been explored for 

weed eradication techniques. None have provided effective long-term results. 

The team is continuing research in an attempt to develop efficient techniques for 

weed control that would be applicable for large-scale land retirement. 

The observed succession of weed species as seen on the HRS plots, fallowed 

lands and reserves is tumbling saltweed (Atriplex argentea), mustards, and finally 

non-native Mediterranean grasses. The general weed succession after fallowing 

appears to start with nearly 100 percent cover of A. argentea that begins to 

decline after 4-5 years. Each year, A. argentea dies and forms a skeleton that can 

carry for miles in a stiff wind. The skeleton eventually begins to break down but 

the process can takes years and in the meantime it makes a dense cover layer of 

dead and dry vegetation. The mustards begin to grow underneath these skeletons 

in the second year; A. argentea itself does not reproduce under them. These 

continue as co-dominant plants through the third and fourth years. After four or 
Land Retirement Demonstration Project 

Five Year Report 

182 

five years, Mediterranean grasses begin to establish, ultimately becoming the 

climax community. This pattern of succession must be overcome for native plant 

restoration to be effective. 

No source of native plant seed is available in sufficient amounts to perform 

significant restoration in the San Joaquin Valley. The majority of plant species 

occurring in the targeted upland habitats are no longer found in the vicinity of the 

project site (within 80 km or 50 miles). Consequently, local ecotypes of native 

plants are largely absent or exceedingly rare and seed is extremely limited. The 

prime sources for seed have been Ecological Reserves and small, isolated 

remnants of habitat existing along roadsides. Seed from 100 species of native 

plants collected from the project vicinity were planted in the on-site native plant 

nursery. The nursery provides the seed used in the research trials and restoration 

activities. 

Information on appropriate seed delivery techniques, germination, propagation, 

harvesting, and seed cleaning techniques is non-existent or insufficient for a 

majority of the targeted native species. The seed imprinter that was used in the 

initial restoration effort proved to be less effective on heavy clay soils than other 

seed delivery techniques. Valuable information on seed production is being 

generated through research in the native plant nursery and through partnership 

with the NRCS Plant Materials Center in Lockeford, California. Numerous 

research trials have been implemented and are ongoing (Appendix 3). Through 

these trials, we are exploring a variety of techniques to address the challenges 

encountered and to expand their applications to large-scale restoration. 

Of the native species used in the work to date, the shrubs have proven to be easier 

to establish and maintain than winter and summer annuals. Shrubs survive better 

long-term against weeds, seem to be less susceptible to competition from weeds, 

and set seed better than annuals. The deep root system of established shrubs 

allows them to persist through drought conditions. Winter annuals cease to grow 

when overtopped by weeds and, without weed control, they quickly expire. Soil 

moisture is reduced by weeds causing a lack of germination in summer annuals. 

Drought exacerbates the competition between natives and weeds. Weed 

suppression will alleviate this competition for soil moisture and enhance success 

of annuals. 

The restoration of a fully functioning ecosystem is much more involved than the 

successful planting of a few native species. A simplified ecosystem will tend to 

degrade to a weedy landscape. Even in many of the Ecological Reserves where 

the ecosystem has been degraded, intensive management is required to maintain 

the native floral diversity. Successful restoration must include a high diversity of 

sustainable populations of plants and animals. 
Chapter 5. Overview of the Implications and Concerns of 

Agricultural Land Retirement in the San Joaquin Valley 

183 

5.8. Agricultural Pests 

Although there have been some instances of agricultural pest outbreaks and weeds 

which required control measures, there were no indications that the HRS lands 

supported greater pest densities than did surrounding retired and fallowed lands or 

agricultural lands. Predatory insects were common on the site, which has likely 

kept the potential for pest infestation to a minimum. Agriculturally beneficial 

species were much more common and widespread on the site, especially in 

restored areas. 

A few weed and insect pests are worthy of mention. Russian thistle is an invasive 

weed that has a high potential to become established on retired farmlands and 

adjacent agricultural fields. It is fairly widespread on the site, but has been 

present only in small patches and in low abundance. Both its distribution and 

abundance on the site decreased over the five-year study period. London rocket 

and black mustard are not generally considered agricultural pests, but they 

provide prime habitat for false chinch bugs and lygus bugs. There were two 

serious infestations of false chinch bugs. These infestations were regionally 

widespread, not restricted to the study site, and not influenced by land retirement 

or restoration activities. Lygus bugs were widespread on the study site, but they 

were not encountered in any great abundance. Few beet leafhoppers were 

observed. Predatory insects likely controlled their numbers. 

5.9. Recommendation 

Based upon the findings presented in this report and experiences gained during 

this 5-year project, the Land Retirement Team and the Endangered Species 

Recovery Program fully support land retirement. We believe that land retirement 

has the potential to solve a variety of drainage issues, including drainage 

reduction, and improved reliability of water supply. Restoration can improve the 

overall ecosystem function by improving air quality, reducing weed loads, 

creating wildlife habitat, and assisting with recovery of sensitive species. Land 

retirement is compatible with a variety of land uses including grazing, dryland 

farming, and enhanced recreational opportunities. Land retirement is expected to 

benefit adjacent farming operations by improving water quality, improving air 

quality through dust abatement, increasing abundance and diversity of 

invertebrate pollinators and predators. 

These benefits are justification for the continuation and expansion of retiring 

drainage impacted lands, continued research of restoration techniques, and 

restoration of selected parcels of retired lands in the San Joaquin Valley. 

The project objectives and associated performance criteria established by the 

USFWS have been met. Many of these criteria were based upon the premise that 

if met, retired lands could qualify for consideration of inclusion in the federal 

National Wildlife Refuge system. The retired lands at Tranquillity and Atwell 
Land Retirement Demonstration Project 

Five Year Report 

184 

Island clearly meet the established criteria. The BLM recognized the potential 

value of the Atwell Island site and manages and restores the retired agricultural 

lands to meet wildlife values, including those of sensitive species. The Land 

Retirement Team and the Endangered Species Recovery program encourage the 

FWS to consider acquiring and managing the Tranquilllity site in a similar 

manner. 
Appendix 1. CVPIA Land Retirement 

Program Chronology 

Appendix 1-1 

Appendix 1. CVPIA Land Retirement 

Program Chronology 

by Beatrice A. Olsen 

Introduction 

This appendix provides an overview of the activities undertaken by the CVPIA 

Land Retirement Team (LRT) and the Endangered Species Recovery Program 

(ESRP) during the course of the Land Retirement Demonstration Project (LRDP) 

1996-2005. Topics are presented in the calendar year they occurred. Some 

activities were repeated annually and are only briefly noted in Appendix 1. 

Appendix 3 contains more details of research and site activities that may only be 

mentioned in Appendix 1. 

For each year included in this chronology, five sub-sections are described (except 

for 1996). Program Administration deals with personnel, key meetings, laws, 

planning, and documentation. Land Acquisition lists actions involved in retiring 

drainage impacted lands. Research and Monitoring lists actions related to the 

measurements of physical and biological impacts due to land retirement. The 

Restoration and Site Management sub-section describes and lists actions debated, 

planned, or taken on the Tranquillity and Atwell Island Demonstration site lands. 

Throughout the course of the project, members of the Land Retirement Team and 

Endangered Species Recovery Program staff have participated in, or taken the 

lead on, a variety of outreach activities. The final subsection for each year is a 

listing of these activities. 

Year 1996 Accomplishments 

Program Administration 

In this year, the Bureau of Reclamation (Reclamation), Fish and Wildlife Service 

(FWS) and Bureau of Land Management (BLM) agreed to cooperatively 

accomplish the Land Retirement Program (LRP) authorized by the Central Valley 

Project Improvement Act (CVPIA) enacted by Congress in 1992 as Public Law 

102-575. The LRP Office was established in Reclamation’s South-Central 

California Area Office in Fresno. Robert May was hired as the Program Manager. 

The Fish and Wildlife Service (FWS) Land Retirement Team representative John 

Castellanos started working for James McKevitt in Sacramento. The Bureau of 

Land Management (BLM) team member Tracy Rowland reported for duty. A 

CVPIA Land Retirement Reclamation/FWS Monthly Coordination Meeting was 

established to discuss the program status and coordination between Reclamation 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 1-2 

and FWS. The Interim Program Guidelines drafted with Reclamation, BLM, FWS 

and DWR and state agencies, water districts, environmental groups, farmers, and 

academic representatives. 

Outreach 

Public information meetings were held in January 1996 to explain the program. 

The Draft Interim Program Guidelines released to public. Co-written with 

Department of Water Resources, they were mailed to water districts, farmers, 

federal and state agencies, county governments, and other interested parties. 

Year 1997 Accomplishments 

Program Administration 

The Reclamation team member hydrologist Stephen Lee reported for duty, as did 

the FWS team member Bea Olsen, who replaced the representative from the 

Sacramento FWS office. 

The Interim Guidelines and Selection Criteria were revised to add selenium ppm 

in soil criteria. A Memorandum of Understanding (MOU) between Westlands 

Water District (WWD) and Department of the Interior (DOI) was drafted 

regarding LRP partnership for program implementation. A DOI MOU was drafted 

that defined roles, responsibilities and implementation procedures for LRP. 

Regional and State Directors for Reclamation, FWS, and BLM signed the MOU 

for three agencies to implement and manage CVPIA Land Retirement Program. A 

third MOU between federal, state, and local agencies was drafted that outlined the 

shared vision and solidified support for the land retirement program. 

The National Environmental Policy Act (NEPA) strategy defined the Prepared 

Scope of Work for a NEPA contract bid request. A Scope of Work was prepared 

and the contracting process was begun to acquire the services of a consulting firm 

to prepare an environmental assessment (EA) for the acquisition of selected 

parcels. Applications for parcels by Sumner-Peck were dropped due to the 

Settlement Agreement for the Sumner-Peck lawsuit. 

A CALFED grant proposal was submitted for the Panoche Creek Riparian Habitat 

and Flood Control corridor project, which seeks to retire farmlands along a creek 

channel and to reestablish a meander zone for the stream. This widening and 

restructuring of the stream channel should reduce flooding and lessen the 

transport of contaminants, such as selenium, to the San Joaquin River. 

Land Acquisition 

The generalized criteria to address drainage, fish and wildlife enhancement, and 

acquisition of water for other purposes of CVPIA and select parcels for 

acquisition was developed by an interagency, multi-disciplinary team of both state 

and federal representatives. DOI began to solicit offers for voluntary land 

retirement from willing sellers within the eligible area. The LRT received 80 
Appendix 1. CVPIA Land Retirement 

Program Chronology 

Appendix 1-3 

applications starting in 1997 and by September 2002 had approximately 22,258 

hectares [ha] (55,000 acres). Applications were accepted on a continuous basis. 

Selections for first round of program totaled 5,108 ha (12,623 acres). Landowner 

applicants were notified of their status within 60 days, in conformance with the 

Interim Guidelines. 

A coordinated appraisal process was performed by Reclamation and title and 

escrow services obtained. Preliminary title reports were requested for selected 

parcels. A coordinated assignment of one regional DOI solicitor to review title 

reports, deeds, etc. for all three agencies’ acquisitions was obtained. A series of 

meetings with applicants was held to explain process and timelines. The first 

appraisal scheduled. 

Bids for hazmat surveys were taken and a contract awarded to BSK. The 

contractor also provided recommendations for cleanup of any such materials. A 

pre-work meeting with hazmat contractor was held and progress monitored. The 

Hazmat Environmental Site Assessment reports were completed for selected 

properties. Pre-work meetings with hazmat contractor were held and progress 

was monitored. Hazmat Environmental Site Assessment reports were completed 

for selected properties. 

Research and Monitoring 

UC Davis was contracted to perform a groundwater model study on Panoche Fan 

area. The Hydrologic Model of Land Retirement: Panoche Water District (UC 

Davis and D. Perkey Model) was completed. 

A 5-year Demonstration Project at Tranquillity and Atwell Island Water District 

was initiated to determine LRP Selection Criteria effectiveness, evaluate physical 

effects of retiring land, and develop effective and economic methods to 

rehabilitate retired lands to suitable upland wildlife habitat. The demonstration 

program would track progress, assess actual results and provide a means to 

determine future land retirement needs and identify actions needed to accomplish 

long-term land retirement objectives. 

Restoration and Site Management 

Parcels submitted in drainage impacted areas were field reviewed for best 

matches to the Interim Guidelines Criteria. 

Outreach 

Public information meetings were held to present Interim Guidelines. 

Advertisements were published in major newspapers, water and drainage district 

newsletters, and agricultural publications throughout the project area, which led to 

receipt of 31 applications, covering approximately 10,927 ha (27,000 acres). 

LRP presentations were given to Westside Resource Conservation District, Fresno 

Co. Public Works and Development Services Director and staff, and separately to 

County Supervisors in Fresno, Tulare, and Kings Counties. Additional LRP 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 1-4 

presentations were given to LR subcommittee for San Joaquin Valley Drainage 

Implementation Plan, at an Open Houses for FWS Draft Recovery Plan for 

Upland Species in San Joaquin Valley and to the Region IV Director, California 

Department of Fish and Game. 

Year 1998 Accomplishments 

Program Administration 

The Environmental Assessment for 526 ha (1,300 acres) of a Land Retirement 

Demonstration Project and a Draft Demonstration Study Plan were completed. 

A scope of work was prepared and the contracting process begun to acquire the 

services of a consulting firm to prepare a programmatic environmental assessment 

for the land retirement program. The focus was the federal CVP service area on 

the western side of the San Joaquin Valley from the Sacramento-San Joaquin 

Delta on the north to the Tehachapi Mountains south of Bakersfield. A contractor 

was selected to prepare a Programmatic Environmental Assessment of the CVPIA 

Land Retirement Program. The Federal Register Notice of Intent (NOI) to 

prepare a Programmatic Environmental Assessment of the CVPIA Land 

Retirement Program, Vol. 63, No. 25/ Friday, February 6, 1998 was listed. A 

Internal Draft Programmatic Environmental Assessment was completed. 

A Finding of No Significant Impact was signed for the Demonstration Project 

which included an agreement DOI made with WWD for the District to participate 

in the LRP. Terms of the cooperative agreement allowed the first 6,070 ha 

(15,000 acres) in WWD to be retired under the agreement. The amount paid 

would be fair market value, absent any appreciation due to the availability of 

Project water; WWD would pay the difference between that value and the full fair 

market value of the land up to $1,150 per acre. WWD would be permitted to 

reallocate the CVP water to which the retired lands are entitled to other lands in 

the District, provided that they do not lie within the designated drainage-impacted 

region of the District. Finally, DOI would apply for an allocation from the 

District supplemental water supply to use in establishing vegetation on retired 

lands for upland habitat. 

A Feasibility Study for Panoche-Silver Creek Corridor Project was begun. The 

Panoche- Silver Creek Corridor Project had the contractor analyze the feasibility 

and cost of developing a riparian habitat and flood control corridor using retired 

agricultural lands in the vicinity of Panoche Creek. At an option to the 

government, all NEPA scoping activities could be performed and an 

environmental assessment prepared. 

Land Acquisition 

Preliminary Title Reports were requested for 5,084 ha (12,563 acres) of drainageimpaired irrigated agricultural land for potential acquisition under the Land 

Retirement Program as outlined in the Interim Guidelines. From work that was 
Appendix 1. CVPIA Land Retirement 

Program Chronology 

Appendix 1-5 

accomplished during 1997, appraisals on these acres were conducted for potential 

acquisition. Appraisals would determine the fair market value of these properties 

and establish the basis of negotiation and/or acquisition of the properties. Lands 

for acquisition under the Land Retirement Program were identified. More lands 

were available to be purchased and retired than funds would allow. A contractor 

conducted HAZMAT site-specific environmental compliance assessments on all 

properties prior to close of escrow. 

Research and Monitoring 

For the Westside San Joaquin Valley Groundwater Flow Model, a selected 

contractor utilized the groundwater flow model developed by Belitz and others to 

evaluate changes in groundwater flow due to land retirement in the central part of 

the western San Joaquin Valley, California. 

At the University of California, Davis, researchers developed for a Water and 

Land Management Economic Study integrated hydrologic, soils, agricultural, and 

economic models for the area surrounding Firebaugh, California. The models 

quantified the economic, environmental, and social impacts of reductions in 

permanent surface water supply, reductions in lands irrigated, and reductions in 

selenium discharged from agricultural drainage in the study area. 

A Groundwater Model (WESTSIM) developed by Reclamation modelers in 

Sacramento provided valuable information about the benefits and measurements 

of success of the program. This model provided a monitoring tool for sub-surface 

drainage reduction effects and potential groundwater table reduction. 

The research design for monitoring biota on twenty 16 ha (40 acre) plots in the 

Demonstration Project in Fresno County was discussed with the Endangered 

Species Recovery Program Office, who will perform the research with CVPIA 

funds. ESRP performed Baseline Biological Survey on Demonstration Project 

lands in Fresno County. A Report of the Baseline Biological Survey was 

submitted to the LRT (See Appendix 2, 1999 Baseline Survey). 

Groundwater monitoring was instituted in 1998 to detect the subsurface level of 

water and test the hypothesis that the water level would decline in the absence of 

surface watering (i.e., the irrigation of crops). Monitoring entailed collecting 

samples from 27 wells and sumps on the Tranquillity site. 

Restoration and Site Management 

Restoration funds were requested to start the conversion of the retired irrigated 

lands to suitable wildlife habitat. Lands were worked up and uniformly planted to 

a barley cover crop on approximately 493 ha (1,220 ac) at the Tranquillity site. 

This planting was done in the hopes of establishing relatively homogenous 

conditions for the Habitat Restoration Study (HRS) plots and to control weeds. 

ESRP contacted Ted St. John to discuss and demonstrate an imprinter and use of 

mychorriza. 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 1-6 

Outreach 

Public meetings were held to scope concerns regarding the Programmatic EA of 

the CVPIA Land Retirement Program. The LRT attended San Joaquin Valley 

Drainage Program Committee Meetings on Land Retirement. 

Year 1999 Accomplishments 

Program Accomplishments 

A contractor was selected for preparation of a Programmatic EA of the CVPIA 

Land Retirement Program. The Expanded Demonstration Project Environmental 

Assessment for the 6,070 ha (15,000 acres) Expanded Demonstration Project area 

was completed. A Finding of No Significant Impact (FONSI) was signed by 

Reclamation, FWS, and BLM. A Biological Opinion as part of Formal Section 7 

Consultation for the CVPIA Land Retirement Program Demonstration Project 

was received. 

A notice was received from Fresno Agricultural Commissioner that sugar beets 

had to be controlled on 97 ha (240 acres) of LRDP lands. 

Land Acquisition 

The first appraisal was completed and the first parcel for the Demonstration 

Project (148 ha or 366 acres) acquired. A total of 666 ha (1,646 acres) in Fresno 

County was completed in FY 1999. Two appraisals in WWD were updated. 

About 24 ha (60 acres) of land were purchased from the WWD within the existing 

demonstration project area. Completed appraisals for purchase of 3,238 ha (8,000 

acres) in Atwell Island WD (Tulare Lake Basin sub-area) were done. Phase 1 

Environmental Site Assessments for approximately 2,428 ha (6,000 acres) of 

agricultural properties were done. The Assessments were completed in 

conformance with ASTM Standard E 1527-97 and Departmental Policy. 

Incoming applications continued to be evaluated and land acquired from a pool of 

applicants previously received. 

Research and Monitoring 

The Feasibility Study for the Panoche-Silver Creek Corridor Project was 

completed. The project proved to be too costly to provide significant flood control 

benefits without partnerships from other federal, state, or local partners. The U.S. 

Army Corps of Engineers (Corps) was identified as appropriate lead agency, but 

LRP may be a partner if project is ever implemented. 

ESRP implemented the HRS on 324 ha (800 acres) of the 846 ha (2,090 acres) 

acquired in Fresno County (See Appendix 3.). The imprinter was built in Dos 

Palos. Surface manipulations were done to form berms. ESRP used seed 

collections and plant propagation on established plots and planted sterile barley to 

control weeds. A reference site was identified near the railroad in Firebaugh that 

is owned by Contra Costa Irrigation District has lots of iodine bush on it. Stuart 
Appendix 1. CVPIA Land Retirement 

Program Chronology 

Appendix 1-7 

Hurlbert, statistician from San Diego State, reviewed the research design for the 

HRS. Soil scientists from UC Davis (Dr. Victor Claassen and David Kelley) and 

the Natural Resources Conservation Service (NRCS) (Kerry Arroues) visited the 

site to discuss soils and reference sites. 

Weather data was collected by the California Irrigation Management System 

(CIMIS) weather station #105 located approximately 2.5 km (1.5 mi) west of the 

Tranquillity site and summarized in the final reports for each year. Data collected 

and summarized included precipitation, temperature, wind, and relative humidity. 

The completed Quality Assurance Plan was implemented to monitor soil, 

groundwater, and surface water at the demonstration project site. A well network 

was installed to monitor groundwater levels and groundwater quality. 

Groundwater quality testing occurred on a quarterly basis during the first year of 

monitoring and annually thereafter. The initial surveys conducted in September 

and October of 1999 established baseline values for soil chemistry including 

salinity, selenium, boron, nitrate, pH, and major anions, cations, and nutrients. 

Unfiltered groundwater samples were analyzed for major ions, trace elements, 

isotopes, electrical conductivity, pH, temperature, and turbidity. Soil samples to 

establish baseline soil chemistry for demonstration project lands were collected. 

The completed groundwater modeling study of various land retirement scenarios 

within the WWD will aid future land retirement planning within WWD. 

Restoration and Site Management 

Plugs of native species were grown and transplanted into “shrub islands.” The 

tillage question about not disturbing mycorrhizal development in buffers was 

discussed. Approximately 24 ha (60 ac) of the Tranquillity site was planted in 

safflower by the California Department of Fish and Game provided for an annual 

dove hunt. 22 hunters harvested 91 mourning doves (Zenaida macroura). 

Outreach 

1999 Partnerships were explored between the California State University system, 

local school districts, local tribal groups, and the proposed Central Valley 

Regional Historical Museum in Fresno, California, for the Tulare Lake artifacts 

and historical farm equipment held by sellers. 

Year 2000 Accomplishments 

Program Administration 

The first Annual Monitoring Report on the Demonstration Project measuring 

physical and biological impacts from land retirement was published and 

distributed, as requested in the 1999 Biological Opinion. 

An Interagency Agreement between Reclamation and BLM was developed that 

would allow BLM to directly acquire approximately 3,238 ha (8,000 acres) in the 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 1-8 

Atwell Island study area that they manage. This 5-year agreement was for 

approximately $12 million, most of which was for land acquisition. 

Land Acquisition 

1,071 ha (2,646 acres) were acquired in the Atwell Island project area: 639 ha 

(1,578.48 acres) in Tulare County and 432 ha (1,067.5 acres) in Kings County, of 

which 184 ha (455 acres) were paid for by Central Valley Project Conservation 

Program. 

Phase 1 Environmental Site Assessments were completed for approximately 2,428 

ha (6,000 acres) of agricultural properties. The Assessments were completed in 

conformance with ASTM Standard E 1527-97 and Departmental Policy. 

Environmental Site assessments will be conducted on all properties purchased for 

land retirement prior to closure of escrow. 

Appraisals for parcels in WWD were conducted by DOI-qualified appraisers to 

determine the fair market value of additional properties to be acquired and to 

establish the basis of negotiation and/or acquisition of the properties. Land 

acquisitions required the services of a title company and escrow to be opened 

prior to county recording of deeds and title processing. 

Processing case files of acquired lands in accordance with federal land acquisition 

standards included locating properties utilizing all available survey records and 

markers and creating Geographic Information System (GIS) databases and maps. 

Research and Monitoring 

Some 32 biotic surveys were conducted each year on the Tranquillity site. The 

majority of surveys were specific to the HRS plots; however, a number of sitewide surveys were also conducted (See Appendix 3). Trials installed included 

imprinting vs. Drilling of Native Seeds Trial in the fall of 2000 (See Appendix 3). 

ESRP was to set up data management of the photo points and other photos and 

provide LRT copies. 

Monitoring wells were installed at the Atwell Island Demonstration Site to 

measure groundwater response as part of the Land Retirement Demonstration 

Project. Groundwater, surface water, and soil samples were collected and 

analyzed for constituents of concern as part of the Land Retirement 

Demonstration Project. The results were shown and discussed in the annual 

monitoring report. As with the monitoring of physical impacts at the Tranquillity 

site, data collected at the Atwell Island site were used to determine the effects, if 

any, of selenium on biota. The groundwater modeling study of various land 

retirement scenarios continued. 

Restoration and Site Management 

The small-scale imprinting and berm trial was installed at Tranquillity. Applying 

adaptive management, those techniques which appeared to be best suited for 

conditions at the Tranquillity site were adopted for the HRS. Additional trials 
Appendix 1. CVPIA Land Retirement 

Program Chronology 

Appendix 1-9 

established tested Native Species, Cover Crops, and Mycorrhiza (See 

Appendix 3). Additionally, seed collecting at sites having remnant populations of 

native plants was initiated on a small scale (See Appendix 3). HRS plots at the 

Atwell Island site were established. Initial restoration efforts on more than 200 

acres began. 

The discussion of mowing techniques for HRS plots suggested that a strip down 

the center should be utilized instead of a circular pattern that would drive fauna to 

the center of the field. 8 ha (20 acres) of clover from the buffer area were offered 

to be harvested by neighbor to be used on idle land nearby. Discussions were 

held on the effects this could have on the buffers. Mowing would not impact 

much because the buffers were dried up already and mowing would act to remove 

another weed seed producer from the buffer. A field meeting with LRT, Karen, 

and Michelle resulted in agreement to mow Atriplex in buffer only (not plots) so 

that it does not spread tremendous numbers of seed over site. Consensus was that 

buffer areas need to be as weed free as possible to maintain the separation of 

experimental units and for aesthetic reasons—weedy areas look terrible to 

neighbors right now. 

A meeting to discuss the serious weed problem at Tranquillity was held with 

Mike Williams of UCSB, Patrick Kelly, Michelle Selmon, and Woody Moise 

about serious weed problem. Sterile barley was found to reproduce and displayed 

recruitment of 50-75 percent cover in the plots. Weeds, such as Sisymbrium irio 

and Senecio vulgare, grew fast and threatened to swamp sprouting native seed. 

Native seed that sprouted 2.5-5 cm (1-2 inches) under the barley and London 

rocket did not do well unless the barley and weeds were controlled. All possible 

solutions, weed-eater, sheep, fire, aerial herbicide, or mowers, have problems. 

Discussion of watering plots at Tranquillity and further plug planting of Atriplex 

and Isocoma. The thick cover of weeds, including sugar beets, was a problem. 

The suggestion was to disk areas slotted for a grass nursery where London rocket 

was seeding. Repeated disking was recommended to eliminate the weed seed 

base prior to restoration. The native grasses would be imprinted in the fall and a 

broadleaf herbicide used the next spring. 

An unauthorized spraying at the Tranquillity site was experienced, most likely 

from the mosquito abatement district spraying. What the county’s abatement 

program schedules are for the area needs to be known, as it affects personnel and 

experiments. This leads to talk of having research signs for the project site. 

The Baseline Biological Surveys were scheduled for Atwell Island site. A field 

meeting with Michelle and Karen of ESRP, Bea and Larry Saslaw of BLM 

located HRS plots at Atwell Island. 

First observation of false chinch bugs at site. “Brown stuff” noted that is sticky 

and appears shiny. Robust native plants were significantly affected. The “Lowtill” situation may or may not have contributed to insect troubles, since false 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 1-10 

chinch bugs are drawn to those areas in addition to being attracted to stressed, thin 

stands of barley and mustard species. 

To maintain the integrity and consistency of the buffer, mowing of the annual 

Atriplex on about 101 ha (250 acres) was warranted. It was agreed to disk weeds 

prior to the fall planting. The barley in the 243 ha (600 acres) of buffers 

surrounding the HRS plots was thrashed and surface disked. Barley was reseeded 

where necessary. A hedgerow with low berms constructed along the edges of the 

seeded area to allow for flood irrigation was installed and planted with 11 native 

species. A previous marsh area was seeded at Tranquillity on 3.2 ha (8 ac) of 

LRDP land where a seasonal wetland had been created by agricultural runoff 

(See Appendix 3). Some native seed was collected. Despite rain delays, 65 ha 

(160 acres) were planted in Tranquillity with berms constructed in a more or less 

random configuration (See Appendix 3). 

Outreach 

Partnerships were explored between the California State University system, local 

school districts, local tribal groups, and the proposed Central Valley Regional 

Historical Museum in Fresno, California. 

Plant ID handout for tours and others working in restoration was discussed. 

A Juvenile Dove Hunt had 45 hunters (quota was 50) on 24 ha (60 ac) of the 

Tranquillity site planted in safflower by the California Department of Fish and 

Game. 

The LRT, in cooperation with FWS, staffed a booth at the Tulare County Farm 

Show which promoted the LRP and agricultural water incentive programs and 

SJV National Wildlife Refuges. Presentations were given by LRT, ESRP, and 

BLM to The Wildlife Society Western Section Conference in Visalia, California. 

A spring tour of the Fresno County site was given for a variety of stakeholders. 

Presentations were given at Kings County Farm Bureau and Westside Resource 

Conservation District Board of Directors. 

Year 2001 Accomplishments 

Program Administration 

The 5-year Interagency Agreement between Reclamation and BLM began 

implementation to allow BLM to directly acquire approximately 3,238 ha (8,000 

acres) in the Atwell Island study area. 

John DiGregoria from Bitterroot Restoration worked on a CalFed project that 

would use Tranquillity to out-plant targeted species at sites in the SJV. Need to 

decide if want to let them use LRDP lands for some 9.1 m X 9.1 m (30 feet X 30 

feet) plots. The grant did not go forward. 
Appendix 1. CVPIA Land Retirement 

Program Chronology 

Appendix 1-11 

A request was received from Sacramento FWS Environmental Contaminants 

Division too late to look for bird eggs (blackbirds) for sampling for selenium. 

Perhaps a sample earlier in season can be done the next year by FWS, as ESRP 

does not have collecting permits for migratory bird eggs. The possibility was 

discussed of taking aerial photos to help define risks associated with water 

standing 30 days or greater, as identified in the Biological Opinion. 

The second annual Land Retirement Demonstration Project Report documenting 

results of physical and biological monitoring programs, and adaptive management 

of retired lands was published and posted on the Reclamation website. 

Land Acquisition 

In Atwell Island Water District, 559.4 ha (1,382.22 acres) of land and associated 

water were acquired from willing sellers. A total of 1,630 ha (4,028.20 acres) was 

acquired to date. 862 ha (2,129.88 acres) were in escrow. In Fresno County, 180 

ha (444 acres) (the North Avenue Parcel) was acquired. 

For 160 parcels of land totaling 1,421 ha (3,512 acres) in the Atwell Island Water 

District, Phase II Environmental Site Assessments were completed. The Site 

Assessments directed sellers to address all recognized environmental conditions 

(RECs) prior to transfer of property. The LRT coordinated with appropriate 

regulatory agencies to confirm satisfactory mitigation of RECs prior to property 

transfer. The properties were thus transferred in a clean, safe, and satisfactory 

condition. 

Research and Monitoring 

Ancillary restoration studies at Tranquillity were initiated. Pitfall traps resulted in 

the first shrews and first herp, a western toad. The Imprinting vs. Drilling of 

Native Seeds trial, designed to investigate planting methods that require a 

minimal amount of ground preparation, had the vegetation sampled. Vegetation 

monitoring of the 100 “shrub islands” planted on the western and northern edges 

of the restoration area. Various habitat rehabilitation techniques were tested and 

monitored for adapting management actions on all retired lands. A reference site 

on vacant fields on a willing private landowner’s property was found that may 

provide answers to many of the management and scientific questions raised at the 

Demonstration Project sites. These activities are discussed in more detail in 

Appendix 3. 

Continued monitoring occurred of groundwater levels and groundwater quality in 

accordance with the Quality Assurance Project Plan at the Fresno site. 

Conceptual plans for monitoring groundwater and soils at the Atwell Island site 

were developed. Nitrate and carbonate testing were done at the Atwell Island site 

as had been done for the Fresno site. The irrigation system at the Atwell Island 

site was evaluated for its existing infrastructure; that evaluation provided a basis 

for future management decisions regarding supplemental irrigation applications 

for habitat restoration and land management activities. 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 1-12 

Restoration and Site Management 

At Atwell Island, harvesting of barley buffers was discussed and discouraged due 

to harvest conflicts with birds fledging. Meetings were held to discuss restoration 

activities, HRS plots, baseline surveys, and water purchase and delivery from 

Alpaugh ID. BLM planted 81 ha (200 acres) with a native mix purchased from 

S&S Seed. Atwell Island HRS plots initiated. Additionally, BLM planted 136 ha 

(335 acres) of safflower and hedgerow borders. BLM and LRT worked with the 

California Department of Corrections to mitigate prison fences with habitat work 

at Atwell Island. California Conservation Corps were contracted to set up pitfall 

arrays at Atwell Island in the HRS plots. 

Water use from WWD and the Environmental Water Account (EWA) discussed. 

It is unclear what happens to water turned back that is put in the EWA. 

ESRP got approval from landowners to do seed collection. Sites include railroad 

right-of-ways, golf course along Hwy 180 and CDFG Natural Areas at Alkali 

Sink and Kerman Flats Ecological Reserves. Sugar beets were hand weeded from 

HRS plots after the Agriculture Commissioner sent a second-year notification. 

The Second Annual Report was published and sent to various divisions within the 

FWS per the Biological Opinion reporting requirement. 

Outreach 

ESRP gave a paper on the results to date of the Demonstration Project at the 

Western Section Conference on Restoration Ecology sponsored by the Wildlife 

Society in Sacramento, California. A lecture was given to biology students and 

faculty at California State University, Stanislaus, as part of a symposium series. 

Two presentations were given at the Society for Ecological Restoration, 

California Chapter, at a conference held in San Diego, California. 

The Land Retirement Team gave an annual site tour to interested agency 

personnel and private parties in spring. The LRT gave a poster session on the 

Demonstration Project at the DOI Conference on the Environment in 

Albuquerque, New Mexico. The LRT spoke with the Kings County Farm Bureau 

and Westside Resource Conservation District Board of Directors about the 

program and the Demonstration Project. The LRT helped exhibit displays of SJV 

native plants and land retirement at the Tulare County Farm Show. The LRT gave 

a PowerPoint presentation of the LRDP to the Westlands Resource Conservation 

District. LRT attended a one-day workshop on restoration techniques sponsored 

by the BLM given by Craig Dremann of The Reveg EdgeTM at the Kern National 

Wildlife Refuge. A LRT staff member attended the Central Valley Birding 

Symposium. A presentation was given by LRT, ESRP and BLM to The Wildlife 

Society Western Section Conference in Visalia, California. A LRT staff member 

attended the Central Valley Birding Symposium. Land Retirement Team staff 

attended the national conference of The Wildlife Society held in Reno, Nevada. A 

LRT staff member attended the Point Reyes Bird Observatory Landbird 

Monitoring Training Workshop. 
Appendix 1. CVPIA Land Retirement 

Program Chronology 

Appendix 1-13 

During the summer, BLM cooperated with the California Department of Fish and 

Game (CDFG) and planted 24 ha (60 acres) of safflower and 4 ha (10 acres) of 

barley at the Atwell Island site. A lack of spring rain resulted in poor seed 

production such that only 13 dove were harvested by 27 hunters. At the 

Tranquillity site, the annual dove hunt had 35 hunters who harvested 213 

mourning doves on the 24 ha (60 acres) of safflower planted by the CDFG. 

Year 2002 Accomplishments 

Program Administration 

ESRP obtains permission from California Fish and Game to move a storage 

container and any other equipment or supplies to the Mendota Wildlife Area. This 

should help with controlling vandalism. 

The third annual Land Retirement Demonstration Project Report documenting 

results of physical and biological monitoring programs and adaptive management 

of retired lands is published and posted on Reclamation’s website. 

Land Acquisition 

At Atwell Island 559 ha (1,382.22 acres) of land and associated water from 

willing sellers is acquired. Late in the year 862 ha (2,130 acres) were acquired. 

The total acreage acquired to date in Atwell Island: 2,492 ha (6,158 acres). 

In Fresno County 180 ha (444 acres) (North Avenue Parcel) was acquired. 

Research and Monitoring 

More ancillary trials to learn about alternate planting methods, native seed mixes, 

and cover crops were established. An Atriplex spinifera Planting Trial was 

installed and monitored in April, July, and December 2002, May 2003, and 

January 2004. A Berm and Mycorrhiza Trial was developed to investigate 

methods of enhancing topography and of facilitating recovery of the soil’s 

mycorrhizal communities. 

Annual monitoring activities at both sites occurred on the HRS plots and various 

habitat rehabilitation techniques were tested, results monitored and management 

actions adapted on all retired lands. All data collected for the study from 1999 to 

2002 has been entered into databases, proofed and edited, and have been 

statistically analyzed. 

As with the monitoring of physical impacts at the Tranquillity site, data were 

collected at the Atwell Island site to determine the potential negative effects of 

selenium, and other naturally occurring elements, on the site’s biota. Baseline 

soil monitoring was initiated in 2002 at Atwell Island and comprised 432 samples. 

The groundwater levels and groundwater quality in Fresno continued to be 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 1-14 

monitored in accordance with the Quality Assurance Project Plan at the 

Westlands Demonstration Project site. Soil monitoring included re-sampling of 

all deep borings and a partial sampling of shallow sites where selenium 

concentrations were found to be highest in 1999. Results to date indicate a 

declining shallow water table in response to land retirement. 

An annual bird count was conducted at Atwell Island on December 16, 2002. 

Participants helping with this effort included personnel from BLM, ESRP, and 

volunteers. Data compiled during this survey was intended for the National 

Audubon Society Christmas Bird Count (CBC), which is an annual survey 

conducted simultaneously in the Western Hemisphere during December (early 

winter). A total of 96 species were observed and 11,381 individuals were 

recorded. Thirteen participants equaling 29 party hours were dedicated to this 

survey. 

ESRP conducted a baseline survey of the “North Avenue Property” (formerly, the 

Bell Property), an approximately 162 ha (400 acre) parcel that was added to the 

LRDP property in 2001. 

Restoration and Site Management 

BLM planted 136 (335 acres) safflower and hedgerow borders. 

A fire occurred at Tranquillity site. Seed collecting was amplified in 2002-2003 

Growing Season (See Appendix 3). 

Outreach 

The annual dove hunt, in which 43 hunters harvested 128 mourning doves, was 

held on the 24 ha (60 acres) of the Tranquillity site planted in safflower by the 

California Department of Fish and Game. 

ESRP staff member attended the Partners in Flight Conference in March 2002 and 

presented information on avian responses to restoration in a poster. ESRP 

personnel and senior staff attended The Wildlife Society’s Western Sections 

annual conference held in Visalia, California. Senior staff presented information 

and progress regarding the LRDP project. Another report also was presented at 

this conference on ornate shrews that included information derived from the 

LRDP project. Two articles were featured in the Central Valley Bird Club 

Bulletin submitted by an ESRP staff member. Two ESRP senior staff members 

presented papers on restoration of retired farmlands at a joint Ecological Society 

of America and Society for Ecological Restoration conference held in Tucson, 

Arizona. 

The LRT and BLM gave a presentation on Atwell Island project accomplishments 

for BLM State Office Staff. BLM gave a talk on Atwell Island project for the 
Appendix 1. CVPIA Land Retirement 

Program Chronology 

Appendix 1-15 

Tulare County Audubon Society. A tour of the Atwell Island project was given to 

a group from The Wildlife Society Western Section. 

Year 2003 Accomplishments 

Program Administration 

Requests for restoration costs from San Luis Drainage Feature Re-evaluation 

coordinator Mike Delamore were developed. 

Sign design for Research Site Land Retirement Demonstration Project was 

suggested. A Fire Plan for Tranquillity site was submitted to California 

Department of Forestry. Due to increased costs and logistical complications, BLM 

took over from ESRP all monitoring and management at Atwell Island site. 

Harry McQuillen from FWS meets with WWD, BLM, Reclamation, and the I-5 

Corridor Committee. 

The third Land Retirement Demonstration Project Report was published 

documenting results of physical and biological monitoring programs, and adaptive 

management of retired lands. An electronic copy of this report was posted to 

Reclamation’s website. 

Land Acquisition 

In Atwell Island, 862 ha (2,130 acres) of land and associated water were acquired. 

Total BLM acres acquired now totals 2,492 ha (6,158 acres). 

Research and Monitoring 

LRT and ESRP gave a presentation to the FWS Environmental Contaminants 

Division regarding the potential biological effects of land retirement and 

selenium. The reaction from Dr. Joe Skorupa was that land retirement “is not the 

loaded gun” FWS envisioned, but that the high concentrations in the groundwater 

warranted further monitoring (Joe Skorupa). 

At Tranquillity site, the Pre-irrigation Trial was imprinted, as were the Herbicide 

and Growth Form Trials, and Burn Plots to examine the effectiveness of mowing 

as a pre-treatment and of imprinting induced disturbance following burning for 

restoration in Bromus madritensis dominated habitats (See Appendix 3). 

Three soil samples were taken from near the center of each of the 48 0.8 ha (2 

acre) research plots and groundwater monitored at Atwell Island. The Christmas 

count at Atwell Island had 79 censured bird species. Hedgerows were responsible 

for increases in species (20 to 27) and from 956 to 1,709 individuals from 

previous year. A major population of Horned Lizards and San Joaquin Valley 

Coachwip was discovered at Atwell Island. 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 1-16 

Restoration and Site Management 

Improvements were finalized by ESRP to the imprinter so that smaller amounts of 

seed could be run in the hopper. Study plots for burn, mowing, and 

herbicide/growth form trials (16 0.2 ha [1⁄2 acre] plots) were installed (See 

Appendix 3). 

Quail Unlimited installed a guzzler at Tranquillity in area used for dove hunt. A 

trespass in the North Avenue Parcel occurred due to mismanagement of 

neighbor’s irrigation pond that overflowed and wetted about 0.49 ha (1.2 acres) of 

LRT land. They also rutted up the road with heavy equipment. Hedgerows were 

hand-seeded. Fencing was installed at the nursery to prevent annual Atriplex from 

blowing in and to discourage trespass sheep. On the south side of the nursery, 

donated 3.8 liter (1 gallon) pots of alkali sacaton grass were planted. Barley had to 

be re-bagged at Mendota to be put in mouse-proof container. Large-scale 

restoration of 32 ha (80 acres) Manning Avenue Restoration was attempted. 

The Tranquillity Native Seed Nursery (1.6 ha [4 acres], with an additional 0.8 ha 

[2 acres] being managed for future planting) was moved to a site on better soil 

and nearer a more convenient water supply. Research on seed delivery, plant 

propagation, and seed production methods was conducted on 34 different San 

Joaquin Valley locally collected native plant species. Five species show a high 

potential for mechanized production and harvest. Historical records for particular 

species were investigated from primarily herbarium specimens and site-searches 

initiated. Historical records for particular species were investigated from primarily 

herbarium specimens and site-searches initiated (See Appendix 3). 

BLM established 48 km (30 miles) of hedgerows (about 20 ha [50 acres]), seeded 

32 ha (80 acres) of range land after treatment with propane flamer, planted 150 

trees in riparian-canal areas using hydro-planter, planted 50 potted trees and shrub 

in riparian-canal areas and developed a native seed source by increasing seed 

collection activities through seed collecting contracts and a seed grow-out 

contract. Restoration activities were coordinated with cooperating farmers who 

performed the work. Additionally, BLM developed 4 ha (10 acre) wetland for 

breeding season. 

Outreach 

BLM and LRT helped to establish and work with the newly established Tulare 

Lake Basin Working Group. They worked on developing partnerships with 

Sequoia Riverlands Trust; USDA NRCS; and USDI Fish and Wildlife Service. 

Tours given by BLM of Atwell Island project included The Wildlife Society 

Western Section, representatives of the California Department of Corrections and 

EDAW, the CVPIA Restoration Group from FWS, Patagonia’s Sustainable 

Cotton Tour and to the BLM Bakersfield Field Office management team and 

interagency LRT. Workshops and conferences attended by BLM staff include: 

Seed for Success workshop in Sacramento (Instruction workshop on seed 

collecting), daylong workshop and open house at ConservaSeed in Courtland, tour 
Appendix 1. CVPIA Land Retirement 

Program Chronology 

Appendix 1-17 

of Union Slough restoration project in Yolo Co., and the Ecological Farming 

conference and Wildfarm Alliance Workshop at Asilomar. 

BLM provided a day in the field for 25 school kids from Sierra Elementary 

Schools to tour Atwell Island and trap k-rats and horny toad lizards with BLM 

biologists. ESRP gave a presentation on the LRDP and SJV plant communities to 

the advanced science classes at Kerman High School in Kerman, California. A 

presentation on wildlife population monitoring in the Central Valley was given to 

biology classes at Kerman High School. Interested, biology career-driven 

students were offered the opportunity to accompany ESRP staff biologists on the 

spring blunt-nosed leopard lizard (Gambelia sila) survey at Pixley National 

Wildlife Refuge. ESRP staff members hosted an educational volunteer day for 

Kerman High School advanced placement biology students at the Tranquillity 

Native Plant Nursery. Students worked to remove weeds and transplant native 

species, do birding, and have lessons on local plant communities and habitat 

restoration. ESRP sponsors a student from the Center for Advanced Research and 

Technology who analyzed some of the small mammal data for her class project. 

The LRT provided a Field Tour for the Sacramento Fish and Wildlife Restoration 

Program Implementation Division of CVPIA Land Retirement Demonstration 

Project and SJR Riparian Habitat. LRT member attended the Lemoore NAS 

Revegetation Workshop by John Crane and Craig Dremman and the UC 

Extension Conservation Tillage Workshop at Five Points. The LRT gave a second 

presentation to the Kings County Board of Supervisors. LRT gave a special Land 

Retirement Presentation to Wayne White, FWS. 

LRT site tours were given to 50 members of the Fresno County Economic 

Opportunity Council and I-5 Business Corridor and to Dr. Ken Lair, Research 

Ecologist and Botanist from Reclamation’s Denver Technical Services Center. 

The latter contact resulted in a cooperative effort being established for 2004 with 

the USDA-NRCS Plant Materials Center in Lockeford, California to augment 

seed supply. 

The 2003 an annual dove hunt had 42 hunters who harvested 255 mourning doves 

at the Tranquillity site planted in safflower by the California Department of Fish 

and Game. 

A science education program at Alpaugh School was initiated, with possible 

coordination with the California Institute of Biodiversity using CAL-Alive CDROM, their educators, and the Atwell Island Land Retirement Restoration Project. 

Year 2004 Accomplishments 

Program Administration 

At Tranquillity, work was accomplished with a revised contract with ESRP. 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 1-18 

Research, restoration, and continued acquisition at and Atwell Island continued 

with the Interagency Agreement with the Bureau of Land Management. 

The Land Retirement Demonstration Project Fourth Annual Report was published 

in January 2004. An electronic copy of this report was posted to Endangered 

Species Recovery Program’s website at 

http://esrpweb.csustan.edu/publications/pdf/lrdp/2002ar

A draft of the 5-year analysis and report was started in October 2004. 

Development of an Implementation Plan for recovery of upland species on 

restored retired agricultural lands began. Discussions with listed species experts 

were held. Discussions of how to best utilize the techniques and native plant 

species of the CVPIA Land Retirement Program for upland habitat restoration on 

retired agricultural lands used this information. 

Land Acquisition 

Acquisitions for the Land Retirement Demonstration Site at Atwell Island 

continue to target completing transactions to reach the goal of 3,238 ha (8,000 

acres). During FY 2004, 12 ha (30 acres) were purchased and an additional 62 ha 

(154 acres) closed by the end of FY 2004 (total 74 ha [184 acres]). Other 

acquisition actions began with the acceptance of a DOI offer for a 253 ha (625 

acre) parcel and for an appraisal currently underway on a 65 ha (160 acre) parcel. 

Research and Monitoring 

ESRP met with Dr. Hurlbert about statistical questions and procedures, 

transformations of the data, and how to implement that. 

Potential trials and restoration activities at Tranquillity: showplace, nursery, 

hedgerows, large scale restoration, herbicides vs. growth-forms, pre-irrigation 

trial, imprinting vs. broadcasting trial, seed augmentation, planting method trial 

and water use trial (See Appendix 3). Research for the program continued in field 

trials focused on determining ways to reduce competition between native plants 

and weedy species. Management activities continued in addition to monitoring, 

data gathering and analysis for the habitat Restoration Study at both the 

Tranquillity (ESRP) and Atwell Island (BLM) study sites. 

Data gathering for the 5-year Habitat Restoration Study, designed to determine 

the effects of habitat restoration on wildlife on 20, 4 ha (10 acre) plots at the 

Tranquillity site, was completed. All data were entered into databases, proofed, 

edited and a suite of exploratory data analysis and graphing accomplished for 

selected data sets covering the 5 consecutive years of the study (1999 to 2004). 

The Land Retirement Team, ESRP, and BLM staff assisted Dr. Ken Lair, 

Reclamation Restoration Botanist, to design, establish, and sample plots 

containing 8 native plant species planted with a variety of techniques. Habitat 

rehabilitation techniques in replicated trials were conducted on 64 plots on 6 ha 
Appendix 1. CVPIA Land Retirement 

Program Chronology 

Appendix 1-19 

(15 acres) at the Tranquillity site and inter-planted on 8 ha (20 acres) of alfalfa at 

Atwell Island. 

Awarded grant from Reclamation’s Science and Technology Program enabled 

research to be conducted on the effects of land retirement on project groundwater 

and soil. Continued monitoring of soil and groundwater conditions at both sites. 

Monitoring equipment to gather weather data at Atwell Island site to be integrated 

into California Irrigation Management Information System (CIMIS) was 

purchased. 

The conceptual model of groundwater flow at Tranquillity site was developed in 

preparation for numerical model simulating groundwater response to land 

retirement. 

Restoration and Site Management 

ESRP and BLM noticed Atriplex lentiformes die-off in Mendota area and 

throughout the SJV. 

At the Atwell Island site, hedgerows with native plant species have been 

established. A San Joaquin kit fox was observed using the hedgerows established 

in January 2003. 80 km (50 miles) of hedgerows were established on the Atwell 

Island project site and restoration work initiated on more than 40 ha (100 acres), 

including planting out flamed grasslands, canal banks, tree poles and upland shrub 

planting in formerly alfalfa fields (approximately 8 ha [20 acres]), and 4 ha (10 

acres) of shorebird habitat and planting. Cooperation with an organic farmer to 

grow-out Alkali Sacaton and Indian Rice grass was initiated. 

The SJV native plant nursery at Tranquillity expanded to 2 ha (5 acres) and 

increased from 34 to 64 species (13 shrubs, 30 annual herbs, 19 perennial herbs, 2 

perennial grasses). Collections of 91 species from 78 locations were made on 314 

collecting trips. Additionally, 8 species were established in 0.2 ha (0.5 acre) plots 

using mechanized production and harvesting methods. Mechanized seed cleaning 

equipment was purchased and operations established. Large quantities of seed 

were collected under contracts. 

Research on seed delivery, plant propagation, and seed production methods 

continued with the USDA Plant Material Center in Lockeford, California. Seed 

augmentation of three targeted species will be done in FY 2005. 

Restoration and site management activities at both sites were accomplished with 

cooperating farmers. Barley was planted at Tranquillity on 243 ha (600 acres) in 

buffers that isolate the study plots from one another, inhibit the establishment of 

weeds, and reduce erosion and dust. Additionally, barley was planted on 49 ha 

(120 acres) that was previously used as research trials so that new trials can be 

installed in FY 2005. On 32 ha (80 acres), a new cultivar of barley (UC937) was 

planted that UC Davis developed for use on high saline soils. 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 1-20 

At Atwell Island, a wildlife farming demonstration area was established with 6 ha 

(15 acres) of native shrub plantings interspersed with 8 ha (20 acres) of crops, 2 

ha (5 acres) each of vetch, milo maize, wheat, and safflower. The results of this 

wildlife habitat planting laid the groundwork for a Cooperative Agreement with 

the Westside Resource Conservation District to implement five units in Fresno 

County in FY 2005. 

The existing 8 ha (20 acres) wetland at Atwell Island was managed for wintering 

waterfowl. 

Outreach 

Presentations and posters were given at a number of forums in FY2004. These 

included the Annual Statewide Department of Water Resources Workshop, 

Drainage and Salinity Annual Conference, American Society of Mammalogists, 

California Native Plant Society, Society of Ecological Restoration, and the Raptor 

Research Foundation. 

Outreach to the local high school science classes and science clubs introduced a 

workshop on land retirement. A volunteer day at the native plant nursery was 

held in observance of Earth Day. Two CSU Fresno graduate students are 

conducting research at the Tranquillity site to investigate native plant pollinators’ 

populations and seed delivery methods for seven native plant species. At Atwell 

Island, a CSU Fresno graduate student is studying of post-harvest flooding 

effects. 

Participation in the Tulare Lake Basin Working Group fostered working 

partnerships with Sequoia Riverlands Trust; Tulare County Audubon Society; 

USDA-NRCS; and FWS Refuges and Joint Venture Program. 

A presentation of the CVPIA Land Retirement Program was given to researchers 

Dr. Werner ‘Erik’ Klohn and Dr. Hans-Wilhelm Windhorst of the University of 

Vechta, Germany. These visitors studied and traveled the California water and 

agricultural regions for the past 15 years. Their work is sponsored by the Institute 

of Spatial Analysis and Planning (ISPA) in areas of intensive agriculture at the 

University of Vechta. 

ESRP gave a presentation to two environmental science classes at the Center for 

Advanced Research and Technology (CART) in Clovis, California. ESRP 

biologists, CART students and teachers, and Clovis Botanical Garden personnel 

transplanted more than 150 native plants and installed a drip irrigation system 

along the Clovis Community Trail. Plants were donated from the LRDP nursery. 

ESRP biologists held an interview and volunteer day at the ERSP warehouse. 

The event was open to CART students interested in a part-time seeding 

experiment position with ERSP. The position was offered to and accepted by an 

environmental science student in his junior year of studies at CART. 
Appendix 1. CVPIA Land Retirement 

Program Chronology 

Appendix 1-21 

Various LRT members and ESRP biologists attended the Hedgerows in 

Agriculture workshop sponsored by the Community Alliance with Family 

Farmers at the UC Center in Fresno, California. 

Two presentations were given at the American Society of Mammalogists meeting 

at Humboldt State University, Arcata, California. A presentation was given at the 

Raptor Research Foundation conference in Bakersfield, California. 

The California Department of Fish and Game annual dove hunt at the Tranquillity 

site had 38 hunters who harvested 183 mourning doves. 

Year 2005 Accomplishments 

Program Administration 

The LRT received Reclamation’s Science and Technology Program was awarded 

funds to conduct research on the effects of Land Retirement on project 

groundwater and soil. 

A Cooperative Agreement with the Westside Resource Conservation District in 

Tranquillity, California was developed to establish upland habitat restoration units 

on retired lands in the SJV. 

Participation in the Tulare Lake Basin Working Group fostered further working 

partnerships with Sequoia Riverlands Trust; Tulare County Audubon Society; 

USDA-NRCS; and FWS Refuges and Joint Venture Program for the Atwell 

Island site. 

A California State University Fresno-Agriculture Research Initiative grant 

proposal was submitted with Dr. John Constable of CSUF by Dr. Nur Ritter of 

ESRP. 

The Five-Year Land Retirement Demonstration Project Report (1999-2004) will 

be produced, pursuant to the FWS BO September 1999 for the CVPIA Land 

Retirement Program Demonstration and put on the Reclamation website. 

Land Acquisition 

The acquisition process for two parcels totaling 318 ha (785 acres) of land and 

associated water within the Atwell Island Water District was completed. 

Research and Monitoring 

The fourth year of the 5-year study at the Atwell Island Project Site continued. 

Monitoring soil and groundwater conditions at both sites continued. Numerical 

simulation of groundwater flow and salt transport in the shallow groundwater at 

the Tranquillity Site will be performed. The Hydrosphere groundwater model 

will be utilized to simulate groundwater flow and advective transport of solutes at 

the demonstration project site. 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 1-22 

Research on seed delivery, plant propagation, and seed production methods 

continued with the USDA Plant Material Center in Lockeford, California. Seed 

augmentation of three targeted species will be done in FY 2005. 

Data gathering for the 5-year Habitat Restoration Study, designed to determine 

the effects of habitat restoration on wildlife on 20, 4 ha (10-acre) plots at the 

Tranquillity site, was completed. The fourth year of the 5-year study at the 

Atwell Island Project Site will be done and the restoration activities continue, 

emphasizing previously successful techniques, while developing and testing new 

methods. 

The Reclamation Denver Technical Services Center Restoration Ecologist Dr. 

Ken Lair will help with trials to expedite refinement and continuance of research 

on species adaptation, planting methods, weed control, plant selection, 

propagation, seed increase, plant materials supply for landscape-scale application, 

and interagency development for commercial retail supply 

Joe Brummer, soil scientist at the Technical Service Center will collect and 

analyze soil chemistry data from the Land Retirement Demonstration Project, 

especially salinity, selenium, and boron and findings will be reported in the 

FY2005 report. Numerical simulation of groundwater flow and salt transport in 

the shallow groundwater at the Tranquillity Site will be performed in FY 05. The 

Hydrosphere groundwater model will be utilized to simulate groundwater flow 

and advective transport of solutes at the demonstration project site. 

Restoration and Site Management 

Restoration and site management activities at both sites were accomplished with 

cooperating farmers. Barley was planted at Tranquillity on 243 ha (600 acres) in 

buffers that isolate the study plots from one another, inhibit the establishment of 

weeds, and reduce erosion and dust. Additionally, barley was planted on 49 ha 

(120 acres) that was previously used as research trials, so that new trials can be 

installed in FY 2005. On 32 ha (80 acres), a new cultivar of barley (UC937) was 

planted that UC Davis developed for use on high saline soils. 

Restoration activities at the Atwell Island Project Site will continue, emphasizing 

previously successful techniques, while developing and testing new methods. 

Restoration acreage will expand from the current 61 ha (150 acres) per year to 

more than 101 ha (250 acres). The existing 8 ha (20 acres) wetland at Atwell 

Island, established with the cooperation of the USDA-NRCS, was managed for 

wintering waterfowl. 51 km (32 miles) (32 ha [80 acres]) of hedgerows were 

established with native shrubs. On 8 ha (20 acres) of range land, seeding occurred 

after treatment with propane flamer. Iodine bush was seeded on 2.8 ha (7 acres) 

of a sump (former evaporation pond). A mix of native annuals and perennials 

was planted on 160 acres. A hydro-planter installed 200 tree cuttings in ripariancanal areas along with 150 potted trees and shrubs. BLM developed a native seed 

source by increasing seed collection activities (approx. 8000 pounds) utilizing 

seed collecting contracts and established a 1.5 acre grow-out area for native grass 
Appendix 1. CVPIA Land Retirement 

Program Chronology 

Appendix 1-23 

seed under contract Two acres of perennial grass seed were planted along ditch 

banks. Two more diversified upland habitat units were established on 80 acres. 

BLM coordinated with cooperating farmers to carry out restoration activities. 

Outreach 

Presentations given this year included one by a Reclamation hydrologist and soil 

scientist on research findings regarding soil and groundwater response to land 

retirement in the Western San Joaquin Valley at the International Salinity 

Conference held at Riverside, Ca in April, 2005. At the Society for Ecological 

Restoration, California Chapter annual meeting at Bass Lake, California, ESRP 

had one poster abstract and three oral presentations accepted and BLM and FWS 

another one. 

BLM held a workshop on recreation and tourism potential for Atwell Island and 

the Tulare Basin. BLM established a partnership with AmeriCorp NCCC which 

provided a crew of 10 to work on numerous projects including construction of 0.5 

miles of nature trail, reforestation of 3 miles of ditch and pond banks, and general 

cleanup and maintenance of the administrative site. The crew also worked on a 

greenhouse at the Alpaugh School as a first step to get students involved in the 

restoration project. The crew also conducted a major cleanup event and removed 

over 45 tons of garbage from the community, much of which might otherwise 

have been dumped on the project area. BLM continued to work with the Tulare 

Lake Basin Working Group and to help establish Tulare Basin Wildlife Partners, 

an NGO which will be a cooperator on the project. BLM expanded its work via 

partnerships developed with Tulare County Audubon Society; Alpaugh School 

District; Citizens for a Better Alpaugh; State Park Service – Allensworth SHM; 

USDA NRCS; USDA Forest Service (Trails Unlimited); and USDI Fish and 

Wildlife Service (FWS). 

ESRP gave a day-long tour to the coordinators and nursery staff from the five 

native plant nurseries of the Golden Gate National Recreation Area. ESRP 

sponsored a booth and gave presentations to 100 underprivileged school children 

at the USDA Forest Service Central California Consortium event held at Grizzlies 

Stadium, Fresno, California. 

ESRP developed a web-site that makes information on the Land Retirement 

Demonstration Project and research results available to the public and to 

cooperating agencies. Links are provided to the various annual reports and the 5-

year report. The ESRP web site can be accessed at: 

http://esrp.csustan.edu/projects/lrdp/. 

Appendix 2. Compliance with 

Biological Opinion 

Appendix 2-1 

Appendix 2. Compliance with 

Biological Opinion 

by Beatrice A. Olsen 

The Fish and Wildlife Service (FWS) stated support for land retirement as one of 

several means to manage subsurface agricultural drainage as was recommended in 

the SJVDP 1990. Their belief was that the Land Retirement Demonstration 

Project could benefit the reduction of contaminated subsurface drainage water, 

increase available fresh water for fish and wildlife and provide large blocks of 

land that could potentially be restored to productive upland wildlife habitat, with 

potentially important endangered species benefits. The LRDP was thought likely 

to adversely affect SJ kit fox, Fresno kangaroo rat, blunt-nosed leopard lizard, 

giant garter snake, Aleutian Canada goose, delta smelt, and Sacramento splittail. 

A not-likely-to-adversely-affect determination was found for American peregrine 

falcon, bald eagle, mountain plover, California red-legged frog, vernal pool fairy 

shrimp, valley elderberry longhorn beetle, palmate-bracted birds-beak, San 

Joaquin woolly-threads, Hoover’s eriastrum, and California jewelflower. 

Conservation Measures 

CONSERVATION MEASURES OF CVPIA LAND RETIREMENT 

DEMONSTRATION PROJECT 

Task Action Required Results 

Listed Species 

Recovery 

Prioritize lands for 

acquisition 

1997 Multi-agency LRP 

Guidelines used 

Evaporative Pond 

Closure 

Close pond to State 

Standards 

Required & done prior to 

federal acquisition 

Habitat Revegetation Study options & 

implement habitat 

rehabilitation 

In-depth study @ both sites. 

Mgt plans ongoing. 

Enhancement 

Survival Program 

Service to work w. LRP 

to develop a plan 

Workload of Service 

personnel too great. 

Monitoring Program Tiered Contaminant 

Monitoring Se and GW 

GW drops ave. 1-2 ft/yr. Se 

conc > 50ug/L See Chptr 2. 

Performance 

Standards 

Compare monitoring 

data to Se standards. 

Met Perfc Stds except GW 

quality. See Chptrs 2 & 3. 

Adapt 

Mgt/Contingency 

Plan 

Minimize risk of Se 

exposure w. adaptive 

mgt. 

Restoration uses adaptive 

mgt. Contingency plans not 

needed. 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 2-2 

FWS Conservation Measures were determined to be critical to the conclusion that 

survival and recovery of the listed species in the action area would not be reduced 

appreciably by the LRDP. As noted by FWS, the information gained from the 

LRDP would be used to guide future implementation and future land acquisitions 

of the CVPIA Land Retirement Program. The 1997 Multi-agency Interim Land 

Retirement Guidelines were employed to determine lands for acquisition for the 

Demonstration Project. 

 

Evaporation pond closures for any federal acquisitions had to be done to the State 

Regional Water Quality Standards. The evaporation pond at Atwell Island was 

closed to these standards prior to the LRT acquisition of the property. 

The purpose of Habitat Re-vegetation was described by FWS as the reestablishment of native vegetation to foster the return of native species, which 

will enhance wildflower and wildlife viewing opportunities. Some retired lands 

could be managed for gamebird hunting programs. The extent to which 

recreational activities will be promoted will depend upon the type and success of 

the land management treatments employed. The restoration trials and study have 

been conducted to determine methods to recreate San Joaquin Valley ecosystems. 

For several years a small section has been planted to safflower for a California 

Department of Fish and Game dove hunt. Wildflower viewing, as envisioned by 

the FWS, would be limited to the spring and dependent upon access. It has not 

been a major recreational activity. As noted by the FWS, separate management 

plans will be developed for the lands in WWD and the Atwell Island area. The 

management plans will address contaminant issues for listed species and utilize 

the results described and analyzed in this five-year report. Some level of selenium 

and groundwater depth monitoring will be part of these plans. They will have 

separate section 7 consultation. 

The Enhancement for Survival Program for neighboring landowners, after several 

interagency meetings, was left in the development stage due to the large workload 

of FWS employees. 

The tiered contaminant monitoring program of selenium levels in groundwater 

and biota was cooperatively developed with the FWS specifically for this project 

(FWS 1999). The monitoring of selenium and salinity in soils was not a 

requirement in the FWS Biological Opinion for the LRDP; however, the soil 

monitoring program was implemented to address concerns raised by the scientific 

community over potential impacts to soils that may result from land retirement. 

The hydrologic techniques, results and discussion are thoroughly described in 

Chapter 2. Groundwater level data from the demonstration site support the 

conceptual model of a declining shallow groundwater table in response to land 

retirement. All of the wells monitored at the Tranquillity site have shown a 

declining water level trend over the five year period of record. The hydrographs 

for the drain sumps and wells are representative of the declining groundwater 
Appendix 2. Compliance with 

Biological Opinion 

Appendix 2-3 

level trend observed at the site during the five years of monitoring. Water levels 

measured in three drain sumps during the time period from July 1998 to July 2000 

similarly show an overall declining trend in groundwater levels for the period of 

record. All sumps being monitored were completely dry starting in October 2000. 

The drain sumps have remained dry as of October 2004. 

As discussed in Chapter 2, the slopes of the hydrographs for groundwater show a 

flattening trend over time. Examination of individual wells suggests that the 

extinction depth for groundwater evaporative discharge may be about 10 feet. The 

volume and flow of upflux is so small between a depth of 7 and 10 feet that 

evaporative discharge in the soil cracking system at the 2-4 foot depth may be 

sufficient to maintain a very small amount of unsaturated upward flow. Once the 

water table receded below 10 feet, all discharge is believed to be vertical deep 

percolation through the first barrier layer. The average annual rate of decline was 

about 1.2 feet per year. This rate is expected to decrease as less head is available 

to push water through the barrier layer. 

The shallow, perched groundwater is extremely saline in nature. Salinity in the 

shallow groundwater and drain sump samples, expressed as EC, ranged from 

11,500 to 76,980 μS/cm, with a median value of 43,925 μS/cm. The groundwater 

samples obtained from the underlying semi-confined aquifer are much less saline. 

Salinity in the groundwater samples obtained from the deep wells (> 50 ft deep), 

expressed as EC ranged from 5,630 to 18,580 μS/cm, with a median value of 

7,675 μS/cm. The groundwater found in the perched zone and in the underlying 

semi-confined aquifer is best described as a sodium- sulfate type of water. 

Selenium concentrations measured in the shallow groundwater system (wells < 50 

feet deep) during the first year of monitoring were high, ranging from 5 to 5,390 

μg/l (0.005 to 5.390 mg/l), with a median concentration of 1,280 μg/l (1.280 

mg/l). 

Due to drought conditions, the FWS performance standards for selenium and 

mercury concentrations in surface water that persisted for more than 30 days were 

not observed at the project site. Precipitation at the site was monitored by viewing 

the CIMIS website during the rainy season. The site was also visited during the 

wet season to document any standing water that persisted for more than 30 days in 

duration. 

In Chapter 3 the methods and results of Se monitoring in biota are discussed. The 

FWS Performance Standards required that Se contaminant levels be monitored in 

biota when high physical parameters results were obtained. The potential for 

adverse effects to sensitive species was measured each year in a number of nonlisted species collected and analyzed. Not all Performance Standards were strictly 

utilized, as small sample sizes would have precluded adequate measurement and 

analysis. Samples of items at the base of the food chain were collected and 

analyzed for selenium but not birds or canids. 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 2-4 

The mean selenium concentration in plants varied from 0.31 to 0.51 mg/kg at the 

Tranquillity site and from 0.21 to 0.26 mg/kg at the Atwell Island site. The mean 

selenium concentrations in plants at both sites were below the performance 

standards set for the project by the U.S. Fish and Wildlife Service (2.0 mg/kg) and 

were approximately an order of magnitude less than the selenium concentration in 

plants collected from Kesterson NWR. The mean selenium concentrations for all 

biota measured were higher at the Tranquillity site than at the Atwell Island site. 

At the Tranquillity site the mean concentration of selenium in invertebrates 

remained below the performance standard, except for spiders in 1999 and isopods. 

Mean selenium concentrations generally remained within the range for terrestrial 

invertebrates occurring on non-seleniferous soils in the western United States (2.5 

mg/kg, USDI 1998). At the Atwell Island site the mean concentration of 

selenium in all invertebrate groups remained below the performance standard of 

2.0 mg/kg established for project lands. The selenium levels in all invertebrate 

groups (crickets, beetles, spiders, and isopods) collected from the Tranquillity and 

Atwell Island sites are approximately an order of magnitude less than 

corresponding invertebrate groups collected between 1988 and 1992 in grassland 

habitat at Kesterson NWR. 

All biotic samples were analyzed to determine selenium concentrations by 

Laboratory and Environmental Testing (L.E.T.), Inc., Columbia, MO. Data 

provided include selenium concentration by dry weight, selenium concentration 

by wet weight, sample dry weight, sample percent moisture, and sample detection 

limit. The laboratory also provided reports on duplicates, spikes, and reference 

samples for quality control. Selenium concentration by dry weight was used for 

analysis. 

An adaptive management approach has been the one used by the LRT for the 

project. Measurements of the various monitoring of physical and biotic 

parameters had to be made before management techniques to minimize the risk of 

wildlife exposure to contaminants were exercised. As the LRDP proceeded, the 

results that were reviewed indicated that contingency plans, as outlined in the 

Biological Opinion, would not be necessary. Continued vigilance of especially the 

groundwater depths and selenium levels in biota will be exercised and reported so 

that changes can be made if needed. To establish upland vegetation quickly and 

efficiently, a variety of re-vegetation techniques will continue to be tested and 

monitored and future efforts will be adapted accordingly. 

Incidental Take Statement 

The effect of anticipated take for the Land Retirement Demonstration Project was 

not likely to result in jeopardy to listed species or destruction or adverse 

modification of critical habitat of Fresno k-rat and delta smelt. The rest of the 

species have no designated critical habitat, so no critical habitat for these species 

could be destroyed or modified. 
Appendix 2. Compliance with 

Biological Opinion 

Appendix 2-5 

INCIDENTAL TAKE STATEMENT FOR THE CVPIA LAND RETIREMENT 

DEMONSTRATION PROJECT 

Task Action Required Results 

Reasonable & 

Prudent 

Measures 

Protect/conserve species w. 

monitoring & toxic 

remediation 

Monitored species not need 

toxic remediation. 

Future acquisitions will not 

result in take. 

Data indicated measure met by 

LRDP. 

No converting of existing 

native species habitat. 

DOI-WWD Agreement ensured 

water not go to convert habitat. 

Sent Hill Valley & AI info. 

Terms & 

Conditions 

Fund 5 years of tiered 

monitoring. 

LRP funded ESRP contract and 

BLM biota monitoring & 

USBR for physical monitoring. 

Implement FWS remediation 

measures for bio-available 

toxic levels of Se. 

No remediation bec. GW levels 

declined even w. bad quality. 

Se biota levels generally below 

Performance Standards. 

Close evap pond at Atwell Is 

per CRWQ Standards 

Seller required to do prior to 

federal ownership. 

Reporting 

Requirements 

Provide annual reports to EC 

& ES Divisions of data 

collected from tiered 

monitoring. 

Annual reports provided 2000, 

2001, 2002 & 2004. 5-yr report 

available Aug. 2005. 

Notify SFWO w/in 3 work 

days of dead listed wildlife 

species. 

April 26, 2002 ESRP captured 5 

shrews (BVL). Notice sent to 

SFWO. Roadkill kit fox 

reported by BLM. 

Provide info of recent 

drainage mgt on acquired 

lands 

1 piece of acquired land had 

drains, but no longer intact or 

functional. 

Notify SFWO of species take 

not authorized. 

None taken so none reported. 

Report dead or sick listed 

wildlife species in/adjacent 

pesticide-treated areas. 

None found during restoration 

activities. 

The Reasonable and Prudent Measures necessary and appropriate to minimize the 

impact of the LRDP to listed species were each complied with. The LRDP’s 

requirement to protect and conserve listed species on lands acquired under the 

project by monitoring and remediation of toxic conditions was done and results 

demonstrated that no remediation of toxic conditions was required. Data collected 

indicated that land retirement would insure that future acquisitions for the LRDP 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 2-6 

would not result in increased or unauthorized take of listed species. The 

Agreement with WWD ensured the Land Retirement Team that water would not 

be used to convert existing native species habitat. 

The Land Retirement Demonstration Project met the nondiscretionary Terms and 

Conditions described in the 1999 Biological Opinion (BO). Funding of the tiered 

monitoring program was provided for at least 5 years. CVPIA funding for the 

LRP Demonstration Project met the project costs for the monitoring and 

restoration on the retired agricultural lands. Having a Fish and Wildlife Service 

Land Retirement Team Representative (co-lead) ensured that funds for proper 

monitoring and reporting occurred each year. The FWS Representative prepared 

and helped finalize all annual work plans and their implementation. 

No remediation measures were necessary due to bio-available toxic levels of 

selenium. The groundwater levels showed a declining shallow watertable. This is 

an important aspect of land retirement due to the high salinity and selenium 

concentrations in the shallow groundwater. The high concentrations in the 

shallow groundwater found in the coast range deposits at the site are a result of 

leaching under irrigated conditions and evaporation from the shallow water. The 

access to this contaminated groundwater is very limited because of the increased 

depth after irrigation is removed and the selenium levels in biota tended to be 

within the range typically found in biota occurring on non-seleniferous soils in the 

western United States. Additionally, the mean selenium levels in biota were 

generally below the population-level performance standards set in the BO. 

The evaporation pond in the Atwell Island Water District had to be closed in 

accordance with State of California standards. Adherence to these standards had 

to occur before federal ownership could be obtained of the lands containing the 

evaporation pond. The landowner had to close the evaporation pond to meet the 

California Regional Water Quality (CRWQ) Control Board, Central Valley 

Region Orders and Resolutions. The 16 March 2001 letter from Gary M. Carlton, 

Executive Officer California Regional Water Quality Control Board Central 

Valley Region certified that the discharge to the basin had ceased and that basin 

sediments remaining in the basin were at or near background levels of soils in the 

area. The evaporation pond was closed in accordance with CRWQ requirements. 

Vegetation cover is slowly taking hold and the pond continues to be monitored. 

Reporting Requirements were all met. The first report was of the transactions 

between Atwell Island Water District (AIWD) and Hill Valley Irrigation District 

for the AIWD CVP allotment. These transactions occurred prior to the project 

dealings with AIWD. What historic information was available was forwarded to 

SWFO within 30 days of receipt of the BO in 1999. The lands acquired by the 

LRDP came with associated CVP contract allocations, except for those lands in 

Fresno County. The land purchase agreement with WWD was executed when the 

lands were purchased in the district and followed the language the FWS 

recommended for incorporation in the Agreement. Cover letter and Agreement 
Appendix 2. Compliance with 

Biological Opinion 

Appendix 2-7 

language were agreed upon by the FWS prior to inclusion in the Environmental 

Assessment and the FONSI. Water was not used to convert habitat or where it 

would adversely affect listed species or their habitats and remained within the 

permitted place of use. The Agreement was an Appendix in the CVPIA Land 

Retirement Demonstration Project Environmental Assessment. 

Reporting Requirements for the Biological Opinion centered primarily on an 

annual report that was to be provided to the various divisions for their review of 

the data collected from the Tiered Monitoring Program. These annual reports 

were provided beginning in May 2000 for 1999 data. Subsequent years’ reports 

were produced in July 2001, September 2002, and January 2004 and copies sent 

to each of the interested departments/parties within the Sacramento Fish and 

Wildlife Office (SFWO). The Five Year Report will be available in 

September 2005. 

Notification of the SFWO within 3 working days of the finding of any dead listed 

wildlife species occurred only when five Buena Vista Lake shrew (BVLS) were 

captured on April 26, 2002 at Atwell Island. A notice was sent to the SFWO 

about the captures. Since BVLS had just been listed the previous months, the 

FWS had not yet issued recovery permits to anybody. ESRP applied for and 

received a recovery permit later in 2002, with a take authorization of 20 animals 

as they had requested. Baseline trapping with pitfall traps in 2000, and more 

extensive trapping with Sherman live traps, did not result in the capture of any 

more shrews. The two living shrews were released after taking tail tissue 

samples. The three dead shrews were preserved for genetic analyses. From 

historical map information and air photos, the land where these shrews were 

captured appears to have been in row crops for many years until the restoration 

project in 2001. The LRDP lands were all planted in barley in the winter of 

2000/2001. The nearest water way is a canal about 0.5 miles to the east of the 

plots where it was trapped. The plots are about 11 miles northeast from the center 

of the Kern NWR. 

Information regarding the recent drainage management of the lands acquired in 

WWD was involved only one piece of land where drains were installed as part of 

a WWD experiment. No parcels had subterranean drainage infrastructure. The 

drains which had been installed were no longer intact or functional. This 

information was supplied to the SFWO early in the project. 

The Reporting Requirement to provide the FWS with annual reports describing 

the progress of implementation of all commitments in the Conservation Measures 

were included in detail in the Annual Reports noted above. No take of any listed 

wildlife species not authorized in this opinion occurred. See the note above 

related to the BVLS. Additionally a road kill kit fox was found at the Atwell 

Island site. BLM reported this road kill at the time of its discovery. No dead or 

sick listed wildlife species found in or adjacent to pesticide-treated areas were 

found. 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 2-8 

Conservation Recommendations 

Implementation of any conservation recommendations or applications of the data 

have been included in the Annual Reports. Special presentations to the FWS at 

various times over the past six years have also served to inform them of results 

from the monitoring of land retirement impacts. Each Conservation 

Recommendation is described below with the compliance action. 

CONSERVATION RECOMMENDATIONS OF CVPIA LAND RETIREMENT 

DEMONSTRATION PROJECT 

Task Action Required Results 

Future 

Acquisitions 

Future acquisitions 

should contribute to 

listed species water 

supply 

CVPIA not likely to have largescale LRP in Fresno Co. due to 

WWD’s 70,000 retired acres 

Implementation 

of 

Recovery actions 

LRT should assist FWS 

in implementation of 

various recovery plans 

All plans w. SJV upland habitats 

benefit from CVPIA data & 

monitoring in Annual Reports 

SJVDP 

Recommended 

Plan 

LRT should assist FWS 

in implementation of this 

plan 

SJVDP provided basis of CVPIA 

authorized LRP, but differences 

exist. LR currently considered in 

SLDFR EIS. 

Educated 

Reclamation staff 

Provide education to 

USBR staff at all levels 

on ESA & 7 (a)(1) 

responsibilities. 

USBR staff training done by 

Sacto & Area Offices. 

Outreach Provide outreach to 

public & schools on 

protecting listed species 

Tours, presentations, panel 

discussions, student projects & 

AmeriCorps integral part of LRP 

from its inception. 

Fund USGS 

studies 

Fund GW & contaminant 

levels studies thru 

USGS. 

Physical monitoring done by 

USBR specialists under LRT 

Hydrologist. USGS specialists 

consulted as well. 

Ecosystem 

protection 

components 

Follow ecosystem 

protection components 

for Central Valley & Bay 

Delta of the FWS’s 

Ecoregion Program. 

The LRT Restoration Trials & 

Habitat Restoration Study 

provides background data for 

implementing protection 

measures on remnant populations 

or their habitat. Required & done 

prior to federal acquisition. 
Appendix 2. Compliance with 

Biological Opinion 

Appendix 2-9 

1. The CVPIA Land Retirement Program is not likely to embark on a large scale 

effort to retire more lands in Fresno County beyond those purchased under the 

current project. This is due to the initiation of WWD’s own land retirement 

program which has now retired, either through lawsuit settlements or district 

purchase, approximately 70,000 acres. 

2. All those recovery plans that involve San Joaquin Valley upland habitats can 

benefit from review of the Five Year Report or previous Annual Reports. The 

information from these has also been available on the Endangered Species 

Recovery Program website or the Bureau of Reclamation website. Data on 

physical parameters in retired drainage-impaired agricultural lands and on biota 

presence and habitat restoration techniques could be helpful to those agencies and 

entities responsible for management of the existing listed species habitat 

remnants. Specific funding to implement these recommendations will have to 

come through other means than the CVPIA Land Retirement Program. 

 

3. The SJVDP provided a basis for the CVPIA. Some differences exist in the 

objectives of each, although many are similar, but the CVPIA Land Retirement 

Program is authorized by the CVPIA, which is not required to implement the 

SJVDP. Land retirement is currently being considered in the San Luis Drainage 

Re-Evaluation EIS. 

4. The education of the ESA and 7(a) (1) responsibilities of Reclamation staff at 

all levels are handled by the appropriate division in Sacramento and the Area 

Offices. 

5. Outreach in the form of tours, presentations, panel discussions, student projects 

and professional organization presentations have been an integral part of the 

CVPIA Land Retirement Program since its inception. 

6. The FWS suggested that CVPIA fund studies of groundwater percolation and 

contaminant levels through USGS. Data collection for LRP groundwater 

monitoring and contaminants was accomplished by Bureau of Reclamation 

specialists and their contractors and USGS specialists consulted as well. 

7. The last item recommended that the LRT follow ecosystem protection 

components for the Central Valley and Bay Delta of the FWS’s Ecoregion 

Program. Restoration Trials and the Habitat Restoration Study can provide these 

entities background data for implementing protection measures on remnant 

populations or their habitat. 

Appendix 3. Research and Restoration 

Appendix 3-1 

Appendix 3. Research and Restoration 

by Nor P. Ritter 

Introduction 

In the appendix, an overview is presented of the activities undertaken by the Land 

Retirement Team and Endangered Species Recovery Program (ESRP) during the 

course of the Land Retirement Demonstration Project 1998-2004. Topics are 

presented as follows. 

Baseline Surveys of the Tranquillity and Atwell Island Property were conducted 

prior installing the Habitat Restoration Studies (HRS) plots. 

An established monitoring regime was carried out each year on both the 

Tranquillity and Atwell Island Habitat Restoration Studies. 

ESRP undertook restoration of portions of the Tranquillity property, and 

conducted a large number of restoration trials. 

A native plant nursery was established on the Tranquillity property. Seed 

collecting sites were located throughout the westside of the San Joaquin Valley, 

and seed was collected for use in the nursery and in restoration efforts. These 

activities, as well as a brief overview of the seed processing facility are presented 

in this appendix. 

Biotic monitoring at Atwell Island was conducted by ESRP from 1998 until 

October 2002. Since that time, Bureau of Land Management (BLM) has taken 

over responsibility for all management and research activities at Atwell Island. 

Activities specific to BLM will be presented by that agency in a separate report. 

Baseline Surveys 

Tranquillity Site 

Biotic Survey A baseline biotic survey of the Tranquillity property was 

conducted on December 2, 1998. The survey protocol entailed driving the 

perimeter roads around each quarter section, with periodic foot surveys onto the 

first 15-30 m (50-100 feet) of each field. A preliminary species list was compiled, 

and areas that merited additional surveys were identified. A follow-up field 

survey was conducted on December 7 and 14, 1998, during which time, the 

previously identified high-priority areas were more intensively surveyed. 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 3-2 

Outcomes from the baseline survey included (1) a preliminary catalog of all noted 

plant species and animals (identified visually or by sign) was compiled; and 

(2) areas which potentially might support species of interest were identified. 

Subsequent site work (e.g., tilling and contouring) was structured to avoid these 

areas. A report of the baseline survey was submitted to the Land Retirement 

Team (see Selmon 1999). 

In 2002, ESRP conducted a baseline survey of the “North Avenue Property” 

(formerly, the Bell Property), an approximately 162 ha (400 ac) parcel that was 

purchased by the Land Retirement Team in May of that year. The property was 

surveyed in its entirety (May-June 2002). Monitoring was conducted for 

vegetation, invertebrates, birds, mammals, amphibians, and reptiles. Outcomes 

from this survey included a catalog of species noted on the site, and a survey 

report (included in Uptain et al. 2004). 

Physical Impacts Monitoring Monitoring of physical conditions at the 

Tranquillity site was designed to address the potential for selenium contamination 

of the local biota. Soil monitoring was aimed at detecting changes in levels of 

soil selenium, boron, and salinity that might result from land retirement over the 

5-year life of the Demonstration Project. The initial surveys conducted in 

September and October of 1999 established baseline values for soil chemistry 

including salinity, selenium, boron, nitrate, ph and major anions, cations, and 

nutrients. 

Soil sampling methodologies were as follows. A rectangular sampling grid was 

established and land surface soil sampling was conducted at 124 locations. Soils 

were collected from a depth of 0 to 30.5 cm (0 to 1 foot) at each corner of the 

HRS plot using a shovel. In addition, sampling of soils from 0 to 30.5 cm (0 to 1 

foot), 60.9 to 91.4 cm (2 to 3 feet), and 121.9 to 152.4 cm (4 to 5 feet) was 

performed in the center of each plot, and from an additional six locations per plot, 

using a 10.1 cm (4 in) inside diameter split barrel core sampler driven to a depth 

of 152.4 cm (5 feet). 

Groundwater monitoring was instituted in July of 1998 to detect the subsurface 

level of water and test the hypothesis that the water level would decline in the 

absence of surface watering (i.e. the irrigation of crops). Monitoring entailed 

collecting samples from 27 wells and sumps on the Tranquillity site. 

Atwell Island Site 

Biotic Survey An initial baseline survey of the Atwell Island property was 

conducted in April and May 2000 (see Uptain et al. 2001 for a complete report of 

this survey). The property was divided into three large areas; the delineations 

were based primarily on land-use history. Surveys were conducted for vegetation, 

birds, small mammals, invertebrates, contaminants (selenium), and, peripherally, 

herptiles. Vegetation monitoring methodology consisted of a series of walkover 

surveys, in which all observed species were identified and recorded. Avian 
Appendix 3. Research and Restoration 

Appendix 3-3 

monitoring methodology utilized visual encounter surveys. In these surveys, 

researchers walked transects across designated field. Recorded data included all 

avian species that were heard or observed, as well as any observed mammals or 

reptiles. Small mammals were surveyed by nighttime trapping (Sherman traps). 

Invertebrates were surveyed using pitfall traps. Selenium monitoring followed 

the same general methodologies as were used at the Tranquillity project site. 

Physical Impacts Monitoring As with the monitoring of physical impacts at the 

Tranquillity site, data were collected at the Atwell Island site to determine the 

potential negative effects of selenium and other naturally occurring elements on 

the site’s biota. Baseline soil monitoring was initiated in 2002 and comprised 

432 samples. Three soil samples were taken from near the center of each of the 

48 approximately 0.8 ha (2 ac) research plots. One composite sample consisting 

of four sub-samples was collected from a depth of 0.0 to 30.5 cm (0 to 12 in); 

three of the four sub-samples were taken from within a two-meter radius of the 

center; while the remaining sub-sample was taken from the center. Additionally, 

one sample each from 30.5 to 76 cm (12 to 30 in) and 76 to 152 cm (30 to 60 in) 

was taken. Two field replicate samples were taken from each quarter section. 

Samples were analyzed for selenium, sulfate, chloride, electrical conductivity, and 

moisture. Surface samples were analyzed for boron, magnesium, potassium, 

sodium, carbonate and nitrate. Protocols and procedures taken to ensure quality 

of data in soil collection and analysis are outlined in the Quality Assurance 

Project Plan (QAPP) for the LRDP (CH2M Hill 1999). 

In the fall of 1999, Reclamation installed 17 monitoring wells to measure 

groundwater levels and sample for water quality. Baseline surface and 

groundwater monitoring was conducted in January 2002. 

Annual Monitoring Activities 

Tranquillity HRS 

Biotic Surveys 

Each year, 32 surveys were conducted of the biota on the Tranquillity site. The 

majority of surveys were specific to the HRS plots (Table A3-1); however, a 

number of site-wide surveys were also conducted (Table A3-2). The effort 

required to conduct these surveys was quite variable, with some (e.g., the 

vegetation contaminants monitoring) generally requiring only a couple of persondays to complete. Others, such as the small mammal trapping, required up to 

20 person-days (e.g., five biologists for 4 days). 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 3-4 

Table A3-1. Annual monitoring activities on the Habitat Restoration Study 

plots (Tranquillity site), 1999-2003, with the number of times each survey 

was conducted per year. 

Survey Repetitions 

Avian Nesting Survey 1 

Avian Survey 4A

Fall Shrub Monitoring 1B

Invertebrate Pitfall Survey 1 

Invertebrate Sweep Survey 1 

Photographic Stations Survey 4 

Reptile and Amphibian Coverboard Survey 1 

Reptile and Amphibian Transect Survey 1 

Small Mammal Pitfall surveys 1 

Small Mammal Trapping 4C

Spring Vegetation Monitoring 1 

A. Only conducted 3 times in 1999. 

B. Only conducted in 2002. 

C. Only conducted once in 1999 and 3 times in 2000.

It should be noted that all monitoring activities outlined here were accompanied 

by a significant body of data-related activities. Examples are data entry, data 

proofing, voucher preparation and cataloging, photo archiving, etc. 

Table A3-2. Annual site-wide monitoring activities at the Tranquillity site, 

1999-2003, with the number of times each survey was conducted per year. 

Survey Repetitions 

Invertebrate Contaminants Monitoring 1 

Small mammal Contaminants Monitoring 1 

Spotlighting Survey 4 

Track Station Survey 4 

Vegetation Contaminants Monitoring 1 

Winter Raptor Survey 1 

Physical Impacts Monitoring 

Soil monitoring followed the methodologies outlined, re-sampling of all deep 

borings and a partial sampling of shallow sites where selenium concentrations 

were found to be highest in 1999 were conducted in November 2002. The 

Quality Assurance Project Plan for the LRDP describes the protocols and 

procedures taken to ensure quality of data in soil collection and analysis (CH2M 

Hill 1999). 
Appendix 3. Research and Restoration 

Appendix 3-5 

Weather data have been collected by the California Irrigation Management 

System (CIMIS) weather station #105 located approximately 2.5 km (1.5 mi) west 

of the Tranquillity site and are summarized in the final reports for each year. Data 

collected and summarized included precipitation, temperature, wind, and relative 

humidity. 

Irrigation regimes were reported on an annual basis beginning in 1999. Amount 

of water (in acre-feet) and methods and dates of application are reported. In 

addition to groundwater level monitoring, groundwater quality testing occurred on 

a quarterly basis during the first year of monitoring (October 1999; February, 

May, and July 2000), and annually thereafter. Unfiltered groundwater samples 

were analyzed for major ions, trace elements, isotopes, electrical conductivity, 

pH, temperature, and turbidity. 

Atwell Island HRS 

Biotic Monitoring 

The same suite of surveys that were conducted on the Tranquillity site served as 

the model for the surveys undertaken at the Atwell Island HRS (Table A3-3). As 

with monitoring at the Tranquillity HRS, the effort required to conduct these 

surveys was quite variable, and spanned approximately the same range of persondays as did the surveys at Tranquillity. Likewise, monitoring at Atwell Island 

was accompanied by the same body of associated tasks (e.g., data entry and 

proofing). 

Table A3-3. Annual monitoring activities on the Habitat Restoration Study 

plots (Atwell Island site) 2001-02, with the number of times each survey 

was conducted per year. 

Survey Repetitions 

Avian Nesting Survey 1 

Avian Survey 4A

Fall Shrub Monitoring 1B

Invertebrate Pitfall Survey 1 

Invertebrate Sweep Survey 1 

Photographic Stations Survey 4 

Reptile and Amphibian Coverboard Survey 1 

Reptile and Amphibian Transect Survey 1 

Small Mammal Pitfall surveys 1 

Small Mammal Trapping 4C

Spring Vegetation Monitoring 1 

A. Only conducted 3 times in 2001. 

B. Only conducted in 2002. 

C. Only conducted once in 1999 and 3 times in 2000.
Land Retirement Demonstration Project 

Five Year Report 

Appendix 3-6 

Physical Impacts Monitoring 

Soil monitoring followed the methodologies outlined. All deep borings and the 

shallow sites with the highest selenium concentrations (in 1999) were re-sampled 

in November 2002. 

Weather data were collected from the CIMIS station #21 located approximately 

29 km (18 mi) west of the project site. Data collected included hourly 

precipitation, wind, and relative humidity. 

In the fall of 1999, Reclamation installed 17 monitoring wells to measure 

groundwater levels and sample for water quality. Baseline surface and 

groundwater monitoring was conducted in January 2002; subsequent monitoring 

was conducted on a quarterly basis. To evaluate the influence of irrigation on 

groundwater levels, the amount (in acre-feet) of irrigation water applied, 

application method, and date were recorded throughout the course of the project 

Restoration and Site Management — Tranquillity 

During the course of the Demonstration Project, ESRP has conducted a variety of 

restoration trials and has undertaken restoration of portions of the Tranquillity 

property. Additionally, various management strategies have been utilized on 

portions of the property. These activities are briefly summarized in this section, 

and are presented in the following order: (1) restoration research (includes both 

the HRS and ancillary trials); (2) restoration; and (3) site management. 

In contrast to the other sections of this Appendix, which are organized by calendar 

year, activities in this section are organized by growing season. This approach 

was taken because it better represents the order in which activities were 

undertaken. For example, trial installation would typically be scheduled for the 

latter portions of a particular calendar year (e.g., October to December); however, 

due to various limitations, some of the same year’s trials might not be installed 

until January or February of the following calendar year. Nevertheless, treatment 

applications (e.g., herbicide applications) and monitoring for all the 

aforementioned trials would occur during the same period (generally, spring). By 

presenting the trials in this manner, it allows the reader to distinguish between 

those trials that were installed in the latter part of one growing season (e.g., 

January in the 2001-02 growing season) from those trials that were installed in the 

following fall (e.g., November of the 2002-03 growing season). 

1998-99 Growing Season 

In the fall of 1998, a cover crop of barley was planted on approximately 493 ha 

(1,220 ac) of the Tranquillity property. This planting was done in the hopes of 

establishing relatively homogenous conditions on the areas on which the HRS 

plots were to be sited. 
Appendix 3. Research and Restoration 

Appendix 3-7 

1999-00 Growing Season 

HRS Plot Installation 

Treatments were applied to the HRS plots. Seed of 13 native species was 

imprinted across the 10 “seeded” plots in March 2000. Native seedlings were also 

transplanted onto these experimental plots in March and April 2000. 

Transplanted seedlings were closely grouped in “shrub islands.” 

Microtopographic contours (berms) were created on the ten “bermed” plots. The 

240, approximately 12 m (39.4 foot) long berms were installed on each plot. 

Imprinting Trial 

To investigate the restoration techniques proposed for the HRS, a small-scale 

imprinting and berming trial was undertaken. Berms were constructed using 

various approaches, and the imprinter was pulled over the plot. Those techniques 

which appeared to be best suited for conditions at the Tranquillity site were 

adopted for the HRS. 

Native Species, Cover Crop, and Mycorrhiza Trial 

Another, small-scale trial was installed in which a variety of native species were 

interplanted with potential cover crop species. A second component of this trial 

involved the use of mycorrhizal inoculum, which was incorporated into a portion 

of the test plots. 

Site Management 

The barley in the buffers surrounding the HRS plots (~ 243 ha; 600 ac) was 

thrashed, and the area was surface disked. Barley was reseeded where necessary. 

2000-01 Growing Season 

Imprinting vs. Drilling of Native Species Trial 

The Imprinting vs. Drilling of Native Seeds trial was designed to investigate 

planting methods that require a minimal amount of ground preparation. Tillage 

breaks down the soil structure and can bring weed seeds to the soil surface. It was 

hoped that less soil disturbance would decrease weed density and promote the 

establishment of mycorrhizal networks in the soil, both of which tend to favor 

native plants (cf. St. John 1995). Comparisons were made between two seeding 

methods, imprinting and drilling. 

Plots were ca. 0.6 ha (1.5 ac) in size; treatments were replicated three times. A 

mixture containing seed of nine native species was imprinted. Data (percent 

cover and species composition) were collected from eight quadrats (35 x 70 cm) 

per plot. Installation of the experiment was undertaken in the fall of 2000; 

vegetation sampling was conducted the following spring (14-15 May 2001). 

Imprinting vs. Drilling of Cover Crops Trial 

This trial was designed to (1) investigate appropriate techniques for establishing 

cover crops, and (2) to examine the utility of planting native species in 

combination with a cover crop (i.e., a “nurse species”). The impetus for this trial 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 3-8 

came from the understanding that it will no doubt be necessary to undertake largescale restoration in phases. Cover crops will most likely be an important tool in 

the implementation of restoration, particularly if the cover crops can be planted 

with minimal soil preparation. 

Plots were ca. 0.6 ha (1.5 ac) in size; each treatment was replicated three times. 

Two seed “mixtures” were used: (1) barley and (2) barley in combination with 

three native grasses. Data (percent cover and species composition) were collected 

from eight quadrats (35 x 70 cm) per plot. Installation of the experiment was 

undertaken in the fall of 2000; vegetation sampling was conducted the following 

spring (14-15 May 2001). 

Section 23 Restoration 

Restoration of approximately 64.8 ha (160 ac) was undertaken in December 2000. 

Berms were constructed in a more or less random configuration. Both linear and 

curved berms were constructed; berms were oriented in either a north/south or an 

east/west direction. A mixture containing seed of 17 native species was imprinted 

at a rate of 9 pounds per acre of native seed and 14 pounds per acre of wheat bran 

used to keep variably sized native seeds in suspension). 

One hundred “shrub islands” were planted on the western and northern edges of 

the restoration area. Forty-three seedlings were transplanted at each island: 20 of 

Allenrolfea occidentalis, 11 of Atriplex polycarpa, and 12 of Sporobolus airoides. 

For each island, an additional 5 seedlings of A. occidentalis and 2 seedlings of S. 

airoides were planted on an adjacent berm. In total, 2,500 seedlings of A. 

occidentalis, 1,100 seedlings of A. polycarpa, and 1,400 seedlings of S. airoides

were transplanted. Vegetation monitoring was conducted in the May 2001 and 

again in February 2002. 

Site Management 

HRS Buffer Maintenance The barley in the buffers surrounding the HRS plots 

(~ 243 ha; 600 ac) was thrashed, and the area was surface disked. Barley was 

reseeded where necessary. 

Hedgerow Seeding Vegetation on field borders may harbor pests; therefore, 

these areas are usually disked or sprayed with herbicide. Hedgerows planted with 

native species are a positive alternative to these management practices. 

Hedgerows can be maintained with minimal management, can provide important 

habitat for birds and other wildlife, and may tend to favor beneficial insects. 

In December 2000, an approximately 3 m (10 foot) wide hedgerow was imprinted 

with seed of 11 native species. Low berms were constructed along the edges of 

the seeded area to allow for flood irrigation. In January 2001, seedlings of 

Atriplex lentiformis, Leymus triticoides, Nassella pulchra and Sporobolus 

airoides were planted along one berm at approximately 0.6 m (2 feet) on center. 
Appendix 3. Research and Restoration 

Appendix 3-9 

Marsh Area Seeding During the initial years of the Demonstration Project, a 

seasonal wetland would form annually on lands adjacent to the Tranquillity 

project site. The wetland was created by agricultural runoff, and occasionally this 

water also inundated approximately 3.2 ha (8 ac) of LRDP land. During periods 

of inundation, these areas supported large numbers of herons and other water 

birds. To enrich this habitat, a mixture containing seed of 14 native species was 

imprinted onto the LRDP portion. Species were selected that were typical for 

both mesic and upland habitats. 

Ditch Bank Seeding 

Ditches are a common feature of the agricultural landscape and are often managed 

with herbicides and blading to prevent the accumulation of weedy species. Native 

plants can potentially prevent weedy species from overtaking ditches while 

providing excellent cover for wildlife. In December 2000, a ditch was created on 

the northern and western boundary of the Section 23 Restoration area. Seedlings 

of Leymus triticoides and Nassella pulchra were planted along the ditch banks. 

In January 2001, a mixture of 13 native species has hand-seeded along the ditch. 

2001-02 Growing Season 

Atriplex spinifera Planting 

In this trial, an evaluation was made of the success of Atriplex spinifera (spiny 

saltbush) when planted in various groupings. Atriplex spinifera is an important 

component of the Central Valley’s native habitats. This species was also of 

interest because of its ability to become established in habitats dominated by red 

brome (Bromus madritensis). 

Atriplex spinifera transplants were grown-out from cuttings taken from shrubs on 

Section 10. A local nursery with extensive experience working with California 

native plants (Intermountain Nursery, Auberry, California; Ray LeClerge, owner) 

was contracted to undertake the propagation and grow-out. Plants were 

maintained in approximately gallon-sized peat pots until transplanting, and were 

watered as deemed appropriate (approximately bi-weekly) while in the nursery. 

Two treatment effects were investigated: (1) planting density and (2) plant 

spacing. Shrubs were transplanted in groups (shrub islands) of four different 

configurations. All plants were watered at the time of transplanting. Additional 

watering occurred weekly until the site received soil-soaking rains (late December 

2001). The condition of each plant was monitored in April, July, and December 

2002, May 2003, and January 2004. 

Berm and Mycorrhiza Trial 

The Berm and Mycorrhiza Trial was developed to investigate methods of 

enhancing topography and of facilitating recovery of the soil’s mycorrhizal 

communities. Two factors were considered: (1) berm “architecture” (i.e., the 

manner by which berms were constructed); and (2) mycorrhizal inoculation. Two 

methods of berm construction were compared. The first method (“dressed” 

berms) approximated that used to construct berms in the HRS trial; in the second 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 3-10 

method (“rough” berms), berms were constructed using just the border maker and 

were not compacted. Commercially purchased mycorrhizal was applied to half 

the plots. 

Plot size was approximately 0.2 ha (0.5 ac); each treatment was replicated five 

times. Each plot contained seven berms; berms were evenly-spaced on 

approximately 9.1 m (30 feet) centers and were oriented east to west. A seed 

mixture of thirteen native species was imprinted. Installation of the trial began in 

mid-February 2002. Because of the late seeding date and the low rainfall, the 

plots were irrigated twice during the course of the experiment (March 21 and 

April 20, 2002). Data (percent cover and species composition) were collected 

from 15 quadrats (35 x 70 cm) per plot. Vegetation monitoring was conducted in 

mid-May 2002 (May 6, 11-12, 14, 17-20). 

Succession Trial 

The Succession Trial was developed to examine differences in the dispersal and 

establishment of three different seed mixtures: (1) barley: (2) barley with native 

grasses; and, (3) the native seed mixture that had been used on the HRS plots. 

Two factors were examined — the ability of native grasses to become established 

when imprinted over an existing barley crop; and, the relative abilities of barley 

and imprinted native grasses to spread beyond the confines of the area in which 

they had been seeded. 

The trial was installed on an approximately 32.4 ha (80 ac) area of the 

Tranquillity property. Fifteen plots (five replicates of three treatments) were 

delineated. Plot width for the barley monoculture was approximately 36.6 m (120 

feet); plot width for the other two treatments was ca. 18.3 m (60 feet). Barley had 

previously been planted as a cover crop in this area in the fall of 2000, and had 

been thrashed and harrowed in 2001. This planting had provided sufficient seed 

such that the plots assigned to the barley monoculture did not require replanting. 

Plots assigned to the other two treatments were disked and imprinted with the 

appropriate seed mixture. Trial installation took place during February 13-15, 

2002. 

Because of the low rainfall that year and the relatively late seeding date, 

vegetation establishment was not sufficient to warrant monitoring of this trial. 

Although systematic sampling of the Succession Trial was never conducted, the 

trial area received periodic visits during the following growing season, during 

which time general observations were recorded. 

Suitability Trial 

The Suitability Trial was developed to evaluate the performance (i.e., 

establishment and growth) of various native species under field conditions at the 

Tranquillity Demonstration Site. Forty-three species were initially considered for 

inclusion in the trial. These species represented species that had previously been 

used in restoration activities in California. The species were ranked based on 
Appendix 3. Research and Restoration 

Appendix 3-11 

18 criteria (see, Uptain et al. 2004, p. 136). Six species (five perennial grasses and 

one sub-woody perennial), were selected for inclusion in the trial. 

Each species was planted (imprinted) in a single, approximately 0.13 ha (0.33 ac) 

plot (12’ x 1200’). This approach was adopted because of difficulties associated 

with seeding small plots with an imprinter. Although this experimental design 

promoted a more equitable seeding of the plots, this approach limited the analysis 

options as there were no true replicates (i.e., pseudoreplication, sensu Hurlbert 

1984). Hence, rather than being treated as a rigorous experiment, this trial should 

be interpreted more as a structured step in identifying suitable species for 

inclusion in restoration efforts in the study area. 

Imprinting was undertaken on March 15, 2002. The plots were sprinkler irrigated 

twice during the course of the experiment (March and April 2002). Vegetation 

sampling was conducted during June 16-18, 2002. Plots were divided into 

40 equal-length (ca. 9.2 m; 30 feet) segments; vegetation data were collected 

from one randomly located quadrat (35 x 70 cm) within each segment. 

Suaeda moquinii Salvage Trial 

The Suaeda moquinii Salvage was an attempt to relocate a number of native 

perennials from an area that was undergoing development. The source population 

was located alongside State Route 180 in adjacent to the Kerman Ecological 

Reserve. This portion of the highway was being widened, and numerous native 

plants were threatened with removal. 

Salvage activities were limited to a single species, Suaeda moquinii (bush 

seepweed). This species was selected because there were hundreds of individuals 

available and many were small enough (15 cm to 30.5 cm; 6-12 inches in height) 

to be transplanted with relative ease. Although many individuals of Atriplex 

polycarpa were also present, most were large and would have been problematic to 

transplant. 

A portion of the Native Plant Nursery was prepared for transplanting by removing 

all weeds and working the soil. Transplanting took place on April 18, 2002. The 

soils at the donor site were hard clay and very dry. These conditions proved 

problematic, as the soil would crack when a shovel was put into the ground and 

fall away from the plant, leaving broken bare roots. Care was taken to dig around 

the plants in an attempt to remove them with an intact root ball, but this was 

generally not possible. The root ball was wrapped in a burlap sheet cut to size 

and then kept moist until transplanted. A few plants were also taken bare root. 

One hundred forty individuals were transplanted. Plants were moved by truck to 

the nursery and were planted, with each individual given approximately 3.8 liters 

(1 gallon) of water. The following day, the transplants were flood irrigated to 

provide deep moisture to the plants. 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 3-12 

Manning Avenue Restoration 

Restoration (i.e., contouring and imprinting) of an approximately 32.4 ha (80 ac) 

parcel located south of Manning Avenue was undertaken late January and early 

February 2002. Seeding of this area was also used to refine calibration of the 

imprinter. Imprinting was undertaken when the ground was wet. The soils on the 

property are heavy clay, and imprinting under these conditions had pronounced 

negative effects. The soil was compacted to where it was not possible to push a 

shovel into the ground. As would be expected under these conditions, 

germination of both native and introduced species was very limited. 

Site Management 

HRS Buffer Maintenance The barley in the buffers surrounding the HRS plots 

(~ 243 ha; 600 ac) was thrashed, and the area was surface disked. Barley was 

reseeded where necessary. 

Marsh Mix Planting Following the initial seeding of the “Marsh Mix Area,” the 

area was mistakenly disked by the farmer that had been contracted to conduct site 

maintenance. The area (~ 3.9 ha; 9.6 ac) was re-seeded in January 2002 with a 

mixture of 14 native species. 

2002-03 Growing Season 

Section 23 Restoration Trial 

As noted, rainfall during the first three years of the project was below average. In 

contrast, winter rainfall for the 2002-03 growing season was predicted to be fairly 

high (i.e., mild El Niño conditions were predicted). In anticipation of these wetter 

conditions, an experiment—the Section 23 Restoration Trial—was developed in 

which various species could be evaluated during an above-average rainfall year. 

In this experiment, two species mixtures were compared. The first mixture, the 

“traditional mix” was composed of a subset (9 of 13) of the species that were 

imprinted on the HRS Plots. The second mixture, the “experimental mix” 

incorporated various species that had been used to some success in other 

restoration trials at Tranquillity, augmented by a few species that had 

demonstrated restoration potential elsewhere in California. 

The Section 23 restoration trial occupied an area of approximately 28.3 ha 

(70 ac). This area had received some weed control and was the largest contiguous 

block of “unassigned” land remaining on the Tranquillity site. Plots were ca.3.0 

ha (7.5 ac) in size; a complete randomized block design was applied, with 

treatments replicated four times. Micro-topographic contours (berms) were 

installed in all plots. Berms were aligned east to west and were the full length of 

the plot. Berm spacing was 9.2 m (30 feet), such that part of a flat and half of a 

berm would be imprinted in a single pass and with a final pass through the middle 

of a flat, there would be no overlap in seeding. In this manner, the berms were 

also compacted slightly. Berms were constructed on December 11, 2002. 

Imprinting was scheduled to follow immediately thereafter; however, rainfall 
Appendix 3. Research and Restoration 

Appendix 3-13 

during this period precluded the use of heavy equipment throughout December 

and imprinting was postponed until January 28-31, 2003. 

Pre-Irrigation Trial 

In this trial, the utility of pre-irrigating lands prior to imprinting was investigated. 

Pre-irrigation is a common weed-control practice in agriculture (Lanini et al. 

2003), and is a recommended approach in hedgerow installation (Earnshaw 2004). 

Hence, it appeared that this technique might also have some utility in the 

ecological restoration of retired agricultural lands. 

Pre-irrigation entails irrigating the land before the start of the growing season 

(i.e., the initiation of winter rainfall in late fall-early winter) to promote 

germination of the ‘winter weeds.’ The weeds are then removed, either 

chemically, by tillage, or by burning, and the crop is seeded. In this manner, the 

seeded species hopefully have a competitive advantage over any additional weeds 

that germinate later in the growing season. 

The area designated for the trial had been dominated by a variety of weeds during 

the preceding year, and the area had been disked for weed control during the 

winter of 2001-02. Plots were ca. 0.2 ha (0.5 ac) in size; a complete random 

block design was applied with treatments replicated four times. A single 

treatment factor (pre-irrigation) was evaluated. 

Site preparation was initiated on September 3, 2002. The soil was disked and 

trenches were installed for flood irrigation. To account for the effects of site 

preparation on vegetation establishment, the control plots received the same 

preparation as the treatment plots (i.e., trenches were also dug in the control plots 

but these were not flooded). The pre-irrigated plots were sprinkler-irrigated (cf. 

Lee & Dyer 1997) from September 7-9. After the winter weeds had germinated, 

all plots (treatment and control) were disked (October 14, 2002). 

Following disking, a mixture containing seed of eight native species was 

imprinted in all plots (19 November 2004). Data were collected from 12 quadrats 

(35 x 70 cm) per plot. Vegetation monitoring was conducted on April 29, 2003. 

Growth Form and Herbicide Trial 

The Growth-form and Herbicide trial was developed to examine how specific 

seed mixtures, in combination with specific herbicides could produce good 

ground cover, lower competition from weeds, and ultimately affect long-term 

planting success. Three seed and herbicide “treatments” were applied: (1) the 

“Grasses Treatment,” a mixture of native grasses with an application of broadleaf 

herbicide (Weedar 64); (2) the “Forb Treatment,” a mixture of native forbs with 

an application of a grass-specific herbicide (Sethoxydim); and (3) the “LateSeason Treatment,” a mixture of late-germinating perennial species with an early 

application of a broad-scale herbicide (Glyphosate). 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 3-14 

Plots were ca. 0.2 ha (0.5 ac) in size; a complete randomized block design was 

applied, with each treatment and a control (i.e., no treatment) replicated four 

times. The plots were seeded on November 20, 2002. The Forb and Late-Season 

Treatments were imprinted. Originally, it was intended that the Grass treatment 

would also be imprinted; however, the long awns on some of the seeds did not 

feed properly through the imprinter hopper. Therefore, for this treatment the seed 

was first broadcast over the plot, and was then worked into the soil by a pass with 

an empty imprinter. Herbicide for the Grass Treatment was applied on the last 

week of February; herbicides for the other two treatments were applied in the 

middle of March. 

Vegetation monitoring of the Grass and Forb treatments and the control plots was 

conducted during May 2003. Monitoring of the Late-Season plots was timed to 

coincide with the plants having attained their maximum growth for the season. 

Monitoring of these plots occurred on November 8, 2003. Data were collected 

from twelve quadrats (35 x 70 cm) per plot, for the Grass, Forb and Control plots. 

The Late-Season plots received a higher-density of sampling, with 24 quadrats 

(100 cm x 150 cm) per plot. 

Section 10 Burn and Mowing Trial 

Section 10 on the Tranquillity site is an area dominated by Bromus madritensis 

(red brome), with a characteristically heavy layer of thatch. Prescribed fire is a 

common management tool that also possesses utility in restoration strategies, and 

has been demonstrated to be effective in grass-dominated habitats (Pollak and 

Kan 1998; Wilson and Stubbendieck 2000). 

The Section 10 Burn and Mowing Trial was developed to take advantage an 

accidental fire that burned a large portion of Section 10 in June 2002. The timing 

of the accidental burn was not optimal in terms of controlling the wintergerminating grasses. Nevertheless, it was a good opportunity to evaluate the 

restoration potential of some seemingly fire-adapted native species. Mowing, 

another common management tool was incorporated in the trial as a second 

treatment factor. 

Shortly after the fire, the burned area was mapped using a global positioning 

system receiver in June. Four “blocks” were designated within the burned area; 

these blocks were delineated in such a manner as to “standardize” the burn 

intensity of the areas selected for the study plots. Plots were ca. 0.2 ha (0.5 ac) in 

size; a complete randomized block design was applied, with treatments replicated 

four times. A mixture containing seed of seven native species was imprinted. In 

order to subject the control plots to the same level of disturbance as the treated 

plots, an empty imprinter was run over the control plots. 

Data were collected from 12 quadrats (35 x 70 cm) per plot. Imprinting occurred 

on November 22, 2002. The “mowing” plots were mown a single time 

(March 28, 2003). Although it was anticipated that the plots might need to be 

mowed multiple times, weed growth under that year’s extremely dry conditions 
Appendix 3. Research and Restoration 

Appendix 3-15 

was not sufficient to warrant additional mowing. Vegetation monitoring was 

conducted on May 5, 2003. 

Mowing Trial 

The Mowing Trial was developed to test whether various mowing regimes could 

facilitate the establishment of native species by reducing weed competition. The 

trial was originally intended to be situated on the North Avenue Property; 

however, repeated incidences of trespass grazing on that property necessitated 

that the trial be relocated on Section 23. 

Two treatment factors, seeding and mowing, were incorporated into the design. 

Restoration (imprinting, berming, and transplanting) had been attempted on 

Section 23 in 2000; however, the entire area had been trespass grazed in the 

summer following restoration, and few plants survived the grazing. Hence, 

unseeded plots were incorporated into the study design as it was hoped that 

mowing might help “release” the seed in the seed bank that remained from these 

restoration activities. 

Plots were ca. 0.2 ha (0.5 ac) in size; a complete randomized block design was 

applied, with treatments replicated four times. A mixture containing seed of five 

native species was imprinted. To subject the non-seeded plots to the same level 

of disturbance as the seeded plots, an empty imprinter was run over the nonseeded plots. The plots were imprinted on November 13, 2002. The “mowing” 

plots were mown a single time (March 28, 2003); as with the Section 10 Burn 

Trial, weed growth was not sufficient to warrant additional mowing. Vegetation 

monitoring was conducted on 1 May and 6 May 2003. Data (percent cover and 

species composition) were collected from 12 quadrats (35 x 70 cm) per plot. 

North Avenue Property Restoration 

Restoration efforts were undertaken on an approximately 32.4 ha (80 ac) area at 

the northern end of the North Avenue Property. Restoration included microtopographic contouring (berming) and imprinting of native seed (13 species). 

Berm installation took place from December 5-7, 2002; imprinted was conducted 

from December 8-10, 2002. 

Prior to creating the berms, any large tumbling saltbushes (Atriplex argentea and 

A. rosea) were shredded to ground level. Berms were spaced on 6.1 m (20 feet) 

centers and were oriented east to west. The berms were installed in a serpentine 

manner to produce a more natural look and to maximize micro-habitat 

heterogeneity. The areas between the berms (the “flats”) were not disked, as the 

soils were generally slightly moist and friable, allowing a good imprint without 

soil preparation. In some areas, the thatch of Mediterranean grasses was so thick 

that it prevented a solid imprint from forming; however, we felt that the benefits 

of imprinting into undisturbed soil outweighed the negatives associated with 

establishing vegetation in the thatched areas. 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 3-16 

Manning Avenue Restoration 

As described previously, the attempted restoration of the Manning Avenue 

Property during the 2001-02 growing season met with little success due to the soil 

compaction that resulted from imprinting on wet soils. Another attempt was 

made to restore (berming and seeding) this area during the 2002-03 growing 

season. At this time, the soil was still sufficiently hard-packed and required the 

area to be disked. Following disking, a series of low, serpentine berms were 

installed on approximately 9.1 m (30 feet) centers. Disking and berming took 

place during October 12-14, 2002. 

A mixture of 12 native species was imprinted. Imprinting was originally 

scheduled for the first week of November; however rainfall at that time precluded 

imprinting until late in the month (November 24-30, 2002). 

Site Management 

HRS Buffer Maintenance The barley in the buffers surrounding the HRS plots 

(~ 243 ha; 600 ac) was thrashed, and the area was surface disked. Barley was 

reseeded where necessary. 

Hedgerows Approximately 3 miles of hedgerow were installed during the 2002-

03 growing season. Hedgerows were situated along the roads that parallel the 

HRS study blocks. A number of different mixtures of native seed were used (see 

Uptain et al. 2004), to investigate the potential of various species for their 

applicability in restoration. Seed was both imprinted and spread by hand. The 

hedgerows were watered (flood irrigation) at selected times during the growing 

season. 

2003-04 Growing Season 

Seed Augmentation and Planting Method Trial 

The Seed Augmentation and Planting Method Trial, and the Herbicide and 

Charcoal Treatment Trial represent a collaborative effort involving Reclamation 

(Reclamation; Technical Service Center, Denver; and Land Retirement Program, 

Fresno), the Endangered Species Recovery Program, Dr. Joe DiTomaso 

(University of California, Davis; UCD), and the Lockeford Plant Materials Center 

(USDA-NRCS; Lockeford). 

The Seed Augmentation and Planting Method Trial (5.6 ha; installed 

November 19-25, 2003) is a replicated, [3x4x4] factorial study evaluating effects 

of three factors on establishment success of eight native grass, forb and shrub 

species. Treatment factors were (a) mechanical soil surface (seedbed) 

manipulation, (b) cover crop use, and (c) chemical rhizosphere augmentation. 

Mechanical surface treatments addressed drilled seeding across variable depths 

and row spacing of deep-furrow seed placement (furrow depth: 1 cm [control 

standard], 10 cm, and 20 cm; row spacing: 30 cm [control standard] and 45 cm). 

Deep-furrow seed placement is designed to increase precipitation capture and 

retention, creating seed germination micro-sites exhibiting lower salinity and 
Appendix 3. Research and Restoration 

Appendix 3-17 

increased protection from environmental extremes. Second-level treatment 

involved use of a dryland barley “nurse crop” seeded at typical agronomic rates 

(68 kg ha-1) in alternate rows (60 cm and 90 cm spacing) with seeded natives to 

evaluate effects on weed suppression and further buffering of climatic extremes. 

Third-level rhizosphere augmentation involved combinations of treatments for 

sodium reduction using banded application of HydraHumeTM at 112 kg ha-1; 

banded phosphorous fertilizer (0-45-0 super treble PO4 at 45 kg ha-1); and 

polymerized, clay-based seed coating (2:1 seed weight ratio). Influence of pretreatment soil parameters will also be analyzed, including surface and subsurface 

texture, pH, sodium adsorption ratio (SAR), electrical conductivity (ECe), and 

major nutrients. 

Plant counts for native and weed species, utilizing ten 1,500 cm2

 (30 cm row 

spacing) or 2,300 cm2 (45 cm row spacing) within-row quadrats per row, were 

conducted during the first growing season (April 26-30, 2004) for cool-season 

species to provide estimates of species germination, emergence, and survival 

(stand success). Because of extreme drought conditions after this date, emergence 

of warm-season species was insufficient to warrant data collection in 2004. 

Planting Techniques Trial and Water Use Trial 

These two trials were carried out by CSU, Fresno, Masters Student Emily Magill. 

The Planting Techniques Trial is a field-based experiment that was developed to 

investigate the relative performance of three planting techniques (drilling, 

imprinting, and broadcasting). Four species of native plants—Atriplex polycarpa, 

Hemizonia pungens ̧ Phacelia ciliata, and Suaeda moquinii—were planted as 

monocultures. The study required 60 plots; plot size was approximately 3.7 m by 

7.6 m (12 feet by 25 feet). Each treatment (i.e., species-planting combination) 

was replicated 5 times. Monitoring included measurements of soil moisture, soil 

electrical conductivity, percent cover, photosynthetic rates, and plant height. 

The second trial, the Water Use Trial, was a greenhouse-based experiment that 

investigated how different watering regimes affected the germination and growth 

of native versus invasive species. Native species were represented by a subset of 

the species used in the Planting Techniques Trial (Atriplex polycarpa and 

Phacelia ciliata). Invasive species were represented by a single species, Bromus 

madritensis (red brome). Data collected in this trial included percent cover, 

photosynthetic rate, biomass (above- and below-ground), and water stress. This 

trial was initiated in the 2003-04 growing season and was continued into the 

2004-05 growing season. 

2004-05 Growing Season 

Herbicide and Charcoal Treatment Trial 

Weed control remains the overriding limitation of restoration efforts on LRDP—

retired (dewatered) lands. Chemical methods of weed control can be particularly 

problematic because most potential herbicide choices exhibit activity on nontarget species (i.e., seeded species). Other integrated pest management (IPM) 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 3-18 

strategies such as grazing, fire, and mechanical control are being evaluated, but 

have limited utility or windows of opportunity during seeded species 

establishment periods. Selective, pre-emerge herbicides with longer residual 

activity in conjunction with native seed / seedling safeners are needed to 

maximize this establishment window. The herbicide and Charcoal Treatment 

Trial was developed to determine if significant levels of control can be achieved 

using only natural precipitation to activate and move the herbicides into the root 

zone of the dominant weeds, with the activated charcoal serving as a protectant 

for the seeded natives. If one of the Experimental Use Permit (EUP) herbicides 

should prove more effective than other herbicide options, a special local need 

permit may be pursued for its broader-scale use within the CVPIA-Land 

Retirement project, since 28,329-40,470 ha (70,000-100,000 acres) within the 

project may eventually be targeted for revegetation. 

The experimental design incorporates a [6x3] factorial study (0.9 ha; installed 

December 13-16, 2004), in which four seeded native forb and shrub species were 

drilled without protectant safener (control) or precisely within an incorporated 

powder band or beneath an over-sprayed slurry band of activated charcoal (GroSafe®; Norit Americas; applied at 336 kg ha-1) to protect them from pre-emerge 

herbicides applied broadcast by ground rig. This weed management approach is 

commonly and successfully practiced in ryegrass and turfgrass industries, with 

possibilities for extension to drilled applications of native species. Six preemerge herbicide treatments (no herbicide [control], Landmark MPTM, Telar 

DFTM, Goal 2XLTM, BroadrangeTM, and Cerano 5MEGTM [the latter two of which 

are evaluated under an EUP), compare potential control of a mixed composition 

of black mustard (Brassica nigra), London rocket (Sisymbrium irio), and the 

“tumbling saltbushes” (Atriplex rosea and A. argentea). Initial monitoring for 

seeded species emergence and survival will commence April 25, 2005. 

It is anticipated that a similar study will be undertaken on the North Avenue 

Property in the 2005-06 growing season. This study will be situated in an area 

dominated by cool-season introduced grasses (Hordeum murinum, Bromus 

madritensis, Avena spp.), and will receive similar herbicide and activated charcoal 

treatments. 

Planting Techniques Trial – Year II 

This trial represents Emily Magill’s second year of Masters research. The same 

three planting methods that were compared in the initial Planting Techniques 

Trial were used here; however, two additional species—Grindelia camporum and 

Lessingia glandulifera—were incorporated. The study required 90 plots; plot size 

was approximately 3.7 m by 7.6 m (12 feet by 25 feet). Each treatment was 

replicated 5 times. Data collection will include those parameters as were 

described for the preceding year. 

Seed Delivery and Competition Trial 

This trial was situated on the northernmost portion of the North Avenue Property 

(ca. 16.2 ha; 40 ac). Restoration efforts had previously been applied to this area; 
Appendix 3. Research and Restoration 

Appendix 3-19 

however, almost all of the native vegetation that was established from these 

efforts was situated on the berms (and adjacent trenches). 

The Seed Delivery and Competition Trial was developed to compare two seed 

delivery methods (imprinting and broadcasting). An additional treatment factor, 

seed mixture, was incorporated into the trial. Two seed mixtures, the “Phacelia 

mixture” and the “Late-season Mixture” were compared. Seeding took place only 

on the “flats” (i.e., the portion between berms), as establishment of the previously 

seeded species was deemed sufficient on the berms to preclude re-seeding. Each 

flat was treated as an experimental plot. Treatments (i.e., the four seed deliveryseed mixture combinations) were assigned randomly in a complete randomized 

block design; each treatment was replicated eight times (32 plots total). 

The “Phacelia mixture” (eight species) had a substantial component of Phacelia 

ciliata (great valley Phacelia), an early-germinating native forb that has shown 

promise in the Native Plant Nursery and in various restoration trials. It was hoped 

that P. ciliata would be able to successfully compete with the annual winter 

grasses that dominate much of the North Avenue Property. Phacelia ciliata

possesses a spreading habit; as the species dies back during the summer months, 

the stems disarticulate creating open habitat. A number of the remaining species 

in this seed mixture were late-germinating perennials. It was hoped that these 

species would be able to become established in the (theoretical) open spaces 

formerly occupied by P. ciliata. 

The “Late-Season Mixture” (seven species) was composed entirely of late-season 

species. The areas seeded with this mixture will be treated with herbicide in the 

early spring (i.e., before any of the seeded species are expected to germinate), to 

create suitable conditions for the establishment of the seeded species. 

Originally, it was intended that seeding would occur shortly after the first rains. 

In this way, it was hoped that seeding would precede germination of the winter 

weeds. However, in the fall of 2004, the initial rains were followed by periodic 

rainy periods, such that during an approximately 6-week long period, the soil 

never dried sufficiently to allowed seeding. Therefore, when conditions finally 

allowed seeding, the winter weeds (specifically, the non-native grasses) had 

developed sufficiently to allow them a distinct advantage over the seeded species. 

To control the weeds, seeding was proceeded by worked the soil with a hookchisel. Seeding took place on November 22, 2004 (imprinting) and December 2-3 

(broadcasting). 

Native Release Trial 

The Native Release Trial was developed to examine the possibility of promoting 

germination of native seed in the seed bank by reducing competition from weeds. 

The trial was situated on a portion of the Tranquillity site that possessed a goodsized population of the native annual forb, Malacothrix coulteri (snakes head). 

This area served as a seed collecting site for snakes head during the 2002-03 

growing season. However, during the next two growing seasons, the abundance 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 3-20 

of the invasive grass Bromus madritensis increased dramatically. Concomitantly, 

M. coulteri decreased in abundance to the point that insufficient individuals did 

not allow harvesting. 

It was hoped that by reducing B. madritensis through various weed-control 

methods, M. coulteri might once again proliferate in the area. Four treatments 

were applied: (1) flaming (i.e., burning existing vegetation with an agricultural 

flamer), (2) mowing, (3) spraying with PoastTM, a grass-only herbicide, and 

(4) spraying with RoundupTM, a broad-spectrum herbicide. 

Plots dimensions were approximately 2 m by 3 m (6.7 feet by 9.8 feet). A 

complete randomized block design was applied, with treatments replicated eight 

times (40 plots total). Monitoring will be conducted during the spring of 2005. 

Native Mowing Trial 

The Native Mowing Trial, another small-plot trial, is situated in the same area as 

the Native Release Trial. This trial was developed to better evaluate the potential 

of mowing as a management strategy for promoting the continuance of native 

species in landscapes threatened by invasive species. 

Treatments consisted of four mowing regimes (one to four mowings) and a 

control (no mowing). A complete randomized block design was applied, with 

treatments replicated eight times (40 plots total). Plots dimensions were 

approximately 2 m by 3 m (6.7 feet by 9.8 feet). Treatments will be applied 

during the 2004-05 growing season. Monitoring will be conducted during the 

spring of the following year (2006). 

Restoration Release Trial 

The Restoration Release Trial was another experiment that was developed to 

examine the possibility of promoting germination of native seed in the seed bank 

by reducing competition from weeds. This trial is situated on the Manning 

Avenue Property—an area that had previously undergone restoration efforts. It 

was hoped that by controlling the invasive species, some of the remaining 

imprinted seed might more readily germinate. 

Four treatments were applied; with one exception, the treatments were the same 

as were used in the Native Release Trial. Treatments were (1) flaming (i.e., 

burning existing vegetation with an agricultural flamer), (2) mowing, (3) spraying 

with RoundupTM, a broad-spectrum herbicide, and (4) spraying with BurnOut 

IITM, a broad-spectrum herbicide. 

Plots dimensions were approximately 2 m by 3 m 6.7 feet by 9.8 feet). A 

complete randomized block design was applied, with treatments replicated eight 

times (40 plots total). Monitoring will be conducted during the spring of 2005. 
Appendix 3. Research and Restoration 

Appendix 3-21 

Restoration and Site Management – Atwell Island 

2000-01 Growing Season 

Site Management 

Barley was planted on the areas where the Habitat Restoration Study would be 

sited (ca. 243 ha; 600 ac), to provide a homogenous setting for the HRS plots. 

The barley was flood irrigated in Study Area 1, and was sprinkler irrigated in the 

other two Study Areas. 

2001-02 Growing Season 

HRS Plot Installation 

Treatments were applied to the 48 HRS plots. Seed of the same 13 native species 

as was used for the Tranquillity HRS plots was imprinted across the 24 “seeded” 

plots in December 2001. In contrast to the Tranquillity HRS plots, no 

transplanting occurred on the Atwell Island plots. Microtopographic contours 

(berms) were created on the 24 “bermed” plots. Forty-nine approximately 12 m 

(39.4 foot) long berms were installed on each plot. 

Evaporation Basin Restoration 

The Evaporation Basin—an approximately 13.3 ha (33-acre) former evaporation 

basin located along the western edge of the Atwell Island LRDP property—was 

targeted for a partial restoration in late 2001. The evaporation basin was 

characterized by a flat expanse of highly alkaline, salt-encrusted soil, nearly 

devoid of vegetation; however, adjacent lands, which are managed by the BLM, 

support fair-sized populations of native alkali sink vegetation. 

Restoration efforts occurred during November and December 2001. Only the 

outer edges of the evaporation basin were accessible, as rainfall at that time had 

created extremely wet and muddy conditions. Vegetation was introduced to the 

site by both seeding and transplanting. Areas to be seeded were prepared by 

loosening the soil with rakes. Native seed from adjacent properties was collected 

and then broadcast onto the raked seedbeds. Species planted in this manner were: 

Allenrolfea occidentalis, Distichlis spicata, Frankenia salina, Heliotropium 

curassavicum, and Suaeda moquinii. Two of these, Distichlis spicata and 

Allenrolfea occidentalis, also were introduced to the site through transplanting. 

Rhizomes of D. spicata that were growing along the perimeter and encroaching 

onto the salt flat were transplanted onto the restoration area. Plugs of Allenrolfea 

occidentalis were grown by the Southern California Edison Nursery (Auberry) 

from native seed collected from the Tranquillity area, and were transplanted 

directly onto the site. 

Site Management 

The barley in the buffers around the HRS plots (ca. 155.4 ha; 384 ac) was 

thrashed and worked into the soil by surface disking. Barley was reseeded in 

areas where the yield was poor. 
Land Retirement Demonstration Project 

Five Year Report 

Appendix 3-22 

Native Plant Nursery and Seed Collecting 

The LRDP Native Plant Nursery was established in the 2001-02 growing season 

to serve a variety of essential functions: (1) to augment available commercial 

sources of native seed; (2) to significantly amplify the number of San Joaquin 

Valley species that were available for use in local restoration activities; (3) to 

serve as a "laboratory", where the various species could be screened for their 

potential applicability in restoration settings; and (4) to provide a setting that was 

suited for outreach and volunteer-centered activities. 

The nursery—and associated seed collecting and processing activities—have 

grown significantly throughout the course of the project. The original nursery 

occupied ca. 0.8 ha (2 ac), of which approximately 0.6 ha (1.5 ac) was planted. In 

the second year (2002-03 growing season), the nursery was relocated to a better 

site, and was expanded to approximately 1.6 ha (4 ac), with weed control 

measures applied to an additional 0.8 ha (2 ac) to prepare that area for future 

nursery expansion. During the third year (2003-04 growing season), the nursery 

expanded again. During this time ca. 0.2 ha (0.5 ac) of the area that was prepared 

during the previous year was put into production. Also, an additional 1.6 ha 

(4 ac) to the east of the nursery were established as a “mechanized nursery,” in 

which eight species were grown in single-species blocks (0. 2 ha; 0.5 ac). In 

contrast to the “main” portion of the nursery, which was reliant on extensive hand 

labor, cultivation and harvesting in the mechanized nursery emphasized machinebased technologies (e.g., the tractor, sprayer, and mechanical seed harvester). For 

the current year (2004-05 growing season), the nursery has been slightly reduced 

in area. The main nursery has been reduced to ca. 1.6 ha (4 ac) and the 

mechanized nursery has been reduced by ca. 0.2 ha (0.5 ac). 

Despite the slight reduction in nursery area for the current growing season, the 

number of species in cultivation has grown steadily. Eighteen species were 

cultivated during the first year. The number of species in cultivation rose steadily 

since that time, with 31 species in 2002-03, and 64 species in 2003-04. Planting 

of the 2004-05 nursery was ongoing at the time of this writing, but it is anticipated 

that about 80 species will be in cultivation. 

Seed collecting activities have also grown dramatically during this period. In the 

first year of seed collection (2000-01) seeds were collected from just seven 

locations. In subsequent years, a significant amount of effort was expended on 

locating additional seed collecting sites. As a result, 45 local collecting sites (i.e., 

within 40 miles of the nursery) are now known. To accommodate the seed (i.e., 

dry, clean, and store) from the nursery and from additional seed collecting, an 

approximately 1,500 square foot facility was leased in 2003. Since that time, a 

variety of seed processing equipment has been purchased and/or constructed, and 

the building has been “outfitted” (e.g., dust-collecting equipment has been 

installed, shelving has been built, etc.). 
Appendix 3. Research and Restoration 

Appendix 3-23 

Literature Cited 

CH2M Hill. 1999. Quality Assurance Project Plan, Land Retirement 

Demonstration Project – Soil, Groundwater, and Surface Water Monitoring. 

41 pp. 

Earnshaw, S. 2004. Hedgerows for California Agriculture. A Resource Guide. 

Community Alliance With Family Farmers. Davis, California. 62 pp. 

Lanini, W. T., S. Fennimore and T. Stevenson. 2003. Pre-irrigation followed by 

cultivation or flaming to deplete the weed seed bank prior to crop planting. 

Pest Management Grants Final Report. U. C. Davis, Davis, California. 

Lee, J. & Dyer, D. A. 1997. Organic Processing Tomatoes in Yolo County: 

Moving Towards Sustainability. TN-PLANT MATERIALS-48. USDANRCS Lockeford Plant Materials Center. Lockeford, California. 11 pp. 

Pollack, O. and T. Kan. 1998. The Use of prescribed fire to control invasive 

exotic weeds at Jepson Prairie Preserve. In: C. W. Witham, E. T. Bauder, D. 

Belk, W. R. Ferren Jr. and R. Ornduff, eds. Ecology, conservation and 

management of vernal pool ecosystems. Proceedings from a 1996 

conference, California Native Plant Society, Sacramento, California. pp. 

241-249. 

Selmon, M. G.W. Moise, PA. Kelly, and C.E. Uptain. 1999. Land Retirement 

Demonstration Project Baseline Biological Inventory for Western Fresno 

County Lands. Unpubl. report submitted to the Interagency Land Retirement 

Team, U.S. Bureau of Reclamation, Fresno, California. 9 pp. 

Uptain, C.E., K. Dulik, P. Brandy, M. Selmon, S.L. Lee, J. Brummer, P.A. Kelly, 

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2000 annual report. Unpubl. report submitted to the Interagency Land 

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Uptain, C.E., N.P. Ritter, S.L. Lee, S.A. Laymon, K.E. Kreitinger, S.E. Phillips, 

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Land Retirement Demonstration Project 

Five Year Report 

Appendix 3-24 

Uptain, C.E., N.P. Ritter, S.L. Lee, J. Brummer, S.A. Laymon, K.R. Garcia, A.J. 

Howard, G. Basso, K.E. Kreitinger, S.E. Phillips, S.R. Messer, D.P. 

Newman, E.M. Magill, L.L. Williams, P.A. Kelly, and D.W. Williams. 2004. 

Land retirement demonstration project, year four, 2002 annual report. 

Unpubl. report submitted to the Interagency Land Retirement Team, U.S. 

Bureau of Reclamation, Fresno, California. 272 pp. 

Wilson, G.D. and J. Stubbendieck. 2000. A provisional model for smooth brome 

management in degraded tallgrass prairie. Ecological Restoration 18: 34-38.