i



# Technical Support Document

f or the
Proposed
Aquatic Life and Aquatic

- Dependent
Wild life Selenium Water Quality Criteria

F or the Sa n Francisco Bay and Delta

( June 201 6 )ii Proposed

Aquatic Life and Aquatic

- Dependent Wildlife

Selenium Water Quality Criteria

For the San Francisco Bay and Delta

June, 201 6

Special thanks to Theresa Presser and Sam Luoma of the United States Geological Survey, Tom Maurer, Bill Beckon, an d Joe Skorupa of the U.S. Fish and Wildlife Service, and Joe Dillon of the National Marine Fisheries Service for providing invaluable insight

.

US Environmental Protection Agency Region 9

Water Division
75 Hawthorne St reet San Francisco, CA 94105

Prepared by Diane E. Fleck, P.E., Esq. and Eugenia McNaughton, Ph

. D

.iii

Table of Contents

E XECUTIVE SUMMARY

................................................................................................... . . .... viii

CHAPTER 1 I NTRODUCTION

.................. ........................................................................... . ... . 1

A. Purpose.....................

....................................................................................... .... . 1

B. Background......................................................................................................

. ... .1

C. Chemistry.............................................................................................

............ .. ... 4

D. E ffects on Biota

.......................................................................................... ... ..... .. 4

CHAPTER 2 S ELENIUM MODELING.

............ . ....... ...................................................... ...... . ... . 7

A. Overview of the USGS Ecosystem

- Scale Selenium Model.....................

. ... . ... 8

B. USGS Modeling of the San Francisco Bay and Delta...

.... ..................... . ...... . 11

a

. Overview of Species

- Specific Variables

. ...... ... .............................. . ... 12

b

. Overview of Environment

- Specific Variables

... ........................... . .... 16

c

. Summary of USGS Modeling of the San Francisco Estuary

...... . ...... 19

CHAPTER 3 S ELENIUM BENCHMARK EFFECT CONCENTRATIONS..

.............................. 21

A. Summary of Benchmarks C onsidered...................................................

.. ...... 21

B. FWS Sources: FWS Specie s Reports............................................................... 23

a . Species at Risk from Selenium Exposure in the San Francisco

Estuary; Final Report (USFWS, 2008)......

....................... ...... . .... 23

b. Selenium Effect Levels for Selected Representative/Surrogate

Species (USFWS, 2009)

................. ............ ........................... . ... ... 27

c. Evaluation of Toxicity of Selenium to White and Green Sturgeon

(USFWS, 2012)

........................... ............................................. ..... 31

C. EPA Sources: CWA Section 304(a) National Recommended Water Quality

Criteri on for Seleniu m and Mallard Bird Studies .

....................................... . ... 37iv a. Freshwater Fish Tissue Criterion Element (USEPA, 2016 )

... ......... . . . 37

b. Bird Egg Tissue Criterion (USEPA, 2011 a ).......................................

. . . 47

D. Benchmarks for EPA Use in Ecos ystem

- Scale Selenium Model............

.... . 51

CHAPTER 4 EPA M ODELING AND PROPOSED WATER QUALITY CRITERIA

... ............... 52

A. Designated Uses.......................................................................................

. ... .. .. 5 2

B. EPA Development of Water Qua lity Criteria.............................................

.. . 53

a. M odeling Vari ables........................................................................

... .... 54

i. Species

- Specif ic Variables...................................................... 54

ii. Environment

- Specific Variables............................................ 69

iii. Summary of Variables............................................................ 72

b. Modeling Results

.. ................................................................................ 7 3

C

. Proposed Criteria

................................................................................. ............. 76

a. Applicable Waters; Magnitud e, Duration and Frequency............... 76

b. Acute and Intermitt ent Criteria.......................................................... 78

D . Summary

........................ ........................................................................... . ....... . 82

R EFERENCES.

......... ..... ........................ .............................................................................. . ...83v

Appendix A. Administrativ e Report: Ecosystem

- Scale Selenium Modeling in Support of Fish

and Wildlife Criteria Development for the San Francisco Bay

- Delta Estuary, California ; by T heresa S. Presser and Samuel N. Luoma; U.S. Geological Survey, Menlo Park, California; December, 2010.

Appendix B. Species at Risk from Selenium Exposure in the San Francisco Estuary; Final Report

to the Environmental Protection Agency ; by William N. Beckon and Thomas C. Maurer; U.S. Fish and Wildlife Service, Sacramento, California; March, 2008.

A ppendix C. Selenium Effect Levels for Selected Representative/Surrogate Species ; by William

Beckon; U.S. Fish and Wildlife Service, Sacramento, California; July 31, 2009.

Appendix D. Evaluation of the Toxicity of Selenium to White and Green Sturgeon ; by William

Beckon; U.S. Fish and Wildlife Service, Sacramento, California; March, 2012.

Appendix E. Additional Details for the Derivation of USGS Trophic Transfer Factor for

Potamocorbula amurensis

Appendix F

. EPA Model ing Results for Proposed Criteria

Appendix G

. Comparative Model ing Results (All Transects)

Appendix H. Partitioning Coefficients (K d s)

Appendix I. Uncertainty/Sensitivity Analysisvi

List of Tables

Chapter 2

Table 2

- 1 Summary of Modeling Variables....................................

... ... ........................... 20

Chapter 3

Table 3

- 1 L ist of FWS Species of Concern (A dapted from USFWS, 2008)...............

... . 22

Table 3

- 2 Summary of EC10 EPA and FWS Benchmarks Considered........................

. . 23

Table 3

- 3 Probable Critical Life Stages (A dapted from USFWS, 2008).....................

... 26

Table 3

- 4 Summary of FWS

- Recommended EC10 Selenium Benchmark Values

for Representative or Surrogate Species (A dapted from USFWS, 2009)......

. 27

Table 3

- 5 Summary of FWS

- Recommended EC10 Selenium Benchmarks for

White and Green Sturgeon (A dapt ed from U SFWS, 2012)...........................

... 33

Table 3

- 6 Summary of 304(a) Recommended Freshwater Selenium Ambient Chronic

Water Quality Criterion for the Protection of Aquatic Life (USEPA, 201 6 )... 38

Table 3

- 7 Lowest Four Reproductive

- Effect Egg/Ovary GMCV s

(A dapted from USEPA, 201 6 )...........................................................................

.... 39

Table 3

- 8 Lowest Four Reprodu ctive

- Effect Whole Body GMCVs

( A dapted from USEPA, 201 6 ).........

.................................................................. .... 39

Table 3

- 9 Lowest Four Rep roductive

- Effect Muscle GMCVs

(A dapted from USEPA, 201 6 )...........................................................................

.... 40

Table 3

- 10 Effects of Dietary Selenium Exposure on Egg Selenium Concentrations

and Hatchability in Mallards (Adapted from Ohlendorf, 2003).....................

. 48

Table 3

- 1 1 Selenium and Hatching Data for Mallard Clutches Collected from the

Davis Wastewater Treatment Facility (USFWS, 2011).................................

... .. 49vii

Chapter 4

Table 4

- 1 Model Variables.......................................................................................

.......... 54

Table 4

- 2 Summary of Life Stages and Diet Mixes of Representative Species

Most at Risk........................................................................

........................ ... ......... 63

Table 4

- 3 Trophic Transfer Factors (TTFs)

............................................................ ... ........ 64

Table 4

- 4 Summary of Diet Mixes and TTFs for Representative Species

Most at Risk................................................................................................

... .... .... 67

Table 4

- 5 Summary of Species

- Spec ific Variables...................................................

... .. . 68

Table 4

- 6 Hydrologic Variables.................................................................................

. ....... 70

Table 4

- 7 Available Transects and Calculated K d Values

........................................... 71

Table 4

- 8 Summary of EPA Modeling Variab les................................................

............. 72

Table 4

- 9 Summary of Representative S cenarios and Results..............................

....... 75

Table 4

- 10 Representative Values of the Proposed Intermittent Water

Concentration Criterion...

.............................................................................. ....... 80

Table 4

- 11 Proposed Selenium Water Quality Crit eria for the San Francisco Bay

and Delta

...... ................................................................................................ ... ........ 81

L ist of Figures

Figure 1

- 1 Map of the San Francisco Bay and Delta System

(A dapted from USGS, 2010)

...... ................................................... . ............... ........ 3

Figure 2

- 1 Ecosystem

- Scale Selenium Model

(A dapted from USGS, 2010 Figure 6)

. ......................................................... ........ 10

Figure 4

- 1 Illustration of an Intermittent Spike Exposure....................................

......... 79viii EXECUTIVE SUMMARY

This document provides the U.S. Environmental Protection Agency’s scientific basis and
recommendations for site

- specific selenium water quality criteria for California’s San Francisco Bay and Sacramento

- San Joaquin River Delta. The proposed criteria are d esigned to protect aquatic life and aquatic

- dependent (avian) wildlife , including federally listed threatened and endangered species, from reproductive and developmental effects of elevated levels of selenium in the aquatic environment. The existing water quality criteria, promulgated in 1992 in the National Toxics Rule, do not reflect the latest science on selenium fate and biological uptake. This document considers updated science in dev eloping the revised criteria values.

The recommended criteria co nsist of fish tissue values, prey (clam) tissue values, and dissolved and particulate water column values. All proposed values are considered com parably protective . The water column and clam tissue values are based on detailed modeling of the estuary usi ng the USGS Ecosystem

- Scale Selenium Model (Presser and Luoma, 2010), a model specifically developed to predict the fate and biological uptake of selenium in the San Francisco
estuary. The proposed values are presented in the table below.

Proposed Seleniu m Water Quality Criteria for the San Francisco Bay and Delta

Media Type Tissue Water Column 1

Criteria Fish Whole

Body or Muscle Clam Dissolved
Chronic Intermittent Exposure 2 Particulate Chronic

Magnitude 8.5 μg/g dw

whole body

or 11.3 μg/g dw
muscle 15 μg/g dw 0.2 μg/L WQC int =

0

. 2 μg / L

− C bkgrnd ( 1

− f int )

f int 1 μg/g dw

Duration Instantaneous

measurement Instantaneous

measurement 30 days Number of days/month with
an elevated concentration 30 days

Frequency N ot to be

exceeded N ot to be

exceeded Not more th an

once in three

years Not more tha n once in three

years Not more tha n once in three
years

1 Water column values are based on dissolved total selenium (includes all oxidation states, i.e., selenite, selenate, organic selenium and any other forms) in water.

2 Where C bkgrnd is the average background selenium concentration in μg/L, and f int is the fraction of any 30

- day period during which elevated selenium concentrations occur, with f int assigned a value ≥ 0.033 (corresponding to one day).

Note 1: The criteria apply to all waters of the San Francisco Bay and Delta in which the salinity is greater than 1 part per thousand 95% or more of the time. Note 2: A translator of 1 shall be used to determine total recoverable selenium values from di ssolved selenium criteria values for use in deriving water quality

- based effluent limitations for point sources.1

CHAPTER 1 INTRODUCTION

A. Purpose

The purpose of this document is to provide the U

. S

. E nvironmental P rotection A gency ’s (EPA or Agency ) scientific basis for its proposed site

- specific selenium water quality criteria for California’s San Francisco Bay and Delta estuary ecosystem. The criteria are designed to protect aquatic life and aquatic

- dependent wildlife in cluding federally listed threatened and endangered species. P ursuant to Clean Water Act section 303(c) and EPA’s implementing regulations at 40 CFR 131.11 (a) , water quality criteria must be based on sound scientific rationale and must contain sufficient parameters or constituents to protect designated uses; for

wate rs with multiple use designations, the criteria must support the most sensitive designated

use s

. The site

- specific selenium criteria are intended to be protective of the State’s established aquatic life and wildlife designated uses w hich include: migratio n of aquatic organisms ; spawning, reproduction and early development of fish; estuarine habitat ; warm and cold
freshwater habitat s ; wildlife habitat; and rare, threatened or endangered species

. The information provided herein does not substitute for the C lean Water Act or EPA regulation, nor is this document a regulation itself. Thus, this document cannot, and does not, impose any legally binding requirements on EPA, the State of California, authorized Tribes, the regulated community, or any other party, and might not apply to a particular situation or
circumstance.

B. Background

Under C lean Water Act ( CWA ) section 304(a), EPA is required to publish water quality
criteria guidance values for priority toxic pollutants, for s tates and t ribes to consider in developing water quality standards. Over the years, EPA has developed a number of pollutant criteria documents for the protection of human health and aquatic life. These guidance values

are termed CWA section 304(a) national recommen ded water quality c riteria, and are informally referred to as “ national recommended criteria ” or “304(a) criteria.” National

r ecommended criteria for aquatic life protection have traditionally been developed as water
column concentrations that reflect the toxicity of water

- only exposure of the pollutant t o aquatic biota. Water column concentrations can be implemented directly to control and limit discharges. However, for pollutants such as selenium that accumulate in aquatic biota through
diet and where toxicity is exhibited through dietary exposure, tissue concentrations can better

re present levels of toxicity, particularly for higher order species if the pollutant bioaccumulates through the food chain . Since tissue concentrations may be difficult to im plement directly, it is
useful to translate tissue concentrations to water column values that reflect the
bioaccumulation

, i.e., a water column concentration that is related to the tissue concentration2

of the predator species of concern that is accumulatin g the selenium

. Therefore, E PA has
de velop ed a national recommended criterion for selenium that incorporates both tissue

- based
values and translations to water column values in order to facilitate the monitoring and regulation of pollutant discharges.

The national recommended tissue criterion incorporates fish tissue values based on the empirically measured relationship between reproductive effects and fish tissue values from dietary exposure from a range of field and laboratory studies (USEPA, 2016 )

. Using the U.S. Geological Survey (USGS) Ecosystem

- Scale Selenium Model 1 (Presser and Luoma, 2010), EPA
also included water column values assoc iated with the fish tissue values for lenti c and lotic systems (USEPA, 2016 ).

The current ly applicable aquatic life water quality criteria for selenium in the San Francisco Bay and Delta are those that were promulgated as part of the National Toxics Rule ( NTR) (57 FR 60848, December 22, 1992, as amended by 60 FR 22228, May 4, 1995; codified at

4 0 CFR 131.36). Th e aquatic life chronic criterion value is 5.0 micrograms per liter ( μg/L ) (total recoverable)

. The NTR criteria are based on EPA’s 1987 national aquatic life selenium
freshwater criteria recommendations, Ambient Water Quality Criteria fo r Selenium

- 1987 , EPA

440/5

- 87

- 008, and are represented in terms of water column concentrations. The 1987
national recommended criteria were derived from observed field condition s at a contaminated lake, Belew s Lake, North Carolina, a cooling water reser voir that had been affected by selenium
loads from a coal

- fired power plant, and reflect water column and dietary exposure of selenium (USEPA, 1987).

Since t he most significant exposure pathway of selenium to species of concern in the San Francisco Bay and Delta is through diet

, the currently applicable criteria for selenium from
the NTR no longer adequately protect species in the estuary. This document provides the basis for EPA’s proposed site

- specific water quality criteria for selenium protective of aquatic life and aquatic

- dependent wildlife for the San Francisco Bay and Delta to address bioaccumulation through dietary exposure

.

EPA is proposing t he site

- specific criteria apply to all salt and estuarine waters of the San Francisco Bay and D elta (s ee Figure 1

- 1 Map of the San Francisco Bay and Delta System )

. These
waters are located with in the jurisdictions of the San Francisco Bay Regional Water Quality

1 The model is a predictive tool to delineate the fate and biological uptake of selenium in an aquatic ecosystem, and is discussed in detail in Chapter 2 of this document.3

Control Board (SFRWQCB ) and the Central Valley Regional Water Quality Control Board ( CVRWQCB) of the State of California.

Figure 1

- 1 Map of the San Francisco Bay and Delta System ( A dapted from USGS, 2010)4

C

. Chemistry

In the Periodic Table, selenium is a non

- metal , even though it is often considered a
metalloid

. S elenium exists in several allotropic ( variant molecular structural) forms, and its most stable form, crystalline hexagonal selenium, is a metallic gray substance, exhibiting metal

like characteristics , including photoconductivity and photovoltaic properties

. Selenium often

occurs naturally in organic carbon

- enriched sediments , and is readily mobilized in the
environment and transformed in to bioavailable forms. It bioaccumulate s in organisms over
time and is assimilate d into the food chain.

Seleniu m occurs naturally in sediments of marine origin, and can enter the aquatic
environment when water comes into contact with selenium

– bearing deposits. Aquatic environmental problems occur when selenium is mobilized through human activities, including agricultural irrigation, mountain top mining, and the processing of fossil fuels such as petroleum
refini ng. Once selenium is converted, it tends to remain in a bioavailable form which contributes to its build up in the biotic environment over time ( US EPA, 2011 b ). Un der highly anoxic conditions (e.g., buried sediments), it can be reduced to elemental selenium, but does not readily convert to the elemental form from a bioavailable form ( USEPA, 2011b ). Depending on environmental conditions, one or another selenium spec ies such as selenate, selenite and

organo

- selenium, which differ in transformation rates and bioavailabi li ty, may predominate. The least bioavailable form, selenate, can be reduced by some organisms to selenite, a more bioavailable form, which can then be accumulated as organo

- selenium , the most bioavailable
form of selenium ( USEPA, 2011b).

D. Effects on Biota

Although selenium is an essential micronutrient for bacteria and animals, it is a dose

sensitive nutrient, and the range between essential and to xic levels in many organisms is narrow ( Chapman et al., 2009) . Selenium can be toxic to organisms at very low levels of chronic exposure (Lemly, 1997). It has been a long

- standing hypothesis that selenium t oxicity occurs through biochemical pathways where selenium may not be distinguish ed from sulfur, with
excess selenium substituting i nto proteins and altering protein structure and function ( see USGS Linking Selenium Sources to Ecosystems: Local and Global Perspectives , Modeling at http://wwwrcamnl.wr.usgs.gov/Selenium/modeling.htm ). More recent studies indicate that selenium may affect organisms via oxidative stress (USEPA, 201 6 ). The role of selenium

induced oxidative stress in em bryo toxicity and teratogenesis (embryonic malformations) appears to be related to impacts on metabolic enzyme (glutathione) homeostasis. In a review of bird studies, Hoffman (2002) reported that avian exposure to selenium altered ratios of
reduced to oxi dized glutathione and thus increased measurements of oxidative cell damage.
Pala ce et al. (2004) suggested that, in rainbow trout embryos, oxidative stress due to elevated5

selenium levels results in pericardial and yolk sac edema. For a more detailed dis cussion of the mechanism of toxicity at the biochemical level, including the role of oxidative stress, see Janz et al. (2010). Exposure to elevated selenium in fish and other wildlife causes reduced growth, and reduces reproductive success through effects that lower embryo survival, most notably from teratogenesis (Eisler, 1985 in US FWS, 2 008; Stewart et al., 2004 in US EPA, 2011 b ).

A well

- documented c ase of selenium toxicity to wildlife occurred in the 1980s, when agricultural runoff high in selenium colle cted in a r eservoir consisting of shallow ponds in the
Kesterson Wildlife Refuge , part of the San Luis Wildlife Refuge in the Central Valley of
California

. Built in the early 1970s as part of the San Luis D rain system to discharge agricultural
runoff from the west side of the San Joaquin River basin to the San Francisco Delta

, Kesterson
was to be a tem porary holding area or terminus within the Valley until the drain could be
extended in to the Delta. By 1982, toxic levels of selenium from agricultural irrigation drainage
moved from the aquatic environment into the food chain ( see USGS Understanding O ur Planet
Thr ough Chemistry at http://minerals.cr.usgs.gov/gips/na/elemap.html ). W idespread fish mortality was observed , as well as an unusually high percentage of avian embryo and hatchling deformities such as missing eyes, shortened, twisted or missing legs, an d elongated or missing
beaks , all characteristic of selenium poisoning (USGS Linking Selenium Sources to Ecosystems:
Local and Global Perspectives, Irrigation at http://wwwrcamnl.wr.usgs.gov/Selenium/irrigation.htm ). In 1983
, a 64% rate of deformity and death of embryos and hatc hlings of wild aquatic birds was recorded

. Th e destruction of
wildlife at Kesterson brought the effects of selenium bioaccumulation and assimilation to national attention (see also Ohlendorf et al.

, 19 86a, 1986b, and 1986c).

Selenium can accumulate in the aquatic food web through various routes and at various

rates. Some aquatic food webs are very efficient at taking in and transferring selenium up the
food chain . At the bottom of the food chain

, microorganisms ( bacteria and algae ) can bioaccumulate selenium to levels that greatly exceed water column concentrations, and some inve r tebrates

, namely filter feeding clams

, can very efficiently accumulate selenium from

s uspended organic and inorganic particulate material and bed sediment

. Since exposure to selenium primarily occurs through diet, an organism ’ s exposure to selenium is affected by the
concentration of selenium in its food sources. In the San Francisco Bay and Delta, clam

- based
f ood webs accumulate selenium at a much higher rate than insect

- based food web s

. Potamocorbula amurensis ( P. amurensis) 2 or Corbula

, an introduced clam species
, can now be

2 Also commonly known as Corbula amurensis (C. amurensis) . See : World Register of Marine Species at http://www.marinespecies.org/aphia.php?p=taxdetails&id=397175 on 2014

- 09

- 17; and see the Integrated Taxonomic Information System on

- line data base at: http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=81746

.6

found throughout the San Francisco estuary , primarily in subtidal areas , across the full range of bay salinities (<1 to 33 parts per t housand

, ppt ) (Carlton et al., 1990 ; Thompson and Parchaso

, 2010 )

. Corbula are abundant in S an Pablo Bay , and Suisun Bay and Marsh , and accumulate selenium at roughly three times the rate of supplanted native clam species ( Cohen, 2011 at http://www.exoticsguide.org ; Stewart et al., 2004 ). In San Francisco Bay, p redator species that prefer to feed on Corbula , such as diving birds and sturgeon, are exposed to high er levels of
bioaccumulated selenium than species that feed mainly on insects or higher order species
within an insect

- based food web.

The risk of impacts or vulnerability of a species to selenium is determined by a
combination of facto rs such as the species ’ exposure ( incl uding exposure through diet and
habitat ) , toxicological sensitiv ity 3

, and population status

. O ther important factors include the duration and timing of the exposure and life stage of the species. For example, white sturgeon spend much of their lives in Bay and Delta waters, but may be ove rall less toxicologically
sensitive to selenium in their diet than green sturgeon (De Riu et al., 2014 , USFWS, 2012 ) . O n the other hand, adult gr een sturgeon are believed to spend less time than white sturgeon in the
estuary (US FWS, 2008 and 2012). Concerns have been raised about the sensitivity of juvenile
salmon

, whose preferred habitat includes the Delta and San Joaquin River (USFWS, 2008 and 2009)

. The juvenile or the developing stage of a species

, a critical life stage

, may be more vulnerable to selenium exposure. E xposure to selenium

- laden prey during these stages could
have a significant impact on the survival and growth of the species.

The availability of selenium under different physical and b iological conditions explains why water column concentrations may not by themselves be sufficient indica tors of toxicological effect. In addition, h ydrologic conditions and water chemistry affect the degree to
which selenium is taken up into the food chain at a given site. Lentic water systems, where waters are calm and flushing is limited, enhance the production of bioavailable forms of
selenium (selenite) . Lotic water systems, where waters are flowing and flushing is rapid, limit selenium uptake given the rapid movement of the water and the predominant form of selenium (selenate ) ( Nagpal and Howell , 2001, and Adams et al., 2000 in Simmons and Wallschlager , 2004)

. Where different types of water bodies are contiguous, impacts to
downstream waters shall be taken into account (40 CFR 131.10(b ))

. All of these species

- specific and hydrologic factors have been considered in determining appropriate site

- specific water quality criteria for selenium in the San Francisco Bay and Delta.

3 Toxicological sensitivity to selenium refers to toxicity effects due only to increased levels of selenium, usually determined under laboratory controlled conditions. Different fish species can have very different inherent toxicological sensitivity to selenium (Janz et al., 2010).7

CHAPTER 2 SELENIUM MODELING

EPA has been working collaboratively with the U.S. Fish and Wildlife Service ( FWS ) and
the National Marine Fisheries Service (NMFS) (col lectively, the Services) t o gather information about threatened and endangered species’ vulnerability to selenium, and with USGS to model the biological movement of selenium in the estuary. The Services provided detailed information concerning critical sp ecies and benchmark effect concentrations that are important in the modeling (see Chapter 3). USGS first published a selenium fate, transport and biological uptake methodology in Forecasting Selenium Discharges to the San Francisco Bay

- Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

, USGS Open

- File Report 00

- 416 (USGS, 2000). This publication was revised and superseded by Professional Paper 1646 (USGS, 2006). As discussed in Professional Paper 1646, the methodology was valida ted using field data and peer reviewed through the USGS Fundamental S cience Practices review process before publication 4

. The methodology outlined in Professional Paper 1646 is the basis of the Ecosystem

- Scale Selenium Model, which is explained in Presser and Luoma (2010). When the Services, USGS, and EPA met in September 2002 to discuss the development of selenium criteria for the San Francisco estuary, the agencies agree d that the USGS methodology

, originally developed to evaluate selenium loads to the estuary through the proposed San Luis Drain extension, offered the best available predictive tool to understand the fate and biological uptake of selenium in the Bay and Delta, and that it would be appropriate to use in the development of site

- specific aqu atic life and aquatic

- dependent wildlife criteria.

Starting i n 2003, EPA provided funding for the USGS to model selenium fate and biological uptake in the estuary , using the Ecosystem

- Scale Selenium Model . USGS completed its report Ecosystem

- Scale Selen ium Modeling in Support of Fish and Wildlife Criteria Development for the San Francisco Bay

- Delta Estuary, California, Administrative Report ( the USGS report) and submitted it to EPA in December, 2010 (USGS, 2010; Appendix A). The modeling was validated by comparing existing site

- specific field data sets from 1998

– 2001 to predicted selenium concentrations in prey (specifically Corbula ), water and suspended particulate material. The predicted selenium concentrations compared w ell with observed concentrations (USGS, 2010 pages 24

– 25 and Tables 14, 15, and 16). The report underwent review through the USGS Fundamental S cience Practices process prior to publication.

4 Th e USGS review process incl udes extensive technical review and comment by experts not associated w ith the work and a thorough reconciliation document, prior to public release of the final document. The USGS technical peer review process is outlined in U.S. Geological Survey Fundame ntal Science Practices Circular 1367, at http://www.usgs.gov/quality_integrity/

.8

U SGS used site

- specific data from various sources, and speci es

- specific data from FWS in

two report s: Species at Risk from Selenium Exposure in the San Francisco Estuary , and Selenium Effect Levels for Selected Representative/Surrogate Species (USFWS, 2008 and USFWS, 2009, Appendices B and C, respectively). The US GS report illustrates how selenium moves through the San Francisco ecosystem using site

- specific hydrologic and species

- specific information for the estuary. EPA relied on the Ecosystem

- Scale Selenium Model, the USGS report, the FWS reports, and other mat erials to develop the analyses contained in this document, on which the proposed criteria for the estuary are based (see Chapter 4).

A. Overview of t he USGS Ecosystem

- Scale Selenium Model 5

As selenium bioaccumulates and assimilates into and up through th e food web via predator

- prey food chains, the most important route of exposure to wildlife is through diet. Therefore, to be scientifically credible and for regulatory purposes, m odeling the fate and biological uptake of selenium in an aquatic environment for the protection of aquatic species and aquatic

- dependent species must consider diet . The Ecosystem

- Scale Selenium Model conceptualizes and quantifies the variables that predict how selenium moves from the water environment to wildlife speci es. The model uses biogeochemical and physiological factors from
f ield and laboratory studies, account ing for selenium speciation, loading, transformation between dissolved and particulate selenium, bioavailability and bioaccumulation, and trophic
transfe r and assimilation to higher order species.

Using the model, selenium concentrations in different media can be linked to translate predator tissue concentrations to dissolved water column , particulate water column

, and/ or prey food tissue concentrations. T he flexibility of the model promotes a more complete understanding of how selenium behaves in site

- specific ecosystems . It takes into account the specific food web of the species of interest , as well as site

- specific biogeochemical conditions
such as s elenium partitioning between dissolved and particulate forms in the aquatic
environment . This last variable is critical to determining selenium uptake through phytoplankton and bacteria at the bottom of the food web. Since the efficiency of selenium to
be taken up into the aquatic environment by particular food webs varies widely, choosing the appropriate ecosystem (i.e., food web) and environmental variables, such as partitioning conditions, is key to determining the extent of bioaccumulation and assimila tion to higher

trophic level wildlife species.

5 Some information in this section is paraphrased and/or summarized from A Methodology for Ecosystem

- Scale Modeling of Selenium , published in Integrated Environmental Assessment and Management (IEAM), Volume 6, Number 4, pp 685

- 710, Presser and Luoma, May 26, 2010.9

The model considers source s of selenium, such as agricultural drainage, oil refinery effluent, and mining discharge; dissolved selenium speciation ( selenate, selenite, and organo

selenium ) ; particulate selenium speciation ( elemental selenium, adsorbed selenite and/or selenate, and organo

- selenium ) ; and receiving water type or transformation al environment
such as wetlands, marsh es , pond s , stream s , river s , and estuaries. The model also considers the
bioav ailability potential of different media such as sediment, detritus, phytoplankton , and periphyton; invertebrate

- specific bioaccumulation potential and trophic transfer factors to fish or aquatic birds using species

- specific physiological parameters includi ng ingestion rate, assimilation efficiency, efflux rate, and growth ; health effects endpoints such as reproduction, teratogenesis, decreased growth, and decreased survival; predator life cycle s using species

specific energetics (body weight and ingestion rate) , life stage (breeding, larval, adult)

, distribution (resident, mobile, migratory) , timing (route, duration)

, and feeding behavior (prey availability and preference, etc.) ; and demographics including l oss of individuals, population reduction, and comm unity change (Presser and Luoma, 2010 Table 1).

The linked approach to environmental variables synthesizes the site

- specific fate

, bioaccumulation and assimilation of selenium within a particular ecosystem. Figure 2

- 1
, Ecosystem

- Scale Selenium Model

, is a generalized schematic of variables and linkages involved (USGS, 2010 Figure 6). For a detailed discussion of the model , see A Methodology for Ecosystem

- Scale Modeling of Selenium , published in Integrated Environmental Assessment and Management (IEAM), V olume 6, Number 4, on May 26, 2010 (Presser and Luoma, 2010).10

Figure 2

- 1 E cosystem

- Scale Selenium Model (A dapted from USGS, 2010 Figure 6)11

B. USGS Model ing of the San Francisco Bay and Delta 6

Using site

- specific information for the San Francisco Bay and Delta, USGS ran the Ecosystem

- Scale Selenium Model under several different hydrologic scenarios and ecological endpoints for the Bay and Delta system to help identif y protective selenium values and associated critical flow and loading conditions. The various scenarios and endpoints illustrate the variability and sensitivity of the system under different conditions

, which informs the process to define the best represent ation of the system for der iving protective regulatory
values based on site

- specific conditions. A brief summary is presented here; details of the USGS modeling can be found in the USGS report in Appendix A (USGS, 2010 ).

The estuary m odeling focused on the area of the Bay from th e Golden Gate Bridge through the central and northern Bay and Delta to Rio Vista on the Sacramento River and to Stockton on the San Joaquin River (see Figure 1

- 1 Map of the San Francisco Bay and Delta System)

. T he South Bay area (Lower San Francisco Bay a nd South San Francisco Bay) is shallower and slower moving than the central and northern parts of the Bay. It exchanges water with other parts of the Bay , and shares similar estuarine processes, species, and habitats with the central and northern parts of the Bay and Delta. The South Bay provides habitat for the important species evaluated in the modeling. T herefore, protective selenium values based on the modeling should be appropriate for the entire Bay and the Delta system.

The Sacramento and San Joa quin Rivers are the main sources of inflow to the Delta. T he Sacramento River is the dominant inflow under current flow management conditions. The
rivers mix with seawater in the Delta and with internal selenium sources. T he model considers
the total ri ver inflow from the Sacramento and San Joaquin Rivers, San Joaquin River water diversions and exports, and the total outflow of the estuary to the Pacific Ocean (or Net Delta Outflow Index, or NDOI , which is related to residence time for freshwater in the Delta and Bay).

The model quantif ies selenium concentrations in water, suspended particulate matter, and prey tissue that would be present, given a certain selenium concentration in a predator

s pecies under specific environmental conditions. For a given predator tissue selenium
concentration (e.g., 8.5 micrograms of selenium per gram of tissue dry weight ), the choice of species (e.g., adult white sturgeon) determines the food web to be modeled. Once a food web is chosen, the selenium concentrations of species within the food web can be determined using

tro phic transfer factors, which relate selenium concentrations in species to concentrations in

6 Some Information in this section is paraphrased and/or summarized from the USGS report in Appendix A (USG S, 2010).12

their food. Invertebrate concentrations at the bo ttom of the food web can be linked to their food source concentrations, e.g., the concentration of selenium in clams can be linked to the concentration of selenium in suspended particulate material. Suspended particulate selenium
concentrations can be lin ked to dissolved selenium concentrations by environmental partitioning coefficients

. Determining the protective water column selenium concentration requires that the appropriate range of site

- specific partitioning coefficients be use d in the modeling.

Mo del variables are either species

- specific, i.e., relating to the species of concern, or
environment

- specific, i.e., relating to the physical environment of the system in which the species is found. The s pecies

- specific variables include:

 Choice of specie s to protect and their critical life stage or stages ;

 Food Web of the species of concern, to define prey/predator pairs in their diet;

 Diet Mix and Trophic Transfer Factors ( TTFs ) to define the relative amounts of prey in the species’ diet (diet mix), and to define how much selenium bioaccumulate s and
assimilate s into and through the species’ food chain (TTFs) ; and

 Effect Concentration Guidelines to define how much selenium may be harmful to the species of concern.

The e nvironment

- specific variables include:

 Salinity to constrain locations and thus potential pathways for loading, transformation, and exposure;

 Partitioning Coefficients or K d s to quantify how much selenium is available to enter the base of a food web under specific hydrologic conditi ons; and

 Flow Year Type and Flow Season to reflect appropriate hydrologic conditions.

a. Overview of Species

- Specific Variables

Wildlife Species , Critical Life Stages and Food Web : Since hundreds of wildlife species are present in the San Francisco est uary, FWS identified the species most at

- risk due to elevated levels of selenium in a report, Species at Risk from Selenium Exposure in the San Francisco Estuary (USFWS, 2008). The FWS report considered both migratory 7 and indigenous
b ird and fish species , and i dentified a smaller list of the most potentially vulnerable species (see Chapter 3). For each at

- risk species, t he FWS report included information about th e critical life

7 The San Francisco estuary is located along the Pacific Flyway and is a stopover for many avian species.13

stage or stages , such as adult female reproduction (including egg laying)

, ad ult migration

, and juven ile growth and development

. The FWS analysis also contained detailed information about diet, including whether it was primarily clam

- based or included insects and other prey items such as amphipods . If diet was primarily clam

- base d, the FWS report included an approximate percentage of clams in the species’ diet.

USGS categorized the at

- risk species by food chain (clam

- or insect

- based) and modeled each category separately: clam

- eating fish ; clam

- eating birds ; and insect

- eating f ish (see Chapter 3, Table 3

- 1) . Each category include d at least one threatened or endangered species
listed under the Endangered Species Act (ESA) (16 U.S.C. § 1531 et seq.). The s pecies cons idered

most at

- risk that are federally listed are the California Ridgway’s rail ( Rallus longirostris ) 8 , a clam

- eating bird ; green sturgeon ( Acipenser medirostris ) , a clam

- eating fish; and (juvenile) Chinook salmon ( Oncorhynchus tshawytscha ) and steelhead trout ( O

. mykiss ) , both insect

eating fish (USFWS, 2008)

. Clam

- eating species are considered at

- risk because of the presence of the invasive clam Corbula

.

Corbula

, a small bivalve ( 25 m illimeters [m m ] or less)

, was discovered in Suisun Bay in the northern part of San Francisco Bay after a major flood in the spri ng of 1986 that removed parts of the benthic community in the estuary (Cohen, 2011). I ts increase and spread coincided
with a multi

- year dry period that began in the summer of 1986. Corbula is now found to be
abundant throughout the Bay and most of the Delta

. A dults ca n be found at salinities from 1 to
3 3 ppt , with long

- term survival greatest at salinities over 5 ppt, and recruits from 2 to 30 ppt ;
t hese ranges encompass the Bay and most of the northern estuary in most seasons and years ( Cohen, 2011; Th ompson and Parchaso, 2010; California Department of Water Resources
Benthic BioGuide at http://www.water.ca.gov/bdma/BioGuide/ ). Corbula is also a frequent
and d ominant bivalve species in the South B ay ( Thompson and Parchaso, 2010). It is most often
observed in subtidal waters, but can also be foun d in intertidal mudflat s (Cohen, 2011; Thompson and Parchaso, 2010; California Department of Water Resources Benthic Bio Guide at http://www.water.ca.gov/bdma/BioGuide/ ). Because this clam species is very efficient in

accum ulating selenium from its environment (Stewart et al., 2004), the species most at risk are
believed to be clam

- eating fish and clam

- eating birds.

Diet Mix : Diet mix is the amount of each type of prey in a species’ diet. To evaluate the sensitivity of the model, USGS modeled different diet scenarios: an all

- clam (100% clam) diet and a 50% clam/50% amphipod diet for clam

- eating fish and clam

- eating birds, and an all

- insect

8 The California Ridgway’s rail was formerly known as the California clapper rail (Chesser et al., 2014).14

(100% insect) diet for insect

- eating fish 9

. Other considerations include d how long and during what life stages the species reside in the estuary . For example, a lthough white sturgeon migrate upstream to spawn, they spend most of their life in the estuary. Sturgeon are long

lived (green up to 50, white u p to 100 years), and have a two

- year internal egg maturation period. The longevity and extended reproductive cycle of white sturgeon may increase their dietary exposure to selenium from Corb ula in the estuary, and may contribute to selenium loading in eggs (USGS, 2010 citing Linville, 2006).

Trophic Transfer Factors: T he model uses trophic transfer factors or TTFs to model the uptake or bioaccumulation of selenium from one trophic level t o the next in a food chain. TTFs define the relationship between selenium concentrations in an animal and in its food , and are species

- specific or , lacking specific data may incorporate a n appropriate category of animal with known feeding habits , e.g., fo rage fish (USGS, 2010 ).

TTFs can be determined from physiological parameters using a biodynamic equation or
derived from field data

. The biodynamic equation considers the selenium concentration in the animal, exposure time, assimilation efficiency from ingested particles, the ingestion rate of particles, the selenium concentration of ingested particles, the efflux (excretion) rate, and the growth rate of the animal (USGS, 2010).

If derived from matched data sets of field concentrations, TTFs can be estimated by dividing the concentration of selenium in the animal by the concentration of selenium in its prey species (food source), or TT F (species) = C (species) / C (prey) . F or example:

TTF (i nvertebrate ) = C (i nvertebrate ) / C (s uspended particulate matter )

where the Cs are the concentrations of selenium in the animal (invertebrate) and in its food source (suspended particulate matter 10 ), respectively (USGS, 2010 ). If the species has a mixed diet that includes more than one prey species, the concentration of selenium in its prey specie s can be weighted for each species. The higher the TTF value, the more the animal accumulates

s elenium from its food source.

Information from one method can be compared or combined with information from

an other to refine or verify outcomes for specific species. Once TTFs are known, they can be

9 The detailed dietary informat ion provided in the FWS report (USFWS, 2008) for the species most at

- risk is considered and discussed in Chapter 4, EPA Modeling and Proposed Water Quality Criteria.

10 USGS defines suspended particulate material (spm) as a mixture of living and non

- living material (USGS, 2010).15

combined to represent step

- wise bioaccumulation of selenium from particulate material through an invertebrate to a predator fish or bird species (USGS, 2010).

Bioaccumulation of selenium from suspended particulate matter to invertebrate species
varies w idely . I n general b ivalves accumulate selenium more efficiently than other invertebrates (Presser and Luoma, 2010), and Corbula accumulates selenium much more efficiently than other bivalves in the estuary (Stewart et al

. , 2004; USGS, 2010).

Since bioa ccumulation rates differ widely among invertebrates and accurate characterization is critical to modeling success, USGS developed site

- specific TTFs for Corbula in the estuary . USGS used a mechanistic equation for quantifying the biodynamics of Corbula

, a nd
estuary

- specific data for their food source of suspended particulate material (USGS, 2010 pages 21

– 23 and equations 14, 15 and 16). The mean TTF for Corbula from suspended particulate
material in the estuary is 17.1, and the range across the estuary is 14

– 26 (USGS, 2010). Since the modeling is representative of the estuary, USGS used a rounded mean TTF value of 17 (see Appendix E Additional Details for the Derivation of USGS Trophic Transfer Factor for
Potamocorbula amurensis ).

A discussion of other TTFs used in the modeling for the estuary is included in the USGS report. Calculated TTFs for various freshwater and marine species are summarized in Presser and Luoma (2010) (see Table 3 and Supporting Information).

Selenium Benchmark Effect C oncentrations: A benchmark is the concentration of a pollutant that relates to a level of adverse effect in the population of an animal or a category of animal (e.g., pelagic fish or aquatic birds). Selenium benchmarks are often expressed a s a concentration of selenium in the predator species’ tissue. B enchmarks for fish tissue can be expressed as an egg or ovary , whole body or muscle concentration. Benchmarks for bird tissue

a re expressed as an egg concentration. Benchmarks are expressed in micrograms per gram (μg/g) or milligrams per kilogram ( mg/kg ) in dry weight ( dw ), e.g., 8.5 μg/g dw or 8.5 mg/kg dw. Studies use both; they represent the same unit and are used interchangeably in this document.

Benchmarks or effect concentrations ( ECs ) can be specified at different levels of effect

a nd for different endpoints. ECs are the concentrations of selenium that may negatively affect up to a certain percentage of the species population , i.e., an EC05 level may affect up to 5% of the population, and an EC10 level may affect up to 10% of the population. Endpoints include those associated with reproductive effects and those associated with non

- reproductive effects. For selenium, r eproductive effect endpoints are those associated with maternal diet and
transfer , and most often include reproductive failure (larval mortality for fish, hatchability for16

birds) and larval and juvenile deformity (teratogenesis); non

- reproductive effect endpoints are those associated with diet and most often include reduct ion in or abnormal juvenile growth and development. Hatchlings and juvenile fish born with deformities and/or experiencing stunted growth and development are u nlikely to survive to adulthood. They are much less likely to successfully reproduce, reducing the overall success of the spec ies population in the ecosystem

. Therefore, both reproductive and non

- reproductive effects are important take into
consider ation

.

For several at

- risk species, FWS provided information about selenium benchmarks, or
selenium effect concentrations (USFWS, 2009

, 2012). Mallard ducks ( Anas platyrhincos ) were chosen as the surrogate species for all aquatic

- dependent birds given the lack of available data on listed and/or at

- risk birds, and the relative abundance of data as to th e toxicological sensitivity of mallards to selenium (USFWS, 2009). FWS provided s elenium effect concentrations as a concentration of selenium in the species tissue (whole body for fish and egg tissue for birds), and as a concent ration of selenium in the d iet (USFWS, 2009, 2012)

.

USGS modeled the three food web categories found in the San Francisco Bay and Delta ( clam

- eating fish, clam

- eating birds, and insect

- eating fish), using the FWS values for EC0, EC05, and EC10 effect concentrations as endpoints 11 (USGS, 2010 Table 17 for clam

- eating fish, Table
18 for clam

- eating birds and Table 19 for insect

- eating fish ). The results identified associated water column, particulate, an d prey selenium concentrations for the different scenarios.

b. Overview of Envi ronment

- Specific Variables

Salinity: The two food web s in the estuary (clam

- and insect

- based ) were independently
modeled using salinity

- specific transects in order to represent the dominant habitat used by each predator/prey pair (USGS, 2010) . Landward gradient modeling represents the insect

based food web in the Delta from Benicia to Rio Vista and to Stockton for insect

- eating fish such as juvenile Chinook salmon and steelhead. Seaward gradient modeling represents the clam

based food web in the Bay from the Golden Gate Bridge through Suisun Bay to Chipps Island for
clam

- eating fish and clam

- eating birds such as sturgeon and diving birds (USGS, 2010). A focused seaward gradient approach was also modeled for the area of Suisun Bay and Carquin ez Strait, where critical habitat for sturgeon 12 and important habitat for diving birds 13 are located.

11 Chapter 3, Selenium Benchmark Effect Concentrations , discusses in detail the selenium effect concentration values used in the EPA modeling on which the proposed criteria are based.

12 Critical habitat for green sturgeon specifically includes Suisun Bay and San Pablo Bay, as well as the Sacramento

San Joaquin Delta (see Endangered and Threatened Wildlife and Plants: Final Rulemaking To Designate Critical17

This approach was used to compartmentalize the modeling to reduce uncertainties associated with ocean and freshwater influences, and to focus on the restr icted area where the refineries discharge selenium and the area of critical and important habitat for clam

- eating fish and bird species. Corbula (a dominant prey species) ar e abundant in this area (Cohen, 2011)

.

Partitioning Coefficients: Environmental partitioning factors or coefficients ( K d s) are used to quantify the transformation process to different forms of selenium, and are site

- specific (USGS, 2010). A K d is defined as the ratio of the selenium concentration of particulate material
to the dissol ved selenium concentration in the water:

K d = C particulate material / C water

where C particulate material is in micrograms of selenium per kilogram of material in dry weight ( μg/kg dw) , and C water i s i n micrograms of selenium per liter of water ( μg/L) (USGS, 2010) . Particulate
material is a mixture of living and non

- living particulates and may include phytoplankton, periphyton, detritus, inorganic suspended material, biofilm, sediment and attached vascular plants ( USGS, 2010; Presser and Luoma, 2010). K d represents the efficiency with which dissolved selenium may be converted to particulate selenium material. The potential for phase transformation from dissolved to particulate selenium is important because selenium enters the food web primarily throu gh particulate material (Presser and Luoma, 2010 citing Luoma et al., 1992; Presser and Luoma, 2010; and Stewart et al., 2010). The dominant chemical species or form of selenium (organo

- selenium, elemental selenium, or adsorbed selenium) depends on the ph ysical

- chemical environment, which in turn affects its bioavailability to invertebrates (USGS, 2010) . The form of dissolved selenium also influences the phase transformation reaction. A detailed discussion of phase transformations is included in the USGS report.

A ll available

, relevant data (USGS, 2010 Table 7) were included in calculating K d values across the estuary (USGS, 2010 Tables 8, 9, and 10). S alinity

- specific data were used to
calculate K d s for the two salinity gradients within the estuary : the seaward gradients from the Golden Gate Bridge through Suisun Bay to Chipps Island for the clam

- based food web, and the landward gradients from Benicia to Rio Vista and to Stockton (through the Delta) for the i nsect

based food web (USGS, 2010)

. Speci fic K d s were calculated for the focused seaward gradients

Habitat for the Threatened South ern Distinct Population Segment of North American Green Sturgeon , 74 FR 52300, November 9, 2009).

13 Important habitat for California Ridgway’s rail (previously California clapper rail) includes tidal and brackish marshes around San Francisco Bay (see End angered and Threatened Wildlife and Plants; Final Recovery Plan for Tidal Marsh Ecosystems of Northern and Central California , 79 FR 10830, February 26, 2014). This includes Suisun Marsh and other tidal and brackish areas in Suisun Bay.18

(the area of Suisun Bay and Carquinez Strait) for the clam

- based food web (USGS, 2010). Data from Cutter and Cutter (2004) and Doblin et al. (2006) were used to develop K d values for the
seaward an d focused seaward transects, and from Lucas and Stewart (2007) to develop K d values for landward transects (USGS, 2010). The transect data sets used to determine K d values consisted of samples taken one meter below the surface from 13 to 20 sites, and inc luded salinity, dissolved selenium concentration and speciation, and suspended particulate material selenium concentration and speciation. Mean K d s and ranges of K d values for each transect were calculated (USGS, 2010). To reduce uncertainty further

, a t em poral component was assigned to each dataset. Ea ch transect was assigned a freshwater residence time, a water year type, and a flow season (USGS, 2010)

. The mean K d value for each of four representative
seaward transects and focused seaward transects was used to model the clam

- based food chain in the estuary, and the mean for each of four representative landward transects was used
to model the insect

- based food chain in the estuary (USGS, 2010).

Water Year Type and Flow Season: USGS collects data on surface waters from streamflow gaging stations throughout the United States and publishes them in annual reports ( see USGS Annual Water Data Reports at http://wdr.water.usgs.gov/ ). “Water years” run from October 1st through September 30 th . The observed average long

- term values are the average flow values of a stream or water body from data collected since the early 1930s, when sufficient numbers of streamflow gages were placed across the nation to collect representative data. Water years are labeled by their relative ranking of the yearly average flows within that 80+ year history. The years are classified as normal (falling within a range of observed long

term average values), above normal, much above normal, or highest. Below normal may be classified as below normal, much below normal, or lowest (USGS, 2012).

For San Francisco Bay and Delta, data were available for below normal, above normal, and wet (much above normal) years. The data used for modeling the clam

- based food web (seaward transects) reflected above normal and wet water years; data used for modeling the
insect

- based food web (landward transects) reflected bel ow normal and above normal water years. Since data were not available for critically dry and dry water years, the results may be
less conservative than if drier conditions had been modeled.

Flow season is categorized as either low or high; low flow seaso n refers to the time between June and the end of November when stream flows from runoff are usually at their lowest, and high flow season refers to the time between December and the end of May, when stream flows from runoff are usually at their highest. T he San Francisco Bay and Delta modeling included data from both low and high flow seasons.19

Both water year type and flow season affect partitioning coefficients; the higher the flow (above normal and wet water years

, and high flow seasons), the shorter t he residence time and the lower the partitioning coefficient, resulting in less selenium being available to enter the food web. Conversely, the lower the flow (below normal and dry water years

, and low flow seasons), the longer the residence time, the hig her the partitioning coefficient, resulting in more selenium being available to enter the food web. S cenarios were run using water year types and flow seasons for which data were available.

c. Summary of USGS Model ing of the San Francisco Estuary

Speci es

- specific and site

- specific information for the San Francisco estuary used in the Ecosystem

- Scale Selenium Model illustrates the fate, bioaccumulation and assimilation of selenium in the aquatic environment. The species

- and site

- specific information is critical to the development of appropriate scenarios representative of the estuary

. Table 2

- 1 Summary of Modeling Variables present that information. In Chapters 3 and 4, we discuss the variables that EPA used to populate the model to determine the proposed criteria for the estuary.20

Table 2

- 1 Summary of Modeling Variables

Species

- Specific Variables Considerations Sub

- Categories USGS Choices

1. Most At

- Risk Species Critical Life Stages ; Federal Status; Diet (General Food Web); Diet Mix (prey species). 1. Clam

- Based Food Web

- Fish Trophic Transfer Factors (TTFs) & Diet Mix (%):

TTF

– A mphipod s TTF

– Clam s

- 100%
TTF

– Amphipod/Clam

- 50%/50%
TTF

– Fish

2. Clam

- Based Food Web

- Birds TTF

– A mphipod s

TTF

– Clam s

- 100%
TTF

– Amphipod/Clam

- 50%/50%
TTF

– Bird Egg

3. Insect

- Based Food Web

– Fish TTF

– Insects

– 100%

TTF

– Fish

2. Effect Concentration (EC) Endpoints: Larval Mortality

- Fish; Hatchability

- Birds; Deformity

– Fish & Birds; Reduction in Growth & Development

– Fish & Birds. 1. Whole Body

– Fish Percent of Population Affected:
EC05
E C10

2. Egg Tissue

- Bird EC0

EC05 EC10

3. Diet

– Fish & Birds EC0

EC05 EC10

Environment

- Specific Variables Considerations Sub

- Categories

1. Water Year Type Effect on Partitioning Coefficients 1. Critically Dry

(All available data) 2. Dry
3. Below Normal
4. Normal
5. Above Normal

6. Wet 7. Critically Wet

2. Flow Season Effect on Partitioning Coefficients 1. Low (All available data) 2. High

3. Partitioning Coefficient (K d ) Salinity Gradient; Residence Time (NDOI) Transect Set: 1. Seaward Mean Value of each transect

2. Landward Mean Value of each transect

3. Focused Seaward Mean Value of each transect21

CHAPTER 3 SELENIUM BENCHMARK EFFECT CONCENTRATIONS

As explained in Chapter 2, EPA, the Services and the USGS have been working together using the Ecosystem

- Scale Selenium Model to develop water quality criteria protective of aquatic life and aquatic

- dependent wildlife including federally listed species for the San Francisco estuary. This chapter considers which selenium benchmark effect concentration values EPA chose to use in the Ecosystem

- Scale Selenium Model to develop site

- specific criteria for the San Francisco Bay and Delta.

An important variable in the Ecosystem

- Scale Selenium Model is the selenium effect
concentration , EC, or benchmark, for the species of concern. The EC is the concentration of a pollu tant that relates to a level of adverse effect in the population of an animal or a category of animal (see Chapter 2). Consistent with EPA’s recent national recommendation to states and tribes for a setting selenium water quality criterion, EC10 levels of effect are considered for this analysis (USEPA, 2016). The Ecosystem

- Scale Selenium Model was developed using whole body fish tissue values (Presser and Luoma, 2010), therefore, we consider whole body fish tissue
concentrations to use in the model for th e San Francisco estuary.

A. Summary of Benchmarks Considered

FWS Sources: EPA considered several benchmark recommendations from FWS. At the request of EPA, FWS completed an analysis of species most at risk in the estuary (USFWS, 2008) (see Table 3

- 1 List of FWS Species of Concern), as well as draft site

- specific benchmark values for aquatic life (represented by two food webs in the estuary: clam

- eating fish and insect

- eating fish) and aquatic

- dependent wildlife (represented by clam

- eating birds in the estuary) (USFWS, 2009). FWS also completed a more detailed species

- specific analysis of benchmark recommendations for (clam

- eating) white and green sturgeon (USFWS, 2012). All fish species considered most at risk are indigenous to the estuary, and a ll bird species are either indigenous or migratory, since the estuary is an important stopover along the Pacific Flyway.

EPA Sources : For aquatic life in the San Francisco Bay and Delta, EPA considered all available science, including the fish tissue v alues in EPA’s national recommended freshwater aquatic life criterion for selenium (USEPA, 2016). These values are intended to be protective of aquatic life under a variety of conditions in water bodies across the United States. EPA’s document incorporat es a comprehensive review of selenium effects data currently available in
the literature f or freshwater species, including anadromous fish species. The freshwater fish tissue values used in the national recommended criterion are based on data from quality

assured studies to ensure representativeness and reduce uncertainty, while data from other22

relevant studies are noted and discussed 14 . The studies used to develop the national recommended chronic criterion are evaluated here to consider whether they are

r epresentative of species in the San Francisco estuary, and thus whether the freshwater fish tissue values are appropriate for use as benchmark values in the model for the estuary to develop site

- specific water quality criteria. For aquatic

- dependent wildl ife (clam

- eating birds), EPA considered the egg tissue value that the State of Utah adopted and EPA Region 8 approved for Gilbert Bay of the Great Salt Lake (USEPA, 2011a). During the development of this bird egg tissue criterion, an expert panel reviewed all currently available bird egg data; the studies used to develop the bird egg tissue value are evaluated here to determine whether they are representative of species in the San Francisco estuary, and thus whether the bird egg tissue value is appropriate for EPA to use as a benchmark value in the model for the estuary.

Table 3

- 1 List of FWS Species of Concern (Adapted from USFWS, 2008)

Species (Indigenous/Migratory) Food Web (Clam or Insect) Federal Status under the

Endangered Species Act Clam

- eating Fish Sturgeon: Green & White (Indigenous) Acipenser medirostris & A. transmontanus Clam ( ≤ 40%) Threatened

- Green Sturgeon; Not Listed

- White Sturgeon Sacramento Splittail (Indigenous) Pogonichthys macrolepidotus Clam ( ≤ 34%) Concerned
Clam

- eating Birds California Ridgway’s Rail (Indigenous) (formerly California clapper rail) Rallus longirostris obsoletus Clam ( ≤ 64%) Endangered

Scaup: Greater & Lesser (Migratory) Aythya marila & A. affinis Clam ( 80

- 96%)* Not Listed Scoter: White

- Winged, Surf, & Black (Migratory) Melanitta fusca, M. perspicillata, & M. nigra Clam (75

- 86%)* Not Listed
Insect

- eating Fish Chinook Salmon (Indigenous) Oncorhynchus tshawytscha Insect Threatened & Endangered Steelhead Trout (Indigenous) O. mykiss Insect Threatened Delta Smelt (Indigenous) Hypomesus transpacificus Insect Threatened * When wintering in the estuary. Since n esting and breeding occurs after migration to Alaskan and Canadian
tundra , potential selenium exposure from Bay and Delta clams may not be relevant to breeding.

A summary of the ca tegories of species considered for the San Francisco Bay and Delta
and FWS and EPA EC10 benchmark values are presented in Tab le 3

- 2 Summary of EC10 EPA and
FWS Benchmarks Considered.

14 See EPA Guidel ines for Ensuring and Maximizing the Quality, Objectivity, Utility, and Integrity, of Information Disseminated by the Environmental Protection Agency , commonly known as EPA Data Quality Guidelines (USEPA, 2002).23

Table 3

- 2 Summary of EC10 EPA and FWS Benchmarks Considered

Category EC10

EPA Benchmark EPA

Source EC10

FWS Benchmark FWS Source

Clam

- eating fish 8.5 mg/kg dw

(whole body) USEPA, 2016 3.86

- 9.65 mg/kg dw White Sturgeon (whole body) Using Linville, 2006 and Tashjian et al., 2006 USFWS, 2012

1.97

- 3.71 mg/kg dw Green Sturgeon (whole body) Using Linares

- Casenave et al., 2010, Linville, 2006, and Tashjian et al., 2006

Clam

- eating birds 12.5 mg/kg dw

(egg tissue) USEPA,

2011a 7.73 mg/kg dw (Mallard surrogate)

(egg tissue) USFWS, 2009

Insect

- eating fish 8.5 mg/kg dw

(whole body) USEPA, 2016 1.84 mg/kg dw Chinook Salmon (whole body) Using Hamilton, et al., 1990; 2.19 mg/kg dw Rainbow Trout (whole body) Using Hilton et al., 1980 USFWS, 2009

B. FWS Sources: FWS Species Reports

a. Species at Risk from Selenium Exposure in the San Francisco Estuary; Final Report (USFWS, 2008): Since hundreds of species of wildlife are present in the San Francisco Bay and Delta, EPA asked FWS to provide a list of species most at risk (i.e., vulnerable) in the Bay and Delta due to elevated levels of selenium. In general, some species are affected by selenium in their environment because they are either more toxicologically sensitive to increased selenium levels than other species and/or because they are exposed to significantly elevated selenium levels through diet preferences (i.e., bioaccumulate d selenium concentrations through prey species). FWS completed a report, Species at Risk from Selenium Exposure in the San Francisco Estuary ; Final Report (USFWS, 2008). The report looks at the species in the estuary and their sensitivity and exposure to selenium, and includes an analysis of each species’ diet (prey species) with a focus on how much of each species’ diet consists of clams.

FWS compiled an initial list of approximately 45 species that live in or around the estuary for evaluation; federal ly threatened and endangered species were given priority. FWS then narrowed the list to 13 species considered to be most at risk from selenium exposure. This list includes seven bird and six fish species; all of the species are aquatic or aquatic

depende nt species, and five (four fish and one bird) species are listed as threatened or endangered under the Endangered Species Act (USFWS, 2008).24

The 13 most at

- risk species fall into three general food

- web categories based on their
diet: clam

- eating fish, c lam

- eating birds, and insect

- eating fish (see Table 3

- 1 List of FWS Species of Concern). Since the invasive clam species Corbula is abundant throughout the estuary and efficiently accumulates selenium, the species thought to be most at risk are clam

eating birds and clam

- eating fish. One species, the bald eagle ( Haliaeetus leucocephalus ), was not considered for further evaluation (and is not included in Table 3

- 1) because its diet is not predominantly clam

- based

, 15 nor is the eagle more vulnerable to elevated selenium levels in its environment than the other aquatic

- dependent bird species considered in the analysis (USFWS, 2008).

Clam

- Eating Fish: FWS found that the clam

- eating fish species most at risk from selenium dietary exposure in the estuary are green sturgeon (Acipenser medirostris) listed as federally threatened, white sturgeon ( A. transmontanus ), and Sacramento splittail ( Pogonichth ys macrolepidotus) . FWS estimated the diet of white sturgeon to be approximately
40% clam

- based, and although not firmly established, the diet of green sturgeon to be similar (USFWS, 2008; USFWS, 2012).

FWS concluded that green sturgeon are likely to b e more toxicologically sensitive to the effects of selenium in their diet than white sturgeon, and juvenile sturgeon, both white and green, may be more sensitive than adult sturgeon (USFWS, 2012). Since data exist for white sturgeon, while limited data ex ist for green sturgeon, w hite sturgeon are considered as a surrogate for listed green sturgeon and differences are noted where known. Both species are anadromous, i.e., they are born in freshwater and return to brackish and marine waters as juveniles. Bo th white and green sturgeon are known to migrate and spawn in the Sacramento River, and both have been caught on the San Joaquin River upstream of Stockton; new data confirm that white sturgeon also spawn in the San Joaquin River system (Jackson and

Eenenn aam, 2013). It is currently understood that white sturgeon spend a considerable amount of time over a lifetime in the estuary, and some are year

- round residents; green sturgeon also spend time in the estuary ( from first to third years) but eventually move into open ocean waters (USFWS, 2008).

FWS estimated the diet of Sacramento splittail to be up to 34% clam

- based (USFWS, 2008). Affected critical life stages from selenium exposure for clam

- eating fish species include

15 Approximately 23% of the bald eagle diet consists of waterfowl (USFWS, 2008). Assuming the worst

- case scenario, that all waterfowl consumed are clam

- eating waterfowl, the other bird species considered most at

- risk (California Ridgway’s rail, scoter and scaup) are at a higher risk of adverse effect, as FWS estimated these species consume more than twice as much clam

- based food (see Table 3

- 1 List of FWS Species of Concern).25

im paired reproduction (toxicity to e ggs, including larval mortality and deformity) and impaired juvenile growth and development (USFWS, 2008) (see Table 3

- 3 Probable Critical Life Stages).

Clam

- Eating Birds: FWS identified the clam

- eating birds most at risk from selenium dietary exposure i n the estuary as the California Ridgway’s rail (Rallus longirostris obsoletus), listed as federally endangered, and the diving ducks: the greater scaup (Aythya marila) , lesser

scaup (A. affinis) , white

- winged scoter (Melanitta fusca) , surf scoter (M. persp icillata) , and black

scoter (M. nigra) (USFWS, 2008). California rails are year

- round residents of the estuary, and
FWS estimated their diet to be as much as 64% clam

- based. 16 Affected critical life stages from selenium exposure include impaired reproduct ion (toxicity to embryos, including egg hatchability and deformity) (USFWS, 2008). Scoters and scaups are migratory birds that spend the winter in the estuary, and fly north to breed in the spring. FWS estimated their diet to range from 75% to 96% clam

- b ased while wintering in the estua ry (USFWS, 2008). The FWS report finds that a ffected critical life stages from selenium exposure may include impaired reproduction (toxicity to embryos, including egg hatchability and deformity) and impaired migration (reduced ability to successfully reach breeding grounds)

. Research indicates that surf scoter and greater scaup accumulate elevated level s of selenium in muscle and liver while overwintering in Suisun Bay (De La Cruz, 2010 and De La Cruz et al., 2008), and that these levels might impair their ability to migrate successfully to breeding areas in Alaska and Canada (Ohlendorf and Heinz, 2011).

Insect

- Eating Fish: The FWS report found that the insect

- eating fish species (or species
in an insect

- eating fish food chain) most at risk from selenium dietary exposure in the estuary
are Chinook salmon (Oncorhynchus tshawytscha) listed as federally en dangered 17 (Sacramento
River winter

- run Evolutionary Significant Unit [ ESU] ) and threatened (Central Valley spring

- run ESU), steelhead trout (O. mykiss) listed as federally threatened, and Delta smelt (Hypomesus transpacificus) also listed as federall y thre atened . Chinook salmon and steelhead trout are
anadromo us, and both are considered highly toxicologically sensitive to selenium levels in their environment ( USFWS, 2008 ). Affected critical life stages include impaired reproduction (toxicity to eggs, incl uding larval mortality and deformity) and impaired juvenile growth and

16 California rails are littoral feeders and consume various types of clams. Corbula , which are predominantly found in subtidal waters, are estimated to be no more than 20% of the rail’s diet. See Chapter 4.

17 The National Marine Fisheries Service has identified 17 Evolutionary Significant Units (ESU) of Chinook salmon in California, Oregon, Washington and Idaho; three use the estuary: the Sacramento River winter

- run ESU; the Central Valley spring

- run ESU; and the Central Valley fall/late

- fall run ESU (USFWS, 2008).26

development 18 ( USFWS, 2008). However, none of the species are known to consume Corbula, (or consume fish species that consume Corbula ) so their dietary exposure of selenium in the

estua ry is likely lower than other species that are known to consume Corbula ( USFWS, 2008 ).

Table 3

- 3 Probable Critical Life Stages (Adapted from USFWS, 2008)
Species Probable Critical Life Stage Clam

- eating Fish Sturgeon: Green & White (anadromous) Adult Female/Reproduction (egg/larval mortality; deformity); Juvenile (growth and development)

Sacramento Splittail Adult Female/Reproduction (egg/larval mortality; deformity); Juvenile (growth and development)* Clam

- eating Birds California Ridgway’ s Rail Adult Female/Reproduction (egg hatchability; deformity)

Scaup: Greater & Lesser Adult Female/Reproduction (egg hatchability; deformity); Adult Male & Female/Migration Scoter: White

- Winged, Surf, & Black Adult Female/Reproduction (egg hatchability; deformity); Adult Male & Female/Migration
Insect

- eating Fish

Chinook Salmon (anadromous) Adult Female/Reproduction (egg/larval mortality; deformity); Juvenile/Migration (growth and development)

Steelhea d Trout (anadromous) Adult Female/Reproduction (egg/larval mortality; deformity); Juvenile/Migration (growth and development)

Delta Smelt Adult Female/Reproduction (egg/larval mortality; deformity); Juvenile (growth and development)

* Juvenile splittail (ages 0 to 2 years) range in length from 25 mm to 200 mm (1 to 8 inches) (USFWS, 2008). Splittail are bottom feeders, and although Corbula are small (averaging 0.5 inches), younger splittail juveniles
may consume fewer mollusks than older juveniles.

Summary: The FWS report narrows the list of vulnerable species to 13. These species can be categorized by food chain: clam

- eating fish, clam

- eating birds, and insect

- eating fish, with each category including at least one federally list ed species. Therefore, the analysis focuses on these three categories of species and the representative species within each category. For clam

- eating fish, target species are white and green sturgeon and splittail, and
the FWS estimates their diets to be approximately 40% and 34% clam

- based, respectively. Green sturgeon are federally listed as endangered. For clam

- eating birds, target species are the California Ridgway’s rail which is federally listed as endangered, and the five species of migratory divi ng ducks, the scoters and scaups. FWS estimates the rail diet to be approximately
64% clam

- based, and the scoters and scaups to be approximately 75

- 96% clam

- based when

18 Adult Chinook salmon and steelhead spend most of their lives in the open ocean, and only in

- migrate through the Bay and Delta to natal waters just prior to spawning; they are unlikely to consume food from the estuary. Juvenile salmon and steelhead out

- migrate through the estuary on their way to the ocean . During that time, they may consume f ood items fr om the estuary that are low in selenium (insects, zooplankton, etc.) for a short period of time. See more detailed discussion in Chapter 4.27

overwintering in the estuary. For insect

- eating fish, target species are Chinook salmo n, listed as endangered, and steelhead trout and delta smelt, both listed as threatened.

b. Selenium Effect Levels for Selected Representative/Surrogate Species (USFWS, 2009): In July 2009, FWS provided recommended benchmark values for representative and/or surrogate species 19 living in the San Francisco estuary to EPA (USFWS, 2009). Representative or surrogate species include mallard ducks ( Anas platy rhynchos ) for clam

- eating birds, white sturgeon ( A. transmontanus ) and green sturgeon ( A. medirostris ) for clam

- eating fish, and Chinook salmon ( O. tshawytscha ) and rainbow trout ( O. mykiss ) for insect

- eating fish. The report includes benchmark values for EC0, EC05 and EC10 for whole body tissue (for fish) and egg tissue (for birds). Since FWS provided E PA with detailed benchmark values for white and green sturgeon in a more recent report (USFWS, 2012), this section discusses the benchmarks
for clam

- eating birds and insect

- eating fish. Benchmarks for sturgeon, the representative species for clam

- eating f ish, are discussed in the next section. Table 3

- 4 summarizes the relevant EC10 FWS recommended bird egg tissue and fish whole body benchmark values for
clam

- eating birds and insect

- eating fish, respectively.

Table 3

- 4 Summary of FWS

- Recommended EC10 Se lenium Benchmark Values for Representative or Surrogate Species (Adapted from USFWS, 2009)

Species Selenium

Tissue Value μg/g dw Effect Dietary Exposure duration (days) Form of

Selenium (in food) Model Data Source*

Mallard duck 7.73

(egg tissue) Hatchability > 40 (parental) Seleno

- DL

methionine Beckon et al.,

2008 (biphasic) Heinz et al.,

1989

Chinook salmon 1.84

(whole body) Mortality 90 (juvenile) Seleno

- DL

methionine Brain and

Cousens, 1989 (biphasic) Hamilton et

al., 1990

Rainbow
trout 2.19

(whole body) Reduction

in growth 140

(juvenile) Sodium

selenite Beckon et al.,

2008 (biphasic) Hilton et al.,

1980 * T he Hamilton et al., 1990 study and the Hilton et al., 1980 study are not used in USEPA, 2016 to derive criteria values due to data quality concerns.

Clam

- Eating birds: Since toxicity studies have not been performed on any of the avian species identified as most at

- risk, the FWS report uses mallard ducks as the surrogate species
for clam

- eating birds (USFWS, 2009 ). FWS relies on a detailed dietary study by Heinz et al.

19 Data do not exist for some of the at

- risk species living in the estuary. In those cases, we rely on data from other species (i.e., surrogate species) that we believe will respond in a manner similar to how the at

- risk species would respond to the same environmental condition, and discuss where differences might occur.28

(1989) that investigated the reproductive success of several groups of mallards that were fed diets containing different concentrations of selenium; the data collected included selenium egg
and liv er concentrations. Mallard ducks are commonly found in the San Francisco Bay area, and live in fresh, brackish and salt waters (National Geographic at http://animals.nationa lgeographic.com/animals/birds/mallard

- duck/ ). FWS uses the egg concentration data from the Heinz (1989) study to determin e an EC10 egg value

.

In 2008, Tetra Tech, Inc. (Tetra Tech ), in association with the Western States Petroleum
Association (WSPA) , co mpleted a detailed review of all available avian studies, in an effort to assist the San Francisco Region al Water Quality Control Board in completing a selenium TMDL for the North San Francisco Bay (Tetra Tech, 2008). The Tetra Tech review indicated that although many avian toxicity studies on selenium have been conducted to determine dietary
benchmarks and several of these studies are a ssociated with reproductive success, only a few studies measured egg selenium concentrations. 20 Tetra Tech reviewed studies available in the literature on the reproductive success of avian species including chickens, mallards, pheasants, and screech owls; these studies indicate that mallards are the most sensitive of the species studied. Key reproductive studies on mallards include Heinz, et al., 1987, and 1989, Heinz and Hoffman 1996, and 1998, and Stanley et al., 1994, and 1996 (Tetra Tech, 2008).

In the 2009 report, FWS selected the Heinz et al. (1989) study on mallards and applied a biphasic (log

- logistic 2 ) 21 model to the egg selenium concentration data (USFWS, 2009 and Beckon et al., 2008). A biphasic model is one in which the dependent variable is maximal or minimal at an intermediate level of the independent variable, i.e., the relationship is depicted
either as a hill

- shaped or valley

- shaped curve (Beckon et al., 2008). Using a biphasic model on the Heinz et al. (1989) data, FWS estimated an EC1 0 bird egg value of 7.73 μg/g dw (USFWS, 2009).

Insect

- Eating fish: For rainbow trout, a representative species for insect

- eating juvenile fish, FWS calculated a whole body EC10 value using the data from the Hilton et al. (1980) study, using a biphas ic model (USFWS, 2009 and Beckon et al., 2008). In the Hilton study, juvenile rainbow trout were fed diets spiked with six different concentrations of selenium ranging from between 0.07 and 13.06 μg/g dw over 20 weeks (140 days). Over the course of the s tudy, fish were sacrificed and data were collected including carcass, liver and kidney selenium

20 Research on selenium toxicity indicates th at for most bird species, similar to fish species, reproductive endpoints appear to be more sensitive than non

- reproductive endpoints (USFWS, 2009 and Tetra Tech, 2008).

21 The term log

- logistic 2 (i.e., log

- logistic squared) reflects a model that is form ed by the multiplicative combination of two log

- logistic models (Beckon et al., 2008).29

concentrations. Fish that were fed the higher concentration selenium diets exhibited reduced growth, food avoidance and mortality.

FWS took the carcass, liv er and kidney data from Hilton et al. (1980) to calculate whole body selenium concentrations, and performed a regression analysis against weight (USFWS, 2009 Figure 11). The FWS analysis indicated that juvenile rainbow trout exhibit reduced growth
at diet s containing 13.06 μg/g dw of selenium, and that effects (10%) began to be observed at whole body concentrations of approximately 2 μg/g dw. Using a biphasic model, FWS calculated a whole body EC10 value for reduction of growth (non

- reproductive effect) i n juvenile rainbow trout of 2.19 μg/g dw (USFWS, 2009).

For Chinook salmon, FWS calculated a whole body EC10 value with data from Hamilton et al. (1990), using the biphasic model (USFWS, 2009 and Brain and Cousens, 1989). In the Hamilton study, juven ile Chinook salmon were exposed to three different types of diets for 90 days at various concentrations: a control diet containing meal with low

- selenium mosquitofish collected from a reference site; a diet containing meal with high

- selenium mosquitofish

c ollected from the San Luis Drain in California (the SLD diet); and a diet containing meal with
low

- selenium mosquitofish fortified with seleno

- DL

- methionine (the SeMet diet). For the SLD and the SeMet diets, fish were fed six different concentrations of s elenium, ranging from 3.2 μg/g dw to 35.4 μg/g dw of selenium (Hamilton et al., 1990). Mortality in each test group was recorded daily, and growth was recorded and whole body tissue samples were taken at 30

- day intervals. The authors reported that there was a positive correlation between whole

- body concentrations of selenium and increased concentrations of dietary selenium, regardless of diet type. However, between 60 and 90 days, mortality in all three dietary scenarios increased noticeably; for the con trol scenario, percent survival decreased from 99% to 67%; for the SLD diets, percent survival decreased from 89

- 97% to 18

- 51%. For the SeMet diets, percent
survival decreased from 63

– 100% to 11

- 73% (Hamilton et al., 1990).

FWS used the 90

- day data on percent survival and whole body concentrations for the SLD diet and SeMet diet scenarios, and performed a regression analysis using a biphasic model (USFWS, 2009 Figure 9 and Table 6). The model yielded a whole body EC10 value for mortality (non

- r eproductive effect) in Chinook salmon of 1.84 μg/g dw (USFWS, 2009).

Summary: In all three analyses, FWS used a biphasic model. For clam

- eating birds, FWS used (mallard) data from Heinz, et al. (1989) and applied a biphasic model (Beckon et al., 2008) to derive an EC10 egg tissue value of 7.73 μg/g dw (USFWS, 2009). For insect

- eating fish, FWS used (rainbow trout) data from Hilton et al. (1980) and applied a biphasic model (Beckon et al., 2008) to derive an EC10 whole body fish tissue value of 2.19 μg/ g dw; and (Chinook salmon)30

data from Hamilton et al. (1990) and applied a biphasic model (Brain and Cousens, 1989) to derive an EC10 whole body fish tissue value of 1.84 μg/g dw (USFWS, 2009).

Biphasic relationships occur in toxicology, and reflect the type of effect that selenium has on many species, i.e., selenium is a micronutrient having a negative effect at zero or very small (deficient) concentrations, a positive effect at small or moderate concentrations, and a negative effect at higher concentrat ions

. Biphasic modeling may be more appropriate than log

logistic modeling if sufficient data points are available in both the lower and higher dose regions, and the measured effect occurs in both a deficient and in an excess of the constituent, e.g., imp aired growth for selenium (non

- reproductive effects). 22 However, if sufficient data are not available in the deficit range, the resulting modeled chronic values in the excess range may be biased. Most studies in the published literature on selenium were n ot set up experimentally or intended to capture the appropriate effects and range of doses in the deficit region that are necessary for biphasic modeling. EPA reviewed the data sets for the published studies for which FWS used a biphasic model, and did no t find they included appropriate or sufficient data for utilization of a biphasic model. Therefore, EPA supports the use of a standard log

- logistic model to determine EC10 values with data sets from published literature, including the data
sets for the st udies discussed above, and does not use biphasic models to calculate chronic
values.

For bird egg tissue modeling using mallard data, EPA supports the use of standard log

logistic modeling as was done for Gilbert Bay of the Great Salt Lake in Utah, using all available appropriate data (USEPA, 2011a). This is discussed in more detail in section C.

Hilton et al. (1980) fed juvenile rainbow trout a diet consisting of a casein

- torula yeast supplemented with selenium as sodium selenite (inorganic selenium). As discussed in USEPA (2016) for the Ogle and Knight (1989) study with fathead minnow, the reduction in growth observed with fish fed at higher dietary inorganic selenium concentrations may be due to reduced palatability of the food, since much of the fo od remained uneaten, i.e., the diet mix contained an unrealistic fraction of inorganic selenium, causing food avoidance. This is a common observation in early selenium studies, including the Hilton study (USEPA, 2016). The reduced growth at the higher di etary concentration in Hilton et al. is likely due to the observed food avoidance, an artifact of unrealistic spiking of the diet with inorganic selenium in the experimental protocol (USEPA, 201 6 ). Therefore, the results of the study would not be appropri ate for deriving chronic values. Additionally, the range of tested concentrations was

22 Reproductive effects such as embryonic mortality or malformations are known to occur after excessive doses of dietary selenium, but not when there is a dietary defic iency; therefore, reproductive effects should only be modeled using a log

- logistic model (Beckon et al., 2008).31

wide , s o that the NOEC and LOEC are unacceptably far apart ( USEPA, 2016 ). Lastly, since reproductive toxicity tests are available for the genus Onc orhynchus , they are p referable to

non

- reproductive effect studies. As concluded by selenium experts at the 2009 Pellston conference (Chapman et al. 2009 ), the most important toxicological effects of selenium in fish arise following maternal transfer of selenium to eggs during vitellogenesis, resulting in selenium exposure when hatched larvae undergo yolk absorption. Such effects include larval mortality or permanent developmental malformations, such as skeletal and craniofacial deformities.

In Hamilton (1990), mortality i n juvenile Chinook salmon increased in all three test groups between 60 and 90 days including the control group as indicated by a 1% mortality at 60 days and a 33% mortality at 90 days. EPA reviewed the data and determined that the health of
the fish was likely compromised between 60 and 90 days. Therefore, the results of the 90

- day endpoint were excluded from the analysis for the national recommended selenium criterion (USEPA, 2016). The control mortality of 1% was acceptable at 60 days. The Aquatic Lif e Guidelines (USEPA, 1985) and the Manual of Instructions for Preparing Aquatic Life Water Quality Criteria Documents (Stephan, 1987) recommend that excessive control mortality be treated as an exclusionary threshold in data quality assessments for regulatory purposes such as deriving water quality criteria. EPA performed a regression on the 60

- day weight and whole body concentrations, and derived a whole body EC10 value of 7.355 μg/g dw for the SeMet diet for reduced growth, and a whole body EC10 value of 11.14 μg/g dw for the SLD diet for reduced growth. These are the only two EC10 Species Mean Chronic Values ( SMCVs ) acceptable to use for deriving non

- reproductive endpoints for the genus Oncorhynchus , and the Genus Mean
Chronic Value (GMCV ) is 9.052 μg/g dw 23 ( USEPA, 2016 Table 6.2).

Given the concerns with using a biphasic model and data quality concerns with Hilt on et al. (1980) and Hamilton et al. (1990), the FWS

- recommended benchmark values for clam

- eating
birds and insect

- eating fish would not be appropriate for use in the Ecosystem

- Scale Selenium Model for deriving site

- specific criteria for the San Francisco Bay and Delta.

c. Evaluation of Toxicity of Selenium to White and Green Sturgeon (USFWS, 2012): As a follow

- up to the FWS report on effect levels for selected species, FWS provided additional detail and supporting information for the clam

- eating fish t issue values. FWS determined that white and green sturgeon were pivotal species for determining aquatic life water quality standards for selenium in the estuary, and then examined the available studies and data on the two sturgeon species to estimate sele nium benchmarks (USFWS, 2012).

23 These results are discussed under Non

- Reproductive Effect Studies in section C, EPA Sources: CWA Section 304(a) National Recommended Water Qu ality Criterion for Selenium and Mallard Bird Studies.32

FWS identified four key studies (Linville, 2006; Linares

- Casenave et al., 2010; Silvestre et al., 2010; and Tashjian et al., 2006), and used the data and information to develop the report, Evaluation of the Toxicity of Se lenium to White and Green Sturgeon (USFWS, 2012). In Linville (2006) (University of California, Davis, Ph.D. dissertation) white sturgeon larvae from the San Francisco estuary were exposed to elevated levels of selenium in two separate experiments:
one in which L

- selenomethionine was injected into yolk sacs just after hatching (microinjection), and the other in which gravid females were fed selenized yeast for up to 6 months before they deposited their eggs (maternal transfer) (USFWS, 2012 and Linville, 20 06). FWS performed a regression on the data from the Linville (2006) microinjection study to determine the 5% and 10% larval mortality effect levels, and used data from the Linville (2006) maternal transfer study and the Tashjian et al. (2006) study to tr anslate the larval mortality effect levels to egg, muscle and whole body effect levels. FWS translated the microinjection larval effect levels to egg concentrations using the relationship in the Linville (2006) maternal transfer study (USFWS, 2012 Figure 3). Similarly, FWS translated the microinjection larval effect levels to muscle concentrations using the relationship found in the Linville (2006) maternal transfer study (USFWS, 2012 Figure 4). Muscle concentrations were translated to whole body

concen trations using the relationship in Tashjian et al. (2006) on juvenile white sturgeon (USFWS, 2012 Figure 5).

FWS also performed a regression on the data from the maternal transfer study to determine the 5% and 10% larval developmental effect levels (USFWS, 2012). FWS then translated the developmental effect levels to egg, muscle and whole body effect levels, using the relationships calculated from the data in the maternal transfer study and the data in Tashjian et al., in the same way as the larval mortality effect levels from the microinjection study were translated (USFWS, 2012).

To develop benchmarks for green sturgeon, FWS used data from the Linares

- Casenave et al. (2010) microinjection study to determine green sturgeon larval mortality effect levels, which were then translated to egg, muscle and whole body using the relationships previously developed for white sturgeon using Linville (2006) and Tashjian et al. (2006). Lastly, FWS used
data from the Linares

- Casenave microinjection studies on g reen and white sturgeon to develop a sensitivity ratio, which was then applied to the results of the Linville maternal transfer study on white sturgeon to calculate effect levels of maternal transfer on green sturgeon. FWS determined that green sturgeon a re more than twice as sensitive as white sturgeon to selenium (USFWS, 2012). They noted that other studies confirm that green sturgeon are more sensitive to selenium at environmentally relevant concentrations than white sturgeon (USFWS, 2012 citing Kaufma n et al., 2008, Linares

- Casenave et al., 2010, and Silvestre et al., 2010).33

The FWS EC10 sturgeon whole body and egg tissue effect concentrations 24 are summarized in Table 3

- 5 Summary of FWS

- Recommended EC10 Selenium Benchmarks for White and Green Sturg eon.

Table 3

- 5 Summary of FWS

- Recommended EC10 Selenium Benchmarks for White and Green Sturgeon (Adapted from USFWS, 2012)

Species Concentration of

Se in whole body (μg/g dw) Concentration of

Se in egg tissue (μg/g dw) Effect Study Type Data Source

White Sturgeon 3.86 6.83 Larval Mortality Microinjection Linville, 2006; Tashjian et al., 2006

9.65 15.8 Larval abnormality Maternal Diet Linville, 2006; Tashjian et al., 2006

Green Sturgeon 1.97 3.70 Larval
M ortality Microinjection Linares

- Casenave et al., 2010; Linville, 2006; Tashjian et al., 2006

3.71* 6.59* Larval abnormality Maternal Diet*

(estimated from sensitivity ratio) Linares

- Casenave et

al., 2010; Linville, 2006; Tashjian et al., 2006

* Benchmarks are projected using a sensitivity ratio that was developed by comparing the results of microinjection studies on green and white sturgeon (Linares

- Casenave et al., 2010 ) and applying the sensitivity ratio to the results
of the Linville (2006) maternal transfer study on white sturgeon (whole body values derived using data from Tashjian et al., 2006).

The FWS report acknowledges that although the best available information was used, some of the studies (Linares

- Casenave et al. [2016] and Silves tre et al. [2010]) may have limited relevance, as the progeny of only a single individual could be used in the study as the species is federally listed as threatened. Additionally, the report notes that the analysis focuses on a single endpoint (either mo rtality or abnormalities), but in nature, mortality and deformity effects are additive such that the surviving individuals suffer developmental impairment; therefore, they postulate that their analysis may underestimate the extent of the effects of
seleniu m to sturgeon (USFWS, 2012).

The microinjection studies (Linville and Linares

- Casenave et al.) represent an artificial route of exposure that can add uncertainty with respect to metabolism and distribution of selenium in the body. Microinjection is a more efficient route of exposure (higher absorption efficiency) and likely leads to less excretion of selenium than maternal exposure through

24 A complete summary of FWS benchmarks can be found on page 2 of the USFWS report, and includes EC05 and EC10 benchmarks for whole body, muscle and egg tissue.34

ingestion of contaminated prey. In addition, microinjection represents a “bolus” dose of
selenomethionine to the developing embryo, and the metabolic controls associated with maternal transfer to the egg are completely bypassed. Metabolic rates may also vary across the species based on the exposure route, i.e., there is uncertainty whether relative sensitivity
would remain the same via other routes due to absorption and assimilation efficiency. To help evaluate these issues, EPA had an external peer review performed on the FWS analysis.

Peer Review of FWS Report: External Peer Review of Sturgeon Study (ERG, 2012) : E xperts in the field of selenium and/or aquatic ecotoxicology reviewed the FWS study on white and green sturgeon (USFWS, 2012) (ERG, 2012). The charge asked the experts to consider whether the studies cited provided the best available information on gr een and white sturgeon for determining mortality and abnormality benchmarks; whether the use of microinjection studies and maternal transfer studies was comparable and appropriate for the purpose of the report; whether each step in the analysis was reasona ble and appropriate, and explained in sufficient detail; whether the assumptions and conclusions in each step of the analysis were reasonable and supported by the data; and lastly, given the available data, whether the experts would recommend any alternati ve analyses to estimate benchmarks for mortality or
abnormalities.

The conclusions of the experts were consistent in affirming that the report relied on the best available data. In general, they agreed that the maternal transfer studies were more relevant and represented a better depiction of exposure in the field than the microinjection studies, which tend to overestimate toxicity; and that the Linville (2006) maternal transfer study, although not publi shed, is the most relevant study. The reviewers noted that while regressions performed using white sturgeon data for tissue

- to

- tissue relationships are relevant for that species, the relationships should be used with caution for related species, even one as close as green sturgeon, because tissue

- to

- tissue relationships vary between species. They
noted that this issue may be especially relevant to these sturgeon species, since white sturgeon spend more time in the estuary, while green sturgeon spend more time in the ocean, and have adapted to slightly different environments. Lastly, the reviewers noted that although the study reflected an appropriate and thorough analysis given the available data, the limited data in each of the studies, and especially th ose related to green sturgeon, are associated with a high degree of uncertainty, and therefore the results should be used with caution in estimating
benchmark values.

After considering these issues, EPA find s the Linville (2006) maternal transfer study results to have more weight than the microinjection study results. The FWS analysis indicates an EC10 whole body value for white sturgeon of 9.65 μg/g dw for reproductive effects (larval35

abnormalities) using the maternal diet results from Linville (USFWS, 2012)

. Similarly, the FWS analysis indicates an EC10 egg tissue value for white sturgeon of 15.8 μg/g dw for reproductive effects using the maternal diet results from Linville (USFWS, 2012) . This value was calculated from the regression performed on lar val developmental effects data from the maternal transfer study, translated to an egg tissue value using data from the same maternal transfer study. This is the most direct translation in the analysis, and therefore less subject to bias. The resulting

eg g tissue value is also consistent with EPA’s national recommended EC10 fish tissue egg/ovary criterion value of 15.1 mg/kg dw (USEPA, 2016).

The results of the Linares

- Casenave et al. (2010) microinjection study on both white and green sturgeon indicat e that green sturgeon may be more sensitive to selenium than white sturgeon. Other studies have observed the same relative sensitivities (Kaufman et al., 2008 ; Silvestre et al., 2010 ; and De Riu et al., 2014). De Riu et al. (2014), a recent study on juve nile green and white sturgeon from San Francisco Bay published after the FWS sturgeon report, suggests that although juvenile green sturgeon may be more sensitive than juvenile white sturgeon to increasing dietary selenium concentrations, initial whole bod y concentrations (i.e., background concentrations in the controls) were 7.2 ± 0. 3 μ g/g dw in green sturgeon and 4.8 ±
0.5 μ g/g dw in white sturgeon; and after several weeks, the controls had similar concentrations ranging from 6.5 to 7.1 μ g/g dw for green sturgeon and 5.6 to 7.3 μ g/g dw for white sturgeon. These control concentrations are close to EPA’s national recommended EC10 whole body
criterion value of 8.5 μ g/g dw (USEPA, 2016), and suggest that juvenile green and white sturgeon have similar sensitiv ities to selenium at these whole body concentrations. The De Riu et al. study is discussed in more detail later in this chapter.

EPA Analysis of Linville (2006) White Sturgeon Study (USEPA, 2016): EPA independently analyzed the reproductive endpoint d ata from the maternal transfer portion of the Linville (2006) study. The analysis is included in EPA’s derivation of the national recommended criterion for selenium (USEPA, 2016), discussed in the following section.

Linville evaluated the effect of elev ated dietary selenium on the health and reproduction of white sturgeon ( A. transmontanus ). Adult female white sturgeon (approximately 5 years old) were fed either a control diet (no added selenium; 1.4 mg/kg selenium) or a diet spiked with selenized yeast (34 mg/kg selenium) for six months in a freshwater flow through system. At the end of the dietary exposure, females were induced to spawn and eggs were fertilized with non

- exposed male milt. Large cohorts of fertilized eggs
from individual females were collected and separately hatched. After hatching (stage 36), n=500 sets of larvae were randomly distributed into each of six flow through chambers. Progeny from two control females and the three treatment females were examined for length,36

weight, edema a nd deformities. Three of the chambers were earmarked for stage 40 evaluations and 3 for stage 45 evaluations, with stage 36 samples for selenium analysis and abnormality (edema, skeletal deformities) evaluation being taken at the time of distribution.

Mo rtality was monitored as fish matured to the desired stage. At stage 40 and 45, samples were collected for selenium analysis and abnormality evaluations. For deformities, one sample of n=30 progeny was taken from each chamber for five of the cohorts (2 c ontrol, 3 treated).

No selenium effects were observed for length or weight of larvae but effects were observed for both edema and skeletal deformities. Selenium concentrations in eggs from the control fish were 1.61 and 2.68 mg/kg dw, and were 7.61, 11, and 20.5 mg/kg dw in eggs from the treatment fish. EPA evaluated larval survival and abnormality frequency at stage 45. Because the mortalities for each cohort were recorded up to the sample collection time for abnormalities, a combined effects varia ble was derived based on the total proportion of hatched larvae which were both alive and without any abnormalities at stage 45. This can be calculated as PS*(1

- PA), where PS is the proportion survival in the test chambers and PA is the proportion of the sample of surviving larvae with abnormalities. The larvae hatched from these eggs had respectively 0, 0, 13.3, 0 and 27.8% occurrence of the combined effects of edema and deformities; and were 99.7, 99.7, 86.4, 99.7 and 66.2% alive and without abnormaliti es.

Estimation of the E C10 was conducted using weighted nonlinear reg ression analysis with
the thres hold sigmoidal model equation (TRAP version 1.30a ) 25

. The binary data available in this study would normally be analyzed using the tolerance distribution analysis in TRAP, however, the combined survival/abnormalities effects variable in this study precludes its use because of the different sample sizes for survival and abnormality evaluation. When there are insufficient data for TRAP to fit an effects/exp os ure curve, an interpolation i s conducted with the same TRAP equation, but constrained to provide interpolation between two points.

Binomial confidence limits were calculated to evaluate significant differences among data points and between data points an d fitted curves (see Linville summary in USEPA, 2016 Appendix C). Since such confidence limits cannot be directly calculated for the combined effects variable, confidence limits were estimated for the percent survival and percent
abnormalities for each co hort by combining the upper and lower confidence limits of the individual effects variable using the same equation previously mentioned above. These confidence limits are only slightly exaggerated because the survival confidence limits are very

narrow com pared to the abnormality confidence limits.

25 TRAP will fit a sigmoidal toxic response versus an exposure variable relationship to standard toxicity data. For more information, see EPA’s website at https://archive.epa.gov/ med/med_archive_03/web/html/trap.html

.37

Since the study yielded only one definite partial effect, TRAP cannot be used to estimate
a concentration

- response curve. Instead, TRAP was used to interpolate between the last two points to estimate the EC 10 ( see Linville summary in USEPA, 2016 Appendix C for detail). The resultant TRAP slope is 2.96 and the interpolated EC 10 is 15.6 mg/kg.

The white sturgeon egg/ovary EC10 of 15.6 mg/kg dw is included in the data set for the
derivation of the national recomm ended freshwater selenium criterion (USEPA, 2016) . The species is a commercially and recreationally important fish species in California and in the Pacific Northwest. This species also provides taxonomic surrogacy for other sensitive sturgeon species tha t are threatened or endangered, including green sturgeon.

C

. EPA Sources: CWA Section 304(a) National Recommended Water Quality Criterion for
Selenium and Mallard Bird Stud ies

a. Freshwater Fish Tissue Criterion Element (USEPA, 2016): In June, 2016 , EPA published the national recommended criterion document, Aquatic Life Ambient Water Quality Criterion for Selenium

– Freshwater 201 6 (USEPA, 201 6 )

. Th is national recommended criteri on has four elements: two fish tissue

- based elements and two water co lumn

- based elements. The fish tissue elements consist of an EC10 egg or ovary tissue value of 15.1 mg/kg dw, and an EC10 whole body or muscle tissue value of 8.5 and 11.3 mg/kg dw, respectively. The whole body,
muscle and water column elements are determ ined from the egg/ovary element. This is consistent with the Pellston International Expert Workshop sponsored by the Society of Environmental Toxicology and Chemistry ( SETAC ) on selenium in 2009 that affirmed that tissue concentrations are an appropriate media to measure selenium toxicity, since the main route of exposure of selenium to aquatic biota is dietary, and analyses demonstrate that reproductive effects through maternal transfer from diet result in more sensitive (lower) endpoints than non

reprodu ctive effects through diet (USEPA, 2016). Another key finding of the SETAC workshop was that relationships between selenium tissue concentrations in egg/ovary and water can be linked by site

- specific bioaccumulation measurements and modeling.

The nation al recommended criterion also includes water column elements. These consist of a set of chronic water column values, one for lentic systems and one for lotic systems, and an intermittent exposure water column value based on an equation using either
the le ntic or lotic chronic water column value and a time variable. The chronic water column values for lentic and lotic systems are translated from the egg/ovary value, using an equation that represents how selenium accumulates through the food chain, as influ enced by the overall hydrologic and ecosystem conditions represented by the two waterbody types. The equation is based on the Ecosystem

- Scale Selenium Model discussed in Chapter 2. The criterion elements38

are summarized in Table 3

- 6 Summary of Freshwater Selenium Ambient Water Quality Criterion Elements for the Protection of Aquatic Life.

Table 3

- 6 Summary of 304(a) Recommended Freshwater Selenium Ambient Chronic Water Quality Criterion for the Protection of Aquatic Life (USEPA, 2016) Media Type Fish Tissue 1 Water Column 4

Criterion
Element Egg/Ovary 2 Fish Whole Body
or Muscle 3 Monthly

Average Exposure Intermittent Exposure 5

Magnitude 15 .1 mg/kg dw 8. 5 mg/kg dw whole body

or 11.3 mg/kg dw muscle (skinless, boneless filet) 1. 5 μg/L in lentic

aquatic systems

3.1 μg/L in lotic aquatic systems WQC int =

WQC 30

− day − C bkgrnd ( 1

− f int )

f int

Duration Instantaneous

measurement 6 Instantaneous

measurement 6 30 days Number of days/month with an
elevated concentration Frequency Not to be

exceeded N ot to be

excee ded Not more than once

in three years on

average Not more than once

in three years on

average

1 Fish tissue elements are expressed as steady

- state.

2 Egg/Ovary supersedes any whole

- body, muscle, or water column element when fish egg/ovary concentrations are measured.

3 Fish whole

- body or muscle tissue supersedes water column element when both fish tissue and water concentrations are measured.

4 Water column values are based on dissolved total selenium in water and are derived from fish tissue values via bioaccumulation modeling . Water column values are the applicable criterion element in the absence of steady

state condition fish tissue data

. 5 Where WQC 30

- day is the water column monthly element, for either a lentic or lotic waters; C bkgrnd is the average background selenium concentration, and f int is the fraction of any 30

- day period during which elevated selenium concentrations occur, with f int assigned a value ≥ 0.033 (corresponding to 1 day).

6 Fish tissue data provide instantaneous point measurements that reflect integrative accumulation of selenium over time and space in fish population(s) at a given site.

The egg/ovary tissue criterion element of 15.1 mg/kg dw is calculated using the four
lowest EC10 GMCVs from a database of acceptable freshwater fish studies, based on the methodology outlined in the 1985 Aquatic Life Guidelines

. 26 Since reproductive endpoints were found to be the most sensitive endpoints, studies of reproductive effects were considered

. Twelve fish reproductive toxicity studies of sufficient quality and covering eight fish genera

26 As outlined in the 1985 Aquatic Life Guidelines, the Final Chronic Value ( FCV ) of 15.1 mg/kg dw was determined from a regression analysis of the four most sensitive GMCVs and an extrapolation to the 5 th percentile of the distribution represented by the tested genera.39

were available that yielded e ndpoin ts includ ing larval mortality

, larval edema and skeletal/cranial deformities (teratogenicity) through maternal transfer from diet ary exposures

. The four most sensitive genera are, in order of most to least sensitive, Acipenser (white sturgeon), Lepomis (b luegill sunfish), Salmo (brown trout), and Oncorhynchus (rainbow and cutthroat trout). The genera and GMCVs are listed in Table 3

- 7 Lowest Four Reproductive

Effect Egg/Ovary GMCVs.

Table 3

- 7 Lowest Four Reproductive

- Effect Egg/Ovary GMCVs (Adapted from US EPA, 2016) Relative Sensitivity Rank Genus GMCV (mg Se/kg dw egg/ovary)

1 Acipenser 15.6
2 Lepomis 20.6
3 Salmo 21.0
4 Oncorhynchus 25.3

Fish whole body and muscle criterion element values were developed because fish egg or ovary tissue is only available in females at certain times of the year while fish whole body and muscle tissue data are more commonly available. The whole body and musc le tissue values are based on the egg/ovary tissue concentration. The whole body tissue value of 8.5 mg/kg dw is calculated using the same methodology using the four lowest whole body EC10 GMCVs of the same set of reproductive effect studies. The four mos t sensitive genera are, in order of most to least sensitive, Acipenser (white sturgeon), Lepomis (bluegill sunfish), Oncorhynchus (rainbow and cutthroat trout), and Salmo (brown trout). The genera and GMCVs are listed in Table 3

- 8 Lowest Four Reproductive

- Effect Whole Body GMCVs.

Table 3

- 8 Lowest Four Reproductive

- Effect Whole Body GMCVs (Adapted from USEPA, 2016) Relative Sensitivity Rank Genus GMCV (mg Se/kg dw whole

- body)

1 Acipenser 9.2
2 Lepomis 9.9
3 Oncorhynchus 11.6
4 Salmo 13.2

The muscle tissue criterion element value of 11.3 mg/kg dw is calculated using the four
lowest muscle EC10 GMCVs of the same set of reproductive effect studies. The four most sensitive genera are in order of most to least sensitive, Acipenser (white sturge on), Oncorhynchus (rainbow and cutthroat trout), Lepomis (bluegill sunfish), and Salmo (brown trout). The rankings for the muscle criterion element differ from both the egg/ovary rankings and the whole body rankings. This is because the factors used to c onvert the egg/ovary to40

muscle concentrations or to whole body concentrations vary across species. 27 A lthough the muscle criterion element and the whole body criterion element are of different magnitude, they both represent the same level of protection as they were both converted from the egg/ovary criterion element as the starting point. The genera and GMCVs are listed in Table 3

- 9 Lowest Four Reprod uctive

- Effect Muscle GMCVs

.

Table 3

- 9 Lowest Four Reproductive

- Effect Muscle GMCVs (Adapted from USEPA, 2016) Relative Sensitivity Rank Genus GMCV (mg Se/kg dw muscle)

1 Acipenser 11.9
2 Oncorhynchus 14.3
3 Lepomis 15.9
4 Salmo 18.5

If a review of the species used in the underlying studies indicates the species are representative of those that live in the Bay and Delta (i.e., if the same species live in the estuary

or are appropriate surrogates for species that live in the estuary ), t he fish tissue criterion elements may be appropriate to use as benchmarks in the Ecosystem

- Scale Selenium Model

. Species used to determine the egg/ovary element are white sturgeon ( Acipenser

transmontanus ), bluegill sunfish ( Lepomis macrochirus ), brown tr out ( Salmo trutta ) and rainbow and cutthroat trout ( Oncorhynchus mykiss and O. clarki lewisi ). Although these are

t he lowest four genera, nine species covering eight genera were included in the analysis.
Genera and s pecies used to determine the whole body and muscle elements are the same four

genera ( and species) used to determine the egg/ovary element, but are ranked in a slightly
different order. A discussion of each of the species by genera follows.

Acipenser : T he study on white sturgeon ( A. transmontanus ) that is used to determine the egg/ovary, whole body and muscle tissue element value s is the maternal transfer Linville (2006) study discussed in the previous section. This study yielded an egg/ovary EC10 GMCV of 15.6 mg/kg dw, the lowest value of the four GMCVs used to determine the egg/ovary tissue
element value ; and a whole body EC10 GMCV of 9.2 mg/kg dw, and a muscle EC10 GMCV of 11.9 mg/kg dw, each the lowest value of the four GMCVs used to determine the wh ole body
and muscle tissue element values , respectively (USEPA, 2016).

The genus Acipenser includes two species indigenous to the San Francisco Bay and Delta: white sturgeon ( A. transmontanus ) and green sturgeon ( A. medirostris ); green sturgeon (Souther n Distinct Population Segment, DPS) are listed as threatened under the ESA (CA DFG, 2001; Threatened Status for Southern Distinct Population Segment of North American Green

27 For a complete discussion, see EPA’s national recommended freshwater aquatic life criterion for selenium, Aquatic Life Ambient Water Quality Criterion for Selenium

– Freshwater 2016 (US EPA, 2016).41

Sturgeon , 71 FR 17757, April 7, 2006). They are the only two sturgeon species occu rring on the U.S. West Coast, and the San Francisco estuary is listed as critical habitat for the Southern DPS of green sturgeon ( Final Rulemaking to Designate Critical Habitat for the Threatened Southern Distinct Population Segment of the North American G reen Sturgeon , 74 FR 52300, October 9, 2009).

In California, white sturgeon are only found on the Klamath River and in the San Francisco estuary (Sacramento and San Joaquin Rivers) where most are located (CA DFG, 2001; Jackson and Eenennaam, 2013). Whi te sturgeon are the largest freshwater

- inhabiting fish in North America, and can grow to over 13 feet and weigh over 1,300 pounds. White sturgeon have been fished from the estuary since the 1860s; commercial fishing peaked in 1887 with 1.65 million pounds of catch, but because of overfishing, only 0.2 million pounds of catch were caught by 1901 (CA DFG, 2001). The commercial fishing of white sturgeon in the estuary stopped in 1917, and throughout the 1900s, the population of white sturgeon in the estuary fluctuated, including periods of rebound (after wetter years) and decline (after drier years) (CA DFG, 2001). Sport fishing of white sturgeon is currently very popular, but in order to manage the population, size limitations are imposed. 28 Researchers are tagging, tracking and conducting studies on both white and green sturgeon to support recovery efforts (CA DFG, 2001; IEP, 2011). Both sturgeon species are ecologically and economically very important to the San Francisco estuary system.

Lepomis : The studies on bluegill sunfish ( L. macrochirus ) used in determining the egg/ovary, whole body and muscle tissue elements yielded an egg/ovary EC10 GMCV of 20.6 mg/kg dw, the second lowest value of the four GMCVs used to determine the egg/ovary tissue
element value , a whole body EC10 GMCV of 9.9 mg/kg dw, the second lowest value of the four GMCVs used to determine the whole body tissue element value , and a muscle EC10 GMCV of 15.9 mg/kg dw, the third lowest of the four GMCVs used to determine the muscle tissue element value (USEPA, 2016). Bluegill sunfish and a close relative, redear sunfish ( L. microlophus ), both live in the more freshwater reaches of the estuary, although neither are indigenous (USGS at http://nas.er.usgs.gov/queries/factsheet.aspx?SpeciesID=390 and http://nas.er.usgs.gov/queries/factsheet.aspx?SpeciesID=385 ; SacDelta.com at http://www.sacdelta.com/fishing/ ). Bluegill are more common and are found throughout the northern parts of the estuary (Wang, 1986) possibly due to their relatively low salinity tolerance (< 5 ppt) (Stuber et al., 1982), al though some populations of bluegill that are native to coastal

28 Currently, fishing for white sturgeon is open year

- round (with some restrictions). Catch must be between 40 and 60 inches (fork length), and no more than one per day and three per year per person. See California Department of Fish and Wildl ife at https://www.wildlife.ca.gov/Fishing/Ocean/Regulations/Fishing

- Map/SF

- Bay#sturgeon
, updated April 2, 2016.42

rivers can be found in salinities of up to 10 ppt and sometimes 12 ppt (Wallus and Simon, 2008; Peterson et al., 1993).

Bluegill and redear cross or hybridize with each other to produce viab le offspring (USGS

at http://nas.er.usgs.gov/queries/factsheet.aspx?SpeciesID=385 ; Inspired by Nature, Inc. at http:// www.ibnature.com/few

- facts

- on

- sun

- fish ). Although bluegill diet consists mainly of aquatic insects and plant matter, they can be bottom feeders (Inspired by Nature, Inc. at http://www.ibnature. com/few

- facts

- on

- sun

- fish ; Michigan Department of Natural Resources at http://www.michigan.gov/dnr/0,4570,7

- 153

- 10364_18958

- 45644

-- ,00.html ), while redear are mostly botto m feeders and are highly molluscivorous (USGS at http://nas.er.usgs.gov/queries/factsheet.aspx?SpeciesID=385 ). Species of fish that are bottom feeders, especially molluscivorous s pecies, are at greatest risk in the San Francisco estuary from
effects of selenium bioaccumulation.

Salmo : The study on brown trout ( S. trutta ) that is used to determine the egg/ovary and whole body and muscle tissue elements yielded an egg/ovary EC10 GM CV of 21.0 mg/kg dw, the third lowest value of the four GMCVs used to determine the egg/ovary tissue element value, a whole body EC10 GMCV of 13.2 mg/kg dw and a muscle EC10 of 18.5 mg/kg dw, each the highest of the four GMCVs used to determine the whole b ody and muscle tissue element values, respectively (USEPA, 2016). The genus Salmo includes only two species that live in North America, Atlantic salmon, S. salar , and brown trout, S. trutta . The distribution of the remaining 40 or so species within the genus Salmo is mostly European and Asian (FishBase, A Global Information System on Fishes at http://fi shbase.sinica.edu.tw/identification/SpeciesList.php?genus=Salmo ). Brown trout are historically native to Europe, western Asia and northern Africa, but since their introduction to North America in the late 1800s, they are now found throughout the United St ates (Animal Diversity Web at http://animaldiversity.ummz.umich.edu/accounts/Salmo_trutta/ ) including throughout California (California Department of Fish and Wildlife at http://www.dfg.ca.gov/fish/resources/WildTrout/WT_BrownDesc.asp ). Anadromous brown trout, also called sea

- run brown trout or sea trout (Fishbase at http://fishbase.sinica.edu.tw/summary/Salmo

- trutta.html ), can be found in the San Francisco delta (SacDelta.com at http://www.sacdelta.com/fishing/ ), but are not common (Schroeter and Moyle, 2006). Young adult sea

- run brown trout or smolts have been found in the Sacramento River portion of the delta (Schroeter and Moyle, 2006 citing Moyle, 2002). Sea

- run brown trout and freshwater brown trout are the same species.

Onco rhynchus : The studies evaluated and used to determine the egg/ovary, whole body
and muscle tissue element values include several studies on salmonids, including rainbow trout43

( O. mykiss ) and Westslope cutthroat trout ( O. clarki lewisi ). The document calcu lates an egg/ovary EC10 SMCV for rainbow trout as 24.5 mg/kg dw, an egg/ovary EC10 SMCV for cutthroat trout as 26.2 mg/kg dw, and an egg/ovary GMCV (for Oncorhynchus ) as 25.3 mg/kg dw (the geomean of the two SMCVs) (USEPA, 2016). This is the highest value of the four GMCVs used to determine the egg/ovary tissue element value. The studies on cutthroat and rainbow trout yielded a whole body EC10 GMCV of 11.6 mg/kg dw, the third lowest of the four GMCVs used to determine the whole body tissue element value, a nd a muscle EC10 GMCV of 14.3 mg/kg dw, the second lowest of the four GMCVs used to determine the muscle tissue element value (USEPA, 2016).

Rainbow trout are the more sensitive of these two species in this genus. Steelhead
trout are anadromous rainbo w trout, living part of their lives in estuarine and/or marine waters, returning to freshwaters to mate and spawn, while resident rainbow trout live their entire lives in freshwater or spend very short periods of time in estuarine and near

- shore
marine wat ers (Alaska Department of Fish and Game at http://www.adfg.alaska.gov/index.cfm?adfg=steelhead.main ; NOAA Fisheries Offic e of
Protected Resources at http://www.nmfs.noaa.gov/pr/species/fish/steelheadtrout.htm ). Steelhead trout and rainbow trout are the same species. There are no major physical
differences between rainbow and st eelhead, and juveniles are indistinguishable; adults appear different given their different life histories (Alaska Department of Fish and Game at http://www.adfg.alaska.gov/index.cfm? adfg=steelhead.main ).

Both rainbow and steelhead are native to the San Francisco estuary and connecting tributaries, and were historically abundant (Leidy et al., 2005; USFWS, 2008). Populations in the estuary have significantly declined over the last 50 years (Leidy et al., 2005), and two E SUs are currently listed as threatened: the Central California Coast ESU which includes populations in the San Francisco Bay (62 FR 43937, August 18, 1977); and the California Central Valley ESU which includes popula tions in the eastern delta regions (63 FR 13347, March 19, 1998).
Steelhead are in the Salmonidae family. Salmonids are an important part of the economically significant recreational fishing industry in the Bay area, generating millions of dollars of re venue annually (Battelle Memorial Institute, 2008).

Cutthroat trout are close relatives of rainbow/steelhead trout and naturally occurring hybrids have the physical markings of both (Alaska Department of Fish and Game at http://www.adfg.alaska.gov/index.cfm?adfg=steelhead.main ). The rainbow/cutthroat hybrids are viable and fertile, and of the 14 recognized subspecies of cutthroat, all have been impacte d by hybridization (USGS at http://www.nrmsc.usgs.gov/science/feature/hybrid_trout ). Coastal cutthroat trout ( O. clarki clarki ) are a subspecies of cutthroat trout (O. clarki) , and are44

anadromous but prefer to remain close to their natal streams (Washington Department of Fish
and Wildlife at http://wdfw.wa.gov/fishing/salmon/cutthroat.html ); they are found in northern

coas tal California regions north of the San Francisco estuary, but not in the estuary (California Department of Fish and Wildlife at http://www.dfg.ca.gov/fish/resources/WildTrout/W T_CCutDesc.asp ).

Other information considered in the determination of the egg/ovary, whole body and
muscle tissue element values included information on Micropterus salmoides (largemouth bass). The study on largemouth bass ( M. salmoides ) yielded an egg /ovary EC10 GMCV of 26.3 mg/kg dw, the fifth lowest value of the eight genera in the dataset. Largemouth bass are commonly found in the San Francisco delta (California Department of Water Resources at http://www.water.ca.gov/aes/predators/largemouthbass.cfm ; USGS at http://nas.er.usgs.gov/queries/FactSheet.aspx?speciesID=401 ; SacDelta.com at http://www.sacdelta.com/fishing/ ; Trails.com at http://www.trails.com/tcatalog_trail.aspx?trailid=XFA053

- 039 ; and CVRWQCB, 2010). Largemouth bass are non

- native; they were introduced into California in the late 1800s as a sport fish (California Department of Water Resources at http://www. water.ca.gov/aes/predators/largemouthbass.cfm ). Sport fishing is a very important industry in the San Francisco Bay area, and bass, including largemouth bass, are an important source of recreation and economic revenue in the San Francisco delta (Californi a Department of Water Resources at http://www.water.ca.gov/aes/predators/largemouthbass.cfm ; Trails.com at http://www.trails.com/tcatalog_trail.aspx?trailid=XFA053

- 039 ; and California Dep artment of
Fish and Wildlife at https://www.wildlife.ca.gov/Fishing/Inland/Black

- Bass ).

Summary of Ge nera: All species used to determine the egg/ovary, whole body and muscle tissue elements may be found in the San Francisco estuary except cutthroat trout, which is found in waters north of the estuary, and each of these species that are found in the

estua ry are important to the health of the estuary. These species include: white sturgeon, bluegill sunfish 29 ; steelhead/rainbow trout; and brown trout

. White sturgeon, as well as green sturgeon, are indigenous, and both are ecologically and economically impor tant to the estuary. Although brown trout are not common in the estuary, others species such as largemouth bass

, which is represented in the dataset, are prevalent. Although neither largemouth bass nor bluegill are native, they are economically important to the sport fishing industry in the region. Native steelhead are part of the Salmondae family; all salmon species in the estuary are essential as salmon fishing is a large part of the recreational and commercial fishing industry in

29 A closely related species to bluegil l sunfish, the redear sunfish (a molluscivorous species), is also found in the estuary, but was not one of the species used to develop the national recommended criterion.45

the Bay area. Steelh ead are also ecologically important; two ESUs that have historically lived in the estuary are currently listed as threatened. It is important to the economy as well as the ecology of the region to increase the population of this species.

Non

- Reproducti ve Effect Studies: In EPA’s recent 304(a) recommended criterion document, a thorough analysis of dietary studie s of non

- reproductive endpoints, e.g., juvenile survival and growth was completed. This analysis indicates t hat EC10 values are above the
EC10 values for reproductive endpoints , and therefore adverse non

- reproductive effects w ill be prevented if adverse reproductive effects are prevented (USEPA, 2016).

Relevant non

- reproductive studies evaluated in the 304(a) criterion document include
the study by Tashjian et al. (2006) on white sturgeon ( A. transmontanus ). This study indicates

an EC10 whole body value of 15.08 mg/kg dw for reduction in body weight (juvenile growth); this value is higher than the fish tissue whole body criterion element va lue of 8.5 mg/kg dw (USEPA, 2016). Thus, non

- reproductive effects to white sturgeon should be prevented by the EC10 whole body element value.

A dietary study on Sacramento splittail ( P. macrolepidotus ), by Teh et al. (2004),
indicates a No Observed Ef fect Concentration ( NOEC ) and Lowest Observed Effect
Concentration (LOEC) for juvenile deformities of 10.1 and 15.1 mg/kg dw, respectively, in muscle tissue. The Maximum Acceptable Toxicant Concentration (MATC ), which is the geometric mean of the NOEC and LOEC (and considered to be the chronic value) is 12.34 mg/kg
dw. Since the national recommended criterion includes an EC10 muscle tissue element value of 11.3 mg/kg dw , the muscle tissue element should be protective of non

- reproductive endpoints to split tail, as found in the Teh et al. study (USEPA, 2016).

Other relevant non

- reproductive studies include a study on Chinook salmon ( O. tshawytscha ) (Hamilton et al., 1990) (discussed in section B) and other studies on rainbow trout/steelhead. Both Chinook salmon and rainbow/steelhead trout are important ecological species, and important to the recreational and commercial industry in the estuary. Although
the studies were considered , they were not used in the development of criteria values due to quality concerns with the studies including poor control survival and/or confounding factors (e.g., other pollutants in diet) (USEPA, 2016 ). For these and other studies, including studies on bluegill, information indicated that the whole body SMCVs were not lowe r than the reproductive

- effect EC10 whole body element value of 8.5 μg/g dw, the national recommended criterion (USEPA, 2016)

.46

For the Hamilton et al. (1990) study, EPA reviewed the results of the 60

- day test on juvenile Chinook salmon, and derived a who le body EC10 GMCV of 9.052 μ g/g dw for non

reproductive effects (reduced growth) (USEPA, 2016) . Chinook salmon are anadromous, and like other Pacific anadromous salmonid species, spend most of their juvenile and all of their adult lives in the ocean, retu rning to natal inland freshwaters only to spawn. They do not feed during in

- migration, and they are semelparous so there is little dietary selenium exposure to adults from bay, estuarine or even freshwater sources. The EC10 GMCV for non

- reproductive
effe cts calculated at 60 days (Hamilton et al., 1990) is close to the whole body element criterion
value of 8.5 μ g/g dw for reproductive effects ; therefore, the whole body element criterion value should be protective for Pacific juvenile anadromous salmonid sp ecies that may be exposed to bay and estuarine selenium sources during out

- migrating to the ocean (USEPA, 2016).

Relative Sensitivity Studies: An issue of importance for the San Francisco estuary is the issue of whether indigenous green sturgeon (listed as threatened) are more sensitive to selenium than indigenous white sturgeon, to help explain why green sturgeon populations are declining. De Riu et al. (2014) fed juvenile green and white sturgeon (~30 g body weight) diets containing a range of selenium concentrations (selenomethionine added to diet formulation ; 2.2 mg/kg selenium in control diet [no added selenium] and 19.7, 40.1 and 77.7 mg/kg
selenium in three treatment diets ). Several endpoints were monitored over an 8

- week exposure period i ncluding survival and percent body weight increase (% BWI)

. White sturgeon juveniles had no mortalities through the highest dietary treatment

. Green sturgeon juveniles
had 0 % , 7.7 % a n d 23.1% mortality with the three dietary treatments. TRAP analysis (th reshold sigmoid nonlinear regression) of the green sturgeon survival data resulted in a whole body EC10 value of 28.93 mg/kg dw. EC10 values were lower for % BWI using TRAP. For % BWI, the whole body EC10 value for green sturgeon was 16.36 mg/kg dw, and for white sturgeon, 23.94 mg/kg
dw.

Also notable, in the control treatments, t he background concentration s of selenium in the juvenile green and white sturgeon were elevated at 7.2, 6.5 and 7.1 mg/kg dw (green sturgeon whole body), and 4.8, 7.3 and 5.6 m g/kg dw (white sturgeon whole body) at test initiation, and after four and eight weeks of exposure, respectively

.

De Riu et al. (2014) suggests green sturgeon may be more sensitive to selenium than white sturgeon and that the EPA whole body concentratio n of 8.5 mg/kg dw (USEPA, 2016) will be protective , based on the survival and growth data and the observation that the control whole body tissue concentrations (up to 7.2 mg/kg dw) are approaching the whole body
criterion element value

. This is important because white sturgeon, as well as juvenile green47

sturgeon (up to three to four years of age), spend most of their time in the San Francisco
estuary.

b. Bird Egg Tissue Criterion (USEPA, 2011 a ): Relevant avian studies on mallards were
identified and u sed recently to develop bird egg threshold values for the Great Salt Lake in Utah (Tetra Tech, Inc., 2008 citing Ohlendorf, 2007 ; Ohlendorf, 2007). The key studies include d Heinz, et al., 1987, 1989, Heinz and Hoffman 1996, 1998, Stanley et al., 1994, 1996 ( Ohlendorf, 2007) . As part of the development process for the threshold values, the Great Salt Lake Science
Panel 30 looked at data from the key studies to determine EC10 d ietary concentrations and EC10 egg selenium concentrations (Tetra Tech, Inc., 2008 ; Ohlendorf, 2007). Data on hatching
success were used to determine an EC10 egg selenium concentration of 12.5 μg/g dw 31 using a logistic regression , and an EC10 of 11.5 μg/g dw 15 using a hockey stick regression (Tetra Tech, Inc., 2008 ; Ohlendorf, 2007). Other studies considered in the Great Salt Lake analysis indicate relevant egg concentration values ranging from 5.1 μ g/g dw to 16 μ g/g dw (Ohlendorf, 2007 Table 2). Althoug h 12.5 μg/g dw based on the logistic regression was chosen as the relevant value for the Great Salt Lake, not all members of the Science Panel agreed (Ohlendorf, 2007 ; Skorupa, 200 8 ). EPA approved the State of Utah’s criteria in 2011 (USEPA, 2011 a ).

The 12.5 μg/g dw EC10 described in Ohlendorf (2003) was calculated using data from six maternal transfer studies for mallard ducks ( A. platyrhynchos ) in which adults were fed selenomethionine for several weeks prior to breeding and throughout the egg laying p eriod. Percent egg hatchability and selenium concentrations in eggs were measured. Because of the high inter

- study variability in the control percent hatch (Table 3

- 10), egg hatchabilities were
control

- normalized prior to analysis (Ohlendorf, 2003). Fol lowing control normalization, the effects of selenium concentrations in eggs on mallard egg hatchability were analyzed using a

two

- parameter logistic regression model, with a resulting EC10 of 12.5 μg/g dw. Dietary treatment levels, egg selenium concentra tions, and unadjusted and control normalized egg hatchabilities for the six studies as originally reported in Ohlendorf (2003) are provided in Table
3

- 10.

The EC10 value of 12.5 μg/g dw appears protective of mallards upon review of the results of a field study conducted by FWS (USFWS, 2011). In this field study, FWS examined the relationship between selenium concentrations and proportional hatch in mallard eggs collected

30 See http://www.deq.utah.gov/ProgramsServices/programs/water/selenium/index.htm for information on the process used to develop the selenium water quality criteria in the Great Salt Lake, Utah.

31 The logistic egg selenium regression was previous ly reported in Ohlendorf (2003), and the hockey

- stick egg selenium regression was previously reported in Adams et al., 2003 (Tetra Tech, Inc., 2008; Ohlendorf, 2007).48

in the field between 2000 and 2005. Eggs were collected in Da vis, California, from nesting sites in fields irrigated with treated sewage water with slightly elevated selenium levels discharg ed by the city. The objective of the study was to generate sufficient data across a range of selenium concentrations in the eg gs above background levels to facilitate a comparison between two alternative hypothesized thresholds of selenium toxicity in mallard s based on laboratory toxicity testing: a threshold of 6

- 10 μg/g dw versus a threshold of 16

- 20 μg/g dw ( USFWS, 2011 ).

Tab le 3

- 10 Effects of Dietary Selenium Exposure on Egg Selenium Concentrations and Hatchability in Mallards (Adapted from Ohlendorf, 2003)

Dietary Selenium
Treatment (nominal) (mg/kg) Egg Se

(mg/kg) # Hens %Egg

Hatchability %Egg

Hatchability (Control
Norm alized) Reference

Control 0.16 11 65.7 100 Heinz et al., 1987
10 15.2 5 30.9 47.0 Heinz et al., 1987 Control 0.59 32 59.6 100 Heinz et al., 1989
1 2.74 15 70.7 119 Heinz et al., 1989
2 5.28 15 60.0 101 Heinz et al., 1989
4 11.2 15 53.4 89.6 Heinz et al., 1989
8 36.3 15 36.9 61.9 Heinz et al., 1989
16 59.4 9 2.2 3.7 Heinz et al., 1989 Control 1.35 10 41.3 100 Heinz and Hoffman, 1996
10 30.4 15 7.6 18.4 Heinz and Hoffman, 1996
10 29.4 15 6.4 15.5 Heinz and Hoffman, 1996 Control 1.16 12 44.2 100 Heinz and Hoffman, 1998
10 25.1 11 24.0 54.3 Heinz and Hoffman, 1998 Control 1.4 37 88.2 100 Stanley et al., 1994
10 37 35 37.0 22.7 Stanley et al., 1994 Control 0.89 33 62.0 100 Stanley et al., 1996
3.5 11.6 29 61.0 98.4 Stanley et al., 1996
7.0 23.4 34 41.0 66.1 Stanley et al., 1996

Paired hatchability and egg selenium data were available for a total of 96 mallard
clutches c ollected between 2000 and 2005 (USFWS, 2011) . Selenium concentrations in eggs ranged from 1.7

– 14 μg/g dw, with a geometric mean of 4.2 μg/g dw. Hatchability of individual clutches ranged from 40 to 100%, and average yearly hatchability ranged from a low of 82% in 2003 (a year with four clutches collected, one of which had 40% hatchabil ity) to a high of 100%
in 2005

. Average hatchability across all 96 clutches between 2000 and 2005 was 91% . Ranges and average selenium concentration and hatchability results are shown in Table 3

- 11, which is reproduced directly from USFWS (2011).49

The relationships between selenium concentrations and percent hatchability were investigated in a summary of the USFWS (2011) report using correlations and analysis of variance (GLEC, 2014). Correlations between egg selenium concentrations and percent hatchability were performed separately for each year of the study, and for the entire study period. There was no correlation between selenium concentrations and proportional hatch for the full 2000 to 2005 dataset. Similarly, there was no correlation between selenium concentrations and propo rtional hatch for individual years with the exception of 2003, where there was a statistically significant positive correlation (p = 0.04, r 2 = 0.92) between selenium concentrations and hatch. The number of clutches found during 2003 was notably lower tha n for all other years (4 of 96), and the anomalous positive correlation was driven by a single clutch with 40% hatch at a selenium concentration of 2.1 μg/g dw coupled with three clutches with selenium concentrations between 4.5 and 5.7 μg/g dw and hatches between 88% and 100%. The positive correlation between selenium concentration and percent hatch appears to be a consequence of an outlier value with low hatchability combined with a small sample size, as clutches from other years during the study were fo und to have 100% hatch with lower
selenium concentrations.

Table 3

- 11 Selenium and Hatching Data for Mallard Clutches Collected from the Davis Wastewater Treatment Facility (USFWS, 2011)

2000 2001 2002 2 003 2004 2005 All
Years # Clutches Collected 23 17 13 4 28 11 96

Mean [Se]* (Range) 4.1

(1.7

- 14) 3.4

(2.4

– 5.2) 5.0

(3.2

– 7.3) 4.1

(2.1

– 5.7) 4.7

(1.8

– 11) 3.6

(1.9

– 12) 4.2

(1.7

– 14.0)

Mean % Hatch (Range) 87%

(50.00

- 100) 90%

(66.67

- 100) 98%

(83.33

- 100) 82%

(40.00

– 100) 91%

(50.00

– 100) 100% 91% (40.00

– 100)

* Geometric mean presented as μ g/g dry weight.

Analysis of variance ( ANOVA) was used to examine whether or not hatchability of eggs with selenium concentrations above the lower level (6 μg/g dw) of the mallard egg selenium toxicity threshold of 6

- 10 μg/g dw was, as hypothesized by FWS, as follows. T he 96 values for
the entire 2000 to 2005 sampling period were divided into two bins, one with selenium concentration less than 6.0 μg/g dw, and one with selenium concentration of 6.0 μg/g dw and higher. The less than 6.0 μg/g dw bin consisted of 76 clutches, and the 6.0 μg/g dw and higher50

bin consisted of 20 clutches. The geometric mean of the selenium concentration in the less than 6.0 μg/g dw bin was 3.47 μg/g dw, and was 8.32 μg/g dw in the 6.0 μg/g dw and greater bin. Next, a Kruskal

- Wallis (non

- parametric ANOVA) test was perfo rmed to determine whether there were any statistically significant differences in hatch between the two bins. Results of the
Kruskal

- Wallis test revealed no significant differences (p = 0.59) between the two groups, suggesting that for these data, 6.0 μg/ g dw did not represent a selenium toxicity threshold for mallard egg hatchability. The average hatchability for the less than 6.0 μg/g dw bin was 91.4%, and the average hatchability for the 6.0 μg/g dw and higher bin was 91.1%.

Summary of EPA Sources: The national crit erion consists of egg/ovary, whole body and
muscle fish tissue elements, which were developed using information on several fish species that reside in the San Francisco estuary, or species that are appropriate surrogates for fish species t hat reside in the estuary. Therefore, the egg/ovary, whole body and muscle fish tissue
element values can be properly considered as benchmark values for reproductive effects, and
can be used in the Ecosystem

- Scale Selenium Model for the development of wate r quality criteria for aquatic species in the San Francisco estuary. A review of the analyses of bird egg tissue values indicate that an egg tissue value of 12.5 mg/kg dw is appropriate to use in the Ecosystem

- Scale Selenium Model for the development of w ater quality criteria for aquatic

dependent wildlife (avian) species in the estuary.

Site

- Specific Values: The EPA national recommended criterion values are guidance that are nationally applicable; however, they may sometimes be over

- or under

- protecti ve for certain specific water bodies due to local differences in biology and/or water quality. In cases where the guidance values are under

- protective, EPA’s 1985 Aquatic Life Guidelines allows for the lowering of the guidance value when necessary to prot ect a critically important species, such as a recreationally or economically important species 32 (USEPA, 1985). Other methods may be used such as the Recalculation Procedure to develop site

- specific tissue criterion values (USEPA, 2016). These methods all ow regulatory authorities to create tailored water quality criteria that are protective of the specified designated uses based on local species, and can be used to develop criteria to protect more sensitive resident species.

EPA’s national recommended s elenium criterion document includes recommended calculation procedures for states to develop site

- specific water column concentration elements
that better reflect site

- specific conditions. Since the translation of tissue values to water column values depe nds on the target predator species and its diet, and the hydrologic

32 The 1985 guidelines allow for the 5 th percentile of the lowest 4 GMCVs (the calculate d criterion) to be lowered to the SMCV of an economically or recreationally important species.51

conditions of the waterbody, the water column elements can be strongly dependent on site

specific conditions. One method to translate a tissue value is to take a mechanistic modeling approach, which uses an equation based on the Ecosystem

- Scale Selenium Model discussed in Chapter 2 (USEPA, 2016). Since this effort to develop site

- specific criteria for the San Francisco
estuary relies on the Ecosystem

- Scale Selen ium Model using detailed site

- specific data, this effort generate s precise and accurate values for the San Francisco Bay and Delta, and is consistent with EPA’s recommended procedure for developing site

- specific water column
concentration elements.

D

. B enchmarks for EPA Use in the Ecosystem

- Scale Selenium Model

EPA’s 2016 national recommended freshwater selenium criterion has four elements: an egg/ovary element, a whole body or muscle element, lentic or lotic water column elements,
and an intermittent water column exposure element (USEPA, 2016). The San Francisco Bay estuary is a large area, extending from the Golden Gate Bridge southeastward to South San Francisco Bay, and from the Bridge, northeastward to the San Joaquin and Sacramento Rivers,
and inc ludes brackish and marine waters with salinities ranging from 1 ppt and higher. The national recommended freshwater selenium tissue elements are developed using information on several species including anadromous species, most of which reside in the estua ry or are closely taxonomically related and serve as surrogates for the untested estuarine or marine species; therefore the national recommended criterion tissue elements may be appropriately considered as benchmark values in the model for the estuary . Si nce the model uses whole body fish tissue values in its calculations , we propose to use the 304(a) recommended whole body element in the model, an EC10 value of 8.5 mg/kg dw.

EPA recently reviewed all available bird egg tissue studies for aquatic

- depend ent avian species (USEPA, 2011a), and found the appropriate egg tissue EC10 value is 12.5 mg/kg dw,
based on studies of mallards. We include t his avian egg tissue value in the Ecosystem

- Scale
Selenium Model , and use the results to inform our analysis for determining protective water quality criteria for the estuary.52

CHAPTER 4 EPA MODELING AND PROPOSED WATER QUALITY CRITERIA

A. Designated Uses

The site

- specific criteria developed in this document (i.e., proposed criteria) are
intended to be protective of aquatic life and aquatic

- dependent wildlife, including federally listed threatened and endangered species in the San Francisco Bay and Delta. This is consistent with the State’s existing designated (beneficial 33 ) uses for the estuary. Two Re gional Water Quality Control Boards oversee different areas within the San Francisco Bay and Delta: the San Francisco Regional Water Quality Control Board ( SFRWQCB ) and the Central Valley Regional Water Quality Control Board (CVRWQCB). The SFRWQCB oversee s all parts of the Bay and the western part of the Delta; these areas are the South San Francisco Bay, Lower San Francisco Bay, Central San Francisco Bay, San Pablo Bay, Carquinez Strait, Suisun Bay, and the western portion of the Sacramento

- San Joaquin De lta (SFRWQCB, 2013). The CVRWQCB oversees the eastern portions of the Delta, which includes most of the Delta and the confluences of the Sacramento and the San Joaquin Rivers (CVRWQCB, 2011). Each of the Regional Water Boards has regional water quality p lans that include beneficial uses for the waterbodies they oversee (SFRWQCB, 2013; CVRWQCB, 2011).

In 1978, the State Water Resources Control Board ( SWRCB ), which oversees the Regional Water Boards, adopted a comprehensive plan for the estuary, the Wate r Quality Control Plan for the San Francisco Bay/Sacramento

- San Joaquin Delta Estuary. The plan was amended in 1991, 1995, and most recently in December, 2006 (SWRCB, 2006). This plan supplements the other water quality plans that cover the Bay and Delta (SWRCB Resolution
2006

- 0098, Whereas paragraph 8), and includes a comprehensive set of existing beneficial uses for all parts of the estuary. Existing beneficial uses in the SWRCB water quality plan for the protection of aquatic life and aquatic

- dependen t wildlife include:

Warm Freshwater Habitat (WARM)

- Uses of water that support warm water ecosystems including, but not limited to, preservation of aquatic habitats, vegetation, fish, or wildlife, including invertebrates.

Cold Freshwater Habitat (CO LD)

– Uses of water that support cold water ecosystems including, but not limited to, preservation or enhancements of aquatic habitats, vegetation, fish, or wildlife, including invertebrates.

33 The State of California uses the term “beneficial uses” instead of the term “designated uses” as used in the Clean
Water Act.53

Migration of Aquatic Organisms (MIGR)

– Uses of water that support habitats necessary for the migration or other temporary activities by aquatic organisms, such as anadromous fish.

Spawning, Reproduction, and/or Early Development (SPWN)

– Uses of water that support high quality aquatic habitats suitable for repro duction and early development of fish.

Estuarine Habitat (EST)

– Uses of water that support estuarine ecosystems including, but not limited to, preservation or enhancement of estuarine habitats, vegetation, fish, shellfish, or wildlife (e.g., estuarine ma mmals, waterfowl, shorebirds).

Wildlife Habitat (WILD)

– Uses of water that support estuarine ecosystems including, but not limited to, preservation and enhancement of terrestrial habitats, vegetation, wildlife (e.g., mammals, birds, reptiles, amphibians , invertebrates), or wildlife water and food sources.

Rare, Threatened, or Endangered Species (RARE)

– Uses of water that support habitats necessary, at least in part, for the survival and successful maintenance of plant or animal species established unde r State or federal law as being rare, threatened, or endangered.

The SWRCB water quality plan is consistent with the two Regional water quality plans. All parts of the San Francisco Bay and Delta have several existing beneficial uses that are
intended t o fully protect aquatic life and aquatic

- dependent wildlife. For the protection of aquatic life, existing WARM, COLD, MIGR, SPWN, EST and RARE uses apply, and for the protection of aquatic

- dependent wildlife including birds, existing EST, WILD and RARE us es apply (SWRCB, 2006).

B. EPA Development of Water Quality Criteria

Chapter 2, Selenium Modeling

, explains the Ecosystem

- Scale Selenium Model

, and describes the USGS modeling of the San Francisco estuary using the model. S everal scenarios

were run for the Bay and Delta under site

- specific environmental conditions with different endpoints to illustrate the bioaccumulation of selenium through out the estuary’s ecosystem ( USGS, 2010). Endpoints included estimated selenium tissue effect concent ration values for several wildlife species (or surrogate species) known to be living in the estuary modeled through the species’ food web.

Chapter 3, Selenium Benchmark Effect Concentrations, discusses options and choices concerning selenium benchmark e ffect values for EPA to use in the Ecosystem

- Scale Selenium54

Model to inform the analysis to determine water quality criteria for the estuary. This chapter
discusses the options and choices for other variables that EPA used in the model to create
represent ative scenarios from which to develop criteria. EPA’s intent is to identify and protect the most sensitive species in the estuary and to make reasonable assumptions and selections of input values for the model variables, and to use the results of our mode ling to develop protective criteria. Protection of all species in the estuary at all times is not an objective because ecosystems can tolerate some stress and occasional adverse effects (USEPA, 1985). A range of values for some variables, representing a balance in data availability and quality, is used in the model; thus a range of model outputs is presented and discussed.

a. Model ing Variables

The Ecosystem

- Scale Selenium Model integrates two general categories of variables: those attributable to species, and those related to the aquatic environment (Table 4

- 1) . Each of
the variables and values for the variables used in the model for determining water quality
criteria is discussed below.

Table 4

- 1 Model Variables

Species

- Specific Variables Environment

- Specific Variables
1. General Food Web s 1. Partitioning Coefficients ( K d s)
2. Representative Species 2. Hydrologic Water Year Type/Condition
3. Critical Life Stage s 3. Flow Season
4. Diet Mix es (for Representative Species)
5. Trophic Transfer Factors ( TTFs)
6. Effect Concentrations ( ECs)

i. Species

- Specific Variables

General Food Webs, Representative Species, Critical Life Stages , and Diet Mixes : Clam

- Eating Fish: EPA considered the analysis (USFWS, 2008) that identified the following
clam

- eating fish species as most at risk from selenium dietary exposure : green sturgeon (Acipenser medirostris) listed as federally threatened ; white sturgeon ( A. transmontanus ); and
the Sacramento splittail (Pogonichthys macrolepidotus) ( USFWS, 2008) . White sturgeon and Sacramento splittail are not federally listed as either threatened or en dangered. Critical life stages include adult female reproduction and juvenile growth and dev elopment for both sturgeon and splittail (USFWS, 2008). Green sturgeon appear to be more sensitive to selenium
in their diet th an white sturgeon (USFWS, 2012; Kaufman et al., 2008; Linares

- Casenave et al, 2010; Silvestre et al., 2010), however both juveni le and adult white and green sturgeon may be55

similarly sensitive to selenium at environmentally relevant whole body concentrations of around 6 to 7 μg/g dw (De Riu et al, 2014).

Juvenile Sturgeon: B ased on the size of juvenile sturgeon found in coastal estuaries and their natal upstream freshwaters, studies indicate that both green and white juvenile sturgeon spend six months to a year upstream in freshwater 34 . As with other fish species, it is likely that this early life stage is the most sensitive juve nile stage. During this time, diet most likely consists of (freshwater) plankton, larval insects, amphipods, and small benthic invertebrates, including crabs, clams and shrimp (Moyle, 2002; CA DFG, 2001), which are generally low in selenium. When the juv eniles are somewhat larger and older, they migrate down into brackish areas of the estuary, and likely consume some Corbula . Although the specific timing is unknown, juvenile green sturgeon are thought to spend from one to three years in the estuary (i.e. , from approximately age one to age four), before migrating to ocean waters (NOAA
Fisheries at http://www.westcoast.fisheries.noaa.gov/protected_species/green_sturgeon/green_sturgeon_ pg.html ; Moyle, 2002).

Sturgeon are long

- lived animals; white sturgeon are believed to have historically lived up to 100 years (University of California, Davis at http://calfish.ucdavis.edu/species/?ds=241&uid=113 ), and green sturgeon can live up to 70 years (USFWS at http://ecos.fws.gov/speciesProfile/profile/speciesProfile.action?spcode=E09K ). Although sturgeon grow rapidly (up to one foot in length) during their first year in freshwater, older juveniles grow at a much slower rate, reaching 46 inches 35 after 9 t o 16 years (CA DFG, 2001). The time that older juvenile green sturgeon may spend in the estuary before migrating to the ocean is not significant given their lifespan, nor is it the most sensitive or significant period of growth. However, in our analysis for the Bay and Delta we consider the effects of dietary
selenium from Corbula in the estuary on both green and white juvenile sturgeon.

In De Riu et al. (2014), background green and white juvenile sturgeon whole body concentrations in the control (fed a diet of 2.2 ± 0.2 mg Se/kg dw) ranged from approximately

5.6

– 7.3 mg/kg dw; no adverse effects on growth and development (including mortality) were

34 Juvenile sturgeon grow up to one foot (30 cm) in length during their first year of life (CA DFG, 2001). Juvenile sturgeon that have been found in Pacific coastal estuaries are all generally much larger (see Nakamoto et al., 1995 and CA DFG, 2002).

35 White sturgeon can reach 13 feet or more (CA DFG, 2001), and green sturgeon can reach up to 7 feet (NOAA Fisheries at http://www.fisheries.noaa.gov/pr/species/fish/green

- sturgeon.html ).56

recorded in the controls. These values are a p proaching EPA’s national recommended whole body fish tissue c riterion element value of 8.5 mg/kg dw (USEPA, 2016), and EPA proposes that both green and white juvenile sturgeon will be protected by the national whole body tissue
value.

Adult sturgeon: Many adult white sturgeon in the San Francisco estuary are yea r

- round residents ( USFWS, 2008; Moyle, 2002). Thus, our analysis focuses on adult white sturgeon and dietary impacts on reproduction from foraging in the estuary.

Adult green sturgeon are believed to spend the majority of their lives in near shore

ocean ic waters, but are known to forage at times in estuaries and bays (NOAA Fisheries at http://www.westcoast.fisheries.noaa.gov/protecte d_species/green_sturgeon/green_sturgeon_ life_history.html ). Reproductively mature adult green sturgeon have been observed to move rapidly through the San Francisco estuary to spawning areas, and, once in freshwaters, spend
several months there before out

- migrating to marine areas (Israel and Klimley, 2008 at http://essexpartnership.com/wp

- content/uploads/2010/10/GreenSturgeon

- _1_.pdf ). In one study, tagged mature female green sturgeon move d through the San Francisco estuary in a matter of a few days on their way to spawning areas in the Sacr amento River (Heublin et al., 2009 Figures 2, 4 and 6). Although the length of stay of the tagged green sturgeon in the Sacramento River varied, they took a few weeks to two months before passing under the Golden Gate Bridge to the ocean (Heublin et al., 2009).

It is likely that for adult green sturgeon to have reproductive impacts from diet, they would have to be foraging in the estuary at the time when they were undergoing vitellogenesis (nutrient or yolk formation during oogenesis, the formation of e gg cells). There is little published information about vitellogenesis in green sturgeon. However, the reproductive cycle in cultured white sturgeon is lengthy and vitellogenesis can occur over a span of 16 to 18 months; reproductive cycles in wild sturge on have been observed to be even longer, but the specific reasons for these differences are not known (Doroshov et al., 1997). If vitellogenesis in wild green sturgeon is similar, and they forage in the estuary during that critical stage in their
life his tory, they may be at an increased risk of exposure, bioaccumulation and maternal transfer of selenium to their eggs 36 . However, since adult green sturgeon only periodically forage in the estuary, their diet most likely predominantly reflects prey species f rom a marine ocean environment. Existing information about vitellogenesis in green sturgeon and their

36 It is also unkno wn whether energy for vitellogenesis comes more from stored body mass (from oceanic diet) or from body fat (directly from a current diet), or both. The source of energy for vitellogenesis (stored body mass vs. body fat) may determine the source of any sel enium deposited into eggs. Additionally, some uncertainty exists concerning the rate of deposition of vitellogenin, and the overall process of vitellogenesis in green sturgeon.57

foraging habits during vitellogenesis does not allow for more precise quantification of this risk. Therefore, the focus of this analysis is on the dieta ry risk to juvenile green and white sturgeon, and to adult white sturgeon that remain in the estuary most of their lives.

Diet: The FWS report states that t he diet of white sturgeon in the estuary is approximately 40% clam

- based; the diet of the green s turgeon in the estuary, although unknown, is believed to be si milar ( USFWS, 2008 Table 2 citing McKechnie and Fenner, 1971). More recent sources, reporting observations made after the introduction of Corbula to the estuary, indicate a larger percentage of clams, specifically the invasive bivalve Corbula

, in white sturgeon diet (Brodsky et al., 2014; Zeug et al., 2014). However, some studies have observed whole (unopened) and/or live Corbula in the feces of white sturgeon and have suggested that
not all of the Corbula tissue consumed is digested (Kogut, 2008; Urquhart and Regalado, 1991). A recent study by Zeug et al. (2014) found that the gut contents of white sturgeon from the estuary contained between 82 and 93% Corbula by volume, but that stable isot ope analysis found that their assimilated contribution to sturgeon biomass was lower, between 70 to 83%. This indicates that although some sturgeon may consume large amounts of Corbula by volume,

a portion is not digested and assimilated.

Worms and cr ustaceans generally make up the balance of the diet, although sturgeon

may be feeding on smaller fish and clams in greater quantities since the introduction and proliferation of Corbula into the estuary (see University of California, Davis, California Fish
Website at http://calfish.ucdavis.edu/species/?ds=241&uid=113 ; USFWS, 2008; Brodsky et al., 2014; Zeug et al., 2014; and Feyrer et al., 2003).

To evaluate reproductive and non

- reproductiv e effects in clam

- eating fish, we consider
a diet of 40% Corbula , and 60% crustaceans, insects and other invertebrates for adult white sturgeon and juvenile white and green sturgeon. The diet of juvenile green sturgeon while in the Bay and Delta is most likely similar to that of white sturgeon. Although Corbula are v ery abundant in sub

- tidal waters of the estuary inhabited by adult and juvenile white sturgeon, juvenile green sturgeon, and other bottom

- dwelling, clam

- eating fish species, and sturgeon may consume a higher percentage of Corbula by volume, not all is dige sted and assimilated.

The FWS report indicates that the diet of the Sacramento splittail can be up to 34%
clam

- based (USFWS, 2008); other sources calculate a smaller percentage, even after the availability of the splittail’s other benthic food items (i.e. , mysid shrimp) declined once Corbula was introduced into the estuary (Feyrer et al., 2003). The splittail diet consists mainly (70%) of detritus, the remainder is various crustaceans including opossum shrimp (mysids), insect larvae, earthworms, and other invertebrates, including some (< 10%) bivalves (Feyrer et al., 2003;58

University of California, Davis, California Fish Website at http://calfish.ucdavis.edu/species/?uid=83&ds=241 ). Since S acramento splittail consume less
Corbula than white sturgeon (approximately 34% clam

- based, a portion of which may be
Corbula ), if white sturgeon are protected, then splittail should also be protected.

Analyses indicate that the most sensitive endpoint arising from dietary exposure of selenium is adverse effects on reproduction (see Chapter 3 and USEPA, 2016); therefore, if these are prevented in adult female white sturgeon, then adverse non

- reproductive effects such as reduced growth and development in juvenile white and green sturgeon also should be prevented 37

.

Clam

- Eating Birds: EPA reviewed the information in the FWS report that identified the

c lam

- eating birds most at risk from selenium dietary exposure as the California Ridgway’s rail (Rallus lo ngirostris obsoletus)

, listed as f ederally endangered, and the diving ducks: the greater

scaup (Aythya marila) , lesser scaup (A. affinis) , white

- winged scoter (Melanitta fusca) , surf

scoter (M

. perspicillata) , and black scoter (M . n igra) ( USFWS, 2008 ). FWS identified the critical life stage for rails as reproductive, and for diving ducks as migratory. 38

California Ridgway’s rails are year

- round residents of the estuary . The FWS report indicates their diet may contain up to 90% animal matter, with the re maining diet consisting of plant matter, and of the 90% animal matter, up to 64% is comprised of clams and mussels, and 26% is comprised of insects, crabs, worms and snails (USFWS, 2008). Both scoter and scaup winter along the Pacific coast of North Ameri ca including in the San Francisco estuary, then migrate north in the spring to their breeding grounds in Alaska and Canada (USFWS, 2008).
Their diet can range from 75% to 96% clam

- based , with the remainder consisting of snails, crustaceans, insects, and s ome plant material (USFWS, 2008).

California Ridgway’s rails live in the estuary’s tidal salt marshes (see USFWS at http://www.fws.gov/refuge/San_Pablo_Bay/LifeTimesofCCR.html ), and are littoral feeders, i.e., they consume species that are available in the shallow

, near shore and intertidal waters

. Corbula , primarily found in sub

- tidal waters, can also be found in intertidal mudflats. T o evaluate reproductive effects in Califor nia Ridgway’s rail , we consider a diet of up to 20 %
Corbula and 40% other mollusks

, 30 % insects and 10% plant matter. This represent s a 90%

37 See also the discussion in Chapter 3 concerning the background (contro l) whole body concentrations in green and white juvenile sturgeon in the De Riu et al. (2014) study.

38 Although FWS identified the critical life stage as migration for (adult) diving ducks, we also include (adult female) reproduction in this analysis for completeness.59

animal (60 % mollusk and 30% insect ) diet, and includes some (20 %) Corbula in their diet, possibly reflecting a conservative (reasonable high end) estimate of Corbula consumption. More detailed information on the rail’s diet in the estuary is not currently available.

Scoter and scaups are migratory birds that winter in various parts of the estuary and fly north to boreal forests in the springtime. A study on the movements of surf scoters in 2004 and 2005 by De La Cruz et al. (2014) found that scoters concentrated in San Pablo Bay during December and January 39 but their distribu tion shifted in February and March to the Central Bay. The scoters also used Suisun Bay in January and February, then moved into the Central Bay in February and March. Some surf scoters congregated along the San Mateo Coun ty and
south Oakland coastlines throughout the winter season. The study noted that scoter diet in San Pablo and Suisun Bays consists mostly of clams ( Corbula ) likely due to its abundance

, while in the Central Bay it consists of herring roe, Japanese littleneck clams ( Venerupis philipina rium ) and invertebrates found in seagrass beds. The most accurate predictor of scoter presence and density in the estuary was herring roe, which is abundant in the Central Bay starting in January, continuing into February and March when herring spawn (De La Cruz et al., 2014). Lovvorn et al. (2013) looked at the movements and diets of lesser scaup, greater scaup and surf scoter in the San Francisco estuary and found similar migratory patterns and diets.

DeVink et al. (2008), using captive lesser scaup, simulated exposure to spring migration (selenium in staging areas) to determine reproductive and physiological effects. The study included three treatment scenarios: a control group fed 0.65 μg/g dw selenium reflecting
observed levels in uncontaminated b oreal invertebrates; a second group fed 7.7 ± 0.2 μg/g dw selenium, and a third group fed 14.9 ± 0.5 μg/g dw selenium (actual treatment concentrations), to simulate observed mussel concentrations in the St. Lawrence River (7.5 μg/g dw) and in Lake Michigan (15 μg/g), respectively. The groups were fed the treatment diets for 4 weeks (30 days), to simulate stopover exposure on the Great Lakes; elevated selenium was removed from diet shortly before egg

- laying began. Results showed that body mass, breeding pr obability and clutch initiation dates were not affected, and that selenium concentrations in eggs from the two treatment groups decreased rapidly, down to a threshold value of 9 μg/g dw by 8 and 12 days after treatment ceased for the 7.7 and 14.9 μg/g dw d ietary selenium groups, respectively. The study concluded that the limited duration of exposure to dietary selenium in spring staging environments is not sufficient to affect reproduction or body mass in scaup that migrate to uncontaminated breeding areas . The results may reflect the ability of females to depurate excess selenium at breeding sites where dietary selenium is low, or the possibility that

39 Migratory waterfowl arrive in the San Francisco Bay area during the fall starting in October (USFWS at http://www.fws.gov/refuge/Don_Edwards_San_Francisco_Bay/seasons_of_wildlife/index.html ).60

contaminated birds may not be breeding (DeVink et al., 2008). The study noted that scaup departing from the Great Lakes take a minimum of 21 days to reach breeding grounds where they initiate nesting, and during that time excess selenium is likely depurated before egg
formation.

In the San Francisco estuary, although migratory ducks may be eating a high s elenium diet during the first part of the winter in San Pablo and Suisun Bays, they are eating a low selenium diet after moving into the Central Bay where they consume herring roe and invertebrates, before migrating north in March and April. De La Cruz et al. (2009) documented that it took approximately 47 days for scoters to reach breeding grounds once they left the estuary. Over that time, it is likely that selenium will be depurated and neither physiological nor reproductive impairments will occur. Ho wever, this risk has not been quantified, and therefore we include migratory diving ducks in our analysis.

Although the diet of scoters and scaups consists of up to 75 to 96% clam during their stopover, they are part

- time residents of the estuary. Theref ore, to evaluate reproductive and migratory life stages, we consider a yearly diet of 45% Corbula , 5% other plant/animal material from the estuary, and 50% food material from outside the estuary. This reflects a diet consisting of up to 90% Co rbula for th e approximately six months of the year that they reside in the estuary, i.e. from about October to April, (1⁄2 of 90% = 45%) and a diet in the upper end of the estimated range of clams consumed, most of which is Corbula 40

. Although concentrated consumption of Corbula occurs during the winter in the estuary, it precedes northern migration by at least a month, and is not consumed during breeding. Although unknown, prey items consumed from northern breeding areas do not likely contain concentrations of selenium
similar to those found in Corbula from the estuary.

Insect

- Eating Fish: EPA considered the FWS analysis which identified t he insect

- eating fish species most at risk from selenium dietary exposure as Chinook salmon (O ncorhynchus tshawytscha) listed as Federally endangered

, and s teelhead trout (O

. mykiss) and Delta smelt (Hypomesus transpacificus) , both listed as Federally threatened ( USFWS, 2008)

. For smelt,
af fected critical life stages include reproduction, and for all three species, juvenile g rowth and development (USFWS, 2008).

Juvenile Salmonids: Both Chinook salmon and steelhead trout are anadromous species, spending their lives in ocean waters and migrating to freshwaters to reproduce. Juvenile Chinook (or K ing) salmon spend from 3 months to 2 years in freshwater (depending on whether

40 In a study by Richman and Lovvorn (2004), during the 1998

- 99 and 1990

- 2000 winters, 96 percent of the dry mass of the esophagus contents of 13 lesser scaup in San Pablo Bay consisted of Corbula (USFWS, 2008).61

they are ocean

- type or stream

- type), then move into estuaries as smolts, to acclimate to saltwater before migrating to ocean waters (NOAA Fisheries at http://www.nmfs.noaa.gov/pr/species/fish/chinook

- salmon.html ). They spend the majority of their life, usually 2 to 4 years, at sea before returning to their natal freshwaters to reproduce (NOAA Fisheries at http://www.nmfs.noaa.gov/pr/species/fish/chinook

- salmon.html ). Chinook salmon are semelparous, i.e, they breed once before dying.

Juvenile steelhead spend from one to three years in freshwater before moving into estuaries to acclimate; they then migrate to the ocean where most of their growth occurs (USFWS at http://ecos.fws.gov/speci esProfile/profile/speciesProfile.action?spcode=E08D ). They spend one to four years at sea before returning to natal freshwaters to spawn (USFWS at http://ecos.fws.gov/speciesProfile/profile/speciesProfile.action?spcode=E08D ). Steelhead are iteroparous, i.e., they breed more than once

– usually twice

– before dying.

Juveniles of both species, while in the estuary as smolts and acclimating to more saline water, eat mostly terrestrial and aquatic insects and insect larvae when young and small, and also small fish as they grow (NOAA Fisheries at http://www.nmfs.noaa.gov/pr/sp ecies/fish/chinook

- salmon.html ; Moyle, 2002).

Juvenile Chinook salmon and steelhead spend varying amounts of time in the estuary before migrating to the ocean. Fall

- run Chinook are known to spend a few weeks or months in estuaries, while spring

- run Chino ok can spend up to 18 months in estuarine water (State of Oregon at http://www.oregon.gov/dsl/SSNERR/docs/EFS/EFS30salmon.pdf ). Similarly, steelhead can spend several weeks to a few months in estuaries before migrating to the ocean (NMFS, 2012). Since juvenile salmonids may be more sensitive to selenium than other fish species, this analysis looks at the dietary effects of selenium on juvenile salmonids.

Adult Salmonids: Anadromo us salmonids such as Chinook salmon and steelhead trout generally use the estuary as a migratory corridor between their oceanic habitat and natal freshwaters where they reproduce. Mature female Chinook salmon in the Klamath River basin were observed to pa ss very quickly through the estuary (in less than 24 hours) to reach freshwaters (Strange, 2013). Salmon species, once they leave the ocean to migrate to freshwaters, do not feed, and often they will die on the way if they do not have sufficient
stored bo dy fat to complete the trip (USFWS at http://www.fws.gov/species/species_accounts/bio_salm.html ). Since salmonids do not eat during their migration to freshwater, nutrients from oc ean prey are consumed during vitellogenesis, even if that process is not completed prior to entry into the estuary (i.e., is completed upon reaching natal freshwater). Since salmonids do not forage much in the estuary62

if at all, using it as a migratory co rridor, our analysis of dietary effects from prey in the estuary
does not include effects to adult salmonids 41

. Diet: None of the three species considered (juvenile Chinook salmon, juvenile steelhead trout and Delta smelt) consume Corbula (or other bival ve species that efficiently accumulate selenium), so their dietary exposure of selenium in the estuary will be lower than other species
that do

. Juvenile Chinook salmon consume mainly insects, amphipods, copepods, Cladocera or water fleas, and larger salm on also consume smaller fish; juvenile steelhead consume a variety of insects, and larger steelhead also consume smaller fish (USFWS, 2008). The Delta smelt, a small fish, consumes primarily amphipods, copepods, and cladocerans, and to a lesser extent,
in sect larvae (USFWS, 2008).

A summary of the representative species within each general food web, their probable critical life stage, estimated diet mix, and federal status under the ESA is shown in Table 4

- 2 Summary of Life Stages and Diet Mixes of Repre sentative Species Most at Risk.

41 Since steelhead trout are iteroparous, the re is some risk from dietary selenium when adult steelhead pass through the estuary on their return to the ocean after spawning. Sufficient information does not exist to quantify this risk; however, since adult steelhead do not appear to remain in the est uary for prolonged periods, it is unlikely that prey from the estuary would have a significant effect on the next cycle of vitellogenesis.63

Table 4

- 2 Summary of Life Stage s and Diet Mix es of Representative Species Most at Risk
General Food Web and Representative Species Probable Critical Life Stage Estimated Diet Mix Federal Status Under ESA

A. Clam

- Eating Fish

White Sturgeon Adult Female/Reproduction; and Juvenile/Growth and Development Corbula 40%; Annelids & Crustaceans 60% (Not listed) Juvenile Green Sturgeon* Juvenile/Growth and Development Corbula 40%; Annelids & Crustaceans 60% Threatened

Sacramento Splittail** Adult Female/Reproduction; and Juvenile/Growth and Development Corbula ≤ 10%; Insects, Crustaceans, Other Invertebrates ≥ 90% (Not listed)

B. Clam

- Eating (Diving) Birds

California Ridgway’s Rail Adult Female/Reproduction Corbula 20%; Other Mollusks 40%; Insects 30%; Plant 10% Endangered

Greater & Lesser Scaup; White

- Winged, Surf, & Black Scoter Adult Female/Reproduction; and Adult/Migration Corbula 45%; Other Materials 5%; Food Outside Estuary 50% (Not Listed)***

C. Insect

- Eating Fish

Chinook Salmon Juvenile/Larval Mortality, Growth and Development Insects; Amphipods; Copepods; Cladocera Endangered

Steelhead Trout Juvenile/Larval Mortality, Growth and Development Insects 100% Threatened

Delta Smelt Adult Female/Reproduction; and Juvenile/Growth and Development Amphipods; Copepods; Cladocera; Insect larvae Threatened * Since reproductive endpoints are more sensitive than non

- reproductive endpoints, juvenil e green (and white) sturgeon (critical life stage of juvenile growth and development) should be protected if white sturgeon (critical life stage of adult female reproduction) are protected. ** Since Sacramento splittail consume less Corbula (≤ 10%) than white sturgeon (40%), critical life stages in splittail should be protected if white sturgeon are protected. *** Although scoter and scaup species are not listed as threatened or endangered under the Endangered Species Act (16 U.S.C. § 1531 et seq.), they a re protected under the Migratory Bird Treaty Act (16 U.S.C. §703 et seq.).

Trophic Transfer Factors: TTFs represent the bioaccumulation of selenium from one trophic level to the next (see Chapter 2). The food web for clam

- eating birds and clam

- eating fish in the estuary consists mostly of Corbula. Other food sources for clam

- eating birds and fish include other mollusks, annelids, crustaceans, insects and other invertebrates (USFWS, 2008).
For insect

- eating fish, the food web consists mostly of aquatic insects and amphipods , and for higher trophic level fish, smaller fish within an insect

- based food web (USFWS, 2008 ). TTF
values for s pecies living in the San Francisco estuary and considered in the mod eling are shown
in Table 4

- 3 Trophic Transfer Factors (TTFs).64

Table 4

- 3 Trophic Transfer Factors (TTFs )

Food Chain TTF Prey ( Diet ) Source Notes
A . Clam

- Eating Fish Potamocorbula amurensis (Corbula) 17 Suspended particulate material (Spm) USGS, 2010 Site

- Specific Value Annelids ( Lumbriculus variegatus ) 1.3 Spm USEPA, 201 6 Freshwater species
Crustaceans: Copepod

- marine 1.35 Spm USGS, 2010; Presser and Luoma, 2010
Crustaceans: Mysid

- marine 1.3 Spm USGS, 2010; Presser and Luoma, 2010 Next Trophic Level: Fish 1.1 Invertebrates USGS, 2010 ; Presser and Luoma, 2010 B. Clam

- Eating Birds Potamocorbula amurensis (Corbula) 17 Spm USGS, 2010 Site

- Specific Value Other bay/estuarine mollusks ( Corbicula fluminea )* 2.8 Spm USGS, 2010; Presser and Luoma, 2010
Insect

– aquatic (average value) ** 2.8 Spm USGS, 2010; Presser and Luoma, 2010

Next Trophic Level: Bird (egg) 1.8 Invertebrates Presser and Luoma, 2010

0.8 Invertebrates Personal Communication, USFWS (see text) Site

- Spe cific Value

– California rail
C. Insect

- Eating Fish
Insect

– aquatic (average value) ** 2.8 Spm USGS, 2010; Presser and Luoma, 2010
Crustaceans: Amphipod

- marine 0.6 Spm USGS, 2010; Presser and Luoma, 2010
Crustaceans: Copepod

- marine 1.35 Spm USGS, 2010; Presser and Luoma, 2010
Crustaceans: Cladocera ( Daphnia m agna ) 1.9 Spm USGS, 2010; Presser and Luoma, 2010 Next Trophic Level: Fish 1.1 Invertebrates USGS, 2010 ; Presser and Luoma, 2010 * Other common, widespread mollusks inhabiting the Bay include the species Corbicula fluminea (see California
D epartment o f Water Resources at http://www.water.ca.gov/bdma/BioGuide/ ). ** Mean value of TTFs for mayfly, caddisfly, crane fly, stonefly, damselfly, corixid and chironomid (Presser and Luoma, 2010).

For clam

- eatin g birds and clam

- eating fish

, USGS used two diet scenarios to illustrate how the model responds: a n all

- clam ( Corbula ) diet (TTF (Corbula) = 17)

, and a mix ed diet of 50%
Corbula and 50% amphipods (TTF (amphipod) = 0.6), using a weighted TTF of 8.8 (i.e., [0. 5 x 17] + [0.5 x 0.6] = 8.8) (see USGS, 2010 and Chapter 2). For insect

- eating fish, USGS used an all

- insect diet (TTF ( i nsect) = 2.8) to illustrate how the model responds (see USGS, 2010 and Chapter 2). In this section, we consider different diet scenari os and weighted TTF values for use in the Ecosystem

- Scale Selenium Model for developing water quality criteria for the estuary. The TTF65

values we chose reflect more detailed diet mixes for the representative species of interest in the estuary.

Clam

- eatin g Fish: For clam

- eating fish, to model a diet of 40% Corbula (TTF (Corbula) = 17) and 60% annelids and crustaceans (TTF (annelids/crustaceans) = 1.3), we used a representative, weighted TTF of 7.6 (i.e., [0.40 x 17] + [0.60 x 1.3] = 7.6). The TTFs for annelids and crustaceans are taken from the published literature and are referenced in Table 4

- 3.

For the next trophic level for clam

- eating f ish, we used a TT F (fish) of 1.1, the value that was used in the published model of the estuary (USGS, 2010). This is the mean value of a compilation of TTFs for 25 different fish species, from 0.51 to 1.8, a relatively narrow range (USGS, 2010; Presser an d Luoma, 2010). The TTFs for fish were derived from labora tory and
matched field datasets.

Clam

- eating Birds: For California Ridgway’s rails, to calculate a diet consisting of 20%
Corbula (TTF (Corbula) = 17), 40% other mollusks (TTF (bay mollusk) = 2.8) and 30% insects (TTF (insect) = 2.8), we used a representative, weighted TTF of 5.4 (i.e., [0.20 x 17] + [0.40 x 2.8] + [0.30 x 2.8] = 5.4) 42 . For scoter and scaup, to model a diet (for the six months a year that they live in the estuary) consisting of 45% Corbula and 5% other animal material from the estuary (TTF (misc/mollusk/insect) = 2.8), we used a representative, weighted TTF of 7.8 (i.e., [0.45 x 17] + [0.05 x 2.8] = 7.8). The TTFs for other bay mollusks and insects are taken from published reports, an d
are referenced in Table 4

- 3. The TTF for other animal material of 2.8 reflects the TTFs of other sources of invertebrate foods in the estuary, such as insects (2.8) and other mollusks (2.8) (see
Table 4

- 3).

For the next trophic level for clam

- eating bi rds, USGS used a TTF ( bird egg) of 2.6 to illustrate scenarios of bioaccumulation in the estuary in its report to EPA (USGS, 2010). This is
the mean value of a range of bird egg TTFs (0.87 to 4.7) derived from matched data pairs of diet and bird egg tissue in the FWS analysis (USFWS, 2009), compiled from the Heinz et al. (1989) study on mallards (USGS, 2010). Presser and Luoma (2010) found a similar range of TTF (bird egg) values (1.5 to 4.5), calculated from mallard data in Ohlendorf (2003). Mallards are thought to be one of the most sensitive avian species based on reproductive endpoints (Presser and Luoma, 2010). Since species

- specific information is not available, and mallards are found in the estuary but are one of the most sensitive species, we chose a TTF (bird egg) of 1.8, a value toward

42 The small (10%) proportion of plant material consumed by rails is considered a de minimus source of selenium for this analysis.66

the lower end of the range to develop criteria. This value was also used in Presser and Luoma (2010) for scoters and scaups.

Species

- specific information is available for the California Ridgway’s rail, based on co

located selenium concentrations in invertebrates (yellow shore crab, ribbed mussels, mud snails, macoma clams and polychaete worms) and in eggs collected in the Corte Madera Marsh and in Wildcat Marsh (personal communication, Tom Maurer, USFWS, May, 2014). The TTF (bird

egg) for rails in the Corte Madera Marsh is 0.7 based on a rail egg selenium concentration of 1.43 parts per million ( ppm) and an invertebrate selenium concentration of 1.84 ppm (1.43/1.84 = 0.7). Similarly, the TTF (bird egg) for rails in Wildcat Marsh is 0.9 based on a rail egg selenium concentration of 1.57 ppm and an invertebrate selenium concentration of 1.71 ppm (1.57/ 1.71 = 0.9). The TTFs are clo se; we used the mean TTF of 0.8 for modeling the California Ridgway’s rail in the Ecosystem

- Scale Selenium Model.

Insect

- eating Fish: For the insect

- eating fish food web, we used a TTF (insects) of 2.8 in our modeling for the estuary; it is the mean val ue of a compilation of TTFs of freshwater insects (mayfly, caddisfly, crane fly, stonefly damselfly, corixid and chironomid) derived from matched field datasets (USGS, 2010 ; Presser and Luoma, 2010). For the next trophic level, we used a

TTF (fish) of 1.1

, as discussed above. The diet of juvenile steelhead is 100% insect

- based. The diets of juvenile Chinook salmon and delta smelt also include amphipods, copepods and Cladocera; the TTFs for these prey items are 0.6, 1.35 and 1.9, respectively (USGS, 2010; Presser and Luoma, 2010). Since the TTFs for these prey items are less than the TTF for insects (2.8), if juvenile steelhead are protected, then juvenile Chinook salmon and delta smelt should be protected.

Table 4

- 4 Summary of Diet Mixes and TTFs for R epresentative Species Most at Risk shows the representative diets and TTFs for the representative species in the three food web categories.67

Table 4

- 4 Summary of Diet Mixes and TTFs for Representative Species Most at Risk

Food Web / Representative Species Representative Diet Representative TTFs

Clam

- eating Fish White Sturgeon (Adult)* 40% Corbula 60% Annelids/Crustaceans 7.6 (spm to prey) 1.1 (prey to fish)

Clam

- eating Birds

California Ridgway’s rail 20% Corbula 40% Other mollusks 30% Insects (10% Plant) 5.4 (spm to prey) 0.8 (prey to bird egg)

Scoter and Scaup 45% Corbula 5% Other A nimal Material (50% Food Outside Estuary) 7.8 (spm to prey) 1.8 (prey to bird egg)

Insect

- eating Fish Steelhead Trout (Juvenile)** 100% Insect 2.8 (spm to insect) 1.1 (insect to fish) * Analyses based on adult white sturgeon should be protective of juvenile white and green sturgeon, and Sacramento splittail. ** Analyses based on juvenile steelhead trout should be protective of juvenile Chinook salmon a nd delta smelt.

Effect Concentrations: The Clean Water Act (33 U.S.C. § 1251 et seq.) requires a level of protection for ambient surface waters that e nsure s specific uses of the water will be available

, i.e., the protection and propagation of fish

, shellfish and wildlife , and recreation in and on the water (see CWA §101(a)(2)). For the Bay and Delta, consistent with the approach to the national recommended freshwater aquatic life selenium criterion (USEPA, 2016), EPA is choosing to base water qualit y criteria on an EC10 level of protection, i.e., an effect
concentration that r epresent s a ten percent population effect level. An EC10 value is appropriate given the nature of exposure and effects for this bioaccumulative chemical. Where
concentrations of selenium in fish tissue approach an effect threshold, there is potential for sustained impacts on aquatic systems, relative to chemicals that are not bioaccumulative. In order to maintain sufficient protection, choosing a low level of effect is appropr iate. The selenium criteria for the estuary are derived from protective (EC10) egg/ovary tissue values. Water column values vary more frequently over time, and derived values are based on extrapolation from tissue values, whereas tissue values are expect ed to vary more gradually.

As discussed in Chapter 3, this proposed criteria document employs an EC10 reproductive effect concentration value in whole body fish tissue of 8.5 mg/kg dw (USEPA, 2016) for clam

- eating fish and insect

- eating fish in the Ecos ystem

- Scale Selenium Model to determine allowable dissolved and particulate water column values and prey concentration values. EPA is considering an EC10 value and the resulting dissolved and particulate water68

column and prey concentration values in devel oping the water quality criteria for species in the estuary. For clam

- eating birds, we employ an EC10 bird egg value of 12.5 mg/kg dw to determine allowable dissolved and particulate water column values and prey concentration
values.

Table 4

- 5 Summary of Species

- Specific Variables shows the species

- specific values chosen for the San Francisco Bay and Delta using the Ecosystem

- Scale Selenium Model.

Table 4

- 5 Summary of Species

- Specific Variables

Food Web / Representative Species Diet TTFs Effect Concentration ( μg/g , or mg/kg, dw)
EC10

Clam

- eating Fish:

White Sturgeon 40% Corbula 60% Annelids/Crustaceans 7.6 (spm to prey) 1.1 (prey to fish) 8.5 *

(USEPA, 2016)

Clam

- eating Birds:

California Ridgway’s rail 20% Corbula 40% Other mollusks 30% Insects (10% Plant) 5.4 (spm to prey) 0.8 (prey to bird egg) 12.5

(USEPA, 2011)

Scoter and Scaup 45% Corbula 5% Other A nimal Material (50% Food Outside Estuary ) 7.8 (spm to prey) 1.8 (prey to bird egg) 12.5

(USEPA, 2011)

Insect

- eating Fish:

Steelhead Trout 100% Insect 2.8 (spm to insect) 1.1 (insect to fish) 8.5 *

(USEPA, 2016) * This is a whole body value. For modeling reproductive effects, whole body fish tissue ( and bird egg tissue ) values best represent dietary bioaccumulation ; however, a corresponding EC10 muscle fish tissue concentration of 11.3 μg/g dw may be more useful for other purposes, e.g., monit oring (USEPA, 201 6 ; see also discussion in Chapter 1
Introduction ).69

ii. E nvironment

- Specific Variables

Partitioning Coefficient, K d : For seaward modeling of clam

- based food webs, site

specific data from 1998 and 1999 for the estuary from Suisun Bay to the Golden Gate Bridge
were used to determine K d values for four transects ( see USGS, 2010 Table 8 , developed using data from Cutter and Cutter [2004] and Doblin et al. [2006] )

. Calculated K d values ranged from 712 to 26,912 (USGS, 2010 ). Because of the wide range of values, a focused approach to location was taken to eliminate uncertainties associated with the ocean

- influenced variability,
and a subset of K d values for Suisun Bay and Carquinez Strait was used to narrow the ranges of

K d values for the sea ward profiles

. This provid ed a set of e stimates that eliminat ed the highly
variable end member values at the downstream ocean interface at the mouth of the Bay near the Golden Gate Bridge ( see USGS, 2010 Table 9 , developed using data from Cutter and Cutte r [2004] and Doblin et al. [2006] ). Since five oil refineries that discharge selenium are located in Suisun Bay and Carquinez Strait, this is considered an important area for modeling and regulatory oversight

. This area is also habitat for species of con cern including juvenile sturgeon as well as rails and migrating scoter and scaup. 43 The K d values for the constrained transects range from 712 to 7,725 , and mean K d values range from 1,180 to 5,986 (USGS, 2010). The 75 th percentile K d values range from 1

, 414 to 7
, 089. We chose to consider the K d values of the transects through Suisun Bay and Carquinez Strait for the clam

- based food webs f or more focused modeling of the interior Bay area , which is most affected by the refiner ies and other point and non

- poi nt sources , and provides a more compartmentalized representation of the seaward portions of the estuary

. 44

For landward modeling of insect

- based food webs, we used site

- specific data from 2003 and 2004 for the estuary from Rio Vista (on the Sacramento Riv er) and Stockton (on the San Joaquin River) to Beni cia to determine K d values for four transects ( see USGS, 2010 Table 10

, developed using data from Lucas and Stewart [2007]). C alculated K d s range from 554 to 12,650
and mean K d s range from 2,268 to 5,855 ( USGS, 2010). The 75 th percentile K d values range from 3,212 to 8,569

.

Hydrolo gic Variables: Water Year Type and Flow Season: Water year type and flow
season affect K d values. Drier years and low flow seasons, characterized by lower, slower flows
and l onger residence times, are generally associated with higher K d values. Extreme conditions

43 Selenium tissue concentrations in Corbula collected in this area were used to validate the model (USGS, 2010).

44 We note that using a narrower range of K d values lowers the mean K d values used in the model which generally produces less conservative (less stringent) results; using a wider range of K d values increases the mean K d values used in the model which generally produces more conservative (more stringent) results. Using constrained transects with a smaller range of K d values reduces the uncertainty of the K d values for the targeted area.70

are generally found during critically dry or dry water years in a low flow season

. Table 4

- 6, Hydrologic Variables , summarizes water year types and seasons, data ava ilability, and effect on

K d

.

Table 4

- 6 Hydrologic Variables

Variable Type Data Availability Effect on K d

1. Flow Season a
. Low

(June

– Nov) S eaward & landward

transects. L onger residence times → ↑ K d s & S e levels in food webs

b. High (Dec

– May) S eaward & landward

transects. S horter residence times → ↓ K d s & S e levels in food webs

2. Water Year a. Critically Dry

(critical condition ) No data*. L onger residence times → ↑ K d s & S e levels in food webs

b. Dry (critical condition) No data*. L onger residence times → ↑ K d s & S e levels in food webs

c. Below Normal L andward transects

only. L onger residence times → ↑ K d s & S e levels in food webs

d

. Normal No data*.

e
. Above Normal S eaward & landward

t ransects

. S horter residence times → ↓ K d s & S e levels in food webs

f. Wet S eaward transects

only. S horter residence times → ↓ K d s & S e le vels in food webs * This type of water year did not occur during the time in which data were collected.

Data collected during f our seaward transect sampling events were used to model the
clam

- based food webs: June 1998; October 1998; April 1999; and November 1999. The June 1998, October 1998 and April 1999 data are from wet water years, and the November 199 9
data are from an above

- average water year ( see USGS, 2010 Table 8, developed using data from Cutter and Cutter [2004] and Doblin et al. [2006]) . No data from critically dry, dry, below normal, or normal water years are available for seaward modeling. The June 1998, October
1998 , and November 1999 data were collected during the low flow season (June to November), although the early June (late spring) data, with a residence time of 11 days, reflect s the high flow season (USGS, 2010 ) . D ata during critical conditions (data from critically dry or dry water years during the low flow season) are not available. Limited data exist for more conservative conditions, i.e., normal (or dry) water year data in the low flow season. We chose to use the

75 th percentile of all available K d values for each focused seaward transect in the modeling to reflect a larger range of hydrologic conditions represented in the data, given that only wet conditions are represent ed.71

Since data reflecting only above normal and wet years for focused seaward transects were available, the results may underestimate the necessary conditions to protect sensitive species in drier hydrologic conditions. Given that only wet conditions are represented, we
selected a conservative K d value. The data for the focused seaward transects are summarized
in Table 4

- 7 Available Transects and Calculated K d Values.

Data collected during four landward transect sampling events were used to model the
insect

- based food webs: January 2003; April 2003; October 2003 , and January 2004. The
October 2003 and January 2004 data are from below normal water years ; the October 2003
data are from the low flow season and the January 2004 data are from the high flo w season

. The January 2003 and April 2003 data are from above normal water years in the high flow
season. No d ata are available for critical conditions. Here again we chose to consider the 75 th percentile of all available K d values for each transect in the modeling to reflect a larger range of conditions represented in the data, and yield a protective model output. The data for landward
transects are summarized in Table 4

- 7 Available Transects and Calculated K d Values.

Table 4

- 7 Available Transects and Calculated K d Values

Food Web /
Transect Type Transect Date Residence Time (Days) Water Year

Type Flow

Season Observed

Dissolved Se (μg/L)
Mean Observed

Particulate Se (μg/g dw)
Mean K d Mean K d 75 th percentile K d

Range

A . Clam

- Eating Birds and Fish

– Focused Approach: Suisun Bay

– Carquinez Strait Constrained Seaward June 16

- 17, 1998 11 Wet High 0.213 0.252 1,180 1,414 712

- 1,647

Oct 7

- 8, 1998 22 Wet Low 0.135 0.462 3,435 4,498 2,202

- 5,212

April 13

- 14, 1999 16 Wet High 0.118 0.303 2,666 2,861 2,274

- 3,168

Nov 4

- 5, 1999 70 Above Normal Low 0.123 0.740 5,986 7,089 3,496

- 7,725 Mean Values 0.147 0.439 3,317 3,966

-

B . Insect

- Eating Fish

Landward Jan 22, 2003

-- Above Normal High 0.245 0.411 2,268 3,212 554

- 3,503

April 22

- 23, 2003

-- Above Normal High 0.356 0.614 2,684 3,564 927

- 4,351

Oct 10, 2003

-- Below Normal Low 0.174 0.751 5,855 8,569 1,628

- 12,650

Jan 15, 2004

-- Below Normal High 0.215 0.519 2, 981 3,808 1,256

- 6,398 Mean Values 0.248 0.574 3,447 4,788

-72

iii. Summary of Variables

A summary of the species

- specific and environment

- specific variables chosen for scenarios for further analysis are shown in Table 4

- 8 Summary of EPA Modeling Variables.

Table 4

- 8 Summary of EPA Modeling Variables
Food Web; Representative Species; (Federal Status) Effect Level

And Value Diet Mix and

Trophic Transfer
Factors Transect Date

And Type Water

Year Type Flow

Season K d

(Range) K d

(75 th percentile)

A. Clam

- Eating Fish  Reproductive and Non

- reproductive Effects :

White Sturgeon

(protective of juvenile green sturgeon [threatened] and Sacramento splittail) EC10

8.5 μg/g dw whole body fish tissue Mixed:

40% Corbula 60% Annelids/
Crustaceans

TTF (prey) = 7.6 TTF (fish) = 1.1 June 1998

Focused Seaward Wet High 712

- 1,647 1,414 October 1998 Focused Seaward Wet Low 2,202

- 5,212 4,498 April 1999 Focused Seaward Wet High 2,274

- 3,186 2,861 November 1999 Focused Seaward Above

Normal Low 3,496

- 7,725 7,089

3,966 Mean B. Clam

- Eating Birds  Reproduct ive and Non

- reproductive Effects:

California Ridgway ’s Rail ( e ndangered)

Scaup: Greater and
Lesser ; and Scoter:

- White

- winged, Surf, and Black EC10

12.5 μg/g dw egg tissue Rail: Mixed:

20% Corbula 40% Other mollusk 30% Insect (10% Plant)
TTF (prey) = 5.4 TTF (egg) = 0.8

Duck: Mixed: 45% Corbula 5% Other Material (50% outside estuary)
TTF (prey) = 7.8 TTF (egg) = 1.8 June 1998

Focused Seaward Wet High 712

- 1,647 1,414

October 1998 Focused Seaward Wet Low 2,202

- 5,212 4,498

April 1999 Focused Seaward Wet High 2,274

- 3,186 2,861

November 1999 Focused Seaward Above

Normal Low 3,496

- 7,725 7,089

3,966 Mean
C. Insect

- Eating Fish  Reproduct ive and Non

- reproductive Effects: Juvenile Steelhead Trout (t hreatened)

(protective of juvenile Chinook

s almon [endangered] and d elta s melt [threatened]) EC10

8.5 μg/g dw whole body fish tissue Insect 100%

TTF (insect) = 2.8 TTF (fish) = 1.1 January 2003

Landward Above

Normal High 554

– 3,503 3,212 April 2003 Landward Above

Normal High 927

– 4,351 3,564 October 2003 Landward Below

Normal Low 1,628

- 12,650 8,569 January 2004 Landward Below

Normal High 1,256

- 6,398 3,808

4,788 Mean73

b. EPA Model ing Results

Using the species and environmental variables discussed above, the model generated dissolved and particulate selenium concentrations for the water column. The model also predicted invertebrate (prey) selenium values. For mixed diet scenarios, the invertebrate selenium concentrations are the weighted averages of the prey ( Corbula , other mollusks, annelids, crustaceans and insects) contributions to the species’ diet. The results of the modeling for clam

- eating fish, clam

- eating birds, and insect

- eating fish, using white sturgeon, California Ridgway’s rails and scoter and scaup, and steelhead trout as representative species (respectively), are summarized in Table 4

- 9 S ummary of Representative Scenarios and Results. Tables showing the results of each of the model runs are included in Appendix F.

Dissolved Selenium: To protect clam

- eating fish at an EC10 level, the predicted protective dissolved selenium estuarine wat er column concentration is between 0.143 and
0.719 μg/L, or between approximately 0.1 and 0.7 μg/L , based on available data. Using the
mean value of the 75 th percentile K d s (3,966), the predicted protective dissolved selenium estuarine water column concentration is 0.256 μg/L, or approximately 0.3 μg/L

.

To protect clam

- eating birds at an EC10 level, the predicted protective dissolved
selenium estuarine water column conc entration is between 0.126 and 2.046 μg/L, or between approximately 0.1 and 2.0 μg/L , based on available data. Using the mean value of the 75 th percentile K d s (3,966), the predicted protective dissolved selenium estuarine water column
concentration is 0.2 24 μg/L for scoter and scaup 45 , or approximately 0.2 μg/L

.

To protect insect

- eating fish at an EC10 level, the predicted protective dissolved selenium estuarine water column concentration is between 0.322 and 0.859 μg/L, or between approximately 0.3 and 0.9 μg/L , based on available data.

Based on these analyses, the protective dissolved selenium water column concentration
selected is 0.2 μg/L . This value should protect existing species in the estuary most of the time,
under the environmental condit ions used in the modeling. These analyses indicate that if clam

eating birds are protected, clam

- eating fish and insect

- eating fish should also be protected.

Tetra Tech, Inc. collected and analyzed more recent (2010

– 2012) ambient data for the
estuary in a report for the Wester n States Petroleum Association (WSPA, 2012). Inserting the

45 For the California Ridgway’s rail, using a K d value of 3,966 results in a dissolved value of 0.730 μg/L, well above the protective value for clam

- eating ducks. See Appendix F.74

ambient data from the report (for K d values) in the Ecosystem

- Scale Selenium Model, we found
that the range of protective dissolved selenium water column concentrations f or clam

- eating fish (focused seaward transects) was 0.157 to 0.283 μg/L, with a mean value of 0.209 μg/L. For
clam

- eating ducks (focused seaward transects) , the range was 0.138 to 0.248 μg/L, with a mean value of 0.183 μg/L. These correspond well with ou r proposed dissolved water column criterion
value of 0.2 μg/L

. We did not include these data in our analysis to determine criteria values, since the data have not been peer reviewed

, however, we include the results of the model runs in Appendix G for gene ral comparison purposes.

Particulate Selenium: To protect clam

- eating fish at an EC10 level, the predicted protective particulate selenium concentration is 1.017 μg/g dw, or approximately 1 μg/g dw, based on available data. To protect clam

- eating birds at an EC10 level, the predicted protective particulate selenium concentration is between 0.890 and 2.894 μg/g dw, or between approximately 1 and 3 μg/g dw, based on available data. The lower end of this range is approximately equal to the protective valu e for clam

- eating fish. To protect insect

- eating fish at an EC10 level, the predicted protective particulate selenium concentration is 2.760 ug/g dw, or approximately 3 ug/g dw, based on available data. To protect clam

- eating and insect

- eating species in the estuary, the proposed particulate selenium concentration is 1 μg/g dw

.

Clam Tissue: To protect clam

- eating fish at an EC10 level, the predicted protective selenium dietary invertebrate concentration is 7.7 μg/g dw; the predicted protective selenium
d ietary Corbula contribution is 6.9 μg/g dw, based on available data. To protect clam

- eating birds at an EC10 level, the predicted protective selenium dietary Corbula contribution is 9.8 μg/g dw for rails and 6.8 μg/g dw for scoter and scaup, based on available data.

To determine the allowable Corbula tissue concentration in the estuary, the dietary contribution must be divided by the percent of Corbula in the species’ diet. For clam

- eating fish (40% Corbula diet), the allowable Corbula tissue concentration is ≤ 17 μg/g dw (6.9 μg/g dw / 0.40). For clam

- eating rails (20% Corbula diet), the allowable Corbula tissue concentration is ≤ 49 μg/g dw (9. 8 μg/g dw / 0.20). For clam

- eating du cks (45% Corbula diet), the allowable
Corbula tissue concentration is ≤ 15 μg/g dw (6.8 μg/g dw / 0.45). To protect all clam

- eating species in the estuary, the proposed Corbula tissue concentration is 15 μg/g dw

.

All proposed values have been rounded to one significant digit. The rounded values provide a reasonable prediction of the appropriate protective values of allowable dissolved and particulate water column selenium concentrations and prey tissue selenium concentrations that will protect clam

- ea ting fish and birds, and insect

- eating fish in the estuary.75

Table 4

- 9 Summary of Representative Scenarios and Results

Representative Species Effect

Concentration (μg/g dw) Representative

Diet and TTFs Water Year/

Flow Season Transect Type and

Transect Date K d 75 th percentile Predicted

Dissolved Se (μg/l) Predicted

Particulate Se (μg/g dw) Predicted Dietary

Invertebrate Se (μg/g dw) Predicted Dietary

Corbula Se Contribution (μg/g dw) Clam

- eating Fish

Green Sturgeon White Sturgeon

Sacramento Splittail EC10

8.5 Whole Body 40% Corbula

60% Annelids/
Crustaceans

TTF (prey) =7.6 TTF (fish) = 1.1 Wet/ High Focused Seaward June 1998 1,414 0.719 1.017 7.7 6.9

Wet/Low Focused Seaward

October 1998 4,498 0.226 1.017 7.7 6.9

Wet/High Focused Seaward

April 1999 2,861 0.355 1.017 7.7 6.9 Above Normal/
Low Focused Seaward

November 1999 7,089 0.143 1.017 7.7 6.9

Range: 1,414

– 7,089 0.143

– 0.719

- > 0.1

– 0.7 1.017

- > 1 7.7 6.9 3,966 mean 0.256

- > 0.3
Clam

- eating Birds

California Ridgway’s Rail

EC10

12.5 Egg Tissue 20% Corbula

40% Other mollusk 30% Insect (10% Plant)
TTF (prey) = 5.4 TTF (egg) = 0.8 Wet/High Focused Seaward June 1998 1,414 2.046 2.894 15.6 9.8

Wet/Low Focused Seaward

October 1998 4,498 0.643 2.894 15.6 9.8

Wet/High Focused Seaward

April 1999 2,861 1.011 2.894 15.6 9.8 Above Normal/
Low Focused Seaward

November 1999 7,089 0.408 2.894 15.6 9.8 Ducks: Greater Scaup Lesser Scaup

White

- winged Scoter Surf Scoter Black Scoter 45% Corbula 5% Other Animal Material

TTF (prey) = 7.8 TTF (egg) = 1.8 Wet/High Focused Seaward June 1998 1,414 0.630 0.890 6.9 6.8

Wet/Low Focused Seaward

October 1998 4,498 0.198 0.890 6.9 6.8

Wet/High Focused Seaward

April 1999 2,861 0.311 0.890 6.9 6.8 Above Normal/
Low Focused Seaward

November 1999 7,089 0.126 0.890 6.9 6.8

Range: 1,414

– 7,089 0.126

– 2.046

- > 0.1

– 2 0.890

– 2.894

- > 1

- 3 6.9

– 15.6 6.8

– 9.8

- > 7

- 10 3,966 mean 0.224

- > 0.2 duck
Insect

- eating Fish

Chinook Salmon

Steelhead Trout

Delta Smelt EC10

8.5 Whole Body 100% Insect

TTF (insect) = 2.8 TTF (fish) = 1.1 Above Normal/

High Landward

January 2003 3,212 0.859 2.760 7.7 N/A Above Normal/ High Landward

April 2003 3,564 0.774 2.760 7.7 N/A Below Normal/
Low Landward

October 2003 8,569 0.322 2.760 7.7 N/A Below Normal/ High Landward

January 2004 3,808 0.725 2.760 7.7 N/A

Range: 3,212

– 8,569 0.322

– 0.859

- > 0.3

– 0.9 2.760

- > 3 7.7 N/A76

C

. Proposed Criteria

a. Applicable Waters; Magnitude, Duration and Frequency

Applicable Waters: The proposed criteria are intended to apply to all marine waters of the Bay and to all estuarine waters of the Bay and Delta, i.e., all waters of the Bay and Delta in which the salinity is greater than 1 part per thousand (ppt) 95% of the time. This is consistent
with the National Toxics Rule and the California Toxics Rule. 46 Since the invasive Corbula clam species is found in the estuary in waters of salinities between 1 and 33 ppt (Cohen, 2011), the
most vulnerable clam

- eating species should be protec ted. These proposed criteria are intended to replace the selenium aquatic life criteria promulgated in the National Toxics Rule for marine and estuarine “waters of the San Francisco Bay upstream to and including Suisun Bay and the
Sacramento

- San Joaquin D elta” (57 FR at 60921, and 40 CFR 131.36(d)(10)).

Criteria Media and Magnitude: EPA is proposing to apply criteria in various media for the protection of aquatic life and aquatic

- dependent wildlife. The media choices considered for
criteria include:

1

. Selenium water column concentrations (dissolved or total);
2. Selenium particulate concentrations;
3. Selenium predator tissue concentrations (fish, and/or bird egg);

4. Selenium prey/dietary tissue concentrations (e.g., clam or Corbula )

5. Combinations of the above concentrations.

Criteria values for selenium in tissue concentrations directly reflect the biological uptake of selenium in the species’ diet, and depending on the type of tissue, concentrations can be easily monitored, e.g., cl am tissue can be easily monitored while fish egg/ovary tissue is more difficult to obtain. Ambient water quality criteria serve two primary functions: they are used to designate the maximum allowable pollutant level that is protective of the designated us es of the waterbody and to regulate the sources of the pollutant by limiting the amount of the pollutant that may be discharged into the waterbody so that the designated uses are maintained. Discharges are in dissolved water and particulate form, whereas tissue concentrations are most predictive of observed biological effects because they are more closely

46 The Natio nal Toxics Rule and California Toxics Rule aquatic life freshwater criteria apply to waters in which the salinity is equal to or less than 1 ppt 95% or more of the time; the aquatic life saltwater criteria apply to waters in which the salinity is equal to or greater than 10 ppt 95% of the time; and the more stringent of the freshwater or saltwater criteria apply to waters in which the salinity is between 1 and 10 ppt 95% of the time (40 CFR 131.36(c)(3) and 40 CFR 131.38(c)(3), respectively).77

tied to the endpoints of concern and do not require cross

- media extrapolations. Tissue concentrations can present challenges when attempting to use them to regulate or limit sources of a pollutant into a water body. Increased pollutant levels in an ecosystem usually occur as a result of continued and/or elevated discharges of the pollutant from anthropogenic sources, and for the estuary, refinery wastewa ter and agriculture drainage are the largest contributors of selenium. It is most straightforward to establish regulatory limits for effluent discharge and agricultural drainage based on expectations in ambient water column concentrations (both dissolved and particulate). Therefore, in order to set water quality criteria that will be more easily implemented to limit selenium entering the estuary, the proposed criteria include values in fish and clam tissue, and in dissolved and particulate water column

co ncentration values. The dissolved and particulate water column concentration values can be used to regulate selenium discharges into the estuary in order to maintain the existing
beneficial uses.

Chapter 3 discusses appropriate EC10 tissue values for th e San Francisco Bay and Delta ecosystem. Using site

- specific data, the Ecosystem

- Scale Model provides corresponding dissolved and particulate water column and prey tissue concentrations. Thus, the proposed criteria should be equally protective in differe nt media. The proposed criteria are described in
Table 4

- 11 Proposed Selenium Water Quality Criteria for the San Francisco Bay and Delta. All criteria are chronic values; they represent protective levels of selenium through dietary exposure, which reflec ts a long term or chronic exposure.

Duration and Frequency: Each proposed criteri on also has a specified duration and exceedance frequency. Both the proposed dissolved and particulate water column selenium criteria have durations of 30 days (approximately monthly) to reflect the seasonal changes in system hydrology. As discussed earl ier, the partitioning between the particulate and dissolved phases of selenium can change with the time of year and type of water year (i.e., high vs. low season, and wet vs. dry year). The proposed fish tissue and clam tissue criteria durations are
based on an instantaneous measurement, since tissue concentrations provide a point measurement that already reflects an integrative accumulation of selenium over time in response to environmental fluctuations, assuming the system represents a steady state/equil ibrium condition.

The proposed dissolved and particulate water column criteria values have an allowable exceedance frequency of no more than once in three years, which is the typical frequency for EPA’s recommended ambient water quality criteria for aqu atic life. This frequency reflects the78

Agency’s intent to provide for ecological recovery from a variety of severe stresses 47 , including a periodic exceedance of a water column criterion. The proposed fish and clam tissue criteria
values are not to be exc eeded . Since tissue concentrations reflect an accumulation of selenium from the environment over long periods of time, if the tissue concentration was exceeded, it might reflect sustained high levels of selenium in the environment, and require a long peri od of time for tissue levels to return to protective levels. By prohibiting an exceedance, sustained adverse conditions may be avoided.

b. Acute and Intermittent Criteria

Acute Criteri on : The proposed criteria are chronic values. Since dietary exposu re poses the highest risk to wildlife, acute toxicity, or toxicity from a brief exposure of a significantly
elevated concentration of waterborne fo rms of selenium, is not pertinent for regulatory purposes in the Bay and Delta, and we do not include an acut e criterion in any medium. However, if a significantly elevated concentration of waterborne selenium occurs in a waterbody, it may introduce a load of selenium into the system from which it may be difficult to recover. Some high, short

- term exposures of selenium could be more detrimental to the system than lower chronic exposures, as they may have significant long

- term residual bioaccumulative effects, which would be similar to causing the protective chronic exposure level to be exceeded for longer than a llowable periods of time. In order to prevent such an occurrence, we include a proposed intermittent criterion.

Intermittent Criterion : To address intermittent exposures that could cause an
exceedance of the chronic fish tissue criterion or clam tissue criterion, or otherwise contribute to the chronic effects of selenium bioaccumulation, we are proposing an intermittent exposure water column criterion (see intermittent exposure criterion in Aquatic Life Ambient Water Quality Criterion for Selenium

– Fres hwater 2016 ; USEPA, 2016). This intermittent criterion is intended to limit cumulative exposure, and is derived from the chronic 30

- day water column criterion by algebraically rearranging a representative equation based on time and
concentration to establ ish a limit on an intermittent elevated concentration that occurs over a specified percentage of the time. Figure 1, Illustration of an Intermittent Spike Exposure, shows a possible sequence of exposures over a 30 day period; it illustrates a spike exposu re occurring a certain percentage of time (e.g., 10% or 3 days) over a 30

- day period, and background exposure occurring the remaining percentage of time (e.g., 90% or 27 days).

47 For a full discussion of exceedance frequency, see Water Quality Standards Handbook, Second Edition , EPA

- 823

- B

- 94

- 005a, August 1994, Office of Water, U.S Environmental Protection Agency.79 Figure 4

- 1. Illustration of an Intermittent Spike Exposure

The 30

- day average concentration, C 30 day , is given by:

C 30 day = C int f

int + C

bkgrnd ( 1

− f

int )

where C

int is the intermittent spike concentration, f int is the fraction of any 30

- day period during which elevated concentrations occur, and C bkgrnd is the background concentration occurring during the remaining time. C 30 day is not to exceed the proposed c hronic criterion,
WQC 30 day
, or 0.2 μg/L for the estuary. I f the intent is to apply a criterion, WQC int to the intermittent spike concentrations, then replacing C int with WQC

int and C

30

- day with WQC

30

- day or 0.2 μg/L in the above equation, and then solving for WQC int yields:

WQC int = [ WQC 30 day or 0

. 2 μg / L ]

− C bkgrnd ( 1

− f

int ) f int

The above equation expresses the intermittent exposure criterion in terms of the 30

- day

average c hronic criterion, while accounting for the fraction in days of any 30

- day period the intermittent spikes o ccur and for the background concentration occurring during the remaining
time. If the concentrations of the three spikes in Figure 1 differ

, or the background concentrations vary, then the average 48 of the spike concentrations and/or the average of the
bac kground concentrations can be used in the equation, as appropriate. This approach is not

48 A weighted average may also be used if appropriate, i.e., if spikes of largely different volumes and concentrations occur within the same 30

- day period.80

intended to apply to o rdinary
, smoothly varying concentrations, as t hat situation is better addressed by applying the chronic water criterion as a 30

- day average.

Ta ble 4

- 10 illustrates example values for the i ntermittent water criterion concentration.
The values in the last r ow and the far right column demonstrate that WQC int is not an independent criterion but a re

- expression of the 30

- day average water column criterion

. WQC int converges to WQC 30

- day when the background concentration is already at WQC 30

- day or

w hen the intermittent exposure occur s throughout the 30

- day period.

Table 4

- 10 Representative Values of the Proposed I ntermittent Water Concent ration Criterion

Bkgrnd Conc, C bkgrnd
(μg/L) Fraction of Time, f int

0.033 (1 day) 0.05

(1.5 days) 0.1

(3 days) 0.2

(6 days) 0.5

(15 days) 1

(30 days) Intermittent Criterion, WQC int 0 6.00 4.00 2.00 1.00 0.40 0.20 0.08 3.64 2.48 1.28 0.68 0.32 0.20 0.10 3.03 2.10 1.10 0.60 0.30 0.20 0.15 1.52 1.15 0.65 0.40 0.25 0.20 0.20 0.20 0.20 0.20 0.20 0.20 0.20

T he value of f

int , the intermittent exposure fraction of the month, should not be assigned a value less than one day (i.e., f int < 0.033)

, to ensure that the monthly water column value will be met. An extremely high peak or concentrated discharge (greater than approximately 160 μg/L) in one hour (i.e., f int < 0.0013) could exceed water concentration
thresholds that have been sh own to be toxic in 2

- day or 4

- day toxicity tests (compiled in U S EPA
, 2004), and would require zero discharge for the entire remaining averaging period of approximately 30 days in order to meet the 30

- day average water column value. Consequently,
the inter mittent fraction of the month should not be assigned a value less th an 0.033 (corresponding to one day), and a discharge greater than approximately 6 μg/L should not occur for longer than one day during any 30

- day period, assuming a background concentration of 0 μg/L.81

Table 4

- 1 1 Proposed Selenium Water Quality Criteria for the San Francisco Bay and Delta

Media Type Tissue Water Column 1

Criteria Fish Whole

Body Or
Muscle Clam Dissolved
Chronic Intermittent Exposure 2 Particulate Chronic

Magnitude 8.5 μg/g dw

whole body

or 11.3 μ g/ g dw
muscle 15 μg/g dw 0.2 μg/L WQC int =

0

. 2 μg / L

− C bkgrnd ( 1

− f int )

f int 1 μg/g dw

Duration Instantaneous

measurement Instantaneous

measurement 30 days Number of days/month
with an elevated
concentration 30 days

Frequency N ot to be

exceeded N ot to be

exceeded Not more th an

once in three

years Not more tha n once in

three years Not more tha n once in three
years

1 Water column values are based on dissolved total selenium (includes all oxidation states, i.e., selenite, selenate, organic selenium and any other fo rms) in water.

2 Where C bkgrnd is the average background selenium concentration in μg/L, and f int is the fraction of any 30

- day period during which elevated selenium concentrations occur, with f int assigned a value ≥ 0.033 (corresponding to one day).

Note 1: The criteria apply to all waters of the San Francisco Bay and Delta in which the salinity is greater than 1 part per thousand 95% or more of the time.

Note 2: A translator of 1 shall be used to determine total recoverable selenium values from d issolved selenium criteria values for use in deriving water quality

- based effluent limitations for point sources.

The se proposed criteria values are specific to the San Francisco Bay and Delta estuary,
and the low chronic water column value is due to the presence of the abundant and invasive species, Potamocorbula amurensis or Corbula . Corbula very efficiently accumulates selenium (Stewart et al., 2004), and therefore h as an unusually high TTF compared to most other mollusk species for which TT Fs have been derived

. Given the site

- specific nature of Corbula
distribution , this TTF is only applicable in the San Francisco Bay and Delta estuary, unless ( and
until ) other locations are observed with Corbula invasions.

Form of Permit Limits: Although proposed water column criteria values are expressed in dissolved selenium concentrations, water quality

- based permit limits, in most instances, are required to be in total recoverable values (40 CFR §122.45(c)). For most metals, criteria are in
the diss olved form because the dissolved fraction provides a better representation of the82

biologically active portion of the metal than does the total or total recoverable fraction 49 (USEPA, 1996). When water quality criteria are in the dissolved form, a translato r can be used to determine a total recoverable permit limit. The translator is the fraction of the total recoverable metal in the downstream water that is dissolved (USEPA, 1996). However, for selenium, both the dissolved and particulate fractions are bi oavailable to the aquatic biota. Thus, EPA proposes a translator of 1 in the proposed criteria table, Table 4

- 11 (see Note 2), an appropriate assumption for the Bay and Delta

.

D. Summary

The proposed site

- specific criteria for the San Francisco Bay a nd Delta include tissue, and dissolved and particulate water column values, which should be comparably protective based on the detailed modeling of the estuary using the Ecosystem

- Scale Selenium Model. The dissolved and particulate water column criteria a re intended to facilitate implementation from different sources of selenium to the estuary. In addition, the total amount of selenium entering the estuary is more appropriately regulated by limiting both dissolved and particulate selenium
loads. Clam tis sue criteria are designed to ensure the protection of higher trophic level species. For each of the proposed criteria values, a duration and frequency is specified.

49 Total selenium in an unfiltered water column sample is the sum of the dissolved fraction and the particulate fraction of selenium in the sample. The dissolved fraction is operati onally defined as that which passes through a 0.45 μm filter (USGS Water Resources Glossaries, Water Resources Data

– Definition of Terms at: http://water.usgs.gov/glossaries.html ). Total recoverable i s the amount of a constituent that is in solution after a
water

- suspended sediment sample has been “digested by a method (usually using a dilute acid solution) that results in dissolution of only readily soluble substances” (USGS Water Resources Glossaries , Water Resources Data

– Definition of Terms at: http://water.usgs.gov/glossaries.html ). Since digestion does not always result in complete dissolution of particulate matter, the total recoverable amou nt of the constituent is usually less than the total amount of the constituent present in the sample.83

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