Abstract 1

Survival, Transport, and Sources of Fecal Bacteria in 

Streams and Survival in Land-Applied Poultry Litter in 

the Upper Shoal Creek Basin, Southwestern Missouri, 

2001–2002

by John G. Schumacher

Abstract

Densities of fecal coliform bacteria along a 

5.7-mi (mile) reach of Shoal Creek extending 

upstream from State Highway 97 (site 3) to State 

Highway W (site 2) and in two tributaries along 

this reach exceeded the Missouri Department of 

Natural Resources (MDNR) standard of 200 

col/100 mL (colonies per 100 milliliters) for 

whole-body contact recreation. A combination of 

techniques was used in this report to provide information on the source, transport, and survival of 

fecal bacteria along this reach of Shoal Creek. 

Results of water-quality samples collected during 

dye-trace and seepage studies indicated that at 

summer low base-flow conditions, pastured cattle 

likely were a substantial source of fecal bacteria in 

Shoal Creek at the MDNR monitoring site (site 3) 

at State Highway 97. Using repeat element Polymerase Chain Reaction (rep-PCR), cattle were the 

presumptive source of about 50 percent of the 

Escherichia coli (E. coli) isolates in water samples 

from site 3. Cattle, horses, and humans were the 

most common presumptive source of E. coli isolates at sites further upstream. Poultry was identified by rep-PCR as a major source of E. coli in 

Pogue Creek, a tributary in the upper part of the 

study area. Results of the rep-PCR were in general 

agreement with the detection and distribution of 

trace concentrations of organic compounds commonly associated with human wastewater, such as 

caffeine, the antimicrobial agent triclosan, and the 

pharmaceutical compounds acetaminophen and 

thiabendazole (a common cattle anthelmintic).

Significant inputs of fecal bacteria to Shoal 

Creek occurred along a 1.6-mi reach of Shoal 

Creek immediately upstream from site 3. During a 

36-hour period in July 2001, average densities of 

fecal coliform and E. coli bacteria increased from 

less than or equal to 500 col/100 mL upstream 

from this stream reach (sample site 2c) to 2,100 

and 1,400 col/100 mL, respectively, at the MDNR 

sampling site. Fecal bacteria densities exhibited 

diurnal variability at all five sampling sites along 

the 5.7-mi study reach of Shoal Creek, but the 

trends at successive downstream sites were out of 

phase and could not be explained by simple advection and dispersion. At base-flow conditions, the 

travel time of bacteria in Shoal Creek along the 

5.7-mi reach between State Highway W (site 2) 

and the MDNR sampling site (site 3) was about 26 

hours. Substantial dispersion and dilution occurs 

along the upper 4.1 mi of this reach because of 

inflows from a number of springs and tributaries 

and the presence of several long pools and channel 

meanders. Minimal dispersion and dilution occurs 

along the 1.6-mi reach immediately upstream from 

the MDNR sampling site. Measurements of fecal 

bacteria decay in Shoal Creek during July 2001 

indicated that about 8 percent of fecal coliform and 

E. coli bacteria decay each hour with an average 

first-order decay constant of 0.084 h-1 (per hour).

Results of field test plots indicated that substantial numbers of fecal bacteria present in poul-
2 Fecal Bacteria in Streams and Land-Applied Poultry Litter in the Upper Shoal Creek Basin, Southwestern Missouri, 2001–2002

try litter can survive in fields for as much as 8 

weeks after the application of the litter to the land 

surface. Median densities of fecal coliform and E. 

coli in slurry-water samples collected from fields 

increased from less than 60 col/100 mL before the 

application of turkey and broiler litter, to as large 

as 420,000 and 290,000 col/100 mL after the 

application of litter. Bacteria densities in the test 

plots generally decreased in a exponential manner 

over time with decay rates ranging from 0.085 to 

0.185 d-1 (per day) for fecal coliform to between 

0.100 and 0.250 d-1 for E. coli. The apparent survival of significant numbers of fecal bacteria on 

fields where poultry litter has been applied indicates that runoff from these fields is a potential 

source of fecal bacteria to vicinity streams for 

many weeks following litter application. 

INTRODUCTION

Shoal Creek (fig. 1) is located within the Springfield Plateau of the Ozark Plateaus physiographic province in southwestern Missouri. From its headwaters in 

Barry County, Shoal Creek flows about 70 mi (miles) 

through mostly rural agricultural areas until it reaches 

the Missouri-Kansas State line about 8 mi west of the 

city of Joplin. Shoal Creek is an important source of 

drinking-water supply for the cities of Joplin (population about 150,000) and Neosho (population about 

10,000) (U.S. Bureau of the Census, 2000). The lower 

49-mi reach of Shoal Creek from the Missouri State 

line to about 0.5-mi downstream from the mouth of 

Capps Creek has eight designated beneficial uses (irrigation, livestock and wildlife watering, protection of 

warm-water aquatic life and human-health fish consumption, cool-water fishery, whole-body contact recreation, boating and canoeing, drinking-water supply, 

and industrial-water supply)—more than any other 

stream in the State except the Missouri River (Missouri 

Department of Natural Resources, 1996). Whole-body 

contact recreation and boating and canoeing are among 

the stated beneficial uses along a 13.5-mi reach immediately downstream from the mouth of Capps Creek to 

about 1 mi upstream from the mouth of Woodward 

Creek (fig. 1). 

The detection of fecal coliform densities greater 

than the Missouri standard of 200 col/100 mL (colonies 

per 100 milliliters) for whole-body contact recreation 

(Missouri Department of Natural Resources, 1996) at 

the Missouri Department of Natural Resources 

(MDNR) monitoring site at State Highway 97 (site 3, 

fig. 2) resulted in part of Shoal Creek being included on 

the 1998 Clean Water Action Plan (CWP) 303(d) list of 

impaired water bodies by the MDNR. During a 1999–

2000 study of the water quality of the upper 233 mi2

(square miles) of the Shoal Creek Basin, the U.S. Geological Survey (USGS) determined that densities of 

fecal coliform bacteria in Shoal Creek exceeded the 

MDNR standard along a 5.7-mi reach upstream from 

State Highway 97 and in several upstream tributaries 

(Schumacher, 2001). Fecal coliform densities 

decreased significantly downstream from the MDNR 

site. Based on the results of limited deoxyribonucleic 

acid (DNA) fingerprinting of Escherichia coli (E. coli) 

isolated from water samples, the USGS study suggested that most of the E. coli bacteria in water samples 

collected from Shoal Creek probably were from nonhuman sources and that poultry may be an important 

contributor. Schumacher (2001) estimated that more 

than 45,000 tons of poultry litter is generated annually 

within the upper Shoal Creek Basin. This litter is 

applied to the land surface as a source of nutrients 

within a few miles of the poultry barns. Little is known 

about the quantities of fecal bacteria within the poultry 

litter or the survival of the bacteria after the litter is 

applied to the land surface.

During 2001, the Food and Agricultural Policy 

Research Institute (FAPRI) initiated a study to construct a fecal coliform transport model for the Shoal 

Creek Basin upstream from the MDNR sampling site. 

Before accurate models can be developed and remedial 

measures implemented to reduce the levels of fecal 

bacteria at the MDNR sampling site, the host source of 

the bacteria must be identified, and the stream reaches 

located where the bacteria are entering the stream. 

Although the results of the 1999–2000 USGS study 

indicated that non-human sources are an important 

source of fecal bacteria at the MDNR sampling site, the 

specific reach where these bacteria are entering Shoal 

Creek and transport times along this reach were outside 

the scope of that study. Because the specific area where 

the fecal bacteria detected at the MDNR sampling site 

are entering the stream has not been identified, the U.S. 

Environmental Protection Agency (USEPA) and 

MDNR entered into a cooperative agreement with the 

USGS to investigate the survival, transport, and source 

of fecal bacteria in Shoal Creek upstream from the 

MDNR sampling site and to determine if viable fecal 
Introduction 3

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4 Fecal Bacteria in Streams and Land-Applied Poultry Litter in the Upper Shoal Creek Basin, Southwestern Missouri, 2001–2002

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Introduction 5

bacteria are present in poultry litter that is applied to the 

land surface in the area. 

Purpose and Scope

This report describes information on the survival, transport, and source of fecal bacteria in Shoal 

Creek. The information is based on results of dye-trace 

and seepage studies conducted during base-flow conditions along a 5.7-mi reach of Shoal Creek upstream 

from the MDNR sampling site on State Highway 97 

(fig. 1). Concentrations of fecal coliform and E. coli

bacteria that were measured along Shoal Creek during 

the 2-day period of the dye-trace study are presented. In 

addition, water-quality samples were collected as the 

dye peak passed selected sampling sites. Because large 

quantities of poultry litter are applied to fields in the 

Shoal Creek Basin, preliminary data also are presented 

on the concentration and survival of fecal bacteria in 

poultry litter that is applied to the land surface.

During the dye-trace study conducted in July 

2001, 68 water-quality samples were collected from 10 

sites along Shoal Creek and 2 tributaries. Samples were 

analyzed for fecal coliform and E. coli bacteria, and a 

subset of samples were analyzed for total nutrients and 

a suite of organic compounds commonly associated 

with human wastewater and selected pharmaceutical 

compounds. The rate of fecal coliform and E. coli

decay in the stream was measured during the dye-trace 

study using in-situ diffusion chambers. Water-quality 

samples were collected and discharge measurements 

were made along a 1.6-mi reach of Shoal Creek immediately upstream from the MDNR sampling site (site 3, 

fig. 2) during a seepage study in August 2002. During 

the summer of 2001 and spring and summer of 2002, 

four test plots were monitored for the survival of fecal 

coliform and E. coli bacteria in fields where poultry litter or poultry litter compost had been applied to the 

land surface. Relative densities of fecal coliform and E. 

coli bacteria were measured at 7 to 10 locations in each 

of the 4 test plots for up to 8 weeks following the application of poultry litter.

Previous Investigations

The MDNR began ambient monitoring on Shoal 

Creek at the State Highway 97 bridge (site 3) during 

1992. Between 1992 and 1998, densities of fecal 

coliform bacteria at the Shoal Creek site averaged 

13,140 col/100 mL with a median of 320 col/100 mL, 

and ranged from less than 1 to 400,000 col/100 mL 

(data supplied by the Missouri Department of Natural 

Resources, Water Pollution Control Program). Concentrations of total nitrite plus nitrate as nitrogen (NO23t) 

and total phosphorus (Pt

) in these samples averaged 

3.15 and 0.17 mg/L (milligrams per liter).

During 1995, the USEPA and MDNR initiated a 

5-year nonpoint-source study focusing on reducing 

nutrient concentrations in the upper Shoal Creek Basin. 

This 5-year study included the collection of monthly 

grab samples from six stream and four spring sites. The 

study also included technical assistance for the Natural 

Resources Conservation Service (NRCS) to work with 

area poultry producers and farmers to develop nutrient 

management plans and to implement Best Management 

Practices (BMPs). During 1998, the MDNR sponsored 

a Special Area Land Treatment (SALT) project in the 

upper Shoal Creek Basin. The 5-year SALT project is a 

locally led project that focuses on reducing agricultural 

nonpoint-source pollution. The upper Shoal Creek 

SALT project is a cooperative effort between the 

MDNR, NRCS, Missouri Department of Conservation 

(MDOC), University of Missouri Extension Office, 

local volunteers, farmers, and poultry producers. The 

project included nutrient sampling at six stream sites 

and four springs on or near demonstration farms downstream from the MDNR sampling site. 

From 1999 to 2000, the USGS conducted a study 

of the water quality of Shoal Creek and its principal 

tributaries in the upper 233 mi2

 of the Shoal Creek 

Basin (Schumacher, 2001). More than 170 water samples were collected during 13 months from a network 

of 12 stream and 5 spring sites. Analyses of the samples 

indicated that fecal coliform concentrations in Shoal 

Creek exceeded the MDNR standard of 200 col/100 

mL at site 3 (fig. 2), the MDNR sampling site (median 

density of 400 col/100 mL and a range of 43 to 33,000 

col/100 mL), and at site 2 (fig. 2) about 5.7 mi upstream 

at State Highway W (median density of 277 col/100 

mL and a range of 25 to 9,200 col/100 mL). Fecal 

coliform densities also exceeded the 200 

col/100 mL standard in two tributaries upstream from 

the MDNR sampling site—Pogue Creek (median density of 580 col/100 mL) and Joyce Creek (median density of 340 col/100 mL). Results of ribopattern analysis 

of E. coli isolates from a small number of water samples indicated that 85 percent of the E. coli isolates 

extracted were from non-human sources. Humans and 

poultry appeared to be a major source of E. coli bacteria 

at the MDNR sampling site; however, the results were 
6 Fecal Bacteria in Streams and Land-Applied Poultry Litter in the Upper Shoal Creek Basin, Southwestern Missouri, 2001–2002

suspect because known cattle isolates from the study 

area frequently were misidentified by the ribopattern 

analysis. Schumacher (2001) postulated that cattle 

from the study area have unique ribopatterns compared 

to the known cattle patterns used in the ribopattern 

database, which were mostly from central Missouri. 

The study also detected the human pathogen E. coli

O157:H7 (commonly associated with cattle) in a water 

sample collected upstream from the MDNR sampling 

site. Historical data on fecal coliform densities at the 

MDNR sampling site also were examined, and the 

report concluded that an apparent increasing trend of 

fecal coliform bacteria with time at the MDNR sampling site was, in part, related to a general trend of 

increasing stream discharge in response to an increase 

in annual precipitation and not necessarily land-use 

changes or increases in poultry production in the basin.

During 2000, the USGS conducted a groundwater study in the upper Shoal Creek Basin to determine if fecal coliform and nutrient concentrations in 

shallow ground water were increasing as a result of 

poultry operations in the region (Mugel, 2002). Analysis of water samples collected from 47 wells and 8 

springs indicated that ground water in proximity to 

poultry operations did not have statistically larger densities of fecal bacteria or nutrient concentrations than 

water from wells in non-poultry producing areas.

In 2001, the FAPRI began a study to develop a 

transport model for fecal coliform in the upper Shoal 

Creek Basin. This study includes the collection of 

weekly fecal coliform and E. coli samples from several 

sites on Shoal Creek including the MDNR sampling 

site (site 3) and several tributaries upstream. Preliminary data from DNA-fingerprinting of these samples 

indicated that most E. coli patterns probably are from 

cattle, humans, and poultry, and that cattle patterns 

appeared more frequently during the summer months 

(Claire Baffaut, Food and Agricultural Policy Research 

Institute, written commun., 2002).

Acknowledgments

The author is indebted to the many local landowners for granting permission to sample streams or 

springs on their property. Special acknowledgment is 

given to Kari Rhoades and Dan Philbrick of the Barry 

County NRCS and to local poultry producers for providing access and assistance during the field test plots 

to measure the survival of fecal bacteria in land-applied 

poultry litter. The author also is grateful to the family 

of Mr. Joseph Renkoski for allowing the continued 

operation of a stream-gaging and water-quality sampling station on their property.

DESCRIPTION OF THE STUDY AREA

The study area focused on a 5.7-mi reach of 

Shoal Creek from the MDNR sampling site (site 3) 

upstream to State Highway W (site 2) in Barry County 

(fig. 2). This reach of Shoal Creek was selected because 

it is part of the reach listed as impaired by fecal 

coliform bacteria by the MDNR (Missouri Department 

of Natural Resources, 2000), and it was identified by 

the USGS as containing fecal coliform levels above the 

MDNR standard of 200 col/100 mL (Schumacher, 

2001). Samples also were collected from a site several 

miles downstream from this reach (site 4) to verify that 

fecal coliform densities above the MDNR standard 

were confined to the reach previously identified as 

impaired.

Climate

The upper Shoal Creek Basin is characterized by 

temperate climate with warm, humid summers, and 

cool, wet winters. The National Oceanic and Atmospheric Administration (NOAA) operates a climatological station at Monett (fig. 1) with 29 years of record. 

The average annual temperature measured at Monett is 

about 55 °F (degrees Fahrenheit) and the average 

annual precipitation is 42.01 in. (inches). During the 

study period from May 2001 through August 2002, the 

minimum temperature recorded at Monett was 0 °F on 

March 3, 2002, and the maximum recorded temperature was 99 °F on July 25, 2002 (National Oceanic and 

Atmospheric Administration, 2001; 2002). The maximum daily precipitation was 2.57 in. recorded on 

May 8, 2002. Southwest Missouri experienced drought 

conditions that began during the 1999–2000 USGS 

water-quality study (Schumacher, 2001). Overall, 

drought conditions persisted throughout the current 

study period with 59.73 in. of precipitation recorded at 

Monett from May 2001 through August 2002. 

Although only 0.85 in. below normal for this period, 

almost 20 percent of this total (12.07 in.) fell during 

May 2002, which was more than 7 in. above normal for 

the month. Excluding May 2002, precipitation was 

about 8 in. below normal for the study period.
Methods of Study 7

Topography and Geology

Topography in the upper Shoal Creek Basin is 

characterized by gently rolling hills, except near 

streams where local relief can be steep. Elevations in 

the study area range from about 1,200 ft (feet) 

[National Geodetic Vertical Datum of 1929 (NGVD 

29)] at site 3 at State Highway 97 to about 1,570 ft in 

the headwaters of Pogue Creek (fig. 1) on the east side 

of the study area.

Mississippian-age limestones underlie the study 

area. A massive chert bed known as the Grand Falls 

Chert underlies most of the study reach between sites 2 

and 3 (Schumacher, 2001). The Grand Falls Chert is a 

discontinuous unit (0 to 40 ft thick) consisting of massive layers of chert up to 6 ft thick. The chert has a 

gnarled and knotted structure that produces an uneven 

surface where the unit is exposed (Thompson, 1986). 

Where the Grand Falls Chert is exposed in the bed of 

Shoal Creek, it forms shoals, riffles, and small waterfalls. Numerous wet-weather seeps and small springs 

appear in fields along this reach of Shoal Creek where 

the Grand Falls Chert is overlain by a thin veneer of 

soil.

Land Use and Population

The study reach of Shoal Creek drains about 

42 mi2 (this area excludes the drainage area of Shoal 

Creek upstream from site 2). Land use in this area is 

about 91 percent agricultural, 8 percent forested, and 

1 percent urban (fig. 2). Nearly all the agricultural land 

use is pasture, hay crop, or poultry barns. An inventory 

conducted in 2001 (Schumacher, 2001) indicated there 

were 118 active poultry barns in this area, producing an 

estimated 14,200 tons of waste litter annually. Thirtynine barns are used for the production of turkeys, 24 of 

which are located in the Pogue Creek Basin. Liquid 

waste from a poultry processing plant is sprayed onto 

more than 400 acres of fields in the upper part of the 

Pogue Creek Basin (fig. 2). This plant has a design 

capacity of more than 1.6 Mgal/d (million gallons per 

day) (Missouri Department of Natural Resources, 

Water Pollution Control Program, written commun., 

2002). No reliable estimate of the number of cattle is 

available for the study area. During the 2001 study, an 

estimated 25,000 cattle were present within the 233 mi2

study area (Schumacher, 2001), and several thousand 

cattle are assumed to be within the drainage area of the 

study reach of Shoal Creek. 

The population of the study area was estimated at 

1,640. This estimate was calculated by multiplying the 

2000 population of the incorporated towns of Butterfield (397), Purdy (1,103), and Wheaton (721) by their 

respective percent areas contained within the Shoal 

Creek study area (100, 50, and 5 percent), and adding 

this total to the estimated rural population. The rural 

population was estimated by multiplying the number of 

rural homes (243) identified on 1996 aerial photography by the average of 2.7 persons per household estimated by the U.S. Bureau of the Census for rural 

Missouri (U.S. Bureau of the Census, 2000).

METHODS OF STUDY

Three main phases of field activity were conducted to address the purpose of this report. The first 

phase was a dye-trace study conducted during July 

2001 along a 5.7-mi reach of Shoal Creek to determine 

the survival rates, transport characteristics, and temporal variation of fecal coliform and E. coli bacteria in the 

stream. The dye-trace study included the collection of 

water-quality and dye-trace samples. Presumptive 

sources of fecal bacteria were identified by DNA-fingerprinting of E. coli isolates in selected water samples. 

The second phase involved a detailed seepage study in 

August 2002 (fig. 2) focusing on the 1.6-mi reach of 

Shoal Creek upstream from site 3, which was part of 

the reach investigated during the dye-trace study. The 

purpose of the detailed seepage study was to locate 

sources of fecal bacteria input into Shoal Creek immediately upstream from the MDNR sampling site (site 3, 

fig. 2). Both the dye-trace and detailed seepage studies 

were conducted during low base-flow conditions. The 

third phase of field activity was conducted during 2001 

and 2002 using a series of field test plots to provide preliminary data on the survival of fecal coliform and E. 

coli bacteria in poultry litter commonly applied to the 

land surface throughout the Shoal Creek Basin.

Stream Monitoring Network and Water-Quality 

Sample Collection

To determine the survival rates, transport time, 

and temporal variability of fecal bacteria along the 

5.7-mi reach of Shoal Creek previously identified as 

having fecal coliform densities above the MDNR standard of 200 col/100 mL, a network of monitoring sites 

was established along Shoal Creek and on Joyce Creek 
8 Fecal Bacteria in Streams and Land-Applied Poultry Litter in the Upper Shoal Creek Basin, Southwestern Missouri, 2001–2002

and Pogue Creek (fig. 2). The collection of water-quality samples from this network coincided with measurements of fecal bacterial survival rates and the injection 

of fluorescent dye at site 2 to evaluate transport characteristics of fecal bacteria along this stream reach. An 

evaluation of fecal bacteria transport using this combined effort is referred to as the July 2001 dye-trace 

study. During a 36-hr (hour) period beginning on July 

23, 2001, seven to nine water-quality samples were collected and analyzed for fecal bacteria densities at five 

sites along the main stem of Shoal Creek (sites 2, 2a, 

2b, 2c, and 3; fig. 2) and at two sites near the mouths of 

Pogue Creek and Joyce Creek (sites 11 and 12, fig. 2). 

As the dye peak passed each main-stem site, a suite of 

additional water-quality samples were collected and 

analyzed for nutrients, wastewater organic compounds, 

and pharmaceutical compounds; and an additional 

fecal bacterial sample was collected and submitted for 

DNA-fingerprinting. These peak samples would provide information on how densities of fecal bacteria and 

concentrations of selected chemical constituents 

changed as the same parcel of water moved through the 

stream system between sites 2 and 3. 

An additional surface-water site (site 4, fig. 2) 

located on Shoal Creek about 6.7 mi downstream from 

State Highway 97 and two sites in the upper part of the 

Pogue Creek Basin (sites 11a and 11c, fig. 2) were sampled less frequently. Samples from sites 11a and 11c 

were analyzed only for fecal bacteria densities and 

nutrients and samples from site 4 were analyzed only 

for fecal bacteria densities. Because the 1999–2000 

USGS study indicated that water samples from Pogue 

Creek at site 11 contained among the largest fecal 

coliform densities in the upper Shoal Creek Basin, bacteria samples were collected from sites 11a and 11c to 

determine if large densities of fecal coliform also were 

present in the upstream reaches of Pogue Creek. Several fecal bacteria samples were collected at site 4 to 

confirm results of the 1999–2000 USGS study, which 

indicated that fecal coliform densities downstream 

from State Highway 97 were less than the MDNR standard of 200 col/100 mL (Schumacher, 2001). 

Based on results from the 2001 dye-trace study, 

additional sampling was conducted during a detailed 

seepage study along a 1.6-mi reach between site 2c and 

site 3 during August 2002 (fig. 2). During this detailed 

seepage study, the stream channel was waded along this 

reach, and the discharge of all inflows was measured. 

Water-quality measurements were made and samples 

for fecal bacteria analyses were collected at several 

intervals along the reach and from inflows to identify 

specific areas where fecal bacteria were entering the 

creek. Environmental factors such as the general channel characteristics (stream depth and width, bottom 

composition, riparian corridor, and height and steepness of the stream bank) of the reach were noted, and 

cultural features such as the location of fences, density 

and type of livestock, and proximity of homes, farm 

buildings, poultry houses, and livestock feeding areas 

to the stream channel were recorded. Water-quality 

samples also were collected from the main stem of 

Shoal Creek at sites 2, 2c, and 3, from sites 11 and 12 

on Pogue and Joyce Creeks, and from Dilbeck Spring 

along the upper reach of Pogue Creek (fig. 2) at the 

time of the detailed seepage study.

Hydrologic conditions within the upper Shoal 

Creek Basin preceding and during the detailed seepage 

study and dye-trace study were determined using data 

from a continuously recording streamflow-gaging and 

water-quality monitoring station that was installed on 

Shoal Creek about 0.2 mi downstream from site 3 during the 1999–2000 USGS study (Schumacher, 2001). 

The station has been in operation since May 1999 and 

is equipped with a submersible pressure transducer to 

record stage and a probe that measures specific conductance and temperature. Measurements are recorded 

every 15 min (minutes). The FAPRI installed an automatic water-quality sampler at the station in 2001 as 

part of their data collection efforts to model fecal 

coliform transport.

During the dye-trace and detailed seepage studies, measurements of discharge, water temperature, 

specific conductance, dissolved oxygen, and pH were 

made, and water samples were collected and analyzed 

for fecal coliform and E. coli bacteria. One set of samples was collected from selected sites during both studies and analyzed for total (unfiltered) nutrients, 

wastewater organic compounds, and pharmaceutical 

compounds. Nutrient analyses included NO23t, total 

nitrite as nitrogen (NO2t), total ammonia as nitrogen 

(NH3t), Pt

, and total orthophosphorus as phosphorus 

(PO4t).

Water samples for the analysis of chemical constituents were collected according to the general protocols described in Wilde and Radtke (1998). Depth 

integrated, equal-width samples were collected from 

streams and springs using a hand-held USGS DH-81 

isokinetic Teflon sampler. A minimum of five individual subsamples was collected at equal-width intervals 

across the stream or spring channel and composited in 
Methods of Study 9

1- or 3-L (liter) Teflon containers. Where depths were 

less than 1 ft and velocities were less than 1 ft/s (foot 

per second), grab samples were collected by filling a 

1-L Teflon container near the center of flow. No replicate samples were collected, and one field blank was 

collected during the dye-trace study and one during the 

detailed seepage study.

Samples for the determination of nitrogen (N) 

species and PO4t were placed in 125-mL (milliliter) 

amber polyethylene bottles and chilled to 4 °C (degrees 

Celsius). Samples for the determination of Pt

 were 

placed in 125-mL clear polyethylene bottles and preserved to pH less than 2 with sulfuric acid before chilling to 4 °C. Selected water samples were analyzed for 

human wastewater organic compounds and pharmaceutical compounds. These samples were placed in 

baked 1-L amber glass bottles and chilled to 4 °C. The 

wastewater organic compounds were determined in 

unfiltered water samples by continuous liquid-liquid 

extraction with methylene chloride and by capillarycolumn gas chromatography/mass spectrometry 

(Zaugg and others, 2002). Pharmaceutical compounds 

were determined on filtered samples by high performance liquid chromatography/mass spectrometry 

(Koplin and others, 2002). Rigorous method detection 

limits have not been established for many compounds 

for these research methods, which are extremely sensitive to the detection of their respective target analytes, 

and the reported concentrations of many compounds 

are listed as estimated. General information on the 

usage of the wastewater organic compounds is discussed in Zaugg and others (2002).

Bacteria Sampling and Analyses

Bacteria samples were collected in sterilized 

500-mL polyethylene bottles. The bottles were filled 

by plunging them neck downward beneath the water 

surface at three equal-width intervals across the stream. 

After collection, the samples were placed on ice until 

processing and bacteria were enumerated using the 

membrane filter technique according to methods 

described in Wilde and Radtke (1998). Daily blanks 

were prepared by filtering 100 mL of sterile buffer 

water through the appropriate filters and incubating 

with the samples. No fecal coliform or E. coli colonies 

were detected in any of the blank samples. Water samples from five surface-water sites (sites 2, 2a, 2b, 3, and 

11) collected during the July 2001 dye-trace study were 

submitted to the University of Missouri College of Veterinary Medicine for DNA-fingerprinting using the 

repeat element Polymerase Chain Reaction (rep-PCR) 

method modified from Dombek and others (2000). 

Although DNA-fingerprinting was done to identify 

presumptive sources of fecal bacteria, the identification 

of the major sources of fecal bacteria in Shoal Creek 

was made using a combination of data from the dyetrace study, bacterial survival rates, detailed seepage 

study, DNA-fingerprinting, and presence of wastewater 

organic and pharmaceutical compounds.

Streambed-sediment samples were collected 

from sites 2 and 3 and analyzed to determine if fecal 

bacteria were accumulating in the streambed of Shoal 

Creek. Sample locations were biased toward areas of 

fine-grained sediment deposition, such as behind large 

rocks or in eddies and small pools. Approximately 1 kg 

(kilogram) of sediment was collected from the top 2 to 

3 cm (centimeters) of the streambed using a stainless 

steel scoop and placed into sterile 1-L wide-mouth, 

polyethylene containers. The containers were chilled to 

4 °C and transported within 24 hrs to the USGS laboratory in Rolla, Missouri. The containers consisted of 

coarse-grained sediment ranging from sand to small 

cobbles and 3 to 4 cm of overlying water. Because of 

the coarse-grained nature of the sediments, the original 

plan of placing 2 to 3 g (grams) of a subsample from 

each container into sterile buffer water was abandoned, 

and the entire container was shaken violently for 2 min 

and allowed to settle for 2 min. After three cycles of 

shaking and settling, a sterile pipette was used to 

remove a 5-mL sample from the upper 1 cm of the overlying water in the containers. The 5-mL sample was 

placed in a sterile flask with 45 mL of phosphate buffer 

solution and fecal coliform and E. coli density were 

determined on serial dilutions according to the procedures previously described. The mass of sediment in 

the containers was determined by drying at 105 °C for 

48 hrs. Data were reported as colonies per gram as dry 

weight. Because 1 mL of water is approximately 1 g, 

the bacteria densities from the streambed sediment and 

the overlying water could be directly compared.

Bacteria Survival in Shoal Creek

Fecal indicator bacteria such as fecal coliform 

and E. coli normally inhabit the intestinal tracts of 

warm-blooded animals and humans. As these bacteria 

are introduced to the surface-water environment, they 

are exposed to environmental conditions that stress the 

organisms, such as changes in temperature, solution 
10 Fecal Bacteria in Streams and Land-Applied Poultry Litter in the Upper Shoal Creek Basin, Southwestern Missouri, 2001–2002

salinity, pH, nutrient concentrations, and the effects 

of solar radiation and predation (Rozak and Colwell, 

1987; Davis and others, 1995; Mezrioui and others, 

1995; Ozkanca and Flint, 1997; Sinton and others, 

1999). These stresses cause a reduction of indicator 

bacteria densities in streams as a result of injury and 

death. According to Sinton and others (1999), exposure 

to solar radiation and predation are among the most 

important factors. Fecal bacteria are thought to survive 

from several hours to a few days in surface water and 

from several weeks to months in streambed sediments 

(Rozak and Colwell, 1987; Doyle and others, 1992). 

An understanding of how quickly fecal bacteria decay 

in the stream can provide important information on the 

magnitude and location of potential sources. 

Decay rates of fecal coliform and E. coli were 

estimated by fitting an exponential equation to bacterial 

densities measured at various time intervals in diffusion chambers placed at sites 2 and 3 during the July 

2001 dye-trace study. Because of the design of the diffusion chambers, the changes in densities of fecal 

coliform and E. coli with increasing time are attributed 

to the sum of natural processes that occur within the 

stream. The equations were expressed as first order 

decay in the general form of:

Ct = Co * e(-kt),

where Ct = the bacteria density at elapsed time t, in 

colonies per 100 milliliters;

Co = the initial bacteria density in colonies 

per 100 milliliters; 

k = the decay constant in hours-1; and 

t = the elapsed time in hours. 

The initial bacteria density (Co) was set to the bacteria 

density measured at the time the diffusion chambers 

were deployed.

The survival of fecal bacteria in Shoal Creek was 

investigated using diffusion chambers constructed of 

polycarbonate cylinders that were fitted with 0.2-μm 

(micrometer) pore-size filters at each end to form a 

chamber (fig. 3). Except for the polycarbonate cylinders, which were obtained from a plastics manufacturer, and the filters, which were obtained from Gelman 

Sciences, all materials used to construct the chambers 

were available at local hardware stores. The 0.2-μm 

pore-size filters served to isolate bacteria inside the 

chamber, while allowing for the diffusion of water and 

dissolved nutrients into and out of the chambers. Polycarbonate was selected so that results could be generally compared to those obtained in the Cuyahoga River 

by Myers and others (1998). Polycarbonate transmits 

more than 80 percent of visible solar radiation, but 

blocks most ultraviolet (UV) radiation; however, Sinton and others (1999) reported that fecal coliform bacteria are sensitive to a wide range of sunlight radiation 

outside the UV range.

The survival of fecal coliform and E. coli was 

measured at sites 2 and 3 during the July 2001 dyetrace study. Diffusion chambers were deployed at each 

site at the beginning of the dye-trace study on July 23, 

2001. The chambers were filled with native water from 

the stream and submerged near the middle of the stream 

channel at each location. The chambers were suspended with nylon cable ties to bricks so they were submerged parallel to the water surface and at about onehalf the average water depth (about 8 in. below the surface) at each location. Two chambers were removed 

immediately; two more at elapsed times of about 25 

and 40 hrs. At each time interval about 150 mL of water 

was removed from each chamber and placed into separate, sterile 250-mL bottles. Fecal coliform and E. coli

bacteria densities were then enumerated using standard 

membrane-filtration methods previously described.

Bacteria Transport in Shoal Creek

Fecal bacteria densities and concentrations of 

chemical constituents in streams are strongly affected 

by dilution, dispersion, and the areal distribution, timing, and magnitude of input sources as they are transported downstream with the advective flow of the 

water. Dilution and dispersion are important physical 

factors that attenuate or decrease the densities of fecal 

bacteria that enter the stream from specific sources. 

The magnitude of other factors, such as bacteria survival, depends on the elapsed time between the input of 

bacteria into the stream and the collection of waterquality samples. 

Transport characteristics of fecal bacteria in 

Shoal Creek were evaluated during the July 2001 dyetrace study using a fluorescent dye to determine the 

time-of-travel and dilution and dispersion characteristics during low base-flow conditions between sites 2 

and 3. A series of stream discharge measurements and 

background dye concentration measurements were 

made at sites 2, 2a, 2b, 2c, 3, 11, and 12 (fig. 2). At 

1828 hrs on July 23, 2001, 2.5 L of rhodamine-WT 

dye solution was injected into a riffle immediately 

upstream from the State Highway W bridge at site 2 
Methods of Study 11

(fig. 4). Concentrations of dye were measured at sites 

2, 2a, 2b, 2c, 3, and 4 during the next 2 1/2 days to follow the dye peak as it moved downstream. Water samples also were collected periodically from each site to 

determine the temporal variability of fecal coliform and 

E. coli densities along this reach of Shoal Creek, as 

described in the methods of study section of this report. 

Dye concentrations were 

measured only occasionally at site 4. As the dye 

peak passed each successive downstream site, an 

additional set of water 

samples was collected 

and analyzed for fecal 

coliform and E. coli densities, nutrients, wastewater organic compounds, 

and pharmaceutical compounds and DNA-fingerprinting of E. coli.

Concentrations of 

rhodamine-WT dye at 

sites 2a, 2b, 2c, 3, and 4 

were measured using a 

Turner Designs Model 10 

fluorometer according to 

published USGS methods 

(Wilson and others, 

1986). The fluorometer 

was calibrated directly 

using standards at concentrations of 0.1, 1.0, 

10.0, 100, and 1,000 μg/L 

(micrograms per liter). 

Dye concentrations at site 

2 (fig. 5) were measured 

with a Turner Designs 

Aquafluor hand-held fluorometer every 2 to 5 min 

after the dye was injected 

until the dye peak had 

passed, after which the 

measurement frequency 

was decreased. Results of 

the individual analyses 

are listed in Appendix A, 

at the back of this report. 

The Aquafluor fluorometer was calibrated using a 

100 μg/L standard obtained from the manufacturer, and 

calibrations were checked using dye standards prepared for the Model 10 fluorometer. After the dye was 

injected, dye concentrations were measured downstream at site 2a approximately every 10 to 30 min until 

dye was detected, then about every 5 to 10 min until the 

dye peak passed, then less frequently thereafter. As
12 Fecal Bacteria in Streams and Land-Applied Poultry Litter in the Upper Shoal Creek Basin, Southwestern Missouri, 2001–2002
Survival and Transport of Fecal Bacteria in Shoal Creek 13

soon as dye was detected at site 2a, measurements were 

started at the next site downstream (site 2b) following 

the same protocol. In this manner, the dye peak was followed downstream. As the dye peak broadened with 

increasing distance downstream from the injection 

point, the measurement interval was adjusted. Calibration of the fluorometer was checked every 4 to 6 hrs 

using a 100 μg/L standard. 

Bacteria Survival in Land-Applied Poultry 

Litter

Field tests were conducted to determine the concentrations of fecal bacteria in poultry litter generated 

within the upper Shoal Creek Basin and to provide an 

estimate of the survival of these bacteria following the 

land application of poultry litter. The tests were conducted with the assistance of the Barry County NRCS 

and several poultry producers in the area. The conceptual design of the tests was to measure the density of 

fecal coliform and E. coli bacteria in fields before and 

after the land application of poultry litter. Fields 

selected for the tests were hay fields (fescue) where 

domestic livestock had been excluded from grazing for 

a least 2 months. Test plots ranging from 5,000 to 

23,000 ft2 (square feet) were marked in each of four 

fields (fig. 6). The test plots were scattered across the 

upper Shoal Creek Basin (fig. 1). Bacteria were 

“washed” from the surface at seven locations within 

each test plot and at one to three control points located 

upslope and upwind of each field test plot using a steel 

cylinder, bacteria-free well water, and a battery powered paint mixer. All equipment was rinsed with methanol and flame sterilized before sample collection. The 

steel cylinder was tapped about 1 in. into the soil surface and filled with about 10 L of bacteria-free well 

water (pH 7 to 7.3). A flat-bottomed paint mixer was 

placed just below the water surface and the solution 

was agitated at 1,200 rpm (revolutions per minute) for 

25 seconds (fig. 7). After mixing, a sterile 250-mL bottle was used to collect a sample of the slurry water from 

inside the steel cylinder. Fecal coliform and E. coli

were enumerated using the membrane-filter method 

previously described.

Samples were collected at each test plot immediately before and after the poultry litter application and 

weekly for as many as 8 weeks. Poultry litter was 

applied using a truck-mounted broadcast spreader (fig. 

8) or a manure spreader. To avoid leaching the same 

spot at each sample location, the cylinder placement 

was rotated clockwise for each sampling trip (fig. 6). 

Litter application rates at each test plot were measured 

by weighing the amount of litter collected on polyethylene mats placed at two or three locations within each 

test plot before litter application (fig. 6). The application rate was calculated as the total weight of litter collected on the mats divided by the total surface area of 

the mats. Densities of fecal coliform and E. coli bacteria in the initial litter spread at each test plot were measured by leaching a composite litter sample collected 

from the mats. The litter collected on each mat was 

transferred into one or two 8-L plastic bags that were 

weighed to the nearest gram and mixed thoroughly 

with a sterilized stainless steel spatula. A 20- to 25-g 

composite litter sample was made by removing subsamples weighing less than 1 g from the plastic bags 

(alternating between each bag) and placing them into a 

sterile 500-mL glass mixing jar. After the net weight of 

litter in the jar was recorded, 250 mL of sterile-phosphate (PO4) water was added, and the solution was 

mixed at about 600 rpm on a stationary mixer for 1 min, 

then allowed to settle for 10 min. After settling, the 

solution was remixed for 30 seconds and allowed to 

settle for 10 min. After the solution was allowed to settle the second time, a sterile pipette was used to transfer 

5 mL of the solution (collected from just beneath the 

surface) to a sterile bottle, where it was diluted with 

PO4 buffer to a total volume of 200 mL. Densities of 

fecal coliform and E. coli bacteria were determined 

using the membrane-filter method on serial dilutions of 

this final solution.

SURVIVAL AND TRANSPORT OF FECAL 

BACTERIA IN SHOAL CREEK

The study described in this report focused on a 

5.7-mi reach of Shoal Creek between State Highway 97 

(site 3) and State Highway W (site 2) that was determined to have fecal coliform densities exceeding the 

MDNR standard of 200 col/100 mL for whole-body 

contact recreation. A network of five sites on Shoal 

Creek (sites 2, 2a, 2b, 2c, and 3) were monitored during 

this study, in addition to a main stem site further downstream (site 4) and two tributaries—Pogue Creek (sites 

11, 11a, and 11c) and Joyce Creek (site 12)—and a 

spring (Dilbeck Spring). A combination of techniques 

was used to determine the sources of the increased fecal 

coliform densities along this reach of Shoal Creek 

including a determination of decay or “die-off” rates of 

fecal coliform and E. coli in the stream, a dye-trace
14 Fecal Bacteria in Streams and Land-Applied Poultry Litter in the Upper Shoal Creek Basin, Southwestern Missouri, 2001–2002
Survival and Transport of Fecal Bacteria in Shoal Creek 15
16 Fecal Bacteria in Streams and Land-Applied Poultry Litter in the Upper Shoal Creek Basin, Southwestern Missouri, 2001–2002

study to determine travel times and dispersion characteristics along this stream reach, a detailed seepage 

study and water-quality sampling to locate specific 

sources of fecal bacteria input to the stream, and DNAfingerprinting of E. coli isolates from stream samples to 

identify presumptive sources of fecal bacteria. 

Bacterial Survival

During the 42 hrs that the diffusion chambers 

were left in the stream, fecal coliform and E. coli densities decreased (fig. 9) more than 90 percent from initial densities (table 1). Decay constants ranged from a 

minimum of 0.070 h-1 (per hour) for fecal coliform at 

site 2 to a maximum of 0.098 h-1 for fecal coliform at 

site 3. The decay rates for E. coli were similar, ranging 

from 0.075 h-1 at site 2 to 0.095 h-1 at site 3. The stream 

channel at both locations where the diffusion chambers 

were placed was mostly open with scattered trees on 

the bank. Climatic conditions were clear with scattered 

light clouds. A steep hillside west of site 3 resulted in 

diffusion chambers at this site receiving about 2 to 3 hrs 

less sunlight in the late afternoon than those at site 2. 

Because of the limited number of data points, no significant difference (alpha level of 0.05) was detected 

between the calculated decay rates at the two sites or 

between fecal coliform and E. coli densities; therefore, 

the decay rates were averaged to give an estimated fecal 

coliform and E. coli decay rate of 0.084 h-1. This estimated decay rate indicates that about 8 percent of the 

fecal coliform and E. coli bacteria in Shoal Creek “dieoff” each hour. This rate of 0.084 h-1 is larger than 

decay rates of fecal coliform and E. coli of 0.002 to 

0.0407 h-1 measured during the summer in the Cuyahoga River by Myers and others (1998). A likely reason 

for the larger decay rates measured in this study is the 

larger degree of sunlight penetration and warmer water 

in Shoal Creek as compared to that of the Cuyahoga 

River. Sunlight penetration is reduced by water turbidity. Myers and others (1998) measured decay rates during periods of runoff where suspended-sediment 

concentrations ranged from 38 to 848 mg/L. In contrast, suspended-sediment concentrations in Shoal 

Creek at base-flow conditions are less than 20 mg/L. In 

addition, the diffusion chambers in the Cuyahoga River 

were placed 18 in. below the surface, more than twice 

the depth the chambers at sites 2 and 3 were placed. 

The shallower depth of the chambers in Shoal Creek 

would allow additional sunlight, and possible UV radiation, to reach the chambers. Bacteria decay in surface 

water is inversely proportional to water temperature 

(Craig and others, 2002). The median water temperature of Shoal Creek (26.8 °C) during sample collection 

was larger than the median summertime water temperature (21.4 to 25.2 °C) during the Cuyahoga River 

study (Myers and others, 1998).
Survival and Transport of Fecal Bacteria in Shoal Creek 17

Travel Times of Bacteria in Shoal Creek

The transport and travel times of fecal bacteria at 

low base-flow conditions between sites 2 and 3 on 

Shoal Creek were investigated by following the pulse 

of the fluorescent dye (rhodamine-WT) injected into 

the stream immediately upstream from site 2 on July 

23, 2001. The underlying assumption is that the transport of fecal bacteria is similar to that of the dye. Less 

than 0.6 in. of precipitation was recorded by the NOAA 

weather station in Monett during the 7-day period preceding the dye injection, and the record from the 

streamflow-gaging station 0.2 mi downstream from the 

site indicated that Shoal Creek was at stable low baseflow conditions. Shoal Creek discharge generally 

increased downstream from the dye injection site. The 

discharge between sites 2 and 2a more than doubled, 

increasing from 7.30 to 14.8 ft3

/s (cubic feet per second) (table 2). Inflow from Pogue Creek (5.14 ft3/s) 

accounted for most of the 7.50 ft3

/s increase in discharge between sites 2 and 2a. The remaining 2.36 ft3

/s 

(about 16 percent of the increase) was from springs and 

diffuse ground-water inflows. Discharge between sites 

2a and 2b increased only slightly (14.8 to 15.0 ft3

/s) 

and was within 5 percent measurement error, indicating 

no detectable inflow between these sites. Discharge 

increased substantially between sites 2b (15.0 ft3/s) and 

2c (23.6 ft3/s). Inflow from Joyce Creek accounted for 

only 1.55 ft3/s of the increase in discharge between site 

2b and 2c. Most of the increase in discharge between 

sites 2b and 2c was attributed to the presence of several 

large springs between these sites. The discharge 

between sites 2c and 3 increased slightly (23.6 to 

24.6 ft3/s); however, the increase (4 percent) was within 

the accepted discharge measurement error. A small 

spring (discharge estimated at 0.05 ft3/s on August 27, 

2002) about 0.25 mi upstream from site 3 accounted for 

part of the small increase in discharge between sites 2c 

and 3.

A total of 595 g of rhodamine-WT dye was 

injected at 1828 on July 23, 2001, into a riffle immediately upstream from a pool upstream from site 2 (figs. 

4, 5). About 50 percent of this dye was recovered 

downstream at sites 2b, 2c, and 3 (table 2). Dye concentrations at site 3 peaked at about 2100 hrs the following 

day, indicating that the total time of travel from the 

injection to site 3 (distance of 5.7 mi) was about 26 hrs. 

As the dye peak moved downstream, dilution and dispersion resulted in a decrease of the peak dye concentration and broadening of the peak at each successive 

downstream site (fig. 10). The peak dye concentrations 

decreased more than 30-fold between sites 2 and 2a 

from 2,070 to 69.8 μg/L, reflecting substantial dilution 

by the large increase in discharge (which more than

Table 1. Densities of fecal coliform and Escherichia coli bacteria in diffusion chambers placed in Shoal Creek

at sites 2 and 3, July 23 to 25, 2001

[E. coli, Escherichia coli; col/100 mL, colonies per 100 milliliters; k, non-ideal count]

Sample 

chamber 

number Date Time

Water 

temperature 

(degrees 

Celsius)

Elapsed 

time 

(hours)

E. coli 

density (col/100 

mL)

Fecal 

coliform

density (col/100 

mL)

Site 2-initial 07/23/01 1730 28.5 0 880 1,200

tube1 07/24/01 2000 26.8 26.50 120 145

tube2 07/24/01 2000 26.8 26.50 170 160

tube6 07/25/01 1030 25.0 41.00 36 k 80 k

Site 3-initial 07/23/01 1700 26.8 0 900 1,100

tube1 07/24/01 1800 27.5 25.00 80 k 180

tube2 07/24/01 1800 27.5 25.00 56 k 150

tube3 07/24/01 1800 27.5 25.00 72 k 135

tube4 07/25/01 1045 23.9 41.75 25 k 5 k

tube5 07/25/01 1045 23.9 41.75 25 k 25 k

tube6 07/25/01 1045 23.9 41.75 12 k 16 k
18 Fecal Bacteria in Streams and Land-Applied Poultry Litter in the Upper Shoal Creek Basin, Southwestern Missouri, 2001–2002

doubled) and dispersion along this reach. Despite a 

nearly uniform discharge, dye concentrations 

decreased by more than 40 percent between sites 2a and 

2b, indicating substantial dispersion along this reach as 

evidenced by the slight broadening of the dye peak (fig. 

10). The substantial dispersion of the dye peak probably was the result of a number of long pools that were 

present between sites 2a and 2b. Absorption of dye to 

streambed material and organic matter within the channel also contributed to the dye decrease. Dye concentrations decreased by about 64 percent and the peak 

broadened between sites 2b and 2c, whereas the discharge increased by more than 50 percent. Unlike the 

upstream reaches, the peak dye concentrations and 

shape of the dye peak at sites 2c and 3 were similar (fig. 

10), indicating the channel characteristics between 

these sites are different from those sites upstream. The 

reach between sites 2c and 3 is shallow and narrow with 

few pools as compared to the reach upstream from site 

2c. The general lack of pools and eddies also was 

expressed in the slightly larger rate of dye movement 

between sites 2c and 3 [0.28 mi/hr (mile per hour)] 

compared to between sites 2a and 2c (0.21 to 0.18 

mi/hr, table 2).

Assuming that the transport characteristics of the 

dye are similar to fecal bacteria, results of the dye study 

indicate that transport of fecal bacteria during low 

base-flow conditions between sites 2 and 3 occurred in 

about 26 hrs. As bacteria are transported along this 

reach of Shoal Creek, dilution and dispersion will 

cause substantial decreases in bacterial densities 

between sites 2 and 2c. Dilution and dispersion will not 

cause a measurable decrease in bacteria densities 

between sites 2c and 3 at low base-flow conditions.

Distribution of Fecal Bacteria and Nutrients

During the July 2001 dye-trace study, densities 

of fecal coliform bacteria in samples from Shoal, 

Pogue, and Joyce Creeks generally exceeded the 

MDNR standard of 200 col/100 mL for whole-body 

contact recreation. All of the samples collected from 

Shoal Creek at sites 2, 2a, 2b, and 3 and Pogue Creek 

at site 11 had fecal coliform densities larger than the 

MDNR standard. Seven of eight samples collected 

from Shoal Creek at site 2c and five of seven samples 

collected from Joyce Creek at site 12 also had fecal 

Table 2. Summary of travel times and dye quantity recovered from selected sites during the July 2001 dye-trace

study

[--, no data available]

Injectiona

Site number (fig. 2)

2 2a 2b 2c 3

Date of dye peak arrival 07/23/01 07/23/01 07/24/01 07/24/01 07/24/01 07/24/01

Time of dye peak arrival 1828 1843 0205 0745 1505 2048

Maximum dye concentration 

(micrograms per liter)

 -- 2,070 69.8 39.4 14.4 14.1

Discharge (cubic feet per second) 7.30 7.30 14.8 15.0 23.6 24.6

Travel time of dye peak from injection 

site (hours)

 -- .25 7.62 13.28 20.62 26.33

Travel time of dye peak between sites 

(hours)

 -- .25 7.37 5.67 7.33 5.72

Distance from injection point (miles) -- .08 1.6 2.8 4.1 5.7

Average travel rate of dye peak from 

injection point (mile per hour)

 -- .32 .21 .21 .20 .22

Rate of dye peak travel between sites 

(mile per hour)

 -- .32 .21 .21 .18 .28

Estimated mass of dye recovered 

(grams)

595 504 412 333 278 327

Fraction of dye recovered -- .85 .69 .56 .47 .55

a

 Injection site was riffle at the upstream end of a pool about 100 feet upstream from State Highway W bridge. Water samples were 

collected at the pool outlet about 300 feet downstream from State Highway W bridge. 
Distribution of Fecal Bacteria and Nutrients 19

coliform densities larger than the MDNR standard. 

None of the three samples collected from Shoal Creek 

at site 4 contained fecal coliform densities larger than 

the MDNR standard. Samples from site 2a contained 

the largest densities of fecal coliform (average of 2,600 

col/100 mL) and E. coli (average of 2,200 col/100 mL) 

detected in the main stem of Shoal Creek (fig. 11). 

Average fecal coliform and E. coli densities decreased 

to less than or equal to 1,400 col/100 mL downstream 

at site 2b and further decreased to less than 500 col/100 

mL at site 2c, but increased significantly at site 3. The 

average densities of fecal coliform (2,100 col/100 mL) 

and E. coli (1,400 col/100 mL) measured at site 3 during the July 2001 dye-trace study were comparable to 

densities previously reported for this site by Schumacher (2001). At an average decay rate of 0.084 hr-1, 

fecal bacteria densities in a parcel of water at site 2c 

would be expected to decrease about 40 percent during 

the 5.7 hr it takes to travel to site 3. The significant 

increase in fecal bacteria densities between sites 2c and 

3 and lack of measurable inflow between these sites 

indicates a substantial source of fecal bacteria along 

this stream reach. 

Fecal bacteria densities in Pogue Creek (site 11, 

fig. 11) were the largest detected during the July 2001 

dye-trace study. The average fecal coliform and E. coli

densities in Pogue Creek (3,000 and 2,500 col/100 mL) 

measured during the July 2001 dye-trace study were 

about twice the average densities for this site reported 

by Schumacher (2001). Samples from sites 11a and 11c 

had the largest fecal coliform (9,900 and 4,300 col/100 

mL) and E. coli densities (4,900 and 4,300 col/100 mL) 

detected in the 2001 dye-trace study (table 3), indicating substantial sources of fecal bacteria in the upper 

reaches of Pogue Creek. Although not measured, the 

discharge at both sites was estimated to be about onehalf (site 11c) to three-fourths (site 11a) of that measured downstream at site 11, which supports the presence of substantial sources of fecal bacteria in the 

upper reaches of Pogue Creek. Densities of fecal bacte-
20 Fecal Bacteria in Streams and Land-Applied Poultry Litter in the Upper Shoal Creek Basin, Southwestern Missouri, 2001–2002

ria in samples from Pogue Creek were significantly 

larger (alpha level of 0.05) than densities in samples 

from Joyce Creek at site 12 and Shoal Creek at sites 2b 

and 2c (fig. 11). 

Fecal bacteria densities varied substantially during the July 2001 dye-trace study and tended to exhibit 

some type of diurnal or sinusoidal variability. For 

example, densities of E. coli at site 2 tended to peak 

during the early morning hours and decrease in the 

early evening (fig. 12). A similar pattern in E. coli densities was observed at sites 2b and 2c. Densities of E. 

coli at sites 2a and 3 also exhibited some sort of sinusoidal variability, but were out of phase with the other 

main stem sites. E. coli densities tended to peak in the
Distribution of Fecal Bacteria and Nutrients 21

Table 3. Discharge, physical properties, and densities of fecal coliform and Escherichia coli in water samples collected 

from Shoal Creek and selected tributary sites during the July 2001 dye-trace study 

[Q, discharge in cubic feet per second; Temp, temperature in degrees Celsius; SC, specific conductance in microsiemens per centimeter at 25 degrees 

Celsius; DO, dissolved oxygen in milligrams per liter; col/100 mL, colonies per 100 milliliters; E. coli, Escherichia coli; --, no data; pk, sample 

collected at dye peak; k, non-ideal count]

Date Time Q Temp SC DO

DO percent 

saturation

Fecal coliform 

(col/100 mL)

E. coli

(col/100 mL)

Site 2, Shoal Creek at State Highway W

07/23/01 1658 7.3 28.5 258 5.96 76.6 -- --

07/23/01 pk 1850 -- 28.4 318 6.92 89.4 1,000 560

07/23/01 pk 1906 -- -- -- -- -- 880 920

07/24/01 0110 -- 25.9 303 5.06 62.3 1,300k 1,900k

07/24/01 0640 -- 24.7 296 5.47 66.0 3,400k 2,300k

07/24/01 1240 -- 27.2 227 8.60 108.4 2,000k 1,300

07/24/01 1930 -- 26.8 232 5.50 73.0 910k 1,000

07/25/01 0123 -- 24.9 303 5.46 66.0 1,500k 1,400k

07/25/01 0705 -- 24.0 232 5.15 61.4 3,400 2,900

Site 2a, Shoal Creek at County Road 2110

07/23/01 1630 14.8 28.7 331 5.29 75.1 -- --

07/23/01 1857 -- -- -- -- -- 3,600k 3,300

07/24/01 0025 -- -- -- -- -- 3,100k 960k

07/24/01 pk 0225 -- 25.1 329 4.74 57.5 2,400k 2,300k

07/24/01 0655 -- 24.2 321 5.14 61.5 3,000k 1,700k

07/24/01 1255 -- 26.4 322 7.94 98.5 1,500k 1,900k

07/24/01 1850 -- 26.7 314 6.30 79.5 2,300 3,100

07/25/01 0110 -- 24.5 325 5.27 63.3 3,500 2,500

07/25/01 0720 -- 23.5 328 4.74 55.6 1,100k 1,600k

Site 2b, Shoal Creek at County Road 2100

07/23/01 1550 15 28.5 332 5.78 74.5 -- --

07/23/01 1948 -- -- -- -- -- 1,100k 1,500

07/24/01 0010 -- 27.0 325 4.07 51.8 1,800k 1,600k

07/24/01 pk 0805 -- -- -- -- -- 1,300k 1,300

07/24/01 0840 -- 24.9 331 4.96 60.0 2,100k 1,500

07/24/01 1305 -- 27.3 325 7.49 93.9 1,100 530k

07/24/01 1840 -- 27.3 325 6.27 79.2 1,000k 580

07/25/01 0100 -- 25.7 325 4.73 58.0 1,300k 1,200k

07/25/01 0730 -- 24.2 330 4.92 58.4 1,300k 1,600k

Site 2c, Shoal Creek at County Road 2090

07/23/01 1520 23.6 26.5 325 6.28 77.8 -- --

07/23/01 1955 -- -- -- -- -- 110 63

07/24/01 0035 -- 24.8 326 5.89 70.6 460 275

07/24/01 0635 -- 23.9 326 6.05 71.5 780 480k

07/24/01 1318 -- 25.4 319 7.78 94.5 1,000 180

07/24/01 pk 1520 -- 25.9 313 7.66 95.1 280 130

07/24/01 1830 -- 25.6 316 7.55 92.6 360 170k

07/25/01 0040 -- 24.1 321 6.54 78.0 500 280

07/25/01 0738 -- 23.2 325 5.77 67.8 410 800k

Site 3, Shoal Creek at State Highway 97

07/23/01 1430 24.6 26.8 -- -- -- -- --

07/23/01 2010 -- -- -- -- -- 1,100k 1,500

07/23/01 2340 -- 25.9 320 6.10 80.0 1,100k 1,400k

07/24/01 0655 -- 24.2 329 5.84 69.6 1,100k 580

07/24/01 1335 -- 27.2 315 9.06 112.8 3,600k 470k

07/24/01 1950 -- -- -- -- -- 2,100k 1,800k

07/24/01 pk 1956 -- -- -- -- -- 4,400k 2,700k

07/25/01 0047 -- 24.5 322 6.12 73.6 1,400k 1,300

07/25/01 0755 -- 23.5 328 5.73 67.5 2,800 2,200k

07/25/01 1450 -- -- -- -- -- 790 360
22 Fecal Bacteria in Streams and Land-Applied Poultry Litter in the Upper Shoal Creek Basin, Southwestern Missouri, 2001–2002

early evening and decrease during the late morning. 

The patterns of E. coli densities at the various sites indicated that inputs of fecal bacteria to the stream or their 

decay, or both, have some sort of diurnal or sinusoidal 

variability. Unfortunately, the sampling period was not 

sufficiently long enough to determine if the variability 

in fecal bacteria densities had a repeatable frequency. 

The fluctuations in fecal bacteria densities were not a 

simple function of advection and dispersion because 

the patterns at successive downstream sites were not 

shifted in time by the travel time of the dye between the 

sites. For example, at the time of injection, E. coli densities at site 2 were less than 1,000 col/100 mL, but 

increased steadily during the next 12 hrs (fig. 12). As 

the dye peak passed site 2a about 8 hrs after injection, 

the E. coli densities at site 2a (2,300 col/100 mL) were 

larger than those at site 2 when the dye was injected and 

remained generally steady during the next 12 hrs. 

Pogue Creek accounts for a large part of the increase in 

discharge between sites 2 and 2a, but the E. coli densities in Pogue Creek near the time of dye injection 

(3,700 col/100 mL) were not large enough to generate 

the E. coli densities observed as the dye peak passed 

site 2a. This suggests additional inputs of E. coli to 

Shoal Creek between sites 2 and 2a independent of 

Pogue Creek.

Site 4, Shoal Creek

07/25/01 1300 -- -- -- -- -- 73k 20k

07/25/01 1430 -- -- -- -- -- 91k 60k

07/26/01 0915 -- -- -- -- -- 190 130

Site 11a, Pogue Creek at County Road

07/24/01 1530 -- 22.5 350 5.44 63.5 9,900 4,900

Site 11c, Pogue Creek at County Road

07/24/01 1600 -- 16.2 365 6.25 63.3 4,300 4,300

Site 11, Pogue Creek near mouth

07/23/01 1925 5.14 -- -- -- -- -- --

07/23/01 2200 -- -- -- -- -- 3,800 3,700

07/24/01 0115 -- 22.2 358 5.20 58.6 3,000 3,300

07/24/01 0646 -- 20.9 356 5.94 66.5 3,000 2,000

07/24/01 1246 -- 22.6 356 6.84 79.0 4,100 1,000k

07/24/01 1620 -- -- -- -- -- 3,600k 3,200k

07/25/01 0120 -- 21.3 349 5.99 67.8 2,700k 2,500k

07/25/01 0713 -- 20.2 324 5.77 63.8 700 1,500

Site 12, Joyce Creek near mouth

07/23/01 1600 1.55 -- -- -- -- 170 200

07/24/01 0030 -- 26.7 306 4.45 56.4 130 350

07/24/01 0645 -- 26.2 301 4.64 58.0 570k 420k

07/24/01 1325 -- 27.6 297 5.61 74.8 830k 130

07/24/01 1823 -- 27.6 294 5.67 74.7 1,600k 650

07/25/01 0033 -- 26.3 299 4.30 51.8 430 890k

07/25/01 0745 -- 25.5 302 4.66 57.0 860k 1,400k

Bacteria concentrations in streambed-sediment samples (colonies per gram wet weight)

Site 2, Shoal Creek at State Highway W

07/25/01 1045 -- -- -- -- -- 28 30

Site 3, Shoal Creek at State Highway 97

07/25/01 0930 -- -- -- -- -- 8 8

Table 3. Discharge, physical properties, and densities of fecal coliform and Escherichia coli in water samples collected 

from Shoal Creek and selected tributary sites during the July 2001 dye-trace study—Continued

[Q, discharge in cubic feet per second; Temp, temperature in degrees Celsius; SC, specific conductance in microsiemens per centimeter at 25 degrees 

Celsius; DO, dissolved oxygen in milligrams per liter; col/100 mL, colonies per 100 milliliters; E. coli, Escherichia coli; --, no data; pk, sample 

collected at dye peak; k, non-ideal count]

Date Time Q Temp SC DO

DO percent 

saturation

Fecal coliform 

(col/100 mL)

E. coli

(col/100 mL)
Distribution of Fecal Bacteria and Nutrients 23

A comparison of the dye concentrations and E. 

coli densities at sites 2c and 3 indicated that the significant increase in fecal bacteria densities between these 

sites was caused by a large influx of bacteria along this 

stream reach. As the dye peak traveled between sites 2c 

and 3, the fecal bacteria densities in the parcel of water 

carrying the dye peak increased nearly ten-fold (fig. 

12). Because the advection 

of the dye peak along this 

reach occurred during the 

daytime, a time when bacterial decay rates should be at a 

maximum because of 

warmer temperatures and 

sunlight exposure, the 

increase in the E. coli densities at site 3 was caused by 

an influx of bacteria along 

the 1.6-mi reach between 

sites 2c and 3.

A mass balance of 

fecal bacteria loads confirms 

significant sources of fecal 

bacteria to Shoal Creek 

between sites 2 and 2a and 

between sites 2c and 3 during the July 2001 dye-trace 

study. The mass balance 

included summing the measured bacteria loads from 

upstream and tributary sites 

and allowing for bacteria 

decay over the estimated 

transport time between the 

sites. For example, the fecal 

bacteria loads at site 2 and 

Pogue Creek (site 11) were 

summed and then allowed to 

decay (rate of 0.084 h-1) for 

the 7.37 hrs it took the dye 

peak to travel between sites 2 

and 2a (table 2). The results 

are predicted distributions of 

fecal coliform and E. coli

bacteria loads at site 2a (fig. 

13). Results of the KruskalWallis test indicated that the 

predicted fecal coliform and 

E. coli loads at sites 2a and 3 

were significantly smaller 

than the measured loads. At site 3, the predicted loads 

were nearly an order of magnitude smaller than the 

measured loads, indicating an extremely large input of 

fecal bacteria between sites 2c and 3 (fig. 13).

Analysis of streambed-sediment samples from 

sites 2 and 3 indicated that the accumulation of substantial quantities of fecal bacteria in the streambed
24 Fecal Bacteria in Streams and Land-Applied Poultry Litter in the Upper Shoal Creek Basin, Southwestern Missouri, 2001–2002
Sources of Fecal Bacteria in Shoal Creek 25

sediment in Shoal Creek probably does not occur. Fecal 

coliform and E. coli bacteria concentrations in streambed sediment from sites 2 and 3 were less than or 

equal to 30 col/g (colonies per gram) wet weight (table 

3). The relatively small fecal bacteria concentrations in 

streambed sediment from Shoal Creek compared to 

water samples was not surprising because of the 

coarse-grained (sand to cobble) streambed sediment. 

Myers and others (1998) reported that smaller fecal 

bacteria densities were present in sandy sediment as 

compared to silty sediment in the Cuyahoga River. The 

small concentration of fecal bacteria in streambed sediment from Shoal Creek indicates that resuspension of 

streambed sediment during runoff probably is not a 

major source of fecal bacteria to the water column. 

However, the streambed-sediment samples collected 

from Shoal Creek were not from areas where livestock 

had access to the stream and may not represent fecal 

bacteria concentrations in streambed sediment in areas 

of intense livestock activity.

Concentrations of NO23t in water samples collected during the July 2001 dye-trace study from Shoal 

Creek increased from 2.3 mg/L at site 2 to between 2.9 

and 3.2 mg/L at sites 2a, 2b, 2c, and 3 (table 4). Samples from Pogue Creek contained the largest NO23t

concentrations detected (4.5 to 4.8 mg/L). A comparison of instantaneous NO23t loads during the July 2001 

dye-trace study indicated that inflow from Pogue Creek 

accounted for nearly all of the increase in NO23t concentrations between sites 2 and 2a. Schumacher (2001) 

postulated that the large NO23t concentrations in Pogue 

Creek might be the result of liquid waste from a poultry 

processing plant. Liquid wastes from this plant, which 

has a discharge in excess of 1 Mgal/d, are applied to the 

land surface about 1-mi upstream from site 11c (fig. 2). 

All the flow in Pogue Creek at site 11c was attributable 

to two springs (Dilbeck Spring and an unnamed spring) 

between the processing plant and site 11c, and 

upstream from these springs Pogue Creek is usually 

dry. According to data from Schumacher (2001) and 

Mugel (2002), Dilbeck Spring contained NO23t concentrations larger than other springs in the upper Shoal 

Creek Basin. 

Concentrations of NO23t in samples collected 

during August 2002 at all sites were similar or slightly 

smaller than those detected in samples during the July 

2001 dye-trace study. The smaller concentrations during the August 2002 sampling probably were caused by 

dilution, because the discharges measured during 

August 2002 were larger than those measured during 

2001 (table 4). Total phosphorus (Pt

) concentrations at 

all sites were less than 0.1 mg/L, with a tendency for 

concentrations in August 2002 to be larger than those 

in July 2001. Overall, NO23t and Pt

 concentrations in 

water samples collected during this study were similar 

to values reported by Schumacher (2001).

SOURCES OF FECAL BACTERIA IN 

SHOAL CREEK

Attempts were made to identify the potential 

sources of fecal bacteria along the study reach using 

detailed observations and sampling during a seepage 

study of a select reach of Shoal Creek during August 

2002. Additional efforts to identify the sources of fecal 

bacteria included the analysis of wastewater organic 

compounds and pharmaceutical compounds in water 

samples along the study reach and DNA-fingerprinting 

of E. coli isolated from selected water samples. Shoal 

Creek is an important source of water for livestock, and 

livestock generally are not fenced out of the stream. 

Schumacher (2001) observed that the livestock have 

free access to most of Shoal Creek and its tributaries 

upstream from site 3 and may be an important source of 

fecal bacteria to Shoal Creek and its tributaries 

upstream from site 3.

Detailed Seepage Study 

In response to the suspected large source of fecal 

bacteria identified between sites 2c and 3 during the 

dye-trace study, a detailed seepage study was conducted along this 1.6-mi reach during low base-flow 

conditions on August 27, 2002. Results of this detailed 

seepage study indicated that the large increase in fecal 

bacteria densities in Shoal Creek between site 2c and 

site 3 (fig. 14) probably was caused by pastured cattle 

between these sampling sites. Water-quality samples 

collected during the detailed seepage study indicated a 

substantial increase in fecal bacteria densities downstream from areas where cattle had been fed along the 

streambank, or in areas where cattle were wading in the 

stream and congregating under trees along the streambank. Fecal coliform and E. coli densities at site 2c 

were small (100 and 40 col/100 mL), but increased to 

1,100 and 580 col/100 mL at site 2c-L downstream 

from an area of intense cattle activity (fig. 14). Inflow 

from a spring branch (site 2c-J) where more than 100 

cattle were wading or grazing nearby also contained
26 Fecal Bacteria in Streams and Land-Applied Poultry Litter in the Upper Shoal Creek Basin, Southwestern Missouri, 2001–2002 Table 4. Physical properties, nutrient concentrations, and densities of fecal coliform and Escherichia coli bacteria in surface- and groun

during July 2001 and August 2002 [Q, discharge in cubic feet per second; Temp, temperature in degrees Celsius; SC, specific conductance in microsiemens per centimeter at 25 degrees Celsius; pH, pH

ammonia; mg/L, milligrams per liter; NO23t, total nitrite plus nitrate as nitrogen; NO2t, total nitrite as nitrogen; Pt, total phosphorus; PO4t, total orthophosphorus; FC, 

colonies per 100 milliliters; E. coli, Escherichia coli; --, no data; <, less than; e, estimated] Site (fig. 2) Site type Date Time Q Temp SC pH NH3t (mg/L) NO23t (mg/L) NO2t (mg/L)

Pt

(mg/L)

PO4t

(mg/L)

(co

July 2001 dye-trace study

2 Stream 07/23/01 1850 7.3 -- 318 -- 0.06 2.3 0.03 0.04 0.04 

2a Stream 07/24/01 0250 14.8 24.5 329 -- .06 3.2 .03 .04 .05 

2b Stream 07/24/01 0800 15.0 24.9 331 -- .05 3.1 .03 .04 .05 

2c Stream 07/24/01 1520 23.6 -- 313 -- .03 3.1 .01 .03 .04 

3 Stream 07/24/01 1950 24.6 -- 322 -- .06 2.9 .02 .04 .04 

11a Stream 07/24/01 1550 -- -- 350 -- .10 4.5 .03 .08 .07 11c Stream 07/24/01 1600 -- -- 352 -- .05 4.6 .01 .03 .03 

11 Stream 07/24/01 1620 5.1 -- 352 -- .11 4.8 .04 .07 .07 

August 2002 detailed seepage study

2 Stream 08/27/02 1400 12 22.7 320 8.1 <0.01 2.6 <0.01 0.03 0.03 

2c Stream 08/27/02 1552 28 22.6 317 -- .01 3.0 <.01 .03 .04 

2c-E Stream 08/27/02 1645 -- -- -- -- -- -- -- -- -- 

2c-G Stream 08/27/02 1744 -- -- -- -- -- -- -- -- -- 

2c-J Spring 08/27/02 1745 .05 e 30.9 325 -- -- -- -- -- -- 

2c-L Stream 08/27/02 1822 -- -- 319 -- -- -- -- -- -- 

3 Stream 08/27/02 1040 29.5 20.8 337 8.1 .02 3.0 .01 .03 .03 

11 Stream 08/28/02 0830 5.9 17.9 342 7.4 .01 3.6 <.01 .04 .02 

Dilbeck Spring Spring 08/27/02 1635 2.0 14.6 384 7.1 <.01 3.9 <.01 .02 .02 

12 Stream 08/27/02 1210 2.4 21.7 315 8.2 .01 3.1 <.01 .04 .02 
Sources of Fecal Bacteria in Shoal Creek 27
28 Fecal Bacteria in Streams and Land-Applied Poultry Litter in the Upper Shoal Creek Basin, Southwestern Missouri, 2001–2002

large densities of fecal coliform (5,600 col/100 mL) 

and E. coli (4,000 col/100 mL). Fecal coliform densities downstream in the sample from site 3 (200 col/100 

mL) were twice as large as those at the upstream site 

(site 2c), but densities of E. coli at site 3 (660 col/100 

mL) were more than 10 times larger than those at site 

2c (fig. 14). Results of the detailed seepage study are 

consistent with results obtained during the dye-trace 

study and indicate that at low base-flow conditions during the time of these studies, a substantial input of fecal 

bacteria into Shoal Creek occurred between sites 2c 

and 3 likely from cattle pastured along this reach. 

Fecal bacteria densities in samples collected during the August 2002 detailed seepage study tended to 

be smaller than those in samples collected during the 

July 2001 dye-trace study (table 4). The large fecal bacteria densities in the July 2001 samples might be 

related to the higher temperatures and the land application of poultry litter that was occurring at the time of 

the dye-trace study. The average maximum temperature for the 3-day period ending July 26, 2001, was 

93 °F compared to 87 °F for the 3-day period ending 

August 27, 2002. Because the study results indicated 

that cattle are an important source of the fecal bacteria 

measured in Shoal Creek, the cattle may be expected to 

congregate for longer periods in and along the stream 

during hotter weather. According to the NRCS, during 

the July 2001 dye-trace study, several hundred truckloads of poultry litter were spread on fields along Shoal 

Creek between sites 2 and 3. Poultry litter was 

observed along roadsides and on low-water bridges at 

sites 2a and 2b during the July 2001 dye-trace study. In 

contrast, widespread application of poultry litter was 

not known to be occurring at the time of the detailed 

seepage study.

Distribution of Wastewater Organic 

Compounds and Pharmaceutical 

Compounds

To provide additional information on the possible sources of fecal bacteria in Shoal Creek, water samples collected during the July 2001 and August 2002 

sampling trips were analyzed for a suite of organic 

compounds commonly associated with wastewater and 

a suite of pharmaceutical compounds. During the July 

2001 dye-trace study, only water samples from the 

main stem sites (sites 2, 2a, 2b, 2c, and 3) were analyzed for these compounds, whereas during the August 

2002 detailed seepage study, only samples from the 

upstream and downstream sites (sites 2 and 3) and 

major tributaries (Pogue and Joyce Creeks) were analyzed. A sample was collected from Dilbeck Spring 

during August 2002 because a large expansion of the 

poultry processing plant wastewater irrigation system 

upstream from the spring was underway and the spring 

supplies a large part of the flow of Pogue Creek. 

A total of seven wastewater compounds and four 

pharmaceutical compounds were detected in one or 

more water samples collected during this study (table 

5). The most frequently detected compounds were the 

stimulant caffeine (eight detections), the fecal indicator 

cholesterol, and the human drug acetaminophen (three 

detections each). Except for an estimated concentration 

of cholesterol of 1.2 μg/L, concentrations of all compounds were below the method reporting limit and estimated at less than 1 μg/L. Analytical error and the 

potential of sample contamination are substantial at 

these small concentrations and care should be used in 

interpreting the results listed in table 5. Trends in the 

type of compounds and concentrations detected along 

the study reach of Shoal Creek were not clearly evident. The largest number of compounds were detected 

in water samples collected during July 2001 from sites 

2a and 2c (five detections). Samples collected during 

July 2001 from sites 2 and 3 had only four or less detections, and the sample from site 2b had one detection. 

The number of compounds detected had no relation to 

the densities of fecal bacteria because site 2a had 

among the largest fecal densities whereas site 2c had 

among the smallest fecal bacteria densities (fig. 12). 

The detection of acetaminophen at sites 2, 3, and 11, 

and the antimicrobial agent triclosan at sites 2b and 3 

indicated that some human wastewater is entering 

Shoal Creek. Triclosan was detected in a previous study 

from site 3 by Schumacher (2001). The detection of thiabendazole, a common anthelmintic used to treat a 

variety of worm infections in cattle, at sites 2 and 2a, 

may indicate cattle waste was entering Shoal Creek. 

Although the presence of thiabendazole may indicate 

cattle waste, the absence of its detection does not necessarily indicate the absence of cattle waste. For example, the August 2002 sample from site 3 contained no 

thiabendazole, but did contain acetaminophen despite 

evidence from fecal bacteria samples collected during 

the detailed seepage study along this reach that indicated a large influx of fecal bacteria from cattle 

between sites 2c and 3 (fig. 14). The sample from Dilbeck Spring contained phenol (estimated concentration 
Sources of Fecal Bacteria in Shoal Creek 29

Table 5. Concentrations of wastewater organic compounds and selected pharmaceutical compounds in surface- and ground-wa

during July 2001 and August 2002

[All concentrations in micrograms per liter; <, less than; e, estimated concentration below the reporting limit; ND, not detected and method detection level no

Compound

Shoal Creek at 

State Highway W 

(site 2)

Pogue 

Creek near 

mouth

 (site 11) 

Shoal 

Creek 

(site 2a)

Shoal 

Creek

(site 2b)

Joyce 

Creek near 

mouth

(site 12)

Shoal 

Creek

(site 2c)

Shoal Creek a

State Highway 9

(site 3)

07/23/01

1850

08/27/02

1400

08/28/02

0830

07/24/01

0225

07/24/01

0800

08/27/02

1210

07/24/01

1520

07/24/01

1950

08/27

104

Wastewater organic compound analysis

3-beta-Coprostanol <2 <2 <2 0.24 e <2 <2 0.57 e <2 <2 beta-Sitosterol <2 <2 <2 .60 e <2 <2 <2 .93 e <2 Caffeine .13 e <.5 <.5 .13 e <.5 <.5 .33 e <.5 <.5 Cholesterol <2 <2 <2 .58 e <2 <2 .81 e 1.2 e <2 para-Cresol <1 <1 .25 e <1 <1 <1 <1 <1 <1 Phenola

a Phenol was detected at an estimated concentration of 0.26 microgram per liter in the blank sample submitted in July 2001 and at an estimated concentrati

per liter in the August 2002 blank sample.

<.5 <.5 <.5 <.5 <.5 <.5 <.5 <.5 <.5 

Triclosan <1 <1 <1 <1 .21 e <1 <1 .12 e <1 

Pharmaceutical compound analysis

Acetaminophen ND 0.004 e 0.003 e ND ND ND ND ND 0.00Caffeine ND .015 ND ND ND 0.015 0.003 0.0043 .031,7-Dimethylxanthine ND ND ND ND ND ND .012 ND ND Thiabendazole 0.0003 ND ND 0.0004 ND ND ND ND ND 
30 Fecal Bacteria in Streams and Land-Applied Poultry Litter in the Upper Shoal Creek Basin, Southwestern Missouri, 2001–2002

of 0.68 μg/L), which is a common disinfectant used in 

domestic and industrial applications. Phenol is used as 

a disinfectant in the poultry industry in the area and 

also was detected in samples from Dilbeck Spring and 

Shoal Creek at site 3 by Schumacher (2001). However 

small concentrations of phenol (0.22 and 0.26 μg/L) 

were detected in the blank samples submitted with 

these samples.

The variety of wastewater and pharmaceutical 

compounds detected, and their relatively low concentrations, provides indirect evidence of a variety of 

human or industrial and animal waste sources to 

streams in the study area. Interpretation of these data is 

complicated by the small number of samples collected 

and analyzed because of their relatively high cost compared to other analyses, such as indicator bacteria. In 

addition, the potential for substantial laboratory error 

and sample contamination is greatly increased at the 

small concentrations detected. For example, during the 

July 2001 dye-trace study the sample from site 2b contained one detection of these compounds, despite the 

detection of five compounds upstream at site 2a and 

downstream at site 2c. Dilution and dispersion unlikely 

would decrease concentrations detected at site 2a to 

less than detection at site 2b because the discharge at 

sites 2a and 2b was essentially the same and the peak 

dye concentration at site 2b was more than 50 percent 

of that at site 2a. The detection of only one compound 

in the sample from site 2b was unusual and suggests 

that a higher sampling frequency was needed to confirm the detected concentrations; care should be exercised when interpreting the detection of trace 

concentrations of these compounds.

Genetic Identification of Fecal Bacteria

A total of 48 E. coli isolates from 5 sites (2, 2a, 

2b, 3, and 11) sampled during the July 2001 dye-trace 

study were evaluated using the rep-PCR method at the 

University of Missouri-Columbia Department of Veterinary Pathobiology. DNA-fragmentation patterns from 

these isolates were compared to the University library 

of known host patterns using a discriminate analyses 

technique. Results of the analysis yielded the presumptive source of each individual E. coli isolate. An initial 

comparison (two-class problem) was done to determine 

if the isolate patterns from the water samples were 

human or nonhuman. Twenty-five of the 48 patterns 

(52 percent) matched non-human patterns and 6 patterns (13 percent) matched human patterns. Seventeen 

of the patterns (35 percent) were not matched. Using 

discriminate analysis, matching of a pattern from an 

unknown isolate was defined to occur when the pattern 

was matched to known patterns of a particular source 

group in the database at a probability of greater than or 

equal to 70 percent.

Results of a second comparison indicated that E. 

coli in the water samples collected during the July 2001 

dye-trace study were from a variety of sources with cattle, horses, and humans being the most common. The 

second five-class comparison (cattle, chicken, horse, 

human, and turkey) was done only on those patterns 

presumptively identified as either human (n=6) or nonhuman (n=25) in the first comparison. About 80 percent of the E. coli patterns isolated from sites 2 and 3 

were matched to cattle and horses (fig. 15) with 44 percent of the patterns from these sites being matched to 

cattle. This match was consistent with observations of 

large numbers of cattle grazing in fields upstream from 

sites 2 and 3 and the detection of thiabendazole in water 

samples from sites 2 and 2a. Horses are scattered 
Occurrence and Survival of Fecal Bacteria in Land-Applied Poultry Litter 31

throughout the basin but not in as large of a density as 

cattle. Large quantities of poultry litter were being 

applied to fields along the study reach and poultry litter 

was observed along roads and low-water crossings; 

however, the small percentage of isolates matched to 

poultry indicated that measurable amounts of this litter 

had not entered the stream at the time of the dye-trace 

study. Results of DNA-fingerprinting from a sample 

collected at site 3 by the FAPRI on August 27, 2002, 

indicated that 7 of 13 isolates (54 percent) were 

matched to cattle, and only 1 isolate was matched to 

humans (Claire Baffaut, written commun., 2002). 

Results of DNA-fingerprinting of the FAPRI sample 

support the results of the detailed seepage study, which 

identified a large influx of fecal coliform and E. coli to 

Shoal Creek from an area of intense cattle grazing and 

feeding upstream from site 3.

Humans appeared to be an important source of E. 

coli at site 2a, where about 50 percent of the patterns 

were matched to human sources. The presence of 

human patterns at site 2a was consistent with the detection of several wastewater organic compounds, including caffeine, in the July 2001 water sample from this 

site. About 20 percent of the patterns from site 3 were 

matched to humans, which was consistent with the 

detection of triclosan in the July 2001 water sample 

from this site. However, humans accounted for less 

than 10 percent of the patterns in the August 27, 2002, 

water sample collected by the FAPRI at site 3. Pogue 

Creek at site 11 was the only site where an appreciable 

number of the isolates (about 50 percent) were matched 

to poultry. The detection of poultry patterns at site 11 

was consistent with a large density of commercial turkey operations upstream from this site and previous 

DNA-fingerprinting, which indicated a predominance 

of turkey patterns in some water samples from Pogue 

Creek (Schumacher, 2001). In addition, Schumacher 

(2001) identified tylosin, an antibiotic used to treat respiratory infections in poultry, in a sample from Pogue 

Creek.

A summary of the DNA-fingerprinting indicated 

that cattle are an important source (about 50 percent) of 

E. coli at the MDNR sampling site (site 3) on Shoal 

Creek. The identification of cattle patterns at site 3 was 

consistent with the results of the August 2002 seepage 

study, which indicated large influxes of fecal bacteria 

from an area of intense cattle activity. However, 

because of the small number of samples and E. coli isolates examined in this study, absolute identification of 

the source of all water-borne E. coli in the study reach 

cannot be made. A small number of patterns from 

known wildlife in the region, such as turkeys, deer, and 

raccoon, have been examined, and these animals also 

may contribute to E. coli detected in Shoal Creek. In 

addition, most of the cattle isolates in the reference 

library are from outside the study area and this may 

cause some cattle isolates in Shoal Creek to be unidentified and classified as unknown origin. A detailed discussion of some of the limitations of DNAfingerprinting of E. coli isolates from the Shoal Creek 

Basin is given in Schumacher (2001).

OCCURRENCE AND SURVIVAL OF 

FECAL BACTERIA IN LAND-APPLIED 

POULTRY LITTER

Fecal bacteria were detected in all of the poultry 

litter samples examined during the study described in 

this report with concentrations varying nearly three 

orders of magnitude. Concentrations of fecal coliform 

ranged from 73 col/g in the broiler litter compost 

applied at test plot P-3 to 47,000 col/g in the turkey litter applied at test plot P-2 (table 6). Concentrations of 

E. coli generally were similar and ranged from 570 

col/g in broiler litter compost to 45,000 col/g in turkey 

litter. The concentrations of fecal coliform in poultry 

litter samples measured in this study were comparable 

to concentrations reported by Hartel and others (2000). 

Hartel and others (2000) measured fecal coliform bacteria in 10 of 20 samples of fresh poultry litter with concentrations ranging from 103.06 to 106.66 col/g. The 

small fecal bacteria density in the broiler litter compost 

as compared to the turkey litter probably was caused by 

the poor survival of fecal bacteria at the temperatures 

that can exist in compost piles. Compost used at test 

plot P-3 was removed from a covered stacking shed 

with a front-end loader immediately before application 

to the test plot. Temperatures measured by the NRCS 

inside the compost pile immediately before application 

ranged from 120 to 125 °F. The pile had previously 

reached 150 °F and was in the process of cooling down 

(Kari Rhoades, Natural Resources Conservation Service, written commun., 2001). In a comparison of fecal 

coliform survival in fresh and stacked broiler litter, 

Hartel and others (2000) concluded that the rapid 

decrease in fecal coliform concentrations from greater 

than 107

 col/g to less than 10 col/g within 8 days in 

stacked broiler litter was the result of spontaneous heating within the piles and that bacteria survival was 
32 Fecal Bacteria in Streams and Land-Applied Poultry Litter in the Upper Shoal Creek Basin, Southwestern Missouri, 2001–2002

inversely related to temperature. Jeffrey and others 

(2001) also noted that increased temperature was an 

important factor in the poor survival of fecal bacteria in 

stacked broiler litter. The high temperatures in test plot 

P-3 broiler litter compost pile were sufficient to kill 

fecal bacteria, and the small concentrations of fecal 

coliform and E. coli that were measured at the time of 

application may be the result of small pockets of bacteria surviving in cooler parts of the pile or contamination 

of the pile by rodent feces or the manure spreader used 

to apply the litter compost to the test plot.

An important finding of the test plots was that 

fecal bacteria in poultry litter can survive in fields for 

several weeks after the application of the litter to the 

land surface. Densities of fecal coliform and E. coli in 

slurry-water samples from the test plots where litter 

from turkey (test plots P-1 and P-2) or broiler barns 

(test plot P-4) was applied were significantly larger 

after the application of litter than before litter application (tables 7, 8). Excluding the broiler litter compost, 

median densities of fecal coliform and E. coli at each 

test plot increased from less than 60 col/100 mL before 

litter application to at least 40,000 col/100 mL immediately after litter application (tables 7, 8). The largest 

increases were at test plot P-4 (broiler litter) where 

median fecal coliform and E. coli densities immediately after application were 420,000 and 290,000 

col/100 mL. Densities of fecal coliform and E. coli at 

the test plots decreased in a generally exponential manner with increasing time after application (fig. 16). 

Estimated decay rates ranged from 0.085 to 0.185 d-1

(per day) for fecal coliform to between 0.100 and 

0.250 d-1 for E. coli (fig. 16). These values were comparable to the range of die-off rates (0.11 to 0.37 d-1 for 

fecal coliform to 0.17 to 0.94 d-1 for E. coli) measured 

by Teague and Vendrell (1995) in laboratory studies 

using soil amended with broiler litter from Arkansas. 

Median fecal coliform and E. coli densities remained 

significantly larger than the initial densities for 4 to 8 

weeks after application. The larger fecal bacteria densities measured after litter application indicated that 

bacteria in the litter applied to the land surface were 

surviving despite the apparent harsh environmental 

Table 6. Description of litter application test plots and initial fecal coliform and Escherichia coli densities in 

poultry litter

[--, no data; E. coli, Escherichia coli]

Description Unit

Test plot

P-1 P-2 P-3 P-4

Litter type -- Turkey litter Turkey litter Broiler litter 

compost

Broiler litter

Start date -- 05/23/01 05/07/02 08/10/01 04/19/02

End date -- 07/03/01 07/02/02 08/31/01 07/03/02

Plot size Feet 302 x 75 302 x 75 180 x 30 200 x 80

Plot area Square feet 22,650 22,650 5,400 16,000

Acres .5 .5 .1 .4

Litter condition -- Dry Dry Damp-wet Damp

Application rate

Mat 1 Tons per acre 2.1 4.2 7.7 4.2

Mat 2 Tons per acre 3.5 3.4 16.5 3.4

Mat 3 Tons per acre 1.7 -- -- --

Average rate Tons per acre 2.4 3.8 12.1 3.8

Vegetation -- Fescue/hay Fescue/hay Mixed grasses Fescue/hay

Initial fecal coliform density, 

in litter

Colonies per gram 

(dry weight)

17,000 47,000 73 45,000

Initial E. coli density, 

in litter

Colonies per gram 

(dry weight)

17,000 45,000 570 44,000
Occurrence and Survival of Fecal Bacteria in Land-Applied Poultry Litter 33

Table 7. Densities of fecal coliform bacteria in slurry-water samples from test plots of land-applied poultry litter[<, less than; --, no data]

Date Time

Elapsed time 

since application 

(days)

Test plot subsample location

Control 1 Control 2

Sum

a Probability value from analysis of variance on ranked data and Tukeys multiple comparison test comparing average rank to initial conditions before application of poultry litter. Probabili

significant difference from the initial concentration.

s1 s2 s3 s4 s5 s6 s7 Average Me

Turkey litter (Test plot P-1)

05/23/01 1130 0 <10 <10 <10 30 <10 69 80 -- -- 31 05/23/01 1430 .13 26,000 12,000 85,000 20,000 42,000 58,000 57,000 -- -- 43,000 4205/24/01 1200 1.02 48,000 5,200 98,000 32,000 12,000 220,000 64,000 -- -- 68,000 4805/29/01 1100 5.98 136,000 3,400 10,000 12,000 1,700 90,000 42,000 -- -- 42,000 1206/05/01 1200 13.02 5,200 220,000 4,500 2,600 4,600 4,700 4,900 -- -- 35,000 406/12/01 1130 20.00 10 50 160 <20 150 1,400 400 -- -- 362 06/19/01 1130 27.00 940 130 560 4,300 200 910 420 -- -- 1,100 06/26/01 1200 34.02 10 240 10 460 60 10 440 -- -- 180 07/03/01 1130 41.00 44 12 10 40 24 76 40 -- -- 35 

Turkey litter (Test plot P-2)

05/07/02 1030 0 26 5 10 10 20 10 10 10 -- 13 05/07/02 1200 .06 74,000 110,000 170,000 100,000 500,000 290,000 92,000 <1,000 -- 191,000 11005/14/02 1020 6.99 380,000 280,000 110,000 23,000 7,300 140,000 72,000 1,000 -- 140,000 11005/29/02 1030 22.00 15,000 27,000 86,000 200,000 16,000 7,000 10,000 11,000 -- 52,000 1606/13/02 1730 37.29 <330 2,700 1,300 3,300 1,300 11,300 8,000 13,000 -- 4,000 207/02/02 1340 56.13 60 1,900 600 100 1,600 200 1,300 1,800 -- 820 

Broiler litter compost (Test plot P-3)

08/10/01 1445 0 19,000 95 15 24 100 10 900 180 7,900 2,900 08/10/01 1545 .04 2,200 1,900 100 200 600 300 890 -- -- 880 08/11/01 1400 .97 130 210 1,900 100 9,100 180 210 130 2,100 1,700 08/15/01 1030 4.82 20 3,000 2,500 500 20 1,700 8,300 20 9,100 2,300 108/31/01 1310 20.93 4,900 5,300 6,000 6,000 8,700 6,000 -- 4,700 -- 6,200 6

Broiler litter (Test plot P-4)

04/19/02 1300 0 31,000 65 5 2,600 29 5 5 710 -- 4,800 04/19/02 1500 .08 245,000 930,000 250,000 540,000 100,000 1,000,000 420,000 1,200 -- 500,000 42004/20/02 1130 .94 220,000 240,000 840,000 110,000 850,000 190,000 190,000 730 -- 400,000 22004/26/02 1000 6.88 <1,000 21,000 370,000 36,000 67,000 110,000 370,000 <1,000 -- 140,000 6705/06/02 1730 17.19 3,000 57,000 42,000 160,000 2,000 110,000 37,000 <1,000 -- 59,000 4205/22/02 1100 32.92 14,000 2,000 2,000 14,000 220,000 15,000 140,000 30,000 -- 58,000 1406/05/02 1215 46.97 30,000 19,000 6,100 30,000 19,000 2,500 2,100 27 -- 16,000 1907/03/01 1000 74.03 30,000 19,000 6,100 30,000 19,000 2,500 2,100 34 -- 16,000 19
34 Fecal Bacteria in Streams and Land-Applied Poultry Litter in the Upper Shoal Creek Basin, Southwestern Missouri, 2001–2002 Table 8. Densities of Escherichia coli bacteria in slurry-water samples from test plots of land-applied poultry waste [nd, not detected because of overgrowth on plate; --, no data; <, less than; > greater than] Date Time Elapsed time since application (days) Test plot subsample location Control 1 Control 2 Summ

a Probability value from analysis of variance on ranked data and Tukeys multiple comparison test comparing average rank to initial conditions before application of poultry litter. Probab

significant difference from the initial concentration.

s1 s2 s3 s4 s5 s6 s7 Average Media

Turkey litter (Test plot P-1)

05/23/01 1130 0 nd nd nd 30 nd nd 20 -- -- 25 05/23/01 1430 .13 27,000 25,000 110,000 2,700 47,000 53,000 44,000 -- -- 44,000 44,005/24/01 1200 1.02 400,000 9,000 85,000 21,000 8,900 300,000 65,000 -- -- 130,000 65,005/29/01 1100 5.98 500,000 3,000 2,200 27,000 2,400 68,000 134,000 -- -- 100,000 27,006/05/01 1200 13.02 2,000 410,000 3,500 2,400 6,500 8,000 3,800 -- -- 62,000 3,806/12/01 1130 20.00 40 200 20 -- 60 1,000 360 -- -- 280 106/19/01 1130 27.00 456 130 200 10,000 -- 2,600 700 -- -- 2,300 506/26/01 1200 34.02 nd 60 nd 460 40 400 420 -- -- 280 407/03/01 1130 41.00 nd 64 nd nd nd 25 nd -- -- 45 

Turkey litter (Test plot P-2)

05/07/02 1030 0 200 <5 <10 <10 <10 <10 <10 <10 -- 36 05/07/02 1200 .06 99,000 60,000 150,000 77,000 330,000 200,000 79,000 1,000 -- 140,000 99,005/14/02 1020 6.99 340,000 200,000 80,000 18,000 14,000 250,000 96,000 1,000 -- 140,000 96,005/29/02 1030 22.00 16,000 24,000 92,000 100,000 14,000 3,600 10,000 44,000 -- 37,000 16,006/13/02 1730 37.29 <330 330 670 3,000 330 9,300 1,800 6,000 -- 2,300 607/02/02 1340 56.13 nd nd nd 20 6,000 20 20 1,600 -- 1,500 

Broiler litter compost (Test plot P-3)

08/10/01 1445 0 19,000 5 100 5 19 130 500 300 1,000 2,800 108/10/01 1545 .04 100 5,100 100 300 100 100 100 -- -- 840 108/11/01 1400 .97 20 700 20 20 100 900 20 14 700 250 08/15/01 1030 4.82 20 700 20 20 100 900 20 20 5,100 250 08/31/01 1310 20.93 14 14 14 14 14 6,000 6,000 19,000 24,000 1,700 

Broiler litter (Test plot P-4)

04/19/02 1300 0 25,000 68 55 1,400 25 5 5 600 -- 3,800 04/19/02 1500 .08 150,000 590,000 290,000 200,000 140,000 460,000 490,000 2,500 -- 330,000 290,004/20/02 1130 .94 82,000 220,000 880,000 200,000 710,000 194,000 54,000 1,100 -- 330,000 200,004/26/02 1000 6.88 1,000 21,000 370,000 36,000 67,000 110,000 370,000 1,000 -- 139,000 67,005/06/02 1730 17.19 3,000 57,000 42,000 160,000 2,000 110,000 37,000 1,000 -- 59,000 42,005/22/02 1100 32.92 1,500 3,500 10,000 51,000 500 200,000 40,000 15,000 -- 44,000 10,006/05/02 1215 46.97 670 2,700 3,000 8,000 4,000 4,700 <330 <330 -- 3,300 3,007/03/01 1000 74.03 10,000 460 >30,000 10,000 28,000 16,000 1,000 30,000 -- 14,000 10,0
Occurrence and Survival of Fecal Bacteria in Land-Applied Poultry Litter 35

3

0

1

2

3

0

1

2

3

0

1

2

3

0

1

2

DAILY PRECIPITATION, IN INCHES

MAXIMUM DAILY AIR TEMPERATURE, IN DEGREES FAHRENHEIT

100

40

60

80

100

40

60

80

100

40

60

80

100

40

60

80

0 10 20 30 40 50 60

P-3

0

1,000

2,000

3,000

4,000

5,000

6,000

7,000

0 10 20 30 40 50 60

P-3

0

50

100

150

200

250

P-4

0

50,000

100,000

150,000

200,000

250,000

300,000

y=290,000e-0.1016x

r2=0.95

P-2

0

20,000

40,000

60,000

80,000

100,000

120,000

140,000

160,000

y=134,000e-0.0895x

r2=0.98

y=44,000e-0.2456x

r2=0.86

P-4

0

50,000

100,000

150,000

200,000

250,000

300,000

350,000

400,000

450,000

y=415,000e-0.085x

r2=0.59

P-2

0

10,000

20,000

30,000

40,000

50,000

60,000

70,000

80,000

90,000

100,000

y=99,000e-0.1389x

r2=0.95

y=42,000e-0.185x

r2=0.92

P-1

0

10,000

20,000

30,000

40,000

50,000

60,000

P-1

0

10,000

20,000

30,000

40,000

50,000

60,000

70,000

MEDIAN FECAL COLIFORM DENSITY, IN COLONIES PER 100 MILLILITERS

TIME, IN DAYS, SINCE LITTER APPLICATION MEDIAN ESCHERICHIA COLI DENSITY, IN COLONIES PER 100 MILLILITERS

Figure 16. Median densities of fecal coliform and Escherichia coli bacteria, total daily precipitation,

and mean daily air temperature at the poultry litter field plots.

Fecal Coliform Escherichia Coli

EXPLANATION

PRECIPITATION

AIR TEMPERATURE

SAMPLE
36 Fecal Bacteria in Streams and Land-Applied Poultry Litter in the Upper Shoal Creek Basin, Southwestern Missouri, 2001–2002

conditions at the land surface. Bacteria from test plot 

P-1 had the shortest survival times (about 4 weeks) and 

those from test plot P-2 had the largest survival times (6 

to 8 weeks). Fecal bacteria densities at the broiler litter 

compost test plot (P-3) did not decrease significantly 

after the application of the compost and generally 

tended to increase with increasing time (fig. 16) 

because of exhaust dust from a nearby poultry barn.

While generally replicating actual conditions on 

the fields, the uncontrolled conditions of the test plots 

created variability in the data. For example, the erratic 

fecal bacteria densities in the control and test plot samples from broiler litter compost test plot (P-3) probably 

were related to the poor location chosen for the test plot 

and the near absence of fecal bacteria in the compost. 

Because of a lack of access to nearby fields, test plot P3 was located about 60 ft north of a broiler house. 

Although the house was empty when the test began, litter from the house was being removed from the house 

during the first 2 days that test plot P-3 was monitored. 

About 3 weeks after monitoring began, a flock of broilers was moved into the house, and fresh dust and feathers were observed on the test plot near the exhaust fans 

on the north side of the house. Sub-sample locations s6, 

s7, and control 1 and control 2 were located in the 

vicinity of the exhaust fans, and E. coli densities at 

these locations increased during the test (table 8). Fecal 

bacteria densities in control samples at test plot P-4 

also were variable. Sometime after monitoring of test 

plot P-4 began, several cows entered the field where 

test plot P-4 was located. Fresh cow manure was 

observed in the vicinity of the control site during the 

May 22, 2002, sampling visit, and fecal bacteria densities in control samples collected that day were larger 

than expected (tables 7, 8).

The presence of significant densities of fecal 

bacteria at the test plots following the land application 

of poultry litter (test plots P-1, P-2, and P-4) was consistent with the published literature. Edwards and 

Daniel (1994) detected densities in fecal coliform as 

large as about 106.4 col/100 mL in runoff from plots 

where poultry litter had been applied. Coyne and 

Blevins (1995) also reported increased fecal coliform 

densities in runoff from plots amended with poultry litter. Increased total coliform densities [from 0 to 33,000 

col/mL (colonies per milliliter)] were observed in runoff from field plots treated with poultry litter (Giddens 

and Barnett, 1980). Unlike the study described in this 

report none of the published studies, however, 

attempted to monitor the survival of the fecal bacteria 

on the fields for an extended time. 

The apparent survival of significant numbers of 

fecal bacteria on fields where poultry litter has been 

applied indicated that runoff from fields where this litter is applied is a potential source of fecal bacteria to 

vicinity streams for many weeks following application. 

The finding is consistent with the results of previous 

DNA-fingerprinting reported by Schumacher (2001), 

which identified poultry patterns in E. coli isolates 

from water samples collected from Shoal Creek and its 

tributaries, even during the summer months when litter 

application generally was decreased. The potential for 

land application of poultry litter to affect fecal bacteria 

densities in Shoal Creek and its tributaries is compounded by the fact that litter is removed from most 

poultry barns and spread to fields during the spring, a 

time when the potential for runoff from spring thunderstorms probably is the greatest. 

SUMMARY AND CONCLUSIONS

Results of the study described in this report indicate that densities of fecal coliform bacteria along a 

5.7-mi (mile) reach of Shoal Creek between State 

Highway 97 (site 3) and State Highway W (site 2) 

exceeded the Missouri Department of Natural 

Resources (MDNR) standard of 200 col/100 mL (colonies per 100 milliliter). Fecal coliform densities above 

the MDNR standard also were detected in two tributaries, Pogue Creek and Joyce Creek, along this reach of 

Shoal Creek. A combination of techniques was used in 

this study to determine the possible sources of the 

increased fecal coliform densities along this reach of 

Shoal Creek, including a determination of the survival 

or “die-off” rates of fecal coliform and Escherichia coli

(E. coli) in the stream, a dye-trace study to determine 

travel times and dispersion characteristics along this 

stream reach, a detailed seepage study and water-quality sampling to locate specific sources of fecal bacteria 

to the stream, and a field study to monitor the quantity 

and survival of fecal bacteria in land applied poultry litter. A network of five sites on this reach of Shoal Creek 

(sites 2, 2a, 2b, 2c, and 3) was monitored during this 

study, in addition to a downstream site (site 4), and two 

tributaries—Pogue Creek and Joyce Creek.

Measurements of fecal bacteria survival in Shoal 

Creek during July 2001 indicated that about 8 percent 

of fecal coliform and E. coli bacteria decay each hour 

with an average first-order decay constant of 0.084 h-1
Summary and Conclusions 37

(per hour). Results of a dye-trace study indicate that at 

low base-flow conditions, the travel time in Shoal 

Creek between State Highway W (site 2) and the 

MDNR sampling site (site 3) about 5.7-mi downstream 

at State Highway 97 is about 26 hours. Substantial dispersion and dilution of the dye peak occurred between 

the injection site (site 2) and site 2c (about 4.1 mi 

downstream) where there are several inflows, long 

pools, and channel meanders; however, minimal dispersion and dilution of the dye peak occurred between 

site 2c and the MDNR sampling site (site 3) about 1.6-

mi downstream.

Measurements of fecal bacteria densities for 36 

hours during the July 2001 dye-trace study indicated 

that samples from site 2a contained the largest average 

densities of fecal coliform (2,600 col/100 mL) and E. 

coli (2,200 col/100 mL) detected in the main stem of 

Shoal Creek. Average densities of fecal coliform and E. 

coli decreased to less than or equal to 1,400 col/100 mL 

downstream at site 2b, and further decreased to less 

than 500 col/100 mL at site 2c, but increased significantly at site 3. At site 3 the average fecal coliform and 

E. coli densities were 2,100 and 1,400 col/100 mL. The 

largest bacteria densities were detected in two samples 

from the upper reaches of Pogue Creek, where densities of fecal coliform and E. coli exceeded 4,000 

col/100 mL. Densities of fecal bacteria at sampling 

sites along the main stem of Shoal Creek exhibited 

sinusoidal variability with time, with bacterial densities 

at sites 2, 2b, and 2c generally being in phase with each 

other, but out of phase with bacteria densities at sites 2a 

and 3. The variability in the bacteria densities with time 

could not be attributed to simple advection and dispersion because the patterns at successive downstream 

sites were not predictable based solely on travel time 

between the sites. Large concentrations of fecal bacteria were not detected in streambed-sediment samples 

from Shoal Creek, and re-suspension of these sediments during runoff probably is not a large source of 

fecal bacteria to the water column.

Results of a mass balance of bacteria densities 

indicated that substantial amounts of fecal bacteria 

enter Shoal Creek between sites 2 and 2a and between 

sites 2c and the MDNR sampling site (site 3). Results 

of a detailed seepage study upstream from site 3 indicated that cattle likely are a large source of the 

increased fecal bacteria densities at site 3. Substantial 

increases in fecal bacteria densities were observed 

downstream from areas where cattle were fed along the 

stream bank or where cattle were wading in the stream 

and congregating under trees along the stream bank. 

Densities of fecal coliform and E. coli increased from 

100 and 40 col/100 mL at site 2c to 1,100 and 580 

col/100 mL downstream from an area of intense cattle 

activity immediately upstream from the MDNR sampling site (site 3).

Analysis of selected water samples for a suite of 

wastewater organic compounds and pharmaceutical 

compounds detected small (less than 1.5 micrograms 

per liter) concentrations of seven wastewater compounds and four pharmaceutical compounds in one or 

more samples. The most frequently detected compounds were caffeine (eight detections), cholesterol, 

and acetaminophen (three detections each). The antimicrobial agent triclosan was detected at sites 2b and 3, 

and the common cattle anthelmintic thiabendazole was 

detected at sites 2 and 2a. The detection of organic 

compounds associated with human wastewater and thiabendazole indicates that some human and animal 

wastes probably are entering Shoal Creek. 

Results of deoxyribonucleic acid (DNA) fingerprinting of E. coli isolates extracted from water samples collected from Shoal Creek and its tributaries 

during the July 2001 dye-trace study indicated that cattle, horses, and humans were the predominate sources 

of fecal bacteria in the stream. About 50 percent of the 

E. coli isolates from site 2a were matched to a human 

source, which was consistent with the detection of several wastewater organic compounds, including caffeine, at this site. About 50 percent of the E. coli

isolates from Pogue Creek were matched to poultry, 

which was consistent with a large density of poultry 

barns in its basin. DNA-fingerprinting indicated that 

cattle are an important source of E. coli (about 50 percent) at the MDNR site (site 3), which is consistent 

with substantial increases of fecal bacteria densities 

immediately downstream from areas where cattle congregated in and along the stream bank immediately 

upstream from this site. 

Results of field test plots indicated that substantial numbers of fecal bacteria present in poultry litter 

can survive in fields for up to 8 weeks after the application of the litter to the land surface. Experiments were 

done using broiler litter, turkey litter, and composted 

broiler litter. Median densities of fecal coliform and E. 

coli in water samples from fields increased from less 

than 60 col/100 mL before the application of turkey and 

broiler litter to as large as 420,000 and 290,000 col/100 

mL after the application of litter. Bacteria densities in 

the test plots generally decreased in an exponential 
38 Fecal Bacteria in Streams and Land-Applied Poultry Litter in the Upper Shoal Creek Basin, Southwestern Missouri, 2001–2002

manner over time, with decay rates ranging from 0.085 

to 0.185 d-1 (per day) for fecal coliform to between 

0.100 and 0.250 d-1 for E. coli. However, fecal bacteria 

densities at the broiler litter compost test plot did not 

vary significantly after the application. The apparent 

survival of substantial numbers of fecal bacteria on 

fields where poultry litter has been applied indicated 

that runoff from fields where this litter is applied is a 

potential source of fecal bacteria to vicinity streams for 

many weeks following application.

REFERENCES

Coyne, M.S., and Blevins, R.L., 1995, Fecal bacteria in 

surface runoff from poultry-manured fields, in

Animal waste and the land-water interface, K. 

Steele, ed., Lewis Publishers, New York, p. 77–87.

Craig, D.L., Fallowfield, H.J., and Cromar, N.J., 2002, 

Comparison of decay rates of fecal indicator 

organisms in recreational coastal water and sediment: Water Science and Technology, v. 2, no. 3, p. 

131–138.

Davis, C.M., Long, J.A., Donald, H.M., and Ashbolt, 

N.J., 1995, Survival of fecal microorganisms in 

marine and freshwater sediments: Applied and 

Environmental Microbiology, v. 53, no. 6, p. 633–

638.

Dombek, P.E., Johnson, L.K., Zimmerley, S.T., and 

Sadowsky, M.J., 2000, Use of repetitive DNA 

sequences and the PCR to differentiate Escherichia coli isolates from human and animal sources: 

Applied and Environmental Microbiology, v. 66, 

p. 2,572–2,577.

Doyle, J.D., Runnicliff, Brock, Kramer, Rick, Kuehl, 

Robert, and Brickler, S.K., 1992, Instability of 

fecal coliform populations in waters and bottom 

sediments at recreational beaches in Arizona: 

Water Research, v. 26, p. 979–988.

Edwards, D.R., and Daniel, T.C., 1994, A comparison 

of runoff quality effects of organic and inorganic 

fertilizers applied to fescuegrass plots: Water 

Resources Bulletin, v. 30, no. 1, p. 35–41.

Giddens, Joel, and Barnett, A.P., 1980, Soil loss and 

microbiological quality of runoff from land treated 

with poultry litter: Journal of Environmental Quality, v. 9, no. 3, p. 518–520.

Hartel, P.G., Segars, W.I., Summer, J.D., Collins, J.V., 

Phillips, A.T., and Whittle, E., 2000, Survival of 

fecal coliforms in fresh and stacked broiler litter: 

Journal of Applied Poultry Research, v. 9, p. 505–

512.

Jeffrey, J.S., Lazano, Joan, Walton, Elizabeth, and 

Tonooka, Karen, 2001, Inactivation of bacteria in 

stacked poultry litter: U.S. Environmental Protection Agency Report of Investigations, accessed 

January 30, 2003, at URL 

http://www.vmtrc.ucdavis.edu/poultry/pdfvers.pdf.

Koplin, D.W., Furlong, E.T., Meyer, M.T., Thurman, 

E.M., Zaugg, S.D., Barber, L.B., and Buxton, H.T., 

2002, Pharmaceuticals, hormones, and other 

organic wastewater contaminants in U.S. streams, 

1999–2000—A national reconnaissance: Environmental Science and Technology, v. 36, no. 6, p. 

1,202–1,211.

Mezrioui, N., Baleux, B., and Troussellier, M., 1995, A 

microcosm study of the survival of Escherichia 

coli and Salmonella typhimurium in brackish 

water: Water Research, v. 29, no. 2, p. 459–465.

Missouri Department of Natural Resources, 1996, 

Rules of Department of Natural Resources, Chapter 7, Water Quality, Title 10 CSR 20-7.031 Waterquality standards: Jefferson City, Clean Water 

Commission, 100 p.

———2000, Rules of Department of Natural 

Resources, Chapter 7, Water Quality, Title 10 CSR 

20-7.031 Water-quality standards: Jefferson City, 

Clean Water Commission, accessed January 2000, 

at URL 

http://www.dnr.state.mo.us.deq/pmnr99_02.htm.

Mugel, D.N., 2002, Ground-water quality and effects 

of poultry confined animal feeding operations on 

shallow ground water, upper Shoal Creek Basin, 

southwest Missouri, 2000: U.S. Geological Survey 

Water-Resources Investigations Report 02–4125, 

41 p.

Myers, D.N., Koltun, G.F., and Francy, D.S., 1998, 

Effects of hydrologic, biological, and environmental processes on sources and concentrations of 

fecal bacteria in the Cuyahoga River, with implications for management of recreational waters in 

Summit and Cuyahoga Counties, Ohio: U.S. Geological Survey Water-Resources Investigations 

Report 98–4089, 45 p.

National Oceanic and Atmospheric Administration, 

2001, Climatologic data annual summary, Missouri: Asheville, North Carolina, National Climatic Data Center.
References 39

———2002, Climatologic data annual monthly summary, Missouri: Asheville, North Carolina, 

National Climatic Data Center.

Ozkanca, R., and Flint, K.P., 1997, Relationship 

between respiratory enzymes and survival of 

Escherichia coli under starvation stress in lake 

water: Journal of Applied Microbiology, v. 82, p. 

301–309.

Rozak, D.B., and Colwell, R.R., 1987, Survival strategies of bacteria in natural environment: Microbiological Reviews, v. 51, p. 365–379.

Schumacher, J.G., 2001, Water quality in the upper 

Shoal Creek Basin, southwestern Missouri, 1999–

2000: U.S. Geological Survey Water-Resources 

Investigations Report 01–4181, 60 p.

Sinton, L.W., Finlay, R.K., and Lynch, P.A., 1999, Sunlight inactivation of fecal bacteriophages and bacteria in sewage-polluted seawater: Applied and 

Environmental Microbiology, v. 65, no. 8, p. 

3,605–3,613.

Teague, K.A., and Vendrell, P.F., 1995, Survival of 

fecal contamination indicator organisms in soil: 

Fayetteville, Arkansas Water Resources Center, 

report 173, 28 p.

Thompson, T.L., 1986, Paleozoic succession in Missouri, part 4, Mississippian System: Missouri 

Department of Natural Resources, Geological Survey and Resource Assessment (formerly known as 

Division of Geology and Land Survey), Report of 

Investigation No. 70, 182 p.

U.S. Bureau of the Census, 2000, Population Estimates 

Program, Population Division: accessed January 

30, 2003, at URL 

http://www.sos.state.mo.us/library/reference/census/.

Wilde, F.D., and Radtke, D.B., 1998, eds., National 

field manual for the collection of water quality 

data: U.S. Geological Survey Techniques of 

Water-Resources Investigations, book 9, chap. A6, 

variously paginated.

Wilson, J.F., Jr., Cobb, E.D., and Kilpatrick, F.A., 1986, 

Fluorometric procedures for dye tracing: U.S. 

Geological Survey Techniques of WaterResources Investigations, book 3, chap. A12, 34 p.

Zaugg, S.D., Smith, S.G., Schroeder, M.P., Barber, 

L.B., and Burkhardt, M.R., 2002, Methods of analysis by the U.S. Geological Survey National Water 

Quality Laboratory—Determination of wastewater compounds by polystyrene-divinylbenzene 

solid-phase extraction and capillary-column gas 

chromatography/mass spectrometry: U.S. Geological Survey Water-Resources Investigations 

Report 01–4186, 37 p.