2. Background

2.1 Basin Conditions
Contact recreation (REC-1) is the primary waterway use that is affected by the presence of high concentrations of fecal organisms in the Russian River and its tributaries. The Basin Plan describes the numeric standard for fecal coliform bacteria as: “Median 30-day levels (based on a minimum of 5 samples/30 days) should not exceed 50 MPN/100 ml and that no more than 10% of those samples should exceed 400 MPN/100 ml.” The California Department of Public Health (formerly Department of Health Services) has the following guidelines for single samples taken at freshwater beaches: Fecal Coliform <400 MPN/100 ml; Enterococcus <61 MPN/100 ml; E. coli <235 MPN/100 ml. Drinking water quality in the Russian River watershed has not been identified as a beneficial use impaired by fecal bacterial contamination of surface water. However, ground-water used for drinking water can become contaminated by surface waters containing fecal material (Olsen et al., 2002)[1].

The numeric standards for recreational contact must be met be any means available to the Regional Board for waters within the Basin. The Russian River and several major tributaries are used for contact recreation and at certain times of the year, exceed these numeric standards. This resulted in 303(d) listing and initiation of TMDL development for the Russian River main-stem and Santa Rosa Creek.

2.2 Potential Russian River watershed sources

There are several major land-uses and point sources that could contribute fecal matter into tributaries of the Russian River. These include dairy and livestock operations, wastewater treatment facilities, sewer lines, septic systems, municipal area runoff, and manure applications on agricultural fields. Previously-published research has identified all of these sources as potential contributors of fecal material to waterways. These land-uses will serve as inputs at certain times of the year and/or when facilities and best management practices are failing.

Farming involving raising of cows and sheep, and/or application of manure on fields is likely to result in increased fecal bacteria into waterways due to overland flow and poor management of waste material. Many of the sub-watersheds in the southern end of the watershed have agriculture as the largest or one of the largest land-uses in the sub-watershed.

Rural residential development often is accompanied by on-site septic systems that vary in age and efficiency of capture and processing of input material. If and when these systems are over-whelmed or as they age, fecal matter may enter surface and ground waters.

Urban area stormwater runoff can contribute very high loads of fecal bacteria to waterways (Salmore et al., 2006), as can wastewater treatment plant effluent. In Maryland, urban areas are considered the primary contributors to waterway fecal contamination in mixed land-use (agriculture and urban) watersheds (Wickham et al., 2006). In one study in the Southern Appalachians, a stream contaminated with fecal bacteria while running through an urban area, became less contaminated once it ran through National Forest lands (Clinton and Vose, 2006).

2.3 Developing TMDLs

There is existing guidance for TMDL development from the USEPA (citation). This guidance and example TMDLs are instructional for the initial studies phase of TMDL development.

Tomales Bay

In this TMDL, threats from fecal organisms to recreational contact (REC-1 and REC-2) and shellfish harvesting were the basis for the TMDL. Sources of problems included human and domestic animal waste entry into tributaries to the Bay. The detection methods for indicator bacteria were restricted to growth media-based approaches, which quantify the culturable fecal bacteria. Several potential pathogens were examined – Salmonella, coliphage, and E. coli H:O157. Some correlations were made in the background studies based on spatial or temporal proximity of problems (high concentrations) with particular tributaries or storm events. There were fecal bacterial concentration variations by tributary, predominant upstream land-use, and season. Human inputs to the system were thought to be primarily from failing septic systems, municipal runoff, and possibly wastewater treatment plants. Animal inputs to the system were thought to be primarily from domestic animals – grazing, dairies, and equestrian facilities. Hydro-dynamic modeling was conducted to target input tributaries for potential inputs to the Bay violating the SHEL standard. Finally, TMDL implementation was to include continuing E. coli/fecal coliform monitoring with medium spatial resolution (30 sites) and temporal resolution (weekly/monthly and event).

Napa River

In this case, fecal coliform and Enterococci bacteria presented threats to REC-1 and REC-2 uses and were the basis of the TMDL. Sources of problems were much the same as in the Tomales Bay watershed, including exceedance of standards from human and domestic animal sources. Detection was conducted using growth media.
The Kendall Tau statistic was used in correlation analysis to relate wet season E. coli concentrations to various urban area parameters and dry season E. coli to % agriculture. In addition, most of the wet season delivery of fecal bacteria was through surface water pathways and in the dry season through ground-water pathways. Human inputs to the system were determined to be primarily from failing or inadequate septic systems, sewer lines, municipal runoff (thought to be very important), and possibly wastewater treatment plants. Animal inputs were primarily from grazing lands and confined animal feeding operations. The TMDL was based on the REC-1 standard as the use most likely to be impaired.

Charles River, Massachusetts

This TMDL focused on fecal coliform and Enterococcus bacteria in a forested and residential watershed. Tributary watersheds/waterways were rated (e.g., Class A) according to goals for fecal bacterial concentrations. Inputs were thought to be primarily from various human waste disposal mechanisms, urban/storm-water runoff, domestic animals, and wildlife. Upstream areas are more contaminated than downstream and concentrations have generally been declining since 1989. The TMDL included river segment-specific potential causes in dry and wet seasons. Generally, there was a correlation between level of development (pristine to urban/agricultural) and E. coli concentrations. Single family residential areas tended to have higher concentrations than commercial and industrial areas. Finally, wet season concentrations tended to be higher than dry season. Human causes of inputs in the dry season were agriculture, failing septic and sewer systems, and illicit connection of sewer to storm drains. Human inputs in the wet season were domestic animal waste, storm-water runoff, and sewer overflows. Animal causes of inputs were minor inputs from wildlife and some input from domestic animals in the dry season. One statistical analysis in the baseline study was correlation analysis of fecal coliform concentrations and rainfall (using Pearson’s R and Spearman Rank Order Correlation). Current monitoring under this TMDL consists of “gap-filling” and measuring effectiveness of control measures and BMPs. Modeling using MIKE-21 is used to study actual and potential benefits from BMPs.

2.4 Bacterial sampling in waterways

The most commonly used indicator bacteria for fecal matter inputs into the environment are E. coli and Enterococcus sp. The most common sampling procedures, and the ones used in the Russian River watershed, are to take grab samples below the surface of a water-body, briefly store and transport the sample on ice, and grow culturable bacteria in challenging growth conditions in order to isolate the intestinal bacteria E. coli and/or Enterococcus sp. Some studies have sampled other media available for fecal organismal storage and growth, including river-bank soils, benthic sediments, landscape soils, and benthic macro-algae. E. coli and Enterococcus are able to survive and sometimes grow in environmental compartments (e.g., benthic sediments and algae), making their use as a fecal matter indicator more challenging (Anderson et al., 2005; Ishii et al., 2006; Power et al., 2005; Whitman et al., 2003; Whitman et al., 2006). E. coli concentrations can also vary in the same waterbody diurnally (citation) and by depth of sampling (Kleinheinz et al., 2006). Although there are short-comings to using E. coli as an indicator bacterium published in the scientific literature, indicator bacteria E. coli and Enterococcus sp. have been enumerated using the Colilert © and Enterolert © approaches, respectively.

An important study in the region of the Russian River to consider is one conducted by UC Davis and other scientists for the Regional Board (Atwill et al., 2007). In this study, the authors describe appropriate fermentation and chromogenic techniques for enumerating fecal bacteria. They also describe sampling regime considerations that they measured to impact fecal bacterial concentrations. These included a non-linear dependence on

antecedent rainfall, a correlative relationship of benthic fecal bacteria with fine sediments, and a linear relationship with depth of sampling.

2.4 Bacterial identification

Currently, fecal coliform bacteria, Escherichia coli, and Enterococcus sp. concentrations are all used as indicators of fecal matter input. This approach is widely used, but is also regularly criticized in the scientific literature (Anderson et al., 2005; Ishii et al., 2006; Power et al., 2005; Whitman et al., 2003; Whitman et al., 2006) for various reasons.

One critical element to using an indicator bacterium for fecal matter input is to be able to identify the host species for the input in order to manage the input. This is not possible using Colilert © or Enterolert © types of approaches because they are not strain specific. In many studies, this approach is still used and links are made to potential host-animal inputs based on the likely pathway for fecal matter (e,g,. agricultural area runoff vs. septic system).

Most fecal bacterial detection systems (e.g., Colilert ©) depend on the culturability of the bacteria; however, not all viable fecal bacterial cells in the environment are culturable and therefore can’t be detected by conventional methods (Awais et al., 2006).

2.5 Die-off rates and watershed loading

“Typically, conditions favorable to the survival of pathogens in water are lower amounts of light energy, lower salinity, elevated levels of nutrients and organic matter, and lower

temperatures.” (EPA guidance manual)

The rate at which bacteria and other potentially pathogenic micro-organisms die in various environmental conditions is important in understanding the fates and potential sources of these micro-organisms. Microbes living in feces may survive hours to months in the various receiving media (soils, water column, benthic sediments). The faster these microbes die, the less risk they pose in to human health. The slower they die and if they can grow outside host animals (Desmarais et al., 2002; Solo-Gabriele et al., 2000), the greater risk they pose to human health. Oocysts (dormant early life stage) of Cryptosporidium and Giardia lamblia can survive for 2 to 6 months in river water at cold and ambient temperatures (Medema et al., 1997; Adam, 1991; Bingham et al., 1979). Temperature is apparently the major limiting factor for virus and coliform bacteria survival in soils, with an estimated doubling of the die-off rate for each 10 oC rise (Gerba and Bitton, 1984; Reddy et al., 1981; Sampson et al., 2006). Temperature is also the dominant factor affecting virus survival in freshwater, with greater survival occurring at lower temperatures. Enteric viruses can survive from 2 to more than 188 days in freshwater (Novotny and Olem, 1994). In addition, different strains of fecal coliform bacteria may survive at different rates outside of the host organism and the distribution of bacterial strains initially present in fecal matter changes over time in the environment (Anderson et al., 2005).

Die-off, or decay, rates for Enterococcus sp., fecal coliform, and E. coli specifically are used in TMDL studies and planning and vary among TMDLs. The Charles River TMDL (see above) assumes a fecal coliform die-off rate of -0.6 day-1. Other rates range from -0.5 day-1 (Tomales Bay TMDL) to >>-0.5 day-1 (USEPA, 1985). Die-off rates in the literature vary depending on the culture/receiving medium, with fecal coliform bacteria in sediments tending to have lower rates (-0.02 day-1) than water (-0.24 day-1; Anderson et al., 2005). In comparison, Enterococci sp. have much higher die-off rates in sediment (-0.22 day-1) and water (-0.73 day-1; Anderson et al., 2005). Without knowing the actual rate of die-off of bacteria and viruses in a particular water-body, any modeling of fates and potential risks will be speculative. Loading of fecal bacteria and viruses in various parts of a watershed and delivery to receiving waters depends on the combination of die-off rates and environmental conditions conducive to survival and sometimes growth of pathogens. These environmental conditions can determine whether fecal matter entering the water-body will die and no longer pose a risk, or survive and grow.

2.6 Reservoirs for Bacteria and Secondary Growth

Once bacteria and other fecal organisms enter the environment they may survive and even grow in media that have the right physical and chemical conditions. These media include benthic sediments, benthic periphyton (e.g., attached filamentous green algae), and riverbank/floodplain soils where survival rates may be greater than in the water column (Sherer et al., 1992; Burton et al., 1987; Thomann and Mueller, 1987; Whitman et al., 2003; Hoyer et al., 2006; Sampson et al., 2006; Whitman et al., 2006). In waterways near and including the Russian River, investigators have found that fecal bacteria, including E. coli, appear to be deposited during wet season flows, along with fine sediments (atwill et al., 2007). Pathogenic organisms, including indicator bacteria like E. coli may have increased survival times if they are protected from sunlight and extreme temperatures. Enteric and pathogenic bacteria and viruses may survive for months in benthic sediments, increasing the chance of resuspension and health impacts (Burton et al., 1987; LaBelle and Gerba, 1980; Roper and Marshall, 1979; Burton et al., 1987; and Sherer et al., 1992). In some cases, resuspension of sediments can result in higher measured concentrations of fecal bacteria than municipal outfalls to recreational beach areas (Noble et al., 2006).

Survival of indicator fecal organisms in the environment, differential survival among strains, and even subsequent bacterial growth reduces their utility as indicators of primary fecal matter input. If E. coli can survive for months in media downstream from the initial input, then connecting the detection of E. coli months later and miles downstream to the primary input can be very challenging (see Anderson et al., 2005 for related discussion). This does not mean that E. coli have no role in fecal matter detection, but rather detection of primary feces inputs using E. coli must be proximal in time to the initial input. Detection of potential secondary storage and growth sites for E. coli and other fecal matter organisms is a critical element of determining extent and importance of inputs.

2.7 Nitrate and oxygen isotopes as indicators of fecal matter input

Bacteria are not the only indicator of fecal matter inputs to streams.