7. Proposed sampling and identification approach

The following strategy for regular and event sampling of fecal indicator organisms would permit identification of possible source areas, transport processes, and host/source organisms for the fecal material inputs.

7.1 Sampling regime

The sampling regime is the combination of site-level sampling decisions, seasonal timing of sampling, and intensity of sampling.


Sampling depth in the water column can determine the relative concentrations measured at a site (Kleinheinz et al., 2006). Because fecal bacteria concentrations in the water column above undisturbed sediments tend to be highest near the surface, grab samples should be taken consistently within the top few inches of water in order to capture the highest occurring concentrations at a site.

For beach and shore sediments and potentially for different points across still water, fecal bacteria concentrations can vary depending on where the sample is taken (Kleinheinz et al., 2006). To account for this, sites where beach/shore sediments are to be sampled, or where water is relatively still, samples should be taken in a transect across the site.

Sample number (Meays et al., 2006)

7.2 Proposed sampling sites

Spatial distribution of sampled sites should capture inputs from individual sub-watersheds, with resolution at least at the Santa Rosa Creek scale. The list of sub-watersheds that would be at this resolution, including sub-reaches of the Russian River main-stem is shown in the map

7.3 Proposed sampling schedule

Three main types of sampling times should be considered: 1) Wet season base-flow, 2) Wet season event-related sampling, and 3) dry season base-flow.

Wet season tributary and mainstem base-flow may have lower fecal bacterial concentrations than during and after storms, but may still represent a significant proportion of wet-season transport of fecal bacteria. In addition, as storm flows subside, fecal-bacteria-containing sediments may be deposited in-stream or on banks and floodplains and function as reservoirs later in the year. In other words, differences in storm and base flows may represent deposition (as well as death and disintegration) of fecal bacteria within the system. Wet season base-flow sampling should be regular (weekly) and distributed in a way to capture transport from potential source areas to potential deposition areas.

Previous research has found that peaks in E. coli concentrations can depend on the type of waterway (position in the watershed) and antecedent rainfall (Gentry et al., 2006). Storm event-related sampling should include investigations at headwater reaches on tributaries, tributary mainstems, and river mainstem sites. These investigations would include sampling before, during, and after storms for several days to determine when peak concentrations and loads of fecal bacteria occur.

Dry-season base-flows occur when contact recreation is most likely to occur and is also when fecal indicator bacterial concentrations in the river water column have been lowest. However, concentrations have historically been found greater than the basin standard for contact recreation in waters above undisturbed sediments. Sampling should continue at regular intervals during dry seasons base-flows, especially during periods of contact recreation (weekends), because of evidence that sediment and algae disturbance can result in higher water column concentrations of fecal indicator bacteria. In addition, special sampling of benthic sediments and algae should take place in focus locations to determine the possible contributions of these media to surface water concentrations.

7.4 Bacteria identification

Historically, E. coli and Enterococcus sp. concentrations have been used to indicate fecal matter input to waterways, including the Russian River, and therefore are intended to represent concentrations of potentially pathogenic organisms. E. coli may survive for months after introduction into the environment, so does not make an ideal indicator of recent fecal material input. Other bacteria, such as Bacteroides sp. may make better indicators of recent fecal material input. Both E. coli and Bacteroides strains specific to particular vertebrate hosts may be identified based on their DNA. Anderson (2005) found that bacteria from different host organisms may survive in the environment at different rates, complicating the interpretation of linking strains found in the environmental samples with specific vertebrate hosts. This problem can be addressed by also sampling and identifying strains of bacteria with very short survival rates in the environment (e.g., Bacteroides sp.). A combination of E. coli, Enterococcus sp., and Bacteroides sp. sampling and identification may provide answers to multiple questions about long-term fecal matter loading, host organisms, and recent fecal matter inputs. Ideally, DNA finger-printing would be used for strain identification and Colilert/Enterolert types of tests for measuring concentrations of E. coli and Enterococcus sp., respectively.

7.5 Nitrogen and oxygen isotopes

7.5 Optimizing consideration of sampling for distributed land-uses

In order to combine both spatial and temporal sampling rules, knowledge is needed of timing of conditions/activities/effects. This could take place a priori based on existing information about potential sources and times of year. For example, if recreational uses in the River are an important source of bacteria, then sampling would be spaced to capture recreational sites and intensity (very popular vs. infrequently-visited beaches) and timed to capture frequency and intensity (early season week-day vs. Memorial Day weekend).

Urban and agricultural land-uses are likely to contribute fecal material to waterways in the Russian River basin. In almost all studies, these general land-uses are found to be source areas for fecal contamination to surface waters and sometimes to ground waters. Certain of the existing monitoring stations used by the Regional Board or others (e.g., CCWI) in the watershed are downstream of one predominant land-use (e.g., agricultural). These existing stations and a select set of new stations can be used to determine the relative contributions of different predominant land-uses to fecal contamination in sub-watersheds draining to the Russian River.

In the gap analysis above (Section 6), stations CCMWC004, UCDRRPP001, and CCML001 are downstream of predominantly rural/wildland sub-watersheds; stations UCDRRPP004, etc.check

In order to provide a complete picture of land-use contributions of fecal contaminants, this set of stations would be augmented to include a larger representative set of land-use types. For this larger set of stations, E. coli and Enterococcus sp. concentrations would be measured using conventional techniques for one water year. In addition, for one or two focus watersheds with varying land-uses, Bacteroides strains would be identified using strain-specific DNA amplification (PCR). The stations for this approach would be representative of predominant land-uses, such as urban, agrictulture, and wildland and would sampling would be over one water year. Finally, for the same focus watershed, nitrogen and oxygen isotope measurements would be conducted to quantify fecal waste loads to waterways over one water year.