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Long-term survival of pathogenic microorganisms in streams enables long-distance disease transmission. In order to manage water-borne diseases more effectively we need to better predict how microbes behave in freshwater systems, particularly how they are transported downstream in rivers. Microbes continuously immobilize and resuspend during downstream transport owing to a variety of processes including gravitational settling, attachment to in-stream structures such as submerged macrophytes, and hyporheic exchange and filtration within underlying sediments. We developed a stochastic model to describe these microbial transport and retention processes in rivers that also accounts for microbial inactivation. We used the model to assess the transport, retention, and inactivation of Escherichia coli in a small stream and the underlying streambed sediments as measured from multitracer injection experiments. The results demonstrate that the combination of laboratory experiments on sediment cores, stream reach-scale tracer experiments, and multiscale stochastic modeling improves assessment of microbial transport in streams. This study (1) demonstrates new observations of microbial dynamics in streams with improved data quality than prior studies, (2) advances a stochastic modeling framework to include microbial inactivation processes that we observed to be important in these streams, and (3) synthesizes new and existing data to evaluate seasonal dynamics.

The effects of wastewater loading rate and planting with Schoenoplectus validus (soft-stem bulrush) on the accumulation of organic matter were investigated in four pairs of gravel-bed constructed wetlands. The planted and unplanted wetland pairs, each supplied with a different hydraulic loading of dairy farm wastewaters pre-treated in an anaerobic and aerobic lagoon, had received cumulative suspended solids loadings (∼ 82% volatile) of between ∼ 1.6 and 5.4 kg m−2 over a 22 month period. Vertical and horizontal gradients of organic matter accumulation were sampled by stratified coring, and the impact of solids accumulations on wastewater residence times investigated using bromide as a conservative tracer. Mean accumulations of organic matter in the unplanted wetlands ranged between 0.4 and 2.3 kg m−2, while those in the planted wetlands reached mean levels of nearly 4 kg m−2. Highest levels were recorded in influent zones (up to 9.5 kg m−2) and in the upper 100 mm of the substratum. The effective porosity of the highest loaded wetlands was markedly reduced compared to that in the lowest loaded wetlands, with mean retention times decreasing to around half of their theoretical values (corrected for evapotranspirational water losses). The planted wetlands retained higher apparent gravel porosity, despite greater accumulations of organic matter. High evapotranspiration rates during hot summer days, markedly extended retention times and increased tracer dispersion.

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