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The goods and services provided by riverine systems are critical to humanity, and our reliance increases with our growing population and demands. As our activities expand, these systems continue to degrade throughout the world even as we try to restore them, and many efforts have not met expectations. One way to increase restoration effectiveness could be to explicitly design restorations to promote microbial communities, which are responsible for much of the organic matter breakdown, nutrient removal or transformation, pollutant removal, and biomass production in river ecosystems. In this paper, we discuss several design concepts that purposefully create conditions for these various microbial goods and services, and allow microbes to act as ecological restoration engineers. Focusing on microbial diversity and function could improve restoration effectiveness and overall ecosystem resilience to the stressors that caused the need for the restoration. Advances in next-generation sequencing now allow the use of microbial ‘omics techniques (e.g., metagenomics, metatranscriptomics) to assess stream ecological conditions in similar fashion to fish and benthic macroinvertebrates. Using representative microbial communities from stream sediments, biofilms, and the water column may greatly advance assessment capabilities. Microbes can assess restorations and ecosystem function where animals may not currently be present, and thus may serve as diagnostics for the suitability of animal reintroductions. Emerging applications such as ecological metatranscriptomics may further advance our understanding of the roles of specific restoration designs towards ecological services as well as assess restoration effectiveness. 

We investigated environmental, landscape, and microbial factors that could structure the spatiotemporal variability in the nontarget chemical composition of four riverine systems in the Oregon Coast Range, USA. We hypothesized that the nontarget chemical composition in river water would be structured by broad-scale landscape gradients in each watershed. Instead, only a weak relationship existed between the nontarget chemical composition and land cover gradients. Overall, the effects of microbial communities and environmental variables on chemical composition were nearly twice as large as those of the landscape, and much of the influence of environmental variables on the chemical composition was mediated through the microbial community (i.e., environment affects microbes, which affect chemicals). Therefore, we found little evidence to support our hypothesis that chemical spatiotemporal variability was related to broad-scale landscape gradients. Instead, we found qualitative and quantitative evidence to suggest that chemical spatiotemporal variability of these rivers is controlled by changes in microbial and seasonal hydrologic processes. While the contributions of discrete chemical sources are undeniable, water chemistry is undoubtedly impacted by broad-scale continuous sources. Our results suggest that diagnostic chemical signatures can be developed to monitor ecosystem processes, which are otherwise challenging or impossible to study with existing off-the-shelf sensors. 

Abstract There is growing evidence that the composition of river microbial communities gradually transitions from terrestrial taxa in headwaters to unique planktonic and biofilm taxa downstream. Yet, little is known about fundamental controls on this community transition across scales in river networks. We hypothesized that community composition is controlled by flow‐weighted travel time of water, in combination with temperature and dissolved organic matter (DOM), via similar mechanisms postulated in the Pulse‐Shunt Concept for DOM. Bacterioplankton and biofilm samples were collected at least quarterly for 2 yr at 30 sites throughout the Connecticut River watershed. Among hydrologic variables, travel time was a better predictor of both bacterioplankton and biofilm community structure than watershed area, dendritic distance, or discharge. Among all variables, both bacterioplankton and biofilm composition correlated with travel time, temperature, and DOM composition. Bacterioplankton beta‐diversity was highest at shorter travel times (< 1 d) and decreased with increasing travel time, showing progressive homogenization as water flows downstream. Bacterioplankton and biofilm communities were similar at short travel times, but diverged as travel time increased. Bacterioplankton composition at downstream sites more closely resembled headwater communities when temperatures were cooler and travel times shorter. These findings suggest that the pace and trajectory of riverine bacterioplankton community succession may be controlled by temperature‐regulated growth rate and time for communities to grow and change. Moreover, bacterioplankton, and to a lesser extent biofilm, may experience the same hydrologic forcing hypothesized in the Pulse‐Shunt Concept for DOM, suggesting that hydrology controls the dispersal of microbial communities in river networks.