The Roles of Microbes in Stream Restorations.

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.

Microbial communities can predict the ecological condition of headwater streams.

Humanity's reliance on clean water and the ecosystem services provided makes identifying efficient and effective ways to assess the ecological condition of streams ever more important. We used high throughput sequencing of the 16S rRNA region to explore relationships between stream microbial communities, environmental attributes, and assessments of stream ecological condition. Bacteria and archaea in microbial community samples collected from the water column and from stream sediments during spring and summer were used to replicate standard assessments of ecological condition performed with benthic macroinvertebrate collections via the Benthic Index of Biotic Integrity (BIBI). Microbe-based condition assessments were generated at different levels of taxonomic resolution from phylum to OTU (Operational Taxonomic Units) in order to understand appropriate levels of taxonomic aggregation. Stream sediment microbial communities from both spring and summer were much better than the water column at replicating BIBI condition assessment results. Accuracies were as high as 100% on training data used to build the models and up to 80% on validation data used to assess predictions. Assessments using all OTUs usually had the highest accuracy on training data, but were lower on validation data due to overfitting. In contrast, assessments at the order-level had similar performance accuracy for validation data, and a reduced subset of orders also performed well, suggesting the method could be generalized to other watersheds. Subsets of the important orders responded similarly to environmental gradients compared to the entire community, where strong shifts in community structure occurred for known aquatic stressors such as pH, dissolved organic carbon, and nitrate nitrogen. The results suggest the stream microbes may be useful for assessing the ecological condition of streams and especially useful for stream restorations where many eukaryotic taxa have been eliminated due to prior degradation and are unable to recolonize.

Headwater Stream Microbial Diversity and Function across Agricultural and Urban Land Use Gradients.

Anthropogenic activity impacts stream ecosystems, resulting in a loss of diversity and ecosystem function; however, little is known about the response of aquatic microbial communities to changes in land use. Here, microbial communities were characterized in 82 headwater streams across a gradient of urban and agricultural land uses using 16S rRNA gene amplicon sequencing and compared to a rich data set of physicochemical variables and traditional benthic invertebrate indicators. Microbial diversity and community structures differed among watersheds with high agricultural, urban, and forested land uses, and community structure differed in streams classified as being in good, fair, poor, and very poor condition using benthic invertebrate indicators. Microbial community similarity decayed with geodesic distance across the study region but not with environmental distance. Stream community respiration rates ranged from 21.7 to 1,570 mg O2 m-2 day-1 and 31.9 to 3,670 mg O2 m-2 day-1 for water column and sediments, respectively, and correlated with nutrients associated with anthropogenic influence and microbial community structure. Nitrous oxide (N2O) concentrations ranged from 0.22 to 4.41 µg N2O liter-1; N2O concentration was negatively correlated with forested land use and was positively correlated with dissolved inorganic nitrogen concentrations. Our findings suggest that stream microbial communities are impacted by watershed land use and can potentially be used to assess ecosystem health.IMPORTANCE Stream ecosystems are frequently impacted by changes in watershed land use, resulting in altered hydrology, increased pollutant and nutrient loads, and habitat degradation. Macroinvertebrates and fish are strongly affected by changes in stream conditions and are commonly used in biotic indices to assess ecosystem health. Similarly, microbes respond to environmental stressors, and changes in community composition alter key ecosystem processes. The response of microbes to habitat degradation and their role in global biogeochemical cycles provide an opportunity to use microbes as a monitoring tool. Here, we identify stream microbes that respond to watershed urbanization and agricultural development and demonstrate that microbial diversity and community structure can be used to assess stream conditions and ecosystem functioning.

Variations in Tissue Mercury Contents in Three Species of Adult Salamanders in Streams in Western Maryland.

The purpose of this study was to improve our understanding of the relationship between mercury in three species of adult salamanders and relatively pristine first-order streams in western Maryland. We measured the tissue mercury content of 106 northern two-lined salamanders (Eurycea bislineata bislineata), 111 northern dusky (Desmognathus fuscus), and 107 Allegheny mountain dusky (Desmognathus ocrophaeus) salamanders collected during three sampling periods. Averaged over our entire data set, northern two-lined salamanders had significantly greater tissue mercury contents (29.57 ± 1.32 ng g-1) than northern dusky (20.95 ± 0.78 ng g-1) and Allegheny mountain dusky salamanders (22.84 ± 1.23 ng g-1). This may be due in part to the longer larval period of the northern two-lined salamanders (24-36 vs. 0-10 months). A longer larval period suggests that the northern two-lined larvae were consuming a fully aquatic diet for a longer time period, which is likely to be higher in mercury compared with a more terrestrial diet. The tissue mercury content in northern two-lined and northern dusky salamanders were strongly correlated with the average total mercury, methyl mercury, and dissolved organic carbon concentrations in stream water. In contrast, the tissue mercury content of the more terrestrial salamander, the Allegheny mountain dusky, was not correlated with stream water chemistry. This suggest that the mercury in the terrestrial prey consumed by the Allegheny mountain dusky salamanders is not directly linked to the mercury in stream water. Our results also suggest that the aquatic salamanders could be important bioindicators of mercury contamination of small streams.

Mercury Concentrations in Northern Two-Lined Salamanders from Stream Ecosystems in Garrett County, Maryland.

The purpose of this study was to increase our understanding of the bioaccumulation of mercury in northern two-lined salamanders (Eurycea bislineata bislineata) in freshwater stream ecosystems. We collected 111 adults and 131 larval northern two-lined salamanders from six streams in Garrett County, Maryland. These salamanders were collected in April, July, and September 2010. We measured the size and tissue mercury content in all of these salamanders. We also measured the total and methyl mercury concentrations in stream water on monthly basis from April through December 2010. Averaged over all stream ecosystems, adult northern two-lined salamanders had significantly greater total mercury concentrations than larval salamanders (29.6 vs. 23.8 ng g-1). For individual stream ecosystems, the mean tissue mercury contents in adult northern two-lined salamanders were significantly greater than the mean tissue mercury contents in larval northern two-lined salamanders for Bear Pen and Mill Run. Adult and larval salamanders from the Little Savage River and Mud Lick had 1.5-2 times greater mean tissue mercury contents than salamanders in all other streams. These two streams also had significantly greater total and methyl mercury concentrations. Despite their different life-stage feeding behaviors (terrestrial vs. aquatic), the tissue mercury contents of adult (r = 0.76) and larval (r = 0.79) northern two-lined salamanders were strongly linked to the methyl mercury concentrations in stream water. This implies that northern two-lined salamanders may be a useful bioindicator of mercury pollution in relatively pristine stream ecosystems.

Hiding in Plain Sight: A Case for Cryptic Metapopulations in Brook Trout (Salvelinus fontinalis).

A fundamental issue in the management and conservation of biodiversity is how to define a population. Spatially contiguous fish occupying a stream network have often been considered to represent a single, homogenous population. However, they may also represent multiple discrete populations, a single population with genetic isolation-by-distance, or a metapopulation. We used microsatellite DNA and a large-scale mark-recapture study to assess population structure in a spatially contiguous sample of Brook Trout (Salvelinus fontinalis), a species of conservation concern. We found evidence for limited genetic exchange across small spatial scales and in the absence of barriers to physical movement. Mark-recapture and stationary passive integrated transponder antenna records demonstrated that fish from two tributaries very seldom moved into the opposite tributary, but movements between the tributaries and mainstem were more common. Using Bayesian genetic clustering, we identified two genetic groups that exhibited significantly different growth rates over three years of study, yet survival rates were very similar. Our study highlights the importance of considering the possibility of multiple genetically distinct populations occurring within spatially contiguous habitats, and suggests the existence of a cryptic metapopulation: a spatially continuous distribution of organisms exhibiting metapopulation-like behaviors.

Regional and local scale modeling of stream temperatures and spatio-temporal variation in thermal sensitivities.

Understanding variation in stream thermal regimes becomes increasingly important as the climate changes and aquatic biota approach their thermal limits. We used data from paired air and water temperature loggers to develop region-scale and stream-specific models of average daily water temperature and to explore thermal sensitivities, the slopes of air-water temperature regressions, of mostly forested streams across Maryland, USA. The region-scale stream temperature model explained nearly 90 % of the variation (root mean square error = 0.957 °C), with the mostly flat coastal plain streams having significantly higher thermal sensitivities than the steeper highlands streams with piedmont streams intermediate. Model R (2) for stream-specific models was positively related to a stream's thermal sensitivity. Both the regional and the stream-specific air-water temperature regression models benefited from including mean daily discharge from regional gaging stations, but the degree of improvement declined as a stream's thermal sensitivity increased. Although catchment size had no relationship to thermal sensitivity, steeper streams or those with greater amounts of forest in their upstream watershed were less thermally sensitive. The subset of streams with three or more summers of temperature data exhibited a wide range of annual variation in thermal sensitivity at a site, with the variation not attributable to discharge, precipitation patterns, or physical attributes of streams or their watersheds. Our findings are a useful starting point to better understand patterns in stream thermal regimes. However, a more spatially and temporally comprehensive monitoring network should increase understanding of stream temperature variation and its controls as climatic patterns change.

Variation in physicochemical responses to urbanization in streams between two Mid-Atlantic physiographic regions.

Urban development substantially alters the physicochemistry of streams, resulting in biodiversity and ecosystem function loss. However, interregional comparisons of physicochemical impact in urban streams suggest that geoclimatic heterogeneity may influence the extent of degradation. In the Mid-Atlantic United States, the adjacent Coastal Plain and Piedmont physiographic provinces possess distinctly different hydrogeomorphic properties that may influence how stream ecosystems respond to urbanization. Recent bioassessments have demonstrated that biotic sensitivity to urbanization is relatively acute in the Piedmont, suggesting that physicochemical change as a consequence of urbanization may be greater in that province. We compared hydrologic, chemical, and thermal characteristics of Mid-Atlantic Coastal Plain and Piedmont first- through fifth-order streams along gradients of impervious surface cover (ISC) at multiple spatial scales. Linear models were applied to test if conditions in rural streams and the degree of impact from ISC varied between provinces. Mean and maximum summer temperatures in Piedmont streams increased more per unit of ISC than in the Coastal Plain. Contrary to expectations, however, variables that quantified high-flow event frequency, magnitude and duration, exhibited significantly greater impact along the ISC gradient in the Coastal Plain. Most chemical changes associated with increasing ISC were similar in the two provinces, although the interregional chemical composition of rural streams differed substantially for most parameters. Our findings demonstrate consistent interregional heterogeneity in stream ecosystem responses to urbanization. Landscape-scale management decisions with stream ecosystem conservation, mitigation, or restoration as a goal must therefore carefully consider the geoclimatic context in order to maximize effectiveness.

Forecasting the combined effects of urbanization and climate change on stream ecosystems: from impacts to management options.

Streams collect runoff, heat, and sediment from their watersheds, making them highly vulnerable to anthropogenic disturbances such as urbanization and climate change. Forecasting the effects of these disturbances using process-based models is critical to identifying the form and magnitude of likely impacts. Here, we integrate a new biotic model with four previously developed physical models (downscaled climate projections, stream hydrology, geomorphology, and water temperature) to predict how stream fish growth and reproduction will most probably respond to shifts in climate and urbanization over the next several decades.The biotic submodel couples dynamics in fish populations and habitat suitability to predict fish assemblage composition, based on readily available biotic information (preferences for habitat, temperature, and food, and characteristics of spawning) and day-to-day variability in stream conditions.WE ILLUSTRATE THE MODEL USING PIEDMONT HEADWATER STREAMS IN THE CHESAPEAKE BAY WATERSHED OF THE USA, PROJECTING TEN SCENARIOS: Baseline (low urbanization; no on-going construction; and present-day climate); one Urbanization scenario (higher impervious surface, lower forest cover, significant construction activity); four future climate change scenarios [Hadley CM3 and Parallel Climate Models under medium-high (A2) and medium-low (B2) emissions scenarios]; and the same four climate change scenarios plus Urbanization.Urbanization alone depressed growth or reproduction of 8 of 39 species, while climate change alone depressed 22 to 29 species. Almost every recreationally important species (i.e. trouts, basses, sunfishes) and six of the ten currently most common species were predicted to be significantly stressed. The combined effect of climate change and urbanization on adult growth was sometimes large compared to the effect of either stressor alone. Thus, the model predicts considerable change in fish assemblage composition, including loss of diversity.Synthesis and applications. The interaction of climate change and urban growth may entail significant reconfiguring of headwater streams, including a loss of ecosystem structure and services, which will be more costly than climate change alone. On local scales, stakeholders cannot control climate drivers but they can mitigate stream impacts via careful land use. Therefore, to conserve stream ecosystems, we recommend that proactive measures be taken to insure against species loss or severe population declines. Delays will inevitably exacerbate the impacts of both climate change and urbanization on headwater systems.

Relationship between wetlands and mercury in brook trout.

The purpose of this study was to determine if wetlands influence mercury concentrations in brook trout (Salvelinus fontinalis), benthic macroinvertebrates, and stream water. On September 26, 2005, water samples, benthic macroinvertebrates, and brook trout were collected from four streams in western Maryland under low-flow conditions. Water samples were also collected in these four streams under high-flow conditions in January 2006. The watersheds of Blue Lick and Monroe Run did not contain wetlands, but the watersheds of the Upper Savage River (3% of upstream area) and Little Savage River (7% of upstream area) contained wetlands. We found significantly (p = 0.05) higher average total mercury concentration in brook trout from Little Savage River (129 +/- 54 ng g(-1)); intermediate concentrations (66 +/- 19 ng g(-1)) in brook trout from Upper Savage River; and lowest concentrations in brook trout from Blue Lick (28 +/- 11 ng g(-1)) and Monroe Run (23 +/- 19 ng g(-1)). Brook trout in all streams accumulated mercury at the same rate over their lifetimes, but the youngest fish had significantly different mercury concentrations (Little Savage > Upper Savage > Blue Lick = Monroe Run), which may be due to differences in mercury concentrations in the eggs or food for the fry. Mercury concentrations in brook trout were not consistent with mercury concentrations in stream water and benthic macroinvertebrates. The Little Savage River had significantly higher total and methylmercury concentrations in stream water, but mercury concentrations in the other streams and in the benthic macroinvertebrates were not significantly different among streams. The unusually high methylmercury concentrations (0.5 to 2.1 ng L(-1)) in the Little Savage River may have been caused by production of methylmercury in the pools. The relatively low methylmercury concentrations in the Upper Savage River may be caused by a mercury concentration gradient downstream of the wetland.