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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., Competing Interests: The authors have declared that no competing interests exist.

Tidal habitats host a diversity of species and provide hydrological services such as shoreline protection and nutrient attenuation. Accretion of sediment and biomass enables tidal marshes and swamps to grow vertically, providing a degree of resilience to rising sea levels. Even if accelerating sea level rise overcomes this vertical resilience, tidal habitats have the potential to migrate inland as they continue to occupy land that falls within the new tide range elevations. The existence of developed land inland of tidal habitats, however, may prevent this migration as efforts are often made to dyke and protect developments. To test the importance of inland migration to maintaining tidal habitat abundance under a range of potential rates of sea level rise, we developed a spatially explicit elevation tracking and habitat switching model, dubbed the Marsh Accretion and Inundation Model (MAIM), which incorporates elevation-dependent net land surface elevation gain functions. We applied the model to the metropolitan Washington, DC region, finding that the abundance of small National Park Service units and other public open space along the tidal Potomac River system provides a refuge to which tidal habitats may retreat to maintain total habitat area even under moderate sea level rise scenarios (0.7 m and 1.1 m rise by 2100). Under a severe sea level rise scenario associated with ice sheet collapse (1.7 m by 2100) habitat area is maintained only if no development is protected from rising water. If all existing development is protected, then 5%, 10%, and 40% of the total tidal habitat area is lost by 2100 for the three sea level rise scenarios tested., Competing Interests: The authors have declared that no competing interests exist.

In North America, it has been shown that cattle in warmer, drier grasslands have lower quality diets than those cattle grazing cooler, wetter grasslands, which suggests warming will increase nutritional stress and reduce weight gain. Yet, little is known about how the plant species that comprise cattle diets change across these gradients and whether these shifts in dietary quality coincide with shifts in dietary composition, i.e. the relative abundance of different plant species consumed by cattle. To quantify geographic patterns in dietary composition, we analyzed the dietary composition and dietary quality of unsupplemented cattle from 289 sites across the central US by sequence-based analyses of plant DNA isolated from cattle fecal samples. Overall, assuming that the percentage of reads for a species in a sample corresponds to the percentage of protein derived from the species, only 45% of the protein intake for cattle was derived from grasses. Within the Great Plains, northern cattle relied more on grasses than southern cattle, which derived a greater proportion of their protein from herbaceous and woody eudicots. Eastern cattle were also more likely to consume a unique assemblage of plant species than western cattle. High dietary protein was not strongly tied to consumption of any specific plant species, which suggests that efforts to promote individual plant species may not easily remedy protein deficiencies. A few plant species were consistently associated with lower quality diets. For example, the diets of cattle with high amounts of Elymus or Hesperostipa were more likely to have lower crude protein concentrations than diets with less of these grasses. Overall, our analyses suggest that climatic warming will increase the reliance of cattle on eudicots as protein concentrations of grasses decline. Monitoring cattle diet with this DNA-based sequencing approach can be an effective tool for quantifying cattle diet to better increase animal performance and guide mitigation strategies to changing climates., Competing Interests: JMC and NF are co-owners of Jonah Ventures LLC. There are no patents, products in development or marketed products to declare. This does not alter the authors’ adherence to PLOS ONE policies on sharing data and materials.

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.

Stream network density exerts a strong influence on ecohydrologic processes in watersheds, yet existing stream maps fail to capture most headwater streams and therefore underestimate stream density. Furthermore, discrepancies between mapped and actual stream length vary between watersheds, confounding efforts to understand the impacts of land use on stream ecosystems. Here we report on research that predicts stream presence from coupled field observations of headwater stream channels and terrain variables that were calculated both locally and as an average across the watershed upstream of any location on the landscape. Our approach used maximum entropy modeling (MaxEnt), a robust method commonly implemented to model species distributions that requires information only on the presence of the entity of interest. In validation, the method correctly predicts the presence of 86% of all 10-m stream segments and errors are low (<1%) for catchments larger than 10 ha. We apply this model to the entire Potomac River watershed (37,800 km(2)) and several adjacent watersheds to map stream density and compare our results with the National Hydrography Dataset (NHD). We find that NHD underestimates stream density by up to 250%, with errors being greatest in the densely urbanized cities of Washington, DC and Baltimore, MD and in regions where the NHD has never been updated from its original, coarse-grain mapping. This work is the most ambitious attempt yet to map stream networks over a large region and will have lasting implications for modeling and conservation efforts.

Low-density residential development (i.e., exurban development) is often embedded within a matrix of protected areas and natural amenities, raising concern about its ecological consequences. Forest-dependent species are particularly susceptible to human settlement even at low housing densities typical of exurban areas. However, few studies have examined the response of forest birds to this increasingly common form of land conversion. The aim of this study was to assess whether, how, and at what scale forest birds respond to changes in habitat due to exurban growth. We evaluated changes in habitat composition (amount) and configuration (arrangement) for forest and forest-edge species around North America Breeding Bird Survey (BBS) stops between 1986 and 2009. We used Threshold Indicator Taxa Analysis to detect change points in species occurrence at two spatial extents (400-m and 1-km radius buffer). Our results show that exurban development reduced forest cover and increased habitat fragmentation around BBS stops. Forest birds responded nonlinearly to most measures of habitat loss and fragmentation at both the local and landscape extents. However, the strength and even direction of the response changed with the extent for several of the metrics. The majority of forest birds' responses could be predicted by their habitat preferences indicating that management practices in exurban areas might target the maintenance of forested habitats, for example through easements or more focused management for birds within existing or new protected areas.

Background: Archaea are important to the carbon and nitrogen cycles, but it remains uncertain how rising atmospheric carbon dioxide concentrations ([CO(2)]) will influence the structure and function of soil archaeal communities., Methodology/principal Findings: We measured abundances of archaeal and bacterial 16S rRNA and amoA genes, phylogenies of archaeal 16S rRNA and amoA genes, concentrations of KCl-extractable soil ammonium and nitrite, and potential ammonia oxidation rates in rhizosphere soil samples from maize and soybean exposed to ambient (∼385 ppm) and elevated (550 ppm) [CO(2)] in a replicated and field-based study. There was no influence of elevated [CO(2)] on copy numbers of archaeal or bacterial 16S rRNA or amoA genes, archaeal community composition, KCl-extractable soil ammonium or nitrite, or potential ammonia oxidation rates for samples from maize, a model C(4) plant. Phylogenetic evidence indicated decreased relative abundance of crenarchaeal sequences in the rhizosphere of soybean, a model leguminous-C(3) plant, at elevated [CO(2)], whereas quantitative PCR data indicated no changes in the absolute abundance of archaea. There were no changes in potential ammonia oxidation rates at elevated [CO(2)] for soybean. Ammonia oxidation rates were lower in the rhizosphere of maize than soybean, likely because of lower soil pH and/or abundance of archaea. KCl-extractable ammonium and nitrite concentrations were lower at elevated than ambient [CO(2)] for soybean., Conclusion: Plant-driven shifts in soil biogeochemical processes in response to elevated [CO(2)] affected archaeal community composition, but not copy numbers of archaeal genes, in the rhizosphere of soybean. The lack of a treatment effect for maize is consistent with the fact that the photosynthesis and productivity of maize are not stimulated by elevated [CO(2)] in the absence of drought.

Background: Lateral gene transfer (LGT) appears to promote genotypic and phenotypic variation in microbial communities in a range of environments, including the mammalian intestine. However, the extent and mechanisms of LGT in intestinal microbial communities of non-mammalian hosts remains poorly understood., Methodology/principal Findings: We sequenced two fosmid inserts obtained from a genomic DNA library derived from an agar-degrading enrichment culture of marine iguana fecal material. The inserts harbored 16S rRNA genes that place the organism from which they originated within Clostridium cluster IV, a well documented group that habitats the mammalian intestinal tract. However, sequence analysis indicates that 52% of the protein-coding genes on the fosmids have top BLASTX hits to bacterial species that are not members of Clostridium cluster IV, and phylogenetic analysis suggests that at least 10 of 44 coding genes on the fosmids may have been transferred from Clostridium cluster XIVa to cluster IV. The fosmids encoded four transposase-encoding genes and an integrase-encoding gene, suggesting their involvement in LGT. In addition, several coding genes likely involved in sugar transport were probably acquired through LGT., Conclusion: Our phylogenetic evidence suggests that LGT may be common among phylogenetically distinct members of the phylum Firmicutes inhabiting the intestinal tract of marine iguanas.