No abstract

Wang et al. Archaeal Distribution Across Distinct Environments network analysis indicated that only soil Archaea formed stable modules. Keystone species (ASVs) were identified mainly from Methanomassiliicoccales, Nitrososphaerales, Nitrosopumilales. Overall, these results indicate a strong habitat-dependent distribution of Archaea and their functional partitions within the local environments.

IntroductionDamming has substantially fragmented and altered riverine ecosystems worldwide. Dams slow down streamflows, raise stream and groundwater levels, create anoxic or hypoxic hyporheic and riparian environments and result in deposition of fine sediments above dams. These sediments represent a good opportunity to study human legacies altering soil environments, for which we lack knowledge on microbial structure, depth distribution, and ecological function.MethodsHere, we compared high throughput sequencing of bacterial/ archaeal and fungal community structure (diversity and composition) and functional genes (i.e., nitrification and denitrification) at different depths (ranging from 0 to 4 m) in riparian sediments above breached and existing milldams in the Mid-Atlantic United States.ResultsWe found significant location- and depth-dependent changes in microbial community structure. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Chloroflexi, Acidobacteria, Planctomycetes, Thaumarchaeota, and Verrucomicrobia were the major prokaryotic components while Ascomycota, Basidiomycota, Chytridiomycota, Mortierellomycota, Mucoromycota, and Rozellomycota dominated fungal sequences retrieved from sediment samples. Ammonia oxidizing genes (amoA for AOA) were higher at the sediment surface but decreased sharply with depth. Besides top layers, denitrifying genes (nosZ) were also present at depth, indicating a higher denitrification potential in the deeper layers. However, these results contrasted with in situ denitrification enzyme assay (DEA) measurements, suggesting the presence of dormant microbes and/or other nitrogen processes in deep sediments that compete with denitrification. In addition to enhanced depth stratification, our results also highlighted that dam removal increased species richness, microbial diversity, and nitrification.DiscussionLateral and vertical spatial distributions of soil microbiomes (both prokaryotes and fungi) suggest that not only sediment stratification but also concurrent watershed conditions are important in explaining the depth profiles of microbial communities and functional genes in dammed rivers. The results also provide valuable information and guidance to stakeholders and restoration projects.

Microbial community composition varies across stream habitats. However, there is little understanding of how varying hydraulic and geomorphic factors influence microbial distribution along a succession of pools. This study examines how substrate, geomorphological and hydraulic habitat variables may drive bacterial community composition within different stream pool habitats of a temperate headwater stream. Microbial community structures from rock biofilm and sediment samples within each of the 10 selected stream pools of White Clay Creek, PA, were determined by high-throughput sequencing of 16S rRNA genes. The grain size distribution, organic matter content, streamflow velocity, temperature regime and morphology of each pool were quantified to characterize the pool habitats' variability. Multivariate statistical analysis revealed significant differences in the microbial community composition linked to the substrate's stability within the pool units. Indeed, soft and more mobile sediments were dominated by heterotrophic bacteria, while photosynthetic microorganisms (e.g., microalgae and cyanobacteria) were mainly found on rock biofilm. The difference in the distribution of bacterial communities can be explained by variations in the local hydraulic (i.e., depth and velocity) and the thermal conditions (daily fluctuation, min and max). These results highlight the geomorphological and hydrologic drivers for small-scale diversity in bacterial communities and provide a better understanding of how maintaining and promoting variability in streambed physical properties may enhance microbial diversity. Better integration of these drivers into stream restoration practices will allow the inclusion of microorganisms, the trophic levels that are usually overlooked but still play critical roles in stream ecology.