Mill dams impact microbiome structure and depth distribution in riparian sediments

Lateral 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.

Here, 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.

We 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.