Mill dams impact microbiome structure and depth distribution in riparian sediments

Abstract

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.

Back from the past? Assessment of nitrogen removal ability of buried historic wetland soils before and after a 1‐year incubation on a restored floodplain

“…Unamended and amended DEA rates were compared pre-and post-incubation by paired t tests (α = 0.5). Ranges of %C, %N, C:N, nitrate-N, DEA, nitrification, mineralization, and nosZ for pre-incubation buried historic soils were compared to previously published values for ancient subsurface C-rich horizons (Hill & Cardaci 2004;Gurwick et al 2008b;Bernal et al 2016) and legacy sediments (Lutgen et al 2020;Lewis et al 2021;Kan et al 2023;Peck et al 2022). Correlation coefficient matrixes (α = 0.05) were calculated for historic wetland soils pre-and post-incubation to assess relationships between soil characteristics.…”

“…Subsets of samples were selected to be analyzed in Immediately following collection, sub-samples for functional gene abundances were separated using a sterilized spatula, placed in sterile Whirl-Pak bags, and transported on ice before being stored frozen. Functional gene abundance was measured via qPCR analysis (QuantiTect SYBR Green PCR Kit analyzed on a QuantStudio 3 System; see Kan et al 2023 for details). N transformation genes proxied functional gene abundance (reported as gene counts per gram of soil), including nitrousoxide reductase gene (nosZ) for denitrifying microorganisms, and the sum of ammonia monooxygenase gene (amoA) for AoA and AoB (Leininger et al 2006;Sienkiewicz et al 2020).…”

Riparian Groundwater Nitrogen (N) Isotopes Reveal Human Imprints of Dams and Road Salt Salinization

“…We attribute these depleted groundwater δ 15 N-NO 3 values to suppressed denitrification and potentially higher DNRA and anaerobic mineralization in riparian soils at the Cooch site. Indeed, our previous measurements of denitrification potentials (Peck et al, 2022) as well as nosZ denitrification genes (Kan et al, 2023), indicated lower values for the Cooch versus the Roller site. We believe that the suppressed denitrification and higher DNRA at Cooch were a coupled result of milldam induced reducing conditions and presence of naturally occurring iron-rich soils amplified by effects of Na + from road-salt salinization (Inamdar et al, 2022).…”

“…Potential denitrification rates were highest at the upland riparian edge and lowest at the persistently saturated near‐stream position (Peck et al., 2022). Furthermore, soil denitrification rates and denitrification functional genes ( nosZ ) were lower for the road‐salt affected riparian soils suggesting potential suppression of denitrification by salinization (Kan et al., 2023; Peck et al., 2022).…”

Dissimilatory Nitrate Reduction to Ammonium (DNRA) Can Undermine Nitrogen Removal Effectiveness of Persistently Reducing Riparian Sediments

“…10 Rates of DNF and abundance of DNF functional genes (nosZ) were also low in these riparian sediments, particularly for the Cooch site affected by road salt salinization. 11,38 We speculated that in addition to ammonification and suppression of nitrification, DNRA likely contributed to the elevated NH 4 + -N concentrations; however, a direct assessment of DNRA was not performed. 10 Here, we directly assessed and compared the potential for DNF and DNRA by determining the reductive process rates using 15 N labeled NO 3 − -N and characterizing nosZ (DNF) and nrfA (DNRA) functional genes for the two milldam-affected riparian sediment sites.…”