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Introduction Damming 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. Methods 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. Results 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 ( amo A for AOA) were higher at the sediment surface but decreased sharply with depth. Besides top layers, denitrifying genes ( nos Z) 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. Discussion 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. 

Abstract The Upper Clark Fork River (UCFR), Montana, a mid-order well-lit system with contemporary anthropogenic nitrogen (N) enrichment and natural geogenic sources of phosphorus (P), experiences annual algal blooms that influence ecosystem structure and function. This study was designed to assess the occurrence of riverine algal blooms (RABs) in the UCFR by characterizing the succession of periphyton and biogeochemical conditions following annual snowmelt runoff through autumnal baseflow conditions, and to provide a framework for assessing RAB progression in montane mid-order rivers more broadly. Using a 21-year database (2000–2020) collected over the growing season at three sites, historical assessment of the persistent and recurrent character of RABs in the UCFR showed that the magnitude of the summer bloom was, in part, moderated by snowmelt disturbance. Abundance and growth forms of benthic algae, along with river physicochemistry (e.g., temperature) and water chemistry (N and P concentration), were measured over the course of snowmelt recession for three years (2018–2020) at the same three sites. Results documented the onset of major blooms of the filamentous green algaeCladophoraacross all sites, commensurate with declines in dissolved inorganic N. Atomic N:P ratios of river water suggest successional transitions from P- to N-limitation associated with mid-season senescence ofCladophoraand development of a secondary bloom of N-fixing cyanobacteria, dominated byNostoc cf. pruniforme. Rates of N-fixation, addressed at one of the sites during the 2020 snowmelt recession, increased uponCladophorasenescence to a maximal value among the highest reported for lotic systems (5.80 mg N/m²/h) before decreasing again to background levels at the end of the growing season. Based on these data, a heuristic model for mid-order rivers responding to snowmelt disturbance suggests progression from phases of physical stress (snowmelt) to optimal growth conditions, to conditions of biotic stress later in the growing season. Optimal growth is observed as green algal blooms that form shortly after peak snowmelt, then transition to stages dominated by cyanobacteria and autochthonous N production later in the growing season. Accordingly, interactions among algal composition, reactive N abundance, and autochthonous N production, suggest successional progression from reliance on external nutrient sources to increased importance of autochthony, including N-fixation that sustains riverine productivity during late stages of snowmelt recession. 

Abstract The seasonal controls of hydrology, temperature, hypoxia, and biogeochemical conditions for groundwater ammonium–N (NH₄⁺) concentrations are not well understood. Here we investigated these controls for riparian groundwaters located upstream of two milldams over a period of 4 years. Groundwater chemistry was sampled monthly while groundwater elevations, hydraulic gradients, and temperatures were recorded sub‐hourly. Distinct seasonal patterns for NH₄⁺were observed which differed among the wells. For wells that displayed a strong seasonal pattern, NH₄⁺concentrations increased through the summer and peaked in October–November. These elevated concentrations were attributed to ammonification, suppression of nitrification, and/or dissimilatory nitrate reduction to ammonium (DNRA). These processes were driven by high groundwater temperatures, low hydraulic gradients (or long residence times), hypoxic/anoxic groundwater conditions, and increased availability of dissolved organic carbon as an electron donor. In contrast, NH₄⁺concentrations decreased in the riparian groundwater from January to April during cool and wet conditions. A groundwater well with elevated total dissolved iron (TdFe) concentrations had elevated NH₄⁺concentrations but displayed a muted seasonal response. In addition to hydrologic controls, we attributed this response to additional NH₄⁺contribution from Fe‐driven autotrophic DNRA and/or ammonification linked to dissimilatory Fe reduction. Understanding the temporal patterns and factors controlling NH₄⁺in riparian groundwaters is important for making appropriate watershed management decisions and implementing appropriate best management practices. 

Abstract Groundwater nitrate‐N isotopes (δ¹⁵N‐) have been used to infer the effects of natural and anthropogenic change on N cycle processes in the environment. Here we report unexpected changes in groundwater δ¹⁵N‐ for riparian zones affected by relict milldams and road salt salinization. Contrary to natural, undammed conditions, groundwater δ¹⁵N‐ values declined from the upland edge through the riparian zone and were lowest near the stream. Groundwater δ¹⁵N‐ values increased for low electron donor (dissolved organic carbon) to acceptor ratios but decreased beyond a change point in ratios. Groundwater δ¹⁵N‐ values were particularly low for the riparian milldam site subjected to road‐salt salinization. We attributed these N isotopic trends to suppression of denitrification, occurrence of dissimilatory nitrate reduction to ammonium (DNRA), and/or effects of road salt salinization. Groundwater δ¹⁵N‐ can provide valuable insights into process mechanisms and can serve as “imprints” of anthropogenic activities and legacies. 

Abstract Milldams and their legacies have significantly influenced fluvial processes and geomorphology. However, less is known about their effects on riparian zone hydrology, biogeochemistry, and water quality. Here, we discuss the potential effects of existing and breached milldams on riparian nitrogen (N) processing through multiple competing hypotheses and observations from complementary studies. Competing hypotheses characterize riparian zone processes that remove (sink) or release (source) N. Elevated groundwater levels and reducing soil conditions upstream of milldams suggest that riparian zones above dams could be hotspots for N removal via denitrification and plant N uptake. On the other hand, dam removals and subsequent drops in stream and riparian groundwater levels result in drained, oxic soils which could increase soil nitrification and decrease riparian plant uptake due to groundwater bypassing the root zone. Whether dam removals would result in a net increase or decrease of N in riparian groundwaters is unknown and needs to be investigated. While nitrification, denitrification, and plant N uptake have typically received the most attention in riparian studies, other N cycle processes such as dissimilatory nitrate reduction to ammonium (DNRA) need to be considered. We also propose a novel concept of riparian discontinuum, which highlights the hydrologic and biogeochemical discontinuities introduced in riparian zones by anthropogenic structures such as milldams. Understanding and quantifying how milldams and similar structures influence the net source or sink behavior of riparian zones is urgently needed for guiding watershed management practices and for informed decision making with regard to dam removals.