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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. 

Anthropogenic salt inputs have impacted many streams in the U.S. for over a century. Urban stream salinity is often chronically elevated and punctuated by episodic salinization events, which can last hours to days after snowstorms and the application of road salt. Here, we investigated the impacts of freshwater salinization on total dissolved nitrogen (TDN) and NO3−/NO2− concentrations and fluxes across time in urban watersheds in the Baltimore-Washington D.C. metropolitan area of the Chesapeake Bay region. Episodic salinization from road salt applications and snowmelt quickly mobilized TDN in streams likely through soil ion exchange, hydrologic flushing, and other biogeochemical processes. Previous experimental work from other studies has shown that salinization can mobilize nitrogen from sediments, but less work has investigated this phenomenon with high-frequency sensors and targeted monitoring during road salt events. We found that urban streams exhibited elevated concentrations and fluxes of TDN, NO3−/NO2−, and specific conductance that rapidly peaked during and after winter road salt events, and then rapidly declined afterwards. We observed plateaus in TDN concentrations in the ranges of the highest specific conductance values (between 1000 and 2000 μS/cm) caused by road salt events. Plateaus in TDN concentrations beyond a certain threshold of specific conductance values suggested source limitation of TDN in watersheds (at the highest ranges in chloride concentrations and ranges); salts were likely extracting nitrogen from soils and streams through ion exchange in soils and sediments, ion pairing in soils and waters, and sodium dispersion of soils to a certain threshold level. When watershed transport was compared across land use, including a forested reference watershed, there was a positive relationship between Cl− loads and NO3−/NO2− loads. This relationship occurred across all sites regardless of land use, which suggests that the mass transport of Cl− and NO3−/NO2− are likely influenced by similar factors such as soil ion exchange, ion pairing, sodium dispersion of soils, hydrologic flushing, and biogeochemical processes. Freshwater salinization has the potential to alter the magnitude and timing of total dissolved nitrogen delivery to receiving waters during winter months following road salt applications, and further work should investigate the seasonal relationships of N transport with salinization in urban watersheds. 

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 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. 

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 Riparian zones are key ecotones that buffer aquatic ecosystems through removal of nitrogen (N) via processes such as denitrification. However, how dams alter riparian N cycling and buffering capacity is poorly understood. Here, we hypothesized that elevated groundwater and anoxia due to the backup of stream water above milldams may enhance denitrification. We assessed denitrification rates (using denitrification enzyme assays) and potential controlling factors in riparian sediments at various depths upstream and downstream of two relict U.S. mid‐Atlantic milldams. Denitrification was not significantly different between upstream and downstream, although was greater per river km upstream considering deeper and wider geometries. Further, denitrification typically occurred in hydrologically variable shallow sediments where nitrate‐N and organic matter were most concentrated. At depths below 1 m, both denitrification and nitrate‐N decreased while ammonium‐N concentrations substantially increased, indicating suppression of ammonium consumption or dissimilatory nitrate reduction to ammonium. These results suggest that denitrification occurs where dynamic groundwater levels result in higher rates of nitrification and mineralization, while another N process that produces ammonium‐N competes with denitrification for limited nitrate‐N at deeper, more stagnant/poorly mixed depths. Ultimately, while it is unclear whether relict milldams are sources of N, limited denitrification rates indicate that they are not always effective sinks; thus, milldam removal—especially accompanied by removal of ammonium‐N rich legacy sediments—may improve riparian N buffering.