Jinjun Kan

Dams and their legacies have substantially altered riparian ecosystems worldwide and these effects could persist for decades or centuries into the future. However, how biogeochemical characteristics of riparian sediments evolve with depth and time post dam removal is poorly understood. We studied 12 riparian sites across three Mid‐Atlantic watersheds in the United States over a chronosequence of 0–234 years since dam removal/breach. Sediments were sampled every 0.3 m to a maximum depth of 4 m upstream of dams. Sediment physico‐chemical characteristics evolved asynchronously and at different rates with depth and time post dam breach. Gravimetric water content, ammonium nitrogen, ripening index and bioavailable and amorphous forms of iron were elevated in wet and reducing sediment conditions but low in drained and oxic sediments. Bulk density increased while total organic carbon and nitrogen decreased slowly following drainage after dam removal. We attributed these changes to complex interactions of changes in groundwater levels, vertical variation in sediment texture, amount and forms of iron oxides, and organic matter content in post‐dam sediments and buried pre‐dam soil horizons. Given the ubiquity of existing and removed dams globally, understanding and quantifying these changes are important for advancing new paradigms for anthropogenic alteration of riparian ecosystems, assessing effectiveness of riparian buffers for pollution mitigation, and guiding restoration and management options post dam removal.

Agriculture is integrally intertwined with water, yet we have little information about how the different approaches to growing food influence water quality. Food production through different strategies is driven by economic and environmental concerns. Organic agriculture has increased for several decades and is projected to continue. Here, we conducted a literature synthesis of paired field studies documenting water quality differences from conventional and organic agriculture of terrestrial row‐crops. Using the 37 papers that met our criteria, we compiled water quality parameters and calculated the percentage change between conventional and organic treatment paired comparisons. This synthesis revealed that 79% of the 14 nutrient, soil loss, and runoff parameters with at least five paired comparisons more often showed either improvement or no difference with organic. Specifically, nitrogen and overall soil losses were reduced in organic systems; however, soil loss outcomes were strongly influenced by tillage practices, and fertilizer type could change whether an organic field experienced greater or lesser nitrogen losses. Losses of phosphorus and carbon generally increased under organic agriculture, except for total phosphorus in runoff. Paired‐field trial comparisons were rare in the literature and highlighted the need for additional studies, consistency in the parameters measured, and sufficient data collected to account for variation in fertilizers, tillage intensity, soil types, and topography, among other parameters. As publications comparing conventional and organic soil quality increase rapidly, studies of water quality lag, leaving open the potential for a shift in agricultural approaches to have unintended consequences for this essential resource.

The time lag between river-borne sediment input to estuaries and its subsequent effects on estuarine ecosystems is difficult to measure but is a conceptually important time scale that influences managed interventions at watershed scales. This study investigated high-throughput sequencing of microbial fingerprinting as a novel method for tracking fluvial sediment movement through estuaries during the days and weeks following river floods. Bioassay incubation experiments in the Choptank and Pocomoke Rivers, Maryland, U.S.A. revealed that microbial communities in river and tidal waters were more similar to each other than to those in saline waters. Although microbial community composition shifted over time, distinct fingerprints remained identifiable for over 15 days. In tidal water treatments, introduced microbial fingerprints from river and saline sources persisted, while in saline treatments, microbial fingerprints from introduced river and tidal communities faded—highlighting the selective influence of ambient water chemistry and salinity on microbial survival and composition. Applying these methods during storm events, we found that riverine microbial fingerprints were rapidly diluted: 50% of riverine sediment was deposited within the upper 10 km of the estuary and less than 30% of the sediment in the mesohaline estuary was attributable to river sediment inputs during the event. These are the first such measurements of deposition and dilution of river sediment that estuarine models and other approaches might only predict or imply. The results also demonstrate the broader viability of microbial fingerprinting as a tool for tracing short-term sediment dynamics and source contributions in estuarine environments.

Freshwater urban wetlands are important ecosystems that can naturally filter and remove excess nitrogen (N) through the process of denitrification (DNF). However, anthropogenic inputs such as road salt application may affect the N removal capacity of urban wetlands by affecting the relative rates of DNF and another competing reductive process that retains N – dissimilatory nitrate reduction to ammonium (DNRA). Here, we assessed 13 roadside wetlands in urban/suburban areas of Delaware, USA to determine the effects of road salt sodium (Na ⁺ ) on soil physical, chemical, and biological properties and the rates of DNF and DNRA. Based on soil Na ⁺ concentrations, wetlands were grouped into three categories: low (Na ⁺ < 70 mg kg ⁻¹ ), medium (70 mg kg ⁻¹ < Na ⁺ < 150 mg kg ⁻¹ ) and high (Na ⁺ > 150 mg kg ⁻¹ ). Rates of DNF and DNRA ranged from 0.8 – 83 and 0.2 – 24 μg N L ⁻¹ slurry h ⁻¹ , respectively. DNF was significantly lower in high Na ⁺ category wetlands whereas DNRA did not show any significant differences. Similarly, macroaggregates and bioavailable Fe were lowest in the high Na ⁺ category, whereas concentrations of soil NH ₄ ⁺ , NO ₃ ⁻ , TOC, TN, and microbial metrics (biomass and nosZ and nrfA functional genes) did not reveal any consistent patterns. These findings imply that road salt Na ⁺ input exhibited mixed effects on soil properties in these wetlands. Overall, elevated Na ⁺ from road salt could undermine the N removal capacity of the roadside urban wetlands. Therefore, strategies should be implemented to reduce the application of road salt or identify effective alternatives.

Understanding the balance between denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in riparian systems is essential for managing watershed nitrogen (N) budgets and evaluating restoration practices. This balance is influenced by several factors including concentrations and ratio of various organic and inorganic electron donors (dissolved organic carbon [DOC], Fe ²⁺ ) to acceptor (NO ₃ ⁻ ). In riparian sediments, these factors can change rapidly over space and time, complicating measurement and quantification. We used a PFLOTRAN batch reactor model calibrated to laboratory microcosm experiments where the denitrification and DNRA rates in riparian sediments were measured using ¹⁵ N stable isotopes. Although DOC/NO ₃ ⁻ ratios influenced the relative proportions of denitrification and DNRA, the processes were also affected by elemental concentrations. For a starting DOC concentration of 0.12 mgL ⁻¹ , DNRA exceeded denitrification at DOC/NO ₃ ⁻ = 6; however, this shift was not observed within a range of DOC/NO ₃ ⁻ = 30 at higher DOC concentration of 12 mgL ⁻¹ . Heterotrophic pathways dominated NO ₃ ‐N reduction with smaller contribution from autotrophic pathways. These findings suggest that although heterotrophic pathways are important in carbon‐rich sediments, autotrophic pathways can be significant in carbon‐depleted conditions in the presence of inorganic electron donors such as Fe ²⁺ . Our simulations also highlighted key challenges with constraining model rate constants and parameters and the need for site specific calibrations. This work highlights the value of process‐based modeling in quantifying denitrification‐DNRA partitioning and the variable controls of electron donors and acceptors. Such simulations could be extended to riparian buffers to determine if they are effective management sinks for N mitigation.

Little is known about the nitrogen transformation dynamics during the early transition phase from conventional to organic farming. We investigated changes in microbial N‐cycling in agricultural fields transitioning from conventional to organic farming practices by quantifying nitrification/mineralization rates, extracellular enzyme activity (EEA), and nitrogen transformation genes (nitrification and denitrification). The farming practices we investigated contained three binary treatments: Management System (denoting both general approach and fertility source), Tillage, and Cover Crop. Four years after the transition, we found that the process of converting conventionally managed fields to organic agricultural practices significantly reduced net nitrification rates, likely as a result of lower abundances of ammonia‐oxidizing archaea (AOA) and ammonia‐oxidizing bacteria (AOB). In addition to terms pertaining to the experimental treatments, we included a term, Year, in our models to control for noise due to the cash/cover crop rotation and weather‐related differences. We found that the Year covariate to have highly significant variation related to net nitrification, soil NH₄⁺‐N concentration, the EEA ratio of NAG:BG, and the abundances of AOA, AOB, and the denitrifying gene nosZ. In contrast to much of the published literature, our results showed the absence of a significant response to the Tillage and Cover Crop treatments after four years of conversion. Combined with year‐to‐year variation being generally more important of an influence than the Tillage and Cover Crop treatments, our results suggest that nutrient processes change gradually in response to farming practices. Therefore, incorporating research about the inter‐year variations may yield predictive models that would be useful not just to researchers but also to guide farmers engaged in conventional‐to‐organic conversion projects.

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.

Agricultural practices affect soil microbes which are critical to soil health and sustainable agriculture. To understand prokaryotic and fungal assembly under agricultural practices, we use machine learning-based methods. We show that fertility source is the most pronounced factor for microbial assembly especially for fungi, and its effect decreases with soil depths. Fertility source also shapes microbial co-occurrence patterns revealed by machine learning, leading to fungi-dominated modules sensitive to fertility down to 30 cm depth. Tillage affects soil microbiomes at 0-20 cm depth, enhancing dispersal and stochastic processes but potentially jeopardizing microbial interactions. Cover crop effects are less pronounced and lack depth-dependent patterns. Machine learning reveals that the impact of agricultural practices on microbial communities is multifaceted and highlights the role of fertility source over the soil depth. Machine learning overcomes the linear limitations of traditional methods and offers enhanced insights into the mechanisms underlying microbial assembly and distributions in agriculture soils.

Water column removal in streams is a nitrogen (N) cycling pathway that has been historically overlooked. Studies filling this knowledge gap have focused on the role of water column N removal in mid‐to‐large‐order rivers with consistently high suspended sediment concentrations. However, smaller streams may provide comparable suspended sediment concentrations during and after storm events, creating favorable conditions for water column N removal. To assess the presence, magnitude, and control of water column N removal during storms in low‐order watersheds, we measured water column denitrification and heterotrophic assimilatory N uptake rates at three locations in a Mid‐Atlantic watershed during five storm events of different magnitude, sediment loads, and nutrient availability. We found large variations in water column denitrification (0–5.56 mg N g ⁻¹ d ⁻¹ ) and assimilatory uptake (0.003–1.67 mg N g ⁻¹ d ⁻¹ ). Higher rates of N removal occurred during flow recession, with a correlation between suspended sediment organic matter content and denitrification. On average, denitrification rates in the water column were higher when flashy responses to storm events occurred. In contrast to denitrification, water column N removal rates (as both denitrification and heterotrophic assimilation) during storm events were comparable to those measured at baseflow in larger rivers. However, water column denitrification could only account for less than 10% of potential reach‐scale N removal during most of the storm events. Our findings provide insight into the ecological relevance of small stream water columns and suggest that more research is needed to understand the magnitude of stream water column processing on watershed‐scale N removal.