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  1. Abstract

    Interstitial water or pore water occupies the space between soil particles and provides “hotspots” and “fluvial networks” for microbial activities in floodplain soil. However, to date, we know very little about the microorganisms living in pore water and how they respond to environmental changes. This study aimed to understand microbial distribution and assemblage in riparian pore waters, and how they respond to water chemistry and redox gradients associated with hydrological processes.

    We analysed the annual changes of porewater microbial communities from the east and west banks of the White Clay Creek, a site at the Christina River Basin – Critical Zone Observatory, Pennsylvania, USA. Microbial abundances were quantified by epifluorescence microscopy and detailed community structures were characterised by high‐throughput sequencing. Water chemistry and redox gradients were also monitored and recorded, and their interactions with porewater microbiomes were analysed using correlations and multivariate analyses.

    Abundance of microbial cells increased during summer and late autumn. Wetland porewater microbiomes mainly contained Acidobacteria, Bacteroidetes, Nitrospirae and Proteobacteria, and microbiome structures were easily distinguishable from those in the underlying hyporheic gravel layer. Seasonal dynamics of bacterial community structure in the east and west wetlands were distinct, responding to floodplain topography and associated hydrological/geochemical processes. Iron (Fe)‐cycling bacteria (mainly Gallionellaceae andRhodoferaxspp.) dominated the porewater microbiome, and their relative abundance was significantly higher in the east than the west wetland. Furthermore, Fe‐oxidising bacteria (Gallionellaceae) were negatively correlated with Fe‐reducing bacteria (Rhodoferaxspp.) at the east wetland.

    Microbial abundances (cell density) in pore waters showed similar seasonal patterns across stream banks, but microbial community structure did not. Microbiome assembly in pore water is correlated with water chemistry and redox gradients primarily associated with local hydrological processes.

    As a consequence of their significance for carbon (C) mineralisation and Fe reduction at terrestrial–aquatic interfaces, microbiomes in riparian pore waters and associated microbial activity play an essential role in C and mineral dynamics. These findings will inform future studies of the response of freshwater ecosystems to hydrological dynamics influenced by global climate change.

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  2. 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. 
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  3. Abstract

    Arsenic (As) and mercury (Hg) were examined in the Yellowstone Lake food chain, focusing on two lake locations separated by approximately 20 km and differing in lake floor hydrothermal vent activity. Sampling spanned from femtoplankton to the main fish species, Yellowstone cutthroat trout and the apex predator lake trout. Mercury bioaccumulated in muscle and liver of both trout species, biomagnifying with age, whereas As decreased in older fish, which indicates differential exposure routes for these metal(loid)s. Mercury and As concentrations were higher in all food chain filter fractions (0.1‐, 0.8‐, and 3.0‐μm filters) at the vent‐associated Inflated Plain site, illustrating the impact of localized hydrothermal inputs. Femtoplankton and picoplankton size biomass (0.1‐ and 0.8‐μm filters) accounted for 30%–70% of total Hg or As at both locations. By contrast, only approximately 4% of As and <1% of Hg were found in the 0.1‐μm filtrate, indicating that comparatively little As or Hg actually exists as an ionic form or intercalated with humic compounds, a frequent assumption in freshwaters and marine waters. Ribosomal RNA (18S) gene sequencing of DNA derived from the 0.1‐, 0.8‐, and 3.0‐μm filters showed significant eukaryote biomass in these fractions, providing a novel view of the femtoplankton and picoplankton size biomass, which assists in explaining why these fractions may contain such significant Hg and As. These results infer that femtoplankton and picoplankton metal(loid) loads represent aquatic food chain entry points that need to be accounted for and that are important for better understanding Hg and As biochemistry in aquatic systems.Environ Toxicol Chem2023;42:225–241. © 2022 SETAC

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  4. 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.

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  5. Abstract

    A mechanistic understanding of factors that structure spatiotemporal community composition is a major challenge in microbial ecology. Our study of microbial communities in the headwaters of three freshwater stream networks showed significant community changes at the small spatial scale of benthic habitats when compared to changes at mid‐ and large‐spatial scales associated with stream order and catchment. Catchment (which included temperate and tropical catchments) had the strongest influence on community composition followed by habitat type (epipsammon or epilithon) and stream orders. Alpha diversity of benthic microbiomes resulted from interactions between catchment, habitat, and canopy. Epilithon contained relatively moreCyanobacteriaand algae whileAcidobacteriaandActinobacteriaproportions were higher in epipsammic habitats. Turnover from replacement created ~60%–95% of beta diversity differences among habitats, stream orders, and catchments. Turnover within a habitat type generally decreased downstream indicating longitudinal linkages in stream networks while between habitat turnover also shaped benthic microbial community assembly. Our study suggests that factors influencing microbial community composition shift in dominance across spatial scales, with habitat dominating locally and catchment dominating globally.

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  6. Abstract Background

    Annually reoccurring microbial populations with strong spatial and temporal variations have been identified in estuarine environments, especially in those with long residence time such as the Chesapeake Bay (CB). However, it is unclear how microbial taxa cooccurr and how the inter-taxa networks respond to the strong environmental gradients in the estuaries.


    Here, we constructed co-occurrence networks on prokaryotic microbial communities in the CB, which included seasonal samples from seven spatial stations along the salinity gradients for three consecutive years. Our results showed that spatiotemporal variations of planktonic microbiomes promoted differentiations of the characteristics and stability of prokaryotic microbial networks in the CB estuary. Prokaryotic microbial networks exhibited a clear seasonal pattern where microbes were more closely connected during warm season compared to the associations during cold season. In addition, microbial networks were more stable in the lower Bay (ocean side) than those in the upper Bay (freshwater side). Multivariate regression tree (MRT) analysis and piecewise structural equation modeling (SEM) indicated that temperature, salinity and total suspended substances along with nutrient availability, particulate carbon and Chla, affected the distribution and co-occurrence of microbial groups, such as Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, Proteobacteria, and Verrucomicrobia. Interestingly, compared to the abundant groups (such as SAR11, Saprospiraceae and Actinomarinaceae), the rare taxa including OM60 (NOR5) clade (Gammaproteobacteria), Micrococcales (Actinobacteria), and NS11-12 marine group (Bacteroidetes) contributed greatly to the stability of microbial co-occurrence in the Bay. Modularity and cluster structures of microbial networks varied spatiotemporally, which provided valuable insights into the ‘small world’ (a group of more interconnected species), network stability, and habitat partitioning/preferences.


    Our results shed light on how estuarine gradients alter the spatiotemporal variations of prokaryotic microbial networks in the estuarine ecosystem, as well as their adaptability to environmental disturbances and co-occurrence network complexity and stability.

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  7. 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.

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  8. Abstract

    The compounding effects of anthropogenic legacies for environmental pollution are significant, but not well understood. Here, we show that centennial‐scale legacies of milldams and decadal‐scale legacies of road salt salinization interact in unexpected ways to produce hot spots of nitrogen (N) in riparian zones. Riparian groundwater and stream water concentrations upstream of two mid‐Atlantic (Pennsylvania and Delaware) milldams, 2.4 and 4 m tall, were sampled over a 2 year period. Clay and silt‐rich legacy sediments with low hydraulic conductivity, stagnant and poorly mixed hydrologic conditions, and persistent hypoxia in riparian sediments upstream of milldams produced a unique biogeochemical gradient with nitrate removal via denitrification at the upland riparian edge and ammonium‐N accumulation in near‐stream sediments and groundwaters. Riparian groundwater ammonium‐N concentrations upstream of the milldams ranged from 0.006 to 30.6 mgN L−1while soil‐bound values were 0.11–456 mg kg−1. We attribute the elevated ammonium concentrations to ammonification with suppression of nitrification and/or dissimilatory nitrate reduction to ammonium (DNRA). Sodium inputs to riparian groundwater (25–1,504 mg L−1) from road salts may further enhance DNRA and ammonium production and displace sorbed soil ammonium‐N into groundwaters. This study suggests that legacies of milldams and road salts may undercut the N buffering capacity of riparian zones and need to be considered in riparian buffer assessments, watershed management plans, and dam removal decisions. Given the widespread existence of dams and other barriers and the ubiquitous use of road salt, the potential for this synergistic N pollution is significant.

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  9. Abstract

    Dam removals are on the increase across the US with Pennsylvania currently leading the nation. While most dam removals are driven by aquatic habitat and public safety considerations, we know little about how dam removals impact water quality and riparian zone processes. Dam removals decrease the stream base level, which results in dewatering of the riparian zone. We hypothesized that this dewatering of the riparian zone would increase nitrification and decrease denitrification, and thus result in nitrogen (N) leakage from riparian zones. This hypothesis was tested for a 1.5 m high milldam removal. Stream, soil water, and groundwater N concentrations were monitored over 2 years. Soil N concentrations and process rates andδ15N values were also determined. Denitrification rates and soilδ15N values in riparian sediments decreased supporting our hypothesis but no significant changes in nitrification were observed. While surficial soil water nitrate‐N concentrations were high (median 4.5 mg N L−1), riparian groundwater nitrate‐N values were low (median 0.09 mg N L−1), indicating that nitrate‐N leakage was minimal. We attribute the low groundwater nitrate‐N to denitrification losses at the lower, more dynamic, groundwater interface and/or dissimilatory nitrate reduction to ammonium (DNRA). Stream water nitrate‐N concentrations were high (median 7.6 mg N L−1) and contrary to our dam‐removal hypothesis displayed a watershed‐wide decline that was attributed to regional hydrologic changes. This study provided important first insights on how dam removals could affect N cycle processes in riparian zones and its implications for water quality and watershed management.

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