Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies

Metal-oxide precipitation influences microbiome structure in hyporheic zones receiving acid rock drainage

Streams impacted by historic mining activity are characterized by acidic pH, unique microbial communities, and abundant metal-oxide precipitation, all of which can influence groundwater-surface water exchange. We investigate how metal-oxide precipitates and hyporheic mixing mediate the composition of microbial communities in two streams receiving acid-rock and mine drainage near Silverton, Colorado, USA. A large, neutral pH hyporheic zone facilitated the precipitation of metal particles/colloids in hyporheic porewaters. A small, low pH hyporheic zone, limited by the presence of a low-permeability, iron-oxyhydroxide layer known as ferricrete, led to the formation of steep geochemical gradients and high dissolved-metal concentrations. To determine how these two hyporheic systems influence microbiome composition, we installed well clusters and deployed in situ microcosms in each stream to sample porewaters and sediments for 16S rRNA gene sequencing. Results indicated that distinct hydrogeochemical conditions were present above and below the ferricrete in the low pH system. A positive feedback loop may be present in the low pH stream where microbially mediated precipitation of iron-oxides contributes to additional clogging of hyporheic pore spaces, separating abundant, iron-oxidizing bacteria (Gallionella spp.) above the ferricrete from rare, low-abundance bacteria below the ferricrete. Metal precipitates and colloids that formed in the neutral pH hyporheic zone were associated with a more diverse phylogenetic community of nonmotile, nutrient-cycling bacteria that may be transported through hyporheic pore spaces. In summary, biogeochemical conditions influence, and are influenced by, hyporheic mixing, which mediates the distribution of micro-organisms and, thus, the cycling of metals in streams receiving acid-rock and mine drainage.

IMPORTANCE

In streams receiving acid-rock and mine drainage, the abundant precipitation of iron minerals can alter how groundwater and surface water mix along streams (in what is known as the "hyporheic zone") and may shape the distribution of microbial communities. The findings presented here suggest that neutral pH streams with large, well-mixed hyporheic zones may harbor and transport diverse microorganisms attached to particles/colloids through hyporheic pore spaces. In acidic streams where metal oxides clog pore spaces and limit hyporheic exchange, iron-oxidizing bacteria may dominate and phylogenetic diversity becomes low. The abundance of iron-oxidizing bacteria in acid mine drainage streams has the potential to contribute to additional clogging of hyporheic pore spaces and the accumulation of toxic metals in the hyporheic zone. This research highlights the dynamic interplay between hydrology, geochemistry, and microbiology at the groundwater-surface water interface of acid mine drainage streams.

Comamonas-dominant microbial community in carbon poor aquitard sediments revealed by metagenomic-based growth rate investigation

The microbiological ecology of a low-nutrient shallow aquifer with high arsenic content in the Yinchuan Plain was investigated in this study. Amplicon sequencing data from five samples (depths: 1.5 m, 3.5 m, 11.2 m, 19.3 m, and 25.5 m) revealed diverse and adaptable microbial community. Among the microbial community, Comamonas was the most prominent, accounting for 10.52 % of the total. This genus displayed high growth rates, with a maximum growth rate of 12.06 d-1 and a corresponding doubling time of 1.38 days, as determined through an analysis of codon usage bias. Functional annotation of Metagenome-Assembled Genomes (MAGs) for samples at 1.5 m and 11.2 m depths revealed Comamonas' metabolic versatility, including various carbon pathways, assimilative sulfate reduction (ASR), and dissimilatory reduction to ammonium (DNRA). The TPM (Transcripts Per Kilobase of exon model per Million mapped reads) of MAGs at 11.2 m sample was 15.7 and 12.3. The presence of arsenic resistance genes in Comamonas aligns with sediment arsenic levels (65.8 mg/kg for 1.5 m depth, 32.8 mg/kg for 11.2 m depth). This study highlights the role of Comamonas as a 'generalist' bacteria in challenging oligotrophic sediments, emphasizing the significance of such organisms in community stability and ecological functions. ENVIRONMENTAL IMPLICATION: Low-biomass limits the microbial activity and biogeochemical study in oligotrophic environments, which is the typical condition for underground aquatic ecosystems. Facilitated by growth rate estimation, our research focuses on active functional microorganisms and their biogeochemical metabolic in oligotrophic aquifer sediments, revealing their impact on the environment and response to arsenic threats. Findings illuminate the metabolic advantage of a 'generalist life-style' in carbon-scarce environments and contribute to a broader understanding of bacterial ecosystems and environmental impacts in oligotrophic aquifer sediments worldwide.

Nitrogen removal in freshwater sediments of riparian zone: N-loss pathways and environmental controls

The riparian zone is an important location of nitrogen removal in the terrestrial and aquatic ecosystems. Many studies have focused on the nitrogen removal efficiency and one or two nitrogen removal processes in the riparian zone, and less attention has been paid to the interaction of different nitrogen transformation processes and the impact of in situ environmental conditions. The molecular biotechnology, microcosm culture experiments and 15N stable isotope tracing techniques were used in this research at the riparian zone in Weinan section of the Wei River, to reveal the nitrogen removal mechanism of riparian zone with multi-layer lithologic structure. The results showed that the nitrogen removal rate in the riparian zone was 4.14-35.19 μmol·N·kg-1·h-1. Denitrification, dissimilatory reduction to ammonium (DNRA) and anaerobic ammonium oxidation (anammox) jointly achieved the natural attenuation process of nitrogen in the riparian zone, and denitrification was the dominant process (accounting for 59.6%). High dissolved organic nitrogen and nitrate ratio (DOC:NO3-) would promote denitrification, but when the NO3- content was less than 0.06 mg/kg, DNRA would occur in preference to denitrification. Furthermore, the abundances of functional genes (norB, nirS, nrfA) and anammox bacterial 16S rRNA gene showed similar distribution patterns with the corresponding nitrogen transformation rates. Sedimentary NOX-, Fe(II), dissolved organic carbon (DOC) and the nitrogen transformation functional microbial abundance were the main factors affecting nitrogen removal in the riparian zone. Fe (II) promoted NO3- attenuation through nitrate dependent ferrous oxidation process under microbial mediation, and DOC promotes NO3- attenuation through enhancing DNRA effect. The results of this study can be used for the management of the riparian zone and the prevention and control of global nitrogen pollution.

Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream

Although river ecosystems comprise less than 1% of Earth's total non-glaciated area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. As a result, the relevance of microbiome interactions and the impacts they have over time on biogeochemical cycles are poorly understood. To assess how viral and microbial communities change over time, we sampled surface water and pore water compartments of the wastewater-impacted River Erpe in Germany every 3 hours over a 48-hour period resulting in 32 metagenomes paired to geochemical and metabolite measurements. We reconstructed 6,500 viral and 1,033 microbial genomes and found distinct communities associated with each river compartment. We show that 17% of our vMAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae, which we suggest are potential contributors to carbon and nitrogen cycling. Together, these findings demonstrate that microbial and viral communities in surface waters of this urban river can exist as stable communities along a flowing river; and raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles.

Vertical Hydrologic Exchange Flows Control Methane Emissions from Riverbed Sediments

CH₄ emissions from inland waters are highly uncertain in the current global CH₄ budget, especially for streams, rivers, and other lotic systems. Previous studies have attributed the strong spatiotemporal heterogeneity of riverine CH₄ to environmental factors such as sediment type, water level, temperature, or particulate organic carbon abundance through correlation analysis. However, a mechanistic understanding of the basis for such heterogeneity is lacking. Here, we combine sediment CH₄ data from the Hanford reach of the Columbia River with a biogeochemical-transport model to show that vertical hydrologic exchange flows (VHEFs), driven by the difference between river stage and groundwater level, determine CH₄ flux at the sediment-water interface. CH₄ fluxes show a nonlinear relationship with the magnitude of VHEFs, where high VHEFs introduce O₂ into riverbed sediments, which inhibit CH₄ production and induce CH₄ oxidation, and low VHEFs cause transient reduction in CH₄ flux (relative to production) due to reduced advective CH₄ transport. In addition, VHEFs lead to the hysteresis of temperature rise and CH₄ emissions because high river discharge caused by snowmelt in spring leads to strong downwelling flow that offsets increasing CH₄ production with temperature rise. Our findings reveal how the interplay between in-stream hydrologic flux besides fluvial-wetland connectivity and microbial metabolic pathways that compete with methanogenic pathways can produce complex patterns in CH₄ production and emission in riverbed alluvial sediments.

Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments

Rivers have a significant role in global carbon and nitrogen cycles, serving as a nexus for nutrient transport between terrestrial and marine ecosystems. Although rivers have a small global surface area, they contribute substantially to worldwide greenhouse gas emissions through microbially mediated processes within the river hyporheic zone. Despite this importance, research linking microbial and viral communities to specific biogeochemical reactions is still nascent in these sediment environments. To survey the metabolic potential and gene expression underpinning carbon and nitrogen biogeochemical cycling in river sediments, we collected an integrated data set of 33 metagenomes, metaproteomes, and paired metabolomes. We reconstructed over 500 microbial metagenome-assembled genomes (MAGs), which we dereplicated into 55 unique, nearly complete medium- and high-quality MAGs spanning 12 bacterial and archaeal phyla. We also reconstructed 2,482 viral genomic contigs, which were dereplicated into 111 viral MAGs (vMAGs) of >10 kb in size. As a result of integrating gene expression data with geochemical and metabolite data, we created a conceptual model that uncovered new roles for microorganisms in organic matter decomposition, carbon sequestration, nitrogen mineralization, nitrification, and denitrification. We show how these metabolic pathways, integrated through shared resource pools of ammonium, carbon dioxide, and inorganic nitrogen, could ultimately contribute to carbon dioxide and nitrous oxide fluxes from hyporheic sediments. Further, by linking viral MAGs to these active microbial hosts, we provide some of the first insights into viral modulation of river sediment carbon and nitrogen cycling. IMPORTANCE Here we created HUM-V (hyporheic uncultured microbial and viral), an annotated microbial and viral MAG catalog that captures strain and functional diversity encoded in these Columbia River sediment samples. Demonstrating its utility, this genomic inventory encompasses multiple representatives of dominant microbial and archaeal phyla reported in other river sediments and provides novel viral MAGs that can putatively infect these. Furthermore, we used HUM-V to recruit gene expression data to decipher the functional activities of these MAGs and reconstruct their active roles in Columbia River sediment biogeochemical cycling. Ultimately, we show the power of MAG-resolved multi-omics to uncover interactions and chemical handoffs in river sediments that shape an intertwined carbon and nitrogen metabolic network. The accessible microbial and viral MAGs in HUM-V will serve as a community resource to further advance more untargeted, activity-based measurements in these, and related, freshwater terrestrial-aquatic ecosystems.

Metagenomics to characterize sediment microbial biodiversity associated with fishing exposure within the Stellwagen Bank National Marine Sanctuary

Microbes in marine sediments constitute a large percentage of the global marine ecosystem and function to maintain a healthy food web. In continental shelf habitats such as the Gulf of Maine (GoM), relatively little is known of the microbial community abundance, biodiversity, and natural product potential. This report is the first to provide a time-series assessment (2017–2020) of the sediment microbial structure in areas open and closed to fishing within the Stellwagen Bank National Marine Sanctuary (SBNMS). A whole metagenome sequencing (WMS) approach was used to characterize the sediment microbial community. Taxonomic abundance was calculated across seven geographic sites with 14 individual sediment samples collected during the summer and fall seasons. Bioinformatics analyses identified more than 5900 different species across multiple years. Non-metric multidimensional scaling methods and generalized linear models demonstrated that species richness was inversely associated with fishing exposure levels and varied by year. Additionally, the discovery of 12 unique biosynthetic gene clusters (BGCs) collected across sites confirmed the potential for medically relevant natural product discovery in the SBNMS. This study provides a practical assessment of how fishing exposure and temporal trends may affect microbial community structure in a coastal marine sanctuary.

Fatty acid signatures of sediment microbial community in the chronically polluted mangrove ecosystem

Phospholipid fatty acid (PLFA) analysis was used to examine variation in the distribution of microbial communities in heavily polluted mangrove sediments of Thane creek, west coast of India. A total of 40 individual PLFAs representing 11 functional groups were identified in the sediment and were mainly dominated by saturated fatty acids (anaerobic prokaryotes) >50%. Significant dominance of PUFA, 16:3 ω6c (34.2%) indicators of micro-eukaryotes, in subsurface depth (p < 0.05) suggests input from the remnants of marine microalgae. Declined mean relative abundance of fungi (<6%) and actinomycetes (<1%) were detected in the sediment indicating their sensitivity to anthropic stressors. Homogenous profile of microbial diversity indicating active bioturbation. Cumulative metabolic stress evident from SAT/MUFA (>1), B/F (>1) and G⁺/G^- (<1) ratio and prolonged hypoxia to be prevalent in the creek during the study. In conclusion, PLFA signatures can thus be used as potential biomarkers of environmental monitoring and proxy for interpreting ecosystem health.

Disintegration half-life of biodegradable plastic films on different marine beach sediments

The seafloor is considered the major sink for plastic debris in the world's oceans. Biodegradable polymers are available on the market as a substitute for conventional plastic and could potentially end up in the same environment. To gain more insight into the effects of different sediments on the degradation rate of biodegradable plastic we performed two iterative seawater tank experiments. First, to test the effect of sediment grain size, film of Mater-Bi HF03V, a blend of thermoplastic starch and biodegradable polyesters, was placed on the surface of mud as well as on four different grain size fractions of beach sand. Disintegration half-life was shortest on mud (139 days) and increased with the grain size of the beach sediment fractions (63-250 µm: 296 days; 250-500 µm: 310 days; 500-1,000 µm: 438 days; >1,000 µm: 428 days). We assume that the higher surface-to-volume ratio in fine sediment compared to coarse sediment led to a higher bacterial abundance and thus to faster disintegration rates. In a follow-up experiment, the <500 µm fraction of sediment from four different beaches around Isola d'Elba, Italy, was used to test plastic disintegration as above. Additionally, polyhydroxybutyrate (PHB, MIREL P5001) was used as a positive control and high-density polyethylene (HD-PE) as a negative control. No disintegration was observed for HD-PE. Mater-Bi HF03V and PHB disintegrated significantly differently on sediment from different sites, with half-lives of Mater-Bi HF03V ranging from 72 to 368 days and of PHB from 112 to 215 days. Here, the half-life was shortest on slightly coarser sediment and at potentially anthropogenically impacted sites. We assume that the effect of the grain size on the disintegration rate was masked by other parameters influencing the microbial community and activity. Understanding the parameters driving biodegradation is key to reliably report the range of disintegration rates occurring under the various conditions in different ecosystems.

Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States

Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (< 30 cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤ 10 m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.

Grain size tunes microbial community assembly and nitrogen transformation activity under frequent hyporheic exchange: A column experiment

Hyporheic zones (HZ) are hotspots for biogeochemical reactions where groundwater and surface water mix. River dam buildings and other hydrologic controls alter the sediment grain size distribution and modify the downstream hyporheic exchange, with cascading effects on geochemical and microbial processes in river corridors. In this lab-scale column experiment, the N transformations in HZ filled with sediments in different grain sizes were investigated with a focus on understanding the interplay among variational hydraulic connectivity, microbial community structure, functional potential under frequent groundwater-surface water exchange. Porosity was identified as the main driver determining bacterial community assembly in HZ sediments. Significant microbial zonation was observed along the columns and the degree of co-occurrence of bacterial communities in the Fine column was lower than that in the Coarse and Mix columns. The Coarse column allowed for almost 2.47 times the exchange flux relative to the Fine column, and generates the fastest DO consumption rate (-6.52 μg O₂/L·s). The enrichment of nitrifiers, i.e., Cytophagaceae and Bacillaceae and nitrification functional genes, i.e., amoA_AOA and amoA_AOB revealed the higher nitrification potential in column filled with coarse sediments. In comparison, the highest NH₄⁺ production rates (2.4 × 10^-3 μg N/L·s) took place in Fine column. The higher abundancies of denitrifiers such as Comamonadaceae and Lysobacter and enrichment of functional genes of nirK and nirS interestingly suggested the elevated denitrification potential in Fine column in a more anaerobic environment. The results implied that variations in microbial functional potential and associated nitrogen transformation may occur in size-fractioned HZ to dynamic hyporheic exchange, which added new knowledge to the underlying biogeochemical and ecological processes in regulated river corridors.

Methane and nitrous oxide porewater concentrations and surface fluxes of a regulated river

Greenhouse gas (GHG) emissions from rivers are a critical missing component of current global GHG models. Their exclusion is mainly due to a lack of in-situ measurements and a poor understanding of the spatiotemporal dynamics of GHG production and emissions, which prevents optimal model parametrization. We combined simultaneous observations of porewater concentrations along different beach positions and depths, and surface fluxes of methane and nitrous oxide at a plot scale in a large regulated river during three water stages: rising, falling, and low. Our goal was to gain insights into the interactions between hydrological exchanges and GHG emissions and elucidate possible hypotheses that could guide future research on the mechanisms of GHG production, consumption, and transport in the hyporheic zone (HZ). Results indicate that the site functioned as a net source of methane. Surface fluxes of methane during river water stages at three beach positions (shallow, intermediate and deep) correlated with porewater concentrations of methane. However, fluxes were significantly higher in the intermediate position during the low water stage, suggesting that low residence time increased methane emissions. Vertical profiles of methane peaked at different depths, indicating an influence of the magnitude and direction of the hyporheic mixing during the different river water stages on methane production and consumption. The site acted as either a sink or a source of nitrous oxide depending on the elevation of the water column. Nitrous oxide porewater concentrations peaked at the upper layers of the sediment throughout the different water stages. River hydrological stages significantly influenced porewater concentrations and fluxes of GHG, probably by influencing heterotrophic respiration (production and consumption processes) and transport to and from the HZ. Our results highlight the importance of including dynamic hydrological exchanges when studying and modeling GHG production and consumption in the HZ of large rivers.

Faecal pollution affects abundance and diversity of aquatic microbial community in anthropo-zoogenically influenced lotic ecosystems

The aquatic microbiota is known to be an important factor in the sustainability of the natural water ecosystems. However, the microbial community also might include pathogens, which result in very serious waterborne diseases in humans and animals. Faecal pollution is the major cause of these diseases. Therefore, it is of immense importance to assess the potential impact of faecal pollution, originating from both anthropogenic and zoogenic sources, on the profile of microbial communities in natural water environments. To this end, the microbial taxonomic diversity of lotic ecosystems in different regions of Norway, representing urban and rural areas, exposed to various levels of faecal pollution, was investigated over the course of a 1-year period. The highest microbial diversity was found in rural water that was the least faecally polluted, while the lowest was found in urban water with the highest faecal contamination. The overall diversity of the aquatic microbial community was significantly reduced in severely polluted water. In addition, the community compositions diverged between waters where the dominant pollution sources were of anthropogenic or zoogenic origin. The results provide new insight into the understanding of how faecal water contamination, specifically that of different origins, influences the microbial diversity of natural waters.