Genome-Resolved Metagenomic Analysis of Groundwater: Insights into Arsenic Mobilization in Biogeochemical Interaction Networks

Microbial communities and functions are structured by vertical geochemical zones in a northern peatland

Northern peatlands are important carbon pools; however, differences in the structure and function of microbiomes inhabiting contrasting geochemical zones within these peatlands have rarely been emphasized. Using 16S rRNA gene sequencing, metagenomic profiling, and detailed geochemical analyses, we investigated the taxonomic composition and genetic potential across various geochemical zones of a typical northern peatland profile in the Changbai Mountains region (Northeastern China). Specifically, we focused on elucidating the turnover of organic carbon, sulfur (S), nitrogen (N), and methane (CH4). Three geochemical zones were identified and characterized according to porewater and solid-phase analyses: the redox interface (<10 cm), shallow peat (10-100 cm), and deep peat (>100 cm). The redox interface and upper shallow peat demonstrated a high availability of labile carbon, which decreased toward deeper peat. In deep peat, anaerobic respiration and methanogenesis were likely constrained by thermodynamics, rather than solely driven by available carbon, as the acetate concentrations reached 90 μmol·L-1. Both the microbial community composition and metabolic potentials were significantly different (p < 0.05) among the redox interface, shallow peat, and deep peat. The redox interface demonstrated a close interaction between N, S, and CH4 cycling, mainly driven by Thermodesulfovibrionia, Bradyrhizobium, and Syntrophorhabdia metagenome-assembled genomes (MAGs). The archaeal Bathyarchaeia were indicated to play a significant role in the organic carbon, N, and S cycling in shallow peat. Although constrained by anaerobic respiration and methanogenesis, deep peat exhibited a higher metabolic potential for organic carbon degradation, primarily mediated by Acidobacteriota. In terms of CH4 turnover, subsurface peat (10-20 cm) was a CH4 production hotspot, with a net turnover rate of ∼2.9 nmol·cm-3·d-1, while the acetoclastic, hydrogenotrophic, and methylotrophic methanogenic pathways all potentially contributed to CH4 production. The results of this study improve our understanding of biogeochemical cycles and CH4 turnover along peatland profiles.

Hydrologic changes induced by groundwater abstraction lead to arsenic mobilization in shallow aquifers

Intensive groundwater abstraction leads to hydrologic changes of groundwater. Nevertheless, the effects of hydrologic change on groundwater arsenic (As) mobilization remain controversial. Here, we investigated fluctuations in water levels and their effects on As mobilization in the shallow aquifer of the Hetao Basin. Results showed that large groundwater level fluctuations and high horizontal hydraulic gradients occurred in irrigation seasons. In the groundwater near the wetland with higher surface water levels than groundwater levels, biological index values of dissolved organic matter (DOM) ranged from 0.54 to 0.72, and a positive correlation between δ18O values and dissolved organic carbon (DOC) was observed, indicating that groundwater DOM was mainly sourced from surface water. The degradation of allochthone labile DOM drove the reductive dissolution of As-bearing Fe(III) oxides to Fe(II). Both DOC and humification indices of DOM exhibited positive correlations with horizontal hydraulic gradients downstream of the study area, implying that the humified organic matter flushed from aquifer sediments contributed to groundwater DOM. The humified DOM controlled by hydraulic conditions participated in the redox reactions mainly by shuttling electrons to As-bearing Fe(III) oxides. These findings highlight distinct roles of hydrologic changes induced by groundwater abstraction in As mobilization.

Magnetite enhances As immobilization during nitrate reduction and Fe(II) oxidation by Acidovorax sp. strain BoFeN1

Arsenic (As) cycling in groundwater is commonly coupled to the biogeochemical cycling of iron (Fe) and the associated transformation of Fe minerals present. Numerous laboratory studies suggested that Fe minerals can act as nucleation sites for further crystal growth and as catalysts for abiotic Fe(II) oxidation. In view of the widespread existence of magnetite in anoxic environments where As is often dissolved, we firstly exploited magnetite to enhance As immobilization during nitrate-reducing Fe(II) oxidation (NRFO) induced by Acidovorax sp. strain BoFeN1, a mixotrophic nitrate-reducing Fe(II)-oxidizing bacterium that can oxidize Fe(II) through both enzymatic and abiotic pathways. Subsequently, we investigated how magnetite affects NRFO and As immobilization. Results demonstrated a significant increase in As(III) removal efficiency from 75.4 % to 97.2 % with magnetite, attributed to the higher amount of NRFO and As(III) oxidation promoted by magnetite. It was found that magnetite stimulated the production of extracellular polymeric substances (EPS), which could decrease the diffusion of nitrate in the periplasm of bacteria and shield them against encrustation, resulting in a more rapid reduction of nitrate in the system with magnetite than that without magnetite. Meanwhile, Fe(II) was almost completely oxidized in the presence of magnetite during the whole 72 h experiment, while in the absence of magnetite, 47.7 % of Fe(II) remained, indicating that magnetite could obviously accelerate the chemical oxidation of Fe(II) with nitrite (the intermediates of nitrate bioreduction). Furthermore, the formation of labile Fe(III), an intermediate product of electron transfer between Fe(II) and magnetite, was reasonably deduced to be vital for anoxic As(III) oxidation. Additionally, the XPS analysis of the solid phase confirmed the oxidation of 43.8 % of As(III) to As(V). This study helps to understand the biogeochemical cycling of Fe and As in the environment, and provides a cost-effective and environmentally friendly option for in situ remediation of As-contaminated groundwater.

Hydrogeochemical differences drive distinct microbial community assembly and arsenic biotransformation in unconfined and confined groundwater of the geothermal system

High‑arsenic (As) groundwater in geothermal aquifers poses a serious threat to public health. Assembly processes governing groundwater microbial community related to As biotransformation are still unexplored in geothermal groundwater across different aquifers. To fill this gap, groundwater microorganisms, community assembly processes, and microbially metabolic coupling of carbon (C), nitrogen (N), phosphorus (P), sulfur (S), and arsenic (As) were investigated in unconfined and confined groundwater in the thermal reservoirs of the Guide Basin. The difference in groundwater hydrogeochemicals led to the heterogeneity of the microbial community and microbially mediated C, N, P, S, and As cycling between unconfined and confined groundwater. Higher temperature and As concentrations, low nutrient supply, and reduced conditions in confined groundwater supported stronger interspecific coexistence and environmental selection, thus promoting the proliferation of As-resistant microorganisms (ARMs) and simplifying the community assemblage. Abundant available nutrient supply and oxidizing conditions supported an increased species diversity and metabolic functionality in unconfined groundwater. S oxidizers, C fixation, and C degradation bacteria potentially contributed to the decreased As concentrations in unconfined groundwater. However, ARMs, ammonification, and anaerobic ammonia-oxidizing bacteria potentially caused As mobilization in confined groundwater. Overall, our results give a comprehensive insight into the interaction between As and microorganisms in geothermal groundwater.

Arsenic redox disequilibrium in geogenic contaminated groundwater: Bioenergetic insights from organic molecular characterization and gene-informed modeling

Biotransformation of arsenic (As) influences its speciation and mobility, obscuring mechanistic comprehension on spatiotemporal variation of As concentration in geogenic contaminated groundwater. In particular, unresolved processes underlying As redox disequilibrium in comparison to major redox couples discourage practical efforts to rehabilitate the As-contaminated groundwater. Here, quantitative metagenomic sequencing and ultrahigh-resolution mass spectrometry (FT-ICR-MS) were jointly applied to reveal the links between vertical distribution of As metabolic gene assemblages and that of free energy density of dissolved organic matter (DOM) in As-contaminated groundwater of Datong Basin. Observed small excess of Gibbs free energy available by DOM relative to that required for As(V)-to-As(III) reduction exerts thermodynamic constraint on metabolism-mediated redox transformation of As. Accordingly, the vertical distribution of dissolved As(V)/As(III) ratio correlated significantly with that of ars+acr3 and arr encoding As(V) reduction and aio encoding As(III) oxidation in the moderately/strongly reducing groundwater. Further gene-informed biogeochemical modeling suggests that a net effect of these kinetics-restricted bidirectional metabolic pathways leads to co-preservation of As(V) and As(III) even at relatively high rates of ars+acr3 encoded As(V) reduction. This study therefore provides new insights into bioenergetic constraints on As hydrobiogeochemical behavior, with implications for other redox-sensitive contaminants in the groundwater systems.

Synergistic effects of warming and humic substances on driving arsenic reduction and methanogenesis in flooded paddy soil

Microbially-driven arsenic reduction and methane emissions in anaerobic soils are regulated by widespread humic substances (HS), while how this effect responds to climate change remains unknown. We investigated potential synergistic effects of HS in response to temperature changes in arsenic-contaminated paddy soils treated with humic acid (HA) and fulvic acid (FA) at temperatures ranging from 15 to 45 °C. Our results reveal a significant increase in arsenic reduction (5.6 times) and methane emissions (178 times) driven by HS, which can be exponentially stimulated at 45 °C. Acting as a electron shuttle, HS determines microbial arsenic reduction, further stimulated by warming. The top three sensitive genera are Geobacter, Anaeromyxobacter, and Gaiella which are responsible for enhanced arsenic reduction, as well as for the reduction of iron and HS with their functional genes; arrA and Geobacter spp. The top three sensitive methanogens are Methanosarsina, Methanocella, and Methanoculleus. Our study suggests notable synergistic effects between HS and warming in stimulating arsenic reduction and methanogenesis in paddy soils. Overall, the findings of this work highlight the high sensitivity of HS-mediated microbial arsenic transformation and methanogenesis in response to warming, which add potential value in predicting the biogeochemical cycling of arsenic and methane in soil under the context of climate change.

Activation of iron oxides through organic matter-induced dissolved oxygen penetration depth dynamics enhances iron-cycling driven ammonium oxidation in microaerobic granular sludge

The iron redox cycle can enhance anammox in treating low-strength ammonia wastewater. However, maintaining an effective iron redox cycle and suppressing nitrite-oxidizing bacteria in a one-stage partial nitritation and anammox (PN/A) process poses challenges during long-term aeration. We proposed a novel and simple strategy to achieve an efficient iron redox cycle in an iron-mediated anoxic-microaerobic (A/O) process by controlling organic matter (OM) at medium-strength levels (30-110 mg COD/L) in microaerobic granular sludge (MGS)-dominated reactor. The developed A/O process consistently achieved >90 % OM removal and >75 % nitrogen removal. Medium-strength OM varied the penetration depths of dissolved oxygen (DO) in MGS, regulating redox conditions and promoting redox reactions across MGS layers, thus activating accumulated inert iron oxides. Ammonia-oxidizing bacteria (Nitrosomonas), iron-reducing bacteria (e.g., Ignavibacterium, Geobacter), and anammox bacteria (Ca. Kuenenia) coexisted harmoniously in MGS. This coexistence ensured high anammox and Feammox rates along with a robust iron redox cycle, thereby mitigating the adverse impacts of fluctuating DO and OM on one-stage PN/A process stability. The identification of iron reduction-associated genes within Ca. Kuenenia, Ignavibacterium, and Geobacter suggests their potential roles in supporting Feammox coupled in one-stage PN/A process. This study introduces an iron-cycle-driven A/O process as an energy-efficient alternative for simultaneous carbon and nitrogen removal from low-strength wastewater.

Biogeochemical mechanisms of iron (Fe) and manganese (Mn) in groundwater and soil profiles in the Zhongning section of the Weining Plain (northwest China)

High levels of Iron (Fe) and manganese (Mn) in soils may contribute to secondary contamination of groundwater. However, there is limited understanding of the cycling mechanisms of Fe and Mn in groundwater and soil. This study aimed to investigate the biogeochemical processes constituting the Fe and Mn cycle by combining hydrochemistry, sequential extraction and microbiological techniques. The results indicated a similar vertical distribution pattern of Fe and Mn, with lower levels of the effective form (EFC-Fe/Mn) observed at the oxygenated surface, increasing near the groundwater table and decreasing below it. Generally, there was a tendency for accumulation above the water table, with Mn exhibiting a higher release potential compared to Fe. Iron‑manganese oxides (Ox-Fe/Mn) dominated the effective forms, with Fe and Mn in the soil entering groundwater through the reduction dissolution of Ox-Fe/Mn and the oxidative degradation of organic matter or sulfide (OM-Fe/Mn). Correlation analysis revealed that Fe and Mn tend to accumulate in media with fine particles and high organic carbon (TOC) contents. 16S rRNA sequencing analysis disclosed significant variation in the abundance of microorganisms associated with Fe and Mn transformations among unsaturated zone soils, saturated zone media and groundwater, with Fe/Mn content exerting an influence on microbial communities. Furthermore, functional bacterial identification results from the FAPROTAX database show a higher abundance of iron-oxidizing bacteria (9.3 %) in groundwater, while iron and manganese-reducing bacteria are scarce in both groundwater and soil environments. Finally, a conceptual model of Fe and Mn cycling was constructed, elucidating the biogeochemical processes in groundwater and soil environments. This study provides a new perspective for a deeper understanding of the environmental fate of Fe and Mn, which is crucial for mitigating Fe and Mn pollution in groundwater.

Influence of anti-seasonal inundation on geochemical processes of arsenic speciation in the water-level-fluctuation zone soil of the Three Gorges Reservoir, China

Since the completion of Three Gorges Dam, the water-level-fluctuation zone (WLFZ) of the Three Gorges Reservoir (TGR) experiences the periodic anti-seasonal inundation. However, knowledge for mechanisms of mobilization and transformation of arsenic (As) in WLFZ soils of the TGR remains scarce. To address this gap, a combination of field observation and simulated flooding experiments attempts to illustrate the As mobilization, the transformation between As(V) and As(III), and the factors driving these processes. The study revealed that anti-seasonal inundation (with a temperature at 13 ℃) mitigated As release from submerged soils. Interestingly, the total As and ratio of As(III) (the more toxic form of As) concentrations in porewater at 13 ℃ was lower, and the prevalence of As(III) occurred later than those at 32 °C (imitate the seasonal inundation condition). The results indicated that the As reduction and the corresponding toxic risks in submerged soils were alleviated under anti-seasonal inundation. The study proposes the reduction of As-bearing manganese (Mn) mineral assemblages and competitive adsorption of dissolved organic carbon (DOC) as primary mechanisms for As mobilization. Furthermore, microorganism-mediated detoxification/reduction processes involving DOC, nitrogen, and Mn (oxyhydr)oxides were identified as central pathways for As(III) enrichment under anti-seasonal inundation. This study enhances understandings of the biogeochemical processes and fate of As in WLFZ soils influenced by artificial regulation of the reservoir.

Prediction of arsenic and fluoride in groundwater of the North China Plain using enhanced stacking ensemble learning

Chronic exposure to elevated geogenic arsenic (As) and fluoride (F-) concentrations in groundwater poses a significant global health risk. In regions around the world where regular groundwater quality assessments are limited, the presence of harmful levels of As and F- in shallow groundwater extracted from specific wells remains uncertain. This study utilized an enhanced stacking ensemble learning model to predict the distributions of As and F- in shallow groundwater based on 4,393 available datasets of observed concentrations and forty relevant environmental factors. The enhanced model was obtained by fusing well-suited Extreme Gradient Boosting, Random Forest, and Support Vector Machine as the base learners and a structurally simple Linear Discriminant Analysis as the meta-learner. The model precisely captured the patchy distributions of groundwater As and F- with an AUC value of 0.836 and 0.853, respectively. The findings revealed that 9.0% of the study area was characterized by a high As risk in shallow groundwater, while 21.2% was at high F- risk identified as having a high risk of fluoride contamination. About 0.2% of the study area shows elevated levels of both of them. The affected populations are estimated at approximately 7.61 million, 34.1 million, and 0.2 million, respectively. Furthermore, sedimentary environment exerted the greatest influence on distribution of groundwater As, with human activities and climate following closely behind at 29.5%, 28.1%, and 21.9%, respectively. Likewise, sedimentary environment was the primary factor affecting groundwater F- distribution, followed by hydrogeology and soil physicochemical properties, contributing 27.8%, 24.0%, and 23.3%, respectively. This study contributed to the identification of health risks associated with shallow groundwater As and F-, and provided insights into evaluating health risks in regions with limited samples.

Promoting the transformation of green rust for As immobilization with Acidovorax sp. strain BoFeN1

Microbially mediated Fe(II) oxidation has a great potential for attenuating arsenic (As) mobility in an anoxic groundwaters. Green rust (GR), a common Fe(II)-bearing phase in such environments, could be easily oxidized into Fe (oxyhydr)oxides through microbial activity. This study focused on Acidovorax sp. strain BoFeN1, an anaerobic nitrate-reducing Fe(II)-oxidizing (NRFO) bacterium, to promote the transformation of GR. In biotic GR transformation experiments, magnetite formation occurred at [As]ini = 5 mg/L while lepidocrocite and goethite were formed at [As]ini = 10 mg/L. In the absence of bacterium, the GR persisted throughout the 120-h experiment. Meanwhile, with the addition of strain BoFeN1, the final aqueous As concentration significantly decreased from 0.237 to 0.004 mg/L (C0 = 5 mg/L) and from 1.457 to 0.096 mg/L (C0 = 10 mg/L) at 120 h. It was indicated that strain BoFeN1 played a crucial role in promoting the GR transformation and enhancing As immobilization. Further investigations revealed that the role of strain BoFeN1 extended beyond Fe-oxidation. With nitrite (the intermediate of nitrate bioreduction) as oxidizer, lepidocrocite/goethite were formed in the chemical-oxidation system, excluding magnetite. In the Bio - [As]ini = 5 mg/L, the occurrence of lepidocrocite via the bio-oxidation of Fe(II) in GR at 24 h, along with the metabolism of strain BoFeN1 reducing nitrate accompanied with H+ consumption, it should be reasonably deduced that the alkaline micro-environment of periplasm induced by strain BoFeN1 were vital for the transformation of lepidocrocite to magnetite triggered by trace Fe(II). However, in the Bio - [As]ini = 10 mg/L, more As adsorbed on GR inhibiting the adsorption of bacterium, so the alkaline micro-environment had no obvious effect on such transformation. This study helps to understand the interdependence between GR and anaerobic NRFO bacterium, and provides a new perspective for more effective As remediation strategies in anoxic groundwaters.

Hydrochemical and microbial community characteristics and the sources of inorganic nitrogen in groundwater from different aquifers in Zhanjiang, Guangdong Province, China

Groundwater from different aquifers in the Zhanjiang area suffers from different degrees of nitrogen pollution, which poses a serious threat to the health of urban and rural residents as well as the surrounding aquatic ecological environment. However, neither the water chemistry and microbial community characteristics in different aquifer media nor the sources of inorganic nitrogen pollution have been extensively studied. This study integrated water quality parameters, dual isotopes (δ15N-NO3- and δ18O-NO3-), and 16S rRNA data to clarify the hydrochemical and microbial characteristics of loose rock pore water (LRPW), layered bedrock fissure water (LBFW), and volcanic rock pore fissure water (VRPFW) in the Zhanjiang area and to determine inorganic nitrogen pollution and sources. The results show that the hydrochemistry of groundwater in different aquifers is complex and diverse, which is mainly affected by rock weathering and atmospheric precipitation, and the cation exchange is strong. High NO3- concentration reduces the richness of the microbial community (VRPFW). There are a large number of bacteria related to nitrogen (N) cycle in groundwater and nitrification dominated the N transformation. A quarter of the samples exceeded the relevant inorganic nitrogen index limits specified in the drinking water standard for China. The NO3- content is highest in VRPFW and the NH4+ content is highest in shallow loose rock pore water (SLRPW). In general, NO3-/Cl-, dual isotope (δ15N-NO3- and δ18O-NO3-) data and MixSIAR quantitative results indicate manure and sewage (M&S) and soil organic nitrogen (SON) are the main sources of NO3-. In LRPW, as the depth increases, the contribution rate of M&S gradually decreases, and the contribution rate of SON gradually increases. The results of uncertainty analysis show that the UI90 values of SON and M&S are higher. This study provides a scientific basis for local relevant departments to address inorganic nitrogen pollution in groundwater.

Deciphering the spatial heterogeneity of groundwater arsenic in Quaternary aquifers of the Central Yangtze River Basin

Significant spatial variability of groundwater arsenic (As) concentrations in South/Southeast Asia is closely associated with sedimentogenesis and biogeochemical cycling processes. However, the role of fine-scale differences in biogeochemical processes under similar sedimentological environments in controlling the spatial heterogeneity of groundwater As concentrations is poorly understood. Within the central Yangtze Basin, dissolved organic matter (DOM) and microbial functional communities in the groundwater and solid-phase As-Fe speciation in Jianghan Plain (JHP) and Jiangbei Plain (JBP) were compared to reveal mechanisms related to the spatial heterogeneity of groundwater As concentration. The optical signatures of DOM showed that low molecular terrestrial fulvic-like with highly humified was predominant in the groundwater of JHP, while terrestrial humic-like and microbial humic-like with high molecular weight were predominant in the groundwater of JBP. The inorganic carbon isotope, microbial functional communities, and solid-phase As-Fe speciation suggest that the primary process controlling As accumulation in JHP groundwater system is the degradation of highly humified OM by methanogens, which drive the reductive dissolution of amorphous iron oxides. While in JBP groundwater systems, anaerobic methane-oxidizing microorganisms (AOM) coupled with fermentative bacteria, iron reduction bacteria (IRB), and sulfate reduction bacteria (SRB) utilize low molecular weight DOM degradation to drive biotic/abiotic reduction of Fe oxides, further facilitating the formation of carbonate associated Fe and crystalline Fe oxides, resulting in As release into groundwater. Different biogeochemical cycling processes determine the evolution of As-enriched aquifer systems, and the coupling of multiple processes involving organic matter transformation‑iron cycling‑sulfur cycling-methane cycling leads to heterogeneity in the spatial distribution of As concentrations in groundwater. These findings provide new perspectives to decipher the spatial variability of As concentrations in groundwater.

Can Sb(III)-oxidizing prokaryote also oxidize As(III) under aerobic and anaerobic conditions, and vice versa?

Sb(III) and As(III) share similar chemical features and coexist in the environment. However, their oxidase enzymes have completely different sequences and structures. This raises an intriguing question: Could Sb(III)-oxidizing prokaryotes (SOPs) also oxidize As(III), and vice versa? Regarding this issue, previous investigations have yielded unclear, incorrect and even conflicting data. This work aims to address this matter. First, we prepared an enriched population of SOPs that comprises 55 different AnoA genes, lacking AioAB and ArxAB genes. We found that these SOPs can oxidize both Sb(III) and As(III) with comparable capabilities. To further confirm this finding, we isolated three cultivable SOP strains that have AnoA gene, but lack AioAB and ArxAB genes. We observed that they also oxidize both Sb(III) and As(III) under both anaerobic and aerobic conditions. Secondly, we obtained an enriched population of As(III)-oxidizing prokaryotes (AOPs) from As-contaminated soils, which comprises 69 different AioA genes, lacking AnoA gene. We observed that the AOP population has significant As(III)-oxidizing activities, but lack detectable Sb(III)-oxidizing activities under both aerobic and anaerobic conditions. Therefore, we convincingly show that SOPs can oxidize As(III), but AOPs cannot oxidize Sb(III). These findings clarify the previous ambiguities, confusion, errors or contradictions regarding how SOPs and AOPs oxidize each other's substrate.

Activation of iron oxide minerals in an aquifer by humic acid to promote adsorption of organic molecules

In aquifers, the sequestration and transformation of organic carbon are closely associated with soil iron oxides and can facilitate the release of iron ions from iron oxide minerals. There is a strong interaction between dissolved organic matter (DOM) and iron oxide minerals in aquifers, but the extent to which iron is activated by DOM exposure to active iron minerals in natural aquifers, the microscopic distribution of minerals on the surface, and the mechanisms involved in DOM molecular transformation are currently unclear. This study investigated the nonbiological reduction transformation and coupled adsorption of iron oxide minerals in aquifers containing DOM from both macro- and micro perspectives. The results of macroscopic dynamics experiments indicate that DOM can mediate soluble iron release during the reduction of iron oxide minerals, that pH strongly affects DOM removal, and that DOM is more efficiently degraded at low rather than high pH values, suggesting that a low pH is conducive to DOM adsorption and oxidation. Spherical aberration-corrected scanning transmission electron microscopy (SACTS) indicates that the reacted mineral surfaces are covered with large amounts of carbon and that dynamic agglomeration of iron, carbon, and oxygen occurs. At the nanoscale, three forms of DOM are found in the mineral surface agglomerates (on the surfaces, inside the surface agglomerates, and in the polymer pores). The microscopic organic carbon and iron mineral reaction patterns can form through oxidation reactions and selective adsorption effects. Fourier transform ion cyclotron resonance mass spectra indicate that both synergistic and antagonistic reactions occur between DOM and the minerals, that the release of iron is accompanied by DOM decomposition and humification, that large oxygen- and carbon-containing molecules are broken down into smaller oxygen- and carbon-containing compounds and that more molecules are produced through oxidation under acidic rather than alkaline conditions. These molecules provide adsorption sites for sediment, meaning that more iron can be released. Microscopic evidence for the release of iron was acquired. These results improve the understanding of the geochemical processes affecting iron in groundwater, the nonbiological transformation mechanisms that occur at the interfaces between natural iron minerals and organic matter, groundwater pollution control, and the environmental behavior of pollutants.

Efficient stabilization of arsenic migration and conversion in soil with surfactant-modified iron-manganese oxide: Environmental effects and mechanistic insights

The use of iron-manganese oxide (FMO) as a promising amendment for remediating arsenic (As) contamination in soils has gained attention, but its application is limited owing to agglomeration issues. This study aims to address agglomeration using surfactant-modified FMO and investigate their stabilization behavior towards As and resulting environmental changes upon amendments. The results confirmed the efficacy of surfactants and demonstrated that cetyltrimethylammonium-bromide-modified FMO significantly reduced the leaching concentration of As by 92.5 % and effectively suppressed the uptake of As by 85.8 % compared with the control groups. The ratio of the residual fraction increased from 30.5-41.6 % in unamended soil to 67.9-69.2 %. The number of active sites was through the introduction of surfactants and immobilized As via complexation, ion exchange, and redox reactions. The study also revealed that amendments and the concentration of As influenced the soil physicochemical properties and enriched bacteria associated with As and Fe reduction and changed the distribution of C, N, Fe, and As metabolism genes, which promoted the stabilization of As. The interactions among cetyltrimethylammonium bromide, FMO, and microorganisms were found to have the greatest effect on As immobilization.

Biological oxidation of As(III) and Sb(III) by a novel bacterium with Sb(III) oxidase rather than As(III) oxidase under anaerobic and aerobic conditions

Sb and As are chemically similar, but the sequences and structures of Sb(III) and As(III) oxidase are totally distinct. It is thus interesting to explore whether Sb(III) oxidase oxidizes As(III), and if so, how microbial oxidations of Sb(III) and As(III) influence one another. Previous investigations have yielded ambiguous or even erroneous conclusions. This study aimed to clarify this issue. Firstly, we prepared a consortium of Sb(III)-oxidizing prokaryotes (SOPs) by enrichment cultivation. Metagenomic analysis reveals that SOPs with the Sb(III) oxidase gene, but lacking the As(III) oxidase gene are predominant in the SOP community. Despite this, SOPs exhibit comparable Sb(III) and As(III)-oxidizing activities in both aerobic and anaerobic conditions, indicating that at the microbial community level, Sb(III) oxidase can oxidize As(III). Secondly, we isolated a representative cultivable SOP, Ralstonia sp. SbOX with Sb(III) oxidase gene but without As(III) oxidase gene. Genomic analysis of SbOX reveals that this SOP strain has a complete Sb(III) oxidase (AnoA) gene, but lacks As(III) oxidase (AioAB or ArxAB) gene. It is interesting to discover that, besides its Sb(III) oxidation activities, SbOX also exhibits significant capabilities in oxidizing As(III) under both aerobic and anaerobic conditions. Moreover, under aerobic conditions and in the presence of both Sb(III) and As(III), SbOX exhibited a preference for oxidizing Sb(III). Only after the near complete oxidation of Sb(III) did SbOX initiate rapid oxidation of As(III). In contrast, under anaerobic conditions and in the presence of both Sb(III) and As(III), Sb(III) oxidation notably inhibited the As(III) oxidation pathway in SbOX, while As(III) exhibited minimal effects on the Sb(III) oxidation. These findings suggest that SOPs can oxidize As(III) under both aerobic and anaerobic conditions, exhibiting a strong preference for Sb(III) over As(III) oxidation in the presence of both. This study unveils a novel mechanism of interaction within the Sb and As biogeochemical cycles.

Spatiotemporal successions of N, S, C, Fe, and As cycling genes in groundwater of a wetland ecosystem: Enhanced heterogeneity in wet season

Microorganisms in wetland groundwater play an essential role in driving global biogeochemical cycles. However, largely due to the dynamics of spatiotemporal surface water-groundwater interaction, the spatiotemporal successions of biogeochemical cycling in wetland groundwater remain poorly delineated. Herein, we investigated the seasonal coevolution of hydrogeochemical variables and microbial functional genes involved in nitrogen, carbon, sulfur, iron, and arsenic cycling in groundwater within a typical wetland, located in Poyang Lake Plain, China. During the dry season, the microbial potentials for dissimilatory nitrate reduction to ammonium and ammonification were dominant, whereas the higher potentials for nitrogen fixation, denitrification, methane metabolism, and carbon fixation were identified in the wet season. A likely biogeochemical hotspot was identified in the area located in the low permeable aquifer near the lake, characterized by reducing conditions and elevated levels of Fe2+ (6.65-17.1 mg/L), NH4+ (0.57-3.98 mg/L), total organic carbon (1.02-1.99 mg/L), and functional genes. In contrast to dry season, higher dissimilarities of functional gene distribution were observed in the wet season. Multivariable statistics further indicated that the connection between the functional gene compositions and hydrogeochemical variables becomes less pronounced as the seasons transition from dry to wet. Despite this transition, Fe2+ remained the dominant driving force on gene distribution during both seasons. Gene-based co-occurrence network displayed reduced interconnectivity among coupled C-N-Fe-S cycles from the dry to the wet season, underpinning a less complex and more destabilizing occurrence pattern. The rising groundwater level may have contributed to a reduction in the stability of functional microbial communities, consequently impacting ecological functions. Our findings shed light on microbial-driven seasonal biogeochemical cycling in wetland groundwater.

Arsenic biogeochemical cycling association with basin-scale dynamics of microbial functionality and organic matter molecular composition

Geogenic arsenic (As)-contaminated groundwater is a sustaining global health concern that is tightly constrained by multiple interrelated biogeochemical processes. However, a complete spectrum of the biogeochemical network of high-As groundwater remains to be established, concurrently neglecting systematic zonation of groundwater biogeochemistry on the regional scale. We uncovered the geomicrobial interaction network governing As biogeochemical pathways by merging in-field hydrogeochemical monitoring, metagenomic analyses, and ultrahigh resolution mass spectrometry (FT-ICR MS) characterization of dissolved organic matter. In oxidizing to weakly reducing environments, the nitrate-reduction and sulfate-reduction encoding genes (narGHI, sat) inhibited the dissolution of As-bearing iron minerals, leading to lower As levels in groundwater. In settings from weakly to moderately reducing, high abundances of sulfate-reduction and iron-transport encoding genes boosted iron mineral dissolution and consequent As release. As it evolved to strongly reducing stage, elevated abundance of methane cycle-related genes (fae, fwd, fmd) further enhanced As mobilization in part by triggering the formation of gaseous methylarsenic. During redox cycling of N, S, Fe, C and As in groundwater, As migration to groundwater and immobilization in mineral particles are geochemically constrained by basin-scale dynamics of microbial functionality and DOM molecular composition. The study constructs a theoretical model to summarize new perspectives on the biogeochemical network of As cycling.

Iron cycle-enhanced anaerobic ammonium oxidation in microaerobic granular sludge

Granule-based partial nitritation and anaerobic ammonium oxidation (PN/A) is an energy-efficient approach for treating ammonia wastewater. When treating low-strength ammonia wastewater, the stable synergy between PN and anammox is however difficult to establish due to unstable dissolved oxygen control. Here, we proposed, the PN/A granular sludge formed by a micro-oxygen-driven iron redox cycle with continuous aeration (0.42 ± 0.10 mg-O2/L) as a novel strategy to achieve stable and efficient nitrogen (N) removal. 240-day bioreactor operation showed that the iron-involved reactor had 37 % higher N removal efficiency than the iron-free reactor. Due to the formation of the microaerobic granular sludge (MGS), the bio(chemistry)-driven iron cycle could be formed with the support of anaerobic ammonium oxidation coupled to Fe3+ reduction. Both ammonia-oxidizing bacteria and generated Fe2+ could scavenge the oxygen as a defensive shield for oxygen-sensitive anammox bacteria in the MGS. Moreover, the iron minerals derived from iron oxidation and Fe-P precipitates were also deposited on the MGS surface and/or embedded in the internal channels, thus reducing the size of the channels that could limit oxygen mass transfer inside the MGS. The spatiotemporal assembly of diverse functional microorganisms in the MGS for the realization of stable PN/A could be achieved with the support of the iron redox cycle. In contrast, the iron-free MGS could not optimize oxygen mass transfer, which led to an unstable and inefficient PN/A. This work provides an alternative iron-related autotrophic N removal for low-strength ammonia wastewater.

Identification of methane cycling pathways in Quaternary alluvial-lacustrine aquifers using multiple isotope and microbial indicators

Groundwater rich in dissolved methane is often overlooked in the global or regional carbon cycle. Considering the knowledge gap in understanding the biogeochemical behavior of methane in shallow aquifers, particularly those in humid alluvial-lacustrine plains with high organic carbon content, we investigated methane sources and cycling pathways in groundwater systems at the central Yangtze River basins. Composition of multiple stable isotopes (2H/18O in water, 13C in dissolved inorganic carbon, 13C/2H in methane, and 13C in carbon dioxide) was combined with the characteristics of microbes and dissolved organic matter (DOM) in the study. The results revealed significant concentrations of biogenic methane reaching up to 13.05 mg/L in anaerobic groundwater environments with abundant organic matter. Different pathways for methane cycling (methanogenic CO2-reduction and acetate-fermentation, and methane oxidation) were identified. CO2-reduction dominated acetate-fermentation in the two methanogenic pathways primarily associated with humic DOM, while methane oxidation was more closely associated with microbially derived DOM. The abundance of obligate CO2-reduction microorganisms (Methanobacterium and Methanoregula) was higher in samples with substantial CO2-reduction, as indicated by isotopic composition. The obligate acetate-fermentation microorganism (Methanosaeta) was more abundant in samples exhibiting evident acetate-fermentation. Additionally, a high abundance of Candidatus Methanoperedens was identified in samples with apparent methane oxidation. Comparing our findings with those in other areas, we found that various factors, such as groundwater temperature, DOM abundance and types, and hydrogeological conditions, may lead to differences in groundwater methane cycling. This study offered a new perspective and understanding of methane cycling in worldwide shallow alluvial-lacustrine aquifer systems without geothermal disturbance.

Ammonium-Enhanced Arsenic Mobilization from Aquifer Sediments

Ammonium-related pathways are important for groundwater arsenic (As) enrichment, especially via microbial Fe(III) reduction coupled with anaerobic ammonium oxidation; however, the key pathways (and microorganisms) underpinning ammonium-induced Fe(III) reduction and their contributions to As mobilization in groundwater are still unknown. To address this gap, aquifer sediments hosting high As groundwater from the western Hetao Basin were incubated with 15N-labeled ammonium and external organic carbon sources (including glucose, lactate, and lactate/acetate). Decreases in ammonium concentrations were positively correlated with increases in the total produced Fe(II) (Fe(II)tot) and released As. The molar ratios of Fe(II)tot to oxidized ammonium ranged from 3.1 to 3.7 for all incubations, and the δ15N values of N2 from the headspace increased in 15N-labeled ammonium-treated series, suggesting N2 as the key end product of ammonium oxidation. The addition of ammonium increased the As release by 16.1% to 49.6%, which was more pronounced when copresented with organic electron donors. Genome-resolved metagenomic analyses (326 good-quality MAGs) suggested that ammonium-induced Fe(III) reduction in this system required syntrophic metabolic interactions between bacterial Fe(III) reduction and archaeal ammonium oxidation. The current results highlight the significance of syntrophic ammonium-stimulated Fe(III) reduction in driving As mobilization, which is underestimated in high As groundwater.

Metabolic coupling of arsenic, carbon, nitrogen, and sulfur in high arsenic geothermal groundwater: Evidence from molecular mechanisms to community ecology

Groundwater arsenic (As) poses a global environmental problem and is regulated by complex biogeochemical processes. However, the As biogeochemistry and its metabolic coupling with carbon (C), nitrogen (N), and sulfur (S) in high As geothermal groundwater remain unclear. Here, we reported significant shifts in the geothermal groundwater microbiome and its functional ecological clusters along the flow path with increased As levels and dynamic As-C-N-S biogeochemical cycle from the Guide Basin, China. Strong associations among As(III), NH4+, HCO3-, and corresponding functional microbial taxa suggest that microbe-mediated As transformation, ammonification, and organic carbon biodegradation potentially contributed to the As mobilization in the discharge area. And As oxidizers (coupling with denitrification or carbon fixation) and S oxidizers were closely linked to the transformation of As(III) to immobile As(V) in the recharge area. Our study provides a comprehensive insight into the complex microbial As-C-N-S coupling network and its potential role in groundwater As mobilization under hydrological disturbances.

Unveiling the biogeochemical mechanism of nitrate in the vadose zone-groundwater system: Insights from integrated microbiology, isotope techniques, and hydrogeochemistry

Clarifying the biogeochemical mechanism of nitrate (NO3-) in the vadose zone-groundwater system, particularly in agricultural contexts, is crucial for mitigating groundwater NO3- pollution. However, comprehensive studies on the impacts of changes in chemical indicators and microbial communities on NO3- are still lacking. This paper aims to address this gap by employing hydrogeochemistry, stable isotopes, and microbial techniques to assess the NO3- biogeochemical processes in the vadose zone-groundwater system. The findings suggested that NO3- in upper soil layers was primarily influenced by plant root absorption, assimilation, and nitrification processes. The oxygen contents gradually decreased with the nitrification process, resulting in the occurrence of the denitrification. However, denitrification predominantly occurred in the 60-80 cm soil layer in the study area. The limited thickness of the denitrification layer results in less NO3- consumption, leading to increased NO3- leaching into groundwater. Hydrochemical and isotopic characteristics further indicated that groundwater NO3- concentrations were mainly controlled by nitrification, followed by denitrification and mixing processes. The 16S rRNA sequencing analysis revealed great influences of soil sampling depths and groundwater NO3- concentrations on the microbial community structure. Additionally, the PICRUSt2-based prediction results demonstrated a stronger potential for dissimilatory reduction of NO3- to ammonium (DNRA) in both soil and groundwater compared to the other processes, potentially due to the widespread presence of the nrfH functional genes. However, the chemical indicators and isotopes used in this study did not support the occurrence of DNRA process in the vadose zone-groundwater system. This finding highlights the importance of an integrated approach combining microbiological, isotopic, and hydrogeochemical data to comprehensive understanding biogeochemical processes. The study developed a conceptual model elucidating the NO3- biogeochemical processes in the vadose zone-groundwater system within an agricultural area, contributing to enhanced comprehension and advancement of sustainable management practices for groundwater nitrogen.

Nitrogen fixation and diazotroph diversity in groundwater systems

Biological nitrogen fixation (BNF), the conversion of N2 into bioavailable nitrogen (N), is the main process for replenishing N loss in the biosphere. However, BNF in groundwater systems remains poorly understood. In this study, we examined the activity, abundance, and community composition of diazotrophs in groundwater in the Hetao Plain of Inner Mongolia using 15N tracing methods, reverse transcription qPCR (RT-qPCR), and metagenomic/metatranscriptomic analyses. 15N2 tracing incubation of near in situ groundwater (9.5-585.4 nmol N L-1 h-1) and N2-fixer enrichment and isolates (13.2-1728.4 nmol N g-1 h-1, as directly verified by single-cell resonance Raman spectroscopy), suggested that BNF is a non-negligible source of N in groundwater in this region. The expression of nifH genes ranged from 3.4 × 103 to 1.2 × 106 copies L-1 and was tightly correlated with dissolved oxygen (DO), Fe(II), and NH4+. Diazotrophs in groundwater were chiefly aerobes or facultative anaerobes, dominated by Stutzerimonas, Pseudomonas, Paraburkholderia, Klebsiella, Rhodopseudomonas, Azoarcus, and additional uncultured populations. Active diazotrophs, which prefer reducing conditions, were more metabolically diverse and potentially associated with nitrification, sulfur/arsenic mobilization, Fe(II) transport, and CH4 oxidation. Our results highlight the importance of diazotrophs in subsurface geochemical cycles.

Arsenic removal in flue gas through anaerobic denitrification and sulfate reduction cocoupled arsenic oxidation

Arsenic in flue gas from municipal solid waste incineration can damage to human health and ecological environment. A sulfate-nitrate-reducing bioreactor (SNRBR) for flue gas arsenic removal was investigated. Arsenic removal efficiency attained 89.4%. An integrated metagenomic and metaproteomic investigation showed that three nitrate reductases (NapA, NapB and NarG), three sulfate reductases (Sat, AprAB and DsrAB), and arsenite oxidase (ArxA) regulated nitrate reduction, sulfate reduction and bacterial As(III)-oxidation, respectively. Citrobacter and Desulfobulbus could synthetically regulate the expression of arsenite-oxidizing gene, nitrate reductases and sulfate reducatases, which involved in As(III) oxidation, nitrate and sulfate reduction. A bacterial consortium containing Citrobacter, UG_Enterobacteriaceas, Desulfobulbus and Desulfovibrio could capable of simultaneously arsenic oxidation, sulfate reduction and denitrification. Anaerobic denitrification and sulfate reduction were cocoupled to arsenic oxidation. The biofilm was characterized by FTIR, XPS, XRD, EEM, and SEM. XRD and XPS spectra verified the formation of aarsenic species (As(V)) from flue gas As(III) conversion. Arsenic speciation in biofilms of SNRBR consisted of 77% residual arsenic, 15.9% organic matter-bound arsenic, and 4.3% strongly absorbed arsenic. Flue gas arsenic was bio-stabilized in the form of Fe-As-S and As-EPS through biodeposition, biosorption and biocomplexation. This provides a new way of flue gas arsenic removal using the sulfate-nitrate-reducing bioreactor.

Effect of phosphate on ferrihydrite transformation and the associated arsenic behavior mediated by sulfate-reducing bacterium

Although PO₄^3- is commonly found in association with iron (oxyhydr)oxide, the effect of PO₄^3- on ferrihydrite reduction, mineralogical transformation, and associated As behavior in sulfate-reducing bacteria (SRB)-rich environments remains unclear. In this study, batch experiments, together with geochemical, mineralogical, and biological analyses, were conducted to elucidate these processes. The results showed that SRB can reduce ferrihydrite via direct and indirect processes, and PO₄^3- promoted ferrihydrite reduction by supporting SRB growth at low and medium PO₄^3- loadings. However, at high loadings, PO₄^3- stabilized the ferrihydrite. PO₄^3- shifted the transformation of ferrihydrite from magnetite and mackinawite to vivianite, which scavenges As effectively by incorporating As into its particle. In systems with 0.5 mM SO₄^2-, PO₄^3- exerted a weak effect on As mobilization. However, in systems with 10 mM SO₄^2-, substantial amounts of As were released into the solution, and PO₄^3- impacted As behavior strongly. Low PO₄^3- loadings increased the mobilization of As because of the competitive adsorption of PO₄^3- on mackinawite. Medium and high PO₄^3- loadings were beneficial for As immobilization because of the substitution of mackinawite by vivianite. These findings have important implications for understanding the biogeochemistry of iron (oxyhydr)oxide and As behavior in SRB-containing sediments.

The influence mechanism of hydrogeochemical environment and sulfur and nitrogen cycle on arsenic enrichment in groundwater: A case study of Hasuhai basin, China

Hydro-biogeochemical processes control the formation and evolution of high arsenic (As) groundwater. However, the effects of nitrogen and sulfur cycles in groundwater on As migration and transformation are not well understood. Thus, twenty-one groundwater samples were collected from the Hasuhai basin. Hydrochemistry and geochemical modeling were used to analyze the geochemical processes associated with nitrogen and sulfur cycles. An arsenic speciation model (AM) and a sulfide-As model (SAM) were constructed to verify the existence of As species and the formation mechanism of thioarsenate. A hydrous ferric oxide (Hfo)-As adsorption model (HAM) and a competitive adsorption model (CAM) were used to reveal the adsorption and desorption mechanisms of As. The results showed that high arsenic groundwater (As > 10 μg/L) was mainly distributed under reductive conditions, and the highest concentration was 231.5 μg/L. The modeling results revealed that sulfides were widely involved in the geochemical cycle of As, with H₃AsO₃ and H₂AsO₃^- accounting for >70 % of the total As, and thioarsenate accounting for 30 %. S/As < 2.5 and S/Fe < l control the formation of thioarsenate. With the high correlation of NH₄⁺, TFe, sulfide, and TAs, the co-mobilization of N and S cycles may facilitate As enrichment in groundwater. A weak alkaline reduction environment triggered by the decomposition of organic matter was the main factor leading to the transfer of As from the aquifer to the groundwater. This research contributes to the development of high-As groundwater, and the findings are of general significance for drinking water in the Hasuhai Basin.

Geogenic arsenic and arsenotrophic microbiome in groundwater from the Hetao Basin

High arsenic (As) in groundwater is an environmental issue of global concern, which is closely related to microbe-mediated As biogeochemical cycling. However, the distribution of genes related to As cycling and underlying microbial As biogeochemical processes in high As groundwater remain elusive. Hence, we profiled the As cycling genes (arsC, arrA, and aioA genes) and indigenous microbial communities in groundwater from a typical high As area, the Hetao Basin from China, using amplicon sequencing and qPCR techniques. Here, we revealed the significant difference in microbial community structure between low As groundwater samples (LG) and high As groundwater samples (HG). Acinetobacter, Thiovirga, Hydrogenophaga, and Sulfurimonas were dominant in LG, while Aquabcterium, Acinetobacter, Sphingomonas, Pseudomonas, Desulfomicrobium, Hydrogenophaga, and Nitrospira were predominant in HG. Shannon and Chao indices of the microbial communities in HG were significantly higher than those of in LG. Alpha diversity and abundance of arsC and arrA genes were higher than those of aioA genes. The significant positive correlation was uncovered between the abundances of arsC and aioA genes, suggesting the cooccurrence of As functional genes in groundwater. Sphingopyxis, Agrobacterium, Klebsiella, Hoeflea, and Aeromonas represented the dominant taxa within the As (V) reducers communities. Distance-based redundancy analysis showed that ORP, pH, As_tot, Mn, and DOC were the key factors shaping the diverse microbial populations, while ORP, S^2-, As(III), Fe(II), NH₄⁺, pH, Mn, SO₄^2-, As(V), temperature, and P as the main drivers affecting arsenotrophic microbiota. This work provides an insight into microbial communities linked to As biogeochemical processes in high As groundwater, playing a fundamental role in groundwater As cycling.