Geogenic arsenic and arsenotrophic microbiome in groundwater from the Hetao Basin

Ecological adaptation of antimony-oxidizing bacteria (SbOB) drives habitat-specific bioremediation potential

Antimony-oxidizing bacteria (SbOB) play vital roles in Sb detoxification, yet their environmental adaptation mechanisms remain unclear. Through comparative analysis of Sb-contaminated groundwater and soil ecosystems in Xikuangshan mining area, we revealed striking habitat-driven divergence in SbOB survival strategies, focusing on community diversity, ribosomal RNA operon (rrn) copies, niche breadth, and gene profiles. Results showed that SbOB markedly enhanced α-diversity in groundwater but minimally affected soil communities. Taxonomically, Hydrogenophaga, Pseudomonas, and Aeromonas prevailed in groundwater, whereas Acidobacteria, Chloroflexi, and Gemmatimonadaceae dominated soil ecosystems. Genomic traits revealed groundwater SbOB uniquely linked Sb oxidation (aioA) and metabolic pathways for sulfur oxidation (soxB), CO2 fixation (cbbL), and N2 fixation (nifH), enabling versatile energy acquisition. These taxa demonstrated rapid responses to fluctuating organic inputs via higher rrn copies, expanding their niche through autotrophy. Additionally, oxidative stress tolerance genes enabled them to thrive under oxygen fluctuations in groundwater. Conversely, soil SbOB with lower rrn copies prioritized antibiotic resistance for niche competition. These findings establish a habitat-specific framework for Sb bioremediation. Groundwater SbOB consortia, with their multifunctional metabolic toolkit, are prime candidates for engineering bioaugmentation systems to simultaneously detoxify Sb(III) and mitigate co-contaminants (e.g., sulfides, nitrate) in mining-impacted aquifers.

Unraveling methanogenesis processes and pathways for Quaternary shallow biogenic gas in aquifer systems through geochemical, genomic and transcriptomic analyses

Shallow biogenic gas is crucial in global warming and carbon cycling. Considering the knowledge gap in the understanding of methanogenesis and metabolic mechanisms within shallow groundwater systems, we investigated Quaternary shallow biogenic gas resources from the Hetao Basin in North China, which were previously underexplored. We systematically analyzed the genesis of gas and formation water, microbial communities, methanogenic processes, and pathways using geochemistry, genomics, and transcriptomics. Our findings indicated that active freshwater environments are conducive to microbial activity and the generation of primary microbial gases. A diverse range of microbes with functions, such as hydrolysis (e.g., Caulobacter), acidogenesis, and hydrogen production (e.g., Sediminibacterium), synergistically contributed to the methanogenic process. Methanogens predominantly comprised hydrogenotrophic methanogens (e.g., Methanobacteriales), although H2-dependent methylotrophic methanogens (e.g., Methanofastidiosa) were also prevalent. The metabolic processes of the different methanogenic pathways were revealed based on functional gene analysis and mapping results. Furthermore, the composition of the community structure, functional predictions, metagenomics, and metatranscriptomics underscored the contribution of the hydrogenotrophic pathway, which ranged from 52.22 % to 79.23 %. The aceticlastic pathway exhibited high gene abundance and was primarily associated with methylotrophs and other potential pathways. The H2-dependent methylotrophic methanogenesis pathway was constrained by low metabolic activity. By revealing the methane production mechanism of biogenic gas in shallow aquifer systems, this study provides a new perspective and profound comprehension of its ecological and environmental implications worldwide.

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.

Identification of key factors and mechanism determining arsenic mobilization in paddy soil-porewater-rice system

Arsenic (As) mobilization in paddy fields poses significant health risks, necessitating a thorough understanding of the controlling factors and mechanisms to safeguard human health. We conducted a comprehensive investigation of the soil-porewater-rice system throughout the rice life cycle, focusing on monitoring arsenic distribution and porewater characteristics in typical paddy field plots. Soil pH ranged from 4.79 to 7.98, while porewater pH was weakly alkaline, varying from 7.2 to 7.47. Total arsenic content in paddy soils ranged from 6.8 to 17.2 mg/kg, with arsenic concentrations in porewater during rice growth ranging from 2.97 to 14.85 μg/L. Specifically, arsenite concentrations in porewater ranged from 0.48 to 7.91 μg/L, and arsenate concentrations ranged from 0.73 to 5.83 μg/L. Through principal component analysis (PCA) and analysis of redox factors, we identified that arsenic concentration in porewater is predominantly influenced by the interplay of reduction and desorption processes, contributing 43.5 % collectively. Specifically, the reductive dissolution of iron oxides associated with organic carbon accounted for 23.3 % of arsenic concentration dynamics in porewater. Additionally, arsenic release from the soil followed a sequence starting with nitrate reduction, followed by ferric ion reduction, and subsequently sulfate reduction. Our findings provide valuable insights into the mechanisms governing arsenic mobilization within the paddy soil-porewater-rice system. These insights could inform strategies for irrigation management aimed at mitigating arsenic toxicity and associated health risks.

Occurrence and spatiotemporal distribution of arsenic biotransformation genes in urban dust

Microbially-mediated arsenic biotransformation plays a pivotal role in the biogeochemical cycling of arsenic; however, the presence of arsenic biotransformation genes (ABGs) in urban dust remains unclear. To investigate the occurrence and spatiotemporal distributions of ABGs, a total of one hundred and eighteen urban dust samples were collected from different districts of Xiamen city, China in summer and winter. Although inorganic arsenic species, including arsenate [As(V)] and arsenite [As(III)], were found to be predominant, the methylated arsenicals, particularly trimethylarsine oxide [TMAs(V)O] and dimethylarsenate [DMAs(V)], were detected in urban dust. Abundant ABGs were identified in urban dust via AsChip analysis (a high-throughput qPCR chip for ABGs), of which As(III) S-adenosylmethionine methyltransferase genes (arsM), As(V) reductase genes (arsC), As(III) oxidase genes (aioA), As(III) transporter genes (arsB), and arsenic-sensing regulator genes (arsR) were the most prevalent, collectively constituting more than 90 % of ABGs in urban dust. Microbes involved in arsenic methylation were assigned to bacteria (e.g., Actinomycetes and Alphaproteobacteria), archaea (e.g., Halobacteria), and eukaryotes (e.g., Chlamydomonadaceae) in urban dust via the arsM amplicon sequencing. Temperature, a season-dependent environmental factor, profoundly affected the abundance of ABGs and the composition of microbes involved in arsenic methylation. This study provides new insights into the presence of ARGs within the urban dust.

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.

Functional features of a novel Sb(III)- and As(III)-oxidizing bacterium: Implications for the interactions between bacterial Sb(III) and As(III) oxidation pathways

Antimony (Sb) and arsenic (As) share similar chemical characteristics and commonly coexist in contaminated environments. It has been reported that the biogeochemical cycles of antimony and arsenic affect each other. However, there is limited understanding regarding microbial coupling between the biogeochemical processes of antimony and arsenic. Here, we aimed to solve this issue. We successfully isolated a novel bacterium, Shinella sp. SbAsOP1, which possesses both Sb(III) and As(III) oxidase, and can effectively oxidize both Sb(III) and As(III) under aerobic and anaerobic conditions. SbAsOP1 exhibits greater aerobic oxidation activity for the oxidation of As(III) or Sb(III) compared to its anaerobic activity. SbAsOP1 also significantly catalyzes the oxidative mobilization of solid-phase Sb(III) under aerobic conditions. The activity of SbAsOP1 in oxidizing solid Sb(III) is 3 times lower than its activity in oxidizing soluble form. It is noteworthy that, in the presence of both Sb(III) and As(III) under aerobic conditions, either As(III) or Sb(III) significantly inhibits the oxidation of Sb(III) or As(III), respectively. In comparison, under anaerobic conditions and in the coexistence of Sb(III) and As(III), As(III) significantly inhibits Sb(III) oxidation, whereas Sb(III) almost completely inhibits As(III) oxidation. These findings suggest that under both aerobic and anaerobic conditions, SbAsOP1 demonstrates a partial preference for Sb(III) oxidation. Additionally, bacterial oxidations of Sb(III) and As(III) mutually inhibit each other to varying degrees. These observations gain a novel understanding of the interplay between the biogeochemical processes of antimony and arsenic.

Fundamentals and application in phytoremediation of an efficient arsenate reducing bacterium Pseudomonas putida ARS1

Arsenic is a ubiquitous environmental pollutant. Microbe-mediated arsenic bio-transformations significantly influence arsenic mobility and toxicity. Arsenic transformations by soil and aquatic organisms have been well documented, while little is known regarding effects due to endophytic bacteria. An endophyte Pseudomonas putida ARS1 was isolated from rice grown in arsenic contaminated soil. P. putida ARS1 shows high tolerance to arsenite (As(III)) and arsenate (As(V)), and exhibits efficient As(V) reduction and As(III) efflux activities. When exposed to 0.6 mg/L As(V), As(V) in the medium was completely converted to As(III) by P. putida ARS1 within 4 hr. Genome sequencing showed that P. putida ARS1 has two chromosomal arsenic resistance gene clusters (arsRCBH) that contribute to efficient As(V) reduction and As(III) efflux, and result in high resistance to arsenicals. Wolffia globosa is a strong arsenic accumulator with high potential for arsenic phytoremediation, which takes up As(III) more efficiently than As(V). Co-culture of P. putida ARS1 and W. globosa enhanced arsenic accumulation in W. globosa by 69%, and resulted in 91% removal of arsenic (at initial concentration of 0.6 mg/L As(V)) from water within 3 days. This study provides a promising strategy for in situ arsenic phytoremediation through the cooperation of plant and endophytic bacterium.

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.

Insight into the enhancement effect of humic acid on microbial degradation of triclosan in anaerobic sediments

Humic acid (HA) as one class of macromolecular substances plays important roles in mediating environmental behaviors of pollutants in sediments, but its effect on microbial degradation of triclosan (TCS), a common antibacterial drug, remains unclear. In this study, the effects of HA addition with different dosages (0-5%) on TCS degradation in anaerobic sediment slurries and the underlying microbial mechanisms were investigated. The results showed that HA addition significantly accelerated the TCS removal and the maximum removal percentage (30.2%) was observed in the sediment slurry with 5% HA addition. The iron reduction rate, relative abundances of the genera Comamonas, Pseudomonas and Geobacter, and bacterial network complexity in sediment slurry were significantly enhanced due to HA addition. Based on the partial least squares path modeling analysis, the enhancement effect of HA on TCS degradation was mainly explained by Fe(II):Fe(III) ratio with the highest influence on TCS removal (total effect: 0.723), followed by dominant genera abundances (total effect: 0.391), module relative abundance (total effect: 0.272), and network topological features (total effect: 0.263). This finding enhanced our understanding of the role of HA in TCS biodegradation in contaminated sediments for bioremediation purposes.

The application of mixed stabilizing materials promotes the feasibility of the intercropping system of Gynostemma pentaphyllum/Helianthus annuus L. on arsenic contaminated soil

Intercropping technology and stabilizing materials are common remediation techniques for soils contaminated with heavy metals. This study investigated the feasibility of the Gynostemma pentaphyllum (G. pentaphyllum)/Helianthus annuus L. (H. annuus) intercropping system on arsenic (As) contaminated farmland through field and pot experiments and the regulation of plant As absorption by the application of mixed stabilizing materials in this intercropping system. Field experiments demonstrated that intercropping with H. annuus increased the As concentration in G. pentaphyllum leaves to 1.79 mg kg-1 but still met the requirements of the national food standard of China (2 mg kg-1) (GB2762-2017). Meanwhile, G. pentaphyllum yield in the intercropping system decreased by 15.09%, but the difference was insignificant (P > 0.05). Additionally, the As bioconcentration (BCA) per H. annuus plant in the intercropping system was significantly higher than that in the monoculture system, increasing by 76.37% (P < 0.05). The pot experiment demonstrated that when granite powder, iron sulfate mineral, and "Weidikang" soil conditioner were applied to the soil collectively, G. pentaphyllum leaf As concentration in the intercropping system could be significantly reduced by 42.17%. Rhizosphere pH is the most crucial factor affecting As absorption by G. pentaphyllum in intercropping systems. When these three stabilizing materials were applied simultaneously, the As bioaccumulation (BCA) per H. annuus plant was significantly higher than that of normal intercropping treatment, which increased by 71.12% (P < 0.05), indicating that the application of these stabilizing materials significantly improved the As removal efficiency of the intercropping system. Dissolved organic carbon (DOC) concentration in the rhizosphere soil is the most pivotal factor affecting As absorption by H. annuus. In summary, the G. pentaphyllum-H. annuus intercropping model is worthy of being promoted in moderately As polluted farmland. The application of granite powder, iron sulfate mineral, and "Weidikang" soil conditioner collectively to the soil can effectively enhance the potential of this intercropping model to achieve "production while repairing" in the As polluted farmland.

Deciphering spatio-seasonal patterns, driving forces, and human health risks of nitrate and fluoride enriched water bodies in the Inner Mongolia Reaches of the Yellow River Basin, China

The ecology and environment of the Yellow River Basin is threatened by fluoride and nitrate contamination induced by anthropogenic activity and geogenic factors. As a result, deciphering the spatio-temporal variability of fluoride and nitrate contamination in this area remains a challenge. Three hundred eighty-six samples of surface water and groundwater from the Inner Mongolia Reaches of the Yellow River Basin were taken for this investigation. According to the results of the multivariate statistical and geostatistical analyses, the fluoride pollution was primarily discovered in the middle and lower reaches of the study area and was determined to be more severe during the dry season. In contrast, nitrate contamination was found to be more severe during the wet season while being widely distributed in groundwater and concentrated in areas with intensive agricultural activities. The primary mechanisms governing the spatial-seasonal patterns of NO3- and F- pollution were shown by the principal component analysis, isotopic, and hydrochemical diagrams. The water-rock interaction or evaporation was crucial in the enrichment of F-. The human inputs (e.g., fertilizer or sewage) dominated fluoride and nitrate contamination. Additionally, the alkaline environment played a role in the generation of NO3- and F-. The health risk assessment concluded that the threat of fluoride contamination was greater than that of nitrate contamination. Children faced the greatest health risks, followed by females and males. These findings would serve as a guide for water management and pollution control in the Yellow River Basin.