Microbial community in high arsenic shallow groundwater aquifers in Hetao Basin of Inner Mongolia, China

Effects of simulated acid rain on hydrochemical factors and microbial community structure in red soil aquifers

Acid rain can lower the pH of groundwater and affect its hydrogeochemistry and microbial ecology. However, the effects of acid rain on the hydrogeochemistry and microbial ecology of red soil groundwater systems in southern China are poorly understood. Previous research had mainly investigated the sources and patterns of groundwater acidification, but not the microbial mechanisms that contribute to this process and their associations with hydrochemical factors. To address this knowledge gap, we conducted a soil column experiment to simulate the infiltration of acid rain through various filter materials (coarse, medium, and fine sand) and to examine the hydrochemical and microbial features of the infiltrate, which can reveal how simulated acid rain (pH 3.5-7.0) alters the hydrochemistry and microbial community composition in red soil aquifers. The results showed that the pH of the leachate decreased due to simulated acid rain, and that the leaching efficiency of nitrogen and metal ions was influenced by the particle size of the filter media. Illumina 16S rRNA gene sequencing revealed that the leachate was dominated by Proteobacteria, Patescibacteria, Actinobacteria, and Acidobacteria, with Proteobacteria accounting for 67.04-74.69% of the bacterial community and containing a high proportion of nitrifying and denitrifying bacteria. Additionally, several genera with heavy metal tolerance, such as Burkholderia-Caballeronia-Paraburkholderia, Delftia, Methylversatilis, Aquicella, and Ralstonia, were widely distributed in the leachate, indicating the strong adaptive capacity of the microbial population. A correlation analysis between the hydrochemical factors and the microbial community structure revealed that pH was the most influential factor, followed by NO2--N, Fe, Al, Cu, Mn, and others. These results indicate that acidification modifies the hydrochemical conditions of the aquifer, creating an environment that is unfavorable for microbial growth and survival. However, some microorganisms may acquire resistance genes to cope with environmental changes.

Arsenic Contamination of Groundwater Is Determined by Complex Interactions between Various Chemical and Biological Processes

At a great many locations worldwide, the safety of drinking water is not assured due to pollution with arsenic. Arsenic toxicity is a matter of both systems chemistry and systems biology: it is determined by complex and intertwined networks of chemical reactions in the inanimate environment, in microbes in that environment, and in the human body. We here review what is known about these networks and their interconnections. We then discuss how consideration of the systems aspects of arsenic levels in groundwater may open up new avenues towards the realization of safer drinking water. Along such avenues, both geochemical and microbiological conditions can optimize groundwater microbial ecology vis-à-vis reduced arsenic toxicity.

Exogenous-organic-matter-driven mobilization of groundwater arsenic

The potential release capacity of arsenic (As) from sediment was evaluated under a high level of exogenous organic matter (EOM) with both bioreactive and chemically reactive organic matters (OMs). The OMs were characterized by FI, HIX, BIX, and SUVA₂₅₄ fluorescence indices showing the biological activities were kept at a high level during the experimental period. At the genus level, Fe/Mn/As-reducing bacteria (Geobacter, Pseudomonas, Bacillus, and Clostridium) and bacteria (Paenibacillus, Acidovorax, Delftia, and Sphingomonas) that can participate in metabolic transformation using EOM were identified. The reducing condition occurs which promoted As, Fe, and Mn releases at very high concentrations of OM. However, As release increased during the first 15-20 days, followed by a decline contributed by secondary iron precipitation. The degree of As release may be limited by the reactivity of Fe (hydro)oxides. The EOM infiltration enhances As and Mn releases in aqueous conditions causing the risk of groundwater pollution, which could occur in specific sites such as landfills, petrochemical sites, and managed aquifer recharge projects.

Microbial community composition analysis to decipher the possible role of inherent bacteria for in-situ arsenic (As) bioremediation

Biogeochemical reduction and mobilization of sediment-bound arsenic (As) is the major concern for widespread groundwater As contamination in the middle Gangetic plains. The present work examines a microcosm based bio-stimulation study and substrate amendments over 45 days to analyze the bacterial community structure and distribution to indicate the possible in-situ bioremediation strategy in the area. Initially, Bacterial phyla Proteobacteria was predominantly present in all the samples, followed by Actinobacteria, Bacteroidetes, and Firmicutes whereas Cyanobacteria was noted as the minor group. In genus level, Delftia, Acinetobacter, Lysobacter, Bacillus, and Pseudomonas were the major groups of bacteria in the As-rich aquifer system, while Planctomycetes dominated the bio-stimulated samples, followed by a minute portion of Proteobacteria. Alpha diversity and Chaol curve further determined the species richness in the samples with an As tolerant capacity of 152.28 ppb. The presence of γ-Proteobacteria as the dominating member in high As-content water indicated their predominant role in As mobilization, whereas, dominance of α-Proteobacterial members in low As-content water indicated their involvement in As detoxification. The complete change in microbial community structure within the bio-stimulated conditions indicated the extensive role of arsenite-oxidizing microbial communities within different levels of As-contaminated areas in Bihar that will enlighten the significant role of these communities in As-biogeochemical cycle.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03612-0.

The distribution characteristics and geological control factors of shallow high-arsenic groundwater in the Hetao Plain, Inner Mongolia, from the perspective of Late Pleistocene-Holocene depositional environments

The alluvial-lacustrine strata that were formed by the evolution of rivers and lakes in the Hetao Plain during the Late Quaternary have an important influence on the formation and distribution of shallow high-arsenic groundwater. This study analyzed the distribution characteristics and depositional environments of shallow high-arsenic groundwater in study area using 1179 groundwater samples and more than 1100 pieces of drilling data. The indicator kriging statistics and the study results of the Quaternary lithofacies paleogeography show that the study area can be divided into three high-arsenic probabilistic distribution areas, namely, the Houtao Plain (HTP), the Yellow River Channel Belt (YRCB), and the Eastern Hubao Plain (EHBP). The depositional environment of the HTP was shaped by the alluviation of the Yellow River during the Late Pleistocene-Holocene. The YRCB is still affected by the alluviation of the Yellow River presently, and the EHBP was almost unaffected by the Yellow River. The high-arsenic groundwater in the EHBP is mostly distributed in the relatively continuous alluvial-lacustrine strata and has a typical hydrochemical type of HCO₃, with the highest Meq(HCO₃^-/SO₄^2-) and the highest reduction degree of SO₄^2-. By contrast, the high-arsenic groundwater in the alluvial-lacustrine environments of the HTP and the YRCB accounts for only 14.77% and 20.13%, respectively, and has only less than 40% of HCO₃ dominant type water. The high-arsenic groundwater in these two areas is generally located in the alluvial or alternating fluvial-lacustrine strata. However, the two areas exist more than three alluvial-lacustrine layers with a thickness of over 2 m each, which play a critical role in the formation of high-arsenic groundwater. Moreover, affected by alluvial aquifers in the same system, the high-arsenic groundwater in both the HTP and the YRCB is not intensively distributed and does not represent a typical HCO₃ dominant type. The S^2- produced by the massive reduction of SO₄^2- might co-precipitate with Fe and As, which may explain why the EHBP has lower arsenic concentration than the HTP and the YRCB, both of which have a lower reduction degree of SO₄^2-.

Metagenome based analysis of groundwater from arsenic contaminated sites of West Bengal revealed community diversity and their metabolic potential

The study of microbial community in groundwater systems is considered to be essential to improve our understanding of arsenic (As) biogeochemical cycling in aquifers, mainly as it relates to the fate and transport of As. The present study was conducted to determine the microbial community composition and its functional potential using As-contaminated groundwater from part of the Bengal Delta Plain (BDP) in West Bengal, India. Geochemical analyses indicated low to moderate dissolved oxygen (0.42-3.02 mg/L), varying As (2.5-311 µg/L) and Fe (0.19-1.2 mg/L) content, while low concentrations of total organic carbon (TOC), total inorganic carbon (TIC), nitrate, and sulfate were detected. Proteobacteria was the most abundant phylum, while the indiscriminate presence of an array of archaeal phyla, Euryarchaeota, Crenarchaeota, Nanoarchaeota, etc., was noteworthy. The core community members were affiliated to Sideroxydans, Acidovorax, Pseudoxanthomonas, Brevundimonas, etc. However, diversity assessed over multiple seasons indicated a shift from Sideroxydans to Pseudomonas or Brevundimonas dominant community, suggestive of microbial response to seasonally fluctuating geochemical stimuli. Taxonomy-based functional potential showed prospects for As biotransformation, methanogenesis, sulfate respiration, denitrification, etc. Thus, this study strengthened existing reports from this region by capturing the less abundant or difficult-to-culture taxa collectively forming a major fraction of the microbial community.

Rhizosphere Microbial Communities and Geochemical Constraining Mechanism of Antimony Mine Waste-Adapted Plants in Southwestern China

Antimony (Sb) and arsenic (As) are two hazardous metalloid elements, and the biogeochemical cycle of Sb and As can be better understood by studying plant rhizosphere microorganisms associated with Sb mine waste. In the current study, samples of three types of mine waste—Sb mine tailing, waste rocks, and smelting slag—and associated rhizosphere microorganisms of adapted plants were collected from Qinglong Sb mine, southwest China. 16S rRNA was sequenced and used to study the composition of the mine waste microbial community. The most abundant phylum in all samples was Proteobacteria, followed by Bacteroidota, Acidobacteriota, and Actinobacteriota. The community composition varied among different mine waste types. Gammaproteobacteria was the most abundant microorganism in tailings, Actinobacteria was mainly distributed in waste rock, and Saccharimonadia, Acidobacteriae, and Ktedonobacteria were mainly present in slag. At the family level, the vast majority of Hydrogenophilaceae were found in tailings, Ktedonobacteraceae, Chthoniobacteraceae, and Acidobacteriaceae (Subgroup 1) were mostly found in slag, and Pseudomonadaceae and Micrococcaceae were mainly found in waste rock. Actinobacteriota and Arthrobacter are important taxa for reducing heavy metal(loid) mobility, vegetation restoration, and self-sustaining ecosystem construction on antimony mine waste. The high concentrations of Sb and As reduce microbial diversity.

Diversity and biogenesis contribution of sulfate-reducing bacteria in arsenic-contaminated soils from realgar deposits

Microbial sulfate reduction, a vital mechanism for microorganisms living in anaerobic, sulfate-rich environments, is an essential aspect of the sulfur biogeochemical cycle. However, there has been no detailed investigation of the diversity and biogenesis contribution of sulfate-reducing bacteria in arsenic-contaminated soils from realgar deposits. To elucidate this issue, soil samples from representative abandoned realgar deposits were collected. Microcosm assays illustrated that all three samples (2-1, 2-2, and 2-3) displayed efficient sulfate and As(V)-respiring activities. Furthermore, a total of 28 novel sequence variants of dissimilatory sulfite reductase genes and 2 new families of dsrAB genes were successfully identified. A novel dissimilatory sulfate-reducing bacterium, Desulfotomaculum sp. JL1, was also isolated from soils, and can efficiently respiratory reduce As(V) and sulfate in 4 and 5 days, respectively. JL1 can promote the generation of yellow precipitates in the presence of multiple electron acceptors (both contain sulfate and As(V) in the cultures), which indicated the biogenesis contribution of sulfate-reducing bacteria to the realgar mine. Moreover, this area had unique microbial communities; the most abundant populations belonged to the phyla Proteobacteria, Chloroflexi, and Acidobacteriota, which were attributed to the unique geochemistry characteristics, such as total organic carbon, total As, NO₃^-, and SO₄^2-. The results of this study provide new insight into the diversity and biogenesis contributions of sulfate-reducing bacteria in arsenic-contaminated soils from realgar deposits.

Arsenic speciation, the abundance of arsenite-oxidizing bacteria and microbial community structures in groundwater, surface water, and soil from a gold mine

The arsenic speciation, the abundance of arsenite-oxidizing bacteria, and microbial community structures in the groundwater, surface water, and soil from a gold mining area were explored using the PHREEQC model, cloning-ddPCR of the aioA gene, and high-throughput sequencing of the 16S rRNA gene, respectively. The analysis of the aioA gene showed that arsenite-oxidizing bacteria retrieved from groundwater, surface water, and soil were associated with Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. In groundwaters from the mining area, there were relatively high ratios of aioA/total 16S rRNA gene copies and the dominance of As⁵⁺, which suggested the presence and activity of arsenite-oxidizing bacteria. Metagenomic analysis revealed that the majority of the soil and surface water microbiomes were Proteobacteria, Actinobacteria, Bacteroidetes, and Chloroflexi, whereas the groundwater microbiomes were dominated exclusively by Betaproteobacteria and Alphaproteobacteria. Geochemical factors influencing the microbial structure in the groundwater were As, residence time, and groundwater flowrate, while those showing a positive correlation to the microbial structure in the surface water were TOC, ORP, and DO. This study provides insights into the groundwater, surface water, and soil microbiomes from a gold mine and expands the current understanding of the diversity and abundance of arsenite-oxidizing bacteria, playing a vital role in global As cycling.

Adaptation of Microbial Communities to Environmental Arsenic and Selection of Arsenite-Oxidizing Bacteria From Contaminated Groundwaters

Arsenic mobilization in groundwater systems is driven by a variety of functionally diverse microorganisms and complex interconnections between different physicochemical factors. In order to unravel this great ecosystem complexity, groundwaters with varying background concentrations and speciation of arsenic were considered in the Po Plain (Northern Italy), one of the most populated areas in Europe affected by metalloid contamination. High-throughput Illumina 16S rRNA gene sequencing, CARD-FISH and enrichment of arsenic-transforming consortia showed that among the analyzed groundwaters, diverse microbial communities were present, both in terms of diversity and functionality. Oxidized inorganic arsenic [arsenite, As(III)] was the main driver that shaped each community. Several uncharacterized members of the genus Pseudomonas, putatively involved in metalloid transformation, were revealed in situ in the most contaminated samples. With a cultivation approach, arsenic metabolisms potentially active at the site were evidenced. In chemolithoautotrophic conditions, As(III) oxidation rate linearly correlated to As(III) concentration measured at the parental sites, suggesting that local As(III) concentration was a relevant factor that selected for As(III)-oxidizing bacterial populations. In view of the exploitation of these As(III)-oxidizing consortia in biotechnology-based arsenic bioremediation actions, these results suggest that contaminated aquifers in Northern Italy host unexplored microbial populations that provide essential ecosystem services.

Microbial community structure in aquifers associated with arsenic: analysis of 16S rRNA and arsenite oxidase genes

The microbiomes of deep and shallow aquifers located in an agricultural area, impacted by an old tin mine, were explored to understand spatial variation in microbial community structures and identify environmental factors influencing microbial distribution patterns through the analysis of 16S rRNA and aioA genes. Although Proteobacteria, Cyanobacteria, Actinobacteria, Patescibacteria, Bacteroidetes, and Epsilonbacteraeota were widespread across the analyzed aquifers, the dominant taxa found in each aquifer were unique. The co-dominance of Burkholderiaceae and Gallionellaceae potentially controlled arsenic immobilization in the aquifers. Analysis of the aioA gene suggested that arsenite-oxidizing bacteria phylogenetically associated with Alpha-, Beta-, and Gamma proteobacteria were present at low abundance (0.85 to 37.13%) and were more prevalent in shallow aquifers and surface water. The concentrations of dissolved oxygen and total phosphorus significantly governed the microbiomes analyzed in this study, while the combination of NO₃ ^--N concentration and oxidation-reduction potential significantly influenced the diversity and abundance of arsenite-oxidizing bacteria in the aquifers. The knowledge of microbial community structures and functions in relation to deep and shallow aquifers is required for further development of sustainable aquifer management.

Microbes involved in arsenic mobilization and respiration: a review on isolation, identification, isolates and implications

Microorganisms play an important role in arsenic (As) cycling in the environment. Microbes mobilize As directly or indirectly, and natural/geochemical processes such as sulphate and iron reduction, oxidative sulphide mineral dissolution, arsenite (AsO₃^3-) oxidation and arsenate (AsO₄^3-) respiration further aid in As cycle in the environment. Arsenate serves as an electron donor for the microbes during anaerobic conditions in the sediment. The present work reviews the recent development in As contamination, various As-metabolizing microbes and their phylogenetic diversity, to understand the role of microbial communities in As respiration and mobilization. It also summarizes the contemporary understanding of the intricate biochemistry and molecular biology of natural As metabolisms. Some successful examples of engineered microbes by harnessing these natural mechanisms for effective remediation are also discussed. The study indicates that there is an exigent need to have a clear understanding of environmental aspects of As mobilization and subsequent oxidation-reduction by a suitable microbial consortium.

Molecular and taxonomic characterization of arsenic (As) transforming Bacillus sp. strain IIIJ3-1 isolated from As-contaminated groundwater of Brahmaputra river basin, India

Background

Microbe-mediated redox transformation of arsenic (As) leading to its mobilization has become a serious environmental concern in various subsurface ecosystems especially within the alluvial aquifers. However, detailed taxonomic and eco-physiological attributes of indigenous bacteria from As impacted aquifer of Brahmaputra river basin has remained under-studied.

Results

A newly isolated As-resistant and -transforming facultative anaerobic bacterium IIIJ3–1 from As-contaminated groundwater of Jorhat, Assam was characterized. Near complete 16S rRNA gene sequence affiliated the strain IIIJ3–1 to the genus Bacillus and phylogenetically placed within members of B. cereus sensu lato group with B. cereus ATCC 14579(T) as its closest relative with a low DNA-DNA relatedness (49.9%). Presence of iC17:0, iC15:0 fatty acids and menaquinone 7 corroborated its affiliation with B. cereus group, but differential hydroxy-fatty acids, C18:2 and menaquinones 5 & 6 marked its distinctiveness. High As resistance [Maximum Tolerable Concentration = 10 mM As³⁺, 350 mM As⁵⁺], aerobic As³⁺ (5 mM) oxidation, and near complete dissimilatory reduction of As ⁵⁺ (1 mM) within 15 h of growth designated its physiological novelty. Besides O₂, cells were found to reduce As⁵⁺, Fe³⁺, SO₄²⁻, NO₃⁻, and Se⁶⁺ as alternate terminal electron acceptors (TEAs), sustaining its anaerobic growth. Lactate was the preferred carbon source for anaerobic growth of the bacterium with As⁵⁺ as TEA. Genes encoding As⁵⁺ respiratory reductase (arr A), As³⁺ oxidase (aioB), and As³⁺ efflux systems (ars B, acr3) were detected. All these As homeostasis genes showed their close phylogenetic lineages to Bacillus spp. Reduction in cell size following As exposure exhibited the strain’s morphological response to toxic As, while the formation of As-rich electron opaque dots as evident from SEM-EDX possibly indicated a sequestration based As resistance strategy of strain IIIJ3–1.

Conclusion

This is the first report on molecular, taxonomic, and ecophysiological characterization of a highly As resistant, As³⁺ oxidizing, and dissimilatory As⁵⁺ reducing Bacillus sp. IIIJ3–1 from As contaminated sites of Brahmaputra river basin. The strain’s ability to resist and transform As along with its capability to sequester As within the cells demonstrate its potential in designing bioremediation strategies for As contaminated groundwater and other ecosystems.

Groundwater microbial communities and their connection to hydrochemical environment in Golmud, Northwest China

Groundwater microbial community normally co-varies with the associated geochemical transect in some hydrogeological sections along flowpath. However, in hydrogeological section with similar geochemical transect (e.g., salinity, ion compositions) how microbial community in groundwater varies are poorly understood. In this study, groundwater samples were collected at six boreholes vertically and horizontally along a generalized groundwater flowpath in the Golmud area, Qaidam Basin, northwest China. High-throughput sequencing and multivariate statistical analysis were applied to explore the underlying relationships between microbial community structure and hydrogeochemical environment. The result showed that microbial communities changed considerably at both horizontal and vertical scales, although the groundwater samples were of relatively stable ionic compositions and hydrochemical types. The dominant bacterial phyla in groundwater varied from Alphaproteobacteria, Betaproteobacteria and Flavobacteriia in 'phreatic and phreatic-like' groundwater in the recharge area to Gammaproteobacteria in the confined groundwater in the lacustrine plain. At both vertical and horizontal scale, Gammaproteobacteria increased while Alpha- and Betaproteobacteria decreased as the function of distance. Genera Roseateles, Aquabacterium, Sphingomonas, Acinetobacter, Acidovorax and Flavobacterium presented in phreatic groundwater, while Pseudomonas, Hydrogenophaga and Perlucidibaca presented in confined groundwater. Spatial distribution of microbial community was highly affected by the pH (for 'phreatic and phreatic-like' groundwater) and ORP (for confined groundwater) of groundwater that had similar salinity or ion compositions. This research extends our knowledge about microbial communities' variation along groundwater flowpath in studied area and similar arid or semi-arid areas.

Arsenic mobilization in a high arsenic groundwater revealed by metagenomic and Geochip analyses

Microbial metabolisms of arsenic, iron, sulfur, nitrogen and organic matter play important roles in arsenic mobilization in aquifer. In this study, microbial community composition and functional potentials in a high arsenic groundwater were investigated using integrated techniques of RNA- and DNA-based 16S rRNA gene sequencing, metagenomic sequencing and functional gene arrays. 16S rRNA gene sequencing showed the sample was dominated by members of Proteobacteria (62.3-75.2%), such as genera of Simplicispira (5.7-6.7%), Pseudomonas (3.3-5.7%), Ferribacterium (1.6-4.4%), Solimonas (1.8-3.2%), Geobacter (0.8-2.2%) and Sediminibacterium (0.6-2.4%). Functional potential analyses indicated that organics degradation, assimilatory sulfate reduction, As-resistant pathway, iron reduction, ammonification, nitrogen fixation, denitrification and dissimilatory nitrate reduction to ammonia were prevalent. The composition and function of microbial community and reconstructed genome bins suggest that high level of arsenite in the groundwater may be attributed to arsenate release from iron oxides reductive dissolution by the iron-reducing bacteria, and subsequent arsenate reduction by ammonia-producing bacteria featuring ars operon. This study highlights the relationship between biogeochemical cycling of arsenic and nitrogen in groundwater, which potentially occur in other aquifers with high levels of ammonia and arsenic.

Metagenomic insights into microbial diversity in a groundwater basin impacted by a variety of anthropogenic activities

Microbial communities in groundwater are diverse and each may respond differently to environmental change. The goal of this study was to investigate the diversity, abundance, and dynamics of microbial communities in impacted groundwater and correlate them to the corresponding land use and groundwater geochemistry, using an Illumina MiSeq platform targeting the V3 and V4 regions of the 16S rRNA gene. The resulting MiSeq sequencing revealed the co-occurrence patterns of both abundant and rare microbial taxa within an impacted groundwater basin. Proteobacteria were the most common groundwater-associated bacterial phylum, mainly composed of the classes Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria. The phyla detected at less abundances were the Firmicutes, Bacteroidetes, Planctomycetes, Actinobacteria, OD1, and Nitrospirae. The members of detected groundwater microorganisms involved in natural biogeochemical processes such as nitrification, anammox, methane oxidation, sulfate reduction, and arsenic transformation. Some of the detected microorganisms were able to perform anaerobic degradation of organic pollutants. The resulting PCA indicates that major land usage within the sampling area seemed to be significantly linked to the groundwater microbial distributions. The distinct microbial pattern was observed in the groundwater collected from a landfill area. This study suggests that the combinations of anthropogenic and natural effects possibly led to a unique pattern of microbial diversity across different locations at the impacted groundwater basin.

Microbial diversity along a gradient in peatlands treating mining-affected waters

Peatlands are used for the purification of mining-affected waters in Northern Finland. In Northern climate, microorganisms in treatment peatlands (TPs) are affected by long and cold winters, but studies about those microorganisms are scarce. Thus, the bacterial, archaeal and fungal communities along gradients of mine water influence in two TPs were investigated. The TPs receive waters rich in contaminants, including arsenic (As), sulfate (SO42-) and nitrate (NO3-). Microbial diversity was high in both TPs, and microbial community composition differed between the studied TPs. Bacterial communities were dominated by Proteobacteria, Actinobacteria, Chloroflexi and Acidobacteria, archaeal communities were dominated by Methanomicrobia and the Candidate phylum Bathyarchaeota, and fungal communities were dominated by Ascomycota (Leotiomycetes, Dothideomycetes, Sordariomycetes). The functional potential of the bacterial and archaeal communities in TPs was predicted using PICRUSt. Sampling points affected by high concentrations of As showed higher relative abundance of predicted functions related to As resistance. Functions potentially involved in nitrogen and SO42- turnover in TPs were predicted for both TPs. The results obtained in this study indicate that (i) diverse microbial communities exist in Northern TPs, (ii) the functional potential of the peatland microorganisms is beneficial for contaminant removal in TPs and (iii) microorganisms in TPs are likely well-adapted to high contaminant concentrations as well as to the Northern climate.

Exploring Biodiversity and Arsenic Metabolism of Microbiota Inhabiting Arsenic-Rich Groundwaters in Northern Italy

Arsenic contamination of groundwater aquifers is an issue of global concern. Among the affected sites, in several Italian groundwater aquifers arsenic levels above the WHO limits for drinking water are present, with consequent issues of public concern. In this study, for the first time, the role of microbial communities in metalloid cycling in groundwater samples from Northern Italy lying on Pleistocene sediments deriving from Alps mountains has been investigated combining environmental genomics and cultivation approaches. 16S rRNA gene libraries revealed a high number of yet uncultured species, which in some of the study sites accounted for more of the 50% of the total community. Sequences related to arsenic-resistant bacteria (arsenate-reducing and arsenite-oxidizing) were abundant in most of the sites, while arsenate-respiring bacteria were negligible. In some of the sites, sulfur-oxidizing bacteria of the genus Sulfuricurvum accounted for more than 50% of the microbial community, whereas iron-cycling bacteria were less represented. In some aquifers, arsenotrophy, growth coupled to autotrophic arsenite oxidation, was suggested by detection of arsenite monooxygenase (aioA) and 1,5-ribulose bisphosphate carboxylase (RuBisCO) cbbL genes of microorganisms belonging to Rhizobiales and Burkholderiales. Enrichment cultures established from sampled groundwaters in laboratory conditions with 1.5 mmol L^-1 of arsenite as sole electron donor were able to oxidize up to 100% of arsenite, suggesting that this metabolism is active in groundwaters. The presence of heterotrophic arsenic resistant bacteria was confirmed by enrichment cultures in most of the sites. The overall results provided a first overview of the microorganisms inhabiting arsenic-contaminated aquifers in Northern Italy and suggested the importance of sulfur-cycling bacteria in the biogeochemistry of arsenic in these ecosystems. The presence of active arsenite-oxidizing bacteria indicates that biological oxidation of arsenite, in combination with arsenate-adsorbing materials, could be employed for metalloid removal.

Diversity and abundance of arsenic methylating microorganisms in high arsenic groundwater from Hetao Plain of Inner Mongolia, China

Arsenic methylation is regarded as an effective way of arsenic detoxification. Current knowledge about arsenic biomethylation in high arsenic groundwater remains limited. In the present study, 16 high arsenic groundwater samples from deep wells of the Hetao Plain were investigated using clone library and quantitative polymerase chain reaction (qPCR) analyses of arsM genes as well as geochemical analysis. The concentrations of methylated arsenic (including monomethylarsonic acid (MMA) and dimethylarsinic acid (DMA)) varied from 2.40 to 16.85 μg/L. Both bacterial and archaeal arsenic methylating populations were detected in the high arsenic aquifer. They were dominated by Proteobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Methanomicrobia and a large unidentified group. The abundances of predominant populations were correlated positively to either total organic carbon or total arsenic and arsenite concentrations. The arsM gene abundances in high arsenic groundwater ranged from below detection to 5.71 × 10⁶ copies/L and accounted for 0-3.32‰ of total bacterial and archaeal 16S rRNA genes. The arsM gene copies in high arsenic groundwater showed closely positive correlations with methylated arsenic concentrations. The overall results implied that arsenic methylating microorganisms were abundant and diverse in high arsenic groundwater. This was the first study of arsenic methylating microbial communities in high arsenic groundwater aquifers and might provide useful information for arsenic bioremediation in groundwater systems.

Molecular and eco-physiological characterization of arsenic (As)-transforming Achromobacter sp. KAs 3-5T from As-contaminated groundwater of West Bengal, India

Molecular and eco-physiological characterization of arsenic (As)-transforming and hydrocarbon-utilizing Achromobacter type strain KAs 3-5^T has been investigated in order to gain an insight into As-geomicrobiology in the contaminated groundwater. The bacterium is isolated from As-rich groundwater of West Bengal, India. Comparative 16S rRNA gene sequence phylogenetic analysis confirmed that the strain KAs 3-5^T is closely related to Achromobacter mucicolens LMG 26685^T (99.17%) and Achromobacter animicus LMG 26690^T (99.17%), thus affiliated to the genus Achromobacter. Strain KAs 3-5^T is nonflagellated, mesophilic, facultative anaerobe, having a broad metabolic repertoire of using various sugars, sugar-/fatty acids, hydrocarbons as principal carbon substrates, and O₂, NO₃^-, NO₂^-, and Fe³⁺ as terminal electron acceptors. Growth with hydrocarbons led to cellular aggregation and adherence of the cells to the hydrocarbon particles confirmed through electron microscopic observations. The strain KAs 3-5^T showed high As resistance (MIC of 5 mM for As³⁺, 25 mM for As⁵⁺) and reductive transformation of As⁵⁺ under aerobic conditions while utilizing both sugars and hydrocarbons. Molecular taxonomy specified a high genomic GC content (65.5 mol %), ubiquinone 8 (UQ-8) as respiratory quinone, spermidine as predominant polyamine in the bacterium. The differential presence of C_12:0, C_14:0 2-OH, C_18:1 ω7c, and C _14:0 iso 3-OH/ C_16:1 iso fatty acids, phosphatidylglycerol (PG), phosphatidylcholine (PC), two unknown phospholipid (PL1, PL2) as polar lipids, low DNA-DNA relatedness (33.0-41.0%) with the Achromobacter members, and unique metabolic capacities clearly indicated the distinct genomic and physiological properties of strain KAs 3-5^T among known species of the genus Achromobacter. These findings lead to improve our understanding on metabolic flexibility of bacteria residing in As-contaminated groundwater and As-bacteria interactions within oligotrophic aquifer system.

Exposure to Arsenic Alters the Microbiome of Larval Zebrafish

Exposure to environmental toxins such as heavy metals can perturb the development and stability of microbial communities associated with human or animal hosts. Widespread arsenic contamination in rivers and riparian habitats therefore presents environmental and health concerns for populations living near sources of contamination. To investigate how arsenic affects host microbiomes, we sequenced and characterized the microbiomes of twenty larval zebrafish exposed to three concentrations of arsenic that are found in contaminated water—low (10 ppb), medium (50 ppb), and high (100 ppb) for 20 days. We found that even a small concentration of arsenic changed the overall microbial composition, structure and diversity of microbial communities, causing dysbiosis in developing larval zebrafish microbiota. In addition, we found that a high concentration of arsenic also increased the abundance of a class 1 integron, an integrase-dependent system facilitating the horizontal transfer of genes conferring resistance to heavy metals and antibiotics.

Temporal dynamics of total and free-living nitrogen-fixing bacterial community abundance and structure in soil with and without history of arsenic contamination during a rice growing season

Despite the fact that the nitrogen (N) fixers act as the key regulator of ecosystem process, a detailed study of their abundance, diversity, and dynamics in arsenic (As)-contaminated rice fields is missing so far. DNA extracted from soil followed by 16S rRNA and nifH gene-based real-time qPCR, clone library analysis, and DNA sequencing were used to examine the status of the total and diazotrophic communities in two agricultural fields with and without arsenic contamination history during one rice cultivation season. In general, higher nifH and 16S rRNA gene copy numbers were observed in rice growing soils with lesser As than that with higher As. Elevated levels of 16S rRNA and nifH genes in soil is directly associated with total and nitrogen fixers abundance in the agricultural land without As contamination history through the cultivation period, but the copy number of 16S rRNA gene was decreased, and the nifH gene remained unchanged in the As-contaminated land. Additionally, Canonical Correspondence Analysis (CCA) indicated the possible suppression of nifH gene abundance by soil pH, phosphate, and As content. Increased abundance of total and Acidobacterial lineages in low As-containing soil and the detection of several uncultured groups among nifH gene sequence in higher frequency indicated the presence of novel nifH bearing bacterial groups. Conversely, the abundance of copiotrophic Proteobacterial lineages gradually increased in soil with higher As. Herein, our study demonstrated that the dynamics of free-living nitrogen-fixing bacterial communities were perturbed due to As contamination in agricultural land.

Bacterial community profile of contaminated soils in a typical antimony mining site

The soils around the world's largest antimony mine have been contaminated by high concentrations of Sb and As, which might influence microbial diversity in the surrounding soils. The ecological effects of bioavailable Sb and As on the composition and diversity of microbial community in soils remain unknown. In this study, the relative abundance, taxonomic diversity and composition of bacterial community in soils from a typical Sb mine area, and the relationship between the bacterial community and bioavailable concentrations as well as environmental factors have been investigated comprehensively using high-throughput sequencing (HTS) and diffusive gradients in thin films (DGT). The results indicated that Proteobacteria, Acidobacteria, Chloroflexi, Bacteroidetes, Actinobacteria, Gemmatimonadetes, and Cyanobacteria were the dominant bacterial populations at phylum level in all soil samples, accounting for more than 80% of the bacteria sequenced. The abundance and diversity of bacterial community vary along a metal contamination gradient. Redundancy discriminate analysis (RDA) revealed that 74.74% of bacterial community variation in the contaminated soils was explained by six environmental factors (pH, Sb_DGT, As_DGT, potential ecological risk index (RI), TC, TN), among which pH, Sb_DGT, and As_DGT were dominant factors influencing the composition and diversity of bacteria. This study contributes to our understanding of microbial diversity in a local ecosystem and introduces the option of studying bioavailable Sb and As using DGT.

Novel arsenic-transforming bacteria and the diversity of their arsenic-related genes and enzymes arising from arsenic-polluted freshwater sediment

Bacteria are essential in arsenic cycling. However, few studies have addressed 16S rRNA and arsenic-related functional gene diversity in long-term arsenic-contaminated tropical sediment. Here, using culture-based, metagenomic and computational approaches, we describe the diversity of bacteria, genes and enzymes involved in AsIII and AsV transformation in freshwater sediment and in anaerobic AsIII- and AsV-enrichment cultures (ECs). The taxonomic profile reveals significant differences among the communities. Arcobacter, Dechloromonas, Sedimentibacter and Clostridium thermopalmarium were exclusively found in ECs, whereas Anaerobacillus was restricted to AsV-EC. Novel taxa that are both AsV-reducers and AsIII-oxidizers were identified: Dechloromonas, Acidovorax facilis, A. delafieldii, Aquabacterium, Shewanella, C. thermopalmarium and Macellibacteroides fermentans. Phylogenic discrepancies were revealed among the aioA, arsC and arrA genes and those of other species, indicating horizontal gene transfer. ArsC and AioA have sets of amino acids that can be used to assess their functional and structural integrity and familial subgroups. The positions required for AsV reduction are conserved, suggesting strong selective pressure for maintaining the functionality of ArsC. Altogether, these findings highlight the role of freshwater sediment bacteria in arsenic mobility, and the untapped diversity of dissimilatory arsenate-reducing and arsenate-resistant bacteria, which might contribute to arsenic toxicity in aquatic environments.

Response of soil microbial communities to roxarsone pollution along a concentration gradient

The extensive use of roxarsone (3-nitro-4-hydroxyphenylarsonic acid) as a feed additive in the broiler poultry industry can lead to environmental arsenic contamination. This study was conducted to reveal the response of soil microbial communities to roxarsone pollution along a concentration gradient. To explore the degradation process and degradation kinetics of roxarsone concentration gradients in soil, the concentration shift of roxarsone at initial concentrations of 0, 50, 100, and 200 mg/kg, as well as that of the arsenic derivatives, was detected. The soil microbial community composition and structure accompanying roxarsone degradation were investigated by high-throughput sequencing. The results showed that roxarsone degradation was inhibited by a biological inhibitor, confirming that soil microbes were absolutely essential to its degradation. Moreover, soil microbes had considerable potential to degrade roxarsone, as a high initial concentration of roxarsone resulted in a substantially increased degradation rate. The concentrations of the degradation products HAPA (3-amino-4-hydroxyphenylarsonic acid), AS(III), and AS(V) in soils were significantly positively correlated. The soil microbial community composition and structure changed significantly across the roxarsone contamination gradient, and the addition of roxarsone decreased the microbial diversity. Some bacteria tended to be inhibited by roxarsone, while Bacillus, Paenibacillus, Arthrobacter, Lysobacter, and Alkaliphilus played important roles in roxarsone degradation. Moreover, HAPA, AS(III), and AS(V) were significantly positively correlated with Symbiobacterium, which dominated soils containing roxarsone, and their abundance increased with increasing initial roxarsone concentration. Accordingly, Symbiobacterium could serve as indicator of arsenic derivatives released by roxarsone as well as the initial roxarsone concentration. This is the first investigation of microbes closely related to roxarsone degradation.

Functional genes and thermophilic microorganisms responsible for arsenite oxidation from the shallow sediment of an untraversed hot spring outlet

Hot Springs have unique geochemical features. Microorganisms-mediated arsenite oxidation is one of the major biogeochemical processes occurred in some hot springs. This study aimed to understand the diversities of genes and microorganisms involved in arsenite oxidation from the outlet of an untraversed hot spring located at an altitude of 4226 m. Microcosm assay indicated that the microbial community from the hot spring was able to efficiently oxidize As(III) using glucose, lactic acid, yeast extract or sodium bicarbonate as the sole carbon source. The microbial community contained 7 phyla of microorganisms, of which Proteobacteria and Firmicutes are largely dominant; this composition is unique and differs significantly from those of other described hot springs. Twenty one novel arsenite oxidase genes were identified from the samples, which are affiliated with the arsenite oxidase families of α-Proteobacteria, β-Proteobacteria or Archaea; this highlights the high diversity of the arsenite-oxidizing microorganisms from the hot spring. A cultivable arsenite-oxidizer Chelatococcu sp. GHS311 was also isolated from the sample using enrichment technique. It can completely convert 75.0 mg/L As(III) into As(V) in 18 days at 45 °C. The arsenite oxidase of GHS311 shares the maximal sequence identity (84.7%) to that of Hydrogenophaga sp. CL3, a non-thermotolerant bacterium. At the temperature lower than 30 °C or higher than 65 °C, the growth of this strain was completely inhibited. These data help us to better understand the diversity and functional features of the thermophilic arsenite-oxidizing microorganisms from hot springs.

Arsenic Methylation and its Relationship to Abundance and Diversity of arsM Genes in Composting Manure

Although methylation is regarded as one of the main detoxification pathways for arsenic (As), current knowledge about this process during manure composting remains limited. In this study, two pilot-scale compost piles were established to treat manure contaminated with As. An overall accumulation of methylated As occurred during 60 day-composting time. The concentration of monomethylarsonic acid (MMA) increased from 6 to 190 μg kg^-1 within 15 days and decreased to 35 μg kg^-1 at the end of the maturing phase; while the concentration of dimethylarsinic acid (DMA) continuously increased from 33 to 595 μg kg^-1 over the composting time. The arsM gene copies increased gradually from 0.08 × 10⁹ to 6.82 × 10⁹ copies g^-1 dry mass over time and correlated positively to the concentrations of methylated As. 16S rRNA gene sequencing and arsM clone library analysis confirmed the high abundance and diversity of arsM genes. Many of these genes were related to those from known As-methylating microbes, including Streptomyces sp., Amycolatopsis mediterranei and Sphaerobacter thermophiles. These results demonstrated that As methylation during manure composting is significant and, for the first time, established a linkage between As biomethylation and the abundance and diversity of the arsM functional genes in composting manure.

Response of microbial communities to roxarsone under different culture conditions

Roxarsone is a feed additive widely used in the broiler and swine industries that has the potential to contaminate the environment, mainly via the use of poultry manure as fertilizer, which results in release of inorganic arsenic to the soil and water. This study was conducted to investigate roxarsone degradation and the response of the microbial community under different culture conditions using high-throughput sequencing technology. Poultry litter was incubated for 288 h in the presence of roxarsone under light aerobic, dark aerobic, or dark anaerobic conditions. The results showed that roxarsone was completely degraded after 48 h of dark anaerobic incubation, while 79.9% and 94.5% of roxarsone was degraded after 288 h of dark aerobic and light aerobic incubation, respectively. Under dark aerobic conditions with microbial inhibitor sodium azide, roxarsone was rarely degraded during the 288 h of incubation, illustrating that microorganisms play an important role in roxarsone degradation. Microbial community structure was significantly different among various culture conditions. Olivibacter, Sphingobacterium, and Proteiniphilum were the top 3 genera in the control samples. Sphingobacterium and Alishewanella dominated the light aerobic samples, while the dominant microflora of the dark aerobic samples were Acinetobacter spp. Pseudomonas and Advenella were the predominant genera of dark anaerobic samples. This study emphasizes the potential importance of microbes in roxarsone degradation and expands our current understanding of microbial ecology during roxarsone degradation under different environmental conditions.

Wells provide a distorted view of life in the aquifer: implications for sampling, monitoring and assessment of groundwater ecosystems

When compared to surface ecosystems, groundwater sampling has unique constraints, including limited access to ecosystems through wells. In order to monitor groundwater, a detailed understanding of groundwater biota and what biological sampling of wells truly reflects, is paramount. This study aims to address this uncertainty, comparing the composition of biota in groundwater wells prior to and after purging, with samples collected prior to purging reflecting a potentially artificial environment and samples collected after purging representing the surrounding aquifer. This study uses DNA community profiling (metabarcoding) of 16S rDNA and 18S rDNA, combined with traditional stygofauna sampling methods, to characterise groundwater biota from four catchments within eastern Australia. Aquifer waters were dominated by Archaea and bacteria (e.g. Nitrosopumilales) that are often associated with nitrification processes, and contained a greater proportion of bacteria (e.g. Anaerolineales) associated with fermenting processes compared to well waters. In contrast, unpurged wells contained greater proportions of pathogenic bacteria and bacteria often associated with denitrification processes. In terms of eukaryotes, the abundances of copepods, syncarids and oligochaetes and total abundances of stygofauna were greater in wells than aquifers. These findings highlight the need to consider sampling requirements when completing groundwater ecology surveys.

Microbial Community of High Arsenic Groundwater in Agricultural Irrigation Area of Hetao Plain, Inner Mongolia

Microbial communities can play important role in arsenic release in groundwater aquifers. To investigate the microbial communities in high arsenic groundwater aquifers in agricultural irrigation area, 17 groundwater samples with different arsenic concentrations were collected along the agricultural drainage channels of Hangjinhouqi County, Inner Mongolia and examined by illumina MiSeq sequencing approach targeting the V4 region of the 16S rRNA genes. Both principal component analysis and hierarchical clustering results indicated that these samples were divided into two groups (high and low arsenic groups) according to the variation of geochemical characteristics. Arsenic concentrations showed strongly positive correlations with NH4+ and total organic carbon (TOC). Sequencing results revealed that a total of 329–2823 operational taxonomic units (OTUs) were observed at the 97% OTU level. Microbial richness and diversity of high arsenic groundwater samples along the drainage channels were lower than those of low arsenic groundwater samples but higher than those of high arsenic groundwaters from strongly reducing areas. The microbial community structure in groundwater along the drainage channels was different from those in strongly reducing arsenic-rich aquifers of Hetao Plain and other high arsenic groundwater aquifers including Bangladesh, West Bengal, and Vietnam. Acinetobacter and Pseudomonas dominated with high percentages in both high and low arsenic groundwaters. Alishewanella, Psychrobacter, Methylotenera, and Crenothrix showed relatively high abundances in high arsenic groundwater, while Rheinheimera and the unidentified OP3 were predominant populations in low arsenic groundwater. Archaeal populations displayed a low occurrence and mainly dominated by methanogens such as Methanocorpusculum and Methanospirillum. Microbial community compositions were different between high and low arsenic groundwater samples based on the results of principal coordinate analysis and co-inertia analysis. Other geochemical variables including TOC, NH4+, oxidation-reduction potential, and Fe might also affect the microbial composition.

Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine

The tailings of the Shimen realgar mine have unique geochemical features. Arsenite oxidation is one of the major biogeochemical processes that occurs in the tailings. However, little is known about the functional and molecular aspects of the microbial community involved in arsenite oxidation. Here, we fully explored the functional and molecular features of the microbial communities from the tailings of the Shimen realgar mine. We collected six samples of tailings from sites A, B, C, D, E, and F. Microcosm assays indicated that all of the six sites contain both chemoautotrophic and heterotrophic arsenite-oxidizing microorganisms; their activities differed considerably from each other. The microbial arsenite-oxidizing activities show a positive correlation with soluble arsenic concentrations. The microbial communities of the six sites contain 40 phyla of bacteria and 2 phyla of archaea that show extremely high diversity. Soluble arsenic, sulfate, pH, and total organic carbon (TOC) are the key environmental factors that shape the microbial communities. We further identified 114 unique arsenite oxidase genes from the samples; all of them code for new or new-type arsenite oxidases. We also isolated 10 novel arsenite oxidizers from the samples, of which 4 are chemoautotrophic and 6 are heterotrophic. These data highlight the unique diversities of the arsenite-oxidizing microorganisms and their oxidase genes from the tailings of the Shimen realgar mine. To the best of our knowledge, this is the first report describing the functional and molecular features of microbial communities from the tailings of a realgar mine.

IMPORTANCE

This study focused on the functional and molecular characterizations of microbial communities from the tailings of the Shimen realgar mine. We fully explored, for the first time, the arsenite-oxidizing activities and the functional gene diversities of microorganisms from the tailings, as well as the correlation of the microbial activities/diversities with environmental factors. The findings of this study help us to better understand the diversities of the arsenite-oxidizing bacteria and the geochemical cycle of arsenic in the tailings of the Shimen realgar mine and gain insights into the microbial mechanisms by which the secondary minerals of the tailings were formed. This work also offers a set of unique arsenite-oxidizing bacteria for basic research of the molecular regulation of arsenite oxidation in bacterial cells and for the environmentally friendly bioremediation of arsenic-contaminated groundwater.

Draft genomic sequence of a chromate- and sulfate-reducing Alishewanella strain with the ability to bioremediate Cr and Cd contamination

Alishewanella sp. WH16-1 (= CCTCC M201507) is a facultative anaerobic, motile, Gram-negative, rod-shaped bacterium isolated from soil of a copper and iron mine. This strain efficiently reduces chromate (Cr⁶⁺) to the much less toxic Cr³⁺. In addition, it reduces sulfate (SO₄²⁻) to S²⁻. The S²⁻ could react with Cd²⁺ to generate precipitated CdS. Thus, strain WH16-1 shows a great potential to bioremediate Cr and Cd contaimination. Here we describe the features of this organism, together with the draft genome and comparative genomic results among strain WH16-1 and other Alishewanella strains. The genome comprises 3,488,867 bp, 50.4 % G + C content, 3,132 protein-coding genes and 80 RNA genes. Both putative chromate- and sulfate-reducing genes are identified.