New Arsenate Reductase Gene (arrA) PCR Primers for Diversity Assessment and Quantification in Environmental Samples

Soil Microbiomes and their Arsenic Functional Genes in Chronically High-Arsenic Contaminated Soils

Microbial arsenic transformations play essential roles in controlling pollution and ameliorating risk. This study combined high-throughput sequencing and PCR-based approaches targeting both the 16 S rRNA and arsenic functional genes to investigate the temporal and spatial dynamics of the soil microbiomes impacted by high arsenic contamination (9.13 to 911.88 mg/kg) and to investigate the diversity and abundance of arsenic functional genes in soils influenced by an arsenic gradient. The results showed that the soil microbiomes were relatively consistent and mainly composed of Actinobacteria (uncultured Gaiellales and an unknown_67 - 14 bacterium), Proteobacteria, Firmicutes (particularly, Bacillus), Chloroflexi, and Acidobacteria (unknown_Subgroup_6). Although a range of arsenic functional genes (e.g., arsM, arsC, arrA, and aioA) were identified by shotgun metagenomics, only the arsM gene was detected by the PCR-based method. The relative abundance of the arsM gene accounted for 0.20%-1.57% of the total microbial abundance. Combining all analyses, arsenic methylation mediated by the arsM gene was proposed to be a key process involved in the arsenic biogeochemical cycle and mitigation of arsenic toxicity. This study advances our knowledge about arsenic mechanisms over the long-term in highly contaminated soils.

Unraveling seasonal shifts in microbial and geochemical mediated arsenic mobilization at the estuarine sediment-water interface under redox changes

The mobilization of arsenic (As) at the sediment-water interface (SWI) is crucial for determining the accumulation of dissolved As to potentially toxic levels. However, the specific impacts of redox processes involving iron (Fe) and sulfur (S), as well as microbial activities occurring in sediments, on As mobilization at the marine SWI remain poorly understood. In this study, we investigated As mobilization at the SWI in the Changjiang Estuary during three different seasons with different benthic redox conditions. The preferential reduction of arsenate (As(V)) to arsenite (As(III)) and subsequent re-adsorption onto newly formed crystalline Fe oxides restricted As release in the As(V) reduction layer. Enhanced Fe(III) reduction in the Fe(III) reduction layer contributed to As release, while the presence of low As-high Fe-high SO42- levels resulted in As removal through adsorption onto pyrite in the sulfate reduction layer. Analysis of functional genes indicated that As(V) in sediments was released into porewater through the reductive dissolution of As(V)-bearing Fe(III) oxides by Geobacter species, followed by microbial reduction of the liberated As(V) to As(III) by microbes carrying the arrA gene. The dominant pathway governing As mobilization at the SWI in the Changjiang Estuary shifted from microbial reduction control during the hypoxic summer to Fe redox control during the aerobic autumn and winter. These findings provide valuable insights into the complex mechanisms driving As mobilization and highlight the importance of considering seasonal variations in understanding As dynamics at the marine SWI.

Selective pressure of arsenic and antimony co-contamination on microbial community in alkaline sediments

Although response of microbial community to arsenic (As) and antimony (Sb) co-contamination has been investigated in neutral and acidic environments, little is known in alkaline environment. Herein, the microbial response and survival strategies under the stress of As and Sb co-contamination were determined in the alkaline sediments. Elevated concentrations of As (13700 ± 5012 mg/kg) and Sb (10222 ± 1619 mg/kg) were introduced into the alkaline sediments by the mine drainage, which was partially adopted in the aquatic environment and resulted in a relatively lower contamination (As, 6633 ± 1707 mg/kg; Sb, 6108 ± 1095 mg/kg) in the downstream sediments. The microbial richness was significantly damaged and the microbial compositions were dramatically shifted by the As and Sb co-contamination. Metagenomic analysis shed light on the survival strategies of the microbes under the pressure of As and Sb co-contamination including metal oxidation coupled with denitrification, metal reduction, and metal resistance. The representative microbes were revealed in the sediments with higher (Halomonas) and lower (Thiobacillus, Hydrogenophaga and Flavihumibacter) As and Sb concentration, respectively. In addition, antibiotic resistance genes were found to co-occur with metal resistance genes in the assembled bins. These findings might provide theoretical guidance for bioremediation of As and Sb co-contamination in alkaline environment.

Soil Humic Acid Stimulates Potentially Active Dissimilatory Arsenate-Reducing Bacteria in Flooded Paddy Soil as Revealed by Metagenomic Stable Isotope Probing

Dissimilatory arsenate reduction contributes a large proportion of arsenic flux from flooded paddy soil, which is closely linked to soil organic carbon input and efflux. Humic acid (HA) represents a natural ingredient in soil and is shown to enhance microbial arsenate respiration to promote arsenic mobility. However, the community and function profiles of metabolically active arsenate-respiring bacteria and their interactions with HA in paddy soil remain unclear. To probe this linkage, we performed a genome-centric comparison of potentially active arsenate-respiring bacteria in anaerobic microcosms amended with 13C-lactate and HA by combining stable-isotope probing with genome-resolved metagenomics. Indeed, HA greatly accelerated the microbial reduction of arsenate to arsenite. Enrichment of bacteria that harbor arsenate-respiring reductase genes (arrA) in HA-enriched 13C-DNA was confirmed by metagenomic binning, which are affiliated with Firmicutes (mainly Desulfitobacterium, Bacillus, Brevibacillus, and Clostridia) and Acidobacteria. Characterization of reference extracellular electron transfer (EET)-related genes in these arrA-harboring bacteria supports the presence of EET-like genes, with partial electron-transport chain genes identified. This suggests that Gram-positive Firmicutes- and Acidobacteria-related members may harbor unspecified EET-associated genes involved in metal reduction. Our findings highlight the link between soil HA and potentially active arsenate-respiring bacteria, which can be considered when using HA for arsenic removal.

Microbially mediated sulfur oxidation coupled with arsenate reduction within oligotrophic mining-impacted habitats

Arsenate [As(V)] reduction is a major cause of arsenic (As) release from soils, which threatens more than 200 million people worldwide. While heterotrophic As(V) reduction has been investigated extensively, the mechanism of chemolithotrophic As(V) reduction is less studied. Since As is frequently found as a sulfidic mineral in the environment, microbial mediated sulfur oxidation coupled to As(V) reduction (SOAsR), a chemolithotrophic process, may be more favorable in sites impacted by oligotrophic mining (e.g. As-contaminated mine tailings). While SOAsR is thermodynamically favorable, knowledge regarding this biogeochemical process is still limited. The current study suggested that SOAsR was a more prevalent process than heterotrophic As(V) reduction in oligotrophic sites, such as mine tailings. The water-soluble reduced sulfur concentration was predicted to be one of the major geochemical parameters that had a substantial impact on SOAsR potentials. A combination of DNA stable isotope probing and metagenome binning revealed members of the genera Sulfuricella, Ramlibacter, and Sulfuritalea as sulfur oxidizing As(V)-reducing bacteria (SOAsRB) in mine tailings. Genome mining further expanded the list of potential SOAsRB to diverse phylogenetic lineages such as members associated with Burkholderiaceae and Rhodocyclaceae. Metagenome analysis using multiple tailing samples across southern China confirmed that the putative SOAsRB were the dominant As(V) reducers in these sites. Together, the current findings expand our knowledge regarding the chemolithotrophic As(V) reduction process, which may be harnessed to facilitate future remediation practices in mine tailings.

Arsenic (As) oxidation by core endosphere microbiome mediates As speciation in Pteris vittata roots

Pteris vittata is an arsenic(As)-hyperaccumulator that may be employed in phytoremediation of As-contaminated soils. P. vittata-associated microbiome are adapted to elevated As and may be important for host survival under stresses. Although P. vittata root endophytes could be critical for As biotransformation in planta, their compositions and metabolisms remain elusive. The current study aims to characterize the root endophytic community composition and As-metabolizing potentials in P. vittata. High As(III) oxidase gene abundances and rapid As(III) oxidation activity indicated that As(III) oxidation was the dominant microbial As-biotransformation processes compared to As reduction and methylization in P. vittata roots. Members of Rhizobiales were the core microbiome and the dominant As(III) oxidizers in P. vittata roots. Acquasition of As-metabolising genes, including both As(III) oxidase and As(V) detoxification reductase genes, through horizontal gene transfer was identified in a Saccharimonadaceae genomic assembly, which was another abundant population residing in P. vittata roots. Acquisition of these genes might improve the fitness of Saccharimonadaceae population to elevated As concentrations in P. vittata. Diverse plant growth promoting traits were encoded by the core root microbiome populations Rhizobiales. We propose that microbial As(III) oxidation and plant growth promotion are critical traits for P. vittata survival in hostile As-contaiminated sites.

Arsenic release from microbial reduction of scorodite in the presence of electron shuttle in flooded soil

Scorodite (FeAsO₄·H₂O) is a common arsenic-bearing (As-bearing) iron mineral in near-surface environments that could immobilize or store As in a bound state. In flooded soils, microbe induced Fe(III) or As(V) reduction can increase the mobility and bioavailability of As. Additionally, humic substances can act as electron shuttles to promote this process. The dynamics of As release and diversity of putative As(V)-reducing bacteria during scorodite reduction have yet to be investigated in detail in flooded soils. Here, the microbial reductive dissolution of scorodite was conducted in an flooded soil in the presence of anthraquinone-2,6-disulfonate (AQDS). Anaeromyxobacter, Dechloromonas, Geothrix, Geobacter, Ideonella, and Zoogloea were found to be the dominant indigenous bacteria during Fe(III) and As(V) reduction. AQDS increased the relative abundance of dominant species, but did not change the diversity and microbial community of the systems with scorodite. Among these bacteria, Geobacter exhibited the greatest increase and was the dominant Fe(III)- and As(V)-reducing bacteria during the incubation with AQDS and scorodite. AQDS promoted both Fe(III) and As(V) reduction, and over 80% of released As(V) was microbially transformed to As(III). The increases in the abundance of arrA gene and putative arrA sequences of Geobacter were higher with AQDS than without AQDS. As a result, the addition of AQDS promoted microbial Fe(III) and As(V) release and reduction from As-bearing iron minerals into the environment. These results contribute to exploration of the transformation of As from As-bearing iron minerals under anaerobic conditions, thus providing insights into the bioremediation of As-contaminated soil.

Environmental Mn(II) enhances the activity of dissimilatory arsenate-respiring prokaryotes from arsenic-contaminated soils

Many investigations suggest that dissimilatory arsenate-respiring prokaryotes (DARPs) play a key role in stimulating reductive mobilization of As from solid phase into groundwater, but it is not clear how environmental Mn(II) affects the DARPs-mediated reductive mobilization of arsenic. To resolve this issue, we collected soil samples from a realgar tailings-affected area. We found that there were diverse arsenate-respiratory reductase (arr) genes in the soils. The microbial communities had high arsenate-respiring activity, and were able to efficiently stimulate the reductive mobilization of As. Compared to the microcosms without Mn(II), addition of 10 mmol/L Mn(II) to the microcosms led to 23.99%-251.79% increases in the microbial mobilization of As, and led to 133.3%-239.2% increases in the abundances of arr genes. We further isolated a new cultivable DARP, Bacillus sp. F11, from the arsenic-contaminated soils. It completely reduced 1 mmol/L As(V) in 5 days under the optimal reaction conditions. We further found that it was able to efficiently catalyze the reductive mobilization and release of As from the solid phase; the addition of 2 mmol/L Mn(II) led to 98.49%-248.78% increases in the F11 cells-mediated reductive mobilization of As, and 70.6%-104.4% increases in the arr gene abundances. These data suggest that environmental Mn(II) markedly increased the DARPs-mediated reductive mobilization of As in arsenic-contaminated soils. This work provided a new insight into the close association between the biogeochemical cycles of arsenic and manganese.

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.

Iron-based passivator mitigates the coupling process of anaerobic methane oxidation and arsenate reduction in paddy soils

Arsenic (As) is a toxic metalloid that is ubiquitous in paddy soils, where passivation is the most widely used method for remediating As contamination. Recently, anaerobic methane oxidation coupled with arsenate (As(V)) reduction (AOM-AsR) has been shown to act as a critical driver for As release in paddy fields. However, the effect and mechanism of the passivators on the AOM-AsR process remain unclear. In this study, we incubated arsenate-contaminated paddy soils under anaerobic conditions. Using isotopically labelled methane and different passivators, we found that an iron-based passivator containing calcium sulfate and iron oxide (9:1, m/m) named IBP showed a much better performance than the other passivators. Adding IBP decreased the arsenite (As(III)) concentration in the soil solution by 78% and increased the AOM rate by 55%. Furthermore, we employed high-throughput sequencing and real-time quantitative polymerase chain reaction (qPCR) to investigate the ability of IBP to control As release mediated by AOM-AsR in paddy fields, as well as its underlying mechanism. Our results showed that IBP addition significantly increased anaerobic methanotrophic (ANME) archaea (ANME-2a-c, ANME-2d, and ANME-3) by 91%, and increased the methane-oxidizing bacterium Methylobacter by 262%. Similarly, IBP addition significantly increased the Fe(III) concentration in soil solution by 39% and increased the absolute abundance of Fe(III)-reducing bacteria (Geobacteraceae) by 21 times in soil. Adding IBP may significantly promote AOM coupled with Fe(III) reduction, significantly reducing electron transfer from AOM to As(V) reduction. Hence, IBP may be used as an efficient passivator to remediate As-contaminated soil using an active AOM-AsR process. These results provide a novel insight into controlling soil As release by regulating an active and critical As mobilization pathway in the environment.

Characterization of arsenic-metabolizing bacteria in an alkaline soil

Arsenite (As(III)) is more toxic, mobilizable and bioavailable than arsenate (As(V)). Hence, the transformations between As(III) and As(V) are crucial for the toxicity and mobility of arsenic (As). However, As transformation and microbial communities involved in alkaline soils are largely unknown. Here we investigate two major pathways of As transformation, i.e., As(III) oxidation and As(V) reduction, and identify the bacteria involved in the alkaline soil by combining stable isotope probing with shotgun metagenomic sequencing. As(III) oxidation and significant increase of the aioA genes copies were observed in the treatments amended with As(III) and NO₃^-, suggesting that As(III) oxidation can couple with nitrate reduction and was mainly catalyzed by the microorganisms containing aioA genes. As(V) reduction was detected in the treatments amended with As(V) and acetate where the abundance of arrA gene significantly increased, indicating that microorganisms with arrA genes were the key As(V) reducers. Acidovorax, Hydrogenophaga, and Ramlibacter were the putative nitrate-dependent As(III) oxidizers, and Deinococcus and Serratia were the putative respiratory As(V) reducers. These findings will improve our understanding of As metabolism and are meaningful for mapping out bioremediation strategies of As contamination in alkaline environment.

Coupled Aerobic Methane Oxidation and Arsenate Reduction Contributes to Soil-Arsenic Mobilization in Agricultural Fields

Microbial oxidation of organic compounds can promote arsenic release by reducing soil-associated arsenate to the more mobile form arsenite. While anaerobic oxidation of methane has been demonstrated to reduce arsenate, it remains elusive whether and to what extent aerobic methane oxidation (aeMO) can contribute to reductive arsenic mobilization. To fill this knowledge gap, we performed incubations of both microbial laboratory cultures and soil samples from arsenic-contaminated agricultural fields in China. Incubations with laboratory cultures showed that aeMO could couple to arsenate reduction, wherein the former bioprocess was carried out by aerobic methanotrophs and the latter by a non-methanotrophic bacterium belonging to a novel and uncultivated representative of Burkholderiaceae. Metagenomic analyses combined with metabolite measurements suggested that formate served as the interspecies electron carrier linking aeMO to arsenate reduction. Such coupled bioprocesses also take place in the real world, supported by a similar stoichiometry and gene activity in the incubations with natural paddy soils, and contribute up to 76.2% of soil-arsenic mobilization into pore waters in the top layer of the soils where oxygen was present. Overall, this study reveals a previously overlooked yet significant contribution of aeMO to reductive arsenic mobilization.

Microbial mediated reaction of dimethylarsinic acid in wetland water and sediments

The biogeochemical reactions of dimethylarsinic acid (DMAs(V)) were investigated using simulated wetland systems in a laboratory. DMAs(V) was injected into the wetland water, and the As concentrations in the water, plants, and sediments were monitored. Aqueous and solid-phase As speciation was evaluated, and the results revealed that the DMAs(V) was completely transported to the sediments and plants. X-ray absorption spectroscopic measurement of the As in the sediment revealed that approximately 85-95% of As existed as inorganic As species, demonstrating the important role of microorganisms in the biogeochemical reaction of DMAs(V). The influences of microbes were further investigated in smaller batches under aerobic and anaerobic conditions. The microbial batch results showed that DMAs(V) demethylation reduced the total aqueous As concentration, demonstrating that As(V) has higher affinity to wetland sediment than DMAs(V). The redox conditions were also revealed as an important controlling factor of the As reaction and, under anaerobic conditions, we observed the presence of the most toxic form of inorganic As(III) in the aqueous phase. Although this study reports one example from a specific wetland, the important roles of the redox conditions and microbial influences were identified from the comprehensive analysis of As speciation and mass balance.

Arsenic Mobilization and Transformation by Ammonium-Generating Bacteria Isolated from High Arsenic Groundwater in Hetao Plain, China

Arsenic (As) mobilization in groundwater involves biogeochemical cycles of carbon, iron, and sulfur. However, few studies have focused on the role of nitrogen-metabolizing bacteria in As mobilization, as well as in the transformation between inorganic and organic As in groundwater. In this study, the nitrogen and As metabolisms of Citrobacter sp. G-C1 and Paraclostridium sp. G-11, isolated from high As groundwater in Hetao Plain, China, were characterized by culture experiments and genome sequencing. The results showed Citrobacter sp. G-C1 was a dissimilatory nitrate-reducing bacterium. The dissimilatory nitrate reduction to ammonia (DNRA) and As-detoxifying pathways identified in the genome enabled Citrobacter sp. G-C1 to simultaneously reduce As(V) during DNRA. Paraclostridium sp. G-11 was a nitrogen-fixing bacterium and its nitrogen-fixing activity was constrained by As. Nitrogen fixation and the As-detoxifying pathways identified in its genome conferred the capability of As(V) reduction during nitrogen fixation. Under anaerobic conditions, Citrobacter sp. G-C1 was able to demethylate organic As and Paraclostridium sp. G-11 performed As(III) methylation with the arsM gene. Collectively, these results not only evidenced that ammonium-generating bacteria with the ars operon were able to transform As(V) to more mobile As(III) during nitrogen-metabolizing processes, but also involved the transformation between inorganic and organic As in groundwater.

Isolation and molecular identification of native As-resistant bacteria: As(III) and As(V) removal capacity and possible mechanism of detoxification

The study of arsenic (As)-resistant microorganisms with high As removal capacity is fundamental for the development of economically sustainable technologies used for the treatment of water contaminated with metalloid. In the current study, four bacterial strains were isolated from As-contaminated water samples of the Xichu region, Mexico. Based on 16S rRNA gene sequencing and phylogenetic analysis of the isolated strains, Rhodococcus gordoniae, Microbacterium hydrocarbonoxydans, Exiguobacterium indicum, and Pseudomonas kribbensis were identified as potential As removal strains. R. gordoniae shows the highest growth capacity in both As(III) and As(V). R. gordoniae, M. hydrocarbonoxydans, and E. indicum removed approximately 81.6, 79.9, and 61.7% of As(III), as well as 77.2, 68.9, and 74.8% of As(V), respectively. P. kribbensis removed only about 80.2% of As(V). This study contributes to the possible detoxification mechanisms employed by these bacteria. Such insight could be crucial in the successful implementation of in situ bioremediation programs using these little-known bacteria.

Effects of anode/cathode electroactive microorganisms on arsenic removal with organic/inorganic carbon supplied

This study reports the effects of an external voltage (0 V, 0.4 V and 0.9 V) on soil arsenic (As) release and sequestration when amended with organic carbon (NaAc) and inorganic carbon (NaHCO₃), respectively, in a soil bioelectrochemistry system (BES). The results demonstrated that although an external voltage had no effect on the As removal capacity in an oligotrophic environment fueled with NaHCO_3, 93.6% of As(III) in the supernatant was removed at 0.9 V with an NaAc amendment. Interestingly, the content of As detected on the electrodes was higher than that removed from the supernatant, implying a continuous release of soil As under external voltages and rapid adsorption onto the electrodes, especially the cathode. In addition, the species of As on the cathode were similar to those in the supernatant (the As(III)/As(V) ratio was approximately 3:1), indicating that the removal capacity was independent of preoxidation. From the viewpoint of electroactive microorganisms (EABs), the relative abundances of the arrA gene and Geobacter genus were specifically enriched at the anode, thus signifying stimulation of the reduction and release of soil As in the anode region. By comparison, Bacillus was particularly abundant at the cathode, which could contribute to the oxidation and sequestration of As in the cathode region. Additionally, specific extracellular polymeric substances (EPSs) secreted by EABs could combine with As, which was followed by electrostatic attraction to the cathode under the effect of an electric field. Furthermore, the formation of secondary minerals and coprecipitation in the presence of iron (Fe) may have also contributed to As removal from solution. The insights from this study will enable us to further understand the biogeochemical cycle of soil As and to explore the feasibility of in situ As bioremediation techniques, combining the aspects of microbial and physicochemical processes in soil bioelectrochemical systems.

Impacts of Redox Conditions on Arsenic and Antimony Transformation in Paddy Soil: Kinetics and Functional Bacteria

Arsenic (As) and antimony (Sb) are known carcinogens and are present as contaminants in paddy soils. However, the complicated dynamics of the mobility of these metalloids have not been well understood due to changing redox conditions in paddy soils. Herein, the kinetics of dissolved As and Sb, and functional bacteria/genes were examined in a paddy soil cultured under aerobic and anaerobic conditions. Under aerobic condition, dissolved As(V) and Sb(V) increased constantly due to sulfide oxidation by O₂ and bound As and Sb were released. Under anaerobic condition, the reduction of As(V) and Sb(V) occurred, and the mobility of As and Sb were affected by soil redox processes. The bacteria with functional genes aioA and arrA were responsible for the direct As/Sb transformation, while Fe- and N-related bacteria had an indirect effect on the fate of As/Sb via coupling with the redox processes of Fe and N. These findings improve understanding of the mobility of As and Sb in paddy soil systems under different redox conditions.

New Arsenite Oxidase Gene (aioA) PCR Primers for Assessing Arsenite-Oxidizer Diversity in the Environment Using High-Throughput Sequencing

Gene encoding the large subunit of As(III) oxidase (AioA), an important component of the microbial As(III) oxidation system, is a widely used biomarker to characterize As(III)-oxidizing communities in the environment. However, many studies were restricted to a few sequences generated by clone libraries and Sanger sequencing, which may have underestimated the diversity of As(III)-oxidizers in natural environments. In this study, we designed a primer pair, 1109F (5'-ATC TGG GGB AAY RAC AAY TA-3') and 1548R (5'-TTC ATB GAS GTS AGR TTC AT-3'), targeting gene sequence encoding for the conserved molybdopterin center of the AioA protein, yielding amplicons approximately 450 bp in size that are feasible for highly parallel amplicon sequencing. By utilizing in silico analyses and the experimental construction of clone libraries using Sanger sequencing, the specificity and resolution of 1109F/1548R are approximated with two other previously published and commonly used primers, i.e., M1-2F/M3-2R and deg1F/deg1R. With the use of the 1109F/1548R primer pair, the taxonomic composition of the aioA genes was similar both according to the Sanger and next-generation sequencing (NGS) platforms. Furthermore, high-throughput amplicon sequencing using the primer pair, 1109F/1548R, successfully identified the well-known As(III)-oxidizers in paddy soils and sediments, and they also revealed the differences in the community structure and composition of As(III)-oxidizers in above two biotopes. The random forest analysis showed that the dissolved As(III) had the highest relative influence on the Chao1 index of the aioA genes. These observations demonstrate that the newly designed PCR primers enhanced the ability to detect the diversity of aioA-encoding microorganisms in environments using highly parallel short amplicon sequencing.

Warming facilitates microbial reduction and release of arsenic in flooded paddy soil and arsenic accumulation in rice grains

Global warming severely hinders both rice (Oryza sativa L.) quality and yield by increasing arsenic (As) bioavailability in paddy soils. However, details regarding As biotransformation and migration in the rice-soil system at elevated temperatures remain unclear. This study investigated the effects of increasing temperature on As behavior and translocation in rice grown in As-contaminated paddy soil at two temperature treatments (33 °C warmer temperature and 28 °C as control). The results showed that increasing temperature from 28 °C to 33 °C significantly favored total As, arsenite (As(III)) and arsenate (As(Ⅴ)) release into the soil pore-water. This increase in As bioavailability resulted in significantly higher As(III) accumulation in the whole grains at warmer treatment relative to the control. Moreover, the results suggest that increasing temperature to 33 °C promoted As(III) migration from the roots to the whole grains. Furthermore, the As(V)-reducing Xanthomonadales order and Alcaligenaceae family, and As(V) reductase-encoding arsC gene were enriched in the rhizosphere soils incubated at 33 °C. This suggests that the increase in As bioavailability in that treatment was due to enhanced As(V) reductive dissolution into the soil pore-water. Overall, this study provides new insights on how warmer future temperatures will exacerbate As accumulation in rice grains.

Microbiomes in agricultural and mining soils contaminated with arsenic in Guanajuato, Mexico

In this report, physical and chemical properties, and total arsenic (As) concentrations were analyzed in agricultural (MASE) and mining soils (SMI) in the State of Guanajuato, México. Additionally, a metagenomic analysis of both types of soils was the bases for the identification and selection of bacteria and fungi resistant to As. The SMI soil showed higher concentration of As (39 mg kg^-1) as compared to MASE soil (15 mg kg^-1). The metagenome showed a total of 175,240 reads from both soils. MASE soil showed higher diversity of bacteria, while the SMI soil showed higher diversity of fungi. 16S rRNA analysis showed that the phylum Proteobacteria showed the highest proportion (39.6% in MASE and 36.4% in SMI) and Acidobacteria was the second most representative (24.2% in SMI and 11.6% in MASE). 18S rRNA analysis, showed that the phylum Glomeromycota was found only in the SMI soils (11.6%), while Ascomycota was the most abundant, followed by Basidiomycota, and Zygomycota, in both soils. Genera Bacillus and Penicillium were able to grow in As concentrations as high as 5 and 10 mM, reduced As (V) to As (III), and removed As at 9.8% and 12.1% rates, respectively. When aoxB, arsB, ACR3(1), ACR3(2,) and arrA genes were explored, only the arsB gene was identified in Bacillus sp., B. simplex, and B. megaterium. In general, SMI soils showed more microorganisms resistant to As than MASE soils. Bacteria and fungi selected in this work may show potential to be used as bioremediation agents in As contaminated soils.

Behaviors of heavy metal(loid)s in a cocontaminated alkaline paddy soil throughout the growth period of rice

A pot experiment was conducted to investigate uptake of cadmium (Cd), arsenic (As) and antimony (Sb) by rice from a lime-treated paddy soil contaminated with the three pollutants. The results showed that the content of Cd in the total rice plants decreased as the plant grew, whereas the As and Sb contents increased steadily. The concentration of As in the pore water showed steady increase throughout the growth period, likely due to the reductive dissolution of iron (Fe)-bearing minerals and the reduction of As(V). In contrast, the concentrations of Cd and Sb in the pore water increased initially, likely attributable to the reductive dissolution of Fe-bearing minerals, and then decreased likely due to their adsorptions onto carbonate and Fe sulfides, the reduction of Sb(V), and the formation of CdS. A random forest model was used to quantitatively evaluate the relative contributions of environmental factors to the accumulation of Cd, As, and Sb in the rice plants. The results suggest that sulfides produced through sulfate reduction and the formation of Cd forms associated with sulfur (S) might significantly affected the Cd content in the rice plants. In addition, the dissolved Fe species, the oxidation-reduction potential, and the abundance of the As(V)-respiring gene were major contributors to the As content in the rice plants, suggesting the important role of the reduction of Fe-bearing minerals and As(V). The results also showed that the Sb content in the rice plants was correlated with Fe species, Sb(V) reduction, and acid volatile S. The environmental behaviors of Cd, As, and Sb in the cocontaminated paddy soil exhibited significant differences. Such differences should be considered in remedy of soils contaminated with multiple heavy metals and metalloids.

Microbial reactions and environmental factors affecting the dissolution and release of arsenic in the severely contaminated soils under anaerobic or aerobic conditions

The soils near the abandoned Shimen Realgar Mine are characterized by containing extremely high contents of total and soluble arsenic. To determine the microbial reactions and environmental factors affecting the mobilization and release of arsenic from soils phase into pore water, we collected 24 soil samples from the representative points around the abandoned Shimen Realgar Mine. They contained 8310.84 mg/kg total arsenic and 703.21 mg/kg soluble arsenic in average. The soluble arsenic in the soils shows significant positive and negative correlations with environmental SO₄^2-/TOC/pH/PO₄^3-, and Fe/Mn, respectively. We found that diverse dissimilatory As(V)-respiring prokaryotes (DARPs) and As(III)-oxidizing bacteria (AOB) exist in all the examined soil samples. The activities of DARPs led to 65-1275% increase of soluble As(III) in the examined soils after 21.0 days of anaerobic incubation, and the microbial dissolution and releases of arsenic show significant positive and negative correlations with the environmental pH/TN and NH₄⁺/PO₄^3-, respectively. In comparison, the activities of AOB led to 24-346% inhibition of the dissolved oxygen-mediated dissolution of arsenic in the soils, and the AOB-mediated releases of As(V) show significant positive and negative correlations with the environmental SO₄^2- and pH/NH₄⁺, respectively. The microbial communities of 24 samples contain 54 phyla of bacteria that show extremely high diversities. Total arsenic, TOC, NO₃^- and pH are the key environmental factors that indirectly controlled the mobilization and release of arsenic via influencing the structures of the microbial communities in the soils. This work gained new insights into the mechanism for how microbial communities catalyze the dissolution and releases of arsenic from the soils with extremely high contents of arsenic.

Expression of Genes and Proteins Involved in Arsenic Respiration and Resistance in Dissimilatory Arsenate-Reducing Geobacter sp. Strain OR-1

The reduction of arsenate [As(V)] to arsenite [As(III)] by dissimilatory As(V)-reducing bacteria, such as Geobacter spp., may play a significant role in arsenic release from anaerobic sediments into groundwater. The biochemical and molecular mechanisms by which these bacteria cope with this toxic element remain unclear. In this study, the expression of several genes involved in arsenic respiration (arr) and resistance (ars) was determined using Geobacter sp. strain OR-1, the only cultured Geobacter strain capable of As(V) respiration. In addition, proteins expressed differentially under As(V)-respiring conditions were identified by semiquantitative proteomic analysis. Dissimilatory As(V) reductase (Arr) of strain OR-1 was localized predominantly in the periplasmic space, and the transcription of its gene (arrA) was upregulated under As(V)-respiring conditions. The transcription of the detoxifying As(V) reductase gene (arsC) was also upregulated, but its induction required 500 times higher concentration of As(III) (500 μM) than did the arrA gene. Comparative proteomic analysis revealed that in addition to the Arr and Ars proteins, proteins involved in the following processes were upregulated under As(V)-respiring conditions: (i) protein folding and assembly for rescue of proteins with oxidative damage, (ii) DNA replication and repair for restoration of DNA breaks, (iii) anaplerosis and gluconeogenesis for sustainable energy production and biomass formation, and (iv) protein and nucleotide synthesis for the replacement of damaged proteins and nucleotides. These results suggest that strain OR-1 copes with arsenic stress by orchestrating pleiotropic processes that enable this bacterium to resist and actively metabolize arsenic.IMPORTANCE Dissimilatory As(V)-reducing bacteria, such as Geobacter spp., play significant roles in arsenic release and contamination in groundwater and threaten the health of people worldwide. However, the biochemical and molecular mechanisms by which these bacteria cope with arsenic toxicity remain unclear. In this study, it was found that both respiratory and detoxifying As(V) reductases of a dissimilatory As(V)-reducing bacterium, Geobacter sp. strain OR-1, were upregulated under As(V)-respiring conditions. In addition, various proteins expressed specifically or more abundantly in strain OR-1 under arsenic stress were identified. Strain OR-1 actively metabolizes arsenic while orchestrating various metabolic processes that repair oxidative damage caused by arsenic. Such information is useful in assessing and identifying possible countermeasures for the prevention of microbial arsenic release in nature.

A global survey of arsenic-related genes in soil microbiomes

BACKGROUND

Environmental resistomes include transferable microbial genes. One important resistome component is resistance to arsenic, a ubiquitous and toxic metalloid that can have negative and chronic consequences for human and animal health. The distribution of arsenic resistance and metabolism genes in the environment is not well understood. However, microbial communities and their resistomes mediate key transformations of arsenic that are expected to impact both biogeochemistry and local toxicity.

RESULTS

We examined the phylogenetic diversity, genomic location (chromosome or plasmid), and biogeography of arsenic resistance and metabolism genes in 922 soil genomes and 38 metagenomes. To do so, we developed a bioinformatic toolkit that includes BLAST databases, hidden Markov models and resources for gene-targeted assembly of nine arsenic resistance and metabolism genes: acr3, aioA, arsB, arsC (grx), arsC (trx), arsD, arsM, arrA, and arxA. Though arsenic-related genes were common, they were not universally detected, contradicting the common conjecture that all organisms have them. From major clades of arsenic-related genes, we inferred their potential for horizontal and vertical transfer. Different types and proportions of genes were detected across soils, suggesting microbial community composition will, in part, determine local arsenic toxicity and biogeochemistry. While arsenic-related genes were globally distributed, particular sequence variants were highly endemic (e.g., acr3), suggesting dispersal limitation. The gene encoding arsenic methylase arsM was unexpectedly abundant in soil metagenomes (median 48%), suggesting that it plays a prominent role in global arsenic biogeochemistry.

CONCLUSIONS

Our analysis advances understanding of arsenic resistance, metabolism, and biogeochemistry, and our approach provides a roadmap for the ecological investigation of environmental resistomes.

Humic Substances Facilitate Arsenic Reduction and Release in Flooded Paddy Soil

Organic matter is important for controlling arsenic reduction and release under anoxic conditions. Humic substances (HS) represent an important fraction of natural organic matter, yet the manner in which HS affect arsenic transformation in flooded paddy soil has not been thoroughly elucidated. In this study, anaerobic microcosms were established with arsenic-contaminated paddy soil and amended with three extracted humic fractions (fulvic acid, FA; humic acid, HA; and humin, HM). The HS substantially enhanced the extent of arsenic reduction and release in the order FA > HA > HM. It was confirmed that microbially reduced HS acted as an electron shuttle to promote arsenate reduction. HS, particularly FA, provided labile carbon to stimulate microbial activity and increase the relative abundances of Azoarcus, Anaeromyxobacter, and Pseudomonas, all of which may be involved in the reduction of HS, Fe(III), and arsenate. HS also increased the abundance of transcripts for an arsenate-respiring gene ( arrA) and overall transcription in arsenate-respiring Geobacter spp. The increase in both abundances lagged behind the increases in dissolved arsenate levels. These results help to elucidate the pathways of arsenic reduction and release in the presence of HS in flooded paddy soil.

Dissimilatory arsenate-respiring prokaryotes catalyze the dissolution, reduction and release of arsenic from paddy soils into groundwater: implication for the effect of sulfate

The paddy soils in some areas in Jianghan Plain were severely contaminated by arsenic. However, little is known about the activity and diversity of the dissimilatory arsenate-respiring prokaryotes (DARPs) in the paddy soils, and the effects of sulfate on the microbial mobilization and release of arsenic from soils into solution. To address this issue, we collected arsenic-rich soils from the depths of 1.6 and 4.6 m in a paddy region in the Xiantao city, Hubei Province, China. Microcosm assays indicated that all of the soils have significant arsenate-respiring activities using lactate, pyruvate or acetate as the sole electron donor. Functional gene cloning and analysis suggest that there are diverse DARPs in the indigenous microbial communities of the soils. They efficiently promoted the mobilization, reduction and release of arsenic and iron from soils under anaerobic conditions. Remarkably, when sulfate was amended into the microcosms, the microorganisms-catalyzed reduction and release of arsenic and iron were significantly increased. We further found that sulfate significantly enhanced the arsenate-respiring reductase gene abundances in the soils. Taken together, a diversity of DARPs in the paddy soils significantly catalyzed the dissolution, reduction and release of arsenic and iron from insoluble phase into solution, and the presence of sulfate significantly increased the microbial reactions.

Structural and mechanistic analysis of the arsenate respiratory reductase provides insight into environmental arsenic transformations

Arsenate respiration by bacteria was discovered over two decades ago and is catalyzed by diverse organisms using the well-conserved Arr enzyme complex. Until now, the mechanisms underpinning this metabolism have been relatively opaque. Here, we report the structure of an Arr complex (solved by X-ray crystallography to 1.6-Å resolution), which was enabled by an improved Arr expression method in the genetically tractable arsenate respirer Shewanella sp. ANA-3. We also obtained structures bound with the substrate arsenate (1.8 Å), the product arsenite (1.8 Å), and the natural inhibitor phosphate (1.7 Å). The structures reveal a conserved active-site motif that distinguishes Arr [(R/K)GRY] from the closely related arsenite respiratory oxidase (Arx) complex (XGRGWG). Arr activity assays using methyl viologen as the electron donor and arsenate as the electron acceptor display two-site ping-pong kinetics. A Mo(V) species was detected with EPR spectroscopy, which is typical for proteins with a pyranopterin guanine dinucleotide cofactor. Arr is an extraordinarily fast enzyme that approaches the diffusion limit (K_m = 44.6 ± 1.6 μM, k_cat = 9,810 ± 220 seconds^-1), and phosphate is a competitive inhibitor of arsenate reduction (K_i = 325 ± 12 μM). These observations, combined with knowledge of typical sedimentary arsenate and phosphate concentrations and known rates of arsenate desorption from minerals in the presence of phosphate, suggest that (i) arsenate desorption limits microbiologically induced arsenate reductive mobilization and (ii) phosphate enhances arsenic mobility by stimulating arsenate desorption rather than by inhibiting it at the enzymatic level.

Effect of microbially mediated iron mineral transformation on temporal variation of arsenic in the Pleistocene aquifers of the central Yangtze River basin

Significant seasonal variation of groundwater arsenic (As) concentrations in shallow aquifers of the Jianghan Plain, central Yangtze River Basin has been reported recently, but the underlying mechanisms remain not well understood. To elaborate biogeochemical processes responsible for the observed As concentration variation, 42-day incubation experiments were done using sediment samples collected respectively from the depth of 26, 36 and 60m of the As-affected aquifer which were labeled respectively as JH26, JH36, JH60. Where JH denotes Jianghan Plain, and the number indicates the depth of the sediment sample. The results indicated that As could be mobilized from the sediments of 26m and 36m depth under the stimulation of exogenous organic carbon, with the maximum As release amount of 1.60 and 1.03mgkg^-1, respectively, while the sediments at 60m depth did not show As mobilization. The microbially mediated reductive dissolution of amorphous iron oxides and reduction of As(V) to As(III) could account for the observed As mobilization. The 16S rRNA high-throughput sequencing results indicated that the variation of microbial community correlated with the released As concentration (R=0.7, P<0.05) and the iron-reducing bacteria, including Pseudomonas, Clostridium and Geobacter, were the main drivers for the As mobilization from the sediments at 26m and 36m depth. The increase of arsC gene abundance (up to 1.4×10⁵ copies g^-1) during As release suggested that As reduction was mediated by the resistant reduction mechanism. By contrast, in the 60m sediments where the Fe and As release was absent, the iron-reducing bacteria accounted for a very minor proportion and sulfate-reducing bacteria were predominant in the microbial community. In addition, after 30days of incubation, the released As in the 26m sediments was immobilized via co-precipitation with or adsorption onto the Fe-sulfide mineral newly-formed by the bacterial sulfate reduction. These results are consistent with the results of our previous field monitoring, indicating that the bacterial sulfate reduction could lead to the temporal decrease in groundwater As concentrations. This study provides insights into the mechanism for As mobilization and seasonal As concentration variation in the Pleistocene aquifers from alluvial plains.

Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwater

Microbial functional potential in high arsenic (As) groundwater ecosystems remains largely unknown. In this study, the microbial community functional composition of nineteen groundwater samples was investigated using a functional gene array (GeoChip 5.0). Samples were divided into low and high As groups based on the clustering analysis of geochemical parameters and microbial functional structures. The results showed that As related genes (arsC, arrA), sulfate related genes (dsrA and dsrB), nitrogen cycling related genes (ureC, amoA, and hzo) and methanogen genes (mcrA, hdrB) in groundwater samples were correlated with As, SO₄^2-, NH₄⁺ or CH₄ concentrations, respectively. Canonical correspondence analysis (CCA) results indicated that some geochemical parameters including As, total organic content, SO₄^2-, NH₄⁺, oxidation-reduction potential (ORP) and pH were important factors shaping the functional microbial community structures. Alkaline and reducing conditions with relatively low SO₄^2-, ORP, and high NH₄⁺, as well as SO₄^2- and Fe reduction and ammonification involved in microbially-mediated geochemical processes could be associated with As enrichment in groundwater. This study provides an overall picture of functional microbial communities in high As groundwater aquifers, and also provides insights into the critical role of microorganisms in As biogeochemical cycling.