Metagenomic analysis revealed highly diverse microbial arsenic metabolism genes in paddy soils with low-arsenic contents

Inorganic arsenic toxicity and alleviation strategies in rice

Direct or indirect exposure to inorganic arsenic (iAs) in the forms of AsIII (arsenite) and AsV (arsenate) through consumption of As-contaminated food materials and drinking water leads to arsenic poisoning. Rice (Oryza sativa L.) plant potentially accumulates a high amount of iAs from paddy fields than any other cereal crops. This makes it to be a major source of iAs especially among the population that uses it as their dominant source of diet. The accumulation of As in human bodies poses a serious global health risk to the human population. Various conventional methods have been applied to reduce the arsenic accumulation in rice plant. However, the success rate of these techniques is low. Therefore, the development of efficient and effective methods aimed at lowering iAs toxicity is a very crucial public concern. With the current advancement in technology, new strategies aimed at addressing this concern are being developed and utilized in various parts of the world. In this review, we discuss the recent advances in the management of iAs in rice plants emphasizing the use of nanotechnology and biotechnology approaches. Also, the prospects and challenges facing these approaches are described.

Thiourea supplementation mediated reduction of grain arsenic in rice (Oryza sativa L.) cultivars: A two year field study

The present study delineates the interactions of arsenic (As), a carcinogenic metalloid, and thiourea (TU), a non-physiological reactive oxygen species (ROS) scavenger, in rice plants grown in As contaminated fields in West Bengal, India. The study was performed for four consecutive seasons (two boro and two aman) in 2016 and 2017 with two local rice cultivars; Gosai and Satabdi (IET-4786) in a control and two As contaminated experimental fields. Thiourea (0.05% wt/vol) treatment was given in the form of seed priming and foliar spray. Thiourea significantly improved growth and yield of rice plants and reduced As concentration in root, shoot, husk and grains in both cultivars and fields. The reduction in As concentration ranged from 10.3% to 27.5% in four seasons in different fields. The average (four seasons) increase in yield was recorded about ~8.1% and ~11.5% in control, ~20.2% and ~18.6% in experimental field 1, and ~16.2% and ~24.1% in experimental field 2, for gosai and satabdi, respectively. Mean hazard quotient (HQ) and incremental lifetime cancer risk (ILCR) values of As reduced upon TU supplementation for both cultivars as compared to that of non-TU plants. Hence, TU can be effectively used to cultivate rice safely in As contaminated fields.

Development of a whole-cell biosensor based on an ArsR-P ars regulatory circuit from Geobacter sulfurreducens

In this study, an Escherichia coli (E. coli) whole-cell biosensor for the specific detection of bioavailable arsenic was developed by placing a green fluorescent protein (GFP) reporter gene under the control of the ArsR1 (GSU2952) regulatory circuit from Geobacter sulfurreducens. E. coli cells only emitted green fluorescence in the presence of arsenite and were more sensitive to arsenite when they were grown in M9 supplemented medium compared to LB medium. Under optimal test conditions, the Geobacter arsR1 promoter had a detection limit of 0.01 μM arsenite and the GFP expression was linear within a range of 0.03-0.1 μM (2.25-7.5 μg/l). These values were well below World Health Organization's drinking water quality standard, which is 10 μg/l. The feasibility of using this whole-cell biosensor to detect arsenic in water samples, such as arsenic polluted tap water and landfill leachate was verified. The biosensor was determined to be just as sensitive as atomic fluorescence spectrometry. This study examines the potential applications of biosensors constructed with Geobacter ArsR-P _ars regulatory circuits and provides a rapid and cost-effective tool that can be used for arsenic detection in water samples.

Root microbiome assembly of As-hyperaccumulator Pteris vittata and its efficacy in arsenic requisition

The assemblage of root-associated microorganisms plays important roles in improving their capability to adapt to environmental stress. Metal(loid) hyperaccumulators exhibit disparate adaptive capability compared to that of non-hyperaccumulators when faced with elevated contents of metal(loid)s. However, knowledge of the assemblage of root microbes of hyperaccumulators and their ecological roles in plant growth is still scarce. The present study used Pteris vittata as a model plant to study the microbial assemblage and its beneficial role in plant growth. We demonstrated that the assemblage of microbes from the associated bulk soil to the root compartment was based on their lifestyles. We used metagenomic analysis and identified that the assembled microbes were primarily involved in root-microbe interactions in P. vittata root. Notably, we identified that the assembled root microbiome played an important role in As requisition, which promoted the fitness and growth of P. vittata. This study provides new insights into the root microbiome and potential valuable knowledge to understand how the root microbiome contributes to the fitness of its host.

Microbiome-environment interactions in antimony-contaminated rice paddies and the correlation of core microbiome with arsenic and antimony contamination

Mining activities of antimony (Sb) and arsenic (As) typically result in severe environmental contamination. These contaminants accumulate in rice and thus threaten the health of local residents, who consume Sb- and As-enriched rice grains. Microorganisms play a critical role in the transformation and transportation of Sb and As in paddy soil. Thus, an understanding of the microbiology of contaminated sites would promote the production of safe agricultural products. In this study, six Sb- and As-contaminated rice fields near an active Sb-mining area were investigated. The Sb and As concentrations of all samples were elevated compared to the background level in China. Nitrate, total As, total Sb, and Fe(III) were the major determinants of the microbial community structure. Seven bacterial taxa (i.e. Bradyrhizobium, Bryobacter, Candidatus Solibacter, Geobacter, Gemmatimonas, Halingium, and Sphingomonas) were identified as the core microbiome. These taxa were strongly correlated with the As and Sb contaminant fractions and likely to metabolize As and Sb. Results imply that many soil microbes can survival in the Sb/As contaminated sites.

Epiphytic bacterial community enhances arsenic uptake and reduction by Myriophyllum verticillatum

Microbes play an important role in the biotransformation of arsenic (As) speciation in various environments. Nevertheless, whether epiphytic bacteria that attached on submerged macrophytes have the potential to influence As speciation still remains unclear. In this study, sterile or nonsterile Myriophyllum verticillatum was cultured with arsenite (As(III)) or arsenate (As(V)) to investigate the impact of epiphytic bacterial community on As uptake, transformation, and efflux. Results showed that both sterile and nonsterile M. verticillatum did not display substantial As(III) oxidation, suggesting that neither M. verticillatum nor epiphytic bacterial community has the capacities of As(III) oxidation. However, sterile M. verticillatum exhibited capacity for As(V) reduction, and the presence of epiphytic bacterial community substantially enhanced the proportions of As(III) in the medium (from 39.91 to 98.44%), indicating that epiphytic bacterial community contributes significantly to As(V) reduction in the medium. The presence of epiphytic bacterial community elevated As accumulation (by up to 2.06-fold) in plants when exposed to As(V). Results also showed that epiphytic bacterial community contributed little to As(III) efflux. Quantitative PCR of As metabolism genes revealed the dominance of the respiratory As(V) reductase genes (arrA) in epiphytic bacterial community, which might play a significant role in As(V) reduction in aquatic environments. Phylogenetic analysis of the arrA genes revealed the widely distribution and diversity of As(V)-respiring bacteria. These results highlighted the substantial impact of the epiphytic bacterial community associated with submerged aquatic macrophytes on As biogeochemistry in wetland and water environments.

Variability in Arsenic Methylation Efficiency across Aerobic and Anaerobic Microorganisms

Microbially-mediated methylation of arsenic (As) plays an important role in the As biogeochemical cycle, particularly in rice paddy soils where methylated As, generated microbially, is translocated into rice grains. The presence of the arsenite (As(III)) methyltransferase gene (arsM) in soil microbes has been used as an indication of their capacity for As methylation. Here, we evaluate the ability of seven microorganisms encoding active ArsM enzymes to methylate As. Amongst those, only the aerobic species were efficient methylators. The anaerobic microorganisms presented high resistance to As exposure, presumably through their efficient As(III) efflux, but methylated As poorly. The only exception were methanogens, for which efficient As methylation was seemingly an artifact of membrane disruption. Deletion of an efflux pump gene (acr3) in one of the anaerobes, Clostridium pasteurianum, rendered the strain sensitive to As and capable of more efficiently methylating As. Our results led to the following conclusions: (i) encoding a functional ArsM enzyme does not guarantee that a microorganism will actively drive As methylation in the presence of the metalloid and (ii) there is an inverse relationship between efficient microbial As efflux and its methylation, because the former prevents the intracellular accumulation of As.

Exploring novel Cr(VI) remediation genes for Cr(VI)-contaminated industrial wastewater treatment by comparative metatranscriptomics and metagenomics

Microbial remediation is a promising method to treat Cr(VI) in industrial wastewater. The remediation efficiency and stress-resistance ability of Cr(VI) remediation genes in microbes are the limiting factors for their application in industrial wastewater treatment. To screen novel highly efficient Cr(VI) remediation genes, comparative metatranscriptomic and metagenomic analyses were performed on long-term Cr(VI)-contaminated riparian soil with/without additional Cr(VI) treatment. The most suitable Cr(VI) treatment time was determined to be 30 min according to the high quality RNA yield and fold changes in gene expression. Six novel genes, which had complete open reading frames (ORFs) in metagenomic libraries, were identified from unculturable microbes. In the phenotypic functional assay, all novel genes enhanced the Cr(VI) resistance/reduction ability of E. coli. In the industrial wastewater treatment, E-mcr and E-gsr presented at least 50% Cr(VI) removal efficiencies in the presence of 200-600 μM of Cr(VI), without a decrease in efficiency over 17 days. The stress resistance assay showed that gsr increased the growth rate of E. coli by at least 30% under different extreme conditions, and thus, gsr was identified as a general stress-response gene. In the Cr valence distribution assay, E-mcr presented ~40 μM higher extracellular Cr (III) compared to E-yieF. Additionally, transmission electron microscopy (TEM) of E-mcr showed bulk black agglomerates on the cell surface. Thus, mcr was identified as a membrane chromate reductase gene. This research provides a new idea for studying novel highly efficient contaminant remediation genes from unculturable microbes.

Microbial adaptation in vertical soil profiles contaminated by an antimony smelting plant

Antimony mining has resulted in considerable pollution to the soil environment. Although studies on antinomy contamination have been conducted, its effects on vertical soil profiles and depth-resolved microbial communities remain unknown. The current study selected three vertical soil profiles (0–2 m) from the world's largest antimony mining area to characterize the depth-resolved soil microbiota and investigate the effects of mining contamination on microbial adaptation. Results demonstrated that contaminated soil profiles showed distinct depth-resolved effects when compared to uncontaminated soil profiles. As soil depth increased, the concentrations of antimony and arsenic gradually declined in the contaminated soil profiles. Acidobacteria, Chloroflexi, Proteobacteria and Thaumarchaeota were the most variable phyla from surface to deep soil. The co-occurrence networks were loosely connected in surface soil, but obviously recovered and were well-connected in deep soil. The metagenomic results indicated that microbial metabolic potential also changed with soil depth. Genes encoding C metabolism pathways were negatively correlated with antimony and arsenic concentrations. Abundances of arsenic-related genes were enriched by severe contamination, but reduced with soil depth. Overall, soil depth-resolved characteristics are often many meters deep and such effects affected the indigenous microbial communities, as well as their metabolic potential due to different contaminants along vertical depths.

Metagenomic and 14 C tracing evidence for autotrophic microbial CO2 fixation in paddy soils

Autotrophic carbon dioxide (CO₂ ) fixation by microbes is ubiquitous in the environment and potentially contributes to the soil organic carbon (SOC) pool. However, the multiple autotrophic pathways of microbial carbon assimilation and fixation in paddy soils remain poorly characterized. In this study, we combine metagenomic analysis with ¹⁴ C-labelling to investigate all known autotrophic pathways and CO₂ assimilation mechanisms in five typical paddy soils from southern China. Marker genes of six autotrophic pathways are detected in all soil samples, which are dominated by the cbbL genes (67%-82%) coding the ribulose-bisphosphate carboxylase large chain in the Calvin cycle. These marker genes are associated with a broad range of phototrophic and chemotrophic genera. Significant amounts of ¹⁴ C-CO₂ are assimilated into SOC (74.3-175.8 mg ¹⁴ C kg^-1 ) and microbial biomass (5.2-24.1 mg ¹⁴ C kg^-1 ) after 45 days incubation, where more than 70% of ¹⁴ C-SOC was concentrated in the relatively stable humin fractions. These results show that paddy soil microbes contain the genetic potential for autotrophic carbon fixation spreading over broad taxonomic ranges, and can incorporate atmospheric carbon into organic components, which ultimately contribute to the stable SOC pool.

Genomic Variation and Arsenic Tolerance Emerged as Niche Specific Adaptations by Different Exiguobacterium Strains Isolated From the Extreme Salar de Huasco Environment in Chilean - Altiplano

Polyextremophilic bacteria can thrive in environments with multiple stressors such as the Salar de Huasco (SH). Microbial communities in SH are exposed to low atmospheric pressure, high UV radiation, wide temperature ranges, salinity gradient and the presence of toxic compounds such as arsenic (As). In this work we focus on arsenic stress as one of the main adverse factors in SH and bacteria that belong to the Exiguobacterium genus due to their plasticity and ubiquity. Therefore, our aim was to shed light on the effect of niche conditions pressure (particularly arsenic), on the adaptation and divergence (at genotypic and phenotypic levels) of Exiguobacterium strains from five different SH sites. Also, to capture greater diversity in this genus, we use as outgroup five As(III) sensitive strains isolated from Easter Island (Chile) and The Great Salt Lake (United States). For this, samples were obtained from five different SH sites under an arsenic gradient (9 to 321 mg/kg: sediment) and isolated and sequenced the genomes of 14 Exiguobacterium strains, which had different arsenic tolerance levels. Then, we used comparative genomic analysis to assess the genomic divergence of these strains and their association with phenotypic differences such as arsenic tolerance levels and the ability to resist poly-stress. Phylogenetic analysis showed that SH strains share a common ancestor. Consequently, populations were separated and structured in different SH microenvironments, giving rise to multiple coexisting lineages. Hence, this genotypic variability is also evidenced by the COG (Clusters of Orthologous Groups) composition and the size of their accessory genomes. Interestingly, these observations correlate with physiological traits such as growth patterns, gene expression, and enzyme activity related to arsenic response and/or tolerance. Therefore, Exiguobacterium strains from SH are adapted to physiologically overcome the contrasting environmental conditions, like the arsenic present in their habitat.

Community dynamics of As(V)-reducing and As(III)-oxidizing genes during a wet-dry cycle in paddy soil amended with organic matter, gypsum, or iron oxide

Microbe-mediated redox transformations regulate arsenic mobility in paddy soil. However, the community dynamics of the related genes, which might be affected by soil ameliorants, have not been systematically investigated during a wet-dry cycle. This study incubated arsenic-contaminated paddy soil amended with organic matter (OM), gypsum, or hematite in microcosms under alternate watering conditions. Added gypsum and hematite reduced arsenic mobility in the soil by 8-60% during the wet and dry periods. However, added OM increased arsenic mobility by 70-130% during the first 4 weeks (not the last 4 weeks) of submergence and the dry period. The results of quantitative real-time polymerase chain reaction (qPCR) depended heavily on the primers used, so the contribution of relevant genes to arsenic transformation cannot be compared using only the gene abundance assessed by qPCR. However, correlation analyses showed that the abundance and community members of the arrA gene, which mediates dissimilatory As(V) reduction [i.e., As(V) respiration], were related to soil arsenic concentrations. This was not the case for the arsC gene, which mediates cytoplasmic As(V) reduction, or the aioA gene, which mediates As(III) oxidation. These suggest that the dissimilatory pathway was mainly responsible for arsenic reduction and release in the soil studied.

Abundance and diversity of microbial arsenic biotransformation genes in the sludge of full-scale anaerobic digesters from a municipal wastewater treatment plant

Arsenic (As) is a potential contaminant in sewage sludge that may affect waste treatment and limit the use of these waste materials as soil amendments. Anaerobic digestion (AD) is an important and effective process for the treatment of sewage sludge and the chemical speciation of As is particularly important in sludge AD. However, the biotransformation genes of As in sludge during AD has not been fully explored. In this study, the influent and effluent sludge of anaerobic digester in a wastewater treatment plant (WWTP) was collected to investigate the species transformations of As, the abundance and diversity of As biotransformation genes was explored by real-time PCR (qPCR) and metagenomic sequencing, separately. The results showed that arsenite [As(III)] and arsenate [As(V)] were predominant in the influent sludge, whereas the relative abundance of monomethylarsenic acid (MMA) increased by 25.7% after digestion. As biotransformation genes were highly abundant, and the As(III) S-adenosylmethionine methyltransferase (arsM) gene was the predominant which significantly increased after AD by qPCR analysis. Metagenomic analysis indicated that the diversity of the arsM-like sequences also increased significantly after AD. Most of the arsM-like sequences in all the influent and effluent sludge samples were related to Bacteroidetes and Alphaproteobacteria. Furthermore, co-occurrence network analysis indicated a strong correlation between the microbial communities and As. This study provides a direct and reliable reference on As biotransformation genes and microbial community in the AD of sludge.

Dissolved organic matter differentially influences arsenic methylation and volatilization in paddy soils

The effect of dissolved organic matter (DOM), derived from composted pig manure or rice straw, on arsenic methylation and subsequent biovolatilization in paddy soils was investigated. Arsine production following pig manure DOM application was 2.7- and 9.6-fold higher than that of soils treated with rice straw DOM and the control, respectively. Trimethylarsine was the dominant arsine at 54 %, followed by dimethylarsine at 22 %, arsine at 21 %, and monomethylarsine at 3 %. The copy numbers of the total and As-methylating bacteria were significantly enhanced in paddy soils treated with DOM. Pig manure DOM altered soil bacterial profile by increasing the OTU number of As methylation-inducing bacteria, such as Proteobacteria, Bacteroidetes, Geobacter, Sphingomonas, Streptomyces, and Rhodopseudomonas, thereby promoting As volatilization and methylation in paddy soils. The higher relative content of alkyl-C, N-alkyl C, and carboxyl-C in pig manure DOM was responsible for the increase in total and arsM-carrying bacteria in paddy soils, leading to enhanced As methylation. These observations will promote a better understanding of the role of DOM in mediating As methylation and volatilization, along with how organic fertilization affects straighthead disorder of rice, a condition caused by methylated arsenic species.

Metagenomic insights into microbial arsenic metabolism in shallow groundwater of Datong basin, China

Elevated arsenic (As) in groundwater is an urgent environmental problem that has caused serious endemic diseases in Datong basin, China. The fate and toxicity of As are generally regulated by microbial As metabolic processes. However, little is known about the microbial community and As metabolism in Datong basin. Herein, the microbial community structure and As metabolism genes in four wells with different levels of As concentration in Shanyin county were investigated using metagenomics approach. The results showed that the presence of As influenced the microbial communities, and Rhodococcus genus was significantly enriched in elevated As wells. As resistance genes were dominant from low to high As containing wells, and As efflux genes such as arsB and acr3 were positively correlated with As concentrations, suggesting that microbes tend to pump As out of the cell as a strategy for As detoxification. Other environmental factors including oxidation-reduction potential (ORP), total organic carbon (TOC), sulfate, and temperature also played a role in shaping the microbial community structure and As metabolic processes.

Bacterial Communities and Functional Genes Stimulated During Anaerobic Arsenite Oxidation and Nitrate Reduction in a Paddy Soil

Microbial arsenite (As(III)) oxidation associated with nitrate (NO₃^-) reduction might be an important process in diminishing arsenic bioavailability and toxicity to rice when paddy soils are contaminated by arsenic. In a noncontaminated soil, however, the responses of bacterial communities and functional genes to As(III) under nitrate-reducing conditions are poorly understood. In this study, anaerobic paddy soil microcosms were established with As(III) and/or NO₃^- to investigate how the bacterial communities and their functional genes were stimulated during As(III) oxidation and nitrate reduction. Microbial oxidation of As(III) to As(V) was substantially accelerated by nitrate addition, while nitrate reduction was not affected by As(III) addition. Metagenomic analysis revealed that nitrate-reducing bacteria were principally affiliated with Pseudogulbenkiania, with narG, nirS, and norBC genes. Putative As(III)-oxidizing bacteria were dominated by an Azoarcus sp. with As(III) oxidase genes aioA and aioB detected in its draft genome, which also had complete sets of denitrification genes (mainly, napA, nirK, and nosZ). Quantitive PCR analysis confirmed that the abundance of Azoarcus spp., aioA, and nosZ genes was enhanced by As(III) addition. These findings suggest the importance of Azoarcus- and Pseudogulbenkiania-related spp., both of which showed various physio-ecological characteristics for arsenic and nitrogen biogeochemistry, in coupling As(III) oxidation and nitrate reduction in flooded paddy soil.

Metal(loid)s (As, Hg, Se, Pb and Cd) in paddy soil: Bioavailability and potential risk to human health

Rice is one of the principal staple foods, essential for safeguarding the global food and nutritional security, but due to different natural and anthropogenic sources, it also acts as one of the biggest reservoirs of potentially toxic metal(loids) like As, Hg, Se, Pb and Cd. This review summarizes mobilization, translocation and speciation mechanism of these metal(loids) in soil-plant continuum as well as available cost-effective remediation measures and future research needs to eliminate the long-term risk to human health. High concentrations of these elements not only cause toxicity problems in plants, but also in animals that consume them and gradual deposition of these elements leads to the risk of bioaccumulation. The extensive occurrence of contaminated rice grains globally poses substantial public health risk and merits immediate action. People living in hotspots of contamination are exposed to higher health risks, however, rice import/export among different countries make the problem of global concern. Accumulation of As, Hg, Se, Pb and Cd in rice grains can be reduced by reducing their bioavailability, and controlling their uptake by rice plants. The contaminated soils can be reclaimed by phytoremediation, bioremediation, chemical amendments and mechanical measures; however these methods are either too expensive and/or too slow. Integration of innovative agronomic practices like crop establishment methods and improved irrigation and nutrient management practices are important steps to help mitigate the accumulation in soil as well as plant parts. Adoption of transgenic techniques for development of rice cultivars with low accumulation in edible plant parts could be a realistic option that would permit rice cultivation in soils with high bioavailability of these metal(loid)s.

Biotransformation of adsorbed arsenic on iron minerals by coexisting arsenate-reducing and arsenite-oxidizing bacteria

Bacteria with arsenate-reducing (ars) and arsenite-oxidizing (aio) genes usually co-exist in aerobic environments, but their contrast impacts on arsenic (As) speciation and mobility remain unclear. To identify which kind of bacteria dominate As speciation under oxic conditions, we studied the biotransformation of adsorbed As on goethite in the co-existence of Pantoea sp. IMH with ars gene and Achromobacter sp. SY8 with aio gene. The incubation results show that SY8 dominated the dissolved As speciation as As(V), even though aio exhibited nearly 5 folds lower transcription levels than ars in IMH. Nevertheless, our XANES results suggest that SY8 showed a negligible effect on solid-bound As speciation whereas IMH reduced adsorbed As(V) to As(III). The change in As speciation on goethite surfaces led to a partial As structural change from bidentate corner-sharing to monodentate corner-sharing as evidenced by our EXFAS analysis. Our Mössbauer spectroscopic results suggest that the incubation with SY8 reduced the degree of crystallinity of goethite, and the reduced crystallinity can be partly compensated by IMH. The changes in As adsorption structure and in goethite crystallinity had a negligible effect on As release. The insights gained from this study improve our understanding of biotransformation of As in aerobic environment.

Characteristics of Bacterial Community and Function in Paddy Soil Profile around Antimony Mine and Its Response to Antimony and Arsenic Contamination

Research of bacterial communities and metabolism potential of paddy soils contaminated by antimony (Sb) and arsenic (As) are vital to acquire understanding for their bioremediation. Here, the relative abundance of Sb and As metabolism genes, the diversity and composition of the bacterial community, and the influences of geochemical properties and the bacterial community and metabolism potential have been researched by Tax4Fun2 prediction and high-throughput sequencing. LEfSe (linear discriminant analysis effect size) analysis shown different taxa were enriched in dissimilar soil layers. RDA (Redundancy analysis) and relative importance analysis indicated the main properties including total sulfur (TS), total organic carbon (TOC), pH, and the bioavailable fractions of Sb and As affects the bacterial community, which Sbrec, Astot, and Asrec had greater impact on the bacterial taxonomic community. For example, Asrec, Astot, and Sbrec had a positive correlation with Chloroflexi and Rokubacteria, but negatively correlated with Proteobacteria and Actinobacteria. Obtaining metabolic function genes by using the tax prediction method. RDA, relative importance analysis, and co-occurrence network analysis showed the geochemical properties and bacterial community affected Sb and As related bacterial functions. The partial least squares path model (PLS-PM) analysis indicated Sb and As contamination fractions had negative effects on ecological function, bacterial community structure had positive influences on ecological function, and the direct effects of geochemical properties on ecological function was greater than community structure. The direct impact of As contamination fractions on bacterial community structure was greater than Sb, while the direct impact of Sb contamination fractions on bacterial function was more remarkable than As. Obviously, this study provides a scientific basis for the potential of biochemical remediation of Sb and As contamination in paddy soils profile.

Impacts of Arsenic and Antimony Co-Contamination on Sedimentary Microbial Communities in Rivers with Different Pollution Gradients

Arsenic (As) and antimony (Sb) are both toxic metalloids that are of primary concern for human health. Mining activity has introduced elevated levels of arsenic and antimony into the rivers and has increased the risks of drinking water contamination in China. Due to their mobility, the majority of the metalloids originating from mining activities are deposited in the river sediments. Thus, depending on various geochemical conditions, sediment could either be a sink or source for As and Sb in the water column. Microbes are key mediators for biogeochemical transformation and can both mobilize or precipitate As and Sb. To further understand the microbial community responses to As and Sb contamination, sediment samples with different contamination levels were collected from three rivers. The result of the study suggested that the major portions of As and Sb were in strong association with the sediment matrix and considered nonbioavailable. These fractions, however, were also suggested to have profound influences on the microbial community composition. As and Sb contamination caused strong reductions in microbial diversity in the heavily contaminated river sediments. Microorganisms were more sensitive to As comparing to Sb, as revealed by the co-occurrence network and random forest predictions. Operational taxonomic units (OTUs) that were potentially involved in As and Sb metabolism, such as Anaerolinea, Sphingomonas, and Opitutus, were enriched in the heavily contaminated samples. In contrast, many keystone taxa, including members of the Hyphomicrobiaceae and Bradyrhizobiaceae families, were inhibited by metalloid contamination, which could further impair crucial environmental services provided by these members.

Distribution of arsenic and its biotransformation genes in sediments from the East China Sea

Microbial transformation of arsenic (As) plays a key role in As biogeochemical cycling and affects the mobility, bioavailability, and toxicity of As. This study aims to investigate the accumulation of As in marine sediments at different water depths in the East China Sea and reveal the abundance and diversity of the aioA, arrA, arsC, and arsM genes through quantitative real-time polymerase chain reaction (qPCR) and high-throughput sequencing. Results showed that the As content in sediments ranged from 5.53 mg kg^-1 to 17.70 mg kg^-1, which decreased with water depth. Abundant As biotransformation genes with low diversity were identified in these sediments, of which arsM and arrA were the most abundant. Significant positive correlation exists between the arsM and arrA gene abundance and between arsC and aioA, indicating the co-occurrence of the As biotransformation genes in microbes in marine sediments. Metagenomics analysis revealed that arsM gene was mainly distributed in Alphaproteobacteria, Solibacteres, Deltaproteobacteria, Clostridia, and Bacilli in these sediments. Among the sediment properties, total N, total S, C/N, and TOC were important factors that shaped the abundance profile of the genes involved in As transformation. This study provides a picture of As biotransformation genes in marine sediments from the East China Sea, which may affect As transformation and the ultimate fate of As in a marine environment.

Arsenic Response of Three Altiplanic Exiguobacterium Strains With Different Tolerance Levels Against the Metalloid Species: A Proteomics Study

Exiguobacterium is a polyextremophile bacterial genus with a physiology that allows it to develop in different adverse environments. The Salar de Huasco is one of these environments due to its altitude, atmospheric pressure, solar radiation, temperature variations, pH, salinity, and the presence of toxic compounds such as arsenic. However, the physiological and/or molecular mechanisms that enable them to prosper in these environments have not yet been described. Our research group has isolated several strains of Exiguobacterium genus from different sites of Salar de Huasco, which show different resistance levels to As(III) and As(V). In this work, we compare the protein expression patterns of the three strains in response to arsenic by a proteomic approach; strains were grown in absence of the metalloid and in presence of As(III) and As(V) sublethal concentrations and the protein separation was carried out in 2D electrophoresis gels (2D-GE). In total, 999 spots were detected, between 77 and 173 of which showed significant changes for As(III) among the three strains, and between 90 and 143 for As(V), respectively, compared to the corresponding control condition. Twenty-seven of those were identified by mass spectrometry (MS). Among these identified proteins, the ArsA [ATPase from the As(III) efflux pump] was found to be up-regulated in response to both arsenic conditions in the three strains, as well as the Co-enzyme A disulfide reductase (Cdr) in the two more resistant strains. Interestingly, in this genus the gene that codifies for Cdr is found within the genic context of the ars operon. We suggest that this protein could be restoring antioxidants molecules, necessary for the As(V) reduction. Additionally, among the proteins that change their expression against As, we found several with functions relevant to stress response, e.g., Hpf, LuxS, GLpX, GlnE, and Fur. This study allowed us to shed light into the physiology necessary for these bacteria to be able to tolerate the toxicity and stress generated by the presence of arsenic in their niche.

Capability for arsenic mobilization in groundwater is distributed across broad phylogenetic lineages

Despite the importance of microbial activity in mobilizing arsenic in groundwater aquifers, the phylogenetic distribution of contributing microbial metabolisms is understudied. Groundwater samples from Ohio aquifers were analyzed using metagenomic sequencing to identify functional potential that could drive arsenic cycling, and revealed mechanisms for direct (i.e., Ars system) and indirect (i.e., iron reduction) arsenic mobilization in all samples, despite differing geochemical conditions. Analyses of 194 metagenome-assembled genomes (MAGs) revealed widespread functionality related to arsenic mobilization throughout the bacterial tree of life. While arsB and arsC genes (components of an arsenic resistance system) were found in diverse lineages with no apparent phylogenetic bias, putative aioA genes (aerobic arsenite oxidase) were predominantly identified in Methylocystaceae MAGs. Both previously described and undescribed respiratory arsenate reduction potential via arrA was detected in Betaproteobacteria, Deltaproteobacteria, and Nitrospirae MAGs, whereas sulfate reduction potential was primarily limited to members of the Deltaproteobacteria and Nitrospirae. Lastly, iron reduction potential was detected in the Ignavibacteria, Deltaproteobacteria, and Nitrospirae. These results expand the phylogenetic distribution of taxa that may play roles in arsenic mobilization in subsurface systems. Specifically, the Nitrospirae are a much more functionally diverse group than previously assumed and may play key biogeochemical roles in arsenic-contaminated ecosystems.

Vegetation type impacts microbial interaction with antimony contaminants in a mining-contaminated soil environment

Antimony (Sb) contamination is a growing environmental concern due to the increasing use of this metalloid in mining and industrial activities. The remediation of Sb-contaminated soil is a lengthy and costly process. Phytoremediation has been suggested as a cost-effective method for the long-term management of Sb-contaminated sites. Various plant types have been found to thrive in contaminated sites and have the potential to remediate Sb contamination; however, their impacts on Sb speciation and the indigenous microbial community remain unclear. In the current study, soils from three types of vegetation environment (i.e., grass, forest, and agricultural) were collected from two Sb mining areas in Guizhou, China. Comparisons of geochemical and microbiological properties among the three vegetation types revealed that vegetation was a major driver of soil biogeochemical characteristics. Contaminant fractions (i.e., extractable fractions of Sb and As) had a greater influence on microbial communities in grass and forest soil, whereas pH had a greater impact in agricultural soil. This difference may indicate distinct microbe-environment interactions in agricultural soil affected by anthropogenic activity. The dominant taxa, including Flavobacterium, Geobacter, Janthinobacterium, Clostridium, and Mycobacterium responded positively to various contaminant fractions, indicating that the community had adapted to the chronically contaminated environment. However, the regulation of these dominant genera by geochemical properties appears to be taxon-specific. Our results demonstrate that vegetation type has a substantial impact on Sb and As biogeochemical cycles, and should be considered in future remediation efforts.

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.

Effects of Arsenic on Gut Microbiota and Its Biotransformation Genes in Earthworm Metaphire sieboldi

Arsenic biotransformation mediated by gut microbiota can affect arsenic bioavailability and microbial community. Arsenic species, arsenic biotransformation genes (ABGs), and the composition of gut microbial community were characterized after the earthworm Metaphire sieboldi was cultured in soils spiked with different arsenic concentrations. Arsenite (As(III)) was the major component in the earthworm gut, whereas arsenate (As(V)) was predominant in the soil. A total of 16 ABGs were quantified by high-throughput quantitative polymerase chain reaction (HT-qPCR). Genes involved in arsenic redox and efflux were predominant in all samples, and the abundance of ABGs involved in arsenic methylation and demethylation in the gut was very low. These results reveal that the earthworm gut can be a reservoir of microbes with the capability of reducing As(V) and extruding As(III) but with little methylation of arsenic. Moreover, gut microbial communities were dominated by Actinobacteria, Firmicutes, and Proteobacteria at the phylum level and were considerably different from those in the surrounding soil. Our work demonstrates that exposure to As(V) disturbs the gut microbiota of earthworms and provides some insights into arsenic biotransformation in the earthworm gut.

Inhibition of Microbial Methylation via arsM in the Rhizosphere: Arsenic Speciation in the Soil to Plant Continuum

The interplay between rice roots and manuring with respect to arsenic speciation, subsequent assimilation into roots, and translocation to shoots in paddy soil was investigated, alongside bacterial diversity characterization. Planting increased soil Eh and decreased soil solution arsenic species: inorganic arsenic, monomethylarsonic acid, trimethylarsenic oxide, and dimethylarsinic acid. Presence of plant roots increased the copy number of Clostridium and Tumebacillus 16S rRNA as well as Streptomyces arsenic methylating gene ( arsM), but decreased Acidobacteria_GP1 16S rRNA and Rhodopseudomonas. palustris BisB5 arsM. Sum of arsenic species decreased under root influence due to the interplay of inorganic arsenic mobilization in bulk soil under anaerobic and immobilization under oxygenated rhizospheric conditions. Manuring increased all soil solution arsenic species (>90%), shoot total arsenic (60%), copy number of Geobacter 16S rRNA, and R. palustris TIE-1 arsM, indicative of a shift towards microbes with iron reduction and oxidation as well as arsenic methylation capabilities.

Biological As(III) oxidation in biofilters by using native groundwater microorganisms

Arsenic (As) contamination in drinking water represents a worldwide threat to human health. During last decades, the exploitation of microbial As-transformations has been proposed for bioremediation applications. Among biological methods for As-contaminated water treatment, microbial As(III)-oxidation is one of the most promising approaches since it can be coupled to commonly used adsorption removal technologies, without requiring the addition of chemicals and producing toxic by-products. Despite the As(III) oxidation capability has been described in several bacterial pure or enrichment cultures, very little is known about the real potentialities of this process when mixed microbial communities, naturally occurring in As contaminated waters, are used. This study highlighted the contribution of native groundwater bacteria to As(III)-oxidation in biofilters, under conditions suitable for a household-scale treatment system. This work elucidated the influence of a variety of experimental conditions (i.e., various filling materials, flow rates, As(III) inflow concentration, As(III):As(V) ratio, filter volumes) on the microbially-mediated As(III)-oxidation process in terms of oxidation efficiency and rate. The highest oxidation efficiencies (up to 90% in 3 h) were found on coarse sand biofilters treating total initial As concentration of 100 μg L^-1. The detailed microbial characterization of the As(III) oxidizing biofilms revealed the occurrence of several OTUs affiliated with families known to oxidize As(III) (e.g., Burkholderiaceae, Comamonadaceae, Rhodobacteraceae, Xanthomonadaceae). Furthermore, As-related functional genes increased in biofilter systems in line with the observed oxidative performances.

Arsenic contamination influences microbial community structure and putative arsenic metabolism gene abundance in iron plaque on paddy rice root

Iron (Fe) plaque on rice roots contains a unique microbiota that connects the root and rhizosphere environments. However, the factors controlling the microbial community structure and function in Fe plaque are unknown. We performed Illumina sequencing of 16S rRNA gene amplicons and of total community DNA to compare the microbial community structure and metabolic potential of Fe plaques derived from arsenic (As)- and non-contaminated sites. Geobacter and Hydrogenophaga were identified as the genera that differed significantly in abundance between As-contaminated and control samples (P < 0.05). Significant differences were found between contaminated and control samples in the relative abundances of predicted As functional genes of the microbial community in Fe plaque, in which the relative abundances of the arsC (encoding As(V) reductase) and arsB genes (encoding As(III) efflux membrane protein) in Fe plaque from contaminated sites (YH and TP samples) were significantly higher than those from the control samples (P < 0.05). In addition, the As concentration in Fe plaque contributed significantly to the relative abundance of genes related to As metabolism and correlated most strongly with the abundance of arrB genes (encoding respiratory arsenate reductase, FeS subunit). These results suggest that As contamination influences the community structure and metabolic potential of Fe plaque-associated microorganisms and may help in understanding the environmental behavior of As at the interface of Fe plaque.

AsChip: A High-Throughput qPCR Chip for Comprehensive Profiling of Genes Linked to Microbial Cycling of Arsenic

Arsenic (As) is a ubiquitous toxic element adversely affecting human health. Microbe-mediated cycling of As is largely mediated by detoxification and energy metabolism in microorganisms. We here report the development of a novel high-throughput qPCR (HT-qPCR) chip (AsChip) for comprehensive profiling of genes involved in microbial As cycling (here collectively termed "As genes"). AsChip contained 81 primer sets targeting 19 As genes and the 16S rRNA gene as a reference gene. Gene amplicon sequencing showed high identity (>96%) of newly designed primers corresponding to their targets. AsChip displayed high sensitivity (plasmid template serial dilution test; r = -0.99), with more than 96% of all PCR assays yielding true positive signals. R² coefficients for standard curves and PCR amplification efficiencies averaged 0.98 and 0.99, respectively. A high correlation between C_T values obtained by AsChip and conventional qPCR was obtained ( r = 0.962, P < 0.001). Finally, we successfully applied AsChip on soil samples from a chromium-copper-arsenic-contaminated field site and identified diverse As genes with total abundance average of 0.4 As gene copies per 16S rRNA. Our results indicate that AsChip constitutes a robust tool for comprehensive quantitative profiling of As genes in environmental samples.

Impacts of nonpoint source pollutants on microbial community in rain gardens

Low-impact development (LID) techniques are being applied to reduce non-point source (NPS) pollution which are generated from various land uses. Cost-effective LID design requires consideration of influent runoff properties as well as physical and ecological pollutant-removing mechanisms. However, current LID technology design has failed to reflect the different properties of influent water from various land uses, and the biological design factors in LID facilities causing low efficiency and difficulties in maintenance. This study was conducted to identify biological design factors by analyzing the impact of the pollutants included in influent runoff and physical environment on microbial growth in rain garden facilities applied to different land uses. The results showed that the non-point source pollutant loadings were about 1.5-3 times higher in the runoff from parking lots, which are frequently visited by automobiles than in roof runoff. Type of soil, chemical species, and chemical composition were assessed as internal environmental factors having significant impact on the phylum and the count of microorganisms in the facilities. The growth of Cyanobacteria, Streptophyta, Chlorophyta, Bacillariophyta, and Xanthophyceae was good when there was appropriate water content in the soil, light, and sandy soil. Based on these results, the future design of rain garden facilities should be performed by considering a microorganism appropriate to the properties of the influent pollutants, determining appropriate water content, nutrient content and soil type, and choosing plants that contribute to microbial growth.

Metal(loid)-resistant bacteria reduce wheat Cd and As uptake in metal(loid)-contaminated soil

This study characterized the effect of the metal(loid)-resistant bacteria Ralstonia eutropha Q2-8 and Exiguobacterium aurantiacum Q3-11 on Cd and As accumulation in wheat grown in Cd- and As-polluted soils (1 mg kg^-1 of Cd + 40 mg kg^-1 of As and 2 mg kg^-1 of Cd + 60 mg kg^-1 of As). The influence of strains Q2-8 and Q3-11 on water-soluble Cd and As and NH₄⁺concentration and pH in the soil filtrate were also analyzed. Inoculation with these strains significantly reduced wheat plant Cd (12-32%) and As (9-29%) uptake and available Cd (15-28%) and As (22-38%) contents in rhizosphere soils compared to the controls. Furthermore, these strains significantly increased the relative abundances of the arsM bacterial As metabolism gene and of Fe- and Mn-oxidizing Leptothrix species in rhizosphere soils. Notably, these strains significantly reduced water-soluble Cd and As concentrations and increased pH and NH₄⁺ concentration in the soil filtrate. These results suggest that these strains increased soil pH and the abundance of genes possibly involved in metal(loid) unavailability, resulting in reduced wheat Cd and As accumulation and highlight the possibility of using bacteria for in situ remediation and safe production of wheat or other food crops in metal(loid)-polluted soils.

Comparative mangrove metagenome reveals global prevalence of heavy metals and antibiotic resistome across different ecosystems

The mangrove ecosystem harbors a complex microbial community that plays crucial role in biogeochemical cycles. In this study, we analyzed mangrove sediments from India using de novo whole metagenome next generation sequencing (NGS) and compared their taxonomic and functional community structures to mangrove metagenomics samples from Brazil and Saudi Arabia. The most abundant phyla in the mangroves of all three countries was Proteobacteria, followed by Firmicutes and Bacteroidetes. A total of 1,942 genes were found to be common across all the mangrove sediments from each of the three countries. The mangrove resistome consistently showed high resistance to fluoroquinolone and acriflavine. A comparative study of the mangrove resistome with other ecosystems shows a higher frequency of heavy metal resistance in mangrove and terrestrial samples. Ocean samples had a higher abundance of drug resistance genes with fluoroquinolone and methicillin resistance genes being as high as 28.178% ± 3.619 and 10.776% ± 1.823. Genes involved in cobalt-zinc-cadmium resistance were higher in the mangrove (23.495% ± 4.701) and terrestrial (27.479% ± 4.605) ecosystems. Our comparative analysis of samples collected from a variety of habitats shows that genes involved in resistance to both heavy metals and antibiotics are ubiquitous, irrespective of the ecosystem examined.

Influence of environmental changes on the biogeochemistry of arsenic in a soil polluted by the destruction of chemical weapons: A mesocosm study

Thermal destruction of chemical munitions from World War I led to the formation of a heavily contaminated residue that contains an unexpected mineral association in which a microbial As transformation has been observed. A mesocosm study was conducted to assess the impact of water saturation episodes and input of bioavailable organic matter (OM) on pollutant behavior in relation to biogeochemical parameters. Over a period of about eight (8) months, the contaminated soil was subjected to cycles of dry and wet periods corresponding to water table level variations. After the first four (4) months, fragmented litter from the nearby forest was placed on top of the soil. The mesocosm solid phase was sampled by three rounds of coring: at the beginning of the experiment, after four (4) months (before the addition of OM), and at the end of the experiment. Scanning electron microscopy coupled to energy dispersive X-ray spectroscopy observations showed that an amorphous phase, which was the primary carrier of As, Zn, and Cu, was unstable under water-saturated conditions and released a portion of the contaminants in solution. Precipitation of a lead arsenate chloride mineral, mimetite, in soils within the water saturated level caused the immobilization of As and Pb. Mimetite is a durable trap because of its large stability domain; however, this precipitation was limited by a low Pb concentration inducing that high amounts of As remained in solution. The addition of forest litter modified the quantities and qualities of soil OM. Microbial As transformation was affected by the addition of OM, which increased the concentration of both As(III)-oxidizing and As(V)-reducing microorganisms. The addition of OM negatively impacted the As(III) oxidizing rate, however As(III) oxidation was still the dominant reaction in accordance with the formation of arsenate-bearing minerals.

Rapid evaluation of arsenic contamination in paddy soils using field portable X-ray fluorescence spectrometry

Arsenic (As) in paddy fields is deteriorating food security and human health through rice ingestion. Rice is the dominant food source of arsenic exposure to half of the world's population. Therefore, an in situ effective method for As risk evaluation in paddy soil is strongly needed to avoid As exposure through rice ingestion. Herein, we developed a rapid analytical methodology for determination of As in plant tissues using field portable X-ray fluorescence spectrometry (FP-XRF). This method was applied to rice roots in order to evaluate the As contamination in paddy soils. The results showed that rice roots with iron plaques were superior to rhizosphere soils for generating FP-XRF signals, especially for field sites with As concentrations lower than the soil detection limit of FP-XRF (30.0mg/kg). Moreover, the strong linear relationships of As concentrations between the rice roots and corresponding leaves and grains proved that the rice root, rather than the soil, is a better predictor of As concentrations in rice grains. The research provides an efficient As monitoring method for As contaminated paddy fields by using wetland plant roots with iron plaques and XRF-based analytical techniques.

Arsenic Methylation Dynamics in a Rice Paddy Soil Anaerobic Enrichment Culture

Methylated arsenic (As) species represent a significant fraction of the As accumulating in rice grains, and there are geographic patterns in the abundance of methylated arsenic in rice that are not understood. The microorganisms driving As biomethylation in paddy environments, and thus the soil conditions conducive to the accumulation of methylated arsenic, are unknown. We tested the hypothesis that sulfate-reducing bacteria (SRB) are key drivers of arsenic methylation in metabolically versatile mixed anaerobic enrichments from a Mekong Delta paddy soil. We used molybdate and monofluorophosphate as inhibitors of sulfate reduction to evaluate the contribution of SRB to arsenic biomethylation, and developed degenerate primers for the amplification of arsM genes to identify methylating organisms. Enrichment cultures converted 63% of arsenite into methylated products, with dimethylarsinic acid as the major product. While molybdate inhibited As biomethylation, this effect was unrelated to its inhibition of sulfate reduction and instead inhibited the methylation pathway. Based on arsM sequences and the physiological response of cultures to media conditions, we propose that amino acid fermenting organisms are potential drivers of As methylation in the enrichments. The lack of a demethylating capacity may have contributed to the robust methylation efficiencies in this mixed culture.

Identification of Arsenic Resistance Genes from Marine Sediment Metagenome

A metagenomic library of sea sediment metagenome containing 245,000 recombinant clones representing ~ 2.45 Gb of sea sediment microbial DNA was constructed. Two unique arsenic resistance clones, A7 and A12, were identified by selection on sodium arsenite containing medium. Clone A7 showed a six-fold higher resistance to arsenate [As(V)], a three-fold higher resistance to arsenite [As(III)] and significantly increased resistance to antimony [Sb(III)], while clone A12 showed increased resistance only to sodium arsenite and not to the other two metalloids. The clones harbored inserts of 8.848 Kb and 6.771 Kb, respectively. Both the clones possess A + T rich nucleotide sequence with similarity to sequences from marine psychrophilic bacteria. Sequence and transposon-mutagenesis based analysis revealed the presence of a putative arsenate reductase (ArsC), a putative arsenite efflux pump (ArsB/ACR) and a putative NADPH-dependent FMN reductase (ArsH) in both the clones and also a putative transcriptional regulatory protein (ArsR) in pA7. The increased resistance of clone A7 to As(V), As(III) and Sb(III) indicates functional expression of ArsC and ArsB proteins from pA7. The absence of increased As(V) resistance in clone A12 may be due to the expression of a possible inactive ArsC, as conserved Arg60 residue in this protein was replaced by Glu60, while the absence of Sb(III) resistance may be due to the presence of an ACR3p-type arsenite pump, which is known to lack antimony transport ability.

Linking Genes to Microbial Biogeochemical Cycling: Lessons from Arsenic

The biotransformation of arsenic is highly relevant to the arsenic biogeochemical cycle. Identification of the molecular details of microbial pathways of arsenic biotransformation coupled with analyses of microbial communities by meta-omics can provide insights into detailed aspects of the complexities of this biocycle. Arsenic transformations couple to other biogeochemical cycles, and to the fate of both nutrients and other toxic environmental contaminants. Microbial redox metabolism of iron, carbon, sulfur, and nitrogen affects the redox and bioavailability of arsenic species. In this critical review we illustrate the biogeochemical processes and genes involved in arsenic biotransformations. We discuss how current and future metagenomic-, metatranscriptomic-, metaproteomic-, and metabolomic-based methods will help to decipher individual microbial arsenic transformation processes, and their connections to other biogeochemical cycle. These insights will allow future use of microbial metabolic capabilities for new biotechnological solutions to environmental problems. To understand the complex nature of inorganic and organic arsenic species and the fate of environmental arsenic will require integrating systematic approaches with biogeochemical modeling. Finally, from the lessons learned from these studies of arsenic biogeochemistry, we will be able to predict how the environment changes arsenic, and, in response, how arsenic biotransformations change the environment.

Assessment of Cr, Ni and Pb Pollution in Rural Agricultural Soils of Tonalite-Trondjhemite Series in Central India

Chromium (Cr), nickel (Ni) and lead (Pb) contamination was investigated in wheat cultivated rain-fed and irrigated rural agricultural soils (n = 31) of Tonalite-Trondjhemite Series in Central India. The soil sampling was carried out by using stratified random sampling method. The mean concentrations of Cr, Ni and Pb were 54.8, 38.1 and 68.9 mg/kg, respectively. The average values of enrichment factor (EF), geoaccumulation index (I _geo ) and contamination factor (CF) followed the order as: Pb > Ni > Cr. Distribution patterns of soil parent material and weathering processes govern mineral enrichments, irrespective of rainfed or irrigated agricultural practices. Principal component analysis (PCA) showed strong loading of Cr and Ni (PC1) and Pb and clay (PC3). The strong loading on Cr and Ni indicates soils are originating from basic and volcanic rocks in the study area. The strong loading of Pb and clay indicates Pb is strongly adsorbed on clay minerals and Fe-oxides. The cancer risk (CR) index showed negligible carcinogenic risk to the residing population. However, hazard index (HI) values for children exceed the safe limit (HI > 1) for Cr and Pb. Spatial distribution of pollution load index suggest highest pollution in the northeastern part of the district. The study revealed that geogenically enriched soils of the area are suitable for agricultural activities under present conditions.

Land scale biogeography of arsenic biotransformation genes in estuarine wetland

As an analogue of phosphorus, arsenic (As) has a biogeochemical cycle coupled closely with other key elements on the Earth, such as iron, sulfate and phosphate. It has been documented that microbial genes associated with As biotransformation are widely present in As-rich environments. Nonetheless, their presence in natural environment with low As levels remains unclear. To address this issue, we investigated the abundance levels and diversities of aioA, arrA, arsC and arsM genes in estuarine sediments at low As levels across Southeastern China to uncover biogeographic patterns at a large spatial scale. Unexpectedly, genes involved in As biotransformation were characterized by high abundance and diversity. The functional microbial communities showed a significant decrease in similarity along the geographic distance, with higher turnover rates than taxonomic microbial communities based on the similarities of 16S rRNA genes. Further investigation with niche-based models showed that deterministic processes played primary roles in shaping both functional and taxonomic microbial communities. Temperature, pH, total nitrogen concentration, carbon/nitrogen ratio and ferric iron concentration rather than As content in these sediments were significantly linked to functional microbial communities, while sediment temperature and pH were linked to taxonomic microbial communities. We proposed several possible mechanisms to explain these results.

Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations

To understand how soil microbial communities and arsenic (As) functional genes respond to soil arsenic (As) contamination, five soils contaminated with As at different levels were collected from diverse geographic locations, incubated for 54 days under flooded conditions, and examined by both MiSeq sequencing of 16S rRNA gene amplicons and functional gene microarray (GeoChip 4.0). The results showed that both bacterial community structure and As functional gene structure differed among geographical locations. The diversity of As functional genes correlated positively with the diversity of 16S rRNA genes (P< 0.05). Higher diversities of As functional genes and 16S rRNA genes were observed in the soils with higher available As. Soil pH, phosphate-extractable As, and amorphous Fe content were the most important factors in shaping the bacterial community structure and As transformation functional genes. Geographic location was also important in controlling both the bacterial community and As transformation functional potential. These findings provide insights into the variation of As transformation functional genes in soils contaminated with different levels of As at different geographic locations, and the impact of environmental As contamination on the soil bacterial community.

Nitrate Stimulates Anaerobic Microbial Arsenite Oxidation in Paddy Soils

Arsenic (As) bioavailability to rice plants is elevated in flooded paddy soils due to reductive mobilization of arsenite [As(III)]. However, some microorganisms are able to mediate anaerobic As(III) oxidation by coupling to nitrate reduction, thus attenuating As mobility. In this study, we investigated the impact of nitrate additions on As species dynamics in the porewater of four As-contaminated paddy soils. The effects of nitrate on microbial community structure and the abundance and diversity of the As(III) oxidase (aioA) genes were quantified using 16S rRNA sequencing, quantitative PCR, and aioA gene clone libraries. Nitrate additions greatly stimulated anaerobic oxidation of As(III) to As(V) and decreased total soluble As in the porewater in flooded paddy soils. Nitrate additions significantly enhanced the abundance of aioA genes and changed the microbial community structure by increasing the relative abundance of the operational taxonomic units (OTUs) from the genera Acidovorax and Azoarcus. The aioA gene sequences from the Acidovorax related OTU were also stimulated by nitrate. A bacterial strain (ST3) belonging to Acidovorax was isolated from nitrate-amended paddy soil. The strain was able to oxidize As(III) and Fe(II) under anoxic conditions using nitrate as the electron acceptor. Abiotic experiments showed that Fe(II), but not As(III), could be oxidized by nitrite. These results show that nitrate additions can stimulate As(III) oxidation in flooded paddy soils by enhancing the population of anaerobic As(III) oxidizers, offering a potential strategy to decrease As mobility in As-contaminated paddy soils.

Understanding arsenic dynamics in agronomic systems to predict and prevent uptake by crop plants

This review is on arsenic in agronomic systems, and covers processes that influence the entry of arsenic into the human food supply. The scope is from sources of arsenic (natural and anthropogenic) in soils, biogeochemical and rhizosphere processes that control arsenic speciation and availability, through to mechanisms of uptake by crop plants and potential mitigation strategies. This review makes a case for taking steps to prevent or limit crop uptake of arsenic, wherever possible, and to work toward a long-term solution to the presence of arsenic in agronomic systems. The past two decades have seen important advances in our understanding of how biogeochemical and physiological processes influence human exposure to soil arsenic, and this must now prompt an informed reconsideration and unification of regulations to protect the quality of agricultural and residential soils.

Arsenic Detoxification by Geobacter Species

Insight into the mechanisms for arsenic detoxification by Geobacter species is expected to improve the understanding of global cycling of arsenic in iron-rich subsurface sedimentary environments. Analysis of 14 different Geobacter genomes showed that all of these species have genes coding for an arsenic detoxification system (ars operon), and several have genes required for arsenic respiration (arr operon) and methylation (arsM). Genes encoding four arsenic repressor-like proteins were detected in the genome of G. sulfurreducens; however, only one (ArsR1) regulated transcription of the ars operon. Elimination of arsR1 from the G. sulfurreducens chromosome resulted in enhanced transcription of genes coding for the arsenic efflux pump (Acr3) and arsenate reductase (ArsC). When the gene coding for Acr3 was deleted, cells were not able to grow in the presence of either the oxidized or reduced form of arsenic, while arsC deletion mutants could grow in the presence of arsenite but not arsenate. These studies shed light on how Geobacter influences arsenic mobility in anoxic sediments and may help us develop methods to remediate arsenic contamination in the subsurface.

IMPORTANCE

This study examines arsenic transformation mechanisms utilized by Geobacter, a genus of iron-reducing bacteria that are predominant in many anoxic iron-rich subsurface environments. Geobacter species play a major role in microbially mediated arsenic release from metal hydroxides in the subsurface. This release raises arsenic concentrations in drinking water to levels that are high enough to cause major health problems. Therefore, information obtained from studies of Geobacter should shed light on arsenic cycling in iron-rich subsurface sedimentary environments, which may help reduce arsenic-associated illnesses. These studies should also help in the development of biosensors that can be used to detect arsenic contaminants in anoxic subsurface environments. We examined 14 different Geobacter genomes and found that all of these species possess genes coding for an arsenic detoxification system (ars operon), and some also have genes required for arsenic respiration (arr operon) and arsenic methylation (arsM).

Arsenic and phosphate rock impacted the abundance and diversity of bacterial arsenic oxidase and reductase genes in rhizosphere of As-hyperaccumulator Pteris vittata

Microbially-mediated arsenic (As) transformation in soils affects As speciation and plant uptake. However, little is known about the impacts of As on bacterial communities and their functional genes in the rhizosphere of As-hyperaccumulator Pteris vittata. In this study, arsenite (AsIII) oxidase genes (aroA-like) and arsenate (AsV) reductase genes (arsC) were amplified from three soils, which were amended with 50mgkg^-1 As and/or 1.5% phosphate rock (PR) and grew P. vittata for 90 d. The aroA-like genes in the rhizosphere were 50 times more abundant than arsC genes, consistent with the dominance of AsV in soils. According to functional gene alignment, most bacteria belonged to α-, β- and γ-Proteobacteria. Moreover, aroA-like genes showed a higher biodiversity than arsC genes based on clone library analysis and could be grouped into nine clusters based on terminal restriction fragment length polymorphism (T-RFLP) analysis. Besides, AsV amendment elevated aroA-like gene diversity, but decreased arsC gene diversity. Redundancy analysis indicated that soil pH, available Ca and P, and AsV concentration were key factors driving diverse compositions in aroA-like gene community. This work identified new opportunities to screen for As-oxidizing and/or -reducing bacteria to aid phytoremediation of As-contaminated soils.