Dissimilatory arsenate reduction with sulfide as electron donor: experiments with mono lake water and Isolation of strain MLMS-1, a chemoautotrophic arsenate respirer

Biological roles of soil microbial consortium on promoting safe crop production in heavy metal(loid) contaminated soil: A systematic review

Heavy metal(loid) (HM) pollution of agricultural soils is a growing global environmental concern that affects planetary health. Numerous studies have shown that soil microbial consortia can inhibit the accumulation of HMs in crops. However, our current understanding of the effects and mechanisms of inhibition is fragmented. In this review, we summarise extant studies and knowledge to provide a comprehensive view of HM toxicity on crop growth and development at the biological, cellular and the molecular levels. In a meta-analysis, we find that microbial consortia can improve crop resistance and reduce HM uptake, which in turn promotes healthy crop growth, demonstrating that microbial consortia are more effective than single microorganisms. We then review three main mechanisms by which microbial consortia reduce the toxicity of HMs to crops and inhibit HMs accumulation in crops: 1) reducing the bioavailability of HMs in soil (e.g. biosorption, bioaccumulation and biotransformation); 2) improving crop resistance to HMs (e.g. facilitating the absorption of nutrients); and 3) synergistic effects between microorganisms. Finally, we discuss the prospects of microbial consortium applications in simultaneous crop safety production and soil remediation, indicating that they play a key role in sustainable agricultural development, and conclude by identifying research challenges and future directions for the microbial consortium to promote safe crop production.

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.

Different sulfide to arsenic ratios driving arsenic speciation and microbial community interactions in two alkaline hot springs

Arsenic (As) is ubiquitous in geothermal fluids, which threatens both water supply safety and local ecology. The co-occurrence of sulfur (S) and As increases the complexity of As migration and transformation in hot springs. Microorganisms play important roles in As-S transformation processes. In the present study, two Tibetan alkaline hot springs (designated Gulu [GL] and Daba [DB]) with different total As concentrations (0.88 mg/L and 12.42 mg/L, respectively) and different sulfide/As ratios (3.97 and 0.008, respectively) were selected for investigating interactions between As-S geochemistry and microbial communities along the outflow channels. The results showed that As-S transformation processes were similar, although concentrations and percentages of As and S species differed between the two hot springs. Thioarsenates were detected at the vents of the hot springs (18% and 0.32%, respectively), and were desulfurized to arsenite along the drainage channel. Arsenite was finally oxidized to arsenate (532 μg/L and 12,700 μg/L, respectively). Monothioarsenate, total As, and sulfate were the key factors shaping the changes in microbial communities with geochemical gradients. The relative abundances of sulfur reduction genes (dsrAB) and arsenate reduction genes (arsC) were higher in upstream portions of GL explaining high thiolation. Arsenite oxidation genes (aoxAB) were relatively abundant in downstream parts of GL and at the vent of DB explaining low thiolation. Sulfur oxidation genes (soxABXYZ) were abundant in GL and DB. Putative sulfate-reducing bacteria (SRB), such as Desulfuromusa and Clostridium, might be involved in forming thioarsenates by producing reduced S for chemical reactions with arsenite. Sulfur-oxidizing bacteria (SOB), such as Elioraea, Pseudoxanthomonas and Pseudomonas, and arsenite-oxidizing bacteria (AsOB) such as Thermus, Sulfurihydrogenibium and Hydrogenophaga, may be responsible for the oxidation of As-bound S, thereby desulfurizing thioarsenates, forming arsenite and, by further abiotic or microbial oxidation, arsenate. This study improves our understanding of As and S biogeochemistry in hot springs.

Effects of Sulfide Input on Arsenate Bioreduction and Its Reduction Product Formation in Sulfidic Groundwater

Microbes have important impacts on the mobilization of arsenic in groundwater. To study the effects of sulfide on As(V) bioreduction in sulfidic groundwater, Citrobacter sp. JH012-1 isolated from sediments in the Jianghan Plain was used in a microcosm experiment. The results showed that sulfide significantly enhanced As(V) bioreduction as an additional electron donor. The reduction rates of As(V) were 21.8%, 34.5%, 73.6% and 85.9% under 0, 15, 75 and 150 µM sulfide inputting, respectively. The main products of As(V) bioreduction were thioarsenite and orpiment and the concentration of thioarsenite reached to 5.5 and 7.1 µM in the solution with the initial 75 and 150 µM sulfide, respectively. However, under 0 and 15 µM sulfide inputting, the dominant product was arsenite with no thioarsenite accumulation. The decrease in pH enhanced the bioreduction of As(V) and promoted the formation of thioarsenite and orpiment. In addition, the percentage of thioarsenite in total arsenic decreased with the decrease in the ratio of sulfur to arsenic, indicating that the formation of thioarsenite was limited by the concentration of initial sulfide. Therefore, the presence of sulfide had a significant effect on the transformation of arsenic in groundwater. This study provides new insights into the bioreduction of As(V) and the formation of thioarsenite in sulfidic groundwater.

Deciphering the community structure and the functional potential of a hypersaline marsh microbial mat community

Microbial mats are vertically stratified communities of microorganisms characterized by pronounced physiochemical gradients allowing for high species diversity and a wide range of metabolic capabilities. High Throughput Sequencing has the potential to reveal the biodiversity and function of such ecosystems in the cycling of elements. The present study combines 16S rRNA amplicon sequencing and shotgun metagenomics on a hypersaline marsh in Tristomo bay (Karpathos, Greece). Samples were collected in July 2018 and November 2019 from microbial mats, deeper sediment, aggregates observed in the water overlying the sediment, as well as sediment samples with no apparent layering. Metagenomic samples' coassembly and binning revealed 250 bacterial and 39 archaeal metagenome-assembled genomes, with completeness estimates higher than 70% and contamination less than 5%. All MAGs had KEGG Orthology terms related to osmoadaptation, with the 'salt in' strategy ones being prominent. Halobacteria and Bacteroidetes were the most abundant taxa in the mats. Photosynthesis was most likely performed by purple sulphur and nonsulphur bacteria. All samples had the capacity for sulphate reduction, dissimilatory arsenic reduction, and conversion of pyruvate to oxaloacetate. Overall, both sequencing methodologies resulted in similar taxonomic compositions and revealed that the formation of the microbial mat in this marsh exhibits seasonal variation.

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.

Desulfurivibrio spp. mediate sulfur-oxidation coupled to Sb(V) reduction, a novel biogeochemical process

Antimony (Sb) contamination released from mine tailings represents a global threat to natural ecosystems and human health. The geochemical conditions of Sb tailings, which are oligotrophic and replete in sulfur (S) and Sb, may promote the coupled metabolism of Sb and S. In this study, multiple lines of evidence indicate that a novel biogeochemical process, S oxidation coupled to Sb(V) reduction, is enzymatically mediated by Desulfurivibrio spp. The distribution of Desulfurivibrio covaried with S and Sb concentrations, showing a high relative abundance in Sb mine tailings but not in samples from surrounding sites (i.e., soils, paddies, and river sediments). Further, the metabolic potential to couple S oxidation to Sb(V) reduction, encoded by a non-canonical, oxidative sulfite reductase (dsr) and arsenate reductase (arrA) or antimonate reductase (anrA), respectively, was found to be common in Desulfurivibrio genomes retrieved from metal-contaminated sites in southern China. Elucidation of enzymatically-catalyzed S oxidation coupled to Sb(V) reduction expands the fundamental understanding of Sb biogeochemical cycling, which may be harnessed to improve remediation strategies for Sb mine tailings.

Arsenic biotransformation and mobilization: the role of bacterial strains and other environmental variables

Over several decades, arsenic (As) toxicity in the biosphere has affected different flora, fauna, and other environmental components. The majority of these problems are linked with As mobilization due to bacterial dissolution of As-bearing minerals and its transformation in other reservoirs such as soil, sediments, and ground water. Understanding the process, mechanism, and various bacterial species involved in these processes under the influence of some ecological variables greatly contributes to a better understanding of the fate and implications of As mobilization into the environments. This article summarizes the process, role, and various types of bacterial species involved in the transformation and mobilization of As. Furthermore, insight into how Fe(II) oxidation and resistance mechanisms such as methylation and detoxification against the toxic effect of As(III) was highlighted as a potential immobilization and remediation strategy in As-contaminated sites. Furthermore, the significance and comparative advantages of some useful analytical tools used in the evaluation, speciation, and analysis of As are discussed and how their in situ and ex situ applications support assessing As contamination in both laboratory and field settings. Nevertheless, additional research involving advanced molecular techniques is required to elaborate on the contribution of these bacterial consortia as a potential agronomic tool for reducing As availability, particularly in natural circumstances. Graphical abstract. Courtesy of conceptual model: Aminu Darma.

Niche Differentiation of Arsenic-Transforming Microbial Groups in the Rice Rhizosphere Compartments as Impacted by Water Management and Soil-Arsenic Concentrations

Arsenic (As) bioavailability in the rice rhizosphere is influenced by many microbial interactions, particularly by metal-transforming functional groups at the root-soil interface. This study was conducted to examine As-transforming microbes and As-speciation in the rice rhizosphere compartments, in response to two different water management practices (continuous and intermittently flooded), established on fields with high to low soil-As concentration. Microbial functional gene composition in the rhizosphere and root-plaque compartments were characterized using the GeoChip 4.0 microarray. Arsenic speciation and concentrations were analyzed in the rhizosphere soil, root-plaque, pore water, and grain samples. Results confirmed several As-biotransformation processes in the rice rhizosphere compartments, and distinct assemblage of As-reducing and methylating bacteria was observed between the root-plaque and rhizosphere. Results confirmed higher potential for microbial As-reduction and As-methylation in continuously flooded, long term As-contaminated fields, which accumulated highest concentrations of As^III and methyl-As concentrations in pore water and rice grains. Water management treatment significantly altered As-speciation in the rhizosphere, and intermittent flooding reduced methyl-As and As^III concentrations in the pore water, root-plaque and rice grain. Ordination and taxonomic analysis of detected gene-probes indicated that root-plaque and rhizosphere assembled significantly different microbial functional groups demonstrating niche separation. Taxonomic non-redundancy was evident, suggesting that As-reduction, -oxidation and -methylation processes were performed by different microbial functional groups. It was also evident that As transformation was coupled to different biogeochemical cycling processes (nutrient assimilation, carbon metabolism etc.) in the compartments and between treatments, revealing functional non-redundancy of rice-rhizosphere microbiome in response to local biogeochemical conditions and As contamination. This study provided novel insights on As-biotransformation processes and their implications on As-chemistry at the root-soil interface and their responses to water management, which could be applied for mitigating As-bioavailability and accumulation in rice grains.

Quantifying Microbially Mediated Kinetics of Ferrihydrite Transformation and Arsenic Reduction: Role of the Arsenate-Reducing Gene Expression Pattern

The behavior of arsenic (As) is usually coupled with iron (Fe) oxide transformation and mediated by both abiotic reactions and microbial processes in the environment. However, quantitative models for the coupled kinetic processes, which specifically consider the arsenate-reducing gene expression correspondent to different reaction conditions, are lacking. In this study, based on the pure cultured Shewanella putrefaciens incubation experiments, extended X-ray absorption fine structure spectroscopy, high resolution transmission electron microscopy, and a suite of microbial analyses, we developed a coupled kinetics model for microbially mediated As reduction and Fe oxide transformation and specifically quantified the As(V) reduction rate coefficients based on the expression patterns of arrA genes. The model reasonably described the temporal changes of As speciation and distribution. The microbial reduction rates of As(V) varied dramatically during the reactions, which were well represented by the varying transcript abundances of arrA genes at different As concentrations. The contributions of biotic and abiotic reactions to the overall reaction rates were assessed. The results improved our quantitative understanding on the key role of As(V)-reducing genes in regulating the speciation and distribution of As. The kinetic modeling approaches based on microbial gene expression patterns are promising for developing comprehensive biogeochemical models of As involving multiple coupled reactions.

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.

Realgar (As4S4) bioprecipitation in microcosm fed by a natural groundwater and organic matter

Sequestration of arsenic to biogenic sulfide minerals is known from As-contaminated anoxic environments. Despite numerous successful laboratory experiments, the process remains difficult to predict in moderate arsenic conditions. We performed microcosm experiments using naturally contaminated groundwater (containing ca. 6 mg/L As) and natural organic matter (NOM) particles both collected from wetland soil. Macroscopic realgar precipitates, occasionally accompanied by bonazziite, a FeS phase, elementary S, calcite, and whewellite, appeared after 4 to 18 months. Realgar only precipitated in microcosms moderately poisoned by azide or antibiotics and those in which oxidation of hydrogen sulfide to sulfur took place. The biomineralization process was not affected by the presence of additional carbon sources or the diversity, community structure, and functional composition of the microbial community. Hydrogen sulfide concentration was greater in the realgar-free microcosms, suggesting that arsenic thiolation prevented precipitation of realgar. We compared our data to available microbial community data from soils with different rates of realgar precipitation, and found that the communities from realgar-encrusted NOM particles usually showed limited sulfate reduction and the presence of fermentative metabolisms, whereas communities from realgar-free NOM particles were strongly dominated by sulfate reducers. We argue that the limited sulfate supply and intensive fermentation amplify reducing conditions, which make arsenic sulfide precipitation plausible in high-sulfate, low-arsenic groundwaters.

Water management impacts the soil microbial communities and total arsenic and methylated arsenicals in rice grains

The bioavailability of the metalloid arsenic (As) in paddy soil is controlled by microbial cycling of As and other elements such as iron (Fe) and sulfur (S), which are strongly influenced by water management in paddy fields. In this study, we evaluated how water management affects As bioavailability by growing rice plants in a geogenic As-contaminated soil. We determined As speciation in soil porewater and the diversity of the associated microbial community. Continuous flooding enhanced the release of Fe and As and increased arsenite (As(III)) and methylated As species concentrations in the rice grain compared with aerobic treatment. Total inorganic and organic As in the grain was 84% and 81% lower, respectively, in the aerobic treatment compared with the continuous flooding treatment. The amounts of Fe(III)-reducing bacteria (FeRB) increased in the flooded rhizosphere soil. The abundance of FeRB in the soil correlated with the dissolution of Fe and As. Among the As-transformation genes quantified, the aioA gene for As(III) oxidation and arsM gene for As(III) methylation were most abundant. The arsM copy number correlated positively with the levels of dsrB (dissimilatory (bi) sulfite reductase β-subunit), suggesting that dissimilatory sulfate-reducing bacteria (SRB) may play an important role in dimethylarsenate (DMAs(V)) production in soil. Our results show that decreased populations of rhizosphere FeRB and SRB contributed to a lower bioavailability of As, and decreased production of methylated arsenicals under oxic conditions.

Arsenate-dependent growth is independent of an ArrA mechanism of arsenate respiration in the termite hindgut isolate Citrobacter sp. strain TSA-1

Citrobacter sp. strain TSA-1 is an enteric bacterium isolated from the hindgut of the termite. Strain TSA-1 displays anaerobic growth with selenite, fumarate, tetrathionate, nitrate, or arsenate serving as electron acceptors, and it also grows aerobically. In regards to arsenate, genome sequencing revealed that strain TSA-1 lacks a homolog for respiratory arsenate reductase, arrAB, and we were unable to obtain amplicons of arrA. This raises the question as to how strain TSA-1 achieves As(V)-dependent growth. We show that growth of strain TSA-1 on glycerol, which it cannot ferment, is linked to the electron acceptor arsenate. A series of transcriptomic experiments were conducted to discern which genes were upregulated during growth on arsenate, as opposed to those on fumarate or oxygen. For As(V), upregulation was noted for 1 of the 2 annotated arsC genes, while there was no clear upregulation for tetrathionate reductase (ttr), suggesting that this enzyme is not an alternative to arrAB as occurs in certain hyperthermophilic archaea. A gene-deletion mutant strain of TSA-1 deficient in arsC could not achieve anaerobic respiratory growth on As(V). Our results suggest that Citrobacter sp. strain TSA-1 has an unusual and as yet undefined means of achieving arsenate respiration, perhaps involving its ArsC as a respiratory reductase as well as a detoxifying agent.

Autotrophic microbial arsenotrophy in arsenic-rich soda lakes

A number of prokaryotes are capable of employing arsenic oxy-anions as either electron acceptors [arsenate; As(V)] or electron donors [arsenite; As(III)] to sustain arsenic-dependent growth ('arsenotrophy'). A subset of these microorganisms function as either chemoautotrophs or photoautotrophs, whereby they gain sufficient energy from their redox metabolism of arsenic to completely satisfy their carbon needs for growth by autotrophy, that is the fixation of inorganic carbon (e.g. HCO3-) into their biomass. Here we review what has been learned of these processes by investigations we have undertaken in three soda lakes of the western USA and from the physiological characterizations of the relevant bacteria, which include the critical genes involved, such as respiratory arsenate reductase (arrA) and the discovery of its arsenite-oxidizing counterpart (arxA). When possible, we refer to instances of similar process occurring in other, less extreme ecosystems and by microbes other than haloalkaliphiles.

Composition and Activity of Microbial Communities along the Redox Gradient of an Alkaline, Hypersaline, Lake

We compared the composition of microbial communities obtained by sequencing 16S rRNA gene amplicons with taxonomy derived from metatranscriptomes from the same samples. Samples were collected from alkaline, hypersaline Mono Lake, California, USA at five depths that captured the major redox zones of the lake during the onset of meromixis. The prokaryotic community was dominated by bacteria from the phyla Proteobacteria, Firmicutes, and Bacteroidetes, while the picoeukaryotic chlorophyte Picocystis dominated the eukaryotes. Most (80%) of the abundant (>1% relative abundance) OTUs recovered as amplicons of 16S rRNA genes have been reported in previous surveys, indicating that Mono Lake's microbial community has remained stable over 12 years that have included periods of regular, annual overturn interspersed by episodes of prolonged meromixis that result in extremely reducing conditions in bottom water. Metatranscriptomic sequences binned predominately to the Gammaproteobacteria genera Thioalkalivibrio (4–13%) and Thioalkalimicrobium (0–14%); and to the Firmicutes genera Dethiobacter (0–5%) and Clostridium (1–4%), which were also abundant in the 16S rRNA gene amplicon libraries. This study provides insight into the taxonomic affiliations of transcriptionally active communities of the lake's water column under different redox conditions.

Phylogenetic Structure and Metabolic Properties of Microbial Communities in Arsenic-Rich Waters of Geothermal Origin

Arsenic (As) is a toxic element released in aquatic environments by geogenic processes or anthropic activities. To counteract its toxicity, several microorganisms have developed mechanisms to tolerate and utilize it for respiratory metabolism. However, still little is known about identity and physiological properties of microorganisms exposed to natural high levels of As and the role they play in As transformation and mobilization processes. This work aims to explore the phylogenetic composition and functional properties of aquatic microbial communities in As-rich freshwater environments of geothermal origin and to elucidate the key microbial functional groups that directly or indirectly may influence As-transformations across a natural range of geogenic arsenic contamination. Distinct bacterial communities in terms of composition and metabolisms were found. Members of Proteobacteria, affiliated to Alpha- and Betaproteobacteria were mainly retrieved in groundwaters and surface waters, whereas Gammaproteobacteria were the main component in thermal waters. Most of the OTUs from thermal waters were only distantly related to 16S rRNA gene sequences of known taxa, indicating the occurrence of bacterial biodiversity so far unexplored. Nitrate and sulfate reduction and heterotrophic As(III)-oxidization were found as main metabolic traits of the microbial cultivable fraction in such environments. No growth of autotrophic As(III)-oxidizers, autotrophic and heterotrophic As(V)-reducers, Fe-reducers and oxidizers, Mn-reducers and sulfide oxidizers was observed. The ars genes, involved in As(V) detoxifying reduction, were found in all samples whereas aioA [As(III) oxidase] and arrA genes [As(V) respiratory reductase] were not found. Overall, we found that As detoxification processes prevailed over As metabolic processes, concomitantly with the intriguing occurrence of novel thermophiles able to tolerate high levels of As.

Reduction of adsorbed As(V) on nano-TiO2 by sulfate-reducing bacteria

Reduction of surface-bound arsenate [As(V)] and subsequent release into the aqueous phase contribute to elevated As in groundwater. However, this natural process is not fully understood, especially in the presence of sulfate-reducing bacteria (SRB). Gaining mechanistic insights into solid-As(V)-SRB interactions motivated our molecular level study on the fate of nano-TiO₂ bound As(V) in the presence of Desulfovibrio vulgaris DP4, a strain of SRB, using incubation and in situ ATR-FTIR experiments. The incubation results clearly revealed the reduction of As(V), either adsorbed on nano-TiO₂ or dissolved, in the presence of SRB. In contrast, this As(V) reduction was not observed in abiotic control experiments where sulfide was used as the reductant. Moreover, the reduction was faster for surface-bound As(V) than for dissolved As(V), as evidenced by the appearance of As(III) at 45h and 75h, respectively. ATR-FTIR results provided direct evidence that the surface-bound As(V) was reduced to As(III) on TiO₂ surfaces in the presence of SRB. In addition, the As(V) desorption from nano-TiO₂ was promoted by SRB relative to abiotic sulfide, due to the competition between As(V) and bacterial phosphate groups for TiO₂ surface sites. This competition was corroborated by the ATR-FTIR analysis, which showed inner-sphere surface complex formation by bacterial phosphate groups on TiO₂ surfaces. The results from this study highlight the importance of indirect bacteria-mediated As(V) reduction and release in geochemical systems.

Sulfate enhances the dissimilatory arsenate-respiring prokaryotes-mediated mobilization, reduction and release of insoluble arsenic and iron from the arsenic-rich sediments into groundwater

Dissimilatory arsenate-respiring prokaryotes (DARPs) play key roles in the mobilization and release of arsenic from mineral phase into groundwater; however, little is known about how environmental factors influence these processes. This study aimed to explore the effects of sulfate on the dissolution and release of insoluble arsenic. We collected high-arsenic sediment samples from different depths in Jianghan Plain. Microcosm assays indicated that the microbial communities from the samples significantly catalyzed the dissolution, reduction and release of arsenic and iron from the sediments. Remarkably, when sulfate was added into the microcosms, the microorganisms-mediated release of arsenic and iron was significantly increased. To further explore the mechanism of this finding, we isolated a novel DARP, Citrobacter sp. JH001, from the samples. Arsenic release assays showed that JH001 can catalyze the dissolution, reduction and release of arsenic and iron from the sediments, and the presence of sulfate in the microcosms also caused a significant increase in the JH001-mediated dissolution and release of arsenic and iron. Quantitative PCR analysis for the functional gene abundances showed that sulfate significantly increased the arsenate-respiring reductase gene abundances in the microcosms. Thus, it can be concluded that sulfate significantly enhances the arsenate-respiring bacteria-mediated arsenic contamination in groundwater.

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

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

Disguised as a Sulfate Reducer: Growth of the Deltaproteobacterium Desulfurivibrio alkaliphilus by Sulfide Oxidation with Nitrate

This study demonstrates that the deltaproteobacterium Desulfurivibrio alkaliphilus can grow chemolithotrophically by coupling sulfide oxidation to the dissimilatory reduction of nitrate and nitrite to ammonium. Key genes of known sulfide oxidation pathways are absent from the genome of D. alkaliphilus. Instead, the genome contains all of the genes necessary for sulfate reduction, including a gene for a reductive-type dissimilatory bisulfite reductase (DSR). Despite this, growth by sulfate reduction was not observed. Transcriptomic analysis revealed a very high expression level of sulfate-reduction genes during growth by sulfide oxidation, while inhibition experiments with molybdate pointed to elemental sulfur/polysulfides as intermediates. Consequently, we propose that D. alkaliphilus initially oxidizes sulfide to elemental sulfur, which is then either disproportionated, or oxidized by a reversal of the sulfate reduction pathway. This is the first study providing evidence that a reductive-type DSR is involved in a sulfide oxidation pathway. Transcriptome sequencing further suggests that nitrate reduction to ammonium is performed by a novel type of periplasmic nitrate reductase and an unusual membrane-anchored nitrite reductase.

Sulfide oxidation and sulfate reduction, the two major branches of the sulfur cycle, are usually ascribed to distinct sets of microbes with distinct diagnostic genes. Here we show a more complex picture, as D. alkaliphilus, with the genomic setup of a sulfate reducer, grows by sulfide oxidation. The high expression of genes typically involved in the sulfate reduction pathway suggests that these genes, including the reductive-type dissimilatory bisulfite reductases, are also involved in as-yet-unresolved sulfide oxidation pathways. Finally, D. alkaliphilus is closely related to cable bacteria, which grow by electrogenic sulfide oxidation. Since there are no pure cultures of cable bacteria, D. alkaliphilus may represent an exciting model organism in which to study the physiology of this process.

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.

Metatranscriptomic analysis of prokaryotic communities active in sulfur and arsenic cycling in Mono Lake, California, USA

This study evaluates the transcriptionally active, dissimilatory sulfur- and arsenic-cycling components of the microbial community in alkaline, hypersaline Mono Lake, CA, USA. We sampled five depths spanning the redox gradient (10, 15, 18, 25 and 31 m) during maximum thermal stratification. We used custom databases to identify transcripts of genes encoding complex iron-sulfur molybdoenzyme (CISM) proteins, with a focus on arsenic (arrA, aioA and arxA) and sulfur cycling (dsrA, aprA and soxB), and assigned them to taxonomic bins. We also report on the distribution of transcripts related to the ars arsenic detoxification pathway. Transcripts from detoxification pathways were not abundant in oxic surface waters (10 m). Arsenic cycling in the suboxic and microaerophilic zones of the water column (15 and 18 m) was dominated by arsenite-oxidizing members of the Gammaproteobacteria most closely affiliated with Thioalkalivibrio and Halomonas, transcribing arxA. We observed a transition to arsenate-reducing bacteria belonging to the Deltaproteobacteria and Firmicutes transcribing arsenate reductase (arrA) in anoxic bottom waters of the lake (25 and 31 m). Sulfur cycling at 15 and 18 m was dominated by Gammaproteobacteria (Thioalkalivibrio and Thioalkalimicrobium) oxidizing reduced S species, with a transition to sulfate-reducing Deltaproteobacteria at 25 and 31 m. Genes related to arsenic and sulfur oxidation from Thioalkalivibrio were more highly transcribed at 15 m relative to other depths. Our data highlight the importance of Thioalkalivibrio to arsenic and sulfur biogeochemistry in Mono Lake and identify new taxa that appear capable of transforming arsenic.

Microbial communities involved in arsenic mobilization and release from the deep sediments into groundwater in Jianghan plain, Central China

It was shown that groundwater in Jianghan Plain was severely contaminated by arsenic; however, little is known about the mechanism by which the mineral arsenic was mobilized and released into groundwater from the high-arsenic sediments in this area. Here, we collected sediment samples from the depths of 5-230m in Jianghan Plain. Although all of the samples contain high contents of total arsenic, the soluble arsenic was only detectable in few of the shallow sediments, but was readily detectable in all of the deep sediments at the depths of 190-230m. Analysis of the genes of arsenate-respiring reductases indicated that they were not present in all of the shallow sediments from the depths of 5-185m, but were detectable in all of the deep sediments from the depths of 190-230m; all of the identified reductase genes are new or new-type, and they display unique diversity. Microcosm assay indicated that the microbial communities from the deep sediments were able to reduce As(V) into As(III) using lactate, formate, pyruvate or acetate as an electron donor under anaerobic condition. Arsenic release assay demonstrated that these microbial communalities efficiently catalyzed the mobilization and release of the mineral arsenic into aqueous phase. We also isolated a novel cultivable dissimilatory As(V)-respiring bacterium Aeromonas sp. JH155 from the sediments. It is able to completely reduce 2.0mM As(V) into As(III) in 72h, and efficiently promote the reduction and release of the mineral arsenic into aqueous phase. Analysis of the 16S rRNA genes indicated that the deep sediments contain diversities of microbial communities, which were shaped by the environmental factors, such as As, SO₄^2-, NO₃^-, Fe and pH value. These data suggest that the microorganisms in the deep sediments in Jianghan Plain played key roles in the mobilization and release of insoluble arsenic into the groundwater.

Biochar increases arsenic release from an anaerobic paddy soil due to enhanced microbial reduction of iron and arsenic

Previous studies have shown that biochar enhances microbial reduction of iron (Fe) oxyhydroxide under anaerobic incubation. However, there is a lack of data on its influence on arsenic (As) release from As-contaminated paddy soils. In this study, paddy soil slurries (120 mg As kg^-1) were incubated under anaerobic conditions for 60 days with and without the addition of biochar (3%, w/w) prepared from rice straw at 500 °C. Arsenic release, Fe reduction, and As fractionation were determined at 1, 10, 20, 30, and 60 d, while Illumina sequencing and real-time PCR were used to characterize changes in soil microbial community structure and As transformation function genes. During the first month of incubation, As released into soil solution increased sharply from 27.9 and 55.9 to 486 and 630 μg kg^-1 in unamended and biochar amended slurries, with inorganic trivalent As (As^III) being the dominant specie (52.7-91.0% of total As). Compared to unamended slurries, biochar addition increased As and ferrous ion (Fe²⁺) concentrations in soil solution but decreased soil As concentration in the amorphous Fe/Al oxide fraction (F3). Difference in released As between biochar and unamended treatments (ΔAs) increased with incubation time, showing strong linear relationships (R² = 0.23-0.33) with ΔFe²⁺ and ΔF3, confirming increased As release due to enhanced Fe reduction. Biochar addition increased the abundance of Fe reducing bacteria such as Clostridum (27.3% vs. 22.7%), Bacillus (3.34% vs. 2.39%), and Caloramator (4.46% vs. 3.88%). In addition, copy numbers in biochar amended slurries of respiratory As reducing (arrA) and detoxifying reducing genes (arsC) increased 19.0 and 1.70 fold, suggesting microbial reduction of pentavalent As (As^V) adsorbed on Fe oxides to As^III, further contributing to increased As release.

Arsenite as an Electron Donor for Anoxygenic Photosynthesis: Description of Three Strains of Ectothiorhodospira from Mono Lake, California and Big Soda Lake, Nevada

Three novel strains of photosynthetic bacteria from the family Ectothiorhodospiraceae were isolated from soda lakes of the Great Basin Desert, USA by employing arsenite (As(III)) as the sole electron donor in the enrichment/isolation process. Strain PHS-1 was previously isolated from a hot spring in Mono Lake, while strain MLW-1 was obtained from Mono Lake sediment, and strain BSL-9 was isolated from Big Soda Lake. Strains PHS-1, MLW-1, and BSL-9 were all capable of As(III)-dependent growth via anoxygenic photosynthesis and contained homologs of arxA, but displayed different phenotypes. Comparisons were made with three related species: Ectothiorhodospira shaposhnikovii DSM 2111, Ectothiorhodospira shaposhnikovii DSM 243^T, and Halorhodospira halophila DSM 244. All three type cultures oxidized arsenite to arsenate but did not grow with As(III) as the sole electron donor. DNA–DNA hybridization indicated that strain PHS-1 belongs to the same species as Ect. shaposhnikovii DSM 2111 (81.1% sequence similarity), distinct from Ect. shaposhnikovii DSM 243^T (58.1% sequence similarity). These results suggest that the capacity for light-driven As(III) oxidation is a common phenomenon among purple photosynthetic bacteria in soda lakes. However, the use of As(III) as a sole electron donor to sustain growth via anoxygenic photosynthesis is confined to novel isolates that were screened for by this selective cultivation criterion.

Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2(T), a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes

Desulfurivibrio alkaliphilus strain AHT2^T is a strictly anaerobic sulfidogenic haloalkaliphile isolated from a composite sediment sample of eight hypersaline alkaline lakes in the Wadi al Natrun valley in the Egyptian Libyan Desert. D. alkaliphilus AHT2^T is Gram-negative and belongs to the family Desulfobulbaceae within the Deltaproteobacteria. Here we report its genome sequence, which contains a 3.10 Mbp chromosome. D. alkaliphilus AHT2^T is adapted to survive under highly alkaline and moderately saline conditions and therefore, is relevant to the biotechnology industry and life under extreme conditions. For these reasons, D. alkaliphilus AHT2^T was sequenced by the DOE Joint Genome Institute as part of the Community Science Program.

Correlating microbial community profiles with geochemical conditions in a watershed heavily contaminated by an antimony tailing pond

Mining activities have introduced various pollutants to surrounding aquatic and terrestrial environments, causing adverse impacts to the environment. Indigenous microbial communities are responsible for the biogeochemical cycling of pollutants in diverse environments, indicating the potential for bioremediation of such pollutants. Antimony (Sb) has been extensively mined in China and Sb contamination in mining areas has been frequently encountered. To date, however, the microbial composition and structure in response to Sb contamination has remained overlooked. Sb and As frequently co-occur in sulfide-rich ores, and co-contamination of Sb and As is observed in some mining areas. We characterized, for the first time, the microbial community profiles and their responses to Sb and As pollution from a watershed heavily contaminated by Sb tailing pond in Southwest China. The indigenous microbial communities were profiled by high-throughput sequencing from 16 sediment samples (535,390 valid reads). The comprehensive geochemical data (specifically, physical-chemical properties and different Sb and As extraction fractions) were obtained from river water and sediments at different depths as well. Canonical correspondence analysis (CCA) demonstrated that a suite of in situ geochemical and physical factors significantly structured the overall microbial community compositions. Further, we found significant correlations between individual phylotypes (bacterial genera) and the geochemical fractions of Sb and As by Spearman rank correlation. A number of taxonomic groups were positively correlated with the Sb and As extractable fractions and various Sb and As species in sediment, suggesting potential roles of these phylotypes in Sb biogeochemical cycling.

Increasing the Richness of Culturable Arsenic-Tolerant Bacteria from Theonella swinhoei by Addition of Sponge Skeleton to the Growth Medium

Theonella swinhoei is an arsenic hyper-accumulator sponge, harboring a multitude of associated bacteria. These bacteria reside in the mesohyl, the dense extracellular matrix of the sponge. Previous elemental analysis of separated cell fractions from the sponge had determined that arsenic is localized to the associated bacteria. Subsequently, sponge-associated arsenic-tolerant bacteria were isolated here and grouped into 15 operational taxonomic units (OTUs, 97% similarity). Both culture-dependent and culture-independent work had revealed that T. swinhoei harbors a highly diverse bacterial community. It was thus hypothesized the acclimation of bacteria in the presence of a sponge skeleton, better mimicking its natural environment, would increase the yield of isolation of sponge-associated bacteria. Using seven modularly designed media, 380 bacteria isolates were grown and grouped into 22 OTUs. Inclusion of sponge skeleton in the growth medium promoted bacterial growth in all seven media, accounting for 20 of the 22 identified OTUs (the other two in a medium without skeleton). Diversity and richness indices were calculated for each treatment or combination of treatments with shared growth parameters. Integrating data inherent in the modularly designed media with the ecological indices led to the formation of new hypotheses regarding the aeration conditions and expected arsenic form in situ. Both aerobic and anoxic conditions are expected to occur in the sponge (temporally and/or spatially). Arsenate is expected to be the dominant (or even the only) arsenic form in the sponge.

Long-distance electron transfer by cable bacteria in aquifer sediments

The biodegradation of organic pollutants in aquifers is often restricted to the fringes of contaminant plumes where steep countergradients of electron donors and acceptors are separated by limited dispersive mixing. However, long-distance electron transfer (LDET) by filamentous ‘cable bacteria' has recently been discovered in marine sediments to couple spatially separated redox half reactions over centimeter scales. Here we provide primary evidence that such sulfur-oxidizing cable bacteria can also be found at oxic–anoxic interfaces in aquifer sediments, where they provide a means for the direct recycling of sulfate by electron transfer over 1–2-cm distance. Sediments were taken from a hydrocarbon-contaminated aquifer, amended with iron sulfide and saturated with water, leaving the sediment surface exposed to air. Steep geochemical gradients developed in the upper 3 cm, showing a spatial separation of oxygen and sulfide by 9 mm together with a pH profile characteristic for sulfur oxidation by LDET. Bacterial filaments, which were highly abundant in the suboxic zone, were identified by sequencing of 16S rRNA genes and fluorescence in situ hybridization (FISH) as cable bacteria belonging to the Desulfobulbaceae. The detection of similar Desulfobulbaceae at the oxic–anoxic interface of fresh sediment cores taken at a contaminated aquifer suggests that LDET may indeed be active at the capillary fringe in situ.

Arsenic remediation by formation of arsenic sulfide minerals in a continuous anaerobic bioreactor

Arsenic (As) is a highly toxic metalloid that has been identified at high concentrations in groundwater in certain locations around the world. Concurrent microbial reduction of arsenate (As(V) ) and sulfate (SO4 (2-) ) can result in the formation of poorly soluble arsenic sulfide minerals (ASM). The objective of this research was to study As biomineralization in a minimal iron environment for the bioremediation of As-contaminated groundwater using simultaneous As(V) and SO4 (2-) reduction. A continuous-flow anaerobic bioreactor was maintained at slightly acidic pH (6.25-6.50) and fed with As(V) and SO4 (2-) , utilizing ethanol as an electron donor for over 250 d. A second bioreactor running under the same conditions but lacking SO4 (2-) was operated as a control to study the fate of As (without S). The reactor fed with SO4 (2-) removed an average 91.2% of the total soluble As at volumetric rates up to 2.9 mg As/(L · h), while less than 5% removal was observed in the control bioreactor. Soluble S removal occurred with an S to As molar ratio of 1.2, suggesting the formation of a mixture of orpiment- (As2 S3 ) and realgar-like (AsS) solid phases. Solid phase characterization using K-edge X-ray absorption spectroscopy confirmed the formation of a mixture of As2 S3 and AsS. These results indicate that a bioremediation process relying on the addition of a simple, low-cost electron donor offers potential to promote the removal of As from groundwater with naturally occurring or added SO4 (2-) by precipitation of ASM.

Microbiological oxidation of antimony(III) with oxygen or nitrate by bacteria isolated from contaminated mine sediments

Bacterial oxidation of arsenite [As(III)] is a well-studied and important biogeochemical pathway that directly influences the mobility and toxicity of arsenic in the environment. In contrast, little is known about microbiological oxidation of the chemically similar anion antimonite [Sb(III)]. In this study, two bacterial strains, designated IDSBO-1 and IDSBO-4, which grow on tartrate compounds and oxidize Sb(III) using either oxygen or nitrate, respectively, as a terminal electron acceptor, were isolated from contaminated mine sediments. Both isolates belonged to the Comamonadaceae family and were 99% similar to previously described species. We identify these novel strains as Hydrogenophaga taeniospiralis strain IDSBO-1 and Variovorax paradoxus strain IDSBO-4. Both strains possess a gene with homology to the aioA gene, which encodes an As(III)-oxidase, and both oxidize As(III) aerobically, but only IDSBO-4 oxidized Sb(III) in the presence of air, while strain IDSBO-1 could achieve this via nitrate respiration. Our results suggest that expression of aioA is not induced by Sb(III) but may be involved in Sb(III) oxidation along with an Sb(III)-specific pathway. Phylogenetic analysis of proteins encoded by the aioA genes revealed a close sequence similarity (90%) among the two isolates and other known As(III)-oxidizing bacteria, particularly Acidovorax sp. strain NO1. Both isolates were capable of chemolithoautotrophic growth using As(III) as a primary electron donor, and strain IDSBO-4 exhibited incorporation of radiolabeled [(14)C]bicarbonate while oxidizing Sb(III) from Sb(III)-tartrate, suggesting possible Sb(III)-dependent autotrophy. Enrichment cultures produced the Sb(V) oxide mineral mopungite and lesser amounts of Sb(III)-bearing senarmontite as precipitates.

Anaerobic Chemolithotrophic Growth of the Haloalkaliphilic Bacterium Strain MLMS-1 by Disproportionation of Monothioarsenate

A novel chemolithotrophic metabolism based on a mixed arsenic-sulfur species has been discovered for the anaerobic deltaproteobacterium, strain MLMS-1, a haloalkaliphile isolated from Mono Lake, California, U.S. Strain MLMS-1 is the first reported obligate arsenate-respiring chemoautotroph which grows by coupling arsenate reduction to arsenite with the oxidation of sulfide to sulfate. In that pathway the formation of a mixed arsenic-sulfur species was reported. That species was assumed to be monothioarsenite ([H2As(III)S(-II)O2](-)), formed as an intermediate by abiotic reaction of arsenite with sulfide. We now report that this species is monothioarsenate ([HAs(V)S(-II)O3](2-)) as revealed by X-ray absorption spectroscopy. Monothioarsenate forms by abiotic reaction of arsenite with zerovalent sulfur. Monothioarsenate is kinetically stable under a wide range of pH and redox conditions. However, it was metabolized rapidly by strain MLMS-1 when incubated with arsenate. Incubations using monothioarsenate confirmed that strain MLMS-1 was able to grow (μ = 0.017 h(-1)) on this substrate via a disproportionation reaction by oxidizing the thio-group-sulfur (S(-II)) to zerovalent sulfur or sulfate while concurrently reducing the central arsenic atom (As(V)) to arsenite. Monothioarsenate disproportionation could be widespread in nature beyond the already studied arsenic and sulfide rich hot springs and soda lakes where it was discovered.

Diversity and abundance of arsenic biotransformation genes in paddy soils from southern China

Microbe-mediated arsenic (As) biotransformation in paddy soils determines the fate of As in soils and its availability to rice plants, yet little is known about the microbial communities involved in As biotransformation. Here, we revealed wide distribution, high diversity, and abundance of arsenite (As(III)) oxidase genes (aioA), respiratory arsenate (As(V)) reductase genes (arrA), As(V) reductase genes (arsC), and As(III) S-adenosylmethionine methyltransferase genes (arsM) in 13 paddy soils collected across Southern China. Sequences grouped with As biotransformation genes are mainly from rice rhizosphere bacteria, such as some Proteobacteria, Gemmatimonadales, and Firmicutes. A significant correlation of gene abundance between arsC and arsM suggests that the two genes coexist well in the microbial As resistance system. Redundancy analysis (RDA) indicated that soil pH, EC, total C, N, As, and Fe, C/N ratio, SO4(2-)-S, NO3(-)-N, and NH4(+)-N were the key factors driving diverse microbial community compositions. This study for the first time provides an overall picture of microbial communities involved in As biotransformation in paddy soils, and considering the wide distribution of paddy fields in the world, it also provides insights into the critical role of paddy fields in the As biogeochemical cycle.

Role of indigenous arsenate and iron(III) respiring microorganisms in controlling the mobilization of arsenic in a contaminated soil sample

In this study two different treatment options were investigated for the release of arsenic from a contaminated soil sample. The first option was based on the "bioaugmentation" principle and involved addition of a pure Fe(III)-reducing culture, i.e. Desulfuromonas palmitatis. The second option consisted in the "biostimulation" of indigenous bacteria and involved simple addition of nutrients. Due to the strong association of As with soil ferric oxides, the reductive dissolution of soil oxides by D. palmitatis lead to 45 % arsenic release in solution (2.15 mM). When only nutrients were supplied to the soil, the same amounts of Fe and As were dissolved with slower rates and most aqueous As was found to be in the trivalent state, indicating the presence of arsenate reducing species. The arsenate reducing microorganisms were enriched with successive cultures, using Na2HAsO4 as electron acceptor. The phylogenetic analysis revealed that the enriched microbial consortium contained Desulfosporosinus species, which are known arsenate reducers.

Culturable associated-bacteria of the sponge Theonella swinhoei show tolerance to high arsenic concentrations

Sponges are potent filter feeders and as such are exposed to high fluxes of toxic trace elements, which can accumulate in their body over time. Such is the case of the Red Sea sponge Theonella swinhoei, which has been shown to accumulate up to 8500 mg/Kg of the highly toxicelement arsenic. T. swinhoei is known to harbor a multitude of sponge-associated bacteria, so it is hypothesized that the associated-bacteria will be tolerant to high arsenic concentration. This study also investigates the fate of the arsenic accumulated in the sponge to test if the associated-bacteria have an important role in the arsenic accumulation process of their host, since bacteria are key players in the natural arsenic cycle. Separation of the sponge to sponge cells and bacteria enriched fractions showed that arsenic is accumulated by the bacteria. Sponge-associated, arsenic-tolerant bacteria were cultured in the presence of 5 mM of either arsenate or arsenite (equivalent to 6150 mg/Kg arsenic, dry weight). The 54 isolated bacteria were grouped to 15 operational taxonomic units (OTUs) and isolates belonging to 12 OTUs were assessed for tolerance to arsenate at increased concentrations up to 100 mM. Eight of the 12 OTUs tolerated an order of magnitude increase in the concentration of arsenate, and some exhibited external biomineralization of arsenic-magnesium salts. The biomineralization of this unique mineral was directly observed in bacteria for the first time. These results may provide an explanation for the ability of the sponge to accumulate considerable amounts of arsenic. Furthermore arsenic-mineralizing bacteria can potentially be used for the study of bioremediation, as arsenic toxicity affects millions of people worldwide.

Integrated phytobial remediation for sustainable management of arsenic in soil and water

Arsenic (As), cited as the most hazardous substance by the U.S. Agency for Toxic Substance and Disease Registry (ATSDR, 2005), is an ubiquitous metalloid which when ingested for prolonged periods cause extensive health effects leading to ultimate untimely death. Plants and microbes can help mitigate soil and groundwater As problem since they have evolved elaborate detoxification machineries against this toxic metalloid as a result of their coexistence with this since the origin of life on earth. Utilization of the phytoremediation and bioremediation potential of the plants and microbes, respectively, is now regarded as two innovative tools that encompass biology, geology, biotechnology and allied sciences with cutting edge applications for sustainable mitigation of As epidemic. Discovery of As hyperaccumulating plants that uptake and concentrate large amounts of this toxic metalloid in their shoots or roots offered new hope to As phytoremediation, solar power based nature's own green remediation. This review focuses on how phytoremediation and bioremediation can be merged together to form an integrated phytobial remediation which could synergistically achieve the goal of large scale removal of As from soil, sediment and groundwater and overcome the drawbacks of the either processes alone. The review also points to the feasibility of the introduction of transgenic plants and microbes that bring new hope for more efficient treatment of As. The review identifies one critical research gap on the importance of remediation of As contaminated groundwater not only for drinking purpose but also for irrigation purpose and stresses that more research should be conducted on the use of constructed wetland, one of the most suitable areas of application of phytobial remediation. Finally the review has narrowed down on different phytoinvestigation and phytodisposal methods, which constitute the most essential and the most difficult part of pilot scale and field scale applications of phytoremediation programs.

Biomineralization of arsenate to arsenic sulfides is greatly enhanced at mildly acidic conditions

Arsenic (As) is an important water contaminant due to its high toxicity and widespread occurrence. Arsenic-sulfide minerals (ASM) are formed during microbial reduction of arsenate (As(V)) and sulfate (SO4(2-)). The objective of this research is to study the effect of the pH on the removal of As due to the formation of ASM in an iron-poor system. A series of batch experiments was used to study the reduction of SO4(2-) and As(V) by an anaerobic biofilm mixed culture in a range of pH conditions (6.1-7.2), using ethanol as the electron donor. Total soluble concentrations and speciation of S and As were monitored. Solid phase speciation of arsenic was characterized by x-ray adsorption spectroscopy (XAS). A marked decrease of the total aqueous concentrations of As and S was observed in the inoculated treatments amended with ethanol, but not in the non-inoculated controls, indicating that the As-removal was biologically mediated. The pH dramatically affected the extent and rate of As removal, as well as the stoichiometric composition of the precipitate. The amount of As removed was 2-fold higher and the rate of the As removal was up to 17-fold greater at pH 6.1 than at pH 7.2. Stoichiometric analysis and XAS results confirmed the precipitate was composed of a mixture of orpiment and realgar, and the proportion of orpiment in the sample increased with increasing pH. The results taken as a whole suggest that ASM formation is greatly enhanced at mildly acidic pH conditions.

Transformation of monothioarsenate by haloalkaliphilic, anoxygenic photosynthetic purple sulfur bacteria

Thioarsenates are the dominant arsenic species in arsenic-rich, alkaline, and sulfidic waters, but bacterial interactions with these compounds have only recently been examined. Previous studies have shown that microorganisms play a role in the transformation of monothioarsenate to arsenate, including use of monothioarsenate as a chemolithotrophic electron donor coupled with oxygen as an electron acceptor. We obtained enrichment cultures from two saline, alkaline lakes (Mono Lake, CA and Big Soda Lake, NV) that are able to use monothioarsenate as the sole electron donor for anoxygenic photosynthesis. These anoxic cultures were able to convert a 1 mM mixture of thioarsenates completely to arsenate in c. 13 days and 4 mM monothioarsenate to arsenate in c. 17 days. This conversion was light dependent; thus, monothioarsenate can be used as the sole electron donor for anoxygenic photosynthesis. Both of the Mono Lake and Big Soda Lake enrichment cultures were dominated by an organism closely related to Ectothiorhodospira species. We tested additional strains of purple sulfur bacteria and found widespread ability to use monothioarsenate as an electron donor. The ability of bacteria to transform thioarsenates directly via anoxygenic photosynthesis adds a new perspective to the well-studied arsenic and sulfur cycles.

Coregulated genes link sulfide:quinone oxidoreductase and arsenic metabolism in Synechocystis sp. strain PCC6803

Although the biogeochemistry of the two environmentally hazardous compounds arsenic and sulfide has been extensively investigated, the biological interference of these two toxic but potentially energy-rich compounds has only been hypothesized and indirectly proven. Here we provide direct evidence for the first time that in the photosynthetic model organism Synechocystis sp. strain PCC6803 the two metabolic pathways are linked by coregulated genes that are involved in arsenic transport, sulfide oxidation, and probably in sulfide-based alternative photosynthesis. Although Synechocystis sp. strain PCC6803 is an obligate photoautotrophic cyanobacterium that grows via oxygenic photosynthesis, we discovered that specific genes are activated in the presence of sulfide or arsenite to exploit the energy potentials of these chemicals. These genes form an operon that we termed suoRSCT, located on a transposable element of type IS4 on the plasmid pSYSM of the cyanobacterium. suoS (sll5036) encodes a light-dependent, type I sulfide:quinone oxidoreductase. The suoR (sll5035) gene downstream of suoS encodes a regulatory protein that belongs to the ArsR-type repressors that are normally involved in arsenic resistance. We found that this repressor has dual specificity, resulting in 200-fold induction of the operon upon either arsenite or sulfide exposure. The suoT gene encodes a transmembrane protein similar to chromate transporters but in fact functioning as an arsenite importer at permissive concentrations. We propose that the proteins encoded by the suoRSCT operon might have played an important role under anaerobic, reducing conditions on primordial Earth and that the operon was acquired by the cyanobacterium via horizontal gene transfer.

Methodology for assessing thioarsenic formation potential in sulfidic landfill environments

Arsenic leaching and speciation in landfills, especially those with arsenic bearing waste and drywall disposal (such as construction and demolition (C&D) debris landfills), may be affected by high levels of sulfide through the formation of thioarsenic anions. A methodology using ion chromatography (IC) with a conductivity detector was developed for the assessment of thioarsenic formation potential in sulfidic landfill environments. Monothioarsenate (H2AsSO3(-)) and dithioarsenate (H2AsS2O2(-)) were confirmed in the IC fractions of thioarsenate synthesis mixture, consistent with previous literature results. However, the observation of AsSx(-) (x=5-8) in the supposed trithioarsenate (H2AsS3O(-)) and tetrathioarsenate (H2AsS4(-)) IC fractions suggested the presence of new arsenic polysulfide complexes. All thioarsenate anions, particularly trithioarsenate and tetrathioarsenate, were unstable upon air exposure. The method developed for thioarsenate analysis was validated and successfully used to analyze several landfill leachate samples. Thioarsenate anions were detected in the leachate of all of the C&D debris landfills tested, which accounted for approximately 8.5% of the total aqueous As in the leachate. Compared to arsenite or arsenate, thioarsenates have been reported in literature to have lower adsorption on iron oxide minerals. The presence of thioarsenates in C&D debris landfill leachate poses new concerns when evaluating the impact of arsenic mobilization in such environments.

Methane oxidation linked to chlorite dismutation

We examined the potential for CH₄ oxidation to be coupled with oxygen derived from the dissimilatory reduction of perchlorate, chlorate, or via chlorite (ClO⁻₂) dismutation. Although dissimilatory reduction of ClO⁻₄ and ClO⁻₃ could be inferred from the accumulation of chloride ions either in spent media or in soil slurries prepared from exposed freshwater lake sediment, neither of these oxyanions evoked methane oxidation when added to either anaerobic mixed cultures or soil enriched in methanotrophs. In contrast, ClO⁻₂ amendment elicited such activity. Methane (0.2 kPa) was completely removed within several days from the headspace of cell suspensions of Dechloromonas agitata CKB incubated with either Methylococcus capsulatus Bath or Methylomicrobium album BG8 in the presence of 5 mM ClO⁻₂. We also observed complete removal of 0.2 kPa CH₄ in bottles containing soil enriched in methanotrophs when co-incubated with D. agitata CKB and 10 mM ClO⁻₂. However, to be effective these experiments required physical separation of soil from D. agitata CKB to allow for the partitioning of O₂ liberated from chlorite dismutation into the shared headspace. Although a link between ClO⁻₂ and CH₄ consumption was established in soils and cultures, no upstream connection with either ClO⁻₄ or ClO⁻₃ was discerned. This result suggests that the release of O₂ during enzymatic perchlorate reduction was negligible, and that the oxygen produced was unavailable to the aerobic methanotrophs.

Arsenic uptake by rice is influenced by microbe-mediated arsenic redox changes in the rhizosphere

Arsenic (As) uptake by rice is largely determined by As speciation, which is strongly influenced by microbial activities. However, little is known about interactions between root and rhizosphere microbes, particularly on arsenic oxidation and reduction. In this study, two rice cultivars with different radial oxygen loss (ROL) ability were used to investigate the impact of microbially mediated As redox changes in the rhizosphere on As uptake. Results showed that the cultivar with higher ROL (Yangdao) had lower As uptake than that with lower ROL (Nongken). The enhancement of the rhizospheric effect on the abundance of the arsenite (As(III)) oxidase gene (aroA-like) was greater than on the arsenate (As(V)) reductase gene (arsC), and As(V) respiratory reductase gene (arrA), resulting in As oxidation and sequestration in the rhizosphere, particularly for cultivar Yangdao. The community of As(III)-oxidizing bacteria in the rhizosphere was dominated by α-Proteobacteria and β-Proteobacteria and was influenced by rhizospheric effects, rice straw application, growth stage, and cultivar. Application of rice straw into the soil increased As release and accumulation into rice plants. These results highlighted that uptake of As by rice is influenced by microbial processes, especially As oxidation in the rhizosphere, and these processes are influenced by root ROL and organic matter application.

Microbiological reduction of Sb(V) in anoxic freshwater sediments

Microbiological reduction of millimolar concentrations of Sb(V) to Sb(III) was observed in anoxic sediments from two freshwater settings: (1) a Sb- and As-contaminated mine site (Stibnite Mine) in central Idaho and 2) an uncontaminated suburban lake (Searsville Lake) in the San Francisco Bay Area. Rates of Sb(V) reduction in anoxic sediment microcosms and enrichment cultures were enhanced by amendment with lactate or acetate as electron donors but not by H2, and no reduction occurred in sterilized controls. Addition of 2-(14)C-acetate to Stibnite Mine microcosms resulted in the production of (14)CO2 coupled to Sb(V) reduction, suggesting that this process proceeds by a dissimilatory respiratory pathway in those sediments. Antimony(V) reduction in Searsville Lake sediments was not coupled to acetate mineralization and may be associated with Sb-resistance. The microcosms and enrichment cultures also reduced sulfate, and the precipitation of insoluble Sb(III)-sulfide complexes was a major sink for reduced Sb. The reduction of Sb(V) by Stibnite Mine sediments was inhibited by As(V), suggesting that As(V) is a preferred electron acceptor for the indigenous community. These findings indicate a novel pathway for anaerobic microbiological respiration and suggest that communities capable of reducing high concentrations of Sb(V) commonly occur naturally in the environment.

Microscale speciation of arsenic and iron in ferric-based sorbents subjected to simulated landfill conditions

During treatment for potable use, water utilities generate arsenic-bearing ferric wastes that are subsequently dispatched to landfills. The biogeochemical weathering of these residuals in mature landfills affects the potential mobilization of sorbed arsenic species via desorption from solids subjected to phase transformations driven by abundant organic matter and bacterial activity. Such processes are not simulated with the toxicity characteristic leaching procedure (TCLP) currently used to characterize hazard. To examine the effect of sulfate on As retention in landfill leachate, columns of As(V) loaded amorphous ferric hydroxide were reacted biotically at two leachate sulfate concentrations (0.064 mM and 2.1 mM). After 300 days, ferric sorbents were reductively dissolved. Arsenic released to porewaters was partially coprecipitated in mixed-valent secondary iron phases whose speciation was dependent on sulfate concentration. As and Fe XAS showed that, in the low sulfate column, 75-81% of As(V) was reduced to As(III), and 53-68% of the Fe(III) sorbent was transformed, dominantly to siderite and green rust. In the high sulfate column, Fe(III) solids were reduced principally to FeS(am), whereas As(V) was reduced to a polymeric sulfide with local atomic structure of realgar. Multienergy micro-X-ray fluorescence (ME-μXRF) imaging at Fe and As K-edges showed that As formed surface complexes with ferrihydrite > siderite > green rust in the low sulfate column; while discrete realgar-like phases formed in the high sulfate systems. Results indicate that landfill sulfur chemistry exerts strong control over the potential mobilization of As from ferric sorbent residuals by controlling secondary As and Fe sulfide coprecipitate formation.

Arsenic-transforming microbes and their role in biomining processes

It is well known that microorganisms can dissolve different minerals and use them as sources of nutrients and energy. The majority of rock minerals are rich in vital elements (e.g., P, Fe, S, Mg and Mo), but some may also contain toxic metals or metalloids, like arsenic. The toxicity of arsenic is disclosed after the dissolution of the mineral, which raises two important questions: (1) why do microorganisms dissolve arsenic-bearing minerals and release this metal into the environment in a toxic (also for themselves) form, and (2) How do these microorganisms cope with this toxic element? In this review, we summarize current knowledge about arsenic-transforming microbes and their role in biomining processes. Special consideration is given to studies that have increased our understanding of how microbial activities are linked to the biogeochemistry of arsenic, by examining (1) where and in which forms arsenic occurs in the mining environment, (2) microbial activity in the context of arsenic mineral dissolution and the mechanisms of arsenic resistance, (3) the minerals used and technologies applied in the biomining of arsenic, and (4) how microbes can be used to clean up post-mining environments.