Isolation of an arsenate-respiring bacterium from a redox front in an arsenic-polluted aquifer in West Bengal, Bengal Basin

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

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

Contradictory Impacts of Nitrate on the Dissimilatory Arsenate-Respiring Prokaryotes-Induced Reductive Mobilization of Arsenic from Contaminated Sediments: Mechanism Insight from Metagenomic and Functional Analyses

Dissimilatory arsenate-respiring prokaryotes (DARPs) are considered to be a key impetus of the reductive dissolution of solid-phase arsenic. However, little is known about the interaction between nitrate and DARPs so far. In this study, we showed that nitrate either inhibited or promoted the DARP population-catalyzed reductive mobilization of As in sediments. Metagenomic analysis of the microbial communities in the microcosms after seven days of As release assays suggested that microbes mainly consisted of: Type-I DARPs having potential to reduce NO3- into NO2- and Type-II DARPs having potential to reduce NO3- to NH4+. We further isolated two cultivable DARPs, Neobacillus sp. A01 and Paenibacillus sp. A02, which represent Type-I and -II DARPs, respectively. We observed that nitrate suppressed A01-mediated release of As(III) but promoted A02-mediated release of As(III). Furthermore, we demonstrated that this observation was due to the fact that nitrite, the end product of incomplete denitrification by Type-I DARPs, suppressed the arrA gene expression per cell and growth of all DARPs, whereas ammonium, the end product of dissimilatory nitrate reduction to ammonium (DNRA) by Type-II DARPs, enhanced the arrA gene expression per cell and significantly promoted the growth of all DARPs. These findings suggest that the actual effects of nitrate on DARP population-catalyzed reductive mobilization of arsenic, largely depend on the ratio of Type-I to Type-II DARPs in sediments.

Metagenomic and culture-dependent approaches unveil active microbial community and novel functional genes involved in arsenic mobilization and detoxification in groundwater

BACKGROUND

Arsenic (As) and its species are major pollutants in ecological bodied including groundwater in Bangladesh rendering serious public health concern. Bacteria with arsenotrophic genes have been found in the aquifer, converting toxic arsenite [As (III)] to less toxic arsenate [As (V)] that is easily removed using chemical and biological trappers. In this study, genomic and metagenomic approaches parallel to culture-based assay (Graphical abstract) have made it possible to decipher phylogenetic diversity of groundwater arsenotrophic microbiomes along with elucidation of their genetic determinants.

RESULTS

Seventy-two isolates were retrieved from six As-contaminated (average As concentration of 0.23 mg/L) groundwater samples from Munshiganj and Chandpur districts of Bangladesh. Twenty-three isolates harbored arsenite efflux pump (arsB) gene with high abundance, and ten isolates possessing arsenite oxidase (aioA) gene, with a wide range of minimum inhibitory concentration, MICAs (2 to 32 mM), confirming their role in arsenite metabolism. There was considerable heterogeneity in species richness and microbial community structure. Microbial taxa from Proteobacteria, Firmicutes and Acidobacteria dominated these diversities. Through these combinatorial approaches, we have identified potential candidates such as, Pseudomonas, Acinetobacter, Stenotrophomonas, Achromobacter, Paraburkholderia, Comamonas and Klebsiella and associated functional genes (arsB, acr3, arsD, arsH, arsR) that could significantly contribute to arsenite detoxification, accumulation, and immobilization.

CONCLUSIONS

Culture-dependent and -independent shotgun metagenomic investigation elucidated arsenotrophic microbiomes and their functions in As biogeochemical transformation. These findings laid a foundation for further large-scale researches on the arsenotrophic microbiomes and their concurrent functions in As biogeochemical transformation in As-contaminated areas of Bangladesh and beyond.

Effect of manganese oxides on arsenic speciation and mobilization in different arsenic-adsorbed iron-minerals under microbially-reducing conditions

The oxidation and immobilization of arsenic (As) by manganese oxides have been shown to reduce As toxicity and bioavailability under abiotic conditions. In this study, we investigate the impact of manganese oxide (δ-MnO₂) on the fate of different Fe-minerals-adsorbed As in the presence of As(V)-reducing bacteria Bacillus sp. JQ. Results showed that in the absence of δ-MnO₂, As release in goethite was much higher than in ferrihydrite and hematite during microbial reduction. Adding 3.1 mM Mn reduced As release by 0.3%, 46.3%, and 6.7% in the ferrihydrite, goethite, and hematite groups, respectively. However, aqueous As was dominated by As(III) in the end, because the oxidation effect of δ-MnO₂ was limited and short-lived. Additionally, the fraction of solid-phase As(V) increased by 9.8% in ferrihydrite, 39.4% in goethite, and 7.4% in hematite in the high-Mn treatments, indicating that δ-MnO₂ had the most significant oxidation and immobilization effect on goethite-adsorbed As. This was achieved because goethite particles were evenly distributed on δ-MnO₂ surface, which supported As(III) oxidation by δ-MnO₂; while ferrihydrite strongly aggregated, which hindered the oxidation of As(III). Our study shows that As-oxidation and immobilization by manganese oxides cannot easily be assessed without considering the mineral composition and microbial conditions of soils.

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.

Microbial mediated arsenate reducing behavior in landfill leachate-saturated zone

As(V) reduction mediated by microorganisms might be an essential process in resisting As toxicity since As(V) is the major species in the landfill. LSZ has been considered as a trigger of all types of microbial activity inside a landfill site. This research investigated the microbial As(V)-reducing behavior in LSZ. The results revealed that higher As(V)-reduction efficiency in higher As(V) content-stress LSZ scenario. The corresponding microbial diversity also varied with the As(V) content. The microbial community structure was related to arrA and arsC distribution, which encode respiratory As(V) reductase and cytoplasmic As(V) reductase, respectively. The landfill As bio-reduction pathways were modeled, as well as the As functional gene distribution among different As(V) contents at different landfill stages. The C, N, and S metabolic processes generally affected the As(V)-resistance genes distribution. Thiosulfate oxidation, denitrification, and dissimilatory nitrate reduction positively affected arsC, while dissimilatory sulfate reduction and methanogenesis trended to play a negative role. This research provides new insight into As(V) bio-reduction inside a landfill site in terms of functional genes distribution and correlation with nutrient elements metabolic processes.

Comparisons of four As(V)-respiring bacteria from contaminated aquifers: activities to respire soluble As(V) and to reductively mobilize solid As(V)

It was shown that dissimilatory arsenate[As(V)]-respiring prokaryotes (DARPs) play important roles in driving the formation of arsenic-contaminated groundwater. However, because it is tough to isolate cultivable DARPs, the physiological and functional features of DARPs have not been fully elucidated yet; this impedes a deep understanding of the mechanisms for the dynamic fluctuations of As concentrations in contaminated groundwater. Here, four new DARPs were isolated from As-contaminated aquifers using the microbial enrichment technique, which were referred to as Bacillus sp Z01, Bacillus sp. Z02. Achromobacter sp. Z03 and Intrasporangium sp. Z04. We found that the presence of As(V) significantly inhibited the growth of Z03 and Z04, but promoted the growth of Z01 and Z02. The four strains possess significant As(V)-, NO₃^-- and Fe(III)-respiring activities; however, their activities and preferred electron donors differ greatly. NO₃^- was finally reduced to NO₂^- by Z01 and Z02, and to N₂O and N₂ by Z03 and Z04. The optimal pH value for their As(V)-respiring activity was 5 for Z01, and 4 for Z02, Z03 and Z04, whereas their optimal temperature varied between 30 and 37 °C. Microcosm assays with As-contaminated sediments and scorodite suggested that the four DARP strains had highly differential activities to reduce and mobilize solid As(V) under anaerobic conditions. Although the four DARPs have high soluble As(V)-respiring activities, their activities to mobilize solid As are negligibly low, accounting for only 0.006-0.484% of their each corresponding soluble As(V)-respiring activity. Moreover, extreme inconsistency between the size orders of their activities to respire soluble As(V) and to catalyze As reductive mobilization was observed. It is interesting to see that Z04 had high As(V)-respiring activity, but had little ability to catalyze the reductive mobilization of As and Fe. These observations suggest that As(V)-respiring activity is required, but not enough to catalyze the reductive mobilization of solid As(V). These findings provide new knowledge about the physiological and functional features of DARPs, and are helpful for a better understanding of the roles of DARPs in reductive mobilization and release of As from solid phase into groundwater.

The groundwater arsenic contamination in the Bengal Basin-A review in brief

The presence of arsenic in the groundwater of the densely-populated Bengal Basin evolved as a mass-poisoning agent and is a reason for the misery of millions of people living here. High-level arsenic was detected in the shallow aquifer-tube wells of the basin in the late-20th century. The redox conditions and the biogeochemical activities in the shallow aquifers support the existence of arsenic in its most toxic +3 state. The shallow aquifers are constructed by the Holocene reduced grey sands, having a lesser capacity to hold the arsenic brought from the Himalayas by the Ganga-Brahmaputra-Meghna river system. Among several other hypotheses, the reductive dissolution of arsenic bearing Fe-oxyhydroxides coupled with the microbial activities in the organic-matter-rich Holocene grey sands is believed to be the primary reason for releasing arsenic in groundwater of basinal shallow aquifers. The deep aquifers below the late Pleistocene aquifers and the Palaeo-interfluvial aquifers capped by the last glacial maximum Palaeosol generally contain arsenic-free or low-arsenic water. Ingress of arsenic into the deep aquifers from the shallow aquifers was considered to have been caused by extensive non-domestic pumping. However, studies have found that extensive pumping is unlikely to contaminate the deep aquifer water with higher levels of arsenic within decadal time scales. Irrigation-pumping may produce hydraulic barriers between the shallow and deep aquifer-groundwater and distributes arsenic in the topsoil by flushing. Significant disparities have been observed among the Bengal basinal groundwater arsenic concentrations. However, abrupt spatial variation in groundwater arsenic concentrations has been a key feature of the basin.

Identification and Genome Analysis of an Arsenic-Metabolizing Strain of Citrobacter youngae IITK SM2 in Middle Indo-Gangetic Plain Groundwater

Whole-genome sequencing (WGS) data of a bacterial strain IITK SM2 isolated from an aquifer located in the middle Indo-Gangetic plain is reported here, along with its physiological, morphological, biochemical, and redox-transformation characteristics in the presence of dissolved arsenic (As). The aquifer exhibits oxidizing conditions relative to As speciation. Analyses based on 16S rRNA and recN sequences indicate that IITK SM2 was clustered with C. youngae NCTC 13708T and C. pasteuri NCTC UMH17T. However, WGS analyses using the digital DNA-DNA hybridization and Rapid Annotations using Subsystems Technology suggest that IITK SM2 belongs to a strain of C. youngae. This strain can effectively reduce As(V) to As(III) but cannot oxidize As(III) to As(V). It exhibited high resistance to As(V) [32,000 mg L-1] and As(III) [1,100 mg L-1], along with certain other heavy metals typically found in contaminated groundwater. WGS analysis also indicates the presence of As-metabolizing genes such as arsC, arsB, arsA, arsD, arsR, and arsH in this strain. Although these genes have been identified in several As(V)-reducers, the clustering of these genes in the forms of arsACBADR, arsCBRH, and an independent arsC gene has not been observed in any other Citrobacter species or other selected As(V)-reducing strains of Enterobacteriaceae family. Moreover, there were differences in the number of genes corresponding to membrane transporters, virulence and defense, motility, protein metabolism, phages, prophages, and transposable elements in IITK SM2 when compared to other strains. This genomic dataset will facilitate subsequent molecular and biochemical analyses of strain IITK SM2 to identify the reasons for high arsenic resistance in Citrobacter youngae and understand its role in As mobilization in middle Indo-Gangetic plain aquifers.

Geochemical, metagenomic, and physiological characterization of the multifaceted interaction between microbiome of an arsenic contaminated groundwater and aquifer sediment

Geomicrobiological details of the interactions between groundwater microbiome (GWM) and arsenic (As)-rich aquifer sediment of Bengal basin was investigated through microcosm incubations. Role of key microorganisms and their specific interactions with As-bearing minerals was demarcated under organic carbon- amended and -unamended conditions. Acinetobacter (50.8 %), Brevundimonas (7.9 %), Sideroxydans (3.4 %), Alkanindiges (3.0 %) dominated the GWM. The microbiome catalysed considerable alterations in As-bearing mineral [Fe-(hydr)oxide and aluminosilicate] phases resulting in substantial changes in overall geochemistry and release of As (65 μg/L) and Fe (118 μg/L). Synergistic roles of autotrophic, NH₄⁺-oxidizing Archaea (Thaumarchaeota) and chemoheterotrophic bacteria (Stenotrophomonas, Pseudomonas, Geobacter) of diverse metabolic abilities (NH₄⁺-oxidizing, NO₃^-, As/Fe-reducing) were noted for observed changes. Organic carbon supported enhanced microbial growth and As mobilization (upto 403.2 μg As/L) from multiple mineral phases (hematite, magnetite, maghemite, biotite, etc.). In presence of high organic carbon, concerted actions of anaerobic, hydrocarbon-utilizing, As-, Fe-reducing Rhizobium, fermentative Escherichia, anaerobic Bacillales, metal-reducing and organic acid-utilizing Pseudomonas and Achromobacter were implicated in altering sediment mineralogy and biogeochemistry. Increase in abundance of arrA, arsC, bssA genes, and dissolution of Fe, Ca, Mg, Mn confirmed that dissimilatory-, cytosolic-As reduction, and mineral weathering fuelled by anaerobic (hydro)carbon metabolism are the predominant mechanisms of As release in aquifers of Bengal basin.

Citrobacter arsenatis sp. nov., an arsenate-reducing bacterium isolated from freshwater sediment

A novel arsenate-reducing bacterium, LY-1^T, was isolated from freshwater sediment in Huangshi, China. Morphological analysis indicated that the cells were shaped like rods and were gram-negative. The major fatty acids (> 10%) were C_16:0, summed feature 3 (C_16:1 ω7c, C_16:1 ω6c) and summed feature 8 (C_18:1 ω7c, C_18:1 ω6c). An assessment of the phylogeny based on 16S rRNA gene sequences indicated that the strain LY-1^T belonged to the genus Citrobacter, while further analysis based on the recN gene indicated that LY-1^T occupies a distinct phylogenetic niche within the Citrobacter genus. Moreover, average nucleotide identity and digital DNA-DNA hybridization between the strain LY-1^T and the type strains of closely related species of the genus Citrobacter (C. europaeus, C. brakii, C. portucalensis, C. freundii, C. werkmanii, C. cronae, C. youngae, C. pasteurii, C. tructae, C. gillenii, and C. murliniae) were 85.8-93.8% and 31.2-56.9%, respectively. In addition, the LY-1^T strain's capacity to metabolize various compounds and its characteristic G + C content of 51.9% were also distinct from other species of the Citrobacter genus. These discriminatory features cumulatively indicate the LY-1^T strain as a new species within the Citrobacter genus. We propose the species name Citrobacter arsenatis for this new species, with LY-1^T (= CCTCC AB 2019169^T = KCTC 72440^T) as the type strain.

Biofilm for leaching precious metals from waste printed circuit boards using biocyanidation technology

Presently, biocyanidation technology is being usually adopted to recover precious metals from an increasing quantity of waste printed circuit boards. The main aim of this work was to investigate the biofilm formation of Pseudomonas and its ability to leach precious metals. Based on batch experiments, strain 113 showed the highest biofilm-forming activity in optimal culture conditions of pH 7.0, 25 °C, and 1/25 NB medium among the Pseudomonas strains isolated. Both low concentrations of Cu²⁺ (500 ppm) and Ag⁺ (2.5 ppm) promoted biofilm formation. Under the optimal culture conditions for biofilm formation, the concentration of CN^- was up to 5.0 ppm. In the continuous silver leaching experiment, the Ag⁺ concentration reached 4.0 ppm and the leaching efficiency was 14.7 % at 7 d. The results of this study may contribute to the construction of a bioreactor used for continuous leaching of waste printed circuit boards in an attempt to recover precious metals. Our results may also aid in the industrialization of biocyanidation technology.

Biological Reduction of Nitric Oxide for Efficient Recovery of Nitrous Oxide as an Energy Source

Chemical absorption-biological reduction based on Fe(II)EDTA is a promising technology to remove nitric oxide (NO) from flue gases. However, limited effort has been made to enable direct energy recovery from NO through production of nitrous oxide (N₂O) as a potential renewable energy rather than greenhouse gas. In this work, the enhanced energy recovery in the form of N₂O via biological NO reduction was investigated by conducting short-term and long-term experiments at different Fe(II)EDTA-NO and organic carbon levels. The results showed both NO reductase and N₂O reductase were inhibited at Fe(II)EDTA-NO concentration up to 20 mM, with the latter being inhibited more significantly, thus facilitating N₂O accumulation. Furthermore, N₂O accumulation was enhanced under carbon-limiting conditions because of electron competition during short-term experiments. Up to 47.5% of NO-N could be converted to gaseous N₂O-N, representing efficient N₂O recovery. Fe(II)EDTA-NO reduced microbial diversity and altered the community structure toward Fe(II)EDTA-NO-reducing bacteria-dominated culture during long-term experiments. The most abundant bacterial genus Pseudomonas, which was able to resist the toxicity of Fe(II)EDTA-NO, was significantly enriched, with its relative abundance increased from 1.0 to 70.3%, suggesting Pseudomonas could be the typical microbe for the energy recovery technology in NO-based denitrification.

Impact of Organic Matter on Microbially-Mediated Reduction and Mobilization of Arsenic and Iron in Arsenic(V)-Bearing Ferrihydrite

Under anoxic conditions, the interactions between As-bearing ferrihydrite (Fh) and As(V)-reducing bacteria are known to cause Fh transformations and As mobilization. However, the impact of different types of organic matter (OM) on microbial As/Fe transformation in As-bearing Fh-organic associations remains unclear. In our study, we therefore exposed arsenate-adsorbed ferrihydrite, ferrihydrite-PGA (polygalacturonic acid), and ferrihydrite-HA (humic acid) complexes to two typical Fe(III)- and As(V)-reducing bacteria, and followed the fate of Fe and As in the solid and aqueous phases. Results show that PGA and HA promoted the reductive dissolution of Fh, resulting in 0.7-1.6 and 0.8-1.9 times more As release than in the OM-free Fh, respectively. This was achieved by higher cell numbers in the presence of PGA, and through Fe-reduction via electron-shuttling facilitated by HA. Arsenic-XAS results showed that the solid-phase arsenite fraction in Fh-PGA and Fh-HA was 15-19% and 27-28% higher than in pure Fh, respectively. The solid-associated arsenite fraction likely increased because PGA promoted cell growth and As(V) reduction, while HA provided electron shuttling compounds for direct microbial As(V)-reduction. Collectively, our findings demonstrate that As speciation and partitioning during microbial reduction of Fh-organic associations are strongly influenced by PGA and HA, as well as the strains' abilities to utilize electron-shuttling compounds.

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

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

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

Background

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

Results

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

Conclusion

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

The effects of biochar as the electron shuttle on the ferrihydrite reduction and related arsenic (As) fate

The effects of electron shuttles (biochar/anthraquinone-2,6-disulphonate (AQDS)) on the process of the Shewanella oneidensis MR-1-induced As(V)-adsorbed ferrihydrite reduction were studied. The results showed that biochar could stimulate Fe(Ⅱ) and As release during the ferrihydrite bioreduction. After the addition of biochar, more dissolved organic matter (DOM) can be consumed as an electron donor to promote the metabolism of microorganisms by the fluorescence excitation-emission matrix spectra analysis. After microbial treatment, cyclic voltammetry (CV) showed that a unique cathodic peak and a distinct anodic peak appeared, which may represent the reduction of Fe(OH)₃ to Fe(OH)₂ and the complexed oxidation of Fe²⁺ to Fe³⁺. No characteristic peak was associated with arsenate reduction or arsenite oxidation. The mineralogical characterization of the final products indicated that AQDS can promote solid-state conversion from ferrihydrite to vivianite (Fe₃(PO₄)₂·8H₂O). However, the addition of biochar inhibited solid-state conversion of ferrihydrite. It was shown that after 6 d, the secondary mineral vivianite production in the bacteria alone and AQDS treatments was 8.12% and 15.6% respectively by mössbauer spectroscopy analysis. Moreover, the XPS indicated that As(V) has no species transformation. It provided new data for understanding the iron-reducing bacteria induced mineralization process and related biogeochemical cycles of Fe and As.

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

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

Mobilization and transformation of arsenic from ternary complex OM-Fe(III)-As(V) in the presence of As(V)-reducing bacteria

Organic matter (OM) was proved to have a high affinity for arsenic (As) in the presence of ferric iron (Fe(III)), the formed ternary complex OM-Fe(III)-As(V) were frequently studied before; however, the mobilization and transformation of As from OM-Fe(III)-As(V) in the presence of As(V)-reducing bacteria remains unclear. Two different strains (Desulfitobacterium sp. DJ-3, Exiguobacterium sp. DJ-4) were incubated with OM-Fe(III)-As(V) to assess the biotransformation of As and Fe. Results showed that Desulfitobacterium sp. DJ-3 could substantially stimulate the reduction and release of OM-Fe complexed As(V) and resulted in notable As(III) release (30 mg/L). The linear combination fitting result of k³-weighted As K-edge EXAFS spectra showed that 56% of OM-Fe-As(V) was transformed to OM-Fe-As(III) after 144 h. Besides, strain DJ-3 could also reduce OM complexed Fe(III), which lead to the decomposition of ternary complex and the release of 11.8 mg/g Fe(II), this microbial Fe(III) reduction process has resulted in 11% more As liberation from OM-Fe(III)-As(V) than without bacteria. In contrast, Exiguobacterium sp. DJ-4 could only reduce free As(V) but cannot stimulate As release from the complex. Our study provides the first evidence for microbial As reduction and release from ternary complex OM-Fe(III)-As(V), which could be of great importance in As geochemical circulation.

Unique diversity and functions of the arsenic-methylating microorganisms from the tailings of Shimen Realgar Mine

Microbial arsenic (As) methylation plays important roles in the As biogeochemical cycle. However, little is known about the diversity and functions of As-methylating microorganisms from the tailings of a Realgar Mine, which is characterized as containing extremely high concentrations of As. To address this issue, we collected five samples (T1-T5) from the tailings of Shimen Realgar Mine. Microcosm assays without addition of exogenous As and carbon indicated that all the five samples possess significant As-methylating activities, producing 0.8-5.7 μg/L DMAs^V, and 1.1-10.7 μg/L MMAs^V with an exception of T3, from which MMAs^V was not detectable after 14.0 days of incubation. In comparison, addition of 20.0 mM lactate to the microcosms significantly enhanced the activities of these samples; the produced DMAs^V and MMAs^V are 8.0-39.7 μg/L and 5.8-38.3 μg/L, respectively. The biogenic DMAs^V shows significant positive correlations with the Fe concentrations and negative correlations with the total nitrogen concentrations in the environment. A total of 63 different arsM genes were identified from the five samples, which code for new or new-type ArsM proteins, suggesting that a unique diversity of As-methylating microbes are present in the environment. The microbial community structures of the samples were significantly shaped by the environmental total organic carbon, total As contents and NO₃^- contents. These data help to better understand the microorganisms-catalyzed As methylation occurred in the environment with extremely high contents of As.

A review of arsenic interfacial geochemistry in groundwater and the role of organic matter

Recent discoveries on arsenic (As) biogeochemistry in aquifer-sediment system have strongly improved our understanding of As enrichment mechanisms in groundwater. We summarize here the research results since 2015 focusing on the As interfacial geochemistry including As speciation, transformation, and mobilization. We discuss the chemical extraction and speciation of As in environmental matrices, followed by As redox change and (im)mobilization in typical minerals and aquifer system. Then, the microbial-assisted reductive dissolution of Fe (hydr)oxides and As transformation and liberation are summarized from the aspects of bacterial isolates, microbial community and gene analysis by comparing As rich groundwater cases worldwide. Finally, the potential effect of organic matter on As interfacial geochemistry are addressed in the aspects of chemical interactions and microbial respiring activities for Fe and As reductive release.

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.

Inhibitory effect of nitrate/nitrite on the microbial reductive dissolution of arsenic and iron from soils into pore water

It was well established that microbial communities are the major drive for the formation of arsenic-contaminated groundwater. However, it remains to be elucidated for how nitrate/nitrite affects the microorganisms-catalyzed dissolution and reduction of arsenic. To address this issue, we collected soil samples containing high-contents of arsenic from the Shimen Realgar Mine area. Microcosm assay indicated that addition of nitrate/nitrite significantly inhibited the dissolution, reduction and release of As and Fe caused by the biological catalysis of microbial communities in the soils, meanwhile nitrate/nitrite was reduced into N₂. To further investigate the molecular mechanism of this finding, we used a representative dissimilatory arsenate-respiring strain Shewanella sp. GL90 from the soils to perform the arsenic release assay. GL90 can efficiently catalyze the reductive dissolution, and promote the release of As and Fe in soils. It is interesting to see that the addition of nitrate/nitrite to the soils led to marked decreases in the GL90-mediated dissolution of As and Fe in the soils. Moreover, we found that this finding was attributed to that nitrate/nitrite significantly inhibited the transcription of the gene of the respiratory arsenate reductase protein in GL90 cells. This work provided new insights into the mechanisms for the coupling of As, N and Fe geochemical cycles in arsenic-rich soils, and for how environmental factors affect As concentration in groundwater.

The whole genome insight on condition-specific redox activity and arsenopyrite interaction promoting As-mobilization by strain Lysinibacillus sp. B2A1

A gram-positive spore former, Lysinibacillus sp. B2A1 was isolated from a high arsenic containing groundwater of Beimen2A well, Chianan Plain area, Southwestern Taiwan. Noteworthy, in the subsurface-mimicking anoxic incubation with a Na-lactate amendment system, this isolate could interact with arsenic-source mineral arsenopyrite and enhance arsenic mobilization. Further, the isolate showed elevated levels of arsenic resistance, 200 mM and 7.5 mM for arsenate and arsenite, respectively. Lysinibacillus sp. B2A1 demonstrated condition-specific redox activities including salient oxic oxidation of arsenite and anoxic reduction of arsenate. The elevated rate of As(III) oxidation (V_max = 0.13 μM min^-1 per 10⁶ cells, K_m = 15.3 μM) under oxic conditions was potent. Correlating with stout persistence in an arsenic-rich niche, remarkably, the lesser toxic effects of arsenic ions on bacterial sporulation frequency and germination highlight this strain's ability to thrive under catastrophic conditions. Moreover, the whole genome analysis elucidated diverse metal redox/resistance genes that included a potential arsenite S-adenosylmethyltransferase capable of mitigating arsenite toxicity. Owing to its arsenic resistance, conditional redox activities and ability to interact with arsenic minerals leading to arsenic mobilization, the presence of such spore-forming strains could be a decisive indication towards arsenic mobilization in subsurface aquifers having a high concentration of soluble arsenic or its source minerals.

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

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

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

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

Microbially Mediated Methylation of Arsenic in the Arsenic-Rich Soils and Sediments of Jianghan Plain

Almost nothing is known about the activities and diversities of microbial communities involved in As methylation in arsenic-rich shallow and deep sediments; the correlations between As biomethylation and environmental parameters also remain to be elucidated. To address these issues, we collected 9 arsenic-rich soil/sediment samples from the depths of 1, 30, 65, 95, 114, 135, 175, 200, and 223 m in Jianghan Plain, China. We used microcosm assays to determine the As-methylating activities of the microbial communities in the samples. To exclude false negative results, we amended the microcosms with 0.2 mM As(III) and 20.0 mM lactate. The results indicated that the microbial communities in all of the samples significantly catalyzed arsenic methylation. The arsM genes were detectable from all the samples with the exception of 175 m, and 90 different arsM genes were identified. All of these genes code for new or new-type ArsM proteins, suggesting that new As-methylating microorganisms are widely distributed in the samples from shallow to deep sediments. To determine whether microbial biomethylation of As occurs in the sediments under natural geochemical conditions, we conducted microcosm assays without exogenous As and carbons. After 80.0 days of incubation, approximately 4.5–15.5 μg/L DMAs^V were detected in all of the microcosms with the exception of that from 30 m, and 2.0–9.0 μg/L MMAs^V were detected in the microcosms of 65, 114, 135, 175, 200, and 223 m; moreover, approximately 18.7–151.5 μg/L soluble As(V) were detected from the nine sediment samples. This suggests that approximately 5.3, 0, 8.1, 28.9, 18.0, 8.7, 13.8, 10.2, and 14.9% of total dissolved As were methylated by the microbial communities in the sediment samples from 1, 30, 65, 95, 114, 135, 175, 200, and 223 m, respectively. The concentrations of biogenic DMAs^V show significant positive correlations with the depths of sediments, and negative correlations with the environmental NH₄⁺ and NaCl concentrations, but show no significant correlations with other environmental parameters, such as NO₃^-, SO₄²⁺, TOC, TON, Fe, Sb, Cu, K, Ca, Mg, Mn, and Al. This work helps to better understand the biogeochemical cycles of arsenic in arsenic-rich shallow and deep sediments.

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

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

Microbial Community Structure and Arsenic Biogeochemistry in Two Arsenic-Impacted Aquifers in Bangladesh

Long-term exposure to trace levels of arsenic (As) in shallow groundwater used for drinking and irrigation puts millions of people at risk of chronic disease. Although microbial processes are implicated in mobilizing arsenic from aquifer sediments into groundwater, the precise mechanism remains ambiguous. The goal of this work was to target, for the first time, a comprehensive suite of state-of-the-art molecular techniques in order to better constrain the relationship between indigenous microbial communities and the iron and arsenic mineral phases present in sediments at two well-characterized arsenic-impacted aquifers in Bangladesh. At both sites, arsenate [As(V)] was the major species of As present in sediments at depths with low aqueous As concentrations, while most sediment As was arsenite [As(III)] at depths with elevated aqueous As concentrations. This is consistent with a role for the microbial As(V) reduction in mobilizing arsenic. 16S rRNA gene analysis indicates that the arsenic-rich sediments were colonized by diverse bacterial communities implicated in both dissimilatory Fe(III) and As(V) reduction, while the correlation analyses involved phylogenetic groups not normally associated with As mobilization. Findings suggest that direct As redox transformations are central to arsenic fate and transport and that there is a residual reactive pool of both As(V) and Fe(III) in deeper sediments that could be released by microbial respiration in response to hydrologic perturbation, such as increased groundwater pumping that introduces reactive organic carbon to depth.IMPORTANCE The consumption of arsenic in waters collected from tube wells threatens the lives of millions worldwide and is particularly acute in the floodplains and deltas of southern Asia. The cause of arsenic mobilization from natural sediments within these aquifers to groundwater is complex, with recent studies suggesting that sediment-dwelling microorganisms may be the cause. In the absence of oxygen at depth, specialist bacteria are thought able to use metals within the sediments to support their metabolism. Via these processes, arsenic-contaminated iron minerals are transformed, resulting in the release of arsenic into the aquifer waters. Focusing on a field site in Bangladesh, a comprehensive, multidisciplinary study using state-of-the-art geological and microbiological techniques has helped better understand the microbes that are present naturally in a high-arsenic aquifer and how they may transform the chemistry of the sediment to potentially lethal effect.

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.

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.

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.

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

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

IMPORTANCE

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

Genetic identification of arsenate reductase and arsenite oxidase in redox transformations carried out by arsenic metabolising prokaryotes - A comprehensive review

Arsenic (As) contamination in water is a cause of major concern to human population worldwide, especially in Bangladesh and West Bengal, India. Arsenite (As(III)) and arsenate (As(V)) are the two common forms in which arsenic exists in soil and groundwater, the former being more mobile and toxic. A large number of arsenic metabolising microorganisms play a crucial role in microbial transformation of arsenic between its different states, thus playing a key role in remediation of arsenic contaminated water. This review focuses on advances in biochemical, molecular and genomic developments in the field of arsenic metabolising bacteria - covering recent developments in the understanding of structure of arsenate reductase and arsenite oxidase enzymes, their gene and operon structures and their mechanism of action. The genetic and molecular studies of these microbes and their proteins may lead to evolution of successful strategies for effective implementation of bioremediation programs.

Comparison of arsenate reduction and release by three As(V)-reducing bacteria isolated from arsenic-contaminated soil of Inner Mongolia, China

Arsenic (As) contamination has become a worldwide environmental problem: arsenite (As(Ⅲ)) especially has posed a major threat to human health. Here, we report the first three isolates of anaerobic As(Ⅴ)-reducing bacterial strains (strains JQ, DJ-3 and DJ-4) from a soil sample containing 48.7% of total As in the form of As(III) collected in Chifeng, Inner Mongolia, China. Strains JQ, DJ-3 and DJ-4 were phylogenetically closely related to Bacillus, Desulfitobacterium and Exiguobacterium, respectively. Among these strains, JQ and DJ-3 have the arsC gene, DJ-4 possesses the arrA gene. The three strains could all resist and reduce high concentrations of As(Ⅴ) under anoxic conditions. The order of resistance to As(Ⅴ) was DJ-3 > JQ > DJ-4. Strain DJ-3 not only possesses the strongest resistance to As(Ⅴ) but could also reduce 53% of the As(Ⅴ) to As(III) in the treatment of 60 mM As(Ⅴ) in 5 d. All three strains could release As from goethite; strain DJ-4 has the highest ability to promote the release of As (90.5%) from goethite. These results suggested that strains JQ, DJ-3 and DJ-4 may play an important role in the mobilization and transformation of As in soil.

An arsenate-reducing and alkane-metabolizing novel bacterium, Rhizobium arsenicireducens sp. nov., isolated from arsenic-rich groundwater

A novel arsenic (As)-resistant, arsenate-respiring, alkane-metabolizing bacterium KAs 5-22^T, isolated from As-rich groundwater of West Bengal was characterized by physiological and genomic properties. Cells of strain KAs 5-22^T were Gram-stain-negative, rod-shaped, motile, and facultative anaerobic. Growth occurred at optimum of pH 6.0-7.0, temperature 30 °C. 16S rRNA gene affiliated the strain KAs 5-22^T to the genus Rhizobium showing maximum similarity (98.4 %) with the type strain of Rhizobium naphthalenivorans TSY03b^T followed by (98.0 % similarity) Rhizobium selenitireducens B1^T. The genomic G + C content was 59.4 mol%, and DNA-DNA relatedness with its closest phylogenetic neighbors was 50.2 %. Chemotaxonomy indicated UQ-10 as the major quinone; phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as major polar lipids; C_16:0, C_17:0, 2-OH C_10:0, 3-OH C_16:0, and unresolved C_18:1 ɷ7C/ɷ9C as predominant fatty acids. The cells were found to reduce O₂, As⁵⁺, NO₃^-, SO₄^2- and Fe³⁺ as alternate electron acceptors. The strain's ability to metabolize dodecane or other alkanes as sole carbon source using As⁵⁺ as terminal electron acceptor was supported by the presence of genes encoding benzyl succinate synthase (bssA like) and molybdopterin-binding site (mopB) of As⁵⁺ respiratory reductase (arrA). Differential phenotypic, chemotaxonomic, genotypic as well as physiological properties revealed that the strain KAs 5-22^T is separated from its nearest recognized Rhizobium species. On the basis of the data presented, strain KAs 5-22^T is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium arsenicireducens sp. nov. is proposed as type strain (=LMG 28795^T=MTCC 12115^T).

Isolation and Genomic Characterization of 'Desulfuromonas soudanensis WTL', a Metal- and Electrode-Respiring Bacterium from Anoxic Deep Subsurface Brine

Reaching a depth of 713 m below the surface, the Soudan Underground Iron Mine (Soudan, MN, USA) transects a massive Archaean (2.7 Ga) banded iron formation, providing a remarkably accessible window into the terrestrial deep biosphere. Despite organic carbon limitation, metal-reducing microbial communities are present in potentially ancient anoxic brines continuously emanating from exploratory boreholes on Level 27. Using graphite electrodes deposited in situ as bait, we electrochemically enriched and isolated a novel halophilic iron-reducing Deltaproteobacterium, ‘Desulfuromonas soudanensis’ strain WTL, from an acetate-fed three-electrode bioreactor poised at +0.24 V (vs. standard hydrogen electrode). Cyclic voltammetry revealed that ‘D. soudanensis’ releases electrons at redox potentials approximately 100 mV more positive than the model freshwater surface isolate Geobacter sulfurreducens, suggesting that its extracellular respiration is tuned for higher potential electron acceptors. ‘D. soudanensis’ contains a 3,958,620-bp circular genome, assembled to completion using single-molecule real-time (SMRT) sequencing reads, which encodes a complete TCA cycle, 38 putative multiheme c-type cytochromes, one of which contains 69 heme-binding motifs, and a LuxI/LuxR quorum sensing cassette that produces an unidentified N-acyl homoserine lactone. Another cytochrome is predicted to lie within a putative prophage, suggesting that horizontal gene transfer plays a role in respiratory flexibility among metal reducers. Isolation of ‘D. soudanensis’ underscores the utility of electrode-based approaches for enriching rare metal reducers from a wide range of habitats.

Mechanisms of Bacterial Extracellular Electron Exchange

The biochemical mechanisms by which microbes interact with extracellular soluble metal ions and insoluble redox-active minerals have been the focus of intense research over the last three decades. The process presents two challenges to the microorganism. Firstly, electrons have to be transported at the cell surface, which in Gram-negative bacteria presents an additional problem of electron transfer across the ~6nm of the outer membrane. Secondly, the electrons must be transferred to or from the terminal electron acceptors or donors. This review covers the known mechanisms that bacteria use to transport electrons across the cell envelope to external electron donors/acceptors. In Gram-negative bacteria, electron transfer across the outer membrane involves the use of an outer membrane β-barrel and cytochrome. These can be in the form of a porin-cytochrome protein, such as Cyc2 of Acidithiobacillus ferrooxidans, or a multiprotein porin-cytochrome complex like MtrCAB of Shewanella oneidensis MR-1. For mineral-respiring organisms, there is the additional challenge of transferring the electrons from the cell to mineral surface. For the strict anaerobe Geobacter sulfurreducens this requires electron transfer through conductive pili to associated cytochrome OmcS that directly reduces Fe(III)oxides, while the facultative anaerobe S. oneidensis MR-1 accomplishes mineral reduction through direct membrane contact, contact through filamentous extensions and soluble flavin shuttles, all of which require the outer membrane cytochromes MtrC and OmcA in addition to secreted flavin.