Diversity of arsenite oxidizing bacterial communities in arsenic-rich deltaic aquifers in West Bengal, India

Bacteria associated with Comamonadaceae are key arsenite oxidizer associated with Pteris vittata root

Pteris vittata (P. vittata), an arsenic (As) hyperaccumulator commonly used in the phytoremediation of As-contaminated soils, contains root-associated bacteria (RAB) including those that colonize the root rhizosphere and endosphere, which can adapt to As contamination and improve plant health. As(III)-oxidizing RAB can convert the more toxic arsenite (As(III)) to less toxic arsenate (As(V)) under As-rich conditions, which may promote plant survial. Previous studies have shown that microbial As(III) oxidation occurs in the rhizospheres and endospheres of P. vittata. However, knowledge of RAB of P. vittata responsible for As(III) oxidation remained limited. In this study, members of the Comamonadaceae family were identified as putative As(III) oxidizers, and the core microbiome associated with P. vittata roots using DNA-stable isotope probing (SIP), amplicon sequencing and metagenomic analysis. Metagenomic binning revealed that metagenome assembled genomes (MAGs) associated with Comamonadaceae contained several functional genes related to carbon fixation, arsenic resistance, plant growth promotion and bacterial colonization. As(III) oxidation and plant growth promotion may be key features of RAB in promoting P. vittata growth. These results extend the current knowledge of the diversity of As(III)-oxidizing RAB and provide new insights into improving the efficiency of arsenic phytoremediation.

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.

The role of the core microorganisms in the microbial interactions in activated sludge

In order to gain a deeper understanding of the microbial interactions in wastewater treatment plants (WWTPs) in China and clarify the role of the core community in the microbial interactions in activated sludge (AS), this study used a molecular ecological network approach based on random matrix theory to construct co-occurrence networks of the core microorganisms (CoreN), the whole AS community (WholeN) and the microbial communities without the core microorganisms (OtherN), respectively. It was shown that the WholeN had more complex and tighter connections compared with the OtherN, because of its higher total number of nodes, higher average clustering coefficient, and shorter average geodesic distance. The proportions of positive links in the CoreN, WholeN and OtherN were gradually decreased, indicating that the core microorganisms promoted cooperation between AS microorganisms. Moreover, higher robustness after random removal of 50% of the nodes of the WholeN (0.2836 ± 0.0311) was observed than the robustness of the OtherN (0.1152 ± 0.0263). In addition, the vulnerability of OtherN (0.0514) is significantly higher than WholeN (0.0225). Meanwhile, the average ratio of negative/positive cohesion, was significantly decreased when the core microorganisms were removed. These results demonstrated that core community could strengthen the stability of the ecological network in AS. By discerning the key factors affecting ecological network, AS temperature was observed to have a strong correlation with all three networks. Moreover, pollutants in wastewater shown stronger correlations with the CoreN and WholeN, supporting the point that core community play a critical role in pollutant removal in WWTPs to a certain extent.

Biofilm-Mediated Heavy Metal Removal from Aqueous System by Multi-Metal-Resistant Bacterial Strain Bacillus sp. GH-s29

Worldwide ever-augmenting urbanization, modernization, and industrialization have contributed to the release of pernicious compounds and a variety of pollutants into the environment. The pollutants discharged due to industrialization are of global concern. Industrial waste and effluent are comprised of hazardous organic and inorganic chemicals including heavy metals which pose a significant threat to the environment and may bring about numerous diseases or abnormalities in human beings. This brings on greater urgency for remediation of these polluted soil and water using sustainable approaches and mechanisms. In the present research, a multi-metal-resistant, gram-positive, non-virulent bacterial strain Bacillus sp. GH-s29 was isolated from contaminated groundwater of Bhojpur district, Bihar, India. The strain had the potential to develop a biofilm that was able to remediate different heavy metals [arsenic, cadmium, and chromium] from individual and multi-heavy metal solutions. Maximum removal for As (V), Cd (II), and Cr (VI) from individual-metal and the multi-metal solution was observed to be 73.65%, 57.37%, 61.62%, and 48.92%, 28.7%, and 35.46%, respectively. SEM-EDX analysis revealed the sequestration of multi-heavy metals by bacterial biofilm. Further characterization by FTIR analysis ensured that the presence of negatively charged functional groups on the biofilm-EPS such as hydroxyl, phosphate, sulfate, and carboxyl helps in binding to the positively charged metal ions. Thus, Bacillus sp. GH-s29 proved to be an effective and economical alternative for different heavy metal remediation from contaminated sites.

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

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

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.

Anoxic storage to promote arsenic removal with groundwater-native iron

Storage containers are usually used to provide a constant water head in decentralized, community groundwater treatment systems for the removal of iron (Fe) and arsenic (As). However, the commonly practiced aeration prior to storage assists in rapid and complete Fe²⁺ oxidation, resulting in poor As removal, despite sufficient native-Fe²⁺ in the source water. In this study, it was found that application of anoxic storage enhanced As removal from groundwater, containing ≥300 µg/L of As(III) and 2.33 mg/L of Fe²⁺ in an As affected village of Rajshahi district in Bangladesh. Although the oxidation of Fe²⁺ and As(III) during oxic storage was considerably faster, the As/Fe removal ratio was higher during anoxic storage (61-80±5 µgAs/mgFe) compared to the oxic storage (45±5 µgAs/mgFe). This higher As removal efficacy in anoxic storage containers could not be attributed to the speciation of As, since As(V) concentrations were higher during oxic storage due to more favorable abiotic (As(III) oxidation by O₂ and Fenton-like intermediates) and biotic (As(III) oxidizing bacteria, e.g., Sideroxydans, Gallionella, Hydrogenophaga) conditions. The continuous, in-situ hydrous ferric oxide floc formation during flow-through operation, and the favorable lower pH aiding higher sorption capacities for the gradually formed As(V) likely contributed to the improved performance in the anoxic storage containers.

Variable response of arsenic contaminated groundwater microbial community to electron acceptor regime revealed by microcosm based high-throughput sequencing approach

Arsenic (As) mobilization in alluvial aquifers is facilitated by microbially catalyzed redox transformations that depend on the availability of electron acceptors (EAs). In this study, the response of an As-contaminated groundwater microbial community from West Bengal, India towards varied EAs was elucidated through microcosm based 16S rRNA gene amplicon sequencing. Acinetobacter, Deinococcus, Nocardioides, etc., and several unclassified bacteria (Ignavibacteria) and archaea (Bathyarchaeia, Micrarchaeia) previously not reported from As-contaminated groundwater of West Bengal, characterized the groundwater community. Distinct shifts in community composition were observed in response to various EAs. Enrichment of operational taxonomic units (OTUs) affiliated to Denitratisoma (NO₃-), Spirochaetaceae (Mn⁴⁺), Deinococcus (As⁵⁺), Ruminiclostridium (Fe³⁺), Macellibacteroides (SO₄²-), Holophagae-Subgroup 7 (HCO₃-), Dechloromonas and Geobacter (EA mixture) was noted. Alternatively, As³⁺ amendment as electron donor allowed predominance of Rhizobium. Taxonomy based functional profiling highlighted the role of chemoorganoheterotrophs capable of concurrent reduction of NO₃-, Fe³⁺, SO₄²-, and As biotransformation in As-contaminated groundwater of West Bengal. Our analysis revealed two major aspects of the community, (a) taxa selective toward responding to the EAs, and (b) multifaceted nature of taxa appearing in abundance in response to multiple substrates. Thus, the results emphasized the potential of microbial community members to influence the biogeochemical cycling of As and other dominant anions/cations.

Periphyton enhances arsenic release and methylation at the soil-water interface of paddy soils

Periphyton is ubiquitous in rice paddy fields, however its role in paddy soil arsenic (As) biogeochemistry remains unexplored. In this study, microcosm incubations and extensive field sampling were used to better understand the roles of periphyton on As mobility and transformation at the soil-water interface. Microcosm incubations revealed that periphyton on the paddy soil surface enhanced As release to water and increased methylated As contents at the soil-water interface. Experimental additions of dissolved phosphate did not significantly affect these processes. The presence of periphyton increased the dissolved organic carbon (DOC) content of the surface soil which may have played a role in the increased As mobility. However, the increase in methylated As species at the soil-water interface is indicative of detoxification processes of As by periphyton. The results from the field study revealed a high abundance and diversity of As biotransformation and detoxification genes in periphyton. Genera of Kineosporia, Limisphaera, Ornatilinea, Ktedonosporobacter and Anaerolinea played key roles in shaping arsM harboring microbe communities in field periphyton. These results highlight the importance of periphyton in the behavior of As in paddy soils and can potentially facilitate improved management of As contamination in paddy soils.

Bacteria responsible for antimonite oxidation in antimony-contaminated soil revealed by DNA-SIP coupled to metagenomics

Antimony (Sb), the analog of arsenic (As), is a toxic metalloid that poses risks to the environment and human health. Antimonite (Sb(III)) oxidation can decrease Sb toxicity, which contributes to the bioremediation of Sb contamination. Bacteria can oxidize Sb(III), but the current knowledge regarding Sb(III)-oxidizing bacteria (SbOB) is limited to pure culture studies, thus underestimating the diversity of SbOB. In this study, Sb(III)-oxidizing microcosms were set up using Sb-contaminated rice paddies as inocula. Sb(III) oxidation driven by microorganisms was observed in the microcosms. The increasing copies and transcription of the arsenate-oxidizing gene, aioA, in the microcosms during biotic Sb(III) oxidation indicated that microorganisms mediated Sb(III) oxidation via the aioA genes. Furthermore, a novel combination of DNA-SIP and shotgun metagenomic was applied to identify the SbOB and predict their metabolic potential. Several putative SbOB were identified, including Paracoccus, Rhizobium, Achromobacter and Hydrogenophaga. Furthermore, the metagenomic analysis indicated that all of these putative SbOB contained aioA genes, confirming their roles in Sb(III) oxidation. These results suggested the concept of proof of combining DNA-SIP and shotgun metagenomics directly. In addition, the identification of the novel putative SbOB expands the current knowledge regarding the diversity of SbOB.

Effects of Arsenic and Iron on the Community and Abundance of Arsenite-Oxidizing Bacteria in an Arsenic-Affected Groundwater Aquifer

Arsenic (As) contamination of groundwater aquifers is a global environmental problem, especially in South and Southeast Asian regions, and poses a risk to human health. Arsenite-oxidizing bacteria that transform As(III) to less toxic As(V) can be potentially used as a groundwater As remediation strategy. This study aimed to examine the community and abundance of arsenite-oxidizing bacteria in groundwater with various As concentrations from Rayong Province, Thailand using PCR-cloning-sequencing and quantitative PCR (qPCR) of catalytic subunit of arsenite oxidase gene (aioA). Key factors influencing their community and abundance were also identified. The results demonstrated that arsenite-oxidizing bacteria retrieved from groundwater were phylogenetically related to Betaproteobacteria and Alphaproteobacteria. The aioA gene abundances ranged from 8.6 × 10¹ to 1.1 × 10⁴ copies per ng of genomic DNA, accounting for 0.16-1.37% of the total 16S rRNA bacterial gene copies. Although the abundance of arsenite-oxidizing bacteria in groundwater was low, groundwater with As(III) dominance likely promoted their abundance which possibly played an important role in chemolithoautotrophic oxidation of As(III) to As(V). Fe and As(III) were the major environmental factors influencing the community and abundance of arsenite-oxidizing bacteria. The knowledge gained from this study can be used to further contribute to the development of bioremediation strategies for As removal from groundwater resources.

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

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

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.

Diversity of Betaproteobacteria revealed by novel primers suggests their role in arsenic cycling

High arsenic concentration in groundwater is a severe environmental problem affecting human health, particularly in countries of South and South-East Asia. The Bengal Delta Plain (BDP) distributed within India and Bangladesh is a major arsenic-affected region where groundwater is the primary source of drinking water. Previous studies have indicated that members of the bacterial class Betaproteobacteria constitute a major fraction of the microbial community in many of the aquifers within this region. Bacteria belonging to this class are known to be involved in redox cycling of arsenic as well as other metals such iron and manganese, thereby impacting arsenic mobilization and immobilization. While microbial diversity in arsenic-contaminated environments is generally assessed using universal 16S rRNA gene primers, targeted evaluation of Betaproteobacteria diversity remains poorly constrained. In this study, bacterial diversity was investigated in the groundwater from two shallow aquifers (West Bengal, India) based on 16S rRNA gene clone libraries and sequencing using a custom-designed pair of primers specific to Betaproteobacteria. Specificity of the primers was confirmed in silico as well as by the absence of PCR amplification of other bacterial classes. Four major families (Burkholderiaceae, Comamonadaceae, Gallionellaceae and Rhodocyclaceae) were detected among which members of Burkholderiaceae represented 59% and 71% of the total community in each aquifer. The four OTUs (operational taxonomic units; 97% sequence identity) within Burkholderiaceae were close phylogenetic relatives of bacteria within the genus Burkholderia known to solubilize phosphate minerals. Additionally, the OTUs belonging to Gallionellaceae were closely related to the members of the genera Gallionella and Sideroxydans, known to oxidize iron under microaerophilic conditions. These results suggest that members of Betaproteobacteria can potentially influence iron and phosphorus cycling which can influence biogeochemistry in arsenic-contaminated aquifers of the BDP.

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

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

Enrichment of indigenous arsenate reducing anaerobic bacteria from arsenic rich aquifer sediment of Brahmaputra river basin and their potential role in as mobilization

Anaerobic enrichment of As⁵⁺ reducing bacteria in the presence and/or absence of organic carbon (OC) and As⁵⁺ from As contaminated soil of Brahmaputra river basin (BRB) (Jorhat, Assam) was performed. Denaturing gradient gel electrophoresis of the 16SrRNA gene sequences amplified from the enriched microbial community indicated occurrence of maximum diversity under conditions receiving no OC (MSM) followed by moderate OC (LB). However, higher OC or As showed antagonistic effect on bacterial enrichment whereas together (BB + As) they showed a synergistic effect. Phylogenetic analysis of the prominent bands revealed an overall abundance of Lachnoanaerobaculum (39%), Clostridium (39%), Bacillus, Peptostreptococcaceae, Anaerostipes (13%), and Desulfotomaculum (8.7%). Moderate OC (LB) led to maximum As mobilization i.e. 27.42 µg/L, whereas presence of added As together with high OC (BB + As) enhanced the mobilization process. Mineralogical analyses of the sediments after incubation showed prominent weathering and loss of crystallinity in MSM and LB. Appearance of a new peak corresponding to arsenolamprite (As) in LB and LB + As indicated opening up of secondary phases of the minerals harboring As due to microbial leaching under moderate OC. This is the first study reporting Lachnoanaerobaculumas a potent As⁵⁺ dissimilating bacterium isolated from As contaminated subsurface sediment of BRB.

K. S, Ghosh D. Arsenic Exposures, Poisoning, and Threat to Human Health

Arsenic (As) is a naturally occurring metalloid which induces high toxicity to both human and animal health. Although As has some applications in industrial, medicinal and agricultural fields, the increasing concentrations of As in drinking water sources had made it a potential threat to living organisms. Inorganic As is naturally present in groundwater and is adsorbed by plants and crops through the irrigation system. This leads to its accumulation in crops and translocation to humans and animals through food. Increased levels of As can cause various health disorders through acute and chronic exposures such as gastrointestinal, hepatic, respiratory, cardiovascular, integumentary, renal, neurological, and reproductive disorders including stillbirth and infant mortality. Arsenic is also capable of inducing epigenetic changes, thereby causing gene mutations. This chapter focuses on the possible sources of As, leading to environmental contamination and followed by its hazardous effects which pave the way to various human health manifestations.

Effects of arsenic on the biofilm formations of arsenite-oxidizing bacteria

Arsenite-oxidizing bacteria (AOB) play a key role in the biogeochemical cycle of arsenic in the environment, and are used for the bioremediation of As contaminated groundwater; however, it is not yet known about how arsenic affects biofilm formations of AOB, and how biofilm formations affect bacterial arsenite-oxidizing activities. To address these issues, we isolated seven novel AOB strains from the arsenic-contaminated soils. They can completely oxidize 1.0 mM As(III) in 22-60 h. Their arsenite oxidase sequences show 43-99% identities to those of other known AOB. Strains Cug1, Cug2, Cug3, Cug4, and Cug6 are able to form biofilms with thickness of 15-95 µm, whereas Cug8 and Cug9 cannot form biofilms. It is interesting to see that arsenite inhibited the biofilm formations of heterotrophic AOB strains, but promoted the biofilm formations of autotrophic strains in a concentration-dependent manner. The arsenite-oxidizing rates of Cug1 and Cug4 biofilms are 31.6% and 27.6% lower than those of their suspension cultures, whereas the biofilm activities of other strains are similar to those of their suspension cultures. The biofilm formation significantly promoted the bacterial resistance to arsenic. This work is the first report on the complex correlations among environmental arsenic, bacterial biofilm formations and bacterial arsenite-oxidizing activities. The data highlight the diverse lifestyle of different AOB under arsenic stress, and provide essential knowledge for the screening of efficient AOB strains used for constructions of bioreactors.

Arsenite biotransformation and bioaccumulation by Klebsiella pneumoniae strain SSSW7 possessing arsenite oxidase (aioA) gene

Arsenite oxidizing Klebsiella pneumoniae strain SSSW7 isolated from shipyard waste Goa, India showed a minimum inhibitory concentration of 21 mM in mineral salts medium. The strain possessed a small supercoiled plasmid and PCR amplification of arsenite oxidase gene (aioA) was observed on plasmid as well as chromosomal DNA. It was confirmed that arsenite oxidase enzyme was a periplasmic protein with a 47% increase in arsenite oxidase activity at 1 mM sodium arsenite. Scanning electron microscopy coupled with electron dispersive X-ray spectroscopic (SEM-EDS) analysis of 15 mM arsenite exposed cells revealed long chains of cells with no surface adsorption of arsenic. Transmission electron microscopy combined with electron dispersive X-ray spectroscopic (TEM-EDS) analysis demonstrated plasma membrane disruption, cytoplasmic condensation and periplasmic accumulation of arsenic. The bacterial strain oxidized 10 mM of highly toxic arsenite to less toxic arsenate after 24 h of incubation. Fourier transformed infrared (FTIR) spectroscopy confirmed the interaction of arsenite with functional groups present on the bacterial cell surface. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of 5 mM arsenite exposed cells demonstrated over-expression of 87 kDa and 14 kDa proteins of two subunits aioA and aioB of heterodimer arsenite oxidase enzyme as compared to control cells. Therefore, this bacterial strain might be employed as a potential candidate for bioremediation of arsenite contaminated environmental sites.

Coping with arsenic stress: Adaptations of arsenite-oxidizing bacterial membrane lipids to increasing arsenic levels

Elevated levels of arsenic (As) in aquifers of South East Asia have caused diverse health problems affecting millions of people who drink As-rich groundwater and consume various contaminated agriculture products. The biogeochemical cycling and mobilization/immobilization of As from its mineral-bound phase is controlled by pH, oxic/anoxic conditions, and different microbial processes. The increased As flux generated from ongoing biogeochemical processes in the subsurface in turn affects the in situ microbial communities. This study analyzes how the indigenous arsenite-oxidizing bacteria combat As stress by various biophysical alterations and self-adaptation mechanisms. Fifteen arsenite-oxidizing bacterial strains were isolated and identified using a polyphasic approach. The bacterial strains isolated from these aquifers belong predominantly to arsenite-oxidizing bacterial groups. Of these, the membrane-bound phospholipid fatty acids (PLFA) were characterized in seven selected bacterial isolates grown at different concentrations of As(III) in the medium. One of the significant findings of this study is how the increase in external stress can induce alteration of membrane PLFAs. The change in fatty acid saturation and alteration of their steric conformation suggests alteration of membrane fluidity due to change in As-related stress. However, different bacterial groups can have different degrees of alteration that can affect sustainability in As-rich aquifers of the Bengal Delta Plain.

Exposure to Arsenic Alters the Microbiome of Larval Zebrafish

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

Rethinking anaerobic As(III) oxidation in filters: Effect of indigenous nitrate respirers

Microorganisms play a key role in the redox transformation of arsenic (As) in aquifers. In this study, the impact of indigenous bacteria, especially the prevailing nitrate respirers, on arsenite (As(III)) oxidation was explored during groundwater filtration using granular TiO₂ and subsequent spent TiO₂ anaerobic landfill. X-ray absorption near edge structure spectroscopy analysis showed As(III) oxidation (46% in 10 days) in the presence of nitrate in the simulated anaerobic landfills. Meanwhile, iron (Fe) species on the spent TiO₂ were dominated by amorphous ferric arsenate, ferrihydrite and goethite. The Fe phase showed no change during the anaerobic landfill incubation. Batch incubation experiments implied that the indigenous bacteria completely oxidized As(III) to arsenate (As(V)) in 10 days using nitrate as the terminal electron acceptor under anaerobic conditions. The bacterial community analysis indicated that various kinds of microbial species exist in groundwater matrix. Phylogenetic tree analysis revealed that Proteobacteria was the dominant phylum, with Hydrogenophaga (34%), Limnohabitans (16%), and Simplicispira (7%) as the major bacterial genera. The nitrate respirers especially from the Hydrogenophaga genus anaerobically oxidized As(III) using nitrate as an electron acceptor instead of oxygen. Our study implied that microbes can facilitate the groundwater As oxidation using nitrate on the adsorptive media.

Anaerobic oxidation of methane by aerobic methanotrophs in sub-Arctic lake sediments

Anaerobic oxidation of methane (AOM) is a biological process that plays an important role in reducing the CH₄ emissions from a wide range of ecosystems. Arctic and sub-Arctic lakes are recognized as significant contributors to global methane (CH₄) emission, since CH₄ production is increasing as permafrost thaws and provides fuels for methanogenesis. Methanotrophy, including AOM, is critical to reducing CH₄ emissions. The identity, activity, and metabolic processes of anaerobic methane oxidizers are poorly understood, yet this information is critical to understanding CH₄ cycling and ultimately to predicting future CH₄ emissions. This study sought to identify the microorganisms involved in AOM in sub-Arctic lake sediments using DNA- and phospholipid-fatty acid (PLFA)- based stable isotope probing. Results indicated that aerobic methanotrophs belonging to the genus Methylobacter assimilate carbon from CH₄, either directly or indirectly. Other organisms that were found, in minor proportions, to assimilate CH₄-derived carbon were methylotrophs and iron reducers, which might indicate the flow of CH₄-derived carbon from anaerobic methanotrophs into the broader microbial community. While various other taxa have been reported in the literature to anaerobically oxidize methane in various environments (e.g. ANME-type archaea and Methylomirabilis Oxyfera), this report directly suggest that Methylobacter can perform this function, expanding our understanding of CH₄ oxidation in anaerobic lake sediments.

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.

Molecular Study of Indigenous Bacterial Community Composition on Exposure to Soil Arsenic Concentration Gradient

Community structure of bacteria present in arsenic contaminated agricultural soil was studied with qPCR (quantitative PCR) and DGGE (Denaturing Gradient Gel Electrophoresis) as an indicator of extreme stresses. Copy number of six common bacterial taxa (Acidobacteria, Actinobacteria, α-, β- and γ-Proteobacteria, Firmicutes) was calculated using group specific primers of 16S rDNA. It revealed that soil contaminated with low concentration of arsenic was dominated by both Actinobacteria and Proteobacteria but a shift towards Proteobacteria was observed with increasing arsenic concentration, and number of Actinobacteria eventually decreases. PCA (Principle Component Analysis) plot of bacterial community composition indicated a distinct resemblance among high arsenic content samples, while low arsenic content samples remained separated from others. Cluster analysis of soil parameters identifies three clusters, each of them was related to the arsenic content. Further, cluster analysis of 16S rDNA based DGGE fingerprint markedly distributed the soil bacterial populations into low (< 10 ppm) and high (> 10 ppm) arsenic content subgroups. Following analysis of diversity indices shows significant variation in bacterial community structure. MDS (Multi Dimensional Scaling) plot revealed distinction in the distribution of each sample denoting variation in bacterial diversity. Phylogenetic sequence analysis of fragments excised from DGGE gel revealed the presence of γ-Proteobacteria group across the study sites. Collectively, our experiments indicated that gradient of arsenic contamination affected the shape of the soil bacterial population by significant structural shift.

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

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

Comparative Genomic Analysis Reveals Organization, Function and Evolution of ars Genes in Pantoea spp

Numerous genes are involved in various strategies to resist toxic arsenic (As). However, the As resistance strategy in genus Pantoea is poorly understood. In this study, a comparative genome analysis of 23 Pantoea genomes was conducted. Two vertical genetic arsC-like genes without any contribution to As resistance were found to exist in the 23 Pantoea strains. Besides the two arsC-like genes, As resistance gene clusters arsRBC or arsRBCH were found in 15 Pantoea genomes. These ars clusters were found to be acquired by horizontal gene transfer (HGT) from sources related to Franconibacter helveticus, Serratia marcescens, and Citrobacter freundii. During the history of evolution, the ars clusters were acquired more than once in some species, and were lost in some strains, producing strains without As resistance capability. This study revealed the organization, distribution and the complex evolutionary history of As resistance genes in Pantoea spp.. The insights gained in this study improved our understanding on the As resistance strategy of Pantoea spp. and its roles in the biogeochemical cycling of As.

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

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

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

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

IMPORTANCE

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

Profiling microbial community in a watershed heavily contaminated by an active antimony (Sb) mine in Southwest China

Located in Southwest China, the Chahe watershed has been severely contaminated by upstream active antimony (Sb) mines. The extremely high concentrations of Sb make the Chahe watershed an excellent model to elucidate the response of indigenous microbial activities within a severe Sb-contaminated environment. In this study, water and surface sediments from six locations in the Chahe watershed with different levels of Sb contamination were analyzed. Illumina sequencing of 16S rRNA amplicons revealed more than 40 phyla from the domain Bacteria and 2 phyla from the domain Archaea. Sequences assigned to the genera Flavobacterium, Sulfuricurvum, Halomonas, Shewanella, Lactobacillus, Acinetobacter, and Geobacter demonstrated high relative abundances in all sequencing libraries. Spearman's rank correlations indicated that a number of microbial phylotypes were positively correlated with different speciation of Sb, suggesting potential roles of these phylotypes in microbial Sb cycling. Canonical correspondence analysis further demonstrated that geochemical parameters, including water temperature, pH, total Fe, sulfate, aqueous Sb, and Eh, significantly structured the overall microbial community in Chahe watershed samples. Our findings offer a direct and reliable reference to the diversity of microbial communities in the presence of extremely high Sb concentrations, and may have potential implications for in situ bioremediation strategies of Sb contaminated sites.

Impact of Arsenite on the Bacterial Community Structure and Diversity in Soil

The impact of arsenite (As[III]) on the bacterial community structure and diversity in soil was determined by incubating soil slurries with 50, 500, and 5,000 μM As(III). As(III) was oxidized to arsenate (As[V]), and the microbial contribution to As(III) oxidation was 70–100%. PCR-denaturing gradient gel electrophoresis revealed that soil bacterial diversity decreased in the presence of As(III). Bacteria closely related to the family Bacillaceae were predominant in slurry spiked with 5,000 μM As(III). The population size of culturable As(III)-resistant bacteria was 37-fold higher in this slurry than in unspiked slurry (p < 0.01), indicating that high levels of As(III) stimulate the emergence of As(III)-resistant bacteria. As(III)-resistant bacteria isolated from slurry spiked with 5,000 μM As(III) were mainly affiliated with the genus Bacillus; however, no strains showed As(III)-oxidizing capacity. An As(III)-oxidizing bacterial community analysis based on As(III) oxidase gene (aioA) sequences demonstrated that diversity was the lowest in slurry spiked with 5,000 μM As(III). The deduced AioA sequences affiliated with Alphaproteobacteria accounted for 91–93% of all sequences in this slurry, among which those closely related to Bosea spp. were predominant (48–86%). These results suggest that exposure to high levels of As(III) has a significant impact on the composition and diversity of the soil bacterial community, including the As(III)-oxidizing bacterial community. Certain As(III)-oxidizing bacteria with strong As(III) resistance may be enriched under high As(III) levels, while more sensitive As(III) oxidizers are eliminated under these conditions.