Arsenic detoxification potential of aox genes in arsenite-oxidizing bacteria isolated from natural and constructed wetlands in the Republic of Korea

Perspectives of pteridophytes microbiome for bioremediation in agricultural applications

The microbiome is the synchronised congregation of millions of microbial cells in a particular ecosystem. The rhizospheric, phyllospheric, and endospheric microbial diversity of lower groups of plants like pteridophytes, which includes the Ferns and Fern Allies, have also given numerous alternative opportunities to achieve greener and sustainable agriculture. The broad-spectrum bioactivities of these microorganisms, including bioremediation of heavy metals (HMs) in contaminated soil, have been drawing the attention of agricultural researchers for the preparation of bioformulations for applications in climate-resilient and versatile agricultural production systems. Pteridophytes have an enormous capacity to absorb HMs from the soil. However, their direct application in the agricultural field for HM absorption seems infeasible. At the same time, utilisation of Pteridophyte-associated microbes having the capacity for bioremediation have been evaluated and can revolutionise agriculture in mining and mineral-rich areas. In spite of the great potential, this group of microbiomes has been less studied. Under these facts, this prospective review was carried out to summarise the basic and applied research on the potential of Pteridophyte microbiomes for soil bioremediation and other agricultural applications globally. Gaps have also been indicated to present scopes for future research programmes.

Gamma irradiation in modulating arsenic bioremediation potential of Pseudomonas sp. AK1 and AK9

PURPOSE

Present study deals with the role of gamma irradiation in modulating arsenic bioremediation of Pseudomonas sp. AK1 and AK9 strains.

MATERIALS AND METHODS

The bacterial strains AK1 and AK9 of Pseudomonas sp. were irradiated at different doses (5 Gy, 10 Gy, 15 Gy and 20 Gy) of gamma irradiation. The effect of γ-irradiation on the growth and arsenic modulating ability of AK1 and AK9 strains was determined in the presence and absence of arsenic along with non-irradiated strains. Further, a comparative study of non-irradiated and irradiated strains by protein profiling in absence and presence of arsenic was carried out to confirm of the increased expression ofarsenite oxidase.

RESULTS

Both strains were able to transform AsIII to AsV. Both strains AK1 and AK9 decrease the arsenic concentration by 626.68 ppb (13.36%) and 686.40 ppb (14.71%) after an incubation period of 96 h in presence of arsenic. Gamma irradiated AK9 strains showed doubled growth in presence of arsenic as compared to non-irradiated strains at 10 Gy treatment whereas no changes in growth was observed in irradiated AK1 strains. Gamma irradiated AK9 strain decrease 378.65 ppb (7.27%) more arsenic concentration from natural water sample supplemented with AsIII than non-irradiated AK9 strain. Further, in the protein profile, increased expression of arsenite oxidase (∼85 kDa) was observed in irradiated AK9 strains in presence of arsenic.

CONCLUSIONS

Overall, the results suggested that the gamma irradiated AK9 strain having potential for arsenic accumulation and increased arsenite tolerance may play a great role in the bioremediation of the arsenite at arsenic contaminated sites.

Responses to arsenic stress of rice varieties coinoculated with the heavy metal-resistant and rice growth-promoting bacteria Pseudomonas stutzeri and Cupriavidus taiwanensis

Arsenic (As)-contaminated rice paddy fields are spreading globally, and thus, rice grains with low As accumulation at a safe level for consumption is profoundly needed. Rice is highly susceptible to As accumulation, and the responses to As vary among rice varieties. Here, combinations of the As^III-oxidizing bacteria Pseudomonas stutzeri strains 4.25, 4.27, or 4.44 and Cupriavidus taiwanensis KKU2500-3 were investigated with respect to their responses to As toxicity and rice growth promotion during the early growth stage. All bacterial strains enhanced antioxidant enzyme activities, including SOD, CAT, APX, GPX, and GR, under As stress in vitro. Uninoculated and coinoculated rice seedlings of three rice varieties (KDML105, RD6, RD10) were cultivated in hydroponic solution without and with a combination of toxic As^III and less toxic As^V for 30 days. Compared with uninoculated seedlings, the inoculated seedlings showed higher growth parameters and lower As contents in roots, shoots and throughout the plants. The bioconcentration factor (BCF) and translocation factor were reduced in inoculated seedlings. The effective response of rice to As toxicity influenced by bacteria was highest in KDML105, followed by RD6 and RD10. The root sulfide content was correlated with As accumulation in roots, shoots, and total seedlings and the BCFs. P. stutzeri 4.44 and C. taiwanensis KKU2500-3 were the most promising combinations for application in KDML105 cultivation under As-contaminated conditions. Understanding the basic response of rice coinoculated with effective bacteria at the early stage will provide guidelines for rice cultivation under As conditions at other scales.

Immobile Iron-Rich Particles Promote Arsenic Retention and Regulate Arsenic Biotransformation in Treatment Wetlands

Remediation of arsenic (As)-contaminated wastewater by treatment wetlands (TWs) remains a technological challenge due to the low As adsorption capacity of wetland substrates and the release of adsorbed As to pore water. This study investigated the feasibility of using immobile iron-rich particles (IIRP) to promote As retention and to regulate As biotransformation in TWs. Iron-rich particles prepared were immobilized in the interspace of a gravel substrate. TWs with IIRP amendment (IIRP-TWs) achieved a stable As removal efficiency of 63 ± 4% over 300 days, while no As removal or release was observed in TWs without IIRP after 180 days of continuous operation. IIRP amendment provided additional adsorption sites and increased the stability of adsorbed As due to the strong binding affinity between As and Fe oxides. Microbially mediated As(III) oxidation was intensified by iron-rich particles in the anaerobic bottom layer of IIRP-TWs. Myxococcus and Fimbriimonadaceae were identified as As(III) oxidizers. Further, metagenomic binning suggested that these two bacterial taxa may have the capability for anaerobic As(III) oxidation. Overall, this study demonstrated that abiotic and biotic effects of IIRP contribute to As retention in TWs and provided insights into the role of IIRP for the remediation of As contamination.

Comparative Study of Polycaprolactone Electrospun Fibers and Casting Films Enriched with Carbon and Nitrogen Sources and Their Potential Use in Water Bioremediation

Augmenting bacterial growth is of great interest to the biotechnological industry. Hence, the effect of poly (caprolactone) fibrous scaffolds to promote the growth of different bacterial strains of biological and industrial interest was evaluated. Furthermore, different types of carbon (glucose, fructose, lactose and galactose) and nitrogen sources (yeast extract, glycine, peptone and urea) were added to the scaffold to determinate their influence in bacterial growth. Bacterial growth was observed by scanning electron microscopy; thermal characteristics were also evaluated; bacterial cell growth was measured by ultraviolet-visible spectrophotometry at 600-nm. Fibers produced have an average diameter between 313 to 766 nm, with 44% superficial porosity of the scaffolds, a glass transition around ~64 °C and a critical temperature of ~338 °C. The fibrous scaffold increased the cell growth of Escherichia coli by 23% at 72 h, while Pseudomonas aeruginosa and Staphylococcus aureus increased by 36% and 95% respectively at 48 h, when compared to the normal growth of their respective bacterial cultures. However, no significant difference in bacterial growth between the scaffolds and the casted films could be observed. Cell growth depended on a combination of several factors: type of bacteria, carbon or nitrogen sources, casted films or 3D scaffolds. Microscopy showed traces of a biofilm formation around 3 h in culture of P. aeruginosa. Water bioremediation studies showed that P. aeruginosa on poly (caprolactone)/Glucose fibers was effective in removing 87% of chromium in 8 h.

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

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

Chromosome-Scale Genome of Masked Palm Civet (Paguma larvata) Shows Genomic Signatures of Its Biological Characteristics and Evolution

The masked palm civet (Paguma larvata) is a small carnivore with distinct biological characteristics, that likes an omnivorous diet and also serves as a vector of pathogens. Although this species is not an endangered animal, its population is reportedly declining. Since the severe acute respiratory syndrome (SARS) epidemic in 2003, the public has been particularly concerned about this species. Here, we present the first genome of the P. larvata, comprising 22 chromosomes assembled using single-tube long fragment read (stLFR) and Hi-C technologies. The genome length is 2.41 Gb with a scaffold N50 of 105.6 Mb. We identified the 107.13 Mb X chromosome and one 1.34 Mb Y-linked scaffold and validated them by resequencing 45 P. larvata individuals. We predicted 18,340 protein-coding genes, among which 18,333 genes were functionally annotated. Interestingly, several biological pathways related to immune defenses were found to be significantly expanded. Also, more than 40% of the enriched pathways on the positively selected genes (PSGs) were identified to be closely related to immunity and survival. These enriched gene families were inferred to be essential for the P. larvata for defense against the pathogens. However, we did not find a direct genomic basis for its adaptation to omnivorous diet despite multiple attempts of comparative genomic analysis. In addition, we evaluated the susceptibility of the P. larvata to the SARS-CoV-2 by screening the RNA expression of the ACE2 and TMPRSS2/TMPRSS4 genes in 16 organs. Finally, we explored the genome-wide heterozygosity and compared it with other animals to evaluate the population status of this species. Taken together, this chromosome-scale genome of the P. larvata provides a necessary resource and insights for understanding the genetic basis of its biological characteristics, evolution, and disease transmission control.

Heavy metal tolerance of bacterial isolates associated with overburden strata of an opencast coal mine of Assam (India)

Coal overburden strata (OBS) vary in thickness, geochemical composition, and physical properties from stratum to stratum. Here, we enumerated the cultivable bacterial diversity and their distribution in different OBS taken from the opencast mining of Tikok colliery, Assam. The pH of the coal OBS ranged from 2.46 to 7.93, but 73% of the OBS was acidic. The OBS samples were mostly of shale types except for a few that were sandstone, mudstone, and red soil. The bacterial CFUs per gram OBS samples were highly diverse ranging from 52 to 57.4×10⁴. A total of 79 bacterial pure culture isolates belonging to 19 genera, 12 family, and 3 phyla (Actinobacteria, Firmicutes, and Proteobacteria) were recovered in nutrient agar plates. Firmicutes appeared dominant over the others. All the isolates were screened for heavy metal tolerance in broth culture augmented with five different metals (Ni²⁺, Cu²⁺, Cr⁶⁺, As³⁺, and Cd²⁺) separately. The number of isolates that showed tolerance was 95% for Cr⁶⁺, 69.6% for Ni²⁺, 50.6% each for As³⁺ and Cu²⁺, and 7.6% for Cd²⁺. The bacterial isolates with high metal tolerance, i.e., 5 to 12 mM could be promising for bioremediation of Ni²⁺, Cu²⁺, Cr⁶⁺, and As³⁺ from the sites contaminated with these heavy metals.

Biological characterization of Bacillus flexus strain SSAI1 transforming highly toxic arsenite to less toxic arsenate mediated by periplasmic arsenite oxidase enzyme encoded by aioAB genes

Bacillus flexus strain SSAI1 isolated from agro-industry waste, Tuem, Goa, India displayed high arsenite resistance as minimal inhibitory concentration was 25 mM in mineral salts medium. This bacterial strain exposed to 10 mM arsenite demonstrated rapid arsenite oxidation and internalization of 7 mM arsenate within 24 h. The Fourier transformed infrared (FTIR) spectroscopy of cells exposed to arsenite revealed important functional groups on the cell surface interacting with arsenite. Furthermore, scanning electron microscopy combined with electron dispersive X-ray spectroscopy (SEM-EDAX) of cells exposed to arsenite revealed clumping of cells with no surface adsorption of arsenite. Transmission electron microscopy coupled with electron dispersive X-ray spectroscopic (TEM-EDAX) analysis of arsenite exposed cells clearly demonstrated ultra-structural changes and intracellular accumulation of arsenic. Whole-genome sequence analysis of this bacterial strain interestingly revealed the presence of large number of metal(loid) resistance genes, including aioAB genes encoding arsenite oxidase responsible for the oxidation of highly toxic arsenite to less toxic arsenate. Enzyme assay further confirmed that arsenite oxidase is a periplasmic enzyme. The genome of strain SSAI1 also carried glpF, aioS and aioE genes conferring resistance to arsenite. Therefore, multi-metal(loid) resistant arsenite oxidizing Bacillus flexus strain SSAI1 has potential to bioremediate arsenite contaminated environmental sites and is the first report of its kind.

Arsenic behavior in groundwater in Hanoi (Vietnam) influenced by a complex biogeochemical network of iron, methane, and sulfur cycling

The fate of arsenic (As) in groundwater is determined by multiple interrelated microbial and abiotic processes that contribute to As (im)mobilization. Most studies to date have investigated individual processes related to As (im)mobilization rather than the complex networks present in situ. In this study, we used RNA-based microbial community analysis in combination with groundwater hydrogeochemical measurements to elucidate the behavior of As along a 2 km transect near Hanoi, Vietnam. The transect stretches from the riverbank across a strongly reducing and As-contaminated Holocene aquifer, followed by a redox transition zone (RTZ) and a Pleistocene aquifer, at which As concentrations are low. Our analyses revealed fermentation and methanogenesis as important processes providing electron donors, fueling the microbially mediated reductive dissolution of As-bearing Fe(III) minerals and ultimately promoting As mobilization. As a consequence of high CH₄ concentrations, methanotrophs thrive across the Holocene aquifer and the redox transition zone. Finally, our results underline the role of SO₄^2--reducing and putative Fe(II)-/As(III)-oxidizing bacteria as a sink for As, particularly at the RTZ. Overall, our results suggest that a complex network of microbial and biogeochemical processes has to be considered to better understand the biogeochemical behavior of As in groundwater.

Introducing the ArsR-Regulated Arsenic Stimulon

The microbial ars operon encodes the primary bacterial defense response to the environmental toxicant, arsenic. An important component of this operon is the arsR gene, which encodes ArsR, a member of the family of proteins categorized as DNA-binding transcriptional repressors. As currently documented, ArsR regulates its own expression as well as other genes in the same ars operon. This study examined the roles of four ArsR proteins in the well-developed model Gram-negative bacterium Agrobacterium tumefaciens 5A. RNASeq was used to compare and characterize gene expression profiles in ± arsenite-treated cells of the wild-type strain and in four different arsR mutants. We report that ArsR-controlled transcription regulation is truly global, extending well beyond the current ars operon model, and includes both repression as well as apparent activation effects. Many cellular functions are significantly influenced, including arsenic resistance, phosphate acquisition/metabolism, sugar transport, chemotaxis, copper tolerance, iron homeostasis, and many others. While there is evidence of some regulatory overlap, each ArsR exhibits its own regulatory profile. Furthermore, evidence of a regulatory hierarchy was observed; i.e. ArsR1 represses arsR4, ArsR4 activates arsR2, and ArsR2 represses arsR3. Additionally and unexpectedly, aioB (arsenite oxidase small subunit) expression was shown to be under partial positive control by ArsR2 and ArsR4. Summarizing, this study demonstrates the regulatory portfolio of arsenite-activated ArsR proteins and includes essentially all major cellular functions. The broad bandwidth of arsenic effects on microbial metabolism assists in explaining and understanding the full impact of arsenic in natural ecosystems, including the mammalian gut.

Genomic and transcriptomic analysis unveils population evolution and development of pesticide resistance in fall armyworm Spodoptera frugiperda

The fall armyworm (FAW), Spodoptera frugiperda, is a destructive pest native to America and has recently become an invasive insect pest in China. Because of its rapid spread and great risks in China, understanding of FAW genetic background and pesticide resistance is urgent and essential to develop effective management strategies. Here, we assembled a chromosome-level genome of a male FAW (SFynMstLFR) and compared re-sequencing results of the populations from America, Africa, and China. Strain identification of 163 individuals collected from America, Africa and China showed that both C and R strains were found in the American populations, while only C strain was found in the Chinese and African populations. Moreover, population genomics analysis showed that populations from Africa and China have close relationship with significantly genetic differentiation from American populations. Taken together, FAWs invaded into China were most likely originated from Africa. Comparative genomics analysis displayed that the cytochrome p450 gene family is extremely expanded to 425 members in FAW, of which 283 genes are specific to FAW. Treatments of Chinese populations with twenty-three pesticides showed the variant patterns of transcriptome profiles, and several detoxification genes such as AOX, UGT and GST specially responded to the pesticides. These findings will be useful in developing effective strategies for management of FAW in China and other invaded areas.

Bioremediation of toxic heavy metals (THMs) contaminated sites: concepts, applications and challenges

Heavy metal contamination is a global issue, where the prevalent contaminants are arsenic (As), cadmium (Cd), chromium (Cr)(VI), mercury (Hg), and lead (Pb). More often, they are collectively known as "most problematic heavy metals" and "toxic heavy metals" (THMs). Their treatment through a variety of biological processes is one of the prime interests in remediation studies, where heavy metal-microbe interaction approaches receive high interest for their cost effective and ecofriendly solutions. In this review, we provide an up to date information on different microbial processes (bioremediation) for the removal of THMs. For the same, emphasis is put on oxidation-reduction, biomineralization, bioprecipitation, bioleaching, biosurfactant technology, biovolatilization, biosorption, bioaccumulation, and microbe-assisted phytoremediation with their selective advantages and disadvantages. Further, the literature briefly discusses about the various setups of cleaning processes of THMs in environment under ex situ and in situ applications. Lately, the study sheds light on the manipulation of microorganisms through genetic engineering and nanotechnology for their advanced treatment approaches.

Bioremediation Options for Heavy Metal Pollution

BACKGROUND

Rapid industrialization and anthropogenic activities such as the unmanaged use of agro-chemicals, fossil fuel burning and dumping of sewage sludge have caused soils and waterways to be severely contaminated with heavy metals. Heavy metals are non-biodegradable and persist in the environment. Hence, remediation is required to avoid heavy metal leaching or mobilization into environmental segments and to facilitate their extraction.

OBJECTIVES

The present work briefly outlines the environmental occurrence of heavy metals and strategies for using microorganisms for bioremediation processes as reported in the scientific literature.

METHODS

Databases were searched from different libraries, including Google Scholar, Medline and Scopus. Observations across studies were then compared with the standards for discharge of environmental pollutants.

DISCUSSION

Bioremediation employs microorganisms for removing heavy metals. Microorganisms have adopted different mechanisms for bioremediation. These mechanisms are unique in their specific requirements, advantages, and disadvantages, the success of which depends chiefly upon the kind of organisms and the contaminants involved in the process.

CONCLUSIONS

Heavy metal pollution creates environmental stress for human beings, plants, animals and other organisms. A complete understanding of the process and various alternatives for remediation at different steps is needed to ensure effective and economic processes.

COMPETING INTERESTS

The authors declare no competing financial interests.

Elevated level of arsenic negatively influences nifH gene expression of isolated soil bacteria in culture condition as well as soil system

Comprehensive studies on the effect of arsenic (As) on free-living diazotrophs that play a crucial role in soil fertility by nitrogen fixation are still scanty. Here, we isolated three free-living bacteria from rice field with potential nitrogen-fixing ability and investigated the impact of As on their nifH gene expression and extracellular polysaccharide (EPS) production in culture condition and soil system. 16S rRNA sequence analysis showed that the isolated bacteria were affiliated to β-Proteobacteria, γ-Proteobacteria and Firmicutes. As(III) exposure to bacterial isolates followed by RT-qPCR analysis revealed that elevated levels of As reduced the expression of nifH gene in selective bacteria, both in culture medium and soil condition. We also noticed reduced production of EPS under higher concentration of As. All the three bacteria showed high tolerance to As(III), able to oxidize As and exhibited significant plant growth-promoting traits. This investigation indicated that an environment exposed with higher concentration of As might perturbed the activity of free-living diazotrophs in agricultural soil system.

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.

Mechanism of arsenic resistance in endophytic bacteria isolated from endemic plant of mine tailings and their arsenophore production

Arsenic contamination is an important environmental problem around the world since its high toxicity, and bacteria resist to this element serve as valuable resource for its bioremediation. Aiming at searching the arsenic-resistant bacteria and determining their resistant mechanism, a total of 27 strains isolated from roots of Prosopis laevigata and Spharealcea angustifolia grown in a heavy metal-contaminated region in Mexico were investigated. The minimum inhibitory concentration (MIC) and transformation abilities of arsenate (As⁵⁺) and arsenite (As³⁺), arsenophore synthesis, arsenate uptake, and cytoplasmatic arsenate reductase (arsC), and arsenite transporter (arsB) genes were studied for these strains. Based on these results and the 16S rDNA sequence analysis, these isolates were identified as arsenic-resistant endophytic bacteria (AREB) belonging to the genera Arthrobacter, Bacillus, Brevibacterium, Kocuria, Microbacterium, Micrococcus, Pseudomonas, and Staphylococcus. They could tolerate high concentrations of arsenic with MIC from 20 to > 100 mM for As⁵⁺ and 10-20 mM for As³⁺. Eleven isolates presented dual abilities of As⁵⁺ reduction and As³⁺ oxidation. As the most effective strains, Micrococcus luteus NE2E1 reduced 94% of the As⁵⁺ and Pseudomonas zhaodongensis NM2E7 oxidized 46% of As³⁺ under aerobic condition. About 70 and 44% of the test strains produced arsenophores to chelate As⁵⁺ and As³⁺, respectively. The AREB may absorb arsenate via the same receptor of phosphate uptake or via other way in some case. The cytoplasmic arsenate reductase and alternative arsenate reduction pathways exist in these AREB. Therefore, these AREB could be candidates for the bioremediation process.

Possible bioremediation of arsenic toxicity by isolating indigenous bacteria from the middle Gangetic plain of Bihar, India

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In middle Gangetic plains, high arsenic concentration is present in water, which causes a significant health risk.

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Two bacterial isolates, AK1 (KY569423) and AK9 (KY569424) were isolated and characterised for Arsenic detoxification.

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aoxR, aoxB and aoxC genes were also observed in the isolated starin which help in arsenic detoxification by oxidation method.

In middle Gangetic plain, high arsenic concentration is present in water, which causes a significant health risk. Total 48 morphologically distinct arsenite resistant bacteria were isolated from middle Gangetic plain. The minimum inhibitory concentration (MIC) values of arsenite varied widely in the range 1–15 mM of the isolates. On the basis of their MIC, two isolates, AK1 (KY569423) and AK9 (KY569424) were selected. The analysis of the 16S rRNA gene sequence of selected isolates revealed that they are belong to the genus Pseudomonas. The AgNO₃ test based microplate method revealed that isolates, AK1 and AK9, have potential in transformation of arsenic species. Further, the presence of aoxR, aoxB and aoxC genes in the both isolated strain AK1 and AK9 was confirmed, which play an important role in arsenic bioremediation by arsenite oxidation. Isolated strains also showed heavy metal resistance against Cr(IV), Ni(II), Co(II), Pb(II), Cu(II), Hg(II), Ag(I) and Cd(II).

Metal-tolerant thermophiles: metals as electron donors and acceptors, toxicity, tolerance and industrial applications

Metal-tolerant thermophiles are inhabitants of a wide range of extreme habitats like solfatara fields, hot springs, mud holes, hydrothermal vents oozing out from metal-rich ores, hypersaline pools and soil crusts enriched with metals and other elements. The ability to withstand adverse environmental conditions, like high temperature, high metal concentration and sometimes high pH in their niche, makes them an interesting subject for understanding mechanisms behind their ability to deal with multiple duress simultaneously. Metals are essential for biological systems, as they participate in biochemistries that cannot be achieved only by organic molecules. However, the excess concentration of metals can disrupt natural biogeochemical processes and can impose toxicity. Thermophiles counteract metal toxicity via their unique cell wall, metabolic factors and enzymes that carry out metal-based redox transformations, metal sequestration by metallothioneins and metallochaperones as well as metal efflux. Thermophilic metal resistance is heterogeneous at both genetic and physiology levels and may be chromosomally, plasmid or transposon encoded with one or more genes being involved. These effective response mechanisms either individually or synergistically make proliferation of thermophiles in metal-rich habitats possibly. This article presents the state of the art and future perspectives of responses of thermophiles to metals at genetic as well as physiological levels.

Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire

Arsenic (As), a toxic element, has impacted life since early Earth. Thus, microorganisms have evolved many As resistance and tolerance mechanisms to improve their survival outcomes given As exposure. We isolated As resistant bacteria from Centralia, PA, the site of an underground coal seam fire that has been burning since 1962. From a 57.4°C soil collected from a vent above the fire, we isolated 25 unique aerobic As resistant bacterial strains spanning seven genera. We examined their diversity, resistance gene content, transformation abilities, inhibitory concentrations, and growth phenotypes. Although As concentrations were low at the time of soil collection (2.58 ppm), isolates had high minimum inhibitory concentrations (MICs) of arsenate and arsenite (>300 mM and 20 mM respectively), and most isolates were capable of arsenate reduction. We screened isolates (PCR and sequencing) using 12 published primer sets for six As resistance genes (AsRGs). Genes encoding arsenate reductase (arsC) and arsenite efflux pumps (arsB, ACR3(2)) were present, and phylogenetic incongruence between 16S rRNA genes and AsRGs provided evidence for horizontal gene transfer. A detailed investigation of differences in isolate growth phenotypes across As concentrations (lag time to exponential growth, maximum growth rate, and maximum OD590) showed a relationship with taxonomy, providing information that could help to predict an isolate's performance given As exposure in situ. Our results suggest that microbiological management and remediation of environmental As could be informed by taxonomically-linked As tolerance, potential for resistance gene transferability, and the rare biosphere.

Investigation of Arsenotrophic Microbiome in Arsenic-Affected Bangladesh Groundwater

Arsenotrophic bacteria contribute to the nutrient cycling in arsenic (As) affected groundwater. This study employed a culture-independent and -dependent investigation of arsenotrophic microbiomes in As affected groundwater samples collected from Madhabpur, Sonatengra, and Union Porishod in Singair Upazila, Manikganj, Bangladesh. Total As contents, detected by Atomic Absorption Spectrophotometry (AAS) of the samples, were 47 µg/L (Madhabpur, SNGW-1), 53 µg/L (Sonatengra, SNGW-2), and 12 µg/L (Union porishod, SNGW-3), whereas the control well (SNGW-4; depths >150 m) showed As content of 6 µg/L. Denaturing Gradient Gel Electrophoresis (DGGE) analysis of the amplified 16S rRNA gene from As-affected groundwater samples revealed the dominance of aerobic bacteria Pseudomonas within heterogeneous bacterial populations. DGGE of heterotrophic enrichments supplemented with arsenite [As (III)] for 4 weeks showed the dominance of Chryseobacterium, Flavobacterium, and Aquabacterium, whereas the dominant genera in that of autotrophic enrichments were Aeromonas, Acinetobacter, and Pseudomonas. Cultured bacteria retrieved from both autotrophic and heterotrophic enrichments were distinguished into nine genotypes belonging to Chryseobacterium, Acinetobacter, Escherichia, Pseudomonas, Stenotrophomonas, Janibacter, Staphylococcus, and Bacillus. They exhibited varying range of As(III) tolerance from 4 to 27 mM. As(III) transformation potential was confirmed within the isolates with oxidation rate as high as 0.143 mM/h for Pseudomonas sp. Sn 28. The arsenotrophic microbiome specifies their potential role in groundwater As-cycling and their genetic information provide the scientific basis for As-bioremediation.

Microbial arsenite oxidation with oxygen, nitrate, or an electrode as the sole electron acceptor

The purpose of this study was to identify bacteria that can perform As(III) oxidation for environmental bioremediation. Two bacterial strains, named JHS3 and JHW3, which can autotrophically oxidize As(III)–As(V) with oxygen as an electron acceptor, were isolated from soil and water samples collected in the vicinity of an arsenic-contaminated site. According to 16S ribosomal RNA sequence analysis, both strains belong to the ɤ-Proteobacteria class and share 99% sequence identity with previously described strains. JHS3 appears to be a new strain of the Acinetobacter genus, whereas JHW3 is likely to be a novel strain of the Klebsiella genus. Both strains possess the aioA gene encoding an arsenite oxidase and are capable of chemolithoautotrophic growth in the presence of As(III) up to 10 mM as a primary electron donor. Cell growth and As(III) oxidation rate of both strains were significantly enhanced during cultivation under heterotrophic conditions. Under anaerobic conditions, only strain JHW3 oxidized As(III) using nitrate or a solid-state electrode of a bioelectrochemical system as a terminal electron acceptor. Kinetic studies of As(III) oxidation under aerobic condition demonstrated a higher V  max and K  m from strain JHW3 than strain JHS3. This study indicated the potential application of strain JHW3 for remediation of subsurface environments contaminated with arsenic.

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.

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.

Arsenic redox transformation by Pseudomonas sp. HN-2 isolated from arsenic-contaminated soil in Hunan, China

A mesophilic, Gram-negative, arsenite[As(III)]-oxidizing and arsenate[As(V)]-reducing bacterial strain, Pseudomonas sp. HN-2, was isolated from an As-contaminated soil. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the strain was closely related to Pseudomonas stutzeri. Under aerobic conditions, this strain oxidized 92.0% (61.4μmol/L) of arsenite to arsenate within 3hr of incubation. Reduction of As(V) to As(III) occurred in anoxic conditions. Pseudomonas sp. HN-2 is among the first soil bacteria shown to be capable of both aerobic As(III) oxidation and anoxic As(V) reduction. The strain, as an efficient As(III) oxidizer and As(V) reducer in Pseudomonas, has the potential to impact arsenic mobility in both anoxic and aerobic environments, and has potential application in As remediation processes.

Spontaneous arsenic (III) oxidation with bioelectricity generation in single-chamber microbial fuel cells

Arsenic is one of the most toxic elements commonly found in groundwater. With initial concentration of 200μgL(-1), spontaneous As(III) oxidation is realized completely during 7 days operation in single-chamber microbial fuel cells (MFCs) in the present study, with the maximum power density of 752.6±17mWm(-2). The product is less toxic and mobile As(V), which can be removed from aqueous solution more easily. High-throughput 16S rRNA gene pyrosequencing analysis indicates the existence of arsenic-resistant bacteria as Actinobacteria, Comamonas, Pseudomonas and arsenic-oxidizing bacteria as Enterobacter, with electrochemically active bacteria as Lactococcus, Enterobacter. They interact together and are responsible for As(III) oxidation and bioelectricity generation in MFCs. This study offers a potential attractive method for remediation of arsenic-polluted groundwater.

Arsenic biotransformation by cyanobacteria from mining areas: evidences from culture experiments

Elucidating the role of cyanobacteria in the biotransformation of arsenic (As) oxyanions is crucial to understand the biogeochemical cycle of this element and indicate species with potential for its bioremediation. In this study, we determined the EC50 for As(III) and As(V) and evaluated the biotransformation of As by Synechococcus sp. through high-performance liquid chromatography hyphenated to inductively coupled plasma mass spectrometry (HPLC-ICP-MS) and X-ray absorption fine structure spectroscopy (XAFS). Synechococcus sp. exhibited higher sensitivity to As(III) with an EC(50, 96 h) of 6.64 mg L(-1) that was approximately 400-fold lower than that for As(V). Even though the cells were exposed to concentrations of As(III) (6 mg L(-1)) approximately 67-fold lower than those of As(V) (400 mg L(-1)), similar intracellular concentrations of As (60.0 μg g(-1)) were observed after 30 days. As(V) was the predominant intracellular As species followed by As(III). Furthermore, organic As species such as monomethylarsonic acid (MMA) and dimethylarsinic acid (DMA) were observed in higher proportions after exposure to As(III). The differential toxicity among As oxyanions indicates that determining the redox state of As in the environment is fundamental to estimate toxicity risks to aquatic organisms. Synechococcus sp. demonstrated potential for its application in bioremediation due to the high accumulation of As and production of As organic compounds notably after exposure to As(III).

Determination of physiological, taxonomic, and molecular characteristics of a cultivable arsenic-resistant bacterial community

A collection of 219 bacterial arsenic-resistant isolates was constituted from neutral arsenic mine drainage sediments. Isolates were grown aerobically or anaerobically during 21 days on solid DR2A medium using agar or gelan gum as gelling agent, with 7 mM As(III) or 20 mM As(V) as selective pressure. Interestingly, the sum of the different incubation conditions used (arsenic form, gelling agent, oxygen pressure) results in an overall increase of the isolate diversity. Isolated strains mainly belonged to Proteobacteria (63%), Actinobacteria (25%), and Bacteroidetes (10%). The most representative genera were Pseudomonas (20%), Acinetobacter (8%), and Serratia (15%) among the Proteobacteria; Rhodococcus (13%) and Microbacterium (5%) among Actinobacteria; and Flavobacterium (13%) among the Bacteroidetes. Isolates were screened for the presence of arsenic-related genes (arsB, ACR3(1), ACR3(2), aioA, arsM, and arrA). In this way, 106 ACR3(1)-, 74 arsB-, 22 aioA-, 14 ACR3(2)-, and one arsM-positive PCR products were obtained and sequenced. Analysis of isolate sensitivity toward metalloids (arsenite, arsenate, and antimonite) revealed correlations between taxonomy, sensitivity, and genotype. Antimonite sensitivity correlated with the presence of ACR3(1) mainly present in Bacteroidetes and Actinobacteria, and arsenite or antimonite resistance correlated with arsB gene presence. The presence of either aioA gene or several different arsenite carrier genes did not ensure a high level of arsenic resistance in the tested conditions.

Effect of arsenic on tolerance mechanisms of two plant growth-promoting bacteria used as biological inoculants

Bacterial ability to colonize the rhizosphere of plants in arsenic (As) contaminated soils is highly important for symbiotic and free-living plant growth-promoting rhizobacteria (PGPR) used as inoculants, since they can contribute to enhance plant As tolerance and limit metalloid uptake by plants. The aim of this work was to study the effect of As on growth, exopolysaccharide (EPS) production, biofilm formation and motility of two strains used as soybean inoculants, Bradyrhizobium japonicum E109 and Azospirillum brasilense Az39. The metabolism of arsenate (As(V)) and arsenite (As(III)) and their removal and/or possible accumulation were also evaluated. The behavior of both bacteria under As treatment was compared and discussed in relation to their potential for colonizing plant rhizosphere with high content of the metalloid. B. japonicum E109 growth was reduced with As(III) concentration from 10 μM while A. brasilense Az39 showed a reduction of growth with As(III) from 500 μM. EPS and biofilm production increased significantly under 25 μM As(III) for both strains. Moreover, this was more notorious for Azospirillum under 500 μM As(III), where motility was seriously affected. Both bacterial strains showed a similar ability to reduce As(V). However, Azospirillum was able to oxidize more As(III) (around 53%) than Bradyrhizobium (17%). In addition, both strains accumulated As in cell biomass. The behavior of Azospirillum under As treatments suggests that this strain would be able to colonize efficiently As contaminated soils. In this way, inoculation with A. brasilense Az39 would positively contribute to promoting growth of different plant species under As treatment.

Bacteria and genes involved in arsenic speciation in sediment impacted by long-term gold mining

The bacterial community and genes involved in geobiocycling of arsenic (As) from sediment impacted by long-term gold mining were characterized through culture-based analysis of As-transforming bacteria and metagenomic studies of the arsC, arrA, and aioA genes. Sediment was collected from the historically gold mining impacted Mina stream, located in one of the world’s largest mining regions known as the “Iron Quadrangle”. A total of 123 As-resistant bacteria were recovered from the enrichment cultures, which were phenotypically and genotypically characterized for As-transformation. A diverse As-resistant bacteria community was found through phylogenetic analyses of the 16S rRNA gene. Bacterial isolates were affiliated with Proteobacteria, Firmicutes, and Actinobacteria and were represented by 20 genera. Most were AsV-reducing (72%), whereas AsIII-oxidizing accounted for 20%. Bacteria harboring the arsC gene predominated (85%), followed by aioA (20%) and arrA (7%). Additionally, we identified two novel As-transforming genera, Thermomonas and Pannonibacter. Metagenomic analysis of arsC, aioA, and arrA sequences confirmed the presence of these genes, with arrA sequences being more closely related to uncultured organisms. Evolutionary analyses revealed high genetic similarity between some arsC and aioA sequences obtained from isolates and clone libraries, suggesting that those isolates may represent environmentally important bacteria acting in As speciation. In addition, our findings show that the diversity of arrA genes is wider than earlier described, once none arrA-OTUs were affiliated with known reference strains. Therefore, the molecular diversity of arrA genes is far from being fully explored deserving further attention.

Microbial transformations of arsenic: perspectives for biological removal of arsenic from water

Arsenic is present in many environments and is released by various natural processes and anthropogenic actions. Although arsenic is recognized to cause a wide range of adverse health effects in humans, diverse bacteria can metabolize it by detoxification and energy conservation reactions. This review highlights the current understanding of the ecology, biochemistry and genomics of these bacteria, and their potential application in the treatment of arsenic-polluted water.

Microbial communities in low permeability, high pH uranium mine tailings: characterization and potential effects

AIMS

To describe the diversity and metabolic potential of microbial communities in uranium mine tailings characterized by high pH, high metal concentration and low permeability.

METHODS AND RESULTS

To assess microbial diversity and their potential to influence the geochemistry of uranium mine tailings using aerobic and anaerobic culture-based methods, in conjunction with next generation sequencing and clone library sequencing targeting two universal bacterial markers (the 16S rRNA and cpn60 genes). Growth assays revealed that 69% of the 59 distinct culturable isolates evaluated were multiple-metal resistant, with 15% exhibiting dual-metal hypertolerance. There was a moderately positive correlation coefficient (R = 0·43, P < 0·05) between multiple-metal resistance of the isolates and their enzyme expression profile. Of the isolates tested, 17 reduced amorphous iron, 22 reduced molybdate and seven oxidized arsenite. Based on next generation sequencing, tailings depth was shown to influence bacterial community composition, with the difference in the microbial diversity of the upper (0-20 m) and middle (20-40 m) tailings zones being highly significant (P < 0·01) from the lower zone (40-60 m) and the difference in diversity of the upper and middle tailings zone being significant (P < 0·05). Phylotypes closely related to well-known sulfate-reducing and iron-reducing bacteria were identified with low abundance, yet relatively high diversity.

CONCLUSIONS

The presence of a population of metabolically-diverse, metal-resistant micro-organisms within the tailings environment, along with their demonstrated capacity for transforming metal elements, suggests that these organisms have the potential to influence the long-term geochemistry of the tailings.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study is the first investigation of the diversity and functional potential of micro-organisms present in low permeability, high pH uranium mine tailings.

The prokaryotic community of a historically mining-impacted tropical stream sediment is as diverse as that from a pristine stream sediment

Mining negatively affects the environment by producing large quantities of metallic tailings, such as those contaminated with arsenic, with harmful consequences for human and aquatic life. A culture-independent molecular analysis was performed to assess the prokaryotic diversity and community structural changes of the tropical historically metal-contaminated Mina stream (MS) and the relatively pristine Mutuca stream (MTS) sediments. A total of 234 bacterial operational taxonomic units (OTUs) were affiliated with 14 (MS) and 17 (MTS) phyla and 53 OTUs were associated with two archaeal phyla. Although the bacterial community compositions of these sediments were markedly distinct, no significant difference in the diversity indices between the bacterial communities was observed. Additionally, the rarefaction and diversity indices indicated a higher bacterial diversity than archaeal diversity. Most of the OTUs were affiliated with the Proteobacteria and Bacteroidetes phyla. Alphaproteobacteria, Gemmatimonadetes and Actinobacteria were only found in the MS clone library. Crenarchaeal 16S rDNA sequences constituted 75 % of the MS archaeal clones, whereas Euryarchaeota were dominant in the MTS clones. Despite the markedly different characteristics of these streams, their bacterial communities harbor high diversity, suggesting that historically mining-impacted sediments promote diversity. The findings also provide basis for further investigation of members of Alphaproteobacteria as potential biological indicators of arsenic-rich sediments.

Arsenics as bioenergetic substrates

Although at low concentrations, arsenic commonly occurs naturally as a local geological constituent. Whereas both arsenate and arsenite are strongly toxic to life, a number of prokaryotes use these compounds as electron acceptors or donors, respectively, for bioenergetic purposes via respiratory arsenate reductase, arsenite oxidase and alternative arsenite oxidase. The recent burst in discovered arsenite oxidizing and arsenate respiring microbes suggests the arsenic bioenergetic metabolisms to be anything but exotic. The first goal of the present review is to bring to light the widespread distribution and diversity of these metabolizing pathways. The second goal is to present an evolutionary analysis of these diverse energetic pathways. Taking into account not only the available data on the arsenic metabolizing enzymes and their phylogenetical relatives but also the palaeogeochemical records, we propose a crucial role of arsenite oxidation via arsenite oxidase in primordial life. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.

New clusters of arsenite oxidase and unusual bacterial groups in enrichments from arsenic-contaminated soil

In the present study cultivation-dependent and molecular methods were applied in combination to investigate the arsenite-oxidizing communities in enrichment cultures from arsenic and lead smelter-impacted soils with respect to both 16S rRNA and arsenite oxidase gene diversity. Enrichments with arsenite as the only electron donor resulted in completely different communities than enrichments with yeast extract and the simultaneous presence of arsenite. The lithoautotrophic community appeared to be dominated by Ferrimicrobium-related Actinobacteria, unusual Acidobacteria, Myxobacteria, and α-Proteobacteria but the heterotrophic community comprised many Dokdonella-related γ-Proteobacteria. Gene sequences of clones encoding arsenite oxidase from the enrichment for lithoautotrophs belonged to three major clusters with sequences from non-cultivated microorganisms. So, primers used to detect arsenite oxidase genes could amplify the genes from many α-, β- and γ-Proteobacteria, but not from various strains of the other phyla present in the enrichment for lithotrophs. This was also observed for the isolates where arsenite oxidase genes from new proteobacterial isolates of the genera Burkholderia, Bosea, Alcaligenes, Bradyrhizobium and Methylobacterium could be amplified but the genes of the new Rhodococcus isolate S43 could not. The results indicate that the ability to oxidize arsenite is widespread in various unusual taxa, and molecular methods for their detection require further improvement.

Molecular identification of arsenic-resistant estuarine bacteria and characterization of their ars genotype

In the present study, 44 arsenic-resistant bacteria were isolated through serial dilutions on agar plate with concentrations ≥0.05 mM of sodium arsenite and ≥10 mM of sodium arsenate from Mandovi and Zuari--estuarine water systems. The ars genotype characterization in 36 bacterial isolates (resistant to 100 mM of sodium arsenate) revealed that only 17 isolates harboured the arsA (ATPase), B (arsenite permease) and C (arsenate reductase) genes on the plasmid DNA. The arsA, B and C genes were individually detected using PCR in 16, 9 and 13 bacterial isolates respectively. Molecular identification of the 17 isolates bearing the ars genotype was carried using 16S rDNA sequencing. A 1300 bp full length arsB gene encoding arsenite efflux pump and a 409 bp fragment of arsC gene coding for arsenate reductase were isolated from the genera Halomonas and Acinetobacter. Phylogenetic analysis of arsB and arsC genes indicated their close genetic relationship with plasmid borne ars genes of E. coli and arsenate reductase of plant origin. The putative arsenate reductase gene isolated from Acinetobacter species complemented arsenate resistance in E. coli WC3110 and JM109 validating its function. This study dealing with isolation of native arsenic-resistant bacteria and characterization of their ars genes might be useful to develop efficient arsenic detoxification strategies for arsenic contaminated aquifers.

Removal processes for arsenic in constructed wetlands

Arsenic pollution in aquatic environments is a worldwide concern due to its toxicity and chronic effects on human health. This concern has generated increasing interest in the use of different treatment technologies to remove arsenic from contaminated water. Constructed wetlands are a cost-effective natural system successfully used for removing various pollutants, and they have shown capability for removing arsenic. This paper reviews current understanding of the removal processes for arsenic, discusses implications for treatment wetlands, and identifies critical knowledge gaps and areas worthy of future research. The reactivity of arsenic means that different arsenic species may be found in wetlands, influenced by vegetation, supporting medium and microorganisms. Despite the fact that sorption, precipitation and coprecipitation are the principal processes responsible for the removal of arsenic, bacteria can mediate these processes and can play a significant role under favourable environmental conditions. The most important factors affecting the speciation of arsenic are pH, alkalinity, temperature, dissolved oxygen, the presence of other chemical species--iron, sulphur, phosphate--,a source of carbon, and the wetland substrate. Studies of the microbial communities and the speciation of arsenic in the solid phase using advanced techniques could provide further insights on the removal of arsenic. Limited data and understanding of the interaction of the different processes involved in the removal of arsenic explain the rudimentary guidelines available for the design of wetlands systems.

Unsuspected diversity of arsenite-oxidizing bacteria as revealed by widespread distribution of the aoxB gene in prokaryotes

In this study, new strains were isolated from an environment with elevated arsenic levels, Sainte-Marie-aux-Mines (France), and the diversity of aoxB genes encoding the arsenite oxidase large subunit was investigated. The distribution of bacterial aoxB genes is wider than what was previously thought. AoxB subfamilies characterized by specific signatures were identified. An exhaustive analysis of AoxB sequences from this study and from public databases shows that horizontal gene transfer has likely played a role in the spreading of aoxB in prokaryotic communities.

The potential for reductive mobilization of arsenic [As(V) to As(III)] by OSBH(2) (Pseudomonas stutzeri) and OSBH(5) (Bacillus cereus) in an oil-contaminated site

Microbial reduction of arsenate [As(V)] plays an important role in arsenic (As) mobilization in aqueous environments. In this study, we investigated reduction of arsenate by different bacterial isolates such as OSBH(1) (GU329913), OSBH(2) (GU329914), OSBH(3) (GU329915), OSBH(4) (GU329916) and OSBH(5) (GU329917), isolated from the oil sludge of a sewage treatment plant operated by the China Petroleum Refinery Company in Kaohsiung, southern Taiwan. Bacterial strains of pure culture were identified by 16S rRNA analysis (≥99 % nucleotide similarity). Morphological and 16S rRNA analysis show that the isolate OSBH(1) is similar to E. coli, OSBH(2) is similar to P. stutzeri, OSBH(3) is similar to P. putida, OSBH(4) is similar to P. aeruginosa, and OSBH(5) is similar to B. Cereus. The As(V) was transformed to As(III) in the presence of isolates OSBH(2) and OSBH(5) by a detoxification process. The potential reduction rates of As(V) were higher in the presence of isolate OSBH(5) compared to the isolate OSBH(2). The microbial growth (cell/mL) of isolate OSBH(5) was significantly higher in culture medium compared to OSBH(2). The bacterial isolates such as OSBH(1), OSBH(3) and OSBH(4) were found to be incapable of transforming the As(V). It is concluded that the activity of the oil-degrading bacterial isolates described in this work contributes to the mobilization of As in the more toxic As(III) form that affects biotic life.

Arsenite oxidase from Ralstonia sp. 22: characterization of the enzyme and its interaction with soluble cytochromes

We characterized the aro arsenite oxidation system in the novel strain Ralstonia sp. 22, a beta-proteobacterium isolated from soil samples of the Salsigne mine in southern France. The inducible aro system consists of a heterodimeric membrane-associated enzyme reacting with a dedicated soluble cytochrome c(554). Our biochemical results suggest that the weak association of the enzyme to the membrane probably arises from a still unknown interaction partner. Analysis of the phylogeny of the aro gene cluster revealed that it results from a lateral gene transfer from a species closely related to Achromobacter sp. SY8. This constitutes the first clear cut case of such a transfer in the Aro phylogeny. The biochemical study of the enzyme demonstrates that it can accommodate in vitro various cytochromes, two of which, c(552) and c(554,) are from the parent species. Cytochrome c(552) belongs to the sox and not the aro system. Kinetic studies furthermore established that sulfite and sulfide, substrates of the sox system, are both inhibitors of Aro activity. These results reinforce the idea that sulfur and arsenic metabolism are linked.