Pseudaminobacter arsenicus sp. nov., an arsenic-resistant bacterium isolated from arsenic-rich aquifers

Microbial reductive mobilization of As(V) in solid phase coupled with the oxidation of sulfur compounds: An overlooked biogeochemical reaction affecting the formation of arsenic-contaminated groundwater

Dissimilatory As(V)-respiring prokaryotes (DARPs) are recognized as having a crucial role in the formation of arsenic-contaminated groundwater. DARPs use small-molecule organic acids as electron donor to directly reduce As(V) in solid phase to more mobile As(III). Therefore, DARPs are considered to be heterotrophic bacteria. However, these cannot explain why high concentrations of As(III) are produced in environments lacking soluble organic carbon. We thus propose that reduced sulfur compounds may also be utilized by DARPs and affect the DARPs-mediated arsenic mobilization. This study sought to confirm this hypothesis. Metagenomic investigations on the DARP population derived from As-contaminated soil indicated that approximately 84 % of DARP MAGs possess the enzymes potentially catalyzing the oxidation of S2-, S0, SO32-, or S2O32-. Functional analysis of DARP population and a cultivable strain suggested that DARPs, in addition to small-molecule organic carbon, can effectively use sulfur compounds as electron donor to reduce As(V) to mobile As(III). Arsenic release experiments using DARP population and a cultivable DARP strain showed that DARPs indeed utilized sulfur compounds as the sole electron donors under autotrophic and anaerobic conditions to directly reduce adsorbed As(V) in the soils to mobile As(III). These findings provide new insights into the microbial mechanism responsible for the variation of As(III) concentrations in contaminated groundwater.

Can Sb(III)-oxidizing prokaryote also oxidize As(III) under aerobic and anaerobic conditions, and vice versa?

Sb(III) and As(III) share similar chemical features and coexist in the environment. However, their oxidase enzymes have completely different sequences and structures. This raises an intriguing question: Could Sb(III)-oxidizing prokaryotes (SOPs) also oxidize As(III), and vice versa? Regarding this issue, previous investigations have yielded unclear, incorrect and even conflicting data. This work aims to address this matter. First, we prepared an enriched population of SOPs that comprises 55 different AnoA genes, lacking AioAB and ArxAB genes. We found that these SOPs can oxidize both Sb(III) and As(III) with comparable capabilities. To further confirm this finding, we isolated three cultivable SOP strains that have AnoA gene, but lack AioAB and ArxAB genes. We observed that they also oxidize both Sb(III) and As(III) under both anaerobic and aerobic conditions. Secondly, we obtained an enriched population of As(III)-oxidizing prokaryotes (AOPs) from As-contaminated soils, which comprises 69 different AioA genes, lacking AnoA gene. We observed that the AOP population has significant As(III)-oxidizing activities, but lack detectable Sb(III)-oxidizing activities under both aerobic and anaerobic conditions. Therefore, we convincingly show that SOPs can oxidize As(III), but AOPs cannot oxidize Sb(III). These findings clarify the previous ambiguities, confusion, errors or contradictions regarding how SOPs and AOPs oxidize each other's substrate.

Phylogenomic analyses and reclassification of the Mesorhizobium complex: proposal for 9 novel genera and reclassification of 15 species

BACKGROUD

The genus Mesorhizobium is shown by phylogenomics to be paraphyletic and forms part of a complex that includes the genera Aminobacter, Aquamicrobium, Pseudaminobacter and Tianweitania. The relationships for type strains belong to these genera need to be carefully re-evaluated.

RESULTS

The relationships of Mesorhizobium complex are evaluated based on phylogenomic analyses and overall genome relatedness indices (OGRIs) of 61 type strains. According to the maximum likelihood phylogenetic tree based on concatenated sequences of 539 core proteins and the tree constructed using the bac120 bacterial marker set from Genome Taxonomy Database, 65 type strains were grouped into 9 clusters. Moreover, 10 subclusters were identified based on the OGRIs including average nucleotide identity (ANI), average amino acid identity (AAI) and core-proteome average amino acid identity (cAAI), with AAI and cAAI showing a clear intra- and inter-(sub)cluster gaps of 77.40-80.91% and 83.98-86.16%, respectively. Combined with the phylogenetic trees and OGRIs, the type strains were reclassified into 15 genera. This list includes five defined genera Mesorhizobium, Aquamicrobium, Pseudaminobacter, Aminobacterand Tianweitania, among which 40/41 Mesorhizobium species and one Aminobacter species are canonical legume microsymbionts. The other nine (sub)clusters are classified as novel genera. Cluster III, comprising symbiotic M. alhagi and M. camelthorni, is classified as Allomesorhizobium gen. nov. Cluster VI harbored a single symbiotic species M. albiziae and is classified as Neomesorhizobium gen. nov. The remaining seven non-symbiotic members were proposed as: Neoaquamicrobium gen. nov., Manganibacter gen. nov., Ollibium gen. nov., Terribium gen. nov., Kumtagia gen. nov., Borborobacter gen. nov., Aerobium gen. nov.. Furthermore, the genus Corticibacterium is restored and two species in Subcluster IX-1 are reclassified as the member of this genus.

CONCLUSION

The Mesorhizobium complex are classified into 15 genera based on phylogenomic analyses and OGRIs of 65 type strains. This study resolved previously non-monophyletic genera in the Mesorhizobium complex.

Biological oxidation of As(III) and Sb(III) by a novel bacterium with Sb(III) oxidase rather than As(III) oxidase under anaerobic and aerobic conditions

Sb and As are chemically similar, but the sequences and structures of Sb(III) and As(III) oxidase are totally distinct. It is thus interesting to explore whether Sb(III) oxidase oxidizes As(III), and if so, how microbial oxidations of Sb(III) and As(III) influence one another. Previous investigations have yielded ambiguous or even erroneous conclusions. This study aimed to clarify this issue. Firstly, we prepared a consortium of Sb(III)-oxidizing prokaryotes (SOPs) by enrichment cultivation. Metagenomic analysis reveals that SOPs with the Sb(III) oxidase gene, but lacking the As(III) oxidase gene are predominant in the SOP community. Despite this, SOPs exhibit comparable Sb(III) and As(III)-oxidizing activities in both aerobic and anaerobic conditions, indicating that at the microbial community level, Sb(III) oxidase can oxidize As(III). Secondly, we isolated a representative cultivable SOP, Ralstonia sp. SbOX with Sb(III) oxidase gene but without As(III) oxidase gene. Genomic analysis of SbOX reveals that this SOP strain has a complete Sb(III) oxidase (AnoA) gene, but lacks As(III) oxidase (AioAB or ArxAB) gene. It is interesting to discover that, besides its Sb(III) oxidation activities, SbOX also exhibits significant capabilities in oxidizing As(III) under both aerobic and anaerobic conditions. Moreover, under aerobic conditions and in the presence of both Sb(III) and As(III), SbOX exhibited a preference for oxidizing Sb(III). Only after the near complete oxidation of Sb(III) did SbOX initiate rapid oxidation of As(III). In contrast, under anaerobic conditions and in the presence of both Sb(III) and As(III), Sb(III) oxidation notably inhibited the As(III) oxidation pathway in SbOX, while As(III) exhibited minimal effects on the Sb(III) oxidation. These findings suggest that SOPs can oxidize As(III) under both aerobic and anaerobic conditions, exhibiting a strong preference for Sb(III) over As(III) oxidation in the presence of both. This study unveils a novel mechanism of interaction within the Sb and As biogeochemical cycles.

Functional features of a novel Sb(III)- and As(III)-oxidizing bacterium: Implications for the interactions between bacterial Sb(III) and As(III) oxidation pathways

Antimony (Sb) and arsenic (As) share similar chemical characteristics and commonly coexist in contaminated environments. It has been reported that the biogeochemical cycles of antimony and arsenic affect each other. However, there is limited understanding regarding microbial coupling between the biogeochemical processes of antimony and arsenic. Here, we aimed to solve this issue. We successfully isolated a novel bacterium, Shinella sp. SbAsOP1, which possesses both Sb(III) and As(III) oxidase, and can effectively oxidize both Sb(III) and As(III) under aerobic and anaerobic conditions. SbAsOP1 exhibits greater aerobic oxidation activity for the oxidation of As(III) or Sb(III) compared to its anaerobic activity. SbAsOP1 also significantly catalyzes the oxidative mobilization of solid-phase Sb(III) under aerobic conditions. The activity of SbAsOP1 in oxidizing solid Sb(III) is 3 times lower than its activity in oxidizing soluble form. It is noteworthy that, in the presence of both Sb(III) and As(III) under aerobic conditions, either As(III) or Sb(III) significantly inhibits the oxidation of Sb(III) or As(III), respectively. In comparison, under anaerobic conditions and in the coexistence of Sb(III) and As(III), As(III) significantly inhibits Sb(III) oxidation, whereas Sb(III) almost completely inhibits As(III) oxidation. These findings suggest that under both aerobic and anaerobic conditions, SbAsOP1 demonstrates a partial preference for Sb(III) oxidation. Additionally, bacterial oxidations of Sb(III) and As(III) mutually inhibit each other to varying degrees. These observations gain a novel understanding of the interplay between the biogeochemical processes of antimony and arsenic.

Phyllobacteriaceae: a family of ecologically and metabolically diverse bacteria with the potential for different applications

The family Phyllobacteriaceae is a heterogeneous assemblage of more than 146 species of bacteria assigned to its existing 18 genera. Phylogenetic analyses have shown great phylogenetic diversity and also suggested about incorrect classification of several species that need to be reassessed for their proper phylogenetic classification. However, almost 50% of the family members belong to the genus Mesorhizobium only, of which the majority are symbiotic nitrogen fixers associated with different legumes. Other major genera are Phyllobacterium, Nitratireductor, Aquamicrobium, and Aminobacter. Nitrogen-fixing, legume nodulating members are present in Aminobacter and Phyllobacterium as well. Aquamicrobium spp. can degrade environmental pollutants, like 2,4-dichlorophenol, 4-chloro-2-methylphenol, and 4-chlorophenol. Chelativorans, Pseudaminobacter, Aquibium, and Oricola are the other genera that contain multiple species having diverse metabolic capacities, the rest being single-membered genera isolated from varied environments. In addition, heavy metal and antibiotic resistance, chemolithoautotrophy, poly-β-hydroxybutyrate storage, cellulase production, etc., are the other notable characteristics of some of the family members. In this report, we have comprehensively reviewed each of the species of the family Phyllobacteriaceae in their eco-physiological aspects and found that the family is rich with ecologically and metabolically highly diverse bacteria having great potential for human welfare and environmental clean-up.

Environmental Mn(II) enhances the activity of dissimilatory arsenate-respiring prokaryotes from arsenic-contaminated soils

Many investigations suggest that dissimilatory arsenate-respiring prokaryotes (DARPs) play a key role in stimulating reductive mobilization of As from solid phase into groundwater, but it is not clear how environmental Mn(II) affects the DARPs-mediated reductive mobilization of arsenic. To resolve this issue, we collected soil samples from a realgar tailings-affected area. We found that there were diverse arsenate-respiratory reductase (arr) genes in the soils. The microbial communities had high arsenate-respiring activity, and were able to efficiently stimulate the reductive mobilization of As. Compared to the microcosms without Mn(II), addition of 10 mmol/L Mn(II) to the microcosms led to 23.99%-251.79% increases in the microbial mobilization of As, and led to 133.3%-239.2% increases in the abundances of arr genes. We further isolated a new cultivable DARP, Bacillus sp. F11, from the arsenic-contaminated soils. It completely reduced 1 mmol/L As(V) in 5 days under the optimal reaction conditions. We further found that it was able to efficiently catalyze the reductive mobilization and release of As from the solid phase; the addition of 2 mmol/L Mn(II) led to 98.49%-248.78% increases in the F11 cells-mediated reductive mobilization of As, and 70.6%-104.4% increases in the arr gene abundances. These data suggest that environmental Mn(II) markedly increased the DARPs-mediated reductive mobilization of As in arsenic-contaminated soils. This work provided a new insight into the close association between the biogeochemical cycles of arsenic and manganese.

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

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

Biological effect of phosphate on the dissimilatory arsenate-respiring bacteria-catalyzed reductive mobilization of arsenic from contaminated soils

Dissimilatory arsenate-respiring prokaryotes (DARPs) are considered to be the major drive of the reductive mobilization of arsenic from solid phases. However, it is not fully understood how phosphate, a structural analog of arsenate, affects the DARPs-mediated arsenic mobilization. This work aimed to address this issue. As-contaminated soils were collected from a Shimen Realgar Mine-affected area. We identified a unique diversity of DARPs from the soils, which possess high As(V)-respiring activities using one of multiple small organic acids as the electron donor. After elimination of the desorption effect of phosphate on the As mobilization, the supplement of additional 10 mM phosphate to the active slurries markedly increased the microbial community-mediated reductive mobilization of arsenic as revealed by microcosm tests; this observation was associated to the fact that phosphate significantly increased the As(V)-respiratory reductase (Arr) gene abundances in the slurries. To confirm this finding, we further obtained a new DARP strain, Priestia sp. F01, from the samples. We found that after elimination of the chemical effect of phosphate, the supplement of 10 mM phosphate to the active slurries resulted in an 82.2% increase of the released As(III) in the solutions, which could be contributed to that excessive phosphate greatly increased the Arr gene abundance, and enhanced the transcriptional level of arrA gene and the bacterial As(V)-respiring activity of F01 cells. Considering that phosphate commonly coexists with As in the environment, and is a frequently-used fertilizer, these findings are helpful for deeply understanding why As concentrations in contaminated groundwater are dynamically fluctuated, and also provided new knowledge on the interactions between the biogeochemical processes of P and As.

Proteomics and transcriptomic analysis of Micrococcus luteus strain AS2 under arsenite stress and its potential role in arsenic removal

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M. luteus strain AS2 showed hyper-tolerance against arsenite upto 50 mM.

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Thioredoxin reductase, involved in As-resistance, upregulated 2.8 folds under arsenite stress.

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The maximum metal oxidizing processing ability of the strain AS2 was 90%.

The proteomics and transcriptomic analysis of Micrococcus luteus strain AS2 was carried out through 2D gel electrophoresis and RT-PCR. Seven protein spots were selected randomly from the gel and identified through mass spectrometry. Four proteins including putative metal-dependent hydrolase TatD, thioredoxin reductase, DNA-directed RNA polymerase subunit alpha and chaperone protein DnaK were upregulated while superoxide dismutase [Mn], 3-oxoacyl-[acyl-carrier-protein] reductase FabG, and putative alkyl/aryl-sulfatase YjcS were down-regulated under arsenite stress. No significant difference was observed in aioB gene expression analysis in the presence and absence of arsenite. The optimum arsenite processing ability was determined at 37°C (90%) and at pH 7 (92%). The maximum metal processing ability was determined at 250 mM arsenite/L (90%) while the minimum was estimated at 1250 mM arsenite/L (42%). The maximum arsenite removal ability of strain AS2 determined after 8 days was 68 and 82% from wastewater and distilled water, and the organism can be a good bioresource for green chemistry to eradicate environmental arsenite.

Unraveling the Central Role of Sulfur-Oxidizing Acidiphilium multivorum LMS in Industrial Bioprocessing of Gold-Bearing Sulfide Concentrates

Acidiphilium multivorum LMS is an acidophile isolated from industrial bioreactors during the processing of the gold-bearing pyrite-arsenopyrite concentrate at 38–42 °C. Most strains of this species are obligate organoheterotrophs that do not use ferrous iron or reduced sulfur compounds as energy sources. However, the LMS strain was identified as one of the predominant sulfur oxidizers in acidophilic microbial consortia. In addition to efficient growth under strictly heterotrophic conditions, the LMS strain proved to be an active sulfur oxidizer both in the presence or absence of organic compounds. Interestingly, Ac. multivorum LMS was able to succeed more common sulfur oxidizers in microbial populations, which indicated a previously underestimated role of this bacterium in industrial bioleaching operations. In this study, the first draft genome of the sulfur-oxidizing Ac. multivorum was sequenced and annotated. Based on the functional genome characterization, sulfur metabolism pathways were reconstructed. The LMS strain possessed a complicated multi-enzyme system to oxidize elemental sulfur, thiosulfate, sulfide, and sulfite to sulfate as the final product. Altogether, the phenotypic description and genome analysis unraveled a crucial role of Ac. multivorum in some biomining processes and revealed unique strain-specific characteristics, including the ars genes conferring arsenic resistance, which are similar to those of phylogenetically distinct microorganisms.

Use of heavy metals resistant bacteria-a strategy for arsenic bioremediation

A large number of industries release their untreated wastes in the environment causing an increase in the concentration of toxic pollutants including heavy metal ions in ground and drinking water which is above the WHO limit. The presence of toxic pollutants in the industrial wastes pollutes our environment. Arsenic (As) is a ubiquitous toxic metalloid. Its amount varies in different parts on the earth, and its concentration is increasing in our environment day by day both by natural and anthropogenic activities. It is found in two forms; one is arsenate (As⁵⁺) and other is arsenite (As³⁺) and the latter is more toxic due to high mobility across the cell membrane. The long-term use of arsenic-containing water causes arsenicosis. High arsenic consumption, revealed by skin harms, color change, and spots on hands and feet, may cause skin cancer and affect lungs and kidneys. Hypertension, a state of high blood pressure, and lack of insulin which causes diabetes and many other disorders which relate to reproduction are the consequences of arsenic contamination. Several methods have been employed to decontaminate arsenic pollution, but the bioremediation by using biomass of bacteria, algae, fungi, and yeasts is the most compromising approach and has gained much attention from researchers in the last few decades. The microbial detoxification of arsenic can be achieved by reduction, oxidation, and methylation. High bioremediation potential and feasibility of the process make bacteria an impending foundation for green chemistry to exterminate arsenic in the environment.