Sedimentary arsenite-oxidizing and arsenate-reducing bacteria associated with high arsenic groundwater from Shanyin, Northwestern China

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.

Novel insights into the co-selection of metal-driven antibiotic resistance in bacteria: a study of arsenic and antibiotic co-exposure

The simultaneous development of antibiotic resistance in bacteria due to metal exposure poses a significant threat to the environment and human health. This study explored how exposure to both arsenic and antibiotics affects the ability of an arsenite oxidizer, Achromobacter xylosoxidans CAW4, to transform arsenite and its antibiotic resistance patterns. The bacterium was isolated from arsenic-contaminated groundwater in the Chandpur district of Bangladesh. We determined the minimum inhibitory concentration (MIC) of arsenite, cefotaxime, and tetracycline for A. xylosoxidans CAW4, demonstrating a multidrug resistance (MDR) trait. Following this determination, we aimed to mimic an environment where A. xylosoxidans CAW4 was exposed to both arsenite and antibiotics. We enabled the strain to grow in sub-MIC concentrations of 1 mM arsenite, 40 µg/mL cefotaxime, and 20 µg/mL tetracycline. The expression dynamics of the arsenite oxidase (aioA) gene in the presence or absence of antibiotics were analyzed. The findings indicated that simultaneous exposure to arsenite and antibiotics adversely affected the bacteria's capacity to metabolize arsenic. However, when arsenite was present in antibiotics-containing media, it promoted bacterial growth. The study observed a global downregulation of the aioA gene in arsenic-antibiotic conditions, indicating the possibility of increased susceptibility through co-resistance across the entire bacterial population of the environment. This study interprets that bacterial arsenic-metabolizing ability can rescue the bacteria from antibiotic stress, further disseminating environmental cross-resistance. Therefore, the co-selection of metal-driven antibiotic resistance in bacteria highlights the need for effective measures to address this emerging threat to human health and the environment.

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.

Addition of plantation waste to the bioconversion of pig manure by black soldier fly larvae: Effects on heavy metal content and bioavailability

During the conversion of pig manure by black soldier fly larvae (BSFL), the accumulation and speciation changes of heavy metals (HMs) have adverse effects on the environment. In this study, corn straw, rice straw, bamboo chips (BC), wood chips, and rice husk char were added to a bioconversion system to study the accumulation, migration, speciation changes, and microbial correlations of HMs. The results indicated that the addition of BC was most beneficial for the accumulation of HMs (47-72 %) in the BSFL body. In the BC group, the accumulation effect of the BSFL body on zinc (Zn) and arsenic (As) was the most evident (72 and 71 %, respectively). The results of linear fitting (R2 > 0.90) and redundancy analysis (RDA; 90 %) indicated that the bacterium Bacillaceae (Bacillus) was beneficial for increasing the larval weight (LW) of BSFL, and a higher LW accumulated HMs. The addition of BC helped reduce the total amount (6-51 %) of available states (weak acid extraction and reducible states) in the BSFL residue. The RDA results indicated that bacteria (55-92 %) affected the transformation of HM speciation. For example, Zn and cadmium were mainly affected by Firmicutes, whereas copper and chromium were affected by Bacteroidetes. Proteobacteria and Pseudomonas formosensis affected the conversion of lead and As. This study provides important insights into the adsorption of HMs from pig manure by BSFL.

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.

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.

Microbial community composition analysis to decipher the possible role of inherent bacteria for in-situ arsenic (As) bioremediation

Biogeochemical reduction and mobilization of sediment-bound arsenic (As) is the major concern for widespread groundwater As contamination in the middle Gangetic plains. The present work examines a microcosm based bio-stimulation study and substrate amendments over 45 days to analyze the bacterial community structure and distribution to indicate the possible in-situ bioremediation strategy in the area. Initially, Bacterial phyla Proteobacteria was predominantly present in all the samples, followed by Actinobacteria, Bacteroidetes, and Firmicutes whereas Cyanobacteria was noted as the minor group. In genus level, Delftia, Acinetobacter, Lysobacter, Bacillus, and Pseudomonas were the major groups of bacteria in the As-rich aquifer system, while Planctomycetes dominated the bio-stimulated samples, followed by a minute portion of Proteobacteria. Alpha diversity and Chaol curve further determined the species richness in the samples with an As tolerant capacity of 152.28 ppb. The presence of γ-Proteobacteria as the dominating member in high As-content water indicated their predominant role in As mobilization, whereas, dominance of α-Proteobacterial members in low As-content water indicated their involvement in As detoxification. The complete change in microbial community structure within the bio-stimulated conditions indicated the extensive role of arsenite-oxidizing microbial communities within different levels of As-contaminated areas in Bihar that will enlighten the significant role of these communities in As-biogeochemical cycle.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03612-0.

Mitigation of arsenic toxicity in rice by the co-inoculation of arsenate reducer yeast with multifunctional arsenite oxidizing bacteria

The study aimed to explicate the role of microbial co-inoculants for the mitigation of arsenic (As) toxicity in rice. Arsenate (AsV) reducer yeast Debaryomyces hansenii NBRI-Sh2.11 (Sh2.11) with bacterial strains of different biotransformation potential was attempted to develop microbial co-inoculants. An experiment to test their efficacy (yeast and bacterial strains) on plant growth and As uptake was conducted under a stressed condition of 20 mg kg-1 of arsenite (AsIII). A combination of Sh2.11 with an As(III)-oxidizer, Citrobacter sp. NBRI-B5.12 (B5.12), resulted in ∼90% decrease in grain As content as compared to Sh2.11 alone (∼40%). Reduced As accumulation in rice roots under co-treated condition was validated with SEM-EDS analysis. Enhanced As expulsion in the selected combination under in vitro conditions was found to be correlated with higher As content in the soil during their interaction with plants. Selected co-inoculant mediated enhanced nutrient uptake in association with better production of indole acetic acid (IAA) and gibberellic acid (GA) in shoot, support microbial co-inoculant mediated better biomass under stressful condition. Boosted defense response in association with enhanced glutathione-S-transferase (GST) and glutathione reductase (GR), activities under in vitro and in vivo conditions were observed. These results indicated that the As(III) oxidizer-B5.12 accelerated the As detoxification property of the As(V) reducer-Sh2.11. Henceforth, the results confer that the coupled reduction-oxidation process of the co-inoculant reduces the accumulation of As in rice grain. These co-inoculants can be further developed for field trials to achieve higher biomass with alleviated As toxicity in rice.

Geogenic arsenic and arsenotrophic microbiome in groundwater from the Hetao Basin

High arsenic (As) in groundwater is an environmental issue of global concern, which is closely related to microbe-mediated As biogeochemical cycling. However, the distribution of genes related to As cycling and underlying microbial As biogeochemical processes in high As groundwater remain elusive. Hence, we profiled the As cycling genes (arsC, arrA, and aioA genes) and indigenous microbial communities in groundwater from a typical high As area, the Hetao Basin from China, using amplicon sequencing and qPCR techniques. Here, we revealed the significant difference in microbial community structure between low As groundwater samples (LG) and high As groundwater samples (HG). Acinetobacter, Thiovirga, Hydrogenophaga, and Sulfurimonas were dominant in LG, while Aquabcterium, Acinetobacter, Sphingomonas, Pseudomonas, Desulfomicrobium, Hydrogenophaga, and Nitrospira were predominant in HG. Shannon and Chao indices of the microbial communities in HG were significantly higher than those of in LG. Alpha diversity and abundance of arsC and arrA genes were higher than those of aioA genes. The significant positive correlation was uncovered between the abundances of arsC and aioA genes, suggesting the cooccurrence of As functional genes in groundwater. Sphingopyxis, Agrobacterium, Klebsiella, Hoeflea, and Aeromonas represented the dominant taxa within the As (V) reducers communities. Distance-based redundancy analysis showed that ORP, pH, As_tot, Mn, and DOC were the key factors shaping the diverse microbial populations, while ORP, S^2-, As(III), Fe(II), NH₄⁺, pH, Mn, SO₄^2-, As(V), temperature, and P as the main drivers affecting arsenotrophic microbiota. This work provides an insight into microbial communities linked to As biogeochemical processes in high As groundwater, playing a fundamental role in groundwater As cycling.

Lysobacter selenitireducens sp. nov., isolated from river sediment

A Gram-stain-negative, yellow-pigmented, motile, flagellated and rod-shaped bacterium, designated as 13A^T, was isolated from a river sediment sample of Fuyang River in Hengshui City, Hebei Province, PR China. Strain 13A^T grew at 10-37 °C (optimum, 30 °C), at pH 5.0-11.0 (optimum, pH 7.0) and at 0-7 % (w/v) NaCl concentration (optimum, 0 %). Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain 13A^T belongs to the genus Lysobacter, and was most closely related to Lysobacter spongiicola DSM 21749^T (97.8 %), Lysobacter concretionis DSM 16239^T (97.5 %), Lysobacter daejeonensis GIM 1.690^T (97.3 %) and Lysobacter arseniciresistens CGMCC 1.10752^T (96.9 %). Meanwhile, the type species Lysobacter enzymogenes ATCC 29487^T was selected as a reference strain (95.2 %). The genomic size of strain 13A^T was 3.0 Mb and the DNA G+C content was 69.0 %. The average nucleotide identity values between strain 13A^T and each of the reference type strains L. spongiicola DSM 21749^T, L. concretionis DSM 16239^T, L. daejeonensis GIM 1.690^T, L. arseniciresistens CGMCC 1.10752^T and L. enzymogenes ATCC 29487^T were 75.9, 76.1, 77.7, 78.0 and 73.2 %, respectively. The digital DNA-DNA hybridization values between strain 13A^T and each of the reference type strains were 21.7, 22.2, 21.9, 22.7 and 23.2 %, respectively. The average amino acid identity values between strain 13A^T and each of the reference type strains were 72.5, 72.9, 72.3, 75.0 and 69.2 %, respectively. The major fatty acids were iso-C_15 : 0, iso-C_16 : 0 and summed feature 9 (iso-C_17 : 1  ω9c and/or C_16 : 0 10-methyl). The sole respiratory quinone was identified as ubiquinone-8. The polar lipid profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid, an unidentified lipid, four unidentified phospholipids and two unidentified glycolipids. Based on the phenotypic, physiological, phylogenetic and chemotaxonomic data, strain 13A^T represents a novel species of the genus Lysobacter, for which the name Lysobacter selenitireducens sp. nov. is proposed. The type strain is 13A^T (=JCM 34786^T=GDMCC 1.2722^T).

Antimony redox processes in the environment: A critical review of associated oxidants and reductants

The environmental behavior of antimony (Sb) has recently received greater attention due to the increasing global use of Sb in a range of industrial applications. Although present at trace levels in most natural systems, elevated Sb concentrations in aquatic and terrestrial environments may result from anthropogenic activities. The mobility and toxicity of Sb largely depend on its speciation, which is dependent to a large extent on its oxidation state. To a certain extent, our understanding of the environmental behavior of Sb has been informed by studies of the environmental behavior of arsenic (As), as Sb and As have somewhat similar chemical properties. However, recently it has become evident that the speciation of Sb and As, especially in the context of redox reactions, may be fundamentally different. Therefore, it is crucial to study the biogeochemical processes impacting Sb redox transformations to understand the behavior of Sb in natural and engineered environments. Currently, there is a growing body of literature involving the speciation, mobility, toxicity, and remediation of Sb, and several reviews on these general topics are available; however, a comprehensive review focused on Sb environmental redox chemistry is lacking. This paper provides a review of research conducted within the past two decades examining the redox chemistry of Sb in aquatic and terrestrial environments and identifies knowledge gaps that need to be addressed to develop a better understanding of Sb biogeochemistry for improved management of Sb in natural and engineered systems.

Flavobacterium selenitireducens sp. nov., isolated from rhizosphere soil of ancient mulberry

A Gram-stain-negative, non-motile, aerobic, yellow, convex, rod-shaped mesophilic bacterial strain, designated strain D33T, was isolated from rhizosphere soil of ancient mulberry in Dezhou city, Shandong province, PR China. The strain grew at 8–37 °C (optimum, 30 °C), pH 4–9 (optimum, pH 7) and growth occurred at 0.5–5.5 % (w/v) NaCl (optimally at 1 %). The results of the phylogenetic analyses of 16S rRNA gene and whole genome sequences indicated that D33T was closely related to members of the genus Flavobacterium and had the highest 16S rRNA gene sequence similarity with ‘Flavobacterium agri’ KACC 19300 (95.4 %), Flavobacterium ichthyis NST-5T (94.6 %), Flavobacterium ahnfeltiae KCTC 32467T (93.6 %) and Flavobacterium longum JCM 19141T (93.6 %). The genome size of D33T was 3.8 Mb and the DNA G+C content was 48.0 mol%. The average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH) and average amino acid identity (AAI) values among D33T and reference strains were lower than the threshold values for species delineation. The only respiratory quinone of D33T was menaquinone 6 (MK-6). The predominant fatty acids (>5 %) were C15:0, C16 : 0, C18 : 0, iso-C15:0, iso–C17 : 0 3-OH, anteiso-C15 : 0 and summed feature 9 . The polar lipid profile contained phosphatidylethanolamine, two unidentified aminophospholipids, three unidentified aminolipids and two unidentified lipids. Combined data from phenotypic, phylogenetic and chemotaxonomic studies indicated that D33T is a representative of a novel species of the genus Flavobacterium, for which the name Flavobacterium selenitireducens sp. nov. is proposed. The type strain is D33T (=GDMCC 1.1946T=KACC 22131T).

Recent Progress and Prospects in Catalytic Water Treatment

Presently, conventional technologies in water treatment are not efficient enough to completely mineralize refractory water contaminants. In this context, the implementation of catalytic processes could be an alternative. Despite the advantages provided in terms of kinetics of transformation, selectivity, and energy saving, numerous attempts have not yet led to implementation at an industrial scale. This review examines investigations at different scales for which controversies and limitations must be solved to bridge the gap between fundamentals and practical developments. Particular attention has been paid to the development of solar-driven catalytic technologies and some other emerging processes, such as microwave assisted catalysis, plasma-catalytic processes, or biocatalytic remediation, taking into account their specific advantages and the drawbacks. Challenges for which a better understanding related to the complexity of the systems and the coexistence of various solid-liquid-gas interfaces have been identified.

Bioaccumulation and detoxification of trivalent arsenic by Achromobacter xylosoxidans BHW-15 and electrochemical detection of its transformation efficiency

Arsenotrophic bacteria play an essential role in lowering arsenic contamination by converting toxic arsenite [As (III)] to less toxic and less bio-accumulative arsenate [As (V)]. The current study focused on the qualitative and electrocatalytic detection of the arsenite oxidation potential of an arsenite-oxidizing bacteria A. xylosoxidans BHW-15 (retrieved from As-contaminated tube well water), which could significantly contribute to arsenic detoxification, accumulation, and immobilization while also providing a scientific foundation for future electrochemical sensor development. The minimum inhibitory concentration (MIC) value for the bacteria was 15 mM As (III). Scanning Electron Microscopy (SEM) investigation validated its intracellular As uptake capacity and demonstrated a substantial association with the MIC value. During the stationary phase, the strain’s As (III) transformation efficiency was 0.0224 mM/h. Molecular analysis by real-time qPCR showed arsenite oxidase (aioA) gene expression increased 1.6-fold in the presence of As (III) compared to the untreated cells. The immobilized whole-cell also showed As (III) conversion up to 18 days. To analyze the electrochemical oxidation in water, we developed a modified GCE/P-Arg/ErGO-AuNPs electrode, which successfully sensed and quantified conversion of As (III) into As (V) by accepting electrons; implying a functional As oxidase enzyme activity in the cells. To the best of our knowledge, this is the first report on the electrochemical observation of the As-transformation mechanism with Achromobactersp. Furthermore, the current work highlighted that our isolate might be employed as a promising candidate for arsenic bioremediation, and information acquired from this study may be helpful to open a new window for the development of a cost-effective, eco-friendly biosensor for arsenic species detection in the future.

Hyphomicrobium album sp. nov., isolated from mountain soil and emended description of genus Hyphomicrobium

A soil bacterium, designated XQ2^T, was isolated from Lang Mountain in Hunan province, P. R. China. The strain is Gram stain negative, facultative anaerobic, and the cells are motile and rod-shaped. The 16S rRNA gene sequence of strain XQ2^T shared the highest similarities with Hyphomicrobium sulfonivorans S1^T (97.1%), Pedomicrobium manganicum ACM 3038^T (95.9%) and Hyphomicrobium aestuarii DSM 1564^T (95.4%) and grouped with H. sulfonivorans S1^T. The average nucleotide identity (ANI) values and the DNA-DNA hybridization (dDDH) values between strain XQ2^T and H. sulfonivorans S1^T were 86.6% and 55.4% respectively. Strain XQ2^T had a genome size of 3.91 Mb and the average G+C content was 65.1%. The major fatty acids (> 5%) were C_18:1ω6c, C_18:1ω7c, C_19:0 cyclo ω8c, C_16:0 and C_18:0. The major respiratory quinone was Q-9 (82.8%) and the minor one was Q-8 (17.2%). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, unidentified phospholipid and two unidentified lipids. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, strain XQ2^T represents a novel species of the genus Hyphomicrobium, for which the name Hyphomicrobium album sp. nov. is proposed. The type strain is XQ2^T (= KCTC 82378^T = CCTCC AB 2020178^T). The genus description is also emended.

Blautia liquoris sp. nov., isolated from the mud in a fermentation cellar used for the production of Chinese strong-flavour liquor

A novel Gram-positive, non-motile, non-flagellated, strictly anaerobic, non-spore-forming and dumbbell-shaped, coccoid- or chain-shaped bacterium, designated strain LZLJ-3^T, was isolated from a mud fermentation cellar which has been used for the production of Chinese strong-flavour liquor for over 100 years. Strain LZLJ-3^T grew at 20-40 °C (optimum, 37 °C), at pH 6.0-8.0 (optimum, pH 8.0) and with NaCl concentrations up to 1 % (w/v; optimum, 0 %). Phylogenetic trees established based on 16S rRNA gene sequences showed that strain LZLJ-3^T belonged to the genus Blautia of the family Lachnospiraceae, with the highest sequence similarity to Blautia stercoris GAM6-1^T (91.7 %) and Blautia faecicola KGMB01111^T (91.7 %). Comparative genome analysis showed that the orthologous average nucleotide identity (OrthoANI) and genome-to-genome distance (GGD) values between strain LZLJ-3^T and B. stercoris GAM6-1^T were respectively 69.1 and 22.9 %; the OrthoANI and GGD values between strain LZLJ-3^T and B. faecicola KGMB01111^T were respectively 70.86 and 36 % . The DNA G+C content of strain LZLJ-3^T genome was 42.1 mol%. The predominant celluar fatty acids (>10 %) of strain LZLJ-3^T were C_16 : 0 FAME (27.9 %), C_14 : 0 FAME (17.6 %) and C_16 : 0 DMA (13.0 %). Arabinose, glucose and maltose could be utilized by strain LZLJ-3^T as sole carbon sources for growth, with weak utilization of raffinose and l-fucose. API ZYM analysis gave positive reactions with α-galactosidase, β-galactosidase, α-glucosidase and β-glucosidase. The major end product of glucose fermentation was acetic acid. Based on the results of phenotypic, genotypic and phylogenetic analyses, strain LZLJ-3^T is considered to represent a novel species of Blautia, for which the name Blautia liquoris sp. nov. is proposed. The type strain is LZLJ-3^T (=KCTC 25163^T=CGMCC 1.5299^T=JCM 34225^T).

Diversity and arsenic-metabolizing gene clusters of indigenous arsenate-reducing bacteria in high arsenic groundwater of the Hetao Plain, Inner Mongolia

Dissimilatory arsenate reduction from arsenic (As)-bearing minerals into highly mobile arsenite is one of the key mechanisms of As release into groundwater. To detect the microbial diversity and As-metabolizing gene clusters of indigenous arsenate-reducing bacteria in high As groundwater in the Hetao Plain of Inner Mongolia, China, three anaerobic arsenate-reducing bacteria were isolated and arrA and arsC gene-based clone libraries of four in situ groundwater samples were constructed. The strains IMARCUG-11(G-11), IMARCUG-C1(G-C1) and IMARCUG-12(G-12) were phylogenetically belonged to genera Paraclostridium, Citrobacter and Klebsiella, respectively. They could reduce >99% of 1 mM arsenate under anoxic conditions with lactate as a carbon source in 60 h, 72 h and 84 h, respectively. As far as we know, this was the first report of arsenate reduction by genus Paraclostridium. Compared with strain G-11 (arsC) and G-C1 (arsRBC), strain G-12 contained two incomplete ars operons (operon1: arsABC, operon2: arsBC), indicating that these strains might present different strategies to resist As toxicity. Phylogenetic analysis illuminating by the arrA genes showed that in situ arsenate-reducing bacterial communities were diverse and mainly composed of Desulfobacterales (53%, dominated by Geobacter), Betaproteobacteria (12%), and unidentified groups (35%). Based on the arsC gene analysis, the indigenous arsenate-reducing bacterial communities were mainly affiliated with Omnitrophica (88%) and Deltaproteobacteria (11%, dominated by Geobacter and Syntrophobacterales). Results of this study expanded our understanding of indigenous arsenic-reducing bacteria in high As groundwater aquifers.

Arsenate reducing bacteria isolated from the marine sponge Theonella swinhoei: Bioremediation potential

Arsenic (As) contamination of freshwater resources constitutes a major environmental issue affecting over 200 million people worldwide. Although the use of microorganisms for the bioremediation of As has been well studied, only very few candidates have been identified to date. Here, we investigated bacteria associated with the Red Sea sponge Theonella swinhoei and their potential to reduce As in a low-salinity liquid medium. This Indo-Pacific common sponge has been shown to hyper-accumulate As, at an average concentration of 8600 mg/g^-1 in an environment uncontaminated by arsenic or barium. Four isolated strains of bacteria exhibited arsenic reduction potential by transforming inorganic As in the form of arsenate (iAs^V) to arsenite (iAs^III). Two of these isolates were identified as Alteromonas macleodii and Pseudovibrio ascidisceicola, and the other two isolates, both belonging to the same species, were identified as Pseudovibrio denitrificans. The four isolates were then cultured in a low-salinity iAs^V-rich medium (5 mM) and As concentration was measured over time using a specifically designed high-performance liquid chromatograph coupled to a mass spectrometer (HPLC-MS). Out of the four isolates, A. macleodii and P. ascidisceicola grew successfully in a low-salinity liquid medium and reduced As^V to As^III at an average rate of 0.094 and 0.083 mM/h, respectively, thereby demonstrating great potential for the bioremediation of As-contaminated groundwater.

Steroidobacter gossypii sp. nov., isolated from cotton field soil

A Gram-negative bacterium, designated S1-65^T, was isolated from soil samples collected from a cotton field located in the Xinjiang region of PR China. Results of 16S rRNA gene sequence analysis revealed that strain S1-65^T was affiliated to the genus Steroidobacter with its closest phylogenetic relatives being 'Steroidobacter cummioxidans' 35Y (98.4 %), 'Steroidobacter agaridevorans' SA29-B (98.3 %) and Steroidobacter agariperforans KA5-B^T (98.3 %). 16S rRNA-directed phylogenetic analysis showed that strain S1-65^T formed a unique phylogenetic subclade next to 'S. agaridevorans' SA29-B and S. agariperforans KA5-B^T, suggesting that strain S1-65^T should be identified as a member of the genus Steroidobacter. Further, substantial differences between the genotypic properties of strain S1-65^T and the members of the genus Steroidobacter, including average nucleotide identity and digital DNA-DNA hybridization, resolved the taxonomic position of strain S1-65^T and suggested its positioning as representing a novel species of the genus Steroidobacter. The DNA G+C content of strain S1-65^T was 62.5 mol%, based on its draft genome sequence. The predominant respiratory quinone was ubiquinone-8. The main fatty acids were identified as summed feature 3 (C_16:1ω6c/C_16:1ω7c), C_16 : 0 and iso-C_15 : 0. In addition, its polar lipid profile was composed of aminophospholipid, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Here, we propose a novel species of the genus Steroidobacter: Steroidobacter gossypii sp. nov. with the type strain S1-65^T (=JCM 34287^T=CGMCC 1.18736^T).

Genomic molecular signatures determined characterization of Mycolicibacterium gossypii sp. nov., a fast-growing mycobacterial species isolated from cotton field soil

A Gram-positive, acid-fast and rapidly growing rod, designated S2-37 ^T, that could form yellowish colonies was isolated from one soil sample collected from cotton cropping field located in the Xinjiang region of China. Genomic analyses indicated that strain S2-37 ^T harbored T7SS secretion system and was very likely able to produce mycolic acid, which were typical features of pathogenetic mycobacterial species. 16S rRNA-directed phylogenetic analysis referred that strain S2-37 ^T was closely related to bacterial species belonging to the genus Mycolicibacterium, which was further confirmed by pan-genome phylogenetic analysis. Digital DNA-DNA hybridization and the average nucleotide identity presented that strain S2-37 ^T displayed the highest values of 39.1% (35.7-42.6%) and 81.28% with M. litorale CGMCC 4.5724 ^T, respectively. And characterization of conserved molecular signatures further supported the taxonomic position of strain S2-37 ^T belonging to the genus Mycolicibacterium. The main fatty acids were identified as C_16:0, C_18:0, C_20:3ω3 and C_22:6ω3. In addition, polar lipids profile was mainly composed of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. Phylogenetic analyses, distinct fatty aids and antimicrobial resistance profiles indicated that strain S2-37 ^T represented genetically and phenotypically distinct from its closest phylogenetic neighbour, M. litorale CGMCC 4.5724 ^T. Here, we propose a novel species of the genus Mycolicibacterium: Mycolicibacterium gossypii sp. nov. with the type strain S2-37 ^T (= JCM 34327 ^T = CGMCC 1.18817 ^T).

Integrated Metabolomics and Targeted Gene Transcription Analysis Reveal Global Bacterial Antimonite Resistance Mechanisms

Antimony (Sb)-resistant bacteria have potential applications in the remediation of Sb-contaminated sites. However, the effect of Sb(III) exposure on whole-cell metabolic change has not been studied. Herein, we combined untargeted metabolomics with a previous proteomics dataset and confirmatory gene transcription analysis to identify metabolic responses to Sb(III) exposure in Agrobacterium tumefaciens GW4. Dynamic changes in metabolism between control and Sb(III)-exposed groups were clearly shown. KEGG pathway analysis suggested that with Sb(III) exposure: (1) the branching pathway of gluconeogenesis is down-regulated, resulting in the up-regulation of pentose phosphate pathway to provide precursors of anabolism and NADPH; (2) glycerophospholipid and arachidonic acid metabolisms are down-regulated, resulting in more acetyl-CoA entry into the TCA cycle and increased capacity to produce energy and macromolecular synthesis; (3) nucleotide and fatty acid synthesis pathways are all increased perhaps to protect cells from DNA and lipid peroxidation; (4) nicotinate metabolism increases which likely leads to increased production of co-enzymes (e.g., NAD⁺ and NADP⁺) for the maintenance of cellular redox and Sb(III) oxidation. Expectedly, the total NADP⁺/NADPH content, total glutathione, and reduced glutathione contents were all increased after Sb(III) exposure in strain GW4, which contribute to maintaining the reduced state of the cytoplasm. Our results provide novel information regarding global bacterial responses to Sb(III) exposure from a single gene level to the entire metabolome and provide specific hypotheses regarding the metabolic change to be addressed in future research.

Seasonal variations in arsenic mobility and bacterial diversity: The case study of Huangshui Creek, Shimen Realgar Mine, Hunan Province, China

Rivers throughout the world have been contaminated by arsenic dispersed from mining activities. The biogeochemical cycling of this arsenic has been shown to be due to factors such as pH, Eh, ionic strength and microbial activity, but few studies have examined the effects of both seasonal changes and microbial community structure on arsenic speciation and flux in mining-affected river systems. To address this research gap, a study was carried out in Huangshui Creek, Hunan province, China, which has been severely impacted by long-term historic realgar (α-As₄S₄) mining. Water and sediment sampling, and batch experiments at different temperatures using creek sediment, were used to determine the form, source and mobility of arsenic. Pentavalent (AsO₄³) and trivalent arsenic (AsO₃^3-) were the dominant aqueous species (70-89% and 30-11%, respectively) in the creek, and the maximum concentration of inorganic arsenic in surface water was 10,400 μg/L. Dry season aqueous arsenic concentrations were lower than those in the wet season samples. The sediments contained both arsenate and arsenite, and relative proportions of these varied with season. 8.3 tons arsenic per annum were estimated to be exported from Huangshui Creek. Arsenic release from sediment increased by 3 to 5 times in high water temperature batch experiments (25 and 37 °C) compared to those carried out at low temperature (8 °C). Our data suggest that the arsenic-containing sediments were the main source of arsenic contamination in Huangshui Creek. Microbial community structured varied at the different sample sites along the creek. Redundancy analysis (RDA) showed that both temperature and arsenic concentrations were the main controlling factors on the structure of the microbial community. Protecbacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Verrucomicrobia, and Planctomycetes were the stable dominant phyla in both dry and wet seasons. The genera Flavobacterium, Hydrogenophaga and Sphingomonas occurred in the most highly arsenic contaminated sites, which removed arsenic by related metabolism.Our findings indicate that seasonal variations profoundly control arsenic flux and species, microbial community structure and ultimately, the biogeochemical fate of arsenic.

Paraflavitalea devenefica sp. nov., isolated from urban soil

A Gram-stain-negative, rod-shaped, mesophilic, milky white-pigmented, aerobic, non-spore-forming and non-flagellated bacterium, designated strain X16^T, was isolated from urban soil of Zibo, Shandong, China. According to 16S rRNA gene sequence analysis, the isolate showed highest similarities with Paraflavitalea soli 5GH32-13^T (97.6 %), Pseudoflavitalea soli KIS20-3^T (96.2 %), Pseudobacter ginsenosidimutans Gsoil 221^T (96.0 %) and Pseudoflavitalea rhizosphaerae T16R-265^T (95.8 %). The neighbour-joining tree based on 16S rRNA gene sequences showed that strain X16^T formed a subcluster with Paraflavitalea soli 5GH32-13^T, and the subcluster was closely related to Pseudoflavitalea soli KIS20-3^T, Pseudobacter ginsenosidimutans Gsoil 221^T and Pseudoflavitalea rhizosphaerae T16R-265^T. Strain X16^T also formed a subcluster with Paraflavitalea soli 5GH32-13^T in phylogenetic tree based on genomic sequences. The polar lipids are phosphatidylethanolamine, two unknown aminolipids, two unknown aminophospholipids, two unknown lipids and two unknown phospholipids. The major quinone of strain X16^T is menaquinone-7 and the main fatty acids (>10 % of total fatty acids) of strain X16^T are iso-C_15 : 0, iso-C_17 : 0 3-OH and iso-C_15 : 1 G. The genome length of strain X16^T is 8.7 Mb with a DNA G+C content of 47.4 %. ANI values among strain X16^T and strain Paraflavitalea soli 5GH32-13^T, Pseudobacter ginsenosidimutans Gsoil 221^T, and Pseudoflavitalea rhizosphaerae T16R-265^T are 78.1, 70.7, 70.6 %, respectively. On the basis of the results of the polyphasic characterization presented in this study, it is concluded that strain X16^T represents a novel species. Besides, strain X16^T can detoxify high toxicity selenite [Se(IV)] to low toxicity elemental selenium [Se(0)], for which the name Paraflavitale devenefica sp. nov. is proposed. The type strain is X16^T (=KACC 21698^T=GDMCC1.1757^T).

Simultaneous removal of chromate and arsenite by the immobilized Enterobacter bacterium in combination with chemical reagents

Simultaneous chromate [Cr(VI)] reduction and arsenite [As(III)] oxidation is a promising pretreatment process for Cr and As removal. Here, a facultative anaerobic bacterium, Enterobacter sp. Z1, presented capacities of simultaneous Cr(VI) reduction and As(III) oxidation during anoxic cultivation in a wild range of temperature (20-45 °C) and pH (Cerkez et al., 2015; Chen et al., 2015; China Environmental Prote, 1996; Fan et al., 2008, 2019) conditions. Strikingly, strain Z1 could simultaneously contribute up to 92.8% of the reduction of Cr(VI) and 45.8% of the oxidation of As(III) in wastewater. The cells of strain Z1 were embedded with sodium alginate to produce biobeads, and the biobeads exhibited stable ratio of Cr(VI) reduction (91.8%) and As(III) oxidation (29.6%) even in the 5 continuous cycles of wastewater treatment. Moreover, in a process pretreated with the Z1 biobeads followed a precipitation with Ca(OH)₂ and FeCl₃, the removal efficiencies in wastewater were 98.9% and 98.3% for total Cr and As, respectively, which were 44.1% and 9.8% higher than those of using Ca(OH)₂ and FeCl₃, only. The residual amounts of Cr and As met the national standard levels of wastewater discharge. Proteomics analysis showed that cysteine, sulfur and methionine metabolisms, As resistance and oxidoreductase (CysH, CysI, CysJ, NemA and HemF) were induced by Cr(VI) and As(III). Moreover, the addition of cysteine to the medium also significantly improved bacterial Cr(VI) reduction rate. Our results provide a novel microbial pretreatment approach for enhancing remediation of Cr(VI) and As(III) pollution in wastewater, and reveal the evident that cysteine, sulfur and methionine metabolisms, As resistance and oxidoreductases are associated with the redox conversion of Cr(VI) and As(III).

In silico analysis of the chemotactic system of Agrobacterium tumefaciens

Agrobacterium tumefaciens is an efficient tool for creating transgenic host plants. The first step in the genetic transformation process involves A. tumefaciens chemotaxis, which is crucial to the survival of A. tumefaciens in changeable, harsh and even contaminated soil environments. However, a systematic study of its chemotactic signalling pathway is still lacking. In this study, the distribution and classification of chemotactic genes in the model A. tumefaciens C58 and 21 other strains were annotated. Local blast was used for comparative genomics, and hmmer was used for predicting protein domains. Chemotactic phenotypes for knockout mutants of ternary signalling complexes in A. tumefaciens C58 were evaluated using a swim agar plate. A major cluster, in which chemotaxis genes were consistently organized as MCP (methyl-accepting chemotaxis protein), CheS, CheY1, CheA, CheR, CheB, CheY2 and CheD, was found in A. tumefaciens, but two coupling CheW proteins were located outside the 'che' cluster. In the ternary signalling complexes, the absence of MCP atu0514 significantly impaired A. tumefaciens chemotaxis, and the absence of CheA (atu0517) or the deletion of both CheWs abolished chemotaxis. A total of 465 MCPs were found in the 22 strains, and the cytoplasmic domains of these MCPs were composed of 38 heptad repeats. A high homology was observed between the chemotactic systems of the 22 A. tumefaciens strains with individual differences in the gene and receptor protein distributions, possibly related to their ecological niches. This preliminary study demonstrates the chemotactic system of A. tumefaciens, and provides some reference for A. tumefaciens sensing and chemotaxis to exogenous signals.

Sediminibacterium soli sp. nov., isolated from soil

A Gram-stain-negative, facultative anaerobic strain, designated WSJ-3^T, was isolated from soil. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain WSJ-3^T belongs to genus Sediminibacterium and exhibits the highest sequence similarities to Sediminibacterium roseum SYL130^T (97.0%), Sediminibacterium goheungense DSM 28323^T (96.9%), Sediminibacterium aquarii AA5^T (96.7%), and Sediminibacterium salmoneum NBRC 103935^T (95.2%). The average nucleotide identity values of strain WSJ-3^T/S. roseum SYL130^T and strain WSJ-3^T/S. goheungense DSM 28323^T are 72.2% and 70.4%, respectively, and digital DNA-DNA hybridization values for these are 19.2% and 19.1%, respectively. Strain WSJ-3^T has a genome size of 3.88 Mb, with a DNA G + C content of 50.1 mol% and comprises of 3263 predicted genes. A phylogenetic tree constructed using the genomic core protein coding sequences revealed that strain WSJ-3^T clusters with S. roseum SYL130^T. Strain WSJ-3^T has menaquinone-7 as the only respiratory quinone and phosphatidylethanolamine, three unidentified phospholipids, four unidentified aminophospholipids, two unidentified aminolipids, and three unidentified lipids as the polar lipids. The major fatty acids of strain WSJ-3^T are iso-C_15:0, iso-C_17:0 3-OH, and iso-C_15:1 G. On the basis of the polyphasic results, the isolate represents a novel species of the genus Sediminibacterium, for which the name Sediminibacterium soli sp. nov. is proposed. The type strain is WSJ-3^T (= KCTC 72839^T = CCTCC AB 2019408^T).

Roseomonas selenitidurans sp. nov., isolated from urban soil, and emended description of Roseomonas frigidaquae

An aerobic, non-motile, Gram-stain-negative, pink, convex, coccobacilli-shaped, mesophilic bacterium, designated strain BU-1^T, was isolated from an urban soil sample from Zibo city, Shandong province, PR China. The strain grew at 20-37 °C (optimum, 30 °C), pH 5-10 (optimum, pH 7) and growth occurred with 0-2 % (w/v) NaCl (optimally with 0.5 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that BU-1^T was closely related to members of the genus Roseomonas and had highest 16S rRNA gene sequence similarities with Roseomonas frigidaquae JCM 15073^T (97.8 %), Roseomonas tokyonensis JCM 14634^T (96.9 %), Roseomonas stagni JCM 15034^T (96.5 %), and Roseomonas riguiloci JCM 17520^T (95.9 %). BU-1^T also formed a subcluster with R. frigidaquae JCM 15073^T and R. stagni JCM 15034^T in phylogenetic trees based on genomic sequences. The genome size of BU-1^T was 5.79 Mb and the DNA G+C content was 71.7 %. ANI, dDDH and AAI values between BU-1^T and R. frigidaquae JCM 15073^T were 84.0, 27.2 and 86.7 %, respectively. Furthermore, the genome of BU-1^T contained 5446 predicted protein coding genes and 4945 (90.8%) of them had classifiable functions. BU-1^T contained Q-10 as the main ubiquinone. The predominant fatty acids (>10 %) were summed feature 3, summed feature 8 and C_16:0. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and five unidentified aminolipids. Combined data from phenotypic, phylogenetic and chemotaxonomic studies indicated that strain BU-1^T is a representative of a novel species of the genus Roseomonas. Since strain BU-1^T can reduce highly toxic selenite [Se(IV)] to low toxicity elemental selenium [Se(0)], the name Roseomonas selenitidurans sp. nov. is proposed. The type strain is BU-1^T (=KACC 21750^T =GDMCC 1.1776^T).

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

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

Arsenic mobilization affected by extracellular polymeric substances (EPS) of the dissimilatory iron reducing bacteria isolated from high arsenic groundwater

The factors that control arsenic (As) mobilization by dissimilatory iron reduction (DIR) are complicated. The association between As mobilization and extracellular polymeric substance (EPS) of dissimilatory iron reducing bacteria (DIRB) remained unclear. In this study, three DIRB were isolated from high arsenic groundwater to understand the effects of EPS on As mobilization. In the laboratory settings, strain Klebsiella oxytoca IR-ZA released As into aqueous phase from As-bearing ferrihydrite, while strain Shewanella putrefaciens IAR-S1 and S. xiamenensis IR-S2 re-sequestrated As by forming secondary minerals during ferrihydrite reduction. Characterization of EPS contents with Fourier Transform Infrared Spectroscopy and high-performance liquid chromatography suggested that mannan and succinic acid were the main different EPS contents of the DIRB. The biomineralization processes were tightly regulated by EPS compositions. Mannan secreted by IAR-S1 and IR-S2 promoted while succinic acid secreted by IR-ZA suppressed the biomineralization and As immobilization. Energy-dispersive X-ray Spectroscopy mapping indicated that As in the secondary minerals was wrapped with EPS. X-ray diffraction and room temperature Mössbauer spectroscopy showed these secondary minerals were vivianite and magnetite, respectively. The amount of As mobilized into aqueous phase was strongly affected by available anions (H₂PO₄^- and HCO₃^-). Our results indicated that the EPS of DIRB significantly influenced As mobilization.

Larkinella punicea sp. nov., isolated from manganese mine soil

Strain ZZJ9^T is a Gram-stain-negative, rod-shaped, aerobic bacterium isolated from manganese mine soil. Strain ZZJ9^T showed the highest 16S rRNA gene sequence similarities with Larkinella rosea 15J16-1T3A^T (97.1%), Larkinella terrae 15J8-8^T (97.0%), Larkinella knui 15J6-3T6^T (96.8%), and Larkinella ripae 15J11-1^T (95.3%). The genome size of strain ZZJ9^T was 8.01 Mb and the DNA G+C content was 51.8 mol%. ANI values among strain ZZJ9^T and Larkinella rosea 52004 ^T, Larkinella knui KCTC 42998^T, and Larkinella terrae 52001^T were 80.5%, 82.7%, and 80.5%, respectively. dDDH values among strain ZZJ9^T and Larkinella rosea 52004^T, Larkinella knui KCTC 42998^T, and Larkinella terrae 52001^T were 23.5%, 26.0%, and 23.6%, respectively. Furthermore, the genome of strain ZZJ9^T contained 6302 predicted protein-coding genes and 3114 (49%) of them had classificatory functions. The major quinone of strain ZZJ9^T was menaquinone-7 and the main cellular fatty acids were C_16:1ω5c (39.5%), iso-C_15:0 (25.6%), and iso-C_17:0 3OH (11.5%). The polar lipids of strain ZZJ9^T were phosphatidylethanolamine, unidentified lipid, and two unidentified aminolipids. Based on the results of phylogenetic, genome, phenotypic, and chemotaxonomic analytical, strain ZZJ9^T represents a novel species of the genus Larkinella, for which the name Larkinella punicea sp. Nov. is proposed. The type strain is ZZJ9^T (= KCTC 62876^T = CCTCC AB 2018215^T).

Evolution of microbial community during dry storage and recovery of aerobic granular sludge

Aerobic granular sludge (AGS) was imbedded in agar and stored at 4 °C for 30 days, and then the stored granules were recovered in a sequencing batch reactor fed real wastewater within 11 days. Variations in microbial community compositions were investigated during dry storage and recovery of AGS, aiming to elucidate the mechanism of granular stability loss and recovery. The storage and recovery of AGS involved microbial community evolution. The dominant bacterial genera of the mature AGS were Zoogloea (relative abundance of 22.39%), Thauera (16.03%) and Clostridium_sensu_stricto (11.17%), and those of the stored granules were Acidovorax (26.79%), Macellibacteroides (12.83%) and Pseudoxanthomonas (5.69%), respectively. However, the dominant genera were Streptococcus (43.64%), Clostridium_sensu_stricto (12.3.6%) and Lactococcus (11.47%) in the recovered AGS. Methanogens were always the dominant archaeal species in mature AGS (93.01%), stored granules (99.99%) and the recovered AGS (94.84%). Facultative anaerobes and anaerobes proliferated and dominated in the stored granules, and their metabolic activities gradually led to granular structure destruction and property deterioration. However, the stored granules served as carriers for the microbes originated from the real septic tank wastewater during recovery. They proliferated rapidly and secreted a large number of extracellular polymeric substances which helped to recover the granular structure in 11 days.

Mucilaginibacter terrenus sp. nov., isolated from manganese mine soil

Strain ZH6^T is a Gram-stain-negative, rod-shaped, aerobic bacterium isolated from manganese mine soil. Strain ZH6^T had highest 16S rRNA gene sequence similarities to Mucilaginibacter yixingensis YX-36^T (96.9 %) and Mucilaginibacter psychrotolerans NH7-4^T (96.8 %). The genome size of strain ZH6^T was 4.61 Mb with a DNA G+C content of 44.0 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain ZH6^T and M. yixingensis DSM 26809^T were 70.6 and 19.2 %, respectively. Strain ZH6^T had menaquinone-7 as a major quinone and main cellular fatty acids of iso-C_15 : 0, iso-C_17 : 0 3-OH and summed feature 3 (C_16 : 1ω7c and/or C_16 : 1ω6c). The polar lipids of strain ZH6^T were a phosphatidylethanolamine, an unidentified glycolipid, an unidentified phospholipid, three unidentified aminophospholipids and four unidentified lipids. Based on the phenotypic, chemotaxonomic and phylogenetic results, strain ZH6^T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacterterrenus sp. nov., is proposed. The type strain is ZH6^T (=CCTCC AB 2018373^T=KCTC 72075^T).

Mucilaginibacter hurinus sp. nov., isolated from briquette warehouse soil

A novel bacterial strain, designated ZR32^T, was isolated from briquette warehouse soil in Ulsan (Korea). The strain was aerobic, showing pink-colored colonies on R2A agar. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ZR32^T was closely related to Mucilaginibacter soli R9-65^T (97.0%), Mucilaginibacter gynuensis YC7003^T (96.9%), and Mucilaginibacter lutimaris BR-3^T (96.8%). The values of DNA-DNA relatedness related two highest strains M. soli R9-65^T and M. gynuensis YC7003^T were 31.2 ± 6.9% and 19.7 ± 0.3%, respectively. Its genome size was 3.9 Mb, comprising 3402 predicted genes. The DNA G+C content of strain ZR32^T was 43.0 mol%. The major cellular fatty acids (> 5% of total) were summed feature 3 (C_16:1ω6c and/or C_16:1ω7c), C_16:0, C_16:1ω5c, iso-C_15:0, iso-C_17:0 3-OH, and C_17:1ω9c. The major respiratory quinine was menaquinone-7 (MK-7). The major polar lipids were phosphatidylethanolamine, two unidentified phospholipids, one unidentified sphingolipid, and one unidentified polar lipid. Strain ZR32^T showed distinctive characteristics such as the temperature and pH for growth ranges, being positive for β-glucosidase, salicin production, negative for N-acetyl-glucosamine assimilation, being resistant to carbenicillin and piperacillin to related species. On the basis of phenotypic, chemotaxonomic, and phylogenetic data, strain ZR32^T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter hurinus sp. nov. is proposed. The type strain is ZR32^T (= KCTC 62193 = CCTCC AB 2017285).

Ample Arsenite Bio-Oxidation Activity in Bangladesh Drinking Water Wells: A Bonanza for Bioremediation?

Millions of people worldwide are at risk of arsenic poisoning from their drinking water. In Bangladesh the problem extends to rural drinking water wells, where non-biological solutions are not feasible. In serial enrichment cultures of water from various Bangladesh drinking water wells, we found transfer-persistent arsenite oxidation activity under four conditions (aerobic/anaerobic; heterotrophic/autotrophic). This suggests that biological decontamination may help ameliorate the problem. The enriched microbial communities were phylogenetically at least as diverse as the unenriched communities: they contained a bonanza of 16S rRNA gene sequences. These related to Hydrogenophaga, Acinetobacter, Dechloromonas, Comamonas, and Rhizobium/Agrobacterium species. In addition, the enriched microbiomes contained genes highly similar to the arsenite oxidase (aioA) gene of chemolithoautotrophic (e.g., Paracoccus sp. SY) and heterotrophic arsenite-oxidizing strains. The enriched cultures also contained aioA phylotypes not detected in the previous survey of uncultivated samples from the same wells. Anaerobic enrichments disclosed a wider diversity of arsenite oxidizing aioA phylotypes than did aerobic enrichments. The cultivatable chemolithoautotrophic and heterotrophic arsenite oxidizers are of great interest for future in or ex-situ arsenic bioremediation technologies for the detoxification of drinking water by oxidizing arsenite to arsenate that should then precipitates with iron oxides. The microbial activities required for such a technology seem present, amplifiable, diverse and hence robust.

Efflux proteins MacAB confer resistance to arsenite and penicillin/macrolide-type antibiotics in Agrobacterium tumefaciens 5A

Antibiotic and arsenic (As) contaminations are worldwide public health problems. Previously, the bacterial ABC-type efflux protein MacAB reportedly conferred resistance to macrolide-type antibiotics but not to other metal(loid)s. In this study, the roles of MacAB for the co-resistance of different antibiotics and several metal(loid)s were analyzed in Agrobacterium tumefaciens 5A, a strain resistant to arsenite [As(III)] and several types of antibiotics. The macA and macB genes were cotranscribed, and macB was deleted in A. tumefaciens 5A and heterologously expressed in Escherichia coli AW3110 and E. coli S17-1. Compared to the wild-type strain 5A, the macB deletion strain reduced bacterial resistance levels to several macrolide-type and penicillin-type antibiotics but not to cephalosporin-type antibiotics. In addition, the macB deletion strain showed lower resistance to As(III) but not to arsenate [As(V)], antimonite [Sb(III)] and cadmium chloride [Cd(II)]. The mutant strain 5A-ΔmacB cells accumulated more As(III) than the cells of the wild-type. Furthermore, heterologous expression of MacAB in E. coli S17-1 showed that MacAB was essential for resistance to macrolide, several penicillin-type antibiotics and As(III) but not to As(V). Heterologous expression of MacAB in E. coli AW3110 reduced the cellular accumulation of As(III) but not of As(V), indicating that MacAB is responsible for the efflux of As(III). These results demonstrated that, in addition to macrolide-type antibiotics, MacAB also conferred resistance to penicillin-type antibiotics and As(III) by extruding them out of cells. This finding contributes to a better understanding of the bacterial resistance mechanisms of antibiotics and metal(loid)s.

Regulation of antimonite oxidation and resistance by the phosphate regulator PhoB in Agrobacterium tumefaciens GW4

Microbial oxidation of antimonite [Sb(III)] to antimonate [Sb(V)] is a detoxification process which contributes to Sb(III) resistance. Antimonite oxidase AnoA is essential for Sb(III) oxidation, however, the regulation mechanism is still unknown. Recently, we found that the expressions of phosphate transporters were induced by Sb(III) using proteomics analysis in Agrobacterium tumefaciens GW4, thus, we predicted that the phosphate regulator PhoB may regulate bacterial Sb(III) oxidation and resistance. In this study, comprehensive analyses were performed and the results showed that (1) Genomic analysis revealed two phoB (named as phoB1 and phoB2) and one phoR gene in strain GW4; (2) Reporter gene assay showed that both phoB1 and phoB2 were induced in low phosphate condition (50 μM), but only phoB2 was induced by Sb(III); (3) Genes knock-out/complementation, Sb(III) oxidation and Sb(III) resistance tests showed that deletion of phoB2 significantly inhibited the expression of anoA and decreased bacterial Sb(III) oxidation efficiency and Sb(III) resistant. In contrast, deletion of phoB1 did not obviously affect anoA's expression level and Sb(III) oxidation/resistance; (4) A putative Pho motif was predicted in several A. tumefaciens strains and electrophoretic mobility shift assay (EMSA) showed that PhoB2 could bind with the promoter sequence of anoA; (5) Site-directed mutagenesis and short fragment EMSA revealed the exact DNA binding sequence for the protein-DNA interaction. These results showed that PhoB2 positively regulates Sb(III) oxidation and PhoB2 is also associated with Sb(III) resistance. Such regulation mechanism may provide a great contribution for bacterial survival in the environment with Sb and for bioremediation application.

Hymenobacter edaphi sp. nov., isolated from abandoned arsenic-contaminated farmland soil

A Gram-stain-negative, aerobic, rod-shaped, non-motile, pink-pigmented bacterium, designated NL^T, was isolated from arsenic-contaminated farmland soil. Strain NL^T showed the highest 16S rRNA gene sequence similarities with those of Hymenobacter jeollabukensis 1-3-3-8^T (98.9 %), Hymenobacter gummosus ANT-18^T (97.5 %), Hymenobacter paludis KBP-30^T (97.4 %), Hymenobacter ocellatus Myx2105^T (97.1 %) and Hymenobacter coalescens WW84^T (96.4 %). The values of genomic orthoANI and dDDH between strain NL^T and Hymenobacter jeollabukensis KCTC 52741^T was 90.5 and 41.2 %, respectively, and those between strain NL^T and Hymenobacter gummosus KCTC 52166^T was 84.4 and 28.4 %, respectively. Strain NL^T exhibited DNA-DNA hybridisation values of 41.3 and 44.1 % with Hymenobacter paludis KCTC 32237^T and Hymenobacter ocellatus DSM 11117^T, respectively. Strain NL^T had major fatty acids (>10 %) of summed feature 4 (iso-C_17 : 1 I and/or anteiso-C_17 : 1 B), iso-C_15 : 0 and anteiso-C_15 : 0 and the predominant polyamine of homospermidine. The only respiratory quinone was menaquinone-7. The polar lipids were phosphatidylethanolamine, phospholipid, three unidentified lipids and two amino lipids. Strain NL^T had a genome size of 6.04 Mb and the average G+C content of 65.6 %. Compared to the other Hymenobacter spp., strain NL^T is different in polar lipid profile (without aminophospholipid) and leucine arylamidase activity. Based on the data of the polyphasic analysis, it is considered that strain NL^T represented a novel species of genus Hymenobacter, for which the name Hymenobacter edaphisp. nov. is proposed. The type strain is NL^T (=KCTC 62521^T=CCTCC AB 2018028^T).

Multilayer arsenic mobilization and multimetal co-enrichment in the alluvium (Brahmaputra) plains of India: A tale of redox domination along the depth

The study attempts to understand arsenic (As) mobilization in a shallow aquifer with depth variation while focusing on the potential co-occurrence of As with priority metals (zinc and lead), using a pilot scale multilevel groundwater monitoring system (MGWS). Groundwater samples (n = 72) were collected bi-weekly (every 15 days) from the multilevel sampler (4.6, 9.2 and 13.8 m depths), installed at Tezpur, Sonitpur district of Brahmaputra floodplain (BFP), Assam, India, for a period of 1 year (August 2013-July 2014). Both geogenic and anthropogenic influences were found to affect the studied unconfined aquifer. At 4.6 m, weathering dominated due to interaction with CO₂ and infiltrating water. Prevalent high pH (7.9-8.6) at all three depths in association with strong oxidizing condition (at 4.6 m) during the drier months seem to play a crucial role in desorption based As release. Multivariate analyses revealed that redox potential (ORP) remains the primary controller of As release at all three depths. With depth, stronger anoxic conditions resulted in the dominance of reductive hydrolysis leading to a co-occurrence scenario of As (max 4.6 μgL^-1) with Zn (max 2514 μgL^-1) and Pb (max 740 μL^-1) with influences of anthropogenic modes of activities like agriculture and dry deposition from a brick kiln. Multi-element enrichment is an emerging concern but the bigger picture would be to understand the peculiarities of individual aquifers, as a generalization can lead to missing a ton of information. In this regard, long-term multilevel monitoring can help in the predictive understanding of the vertical stratification and co-occurrences of multi-metals that can subsequently be applied for water production at the safer depths.

Runella aurantiaca sp. nov., isolated from sludge of a manganese mine

A Gram-stain-negative, filamentous rod-shaped, aerobic and non-motile strain, YX9^T, was isolated from sludge of a manganese mine. Analysis of the 16S rRNA gene sequence revealed that strain YX9^T formed the same branch within the members of the genus Runella and showed high relatedness to Runella slithyformis DSM 19594^T (98.1 %), Runella palustris HMF3829^T (96.0 %) and Runella zeae NS12^T (95.4 %). The genome length of strain YX9^T was 7.21 Mb, had 5985 coding sequences and a DNA G+C content of 44.8 mol%. The average nucleotide identity value of the draft genomes between strain YX9^T and R. slithyformis DSM 19594^T was 80.7 %. The major fatty acids of strain YX9^T were iso-C_15 : 0, C_16:1 ω5c and summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c). The predominant respiratory quinone was menaquinone 7. The polar lipids of strain YX9^T were phosphatidylethanolamine, four unidentified lipids, two aminolipids, a phospholipid and a glycolipid. Based on the results of genotypic and phenotypic studies, strain YX9^T represents a novel species within the genus Runella, for which the name Runellaaurantiaca sp. nov. is proposed (=KCTC 62875^T=CCTCC AB 2018214^T).

Chitinophaga lutea sp. nov., isolated from arsenic-contaminated soil

A yellow-coloured bacterial strain, designated ZY74^T, was isolated from arsenic contaminated soil (34 mg kg^-1) sample collected in Longkou, Hubei Province, PR China. Cells were Gram-stain-negative, aerobic, non-motile and rod-shaped. Strain ZY74^T produced round, yellow-pigmented, smooth and opaque colonies. Based on the results of 16S rRNA gene sequence analysis, strain ZY74^T was found to be affiliated with members of the genus Chitinophaga. Its closest members were Chitinophagabarathri YLT18^T (97.72 %) and Chitinophaganiabensis JS13-10^T (97.17 %). The genome size of strain ZY74^T was 6.61 Mb, containing 5351 predicted protein-coding genes, with a DNA G+C content of 55.0 mol%. The average nucleotide identity values of strain ZY74^T with C. barathri YLT18^T and C. niabensis DSM 24787^T were 76.12 and 73.32 %, respectively. The digital DNA-DNA hybridization values of strain ZY74^T with C. barathri YLT18^T and C. niabensis JS13-10^T were 20.60 and 19.40 %, respectively. The major respiratory quinone was menaquinone 7 and the predominant fatty acids (>5 %) were iso-C15:0, C16 : 1ω5c and iso-C17 : 03-OH. On the basis of phylogenetic, genotypic, phenotypic and chemotaxonomic characterization, strain ZY74^T represents a novel species in the genus Chitinophaga, for which the name Chitinophagalutea sp. nov. is proposed. The type strain is ZY74^T (=CCTCC AB2018369^T=KCTC 72039^T).

Adaptation of metal and antibiotic resistant traits in novel β-Proteobacterium Achromobacter xylosoxidans BHW-15

Chromosomal co-existence of metal and antibiotic resistance genes in bacteria offers a new perspective to the bacterial resistance proliferation in contaminated environment. In this study, an arsenotrophic bacterium Achromobacter xylosoxidans BHW-15, isolated from Arsenic (As) contaminated tubewell water in the Bogra district of Bangladesh, was analyzed using high throughput Ion Torrent Personal Genome Machine (PGM) complete genome sequencing scheme to reveal its adaptive potentiality. The assembled draft genome of A. xylosoxidans BHW-15 was 6.3 Mbp containing 5,782 functional genes, 1,845 pseudo genes, and three incomplete phage signature regions. Comparative genome study suggested the bacterium to be a novel strain of A. xylosoxidans showing significant dissimilarity with other relevant strains in metal resistance gene islands. A total of 35 metal resistance genes along with arsenite-oxidizing aioSXBA, arsenate reducing arsRCDAB, and mercury resistance merRTPADE operonic gene cluster and 20 broad range antibiotic resistance genes including β-lactams, aminoglycosides, and multiple multidrug resistance (MDR) efflux gene complex with a tripartite system OM-IM-MFP were found co-existed within the genome. Genomic synteny analysis with reported arsenotrophic bacteria revealed the characteristic genetic organization of ars and mer operonic genes, rarely described in β-Proteobacteria. A transposon Tn21 and mobile element protein genes were also detected to the end of mer (mercury) operonic genes, possibly a carrier for the gene transposition. In vitro antibiotic susceptibility assay showed a broad range of resistance against antibiotics belonging to β-lactams, aminoglycosides, cephalosporins (1st, 2nd, and 3rd generations), monobactams and even macrolides, some of the resistome determinants were predicted during in silico analysis. KEGG functional orthology analysis revealed the potential of the bacterium to utilize multiple carbon sources including one carbon pool by folate, innate defense mechanism against multiple stress conditions, motility, a proper developed cell signaling and processing unit and secondary metabolism-combination of all exhibiting a robust feature of the cell in multiple stressed conditions. The complete genome of the strain BHW-15 stands as a genetic basis for the evolutionary adaptation of metal and the antibiotic coexistence phenomenon in an aquatic environment.

Anaerobic Bacterial Immobilization and Removal of Toxic Sb(III) Coupled With Fe(II)/Sb(III) Oxidation and Denitrification

Antimony (Sb) pollution is a worldwide problem. In some anoxic sites, such as Sb mine drainage and groundwater sediment, the Sb concentration is extremely elevated. Therefore, effective Sb remediation strategies are urgently needed. In contrast to microbial aerobic antimonite [Sb(III)] oxidation, the mechanism of microbial anaerobic Sb(III) oxidation and the effects of nitrate and Fe(II) on the fate of Sb remain unknown. In this study, we discovered the mechanism of anaerobic Sb(III) oxidation coupled with Fe(II) oxidation and denitrification in the facultative anaerobic Sb(III) oxidizer Sinorhizobium sp. GW3. We observed the following: (1) under anoxic conditions with nitrate as the electron acceptor, strain GW3 was able to oxidize both Fe(II) and Sb(III) during cultivation; (2) in the presence of Fe(II), nitrate and Sb(III), the anaerobic Sb(III) oxidation rate was remarkably enhanced, and Fe(III)-containing minerals were produced during Fe(II) and Sb(III) oxidation; (3) qRT-PCR, gene knock-out and complementation analyses indicated that the arsenite oxidase gene product AioA plays an important role in anaerobic Sb(III) oxidation, in contrast to aerobic Sb(III) oxidation; and (4) energy-dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS) and powder X-ray diffraction (XRD) analyses revealed that the microbially produced Fe(III) minerals were an effective chemical oxidant responsible for abiotic anaerobic Sb(III) oxidation, and the generated Sb(V) was adsorbed or coprecipitated on the Fe(III) minerals. This process included biotic and abiotic factors, which efficiently immobilize and remove soluble Sb(III) under anoxic conditions. The findings revealed a significantly novel development for understanding the biogeochemical Sb cycle. Microbial Sb(III) and Fe(II) oxidation coupled with denitrification has great potential for bioremediation in anoxic Sb-contaminated environments.

Groundwater flow and arsenic contamination transport modeling for a multi aquifer terrain: Assessment and mitigation strategies

Arsenic contaminated shallow aquifers evaluation, mitigation, and management strategies are the challenging task to all the hydrologist and provide a safe drinking water demand in the Holocene age, alluvial aquifers. To manage and mitigate such problems, we used numerical groundwater modeling software (GMS 10.2), for the development of 3D transient state predictive (groundwater flow and contaminant transport) conceptual model for two topographically different arsenic contaminated regions. The models were built by using the measured hydro-geological data, empirical values, and equations. Groundwater flow calibration, sensitivity analyses, and validation were performed for each soil parameters, varying boundary conditions and for alternate meteorological scenarios. The MODFLOW results suggested that, the distribution of As contaminant was directly controlled by the complex hydrostratigraphy, surface water bodies and indirectly controlled by the change in meteorological conditions. The MT3DMS model, for As contaminant transport, used for the assessment of shallow and deeper aquifers. The results showed that the downward movement of As has made the deeper aquifer unsafe for drinking water and irrigation purposes. However, the aquifers and regions with high flushing capability, negligible vertical hydraulic conductivity can be delineated as As safe groundwater source, irrespective of their sediment color. Therefore, for the geogenic source of As, both the simulation results inferred that to estimate and mitigate As contaminant groundwater aquifers or regions, the numerical modeling solution is a technically viable means an effective decision-making tool.

Sphingosinicella humi sp. nov., isolated from arsenic-contaminated farmland soil and emended description of the genus Sphingosinicella

A Gram-stain-negative, strictly aerobic bacterium, designated strain QZX222^T, was isolated from arsenic-contaminated farmland soil. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain QZX222^T was clustered with Sphingosinicella vermicomposti YC7378^T (97.0 %), Sphingosinicellaxenopeptidilytica 3-2W4^T (96.1 %), Sphingosinicella microcystinivorans Y2^T (96.0 %) and Sphingosinicella soli KSL-125^T (95.9 %). Compared to strain QZX222^T, Spingomonas olgophenolica JCM 12082^T and Sphingobium boeckii 469^T had 16S rRNA gene similarities of 96.2 and 95.9 %, respectively, but they located in other phylogenetic clusters. DNA-DNA hybridization and genomic ANI values between strain QZX222^T and Sphingosinicella vermicomposti DSM 21593^T (KCTC 22446^T) were 34.8 and 75.0 %, respectively. The genome size of strain QZX222^T was 3.0 Mb including 2982 predicted genes. The strain had a DNA G+C content of 65.9 mol%. Strain QZX222^T had ubiquinone Q-10 as the major respiratory quinone and homospermidine as the major polyamine. The major fatty acids (>10 %) of strain QZX222^T were C17 : 1ω6c, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C17 : 1ω8c. The polar lipids were sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and an unidentified glycolipid. Strain QZX222^T could be distinguished from other Sphingosinicella strains based on the results of phylogenetic and genomic analyses, DNA-DNA hybridization, white colour colony, hydrolysis of urea, alkaline phosphatase activity, lack of phosphatidylmonomethylethanolamine, and presence of phosphatidylcholine. Therefore, strain QZX222^T represents a novel species of Sphingosinicella, for which the name Sphingosinicellahumi sp. nov. is proposed. The type strain is QZX222^T (=KCTC 62519^T=CCTCC AB 2018030^T).