Identification of bacterial dissimilatory antimonate reductase AnrA: genes and proteins involved in antimonate respiration and resistance in Geobacter sp. strain SVR.

Geobacter sp. strain SVR uses antimonate [Sb(V)] as a terminal electron acceptor for anaerobic respiration. Here, we visualized a possible key enzyme, periplasmic Sb(V) reductase (Anr), via active staining and non-denaturing gel electrophoresis. Liquid chromatography-tandem mass spectrometry analysis revealed that a novel dimethyl sulfoxide (DMSO) reductase family protein, WP_173201954.1, is involved in Anr. This protein was closely related with AnrA, a protein suggested to be the catalytic subunit of a respiratory Sb(V) reductase in Desulfuribacillus stibiiarsenatis. The anr genes of strain SVR (anrXSRBAD) formed an operon-like structure, and their transcription was upregulated under Sb(V)-respiring conditions. The expression of anrA gene was induced by more than 1 µM of antimonite [Sb(III)]; however, arsenite [As(III)] did not induce the expression of anrA gene. Tandem mass tag-based proteomic analysis revealed that, in addition to Anr proteins, proteins in the following categories were upregulated under Sb(V)-respiring conditions: (i) Sb(III) efflux systems such as Ant and Ars; (ii) antioxidizing proteins such as ferritin, rubredoxin, and thioredoxin; (iii) protein quality control systems such as HspA, HslO, and DnaK; and (iv) DNA repair proteins such as UspA and UvrB. These results suggest that strain SVR copes with antimony stress by modulating pleiotropic processes to resist and actively metabolize antimony. To the best of our knowledge, this is the first report to demonstrate the involvement of AnrA in Sb(V) respiration at the protein level. Furthermore, this is the first example to show high expression of the Ant system proteins in the Sb(V)-respiring bacterium.IMPORTANCEAntimony (Sb) exists mainly as antimonite [Sb(III)] or antimonate [Sb(V)] in the environment, and Sb(III) is more toxic than Sb(V). Recently, microbial involvement in Sb redox reactions has received attention. Although more than 90 Sb(III)-oxidizing bacteria have been reported, information on Sb(V)-reducing bacteria is limited. Especially, the enzyme involved in dissimilatory Sb(V) reduction, or Sb(V) respiration, is unclear, despite this pathway being very important for the circulation of Sb in nature. In this study, we demonstrated that the Sb(V) reductase (Anr) of an Sb(V)-respiring bacterium (Geobacter sp. SVR) is a novel member of the dimethyl sulfoxide (DMSO) reductase family. In addition, we found that strain SVR copes with Sb stress by modulating pleiotropic processes, including the Ant and Ars systems, and upregulating the antioxidant and quality control protein levels. Considering the abundance and diversity of putative anr genes in the environment, Anr may play a significant role in global Sb cycling in both marine and terrestrial environments.

Corrigendum: Iron corrosion concomitant with nitrate reduction by Iodidimonas nitroreducens sp. nov. isolated from iodide-rich brine associated with natural gas.

[This corrects the article DOI: 10.3389/fmicb.2023.1232866.].

Iron corrosion concomitant with nitrate reduction by Iodidimonas nitroreducens sp. nov. isolated from iodide-rich brine associated with natural gas.

Microbially influenced corrosion (MIC) may contribute significantly to corrosion-related failures in injection wells and iron pipes of iodine production facilities. In this study, the iron (Fe0) corroding activity of strain Q-1 isolated from iodide-rich brine in Japan and two Iodidimonas strains phylogenetically related to strain Q-1 were investigated under various culture conditions. Under aerobic conditions, the Fe0 foil in the culture of strain Q-1 was oxidized in the presence of nitrate and yeast extract, while those of two Iodidimonas strains were not. The amount of oxidized iron in this culture was six times higher than in the aseptic control. Oxidation of Fe0 in aerobic cultures of nitrate-reducing bacterium Q-1 was dependent on the formation of nitrite from nitrate. This Fe0 corrosion by nitrate-reducing bacterium Q-1 started after initial nitrite accumulation by day 4. Nitrate reduction in strain Q-1 is a unique feature that distinguishes it from two known species of Iodidimonas. Nitrite accumulation was supported by the encoding of genes for nitrate reductase and the missing of genes for nitrite reduction to ammonia or nitrogen gas in its genome sequence. Phylogenetic position of strain Q-1 based on the 16S rRNA gene sequence was with less than 96.1% sequence similarity to two known Iodidimonas species, and digital DNA-DNA hybridization (dDDH) values of 17.2-19.3%, and average nucleotide identity (ANI) values of 73.4-73.7% distinguished strain Q-1 from two known species. In addition of nitrate reduction, the ability to hydrolyze aesculin and gelatin hydrolysis and cellular fatty acid profiles also distinguished strain Q-1 from two known species. Consequently, a new species, named Iodidimonas nitroreducens sp. nov., is proposed for the nitrate-reducing bacterium strain Q-1T.

Draft genome sequence of Pelosinus sp. IPA-1, a bacterium isolated from arsenic-contaminated soil in Japan.

Pelosinus sp. strain IPA-1 is a bacterium isolated from arsenic-contaminated soil in Japan. We here report the draft genome sequence of strain IPA-1.

Iodate respiration by Azoarcus sp. DN11 and its potential use for removal of radioiodine from contaminated aquifers.

Azoarcus sp. DN11 was previously isolated from gasoline-contaminated groundwater as an anaerobic benzene-degrading bacterium. Genome analysis of strain DN11 revealed that it contained a putative idr gene cluster (idrABP1P2 ), which was recently found to be involved in bacterial iodate (IO3 -) respiration. In this study, we determined if strain DN11 performed iodate respiration and assessed its potential use to remove and sequester radioactive iodine (129I) from subsurface contaminated aquifers. Strain DN11 coupled acetate oxidation to iodate reduction and grew anaerobically with iodate as the sole electron acceptor. The respiratory iodate reductase (Idr) activity of strain DN11 was visualized on non-denaturing gel electrophoresis, and liquid chromatography-tandem mass spectrometry analysis of the active band suggested the involvement of IdrA, IdrP1, and IdrP2 in iodate respiration. The transcriptomic analysis also showed that idrA, idrP1 , and idrP2 expression was upregulated under iodate-respiring conditions. After the growth of strain DN11 on iodate, silver-impregnated zeolite was added to the spent medium to remove iodide from the aqueous phase. In the presence of 200 µM iodate as the electron acceptor, more than 98% of iodine was successfully removed from the aqueous phase. These results suggest that strain DN11 is potentially helpful for bioaugmentation of 129I-contaminated subsurface aquifers.

The Genus Iodidimonas: From Its Discovery to Potential Applications.

The genus Iodidimonas was recently proposed in the class Alphaproteobacteria. Iodidimonas strains are aerobic, mesophilic, neutrophilic, moderately halophilic, and chemo-organotrophic. They were first discovered in natural gas brine water containing a very high level of iodide (I-). They exhibited a unique phenotypic feature of iodide oxidation to form molecular iodine (I2). Iodidimonas was also enriched and isolated from surface seawater supplemented with iodide, and it is clearer now that their common habitats are those enriched with iodide. In such environments, Iodidimonas species seem to attack microbial competitors with the toxic form I2 to occupy their ecological niche. The iodide-oxidizing enzyme (IOX) purified from the Iodidimonas sp. strain Q-1 exhibited high catalytic efficiency for iodide and consisted of at least two proteins IoxA and IoxC. IoxA is a putative multicopper oxidase with four conserved copper-binding regions but is phylogenetically distinct from other bacterial multicopper oxidases. The IOX/iodide system could be used as a novel enzyme-based antimicrobial system which can efficiently kill Bacillus spores. Furthermore, the IOX/iodide system can be applied to the decolorization of recalcitrant dyes, where iodide may function as a novel inorganic natural redox mediator.

Decolorization of cationic dyes under alkaline conditions by Iodidimonas sp. Q-1 multicopper oxidase.

Previously, we found that a multicopper oxidase (IOX) produced by Iodidimonas sp. Q-1, an iodide (I-)-oxidizing marine bacterium, exhibited significant decolorization activity toward various anionic dyes. In this study, the potential capacity of IOX for decolorization of cationic dyes such as malachite green (MG), crystal violet (CV), and methylene blue (MB) was determined. Decolorization of the dyes by IOX exhibited significant pH dependence, and effective decolorization was observed under alkaline conditions. At an optimum pH of 9.5, IOX decolorized more than 90% of MG, CV, and MB within 30 min, 2 h, and 6 h, respectively. The addition of iodide was indispensable for decolorization, suggesting that this halide ion serves as a redox mediator. Decolorization products of MG showed less toxicity than MG against Escherichia coli cells. These results suggest that this IOX-iodide system can be used for the decolorization and detoxification of cationic dyes under alkaline conditions.

Isolation and identification of Zalaria sp. Him3 as a novel fructooligosaccharides-producing yeast.

AIMS: This study aimed at obtaining a novel fructooligosaccharides (FOS)-producing yeast, which was different from conventional FOS producers, Aureobasidium spp. METHODS AND RESULTS: Strain Him3 was newly isolated from a Japanese dried sweet potato as a FOS producer. The strain exhibited yeast-like cells and melanization on the potato dextrose agar medium, and formed very weak pseudomycelia on the yeast extract polypeptone dextrose agar medium. Based on the internal transcribed spacer (ITS) region of ribosomal DNA and a partial ß-tubulin gene sequences, the strain Him3 was identified as Zalaria sp. The ß-fructofuranosidase (FFase) produced by strain Him3 was localized on the cell surface (CS-FFase) as well as in the culture broth (EC-FFase). The FOS production yields by CS-FFase and EC-FFase from 50% sucrose were 63.8% and 64.6%, respectively, to consumed sucrose after the reaction for 72 h. CONCLUSIONS: We successfully isolated a novel black yeast, Zalaria sp. Him3, with effective capacity for FOS production. Phylogenetic analysis revealed that strain Him3 was distantly related with the conventional FOS producers, Aureobasidium spp. SIGNIFICANCE AND IMPACT OF THE STUDY: Since FFase of strain Him3 demonstrated high production yields of FOS, it could be applied to novel industrial production of FOS, which is different from conventional methods.

Reductive deiodination of 2,4,6-triiodophenol by Vallitalea sp. strain TIP-1 isolated from the marine sponge.

An anaerobic microbial consortium capable of reductively dehalogenating 2,4,6-triiodophenol (2,4,6-TIP) was enriched from the marine sponge Hymeniacidon sinapium. The enrichment reductively deiodinated 100 µM of 2,4,6-TIP to 4-iodophenol (4-IP) and 2-iodophenol (2-IP) in the presence of sterile sponge tissue as the sole carbon source and electron donor. PCR-denaturing gradient gel electrophoresis and 16S rRNA gene sequence analysis revealed that bacteria closely related with Vallitalea guaymasensis and Oceanirhabdus sediminicola, both of which are members of the order Clostridiales, were predominant in the enrichment. When glucose was added to the enrichment as alternative carbon source, one of these bacteria grew predominantly, which was subsequently isolated as a pure culture. The strain, designated as TIP-1, showed 99.7% 16S rRNA gene sequence similarity with V. guaymasensis. In the presence of glucose, strain TIP-1 reductively deiodinated 2,4,6-TIP to 2-IP and 4-IP at a molar ratio of 3:1, during which 2,4-diiodophenol (2,4-DIP) and 2,6-diiodophenol (2,6-DIP) were observed as deiodinated intermediates. Glucose was required for 2,4,6-TIP deiodination, but 2,4,6-TIP was not essential for growth of strain TIP-1. The strain also deiodinated 2,4-DIP to 2-IP and 4-IP at a molar ratio of 1:1, and 2,6-DIP to 2-IP, but further deiodination of the monoiodophenols was not observed. These results suggest that strain TIP-1 removed both ortho- and para-substituted iodines equally. Such deiodinating bacteria could be applied to the mineralization or dehalogenation of triiodobenzene derivatives, which are widely used as X-ray contrast media.

Complete Genome Sequence of Geobacter sp. Strain SVR, an Antimonate-Reducing Bacterium Isolated from Antimony-Rich Mine Soil.

We report here the complete genome sequence of Geobacter sp. strain SVR, isolated from antimony mine soil in Nakase Mine, Hyogo Prefecture, Japan. SVR strains proliferate using antimonate [Sb(V)] as an electron acceptor, providing insights into the antimony reduction mechanism.

Iodidimonas gelatinilytica sp. nov., aerobic iodide-oxidizing bacteria isolated from brine water and surface seawater.

Chemo-organotrophic iodide (I-)-oxidizing bacterial strains Hi-2T and Mie-1 were isolated from iodide-rich natural gas brine water in Chiba and surface seawater in Mie, Japan, respectively. Cells of strains Hi-2T and Mie-1 were aerobic, Gram-negative and rod-shaped (0.3-0.5 µm width and 1.2-4.4 µm in length). Two isolates grew optimally at 30 °C, pH 7.5 and with 3% NaCl (w/v). Iodide oxidation to form molecular iodine (I2) was a biochemically unique trait for strains Hi-2T and Mie-1. The major cellular fatty acids are C18:1ω7c, C16:1ω5c and C18:1 2-OH. A phylogenetic analysis based on the 16S rRNA gene sequence revealed that strains Hi-2T and Mie-1 were located near Iodidimonas muriae C-3T with 99.2% sequence similarity. The calculated digital DNA-DNA hybridization (dDDH) value of 65.7-65.9% between the two isolates and I. muriae C-3T was lower than the threshold of 70%, which was used for prokaryotic species delineation. Strains Hi-2T and Mie-1 differed in the hydrolysis of aesculin, the hydrolysis of gelatin and the major cellular fatty acids composition from I. muriae C-3T. Considering these biochemical properties, the major cellular fatty acids composition and dDDH value, a novel species is proposed for strains Hi-2T (= JCM 17844T = LMG 28661T) and Mie-1 (= JCM 17845 = LMG 28662), to be named Iodidimonas gelatinilytica.

Production of two morphologically different antimony trioxides by a novel antimonate-reducing bacterium, Geobacter sp. SVR.

A novel dissimilatory antimonate [Sb(V)]-reducing bacterium, strain SVR, was isolated from soil of a former antimony (Sb) mine. Strain SVR coupled Sb(V) reduction to acetate oxidation with an apparent reduction rate of 2.4 mM d-1. The reduction of Sb(V) was followed by the precipitation and accumulation of white microcrystals in the liquid medium. The precipitates were initially small and amorphous, but they eventually developed to the crystal phase with a length > 50 µm. Strain SVR removed 96% of dissolved Sb as the precipitates. An X-ray diffraction analysis indicated that the microcrystals were the orthorhombic Sb trioxide (Sb2O3), i.e., valentinite. Phylogenetic and physiological analyses revealed that strain SVR is a member of the genus Geobacter. The cell suspension of strain SVR incubated with acetate and Sb(V) at pH 7.0 was able to form valentinite. Interestingly, at pH 8.0, the cell suspension formed another crystalline Sb2O3 with a cubic structure, i.e., senarmontite. Our findings provide direct evidence that Geobacter spp. are involved in Sb(V) reduction in nature. Considering its superior capacity for Sb removal, strain SVR could be used for the recovery of Sb and the individual productions of valentinite and senarmontite from Sb-contaminated wastewater.

Possible Involvement of a Tetrathionate Reductase Homolog in Dissimilatory Arsenate Reduction by Anaeromyxobacter sp. Strain PSR-1.

Anaeromyxobacter sp. strain PSR-1, a dissimilatory arsenate [As(V)]-reducing bacterium, can utilize As(V) as a terminal electron acceptor for anaerobic respiration. A previous draft genome analysis revealed that strain PSR-1 lacks typical respiratory As(V) reductase genes (arrAB), which suggested the involvement of another protein in As(V) respiration. Dissimilatory As(V) reductase activity of strain PSR-1 was induced under As(V)-respiring conditions and was localized predominantly in the periplasmic fraction. The activity was visualized by partially denaturing gel electrophoresis, and liquid chromatography-tandem mass spectrometry analysis identified proteins involved in the active band. Among these proteins, a protein annotated as molybdopterin-dependent oxidoreductase (PSR1_00330) exhibited the highest sequence coverage, 76%. Phylogenetic analysis revealed that this protein was a homolog of tetrathionate reductase catalytic subunit TtrA. However, the crude extract of strain PSR-1 did not show significant tetrathionate reductase enzyme activity. Comparative proteomic analysis revealed that the protein PSR1_00330 and a homolog of tetrathionate reductase electron transfer subunit TtrB (PSR1_00329) were expressed abundantly and specifically under As(V)-respiring conditions, respectively. The genes encoding PSR1_00330 and PSR1_00329 formed an operon-like structure along with a gene encoding a c-type cytochrome (cyt c), and their transcription was upregulated under As(V)-respiring conditions. These results suggest that the protein PSR1_00330, which lacks tetrathionate reductase activity, functions as a dissimilatory As(V) reductase in strain PSR-1. Considering the wide distribution of TtrA homologs among bacteria and archaea, they may play a hitherto unknown role along with conventional respiratory As(V) reductase (Arr) in the biogeochemical cycling of arsenic in nature.IMPORTANCE Dissimilatory As(V)-reducing prokaryotes play significant roles in arsenic release and contamination in groundwater and threaten the health of people worldwide. Generally, such prokaryotes reduce As(V) by means of a respiratory As(V) reductase designated Arr. However, some dissimilatory As(V)-reducing prokaryotes such as Anaeromyxobacter sp. strain PSR-1 lack genes encoding Arr, suggesting the involvement of other protein in As(V) reduction. In this study, using multiple proteomic and transcriptional analyses, it was found that the dissimilatory As(V) reductase of strain PSR-1 was a protein closely related to the tetrathionate reductase catalytic subunit (TtrA). Tetrathionate reductase is known to play a role in anaerobic respiration of Salmonella on tetrathionate, but strain PSR-1 showed neither growth on tetrathionate nor significant tetrathionate reductase enzyme activity. These results suggest the possibility that TtrA homologs encoded in a wide variety of archaeal and bacterial genomes might function as dissimilatory As(V) reductases.

Diazotrophic Anaeromyxobacter Isolates from Soils.

Biological nitrogen fixation is an essential reaction in a major pathway for supplying nitrogen to terrestrial environments. Previous culture-independent analyses based on soil DNA/RNA/protein sequencing could globally detect the nitrogenase genes/proteins of Anaeromyxobacter (in the class Deltaproteobacteria), commonly distributed in soil environments and predominant in paddy soils; this suggests the importance of Anaeromyxobacter in nitrogen fixation in soil environments. However, direct experimental evidence is lacking; there has been no research on the genetic background and ability of Anaeromyxobacter to fix nitrogen. Therefore, we verified the diazotrophy of Anaeromyxobacter based on both genomic and culture-dependent analyses using Anaeromyxobacter sp. strains PSR-1 and Red267 isolated from soils. Based on the comparison of nif gene clusters, strains PSR-1 and Red267 as well as strains Fw109-5, K, and diazotrophic Geobacter and Pelobacter in the class Deltaproteobacteria contain the minimum set of genes for nitrogenase (nifBHDKEN). These results imply that Anaeromyxobacter species have the ability to fix nitrogen. In fact, Anaeromyxobacter PSR-1 and Red267 exhibited N2-dependent growth and acetylene reduction activity (ARA) in vitro Transcriptional activity of the nif gene was also detected when both strains were cultured with N2 gas as a sole nitrogen source, indicating that Anaeromyxobacter can fix and assimilate N2 gas by nitrogenase. In addition, PSR-1- or Red267-inoculated soil showed ARA activity and the growth of the inoculated strains on the basis of RNA-based analysis, demonstrating that Anaeromyxobacter can fix nitrogen in the paddy soil environment. Our study provides novel insights into the pivotal environmental function, i.e., nitrogen fixation, of Anaeromyxobacter, which is a common soil bacterium.IMPORTANCEAnaeromyxobacter is globally distributed in soil environments, especially predominant in paddy soils. Current studies based on environmental DNA/RNA analyses frequently detect gene fragments encoding nitrogenase of Anaeromyxobacter from various soil environments. Although the importance of Anaeromyxobacter as a diazotroph in nature has been suggested by culture-independent studies, there has been no solid evidence and validation from genomic and culture-based analyses that Anaeromyxobacter fixes nitrogen. This study demonstrates that Anaeromyxobacter harboring nitrogenase genes exhibits diazotrophic ability; moreover, N2-dependent growth was demonstrated in vitro and in the soil environment. Our findings indicate that nitrogen fixation is important for Anaeromyxobacter to survive under nitrogen-deficient environments and provide a novel insight into the environmental function of Anaeromyxobacter, which is a common bacterium in soils.

Draft Genome Sequence of Geobacter sp. Strain SVR, Isolated from Antimony Mine Soil.

We report here the draft genome sequence of Geobacter sp. strain SVR, isolated from antimony mine soil in Hyogo Prefecture, Japan. The genome sequence data in this study will provide useful information for understanding bacterial antimonate reduction.

A novel dimethylsulfoxide reductase family of molybdenum enzyme, Idr, is involved in iodate respiration by Pseudomonas sp. SCT.

Pseudomonas sp. strain SCT is capable of using iodate (IO3 - ) as a terminal electron acceptor for anaerobic respiration. A possible key enzyme, periplasmic iodate reductase (Idr), was visualized by active staining on non-denaturing gel electrophoresis. Liquid chromatography-tandem mass spectrometry analysis revealed that at least four proteins, designated as IdrA, IdrB, IdrP1 , and IdrP2 , were involved in Idr. IdrA and IdrB were homologues of catalytic and electron transfer subunits of respiratory arsenite oxidase (Aio); however, IdrA defined a novel clade within the dimethylsulfoxide (DMSO) reductase family. IdrP1 and IdrP2 were closely related to each other and distantly related to cytochrome c peroxidase. The idr genes (idrABP 1 P 2 ) formed an operon-like structure, and their transcription was upregulated under iodate-respiring conditions. Comparative proteomic analysis also revealed that Idr proteins and high affinity terminal oxidases (Cbb3 and Cyd), various H2 O2 scavengers, and chlorite (ClO2 - ) dismutase-like proteins were expressed specifically or abundantly under iodate-respiring conditions. These results suggest that Idr is a respiratory iodate reductase, and that both O2 and H2 O2 are formed as by-products of iodate respiration. We propose an electron transport chain model of strain SCT, in which iodate, H2 O2 , and O2 are used as terminal electron acceptors.

Soil Microbial Communities Involved in Reductive Dissolution of Arsenic from Arsenate-Laden Minerals with Different Carbon Sources.

The natural microbial communities involved in arsenic (As) extraction under biostimulated conditions are still unclear. In this study, soil slurry was incubated with arsenate [As(V)]-laden Fe(III) or Al (hydr)oxides with lactate or acetate. After 40 d, dissolved As released from As(V)-laden Fe(III) accounted for 54% of the initial solid-phase As in lactate-amended slurries, while much less As was released from acetate-amended slurries. As was released more rapidly from As(V)-laden Al, but the total release was relatively low (45%). High-throughput Illumina sequencing of 16S rRNA genes revealed that dissimilatory metal(loid) reducers such as Desulfitobacterium became predominant in lactate-amended slurries. Moreover, anaerobic fermenters in the Sporomusaceae family were predominant. Interestingly, a Sporomusaceae bacterial strain isolated from the slurry was capable of releasing As from both As(V)-laden (hydr)oxides in the presence of lactate. The strain first released As as As(V) and subsequently reduced it to As(III) in the aqueous phase. These results suggest that lactate is a suitable carbon source for As extraction by natural microbial communities, and that both dissimilatory metal(loid) reducers and certain anaerobic fermenters play significant roles in As extraction. Microbial reductive dissolution of As may be expected to be a cost-effective restoration technique for As-contaminated soils.

Expression of Genes and Proteins Involved in Arsenic Respiration and Resistance in Dissimilatory Arsenate-Reducing Geobacter sp. Strain OR-1.

The reduction of arsenate [As(V)] to arsenite [As(III)] by dissimilatory As(V)-reducing bacteria, such as Geobacter spp., may play a significant role in arsenic release from anaerobic sediments into groundwater. The biochemical and molecular mechanisms by which these bacteria cope with this toxic element remain unclear. In this study, the expression of several genes involved in arsenic respiration (arr) and resistance (ars) was determined using Geobacter sp. strain OR-1, the only cultured Geobacter strain capable of As(V) respiration. In addition, proteins expressed differentially under As(V)-respiring conditions were identified by semiquantitative proteomic analysis. Dissimilatory As(V) reductase (Arr) of strain OR-1 was localized predominantly in the periplasmic space, and the transcription of its gene (arrA) was upregulated under As(V)-respiring conditions. The transcription of the detoxifying As(V) reductase gene (arsC) was also upregulated, but its induction required 500 times higher concentration of As(III) (500 µM) than did the arrA gene. Comparative proteomic analysis revealed that in addition to the Arr and Ars proteins, proteins involved in the following processes were upregulated under As(V)-respiring conditions: (i) protein folding and assembly for rescue of proteins with oxidative damage, (ii) DNA replication and repair for restoration of DNA breaks, (iii) anaplerosis and gluconeogenesis for sustainable energy production and biomass formation, and (iv) protein and nucleotide synthesis for the replacement of damaged proteins and nucleotides. These results suggest that strain OR-1 copes with arsenic stress by orchestrating pleiotropic processes that enable this bacterium to resist and actively metabolize arsenic.IMPORTANCE Dissimilatory As(V)-reducing bacteria, such as Geobacter spp., play significant roles in arsenic release and contamination in groundwater and threaten the health of people worldwide. However, the biochemical and molecular mechanisms by which these bacteria cope with arsenic toxicity remain unclear. In this study, it was found that both respiratory and detoxifying As(V) reductases of a dissimilatory As(V)-reducing bacterium, Geobacter sp. strain OR-1, were upregulated under As(V)-respiring conditions. In addition, various proteins expressed specifically or more abundantly in strain OR-1 under arsenic stress were identified. Strain OR-1 actively metabolizes arsenic while orchestrating various metabolic processes that repair oxidative damage caused by arsenic. Such information is useful in assessing and identifying possible countermeasures for the prevention of microbial arsenic release in nature.

Draft Genome Sequence of a Novel Lactate-Fermenting Bacterial Strain of the Family Sporomusaceae within the Class Negativicutes.

Here, we report a draft genome sequence of the Sporomusaceae bacterial strain FL31, a novel lactate-fermenting bacterium of the family Sporomusaceae within the class Negativicutes. This genome furthers our understanding of the physiological functions of this taxonomic group in natural environments.

Genomic Analysis of Pseudomonas sp. Strain SCT, an Iodate-Reducing Bacterium Isolated from Marine Sediment, Reveals a Possible Use for Bioremediation.

Strain SCT is an iodate-reducing bacterium isolated from marine sediment in Kanagawa Prefecture, Japan. In this study, we determined the draft genome sequence of strain SCT and compared it to complete genome sequences of other closely related bacteria, including Pseudomonas stutzeri A phylogeny inferred from concatenation of core genes revealed that strain SCT was closely related to marine isolates of P. stutzeri Genes present in the SCT genome but absent from the other analyzed P. stutzeri genomes comprised clusters corresponding to putative prophage regions and possible operons. They included pil genes, which encode type IV pili for natural transformation; the mer operon, which encodes resistance systems for mercury; and the pst operon, which encodes a Pi-specific transport system for phosphate uptake. We found that strain SCT had more prophage-like genes than the other P. stutzeri strains and that the majority (70%) of them were SCT strain-specific. These genes, encoded on distinct prophage regions, may have been acquired after branching from a common ancestor following independent phage transfer events. Thus, the genome sequence of Pseudomonas sp. strain SCT can provide detailed insights into its metabolic potential and the evolution of genetic elements associated with its unique phenotype.