Complete Genome Sequence of Geobacter sp. Strain FeAm09, a Moderately Acidophilic Soil Bacterium

ABSTRACT A moderately acidophilic Geobacter sp. strain, FeAm09, was isolated from forest soil. The complete genome sequence is 4,099,068 bp with an average GC content of 61.1%. No plasmids were detected. The genome contains a total of 3,843 genes and 3,608 protein-coding genes, including genes supporting iron and nitrogen biogeochemical cycling.

Characteristics of an Iron-Reducing, Moderately Acidophilic Actinobacterium Isolated from Pyritic Mine Waste, and Its Potential Role in Mitigating Mineral Dissolution in Mineral Tailings Deposits

Reactive pyritic mine tailings can be populated by chemolithotrophic prokaryotes that enhance the solubilities of many metals, though iron-reducing heterotrophic microorganisms can inhibit the environmental risk posed by tailings by promoting processes that are the reverse of those carried out by pyrite-oxidising autotrophic bacteria. A strain (IT2) of Curtobacterium ammoniigenes, a bacterium not previously identified as being associated with acidic mine wastes, was isolated from pyritic mine tailings and partially characterized. Strain IT2 was able to reduce ferric iron under anaerobic conditions, but was not found to catalyse the oxidation of ferrous iron or elemental (zero-valent) sulfur, and was an obligate heterotrophic. It metabolized monosaccharides and required small amounts of yeast extract for growth. Isolate IT2 is a mesophilic bacterium, with a temperature growth optimum of 30 °C and is moderately acidophilic, growing optimally at pH 4.0 and between pH 2.7 and 5.0. The isolate tolerated elevated concentrations of many transition metals, and was able to grow in the cell-free spent medium of the acidophilic autotroph Acidithiobacillus ferrooxidans, supporting the hypothesis that it can proliferate in acidic mine tailings. Its potential role in mitigating the production of acidic, metal-rich drainage waters from mine wastes is discussed.

Halarchaeum grantii sp. nov., a moderately acidophilic haloarchaeon isolated from a commercial salt sample

Three moderately acidophilic, halophilic archaeal strains, MH1-243-3T, MH1-243-5 and MH1-243-6, were isolated from a commercial salt sample made from seawater in Okinawa, Japan. Cells of the three strains were pleomorphic and stained Gram-negative. Colonies of the strains were orange–red-pigmented. Strain MH1-243-3T was able to grow at 15–27 % (w/v) NaCl (optimum 24 °C), at pH 4.5–6.5 (pH 5.5) and at 35–50 °C (45 °C). Strains MH1-243-5 and MH1-243-6 grew within slightly different ranges (shown in text). The 16S rRNA gene sequences of the three strains were identical, and the closest phylogenetic relative was Halarchaeum salinum MH1-34-1T with 97.0 % similarity. The rpoB′ gene sequences of the three strains were also identical, and the closest phylogenetic relative was Halarchaeum acidiphilum JCM 16109T with 92.0 % similarity. The DNA G+C content of MH1-243-3T, MH1-243-5 and MH1-243-6 was 65.2 mol%. The levels of DNA–DNA relatedness amongst the three strains were 84.1–99.8 %, while that between MH1-243-3T and H. salinum MH1-34-1T was 30.6 % and 31.6 % (reciprocally), and those between MH1-243-3T and type strains of other species in the genus Halarchaeum were 42.3–29.4 %. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolates should represent a novel species of the genus Halarchaeum, for which the name Halarchaeum grantii sp. nov. is proposed. The type strain is MH1-243-3T ( = JCM 19585T = KCTC 4142T), isolated from commercial sea salt produced in Okinawa, Japan. MH1-243-5 ( = JCM 19586) and MH1-243-6 ( = JCM 18422) are additional strains of the species.

An ArsR/SmtB Family Member Is Involved in the Regulation by Arsenic of the Arsenite Oxidase Operon in Thiomonas arsenitoxydans

ABSTRACTThe genetic organization of theaioBAoperon, encoding the arsenite oxidase of the moderately acidophilic and facultative chemoautotrophic bacteriumThiomonas arsenitoxydans, is different from that of theaioBAoperon in the other arsenite oxidizers, in that it encodes AioF, a metalloprotein belonging to the ArsR/SmtB family. AioF is stabilized by arsenite, arsenate, or antimonite but not molybdate. Arsenic is tightly attached to AioF, likely by cysteine residues. When loaded with arsenite or arsenate, AioF is able to bind specifically to the regulatory region of theaiooperon at two distinct positions. InThiomonas arsenitoxydans, the promoters ofaioXandaioBare convergent, suggesting that transcriptional interference occurs. These results indicate that the regulation of theaioBAoperon is more complex inThiomonas arsenitoxydansthan in the otheraioBAcontaining arsenite oxidizers and that the arsenic binding protein AioF is involved in this regulation. On the basis of these data, a model to explain the tight control ofaioBAexpression by arsenic inThiomonas arsenitoxydansis proposed.

Halarchaeum nitratireducens sp. nov., a moderately acidophilic haloarchaeon isolated from commercial sea salt

Two halophilic moderately acidophilic archaeal strains, MH1-136-2T and MH1-370-1 were isolated from commercial salt samples made from seawater in Japan and Indonesia, respectively. Cells of the two strains were pleomorphic and Gram-stain-negative. Strain MH1-136-2T was pink pigmented, while MH1-370-1 was orange–red pigmented. Strain MH1-136-2T was able to grow at 9–30 % (w/v) NaCl (with optimum, 21 % NaCl, w/v) at pH 4.5–6.2 (optimum, pH 5.2–5.5) and at 18–55 °C (optimum, 45 °C). Strain MH1-370-1 was able to grow at 12–30 % (w/v) NaCl (optimum, 18 %, w/v) at pH 4.2–6.0 (optimum, pH 5.2–5.5) and 20–50 °C (optimum, 45 °C). Strain MH1-136-2T required at least 1 mM Mg2+, while MH1-370-1 required at least 10 mM for growth. Both strains reduced nitrate and nitrite under aerobic conditions. The 16S rRNA gene sequences of strains MH1-136-2T and MH1-370-1 were identical, and the closest relative was Halarchaeum rubridurum MH1-16-3T with 98.3 % similarity. The level of DNA–DNA relatedness between these strains was 90.9 % and 92.4 % (reciprocally), while that between MH1-136-2T and Halarchaeum acidiphilum MH1-52-1T, Halarchaeum salinum MH1-34-1T and Halarchaeum rubridurum MH1-16-3T was 37.7 %, 44.3 % and 41.1 % (each an average), respectively. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolates represent a novel species of the genus Halarchaeum , for which the name Halarchaeum nitratireducens sp. nov. is proposed. The type strain is MH1-136-2T ( = JCM 16331T = CECT 7573T) isolated from solar salt produced in Japan.

Halarchaeum acidiphilum gen. nov., sp. nov., a moderately acidophilic haloarchaeon isolated from commercial solar salt

A novel halophilic archaeon, strain MH1-52-1T, was isolated from solar salt imported from Australia. Cells were pleomorphic, non-motile and Gram-negative. Strain MH1-52-1T required at least 3.0 M NaCl and 1 mM Mg2+ for growth. Strain MH1-52-1T was able to grow at pH 4.0–6.0 (optimum, pH 4.4–4.5) and 15–45 °C (optimum, 37 °C). The diether phospholipids phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, derived from both C20C20 and C20C25 archaeol, were present. Four unidentified glycolipids were also detected. The 16S rRNA gene sequence showed the highest similarity to that of Halobacterium noricense A1T (91.7 %); there were lower levels of similarity to other members of the family Halobacteriaceae. The G+C content of its DNA was 61.4 mol%. Based on our phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolate should be classified as a representative of a new genus and species, for which the name Halarchaeum acidiphilum gen. nov., sp. nov. is proposed. The type strain of Halarchaeum acidiphilum is MH1-52-1T (=JCM 16109T =DSM 22442T =CECT 7534T).