title: Characterization and Genome Analysis of the First Facultatively AlkaliphilicThermodesulfovibrioIsolated from the Deep Terrestrial Subsurface.
abstract: Members of the genusThermodesulfovibriobelong to theNitrospiraephylum and all isolates characterized to date are neutrophiles. They have been isolated from terrestrial hot springs and thermophilic methanogenic anaerobic sludges. Their molecular signatures have, however, also been detected in deep subsurface. The purpose of this study was to characterize and analyze the genome of a newly isolated, facultatively alkaliphilicThermodesulfovibriofrom a 2 km deep aquifer system in Western Siberia, Russia. The new isolate, designated N1, grows optimally at pH 8.5 and at 65°C. It is able to reduce sulfate, thiosulfate or sulfite with a limited range of electron donors, such as formate, pyruvate, and lactate. Analysis of the 1.93 Mb draft genome of strain N1 revealed that it contains a set of genes for dissimilatory sulfate reduction, including sulfate adenyltransferase, adenosine-5'-phosphosulfate reductase AprAB, membrane-bound electron transfer complex QmoABC, dissimilatory sulfite reductase DsrABC, and sulfite reductase-associated electron transfer complex DsrMKJOP. Hydrogen turnover is enabled by soluble cytoplasmic, membrane-linked, and soluble periplasmic hydrogenases. The use of thiosulfate as an electron acceptor is enabled by a membrane-linked molybdopterin oxidoreductase. The N1 requirement for organic carbon sources corresponds to the lack of the autotrophic C1-fixation pathways. Comparative analysis of the genomes ofThermodesulfovibrio(T. yellowstonii, T. islandicus, T. àggregans, T. thiophilus, and strain N1) revealed a low overall genetic diversity and several adaptive traits. Consistent with an alkaliphilic lifestyle, a multisubunit Na+/H+antiporter of the Mnh family is encoded in theThermodesulfovibriostrain N1 genome. Nitrogenase genes were found inT. yellowstonii, T. aggregans, andT. islandicus, nitrate reductase inT. islandicus, and cellulose synthetase inT. aggregansand strain N1. Overall, our results provide genomic insights into metabolism of theThermodesulfovibriolineage in microbial communities of the deep subsurface biosphere.
authors.affiliation: Laboratory of Biochemistry and Molecular Biology, Tomsk State University Tomsk, Russia.
authors.forename: Yulia A
authors.initials: YA
authors.lastname: Frank
authors.affiliation: Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia.
authors.forename: Vitaly V
authors.initials: VV
authors.lastname: Kadnikov
authors.affiliation: Laboratory of Biochemistry and Molecular Biology, Tomsk State University Tomsk, Russia.
authors.forename: Anastasia P
authors.initials: AP
authors.lastname: Lukina
authors.affiliation: Systems, Power and Energy, School of Engineering, Glasgow UniversityGlasgow, UK; Holymoor Consultancy Ltd.Chesterfield, UK.
authors.forename: David
authors.initials: D
authors.lastname: Banks
authors.affiliation: Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia.
authors.forename: Alexey V
authors.initials: AV
authors.lastname: Beletsky
authors.affiliation: Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia.
authors.forename: Andrey V
authors.initials: AV
authors.lastname: Mardanov
authors.affiliation: Laboratory of Biochemistry and Molecular Biology, Tomsk State University Tomsk, Russia.
authors.forename: Elena I
authors.initials: EI
authors.lastname: Sen'kina
authors.affiliation: Laboratory of Biochemistry and Molecular Biology, Tomsk State University Tomsk, Russia.
authors.forename: Marat R
authors.initials: MR
authors.lastname: Avakyan
authors.affiliation: Laboratory of Biochemistry and Molecular Biology, Tomsk State University Tomsk, Russia.
authors.forename: Olga V
authors.initials: OV
authors.lastname: Karnachuk
authors.affiliation: Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia.
authors.forename: Nikolai V
authors.initials: NV
authors.lastname: Ravin
keywords: Thermodesulfovibrio; alkaliphilic bacteria; deep subsurface biosphere; genome analysis; sulfate reduction