title: Genomic Analysis ofCaldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial PhylumCalditrichaeota.
abstract: The genome ofCaldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochromecnitrite reductase εHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H2, probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes for cytochromecoxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported whenC. abyssiwas first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth ofC. abyssi: starch, cellobiose, glucomannan and xyloglucan. The genomic analysis demonstrated the ability ofC. abyssito synthesize nucleotides and most amino acids and vitamins. Finally, the genomic sequence allowed us to perform a phylogenomic analysis, based on 38 protein sequences, which confirmed the deep branching of this lineage and justified the proposal of a novel phylumCalditrichaeota.
authors.affiliation: Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia.
authors.forename: Ilya V
authors.initials: IV
authors.lastname: Kublanov
authors.affiliation: A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia.
authors.forename: Olga M
authors.initials: OM
authors.lastname: Sigalova
authors.affiliation: Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia.
authors.forename: Sergey N
authors.initials: SN
authors.lastname: Gavrilov
authors.affiliation: Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia.
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Lebedinsky
authors.affiliation: Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia QLD, Australia.
authors.forename: Christian
authors.initials: C
authors.lastname: Rinke
authors.affiliation: Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia.
authors.forename: Olga
authors.initials: O
authors.lastname: Kovaleva
authors.affiliation: Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia.
authors.forename: Nikolai A
authors.initials: NA
authors.lastname: Chernyh
authors.affiliation: DOE Joint Genome Institute, Walnut Creek CA, USA.
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanova
authors.affiliation: DOE Joint Genome Institute, Walnut Creek CA, USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Daum
authors.affiliation: DOE Joint Genome Institute, Walnut Creek CA, USA.
authors.forename: T B K
authors.initials: TB
authors.lastname: Reddy
authors.affiliation: School of Biology, Newcastle University Newcastle upon Tyne, UK.
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Klenk
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Spring
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Göker
authors.affiliation: Center for Bioinformatics and Computational Biology, Department of Biochemistry, University of Pretoria Pretoria, South Africa.
authors.forename: Oleg N
authors.initials: ON
authors.lastname: Reva
authors.affiliation: Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia.
authors.forename: Margarita L
authors.initials: ML
authors.lastname: Miroshnichenko
authors.affiliation: DOE Joint Genome Institute, Walnut Creek CA, USA.
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
authors.affiliation: DOE Joint Genome Institute, Walnut CreekCA, USA; Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, BerkeleyCA, USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of SciencesMoscow, Russia; Department of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State UniversityMoscow, Russia; Skolkovo Institute of Science and TechnologyMoscow, Russia; Faculty of Computer Science, National Research University - Higher School of EconomicsMoscow, Russia.
authors.forename: Mikhail S
authors.initials: MS
authors.lastname: Gelfand
authors.affiliation: Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia.
authors.forename: Elizaveta A
authors.initials: EA
authors.lastname: Bonch-Osmolovskaya
keywords: Caldithrix; bacterial evolution; genomic analysis; phylogenomics; phylum; sequencing; taxonomy