Genomic analysis of Caldithrix abyssi, the thermophilic anaerobic bacterium of the novel bacterial phylum Calditrichaeota

dc.contributor.authorKublanov, IIya V.
dc.contributor.authorSigalova, Olga M.
dc.contributor.authorGavrilov, Sergey N.
dc.contributor.authorLebedinsky, Alexander V.
dc.contributor.authorRinke, Christian
dc.contributor.authorKovaleva, Olga
dc.contributor.authorChernyh, Nikolai A.
dc.contributor.authorIvanova, Natalia
dc.contributor.authorDaum, Chris
dc.contributor.authorReddy, T.B.K.
dc.contributor.authorKlenk, Hans-Peter
dc.contributor.authorSpring, Stefan
dc.contributor.authorGoker, Markus
dc.contributor.authorReva, Oleg N.
dc.contributor.authorMiroshnichenko, Margarita L.
dc.contributor.authorKyrpides, Nikos C.
dc.contributor.authorWoyke, Tanja
dc.contributor.authorGelfand, Mikhall S.
dc.contributor.authorBonch-Osmolovskaya, Elizaveta A.
dc.date.accessioned2017-03-27T10:19:58Z
dc.date.available2017-03-27T10:19:58Z
dc.date.issued2017-02-20
dc.description.abstractThe genome of Caldithrix 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 H2 during 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 cytochrome c nitrite 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 cytochrome c oxidase, 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 when C. abyssi was 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 of C. abyssi: starch, cellobiose, glucomannan and xyloglucan. The genomic analysis demonstrated the ability of C. abyssi to 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 phylum Calditrichaeota.en_ZA
dc.description.departmentBiochemistryen_ZA
dc.description.librarianam2017en_ZA
dc.description.sponsorshipThe work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231. OS and MSG were supported by the Russian Science Foundation (RSF, grant 14-24-00155). EB-O and SG were supported by the RSF grant 14-24-00165. IK, NC, AL, and MM were supported by the Russian Foundation for Basic Research grant 14-04-00503.en_ZA
dc.description.urihttp://www.frontiersin.orgen_ZA
dc.identifier.citationKublanov IV, Sigalova OM, Gavrilov SN, Lebedinsky AV, Rinke C, Kovaleva O, Chernyh NA, Ivanova N, Daum C, Reddy TBK, Klenk H-P, Spring S, Göker M, Reva ON, Miroshnichenko ML, Kyrpides NC, Woyke T, Gelfand MS, Bonch-Osmolovskaya EA (2017) Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota. Front. Microbiol. 8:195. DOI: 10.3389/fmicb.2017.00195.en_ZA
dc.identifier.issn1664-302X
dc.identifier.other10.3389/fmicb.2017.00195
dc.identifier.urihttp://hdl.handle.net/2263/59552
dc.language.isoenen_ZA
dc.publisherFrontiers Research Foundationen_ZA
dc.rights© 2017 Kublanov, Sigalova, Gavrilov, Lebedinsky, Rinke, Kovaleva, Chernyh, Ivanova, Daum, Reddy, Klenk, Spring, Göker, Reva, Miroshnichenko, Kyrpides, Woyke, Gelfand, Bonch-Osmolovskaya. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).en_ZA
dc.subjectBacterial evolutionen_ZA
dc.subjectPhylogenomicsen_ZA
dc.subjectTaxonomyen_ZA
dc.subjectPhylumen_ZA
dc.subjectCaldithrixen_ZA
dc.subjectGenomic analysisen_ZA
dc.subjectSequencingen_ZA
dc.titleGenomic analysis of Caldithrix abyssi, the thermophilic anaerobic bacterium of the novel bacterial phylum Calditrichaeotaen_ZA
dc.typeArticleen_ZA

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