Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota

Kublanov, Ilya V.; Sigalova, Olga M.; Gavrilov, Sergey N.; Lebedinsky, Alexander V.; Rinke, Christian; Kovaleva, Olga; Chernyh, Nikolai A.; Ivanova, Natalia; Daum, Chris; Reddy, T. B. K.; Klenk, Hans -Peter; Spring, Stefan; Goker, Markus; Reva, Oleg N.; Miroshnichenko, Margarita L.; Kyrpides, Nikos C.; Woyke, Tanja; Gelfand, Mikhail S.; Bonch-Osmolovskaya, Elizaveta A.

doi:10.3389/fmicb.2017.00195

Title: Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota

Journal Article · Mon Feb 20 00:00:00 EST 2017 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2017.00195· OSTI ID:1379740

Kublanov, Ilya V. ^[1]; Sigalova, Olga M. ^[1]; Gavrilov, Sergey N. ^[1]; Lebedinsky, Alexander V. ^[1]; Rinke, Christian ^[2]; Kovaleva, Olga ^[1]; Chernyh, Nikolai A. ^[1]; Ivanova, Natalia ^[3]; Daum, Chris ^[3]; Reddy, T. B. K. ^[3]; Klenk, Hans -Peter ^[4]; Spring, Stefan ^[5]; Goker, Markus ^[5]; Reva, Oleg N. ^[6]; Miroshnichenko, Margarita L. ^[1]; Kyrpides, Nikos C. ^[3]; Woyke, Tanja ^[7]; Gelfand, Mikhail S. ^[8]; Bonch-Osmolovskaya, Elizaveta A. ^[1]

Russian Academy of Sciences, Moscow (Russia)
Univ. of Queensland, St. Lucia, QLD (Australia)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Newcastle Univ., Newcastle upon Tyne (United Kingdom)
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
Univ. of Pretoria, Pretoria (South Africa)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Russian Academy of Sciences, Moscow (Russia); M.V. Lomonosov Moscow State Univ., Moscow (Russia); Skolkovo Institute of Science and Technology, Moscow (Russia); National Research Univ. - Higher School of Economics, Moscow (Russia)

The 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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1379740

Journal Information:: Frontiers in Microbiology, Vol. 8, Issue FEB; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 28 works

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