Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments

Handle URI:
http://hdl.handle.net/10754/621722
Title:
Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments
Authors:
Wang, Yong; Gao, Zhao-Ming; Li, Jiang-Tao; Bougouffa, Salim ( 0000-0001-9218-6452 ) ; Tian, Ren Mao; Bajic, Vladimir B. ( 0000-0001-5435-4750 ) ; Qian, Pei-Yuan
Abstract:
Aerophobetes (or CD12) is a recently defined bacterial phylum, of which the metabolic processes and ecological importance remain unclear. In the present study, we obtained the draft genome of an Aerophobetes bacterium TCS1 from saline sediment near the Thuwal cold seep in the Red Sea using a genome binning method. Analysis of 16S rRNA genes of TCS1 and close relatives revealed wide distribution of Aerophobetes in deep-sea sediments. Phylogenetic relationships showed affinity between Aerophobetes TCS1 and some thermophilic bacterial phyla. The genome of TCS1 (at least 1.27 Mbp) contains a full set of genes encoding core metabolic pathways, including glycolysis and pyruvate fermentation to produce acetyl-CoA and acetate. The identification of cross-membrane sugar transporter genes further indicates its potential ability to consume carbohydrates preserved in the sediment under the microbial mat. Aerophobetes bacterium TCS1 therefore probably carried out saccharolytic and fermentative metabolism. The genes responsible for autotrophic synthesis of acetyl-CoA via the Wood–Ljungdahl pathway were also found in the genome. Phylogenetic study of the essential genes for the Wood–Ljungdahl pathway implied relative independence of Aerophobetes bacterium from the known acetogens and methanogens. Compared with genomes of acetogenic bacteria, Aerophobetes bacterium TCS1 genome lacks the genes involved in nitrogen metabolism, sulfur metabolism, signal transduction and cell motility. The metabolic activities of TCS1 might depend on geochemical conditions such as supplies of CO2, hydrogen and sugars, and therefore the TCS1 might be a facultative bacterium in anaerobic saline sediments near cold seeps. © 2016, Science China Press and Springer-Verlag Berlin Heidelberg.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
Wang Y, Gao Z-M, Li J-T, Bougouffa S, Tian RM, et al. (2016) Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments. Science Bulletin 61: 1176–1186. Available: http://dx.doi.org/10.1007/s11434-016-1135-6.
Publisher:
Springer Nature
Journal:
Science Bulletin
Issue Date:
1-Jul-2016
DOI:
10.1007/s11434-016-1135-6
Type:
Article
ISSN:
2095-9273; 2095-9281
Sponsors:
This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB06010201) and the National Natural Science Foundation of China (41476104). This study was also supported by the Strategic Priority Research Program (XDB06010102) and an award from the King Abdullah University of Science and Technology (SA-C0040/UK-C0016) to P.Y. Qian. V.B. Bajic was supported by KAUST Base Research Funds, and S. Bougouffa was supported by a SABIC postdoctoral fellowship.
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorWang, Yongen
dc.contributor.authorGao, Zhao-Mingen
dc.contributor.authorLi, Jiang-Taoen
dc.contributor.authorBougouffa, Salimen
dc.contributor.authorTian, Ren Maoen
dc.contributor.authorBajic, Vladimir B.en
dc.contributor.authorQian, Pei-Yuanen
dc.date.accessioned2016-11-03T13:23:33Z-
dc.date.available2016-11-03T13:23:33Z-
dc.date.issued2016-07-01en
dc.identifier.citationWang Y, Gao Z-M, Li J-T, Bougouffa S, Tian RM, et al. (2016) Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments. Science Bulletin 61: 1176–1186. Available: http://dx.doi.org/10.1007/s11434-016-1135-6.en
dc.identifier.issn2095-9273en
dc.identifier.issn2095-9281en
dc.identifier.doi10.1007/s11434-016-1135-6en
dc.identifier.urihttp://hdl.handle.net/10754/621722-
dc.description.abstractAerophobetes (or CD12) is a recently defined bacterial phylum, of which the metabolic processes and ecological importance remain unclear. In the present study, we obtained the draft genome of an Aerophobetes bacterium TCS1 from saline sediment near the Thuwal cold seep in the Red Sea using a genome binning method. Analysis of 16S rRNA genes of TCS1 and close relatives revealed wide distribution of Aerophobetes in deep-sea sediments. Phylogenetic relationships showed affinity between Aerophobetes TCS1 and some thermophilic bacterial phyla. The genome of TCS1 (at least 1.27 Mbp) contains a full set of genes encoding core metabolic pathways, including glycolysis and pyruvate fermentation to produce acetyl-CoA and acetate. The identification of cross-membrane sugar transporter genes further indicates its potential ability to consume carbohydrates preserved in the sediment under the microbial mat. Aerophobetes bacterium TCS1 therefore probably carried out saccharolytic and fermentative metabolism. The genes responsible for autotrophic synthesis of acetyl-CoA via the Wood–Ljungdahl pathway were also found in the genome. Phylogenetic study of the essential genes for the Wood–Ljungdahl pathway implied relative independence of Aerophobetes bacterium from the known acetogens and methanogens. Compared with genomes of acetogenic bacteria, Aerophobetes bacterium TCS1 genome lacks the genes involved in nitrogen metabolism, sulfur metabolism, signal transduction and cell motility. The metabolic activities of TCS1 might depend on geochemical conditions such as supplies of CO2, hydrogen and sugars, and therefore the TCS1 might be a facultative bacterium in anaerobic saline sediments near cold seeps. © 2016, Science China Press and Springer-Verlag Berlin Heidelberg.en
dc.description.sponsorshipThis work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB06010201) and the National Natural Science Foundation of China (41476104). This study was also supported by the Strategic Priority Research Program (XDB06010102) and an award from the King Abdullah University of Science and Technology (SA-C0040/UK-C0016) to P.Y. Qian. V.B. Bajic was supported by KAUST Base Research Funds, and S. Bougouffa was supported by a SABIC postdoctoral fellowship.en
dc.publisherSpringer Natureen
dc.subjectAerophobetesen
dc.titleDraft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sedimentsen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalScience Bulletinen
dc.contributor.institutionSanya Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Chinaen
dc.contributor.institutionDivision of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, Chinaen
dc.contributor.institutionState Key Laboratory of Marine Geology, Tongji University, Shanghai, Chinaen
kaust.authorBougouffa, Salimen
kaust.authorBajic, Vladimir B.en
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