Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments

Handle URI:
http://hdl.handle.net/10754/325298
Title:
Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments
Authors:
Wang, Yong; Yang, Jiang Ke; Lee, On On; Li, Tie Gang; Al-Suwailem, Abdulaziz M.; Danchin, Antoine; Qian, Pei-Yuan
Abstract:
The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers) of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed. © 2011 Wang et al.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; KAUST Global Collaborative Research Program
Citation:
Wang Y, Yang JK, Lee OO, Li TG, Al-Suwailem A, et al. (2011) Bacterial Niche-Specific Genome Expansion Is Coupled with Highly Frequent Gene Disruptions in Deep-Sea Sediments. PLoS ONE 6: e29149. doi:10.1371/journal.pone.0029149.
Publisher:
Public Library of Science (PLoS)
Journal:
PLoS ONE
Issue Date:
21-Dec-2011
DOI:
10.1371/journal.pone.0029149
PubMed ID:
22216192
PubMed Central ID:
PMC3244439
Type:
Article
ISSN:
19326203
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorWang, Yongen
dc.contributor.authorYang, Jiang Keen
dc.contributor.authorLee, On Onen
dc.contributor.authorLi, Tie Gangen
dc.contributor.authorAl-Suwailem, Abdulaziz M.en
dc.contributor.authorDanchin, Antoineen
dc.contributor.authorQian, Pei-Yuanen
dc.date.accessioned2014-08-27T09:45:42Z-
dc.date.available2014-08-27T09:45:42Z-
dc.date.issued2011-12-21en
dc.identifier.citationWang Y, Yang JK, Lee OO, Li TG, Al-Suwailem A, et al. (2011) Bacterial Niche-Specific Genome Expansion Is Coupled with Highly Frequent Gene Disruptions in Deep-Sea Sediments. PLoS ONE 6: e29149. doi:10.1371/journal.pone.0029149.en
dc.identifier.issn19326203en
dc.identifier.pmid22216192en
dc.identifier.doi10.1371/journal.pone.0029149en
dc.identifier.urihttp://hdl.handle.net/10754/325298en
dc.description.abstractThe complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers) of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed. © 2011 Wang et al.en
dc.language.isoenen
dc.publisherPublic Library of Science (PLoS)en
dc.rightsWang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en
dc.rightsArchived with thanks to PLoS ONEen
dc.subjectbacterial genomeen
dc.subjectcontrolled studyen
dc.subjectdeep seaen
dc.subjectenvironmental changeen
dc.subjectevolutionary adaptationen
dc.subjectframeshift mutationen
dc.subjectgene disruptionen
dc.subjectgene dosageen
dc.subjectgene duplicationen
dc.subjectgenetic conservationen
dc.subjectgenetic parametersen
dc.subjectgenetic variabilityen
dc.subjectgenome expansionen
dc.subjectgenome sizeen
dc.subjectmetagenomeen
dc.subjectparalogyen
dc.subjectpoint mutationen
dc.subjectpseudogeneen
dc.subjectpyrosequencingen
dc.subjectsedimenten
dc.subjectsequence homologyen
dc.subjectbacteriumen
dc.subjectgeneticsen
dc.subjectmicrobiologyen
dc.subjectsea wateren
dc.subjectBacteriaen
dc.subjectGenome, Bacterialen
dc.subjectGeologic Sedimentsen
dc.subjectSeawateren
dc.titleBacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sedimentsen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentKAUST Global Collaborative Research Programen
dc.identifier.journalPLoS ONEen
dc.identifier.pmcidPMC3244439en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionInstitute of Oceanography, Chinese Academy of Sciences, Qingdao, Chinaen
dc.contributor.institutionAMAbiotics, SAS and CEA/Genoscope, Evry, Franceen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorAl-Suwailem, Abdulaziz M.en
kaust.authorLi, Tiegangen

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