Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments
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Yang, Jiang Ke
Lee, On On
Li, Tie Gang
Al-Suwailem, Abdulaziz M.
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
KAUST Global Collaborative Research Program
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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.
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.
PublisherPublic Library of Science (PLoS)
PubMed Central IDPMC3244439
- Hydrothermally generated aromatic compounds are consumed by bacteria colonizing in Atlantis II Deep of the Red Sea.
- Authors: Wang Y, Yang J, Lee OO, Dash S, Lau SC, Al-Suwailem A, Wong TY, Danchin A, Qian PY
- Issue date: 2011 Oct
- Unique prokaryotic consortia in geochemically distinct sediments from Red Sea Atlantis II and discovery deep brine pools.
- Authors: Siam R, Mustafa GA, Sharaf H, Moustafa A, Ramadan AR, Antunes A, Bajic VB, Stingl U, Marsis NG, Coolen MJ, Sogin M, Ferreira AJ, Dorry HE
- Issue date: 2012
- Autotrophic microbe metagenomes and metabolic pathways differentiate adjacent Red Sea brine pools.
- Authors: Wang Y, Cao H, Zhang G, Bougouffa S, Lee OO, Al-Suwailem A, Qian PY
- Issue date: 2013
- Zonation of Microbial Communities by a Hydrothermal Mound in the Atlantis II Deep (the Red Sea).
- Authors: Wang Y, Li JT, He LS, Yang B, Gao ZM, Cao HL, Batang Z, Al-Suwailem A, Qian PY
- Issue date: 2015
- Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments.
- Authors: Adel M, Elbehery AH, Aziz SK, Aziz RK, Grossart HP, Siam R
- Issue date: 2016 Sep 6
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