Phylogenetic and Functional Diversity of Microbial Communities Associated with Subsurface Sediments of the Sonora Margin, Guaymas Basin

Type Article
Date 2014-08
Language English
Author(s) Vigneron AdrienORCID1, 2, 3, Cruaud Perrine1, 2, 3, Roussel ErwanORCID7, Pignet Patricia1, 2, 3, Caprais Jean-Claude4, Callac Nolwenn1, 2, 3, 5, Ciobanu Maria Cristina6, Godfroy AnneORCID1, 2, 3, Cragg Barry A.7, Parkes John R.7, Van Nostrand Joy D.8, 9, He Zhili8, 9, Zhou Jizhong8, 9, 10, 11, Toffin LaurentORCID1, 2, 3
Affiliation(s) 1 : IFREMER, Lab Microbiol Environm Extremes, UMR6197, Plouzane, France.
2 : Univ Bretagne Occidentale, Lab Microbiol Environm Extremes, UMR6197, Plouzane, France.
3 : CNRS, Lab Microbiol Environm Extremes, UMR6197, Plouzane, France.
4 : IFREMER, Lab Etud Environm Profonds, UMR6197, Plouzane, France.
5 : Univ Brest, Domaines Ocean IUEM, UMR6538, Plouzane, France.
6 : IFREMER, Geosci Marines, Lab Environm Sedimentaires, Plouzane, France.
7 : Cardiff Univ, Sch Earth & Ocean Sci, Cardiff CF10 3AX, S Glam, Wales.
8 : Univ Oklahoma, Inst Environm Genom, Norman, OK 73019 USA.
9 : Univ Oklahoma, Dept Microbiol & Plant Biol, Norman, OK 73019 USA.
10 : Tsinghua Univ, Sch Environm, State Key Joint Lab Environm Simulat & Pollut Con, Beijing 100084, Peoples R China.
11 : Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA.
Source Plos One (1932-6203) (Public Library Science), 2014-08 , Vol. 9 , N. 8 , P. e104427
DOI 10.1371/journal.pone.0104427
WOS© Times Cited 16
Note Data Availability: The authors confirm that all data underlying the findings are fully available without restriction. Nucleic acid sequences are available in the EMBL database under the following accession numbers: HF543837–HF543861 for archaeal, HF545450–HF545524 for bacterial 16S rRNA sequences and HF935025–HF935037 for mcrA gene sequences. The raw GeoChip dataset is available at http://ieg.ou.edu/4download/.
Abstract Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments.
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Vigneron Adrien, Cruaud Perrine, Roussel Erwan, Pignet Patricia, Caprais Jean-Claude, Callac Nolwenn, Ciobanu Maria Cristina, Godfroy Anne, Cragg Barry A., Parkes John R., Van Nostrand Joy D., He Zhili, Zhou Jizhong, Toffin Laurent (2014). Phylogenetic and Functional Diversity of Microbial Communities Associated with Subsurface Sediments of the Sonora Margin, Guaymas Basin. Plos One, 9(8), e104427. Publisher's official version : https://doi.org/10.1371/journal.pone.0104427 , Open Access version : https://archimer.ifremer.fr/doc/00203/31408/