Phylogenetic and functional diversity of microbial communities associated with subsurface sediments of the Sonora Margin, Guaymas Basin

• Published in: PloS one 2014-08, Vol.9 (8), p.e104427-104427
• Main Authors: Vigneron, Adrien, Cruaud, Perrine, Roussel, Erwan G, 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
• Format: Article
• Language: English
• Subjects: Archaea; Archaea - classification; Archaea - genetics; Archaean biology; Bacteria; Bacteria - classification; Bacteria - genetics; Base Sequence; BASIC BIOLOGICAL SCIENCES; Basins (Geology); Biodegradation; Biodiversity; Biology and Life Sciences; Chloroflexi; Cold; cold seeps; Communities; Community structure; DNA microarrays; Ecology and Environmental Sciences; Environmental Sciences; Gene expression; Genetic transformation; Genomics; Geochemistry; Hydrocarbons; Laboratories; Lipids; Marine ecosystems; Measuring instruments; Metabolic pathways; Metabolism; methane; Microbial activity; Microbiomes; Microorganisms; Molecular Sequence Data; Monetary incentives; Nitrogen; Ocean floor; Organic carbon; Phylogenetics; Phylogeny; Plant biology; Primers; ribosomal RNA; RNA; RNA, Archaeal - genetics; RNA, Bacterial - genetics; RNA, Ribosomal, 16S - genetics; rRNA 16S; Science; sediment; Sediments; Spacer; Substrates; Transformation; Uranium; Water Microbiology
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0104427

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.