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

Adrien Vigneron,Patricia Pignet,Anne Godfroy,Jean-Claude Caprais,Laurent Toffin,Jizhong Zhou,Barry A Cragg,Nolwenn Callac,Perrine Cruaud,Erwan G Roussel,Joy D Van Nostrand,John R Parkes,Maria-Cristina Ciobanu,Zhili He

doi:10.1371/journal.pone.0104427

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.

Highlights

Deep marine subsurface sediments are one of the most extensive microbial habitats on Earth, covering more than two-thirds of the Earth’s surface and reaching maximal thickness of more than 10 km at some locations [1]
Microbial community structure In this study, we document the taxonomic and functional diversity of the microbial community associated with subsurface sediments from a site adjacent (600 m) to cold seep sediment sites of the Sonora Margin [19,20]
Identical molecular methods were used in both studies, the microbial diversity associated with the subsurface sediments (0.5–9 mbsf) was different from the surface cold seeps (0–0.2 mbsf) of the Sonora Margin

Summary

Introduction

Deep marine subsurface sediments are one of the most extensive microbial habitats on Earth, covering more than two-thirds of the Earth’s surface and reaching maximal thickness of more than 10 km at some locations [1]. Specific lineages of Bacteria (for e.g. Chloroflexi, Candidate division JS1) and Archaea (for e.g. Miscellaneous Crenarchaeotal Group (MCG), Marine Benthic Group D (MBGD), South African Goldmine Euryarchaeotal Group (SAGMEG) [14,15], distinct from the surface biospheres (above 1 mbsf), appear to occur consistently in marine subsurface sediments. Recent single cell genomic approaches indicated the capacity of peptides degradation for members of MCG and MBGD archaeal lineages [18]. Despite these recent advances the metabolic pathways associated to the dominant microbial communities in subsurface sediments remain unclear

Objectives

Methods

Results

Discussion

Conclusion