Integrated metagenomic and metaproteomic analyses of an ANME-1-dominated community in marine cold seep sediments

Environ Microbiol. 2012 May;14(5):1333-46. doi: 10.1111/j.1462-2920.2012.02716.x. Epub 2012 Mar 9.

Abstract

Sulfate-reducing methanotrophy by anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) is a major biological sink of methane in anoxic methane-enriched marine sediments. The physiology of a microbial community dominated by free-living ANME-1 at 14-16 cm below the seafloor in the G11 pockmark at Nyegga was investigated by integrated metagenomic and metaproteomic approaches. Total DNA was subjected to 454-pyrosequencing (829 527 reads), and 16.6 Mbp of sequence information was assembled into 27352 contigs. Taxonomic analysis supported a high abundance of Euryarchaea (70%) with 66% of the assembled metagenome belonging to ANME-1. Extracted sediment proteins were separated in two dimensions and subjected to mass spectrometry (LTQ-Orbitrap XL). Of 356 identified proteins, 245 were expressed by ANME-1. These included proteins for cold-adaptation and production of gas vesicles, reflecting both the adaptation of the ANME-1 community to a permanently cold environment and its potential for positioning in specific sediment depths respectively. In addition, key metabolic enzymes including the enzymes in the reverse methanogenesis pathway (except N(5) ,N(10) -methylene-tetrahydromethanopterin reductase), heterodisulfide reductases and the F(420) H(2) :quinone oxidoreductase (Fqo) complex were identified. A complete dissimilatory sulfate reduction pathway was expressed by sulfate-reducing Deltaproteobacteria. Interestingly, an APS-reductase comprising Gram-positive SRB and related sequences were identified in the proteome. Overall, the results demonstrated that our approach was effective in assessing in situ metabolic processes in cold seep sediments.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anaerobiosis / genetics
  • Archaea / classification
  • Archaea / genetics*
  • Deltaproteobacteria / classification
  • Deltaproteobacteria / genetics
  • Geologic Sediments / microbiology*
  • Metagenome / genetics*
  • Metagenomics*
  • Methane / metabolism
  • Molecular Sequence Data
  • Phylogeny
  • Proteomics*
  • RNA, Ribosomal, 16S / genetics
  • Stress, Physiological / genetics

Substances

  • RNA, Ribosomal, 16S
  • Methane