title: Integrated metagenomic and metaproteomic analyses of an ANME-1-dominated community in marine cold seep sediments.
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.
authors.affiliation: Department of Biology, Centre for Geobiology Department of Earth Science, University of Bergen, Bergen, Norway.
authors.forename: Runar
authors.initials: R
authors.lastname: Stokke
authors.forename: Irene
authors.initials: I
authors.lastname: Roalkvam
authors.forename: Anders
authors.initials: A
authors.lastname: Lanzen
authors.forename: Haflidi
authors.initials: H
authors.lastname: Haflidason
authors.forename: Ida H
authors.initials: IH
authors.lastname: Steen
mesh_terms: D000693:Anaerobiosis / Q000235:genetics; D001105:Archaea / Q000145:classification / Q000235:genetics*; D020564:Deltaproteobacteria / Q000145:classification / Q000235:genetics; D019015:Geologic Sediments / Q000382:microbiology*; D054892:Metagenome / Q000235:genetics*; D056186:Metagenomics; D008697:Methane / Q000378:metabolism; D008969:Molecular Sequence Data; D010802:Phylogeny; D040901:Proteomics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013312:Stress, Physiological / Q000235:genetics
chemical_list: D012336:RNA, Ribosomal, 16S; D008697:Methane