A metagenomic study of methanotrophic microorganisms in Coal Oil Point seep sediments

Abstract

BackgroundMethane oxidizing prokaryotes in marine sediments are believed to function as a methane filter reducing the oceanic contribution to the global methane emission. In the anoxic parts of the sediments, oxidation of methane is accomplished by anaerobic methanotrophic archaea (ANME) living in syntrophy with sulphate reducing bacteria. This anaerobic oxidation of methane is assumed to be a coupling of reversed methanogenesis and dissimilatory sulphate reduction. Where oxygen is available aerobic methanotrophs take part in methane oxidation. In this study, we used metagenomics to characterize the taxonomic and metabolic potential for methane oxidation at the Tonya seep in the Coal Oil Point area, California. Two metagenomes from different sediment depth horizons (0-4 cm and 10-15 cm below sea floor) were sequenced by 454 technology. The metagenomes were analysed to characterize the distribution of aerobic and anaerobic methanotrophic taxa at the two sediment depths. To gain insight into the metabolic potential the metagenomes were searched for marker genes associated with methane oxidation.ResultsBlast searches followed by taxonomic binning in MEGAN revealed aerobic methanotrophs of the genus Methylococcus to be overrepresented in the 0-4 cm metagenome compared to the 10-15 cm metagenome. In the 10-15 cm metagenome, ANME of the ANME-1 clade, were identified as the most abundant methanotrophic taxon with 8.6% of the reads. Searches for particulate methane monooxygenase (pmoA) and methyl-coenzyme M reductase (mcrA), marker genes for aerobic and anaerobic oxidation of methane respectively, identified pmoA in the 0-4 cm metagenome as Methylococcaceae related. The mcrA reads from the 10-15 cm horizon were all classified as originating from the ANME-1 clade.ConclusionsMost of the taxa detected were present in both metagenomes and differences in community structure and corresponding metabolic potential between the two samples were mainly due to abundance differences.The results suggests that the Tonya Seep sediment is a robust methane filter, where taxa presently dominating this process could be replaced by less abundant methanotrophic taxa in case of changed environmental conditions.

Characterization of Methane Degradation and Methane-Degrading Microbes in Alaska Coastal Water

“…Other studies have reported genomic data from anaerobic methane oxidizing archaea in the ANME-1 group (Hallam et al 2004;Meyerdierks et al 2010;Meyerdierks et al 2005), and a recent metagenomic survey similar to ours also found that most ANME sequences were related to those from ANME-1 (Havelsrud et al 2011). Using a PCR-based approach another study also found mostly ANME-1 (Lloyd et al 2011).…”

Rare Branched Fatty Acids Characterize the Lipid Composition of the Intra-Aerobic Methane Oxidizer “Candidatus Methylomirabilis oxyfera”

“…Methylomirabilis oxyfera"-like bacteria in marine sediments based on genomic analyses, but this was only based on 16S rRNA reads and no similarity with functional genes (for methane monooxygenase) of "Ca. Methylomirabilis oxyfera" could be found in the metagenome (24). The contribution of "Ca.…”

Polycyclic aromatic hydrocarbons in deep sea sediments: Microbe–pollutant interactions in a remote environment

“…Functions such as sulfate reduction in hydrothermal vents and cold seeps have been mainly attributed to ε-and δ-Proteobacteria (Desulfococcus and Desulfosarcina) (Longnecker and Reysenbach, 2001;Inagaki et al, 2002;Zeng et al, 2005), sulfur oxidation to γ-and ε-Proteobacteria (Inagaki and Nakagawa, 2008), methane oxidation to members of the uncultured candidate division JS1 (Inagaki et al, 2002), γ-and α-Proteobacteria (Xu et al, 2005) and dechlorination to members of δ-Proteobacteria and Chloroflexi (Inagaki and Nakagawa, 2008). Archaea are also crucial players in the chemosynthetic activity of the DSS microbial community, e.g., in the fixation of dissolved inorganic carbon (Herndl et al, 2005), methane oxidation (Havelsrud et al, 2011) and nitrification (Beman et al, 2008). Archaea have also been shown to be relatively more abundant in DSSs microbial communities (Herndl et al, 2005).…”