Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia Margin as revealed by 16S rRNA molecular analysis

Abstract

The microbial community of a deep (to 234 m below the sea floor) sediment gas hydrate deposit (Cascadia Margin Ocean Drilling Program Site 889/890, Leg 146) was analysed for the first time by molecular genetic techniques. Both bacterial and methanogen diversity were determined by phylogenetic analysis of ribosomal DNA sequences. High molecular mass DNA, indicative of active bacteria, was present in all of the samples. Ribosomal RNA genes were amplified from extracted DNA extracted from sediment using bacteria, and methanogen specific PCR primers, the latter designed in this study. Phylogenetic analysis of approximately 400 bacterial clones demonstrated that 96% were members of the Proteobacteria. These clones were affiliated with the K, L and Q subdivisions, with Caulobacter (Zymomonas group), Ralstonia and Pseudomonas phylotypes predominating. The methanogen clones were of low diversity and clustered in three sub-groups. Two of these sub-groups (contained 96% of the 400 clones) were closely related to Methanosarcina mazeii, while the third sub-group clustered in the Methanobacteriales. This analysis of a deep sediment gas hydrate environment shows a bacteria and methanogen community of limited diversity and confirms that the gas hydrate zone is biogeochemically active. These results are consistent with the presence of bacterial populations capable of methanogenesis throughout the core, and suggest that the methane hydrate at this site is at least partially biogenic in origin. ß

Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor

“…Contrary to our expectations, the methanogen isolates from subseafloor sediments were very closely related to previously characterized (cultivated) methanogens. Although the novelty of the isolated methanogens is unfortunately low from a taxonomic perspective, our results are consistent with previous culture-independent molecular studies, which have also detected sequences closely related to previously isolated methanogens, such as Methanosarcina and Methanobrevibacter (for example, Marchesi et al, 2001;Newberry et al, 2004). Among the bacterial isolates, strains MO-CFX1 and MO-CFX2 belonging to the Chloroflexi subphylum I, and strains MO-SPC1 and MO-SPC2 belonging to the genus Spirochaeta are of note (Figures 5a-d) because these bacterial components have been frequently reported as some of the predominant microbial components in marine subsurface environments (for example, Toffin et al, 2004;Inagaki et al, 2006;Fry et al, 2008;Webster et al, 2009).…”

Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics

“…16S rRNA gene surveys from hydrate-bearing deep subsurface sediments and methane seeps have reported Burkholderiaceaerelated phylotypes (26), suggesting a potential niche for these organisms within methane-rich marine environments; however, their role in this ecosystem remains undefined. There has been some speculation that Betaproteobacteria may participate in methanotrophy (27); however, we are unaware of another study describing a close physical association between these organisms and ANME archaea. The involvement of Betaproteobacteria within the Chlorochromatium symbiosis, and other documented couplings between Betaproteobacteria and bacterial methanotrophs (28) suggest some conferred capacity for interspecies associations by this proteobacterial subdivision.…”

Assessment of a metaviromic dataset generated from nearshore Lake Michigan

“…DNA was prepared without any additional amplification steps, therefore favouring the capture of dsDNA viruses (Kim and Bae 2011). To test for bacterial contamination, each extraction underwent PCR testing using primers for the bacterial 16S rRNA gene (Marchesi et al 2001), alongside an Escherichia coli-positive control. No amplicons were produced by the viral DNA template.…”