Prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin

Abstract

The community compositions of Bacteria and Archaea were investigated in deep, sub-seafloor sediments from the highly productive Peru Margin (ODP Leg 201, sites 1228 and 1229, c. 25 km apart) down to nearly 200 m below the seafloor using taxonomic (16S rRNA) and functional (mcrA and dsrA) gene markers. Bacterial and archaeal groups identified from clone libraries of 16S rRNA gene sequences at site 1229 agreed well with sequences amplified from bands excised from denaturing gradient gel electrophoresis (DGGE) depth profiles, with the exception of the Miscellaneous Crenarchaeotic Group (MCG). This suggested that the prokaryotic community at site 1228, obtained from DGGE profiling alone, was reliable. Sites were dominated by Bacteria in the Gammaproteobacteria, Chloroflexi (green non-sulphur bacteria) and Archaea in the MCG and South African Gold Mine Euryarchaeotic Group, although community composition changed with depth. The candidate division JS1 was present throughout both sites but was not dominant. The populations identified in the Peru Margin sediments consisted mainly of prokaryotes found in other deep subsurface sediments, and were more similar to communities from the Sea of Okhotsk (pelagic clays) than to those from the low organic carbon Nankai Trough sediments. Despite broad similarities in the prokaryotic community at the two sites, there were some differences, as well as differences in activity and geochemistry. Methanogens (mcrA) within the Methanosarcinales and Methanobacteriales were only found at site 1229 (4 depths analysed), whereas sulphate-reducing prokaryotes (dsrA) were only found at site 1228 (one depth), and these terminal-oxidizing prokaryotes may represent an active community component present at low abundance. This study clearly demonstrates that the deep subsurface sediments of the Peru Margin have a large diverse and metabolically active prokaryotic population.

Uncultured archaea in deep marine subsurface sediments: have we caught them all?

“…These crenarchaeotal groups were found in 16S rDNA surveys of push cores retrieved from surficial (Takai and Horikoshi, 1999). Clones of these groups occur in deep subsurface sediments of Leg 201 Sørensen and Teske, 2006;Webster et al, 2006), and in surficial marine sediments from around the world (Knittel et al, 2005). The detection of MBG-D in reverse-transcribed 16S rRNA clone libraries from Sites 1227 and 1228 indicates that the group is metabolically active in subsurface environments.…”

“…However, SAGMEG Archaea were next found in deep marine sediments containing methane hydrates in the Nankai Trough, here labeled NT-A1 group (Reed et al, 2002); in marine subsurface sediments in the Sea of Okhotsk (Inagaki et al, 2003), and repeatedly in marine sediments of the Peru Margin, at ODP Sites 1227 , 1228 and 1229 Webster et al, 2006). The SAGMEG Archaea have been detected by rRNA extraction, reverse transcription, cloning and sequencing, and therefore appear to be a metabolically active archaeal group in deep marine subsurface sediments (Sørensen and Teske, 2006); they are a part of the heterotrophic archaeal community in deep, anaerobic and methanogenic Peru Margin sediments at ODP Site 1227 .…”

Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments

“…A few subgroups from the literature were not explicitly included in the 17 subgroup designations because they are subsets of some of the other MCG subgroups. Subgroup PM-1 fell within the MCG-2, PM-2 fell within the MCG-4, PM-3 through PM-5 fell within the MCG-1, PM-6 fell within the MCG-3, PM-7 fell within the MCG-8 in some treeing methods and PM-8 fell within the MCG-17 (Webster et al, 2006). pMARA-5 (Nercessian et al, 2005) fell within MCG-17.…”

Biogeography of Rhizobium radiobacter and distribution of associated temperate phages in deep subseafloor sediments

“…Furthermore, geochemical characteristics of deeper sediments indicate microbial activity as several chemical transformations are linked to microbial processes (Parkes et al, 2000;D'Hondt et al, 2004). During the last decades we got insights into microbial community composition and diversity within the deep subsurface (Inagaki et al, 2006;Sørensen and Teske, 2006;Webster et al, 2006;Fry et al, 2008;Lipp et al, 2008;Teske and Sørensen, 2008;Durbin and Teske, 2011).…”