Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment

Abstract

The subseafloor marine biosphere may be one of the largest reservoirs of microbial biomass on Earth and has recently been the subject of debate in terms of the composition of its microbial inhabitants, particularly on sediments from the Peru Margin. A metagenomic analysis was made by using whole-genome amplification and pyrosequencing of sediments from Ocean Drilling Program Site 1229 on the Peru Margin to further explore the microbial diversity and overall community composition within this environment. A total of 61.9 Mb of genetic material was sequenced from sediments at horizons 1, 16, 32, and 50 m below the seafloor. These depths include sediments from both primarily sulfate-reducing methane-generating regions of the sediment column. Many genes of the annotated genes, including those encoding ribosomal proteins, corresponded to those from the Chloroflexi and Euryarchaeota. However, analysis of the 16S smallsubunit ribosomal genes suggests that Crenarchaeota are the abundant microbial member. Quantitative PCR confirms that uncultivated Crenarchaeota are indeed a major microbial group in these subsurface samples. These findings show that the marine subsurface is a distinct microbial habitat and is different from environments studied by metagenomics, especially because of the predominance of uncultivated archaeal groups.Archaea ͉ Chloroflexi ͉ marine sediment ͉ quantitative PCR

Insights in the ecology and evolutionary history of the Miscellaneous Crenarchaeotic Group lineage

“…One explanation for this trend, one of the most robust in macroecology (Gaston et al, 2000), is related with the alternative concept of 'jack-of-all-trades is master of all' (Brown, 1984;Gaston et al, 1997;Verberk et al, 2010), in which cosmopolitan species that can tolerate a large spectrum of environmental conditions and use a broad range of resources become locally dominant. This concept seems to characterize very well members of the MCG lineage both in terms of resources (Biddle et al, 2008;Lloyd et al, 2013;Meng et al, 2014) and distribution. The MCG lineage was one of the most frequent archaeal lineage found in the sediment habitat as it occurs in 68% (141 sites) of the 207 sediments analyzed.…”

“…However, most of these abundant microbial groups escape our capacity to understand their ecology and physiology. This is for instance the case of the Miscellaneous Crenarchaeotic Group (MCG), a sister clade of the archaeal phyla Thaumarchaeota and Aigarchaeota, which appears to be particularly abundant and widespread in marine sediments (Biddle et al, 2006(Biddle et al, , 2008Durbin and Teske, 2012;Kubo et al, 2012;Lloyd et al, 2013;Lazar et al, 2014), where it accounts on average for 12% of total prokaryotic cells in CARD-FISH counts (Kubo et al, 2012) and for 30% of all clones in archaeal 16S rRNA gene libraries (Fry et al, 2008). Considering that half of the microbial cells in the oceans are found in sediments (Kallmeyer et al, 2012) and that oceans covers~70% of the surface of the planet, members of the MCG may be one of the most successful lineages on the Earth.…”

Bacterial community structure in maize stubble-amended soils with different moisture levels estimated by bar-coded pyrosequencing

“…This targeted gene region has been shown to be the most appropriate for accurate phylogenetic identification of bacteria (Biddle et al, 2008). PCR reaction mixtures consisted of 0.5 ml (0.25 mM) each of forward/reverse primer, 1 ml (50 ng ml À1 ) of DNA template, 23 ml of ddH 2 O, and 25 ml of Premix Taq (Takara, Shiga, Japan), which contained 1.25 U DNA polymerase, 2 Â dNTP mixture (0.4 mM), 2 Â buffer (3 mM Mg 2+ ) and the marker (tartrazine/xylene cyanol FF).…”

Microbial community composition in sediments resists perturbation by nutrient enrichment

“…nirS and 16S rRNA standards were quantified using Quant-iT Picogreen (Molecular Probes Inc., Eugene, OR, USA) and serially diluted to generate known standards. Environmental DNA from each plot was amplified in triplicate, along with triplicate standards and internal controls, on a Strategene MX-3000 (Stratagene, La Jolla, CA, USA) under the following conditions: 16S rRNA was amplified following the protocol outlined in Biddle et al (2008). For each sample of 16S rRNA, 1.125 ml of 20 mM primers 357F and 519R was added along with 1 ml DNA, 12.5 ml SybrGreen master mix (Applied Biosystems, Carlsbad, CA, USA) and 10.5 ml deionized water.…”