Quantification of microbial communities in near‐surface and deeply buried marine sediments on the Peru continental margin using real‐time PCR

Abstract

Deeply buried marine sediments harbour a large fraction of all prokaryotes on Earth but it is still unknown which phylogenetic and physiological microbial groups dominate the deep biosphere. In this study real-time PCR allowed a comparative quantitative microbial community analysis in near-surface and deeply buried marine sediments from the Peru continental margin. The 16S rRNA gene copy numbers of prokaryotes and Bacteria were almost identical with a maximum of 10(8)-10(10) copies cm(-3) in the near-surface sediments. Archaea exhibited one to three orders of magnitude lower 16S rRNA gene copy numbers. The 18S rRNA gene of Eukarya was always at least three orders of magnitude less abundant than the 16S rRNA gene of prokaryotes. The 16S rRNA gene of the Fe(III)- and Mn(IV)-reducing bacterial family Geobacteraceae and the dissimilatory (bi)sulfite reductase gene (dsrA) of sulfate-reducing prokaryotes were abundant with 10(6)-10(8) copies cm(-3) in near-surface sediments but showed lower numbers and an irregular distribution in the deep sediments. The copy numbers of all genes decreased with sediment depth exponentially. The depth gradients were steeper for the gene copy numbers than for numbers of total prokaryotes (acridine orange direct counts), which reflects the ongoing degradation of the high-molecular-weight DNA with sediment age and depth. The occurrence of eukaryotic DNA also suggests DNA preservation in the deeply buried sediments.

Microorganisms persist at record depths in the subseafloor of the Canterbury Basin

“…), as revealed by molecular, metagenomic and metatranscriptomic studies (Lipp et al, 2008;Roussel et al, 2008;Biddle et al, 2011;Pawlowski et al, 2011;Orsi et al, 2013a). It harbors representatives from the three domains of life, for example, numerous endemic and/or as yet uncultured Archaea and Bacteria (for example, Inagaki et al, 2006;Orcutt et al, 2011), in addition to bacterial endospores (Lomstein et al, 2012), protists and fungi belonging to Eukarya (Schippers and Neretin, 2006;Edgcomb et al, 2011;Orsi et al, 2013a,b). Occurrence of capsid-encoding organisms has also been confirmed (Engelhardt et al, 2011).…”

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

“…Sites 1225 and 1226 are more oligotrophic (1225: 0.01-0.85 wt%, average 0.18 wt%; 1226: 0.25-3.49 wt%, average 0.92 wt%) and represent sediments with lower microbial activity. Thus, the sampling sites comprises a broad range of characteristics in terms of microbial activity, chemical profiles and abundances of prokaryotes (Parkes et al, 2000;D'Hondt et al, 2004;Schippers and Neretin, 2006). Therefore, this area of the deep biosphere is well suited to study the role of viruses for the investigated sites and also allow extrapolating their impact to other marine subsurface habitats.…”

Desulfocurvus vexinensis gen. nov., sp. nov., a sulfate-reducing bacterium isolated from a deep subsurface aquifer

“…Considering only some of the recently published papers, SRB have been found in many deep geological formations including a 4-5 km deep fault (Moser et al, 2005), deep aquifers in Australia (Kimura et al, 2005) and France (Basso et al, 2005b(Basso et al, , 2009, deeply buried marine sediments (Schippers & Neretin, 2006) and oil reservoirs (Grabowski et al, 2005;Magot, 2005;Birkeland, 2005). From the numerous observations already published, it appears that SRB may constitute an important, or even major, component of the subterrestrial biosphere, which is considered to be possibly the largest prokaryotic habitat on our planet (Whitman et al, 1998;Parkes et al, 2005).…”