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

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doi: 10.1111/j.1462-2920.2006.01019.x
Author(s): Schippers, Axel; Neretin, Lev N.
Author Affiliation(s): Primary:
Federal Institute for Geosciences and Natural Resources, Section Geomicrobiology, Hanover, Germany
Volume Title: Environmental Microbiology
Source: Environmental Microbiology, 8(7), p.1251-1260. Publisher: Blackwell Science, Oxford, United Kingdom. ISSN: 1462-2912
Note: In English. 48 refs.; illus., incl. 2 tables
Summary: 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 108-1010 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 106-108 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.
Year of Publication: 2006
Research Program: ODP Ocean Drilling Program
Key Words: 07 Marine Geology and Oceanography; 22 Environmental Geology; Bacteria; Biodegradation; Biosphere; Continental margin; DNA; Deep-water environment; East Pacific; Ecology; Equatorial Pacific; Eukaryotes; Genetics; Geobacter; Habitat; Leg 201; Marine environment; Microorganisms; Molecular dynamics; Nucleic acids; ODP Site 1227; ODP Site 1229; ODP Site 1230; Ocean Drilling Program; Pacific Ocean; Peru; Peru-Chile Trench; Phylogeny; Prokaryotes; RNA; Sediments; South America; South Pacific; Southeast Pacific; Sulfate ion
Coordinates: S090700 S090700 W0803500 W0803500
S105900 S105900 W0775800 W0775800
Record ID: 2015100864
Copyright Information: GeoRef, Copyright 2019 American Geosciences Institute. Reference includes data from John Wiley & Sons, Chichester, United Kingdom