Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
ISME J. 2008 Jan;2(1):3-18. doi: 10.1038/ismej.2007.90. Epub 2007 Nov 8.

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

Author information

  • 1Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. teske@email.unc.edu

Abstract

Deep marine subsurface sediments represent a novel archaeal biosphere with unknown physiology; the sedimentary subsurface harbors numerous novel phylogenetic lineages of archaea that are at present uncultured. Archaeal 16S rRNA analyses of deep subsurface sediments demonstrate their global occurrence and wide habitat range, including deep subsurface sediments, methane seeps and organic-rich coastal sediments. These subsurface archaeal lineages were discovered by PCR of extracted environmental DNA; their detection ultimately depends on the specificity of the archaeal PCR 16S rRNA primers. Surprisingly high mismatch frequencies for some archaeal PCR primers result in amplification bias against the corresponding archaeal lineages; this review presents some examples. Obviously, most archaeal 16S rRNA PCR primers were developed either before the discovery of these deep subsurface archaeal lineages, or without taking their sequence variants into account. PCR surveys with multiple primer combinations, revision and updates of primers whenever possible, and increasing use of PCR-independent methods in molecular microbial ecology will contribute to a more comprehensive view of subsurface archaeal communities.

PMID:
18180743
[PubMed - indexed for MEDLINE]
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Nature Publishing Group
    Loading ...
    Write to the Help Desk