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.
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Acknowledgements
A Teske was supported by the NASA Astrobiology Institutes at MBL (Environmental Genomes, S/C NCC2-1054) and at URI (Subsurface Biospheres NCC2-1275), and by NSF (OCE-Ocean Drilling Program 0527167). K Sørensen was supported by the Marie Curie Transfer of Knowledge program (ABIOS). We thank JF Biddle for critical reading of the manuscript.
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Teske, A., Sørensen, K. Uncultured archaea in deep marine subsurface sediments: have we caught them all?. ISME J 2, 3–18 (2008). https://doi.org/10.1038/ismej.2007.90
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