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Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, Tartu, Estonia;Swedish Univ Agr Sci, Dept Ecol, Ulls Vag 16, S-75651 Uppsala, Sweden.
Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, Tartu, Estonia;Braunschweig Univ Technol, Zool Inst, Mendelssohnstr 4, D-38106 Braunschweig, Germany.
European Mol Biol Lab, Struct & Computat Biol, Heidelberg, Germany.
European Mol Biol Lab, Struct & Computat Biol, Heidelberg, Germany;Max Delbruck Ctr Mol Med, Berlin, Germany;Univ Wurzburg, Bioctr, Dept Bioinformat, Wurzburg, Germany.
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2019 (English)In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 11, no 4, p. 487-494Article in journal (Refereed) Published
Abstract [en]

High-throughput studies of microbial communities suggest that Archaea are a widespread component of microbial diversity in various ecosystems. However, proper quantification of archaeal diversity and community ecology remains limited, as sequence coverage of Archaea is usually low owing to the inability of available prokaryotic primers to efficiently amplify archaeal compared to bacterial rRNA genes. To improve identification and quantification of Archaea, we designed and validated the utility of several primer pairs to efficiently amplify archaeal 16S rRNA genes based on up-to-date reference genes. We demonstrate that several of these primer pairs amplify phylogenetically diverse Archaea with high sequencing coverage, outperforming commonly used primers. Based on comparing the resulting long 16S rRNA gene fragments with public databases from all habitats, we found several novel family- to phylum-level archaeal taxa from topsoil and surface water. Our results suggest that archaeal diversity has been largely overlooked due to the limitations of available primers, and that improved primer pairs enable to estimate archaeal diversity more accurately.

Place, publisher, year, edition, pages
WILEY , 2019. Vol. 11, no 4, p. 487-494
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Evolutionary Biology Microbiology
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URN: urn:nbn:se:uu:diva-390507DOI: 10.1111/1758-2229.12684ISI: 000474226700002PubMedID: 30058291OAI: oai:DiVA.org:uu-390507DiVA, id: diva2:1341975
Funder
EU, European Research Council, ERC-AdG-669830Swedish Research Council, 2017-05019Available from: 2019-08-12 Created: 2019-08-12 Last updated: 2019-08-12Bibliographically approved

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Bahram, Mohammad

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