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High-throughput sequencing shows inconsistent results with a microscope-based analysis of the soil prokaryotic community
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. (Climate Impacts Research Centre (CIRC))
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. (Climate Impacts Research Centre (CIRC) ; Arcum)
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2014 (English)In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 76, 53-56 p.Article in journal (Refereed) Published
Abstract [en]

In the present study, we perform the first direct analysis on how the composition of the prokaryotic soil community differs depending on whether high-throughput sequencing or fluorescent in situ hybridization (FISH) coupled with catalyzed reporter deposition (CARD) is used. Soil samples were collected along short (<3 m) tundra vegetation gradients from Northern Sweden. Relative abundances of Acid-obacteria and Bacteroidetes estimated by the high-throughput sequencing were higher than those estimated by CARD-FISH, while relative abundances of Archaea and alpha-Proteobacteria estimated by high-throughput sequencing were lower than those estimated by CARD-FISH. The results indicated that the high-throughput sequencing overestimates/underestimates the relative abundance of some microbial taxa if we assume that CARD-FISH can provide potentially more quantitative data. Great caution should be taken when interpreting data generated by molecular technologies (both of high-throughput sequencing and CARD-FISH), and supports by multiple approaches are necessary to make a robust conclusion. (C) 2014 Elsevier Ltd. All rights reserved.

Place, publisher, year, edition, pages
Elsevier, 2014. Vol. 76, 53-56 p.
Keyword [en]
Archaea, Bacteria, CARD-FISH, High-throughput sequencing, Soil prokaryotic community, Tundra ecosystem
National Category
Ecology Earth and Related Environmental Sciences
Identifiers
URN: urn:nbn:se:umu:diva-92906DOI: 10.1016/j.soilbio.2014.05.010ISI: 000339695900007OAI: oai:DiVA.org:umu-92906DiVA: diva2:748189
Available from: 2014-09-18 Created: 2014-09-09 Last updated: 2017-12-05Bibliographically approved

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Makoto, KobayashiKlaminder, Jonatan
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