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Appl Environ Microbiol. 2016 Apr 18;82(9):2595-2607. doi: 10.1128/AEM.00019-16. Print 2016 May.

Estimates of Soil Bacterial Ribosome Content and Diversity Are Significantly Affected by the Nucleic Acid Extraction Method Employed.

Author information

1
Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
2
Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany.
3
Institute of Soil Science and Land Evaluation, Soil Biology Section, University of Hohenheim, Stuttgart, Germany.
4
Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany.
5
Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany joerg.overmann@dsmz.de.

Abstract

Modern sequencing technologies allow high-resolution analyses of total and potentially active soil microbial communities based on their DNA and RNA, respectively. In the present study, quantitative PCR and 454 pyrosequencing were used to evaluate the effects of different extraction methods on the abundance and diversity of 16S rRNA genes and transcripts recovered from three different types of soils (leptosol, stagnosol, and gleysol). The quality and yield of nucleic acids varied considerably with respect to both the applied extraction method and the analyzed type of soil. The bacterial ribosome content (calculated as the ratio of 16S rRNA transcripts to 16S rRNA genes) can serve as an indicator of the potential activity of bacterial cells and differed by 2 orders of magnitude between nucleic acid extracts obtained by the various extraction methods. Depending on the extraction method, the relative abundances of dominant soil taxa, in particular Actino bacteria and Proteobacteria, varied by a factor of up to 10. Through this systematic approach, the present study allows guidelines to be deduced for the selection of the appropriate extraction protocol according to the specific soil properties, the nucleic acid of interest, and the target organisms.

PMID:
26896137
PMCID:
PMC4836429
DOI:
10.1128/AEM.00019-16
[Indexed for MEDLINE]
Free PMC Article

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