title: Estimates of Soil Bacterial Ribosome Content and Diversity Are Significantly Affected by the Nucleic Acid Extraction Method Employed.
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.
authors.affiliation: Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors.forename: Pia K
authors.initials: PK
authors.lastname: Wüst
authors.affiliation: Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany.
authors.forename: Heiko
authors.initials: H
authors.lastname: Nacke
authors.affiliation: Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany.
authors.forename: Kristin
authors.initials: K
authors.lastname: Kaiser
authors.affiliation: Institute of Soil Science and Land Evaluation, Soil Biology Section, University of Hohenheim, Stuttgart, Germany.
authors.forename: Sven
authors.initials: S
authors.lastname: Marhan
authors.affiliation: Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Sikorski
authors.affiliation: Institute of Soil Science and Land Evaluation, Soil Biology Section, University of Hohenheim, Stuttgart, Germany.
authors.forename: Ellen
authors.initials: E
authors.lastname: Kandeler
authors.affiliation: Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany.|Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany.
authors.forename: Rolf
authors.initials: R
authors.lastname: Daniel
authors.affiliation: Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany joerg.overmann@dsmz.de.
authors.forename: Jörg
authors.initials: J
authors.lastname: Overmann
mesh_terms: D001419:Bacteria / Q000737:chemistry* / Q000235:genetics; D001431:Bacteriological Techniques / Q000379:methods*; D044822:Biodiversity; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D009696:Nucleic Acids / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification*; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D012336:RNA, Ribosomal, 16S / Q000235:genetics / Q000302:isolation & purification; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods; D012270:Ribosomes / Q000737:chemistry* / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012987:Soil / Q000737:chemistry*; D012988:Soil Microbiology
chemical_list: D004269:DNA, Bacterial; D009696:Nucleic Acids; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012987:Soil