Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems
Simon Roux
Clermont Université, Université Blaise Pascal, Laboratoire ‘Microorganismes: Génome et Environnement’, Clermont-Ferrand, France
CNRS, UMR 6023, LMGE, Aubiere, France
Search for more papers by this authorFrançois Enault
Clermont Université, Université Blaise Pascal, Laboratoire ‘Microorganismes: Génome et Environnement’, Clermont-Ferrand, France
CNRS, UMR 6023, LMGE, Aubiere, France
Search for more papers by this authorGisè le Bronner
Clermont Université, Université Blaise Pascal, Laboratoire ‘Microorganismes: Génome et Environnement’, Clermont-Ferrand, France
CNRS, UMR 6023, LMGE, Aubiere, France
Search for more papers by this authorCorresponding Author
Didier Debroas
Clermont Université, Université Blaise Pascal, Laboratoire ‘Microorganismes: Génome et Environnement’, Clermont-Ferrand, France
CNRS, UMR 6023, LMGE, Aubiere, France
Correspondence: Didier Debroas, Universite Blaise Pascal, Laboratoire de Biologie des Protistes – UMR CNRS 6023, Aubiere 63177, France. Tel.: +334 7340 7837; fax: +334 7340 7670; e-mail: [email protected]Search for more papers by this authorSimon Roux
Clermont Université, Université Blaise Pascal, Laboratoire ‘Microorganismes: Génome et Environnement’, Clermont-Ferrand, France
CNRS, UMR 6023, LMGE, Aubiere, France
Search for more papers by this authorFrançois Enault
Clermont Université, Université Blaise Pascal, Laboratoire ‘Microorganismes: Génome et Environnement’, Clermont-Ferrand, France
CNRS, UMR 6023, LMGE, Aubiere, France
Search for more papers by this authorGisè le Bronner
Clermont Université, Université Blaise Pascal, Laboratoire ‘Microorganismes: Génome et Environnement’, Clermont-Ferrand, France
CNRS, UMR 6023, LMGE, Aubiere, France
Search for more papers by this authorCorresponding Author
Didier Debroas
Clermont Université, Université Blaise Pascal, Laboratoire ‘Microorganismes: Génome et Environnement’, Clermont-Ferrand, France
CNRS, UMR 6023, LMGE, Aubiere, France
Correspondence: Didier Debroas, Universite Blaise Pascal, Laboratoire de Biologie des Protistes – UMR CNRS 6023, Aubiere 63177, France. Tel.: +334 7340 7837; fax: +334 7340 7670; e-mail: [email protected]Search for more papers by this authorAbstract
PCR amplification of the rRNA gene is the most popular method for assessing microbial diversity. However, this molecular marker is often present in multiple copies in cells presenting, in addition, an intragenomic heterogeneity. In this context, housekeeping genes may be used as taxonomic markers for ecological studies. However, the efficiency of these protein-coding genes compared to 16S rRNA genes has not been tested on environmental data. For this purpose, five protein marker genes for which primer sets are available, were selected (rplB, pyrG, fusA, leuS and rpoB) and compared with 16S rRNA gene results from PCR amplification or metagenomic data from aquatic ecosystems. Analysis of the major groups found in these ecosystems, such as Actinobacteria, Bacteroides, Proteobacteria and Cyanobacteria, showed good agreement between the protein markers and the results given by 16S rRNA genes from metagenomic reads. However, with the markers it was possible to detect minor groups among the microbial assemblages, providing more details compared to 16S rRNA results from PCR amplification. In addition, the use of a set of protein markers made it possible to deduce a mean copy number of rRNA operons. This average estimate is essentially lower than the one estimated in sequenced genomes.
Supporting Information
| Filename | Description |
|---|---|
| fem1190-sup-0001-FigureS1.pdfapplication/PDF, 32.3 KB | Fig. S1. Schematic representation of the phylogenetic tree affiliation pipeline. |
| fem1190-sup-0002-FigureS2.pdfapplication/PDF, 44.4 KB | Fig. S2. Taxonomic affiliation for GS12 and GS08 ecosystems, with five protein markers (rplB, pyrG, leuS, fusA and rpoB), metagenomic 16S rRNA and PCR-amplified 16S rRNA. |
| fem1190-sup-0003-FigureS3.pdfapplication/PDF, 47.9 KB | Fig. S3. Taxonomic affiliation for minor groups (i.e. all groups with the exception of Actinobacteria and Proteobacteria) with five protein markers (rplB, pyrG, leuS, fusA and rpoB), metagenomic 16S rRNA and PCR-amplified 16S rRNA. |
| fem1190-sup-0004-TableS1.pdfapplication/PDF, 40.1 KB | Table S1. Main characteristics of protein-coding genes used as phylogenetic markers. |
| fem1190-sup-0005-TableS2.pdfapplication/PDF, 40.1 KB | Table S2. Percentage of correct affiliations for tree affiliation and best blast hit obtained from simulated data. |
| fem1190-sup-0006-TableS3.pdfapplication/PDF, 40.6 KB | Table S3. Alpha-Proteobacteria affiliations for GS08. |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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