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PMID: 16751545 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Potential of a 16S rRNA-based taxonomic microarray for analyzing the rhizosphere effects of maize on Agrobacterium spp. and bacterial communities.

Applied and environmental microbiology ·Vol. 72 ·No. 6 ·2006-06-00 ·Pages 4302-12

Sanguin H, Remenant B, Dechesne A, Thioulouse J, Vogel TM, Nesme X, Moënne-Loccoz Y, Grundmann GL

Abstract

Bacterial diversity is central to ecosystem sustainability and soil biological function, for which the role of roots is important. The high-throughput analysis potential of taxonomic microarray should match the breadth of bacterial diversity. Here, the power of this technology was evidenced through methodological verifications and analysis of maize rhizosphere effect based on a 16S rRNA-based microarray developed from the prototype of H. Sanguin et al. (Environ. Microbiol. 8:289-307, 2006). The current probe set was composed of 170 probes (41 new probes in this work) that targeted essentially the Proteobacteria. Cloning and sequencing of 16S rRNA amplicons were carried out on maize rhizosphere and bulk soil DNA. All tested clones that had a perfect match with corresponding probes were positive in the hybridization experiment. The hierarchically nested probes were reliable, but the level of taxonomic identification was variable, depending on the probe set specificity. The comparison of experimental and theoretical hybridizations revealed 0.91% false positives and 0.81% false negatives. The microarray detection threshold was estimated at 0.03% of a given DNA type based on DNA spiking experiments. A comparison of the maize rhizosphere and bulk soil hybridization results showed a significant rhizosphere effect, with a higher predominance of Agrobacterium spp. in the rhizosphere, as well as a lower prevalence of Acidobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes, a new taxon of interest in soil. In addition, well-known taxonomic groups such as Sphingomonas spp., Rhizobiaceae, and Actinobacteria were identified in both microbial habitats with strong hybridization signals. The taxonomic microarray developed in the present study was able to discriminate and characterize bacterial community composition in related biological samples, offering extensive possibilities for systematic exploration of bacterial diversity in ecosystems.

MeSH Terms
Cloning, Molecular Oligonucleotide Array Sequence Analysis Phylogeny Polymerase Chain Reaction Proteobacteria/classification,genetics,growth & development RNA, Bacterial/genetics RNA, Ribosomal, 16S/genetics Rhizobium/classification,genetics,growth & development Soil Microbiology Zea mays/microbiology
Chemicals
RNA, Bacterial RNA, Ribosomal, 16S
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Sanguin Hervé
UMR CNRS 5557/USC INRA 1193 Ecologie Microbienne, Université Claude Bernard (Lyon 1), 43 bd du 11 Novembre 1918, F-69622 Villeurbanne Cedex, France.
Remenant Benoît
Dechesne Arnaud
Thioulouse Jean
Vogel Timothy M
Nesme Xavier
Moënne-Loccoz Yvan
Grundmann Geneviève L
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Article Info
Journal
Applied and environmental microbiology
Abbr.
Appl Environ Microbiol
ISSN
0099-2240
DOI
10.1128/AEM.02686-05
Published
2006-06-00
Pages
4302-12
Language
English
Region
United States
NLM ID
7605801
PMCID
PMC1489601
Subset
IM
External Links
PubMed source DOI: 10.1128/AEM.02686-05 PMC Full Text View journal details
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