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Applied and Environmental Microbiology, December 2005, p. 8042-8048, Vol. 71, No. 12
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.12.8042-8048.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Microarray-Based Detection and Typing of the Rhizobium Nodulation Gene nodC: Potential of DNA Arrays To Diagnose Biological Functions of Interest{dagger}

Cyril Bontemps,1 Geoffroy Golfier,2 Carine Gris-Liebe,1 Sébastien Carrere,1 Luc Talini,2 and Catherine Boivin-Masson1*

Laboratoire des Interactions Plantes Micro-Organismes (LIPM), UMR CNRS-INRA 2594/441, BP 52627, 31326 Castanet Tolosan cedex, France,1 GeneScore, 10 Rue Vauquelin, 75005 Paris, France2

Received 10 May 2005/ Accepted 2 September 2005

Environmental screening of bacteria for the presence of genes of interest is a challenging problem, due to the high variability of the nucleotide sequence of a given gene between species. Here, we tackle this general issue using a particularly well-suited model system that consists of the nodulation gene nodC, which is shared by phylogenetically distant rhizobia. 41mer and 50mer oligonucleotides featuring the nucleotide diversity of two highly conserved regions of the NodC protein were spotted on glass slides and cross hybridized with the radioactive-labeled target genomic DNA under low-stringency conditions. Statistical analysis of the hybridization patterns allowed the detection of known, as well as new, nodC sequences and classified the rhizobial strains accordingly. The microarray was successfully used to type the nodC gene directly from legume nodules, thus eliminating the need of cultivation of the endosymbiont. This approach could be extended to a panel of diagnostic genes and constitute a powerful tool for studying the distribution of genes of interest in the environment, as well as for bacteria identification.

* Corresponding author. Mailing address: Laboratoire des Interactions Plantes Micro-Organismes, INRA-CNRS, BP 52627, 31326 Castanet-Tolosan cedex, France. Phone: (33) 5 61 28 54 49. Fax: (33) 5 61 28 50 61. E-mail: boivin{at}toulouse.inra.fr.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, December 2005, p. 8042-8048, Vol. 71, No. 12
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.12.8042-8048.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.





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