DNA sequence-based analysis of the Pseudomonas species
Article first published online: 25 FEB 2010
© 2010 Society for Applied Microbiology and Blackwell Publishing Ltd
Special Issue: Pseudomonas. Editors: Professors Burkhard Tummler, Victor de Lorenzo, Alain Filloux and Joyce Loper
Volume 12, Issue 6, pages 1513–1530, June 2010
How to Cite
Mulet, M., Lalucat, J. and García-Valdés, E. (2010), DNA sequence-based analysis of the Pseudomonas species. Environmental Microbiology, 12: 1513–1530. doi: 10.1111/j.1462-2920.2010.02181.x
- Issue published online: 3 JUN 2010
- Article first published online: 25 FEB 2010
- Received 28 October, 2009; accepted 7 January, 2010.
Partial sequences of four core ‘housekeeping’ genes (16S rRNA, gyrB, rpoB and rpoD) of the type strains of 107 Pseudomonas species were analysed in order to obtain a comprehensive view regarding the phylogenetic relationships within the Pseudomonas genus. Gene trees allowed the discrimination of two lineages or intrageneric groups (IG), called IG P. aeruginosa and IG P. fluorescens. The first IG P. aeruginosa, was divided into three main groups, represented by the species P. aeruginosa, P. stutzeri and P. oleovorans. The second IG was divided into six groups, represented by the species P. fluorescens, P. syringae, P. lutea, P. putida, P. anguilliseptica and P. straminea. The P. fluorescens group was the most complex and included nine subgroups, represented by the species P. fluorescens, P. gessardi, P. fragi, P. mandelii, P. jesseni, P. koreensis, P. corrugata, P. chlororaphis and P. asplenii. Pseudomonas rhizospherae was affiliated with the P. fluorescens IG in the phylogenetic analysis but was independent of any group. Some species were located on phylogenetic branches that were distant from defined clusters, such as those represented by the P. oryzihabitans group and the type strains P. pachastrellae, P. pertucinogena and P. luteola. Additionally, 17 strains of P. aeruginosa, ‘P. entomophila’, P. fluorescens, P. putida, P. syringae and P. stutzeri, for which genome sequences have been determined, have been included to compare the results obtained in the analysis of four housekeeping genes with those obtained from whole genome analyses.