Open Access Highly Accessed Open Badges Research

Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere

Miguel A Matilla, Manuel Espinosa-Urgel, José J Rodríguez-Herva, Juan L Ramos and María Isabel Ramos-González*

Author affiliations

Department of Environmental Protection, Estación Experimental de Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, Granada 18008, Spain

For all author emails, please log on.

Citation and License

Genome Biology 2007, 8:R179  doi:10.1186/gb-2007-8-9-r179

Published: 4 September 2007



Mutualistic interactions less well known than those between rhizobia and legumes are commonly found between plants and bacteria, frequently pseudomonads, which colonize roots and adjacent soil areas (the rhizosphere).


A global analysis of Pseudomonas putida genes expressed during their interaction with maize roots revealed how a bacterial population adjusts its genetic program to this lifestyle. Differentially expressed genes were identified by comparing rhizosphere-colonizing populations with three distinct controls covering a variety of nutrients, growth phases and life styles (planktonic and sessile). Ninety rhizosphere up-regulated (rup) genes, which were induced relative to all three controls, were identified, whereas there was no repressed gene in common between the experiments. Genes involved in amino acid uptake and metabolism of aromatic compounds were preferentially expressed in the rhizosphere, which reflects the availability of particular nutrients in root exudates. The induction of efflux pumps and enzymes for glutathione metabolism indicates that adaptation to adverse conditions and stress (oxidative) response are crucial for bacterial life in this environment. The finding of a GGDEF/EAL domain response regulator among the induced genes suggests a role for the turnover of the secondary messenger c-diGMP in root colonization. Several mutants in rup genes showed reduced fitness in competitive root colonization.


Our results show the importance of two selective forces of different nature to colonize the rhizosphere: stress adaptation and availability of particular nutrients. We also identify new traits conferring bacterial survival in this niche and open a way to the characterization of specific signalling and regulatory processes governing the plant-Pseudomonas association.