The electronic version of this article is the complete one and can be
found online at http://genomebiology.com/2007/8/9/R179
[Background] 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).
[Results] 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.
[Conclusion] 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.
This work was supported by
grants GEN2001-4698-CO5-03, BIO2003-0515, and BFU2006-09078 from
the Plan Nacional de I+D+I. MAM is the recipient of a fellowship from the
Ministerio de Educación y Ciencia. Research contract and funding from the
Junta de Andalucía to MIR-G are also acknowledged.
Peer reviewed