Abstract
BackgroundPseudomonas fluorescens is a common inhabitant of soil and the rhizosphere environment. In addition to potential applications in biocontrol and bioremediation, P. fluorescens is of interest as a model for studying bacterial survival and fitness in soil. A previous study using in vivo expression technology (IVET) identified 22 genes in P. fluorescens Pf0-1 which are up-regulated during growth in Massachusetts loam soil, a subset of which are important for fitness in soil. Despite this and other information on adaptation to soil, downstream applications such as biocontrol or bioremediation in diverse soils remain underdeveloped. We undertook an IVET screen to identify Pf0-1 genes induced during growth in arid Nevada desert soil, to expand our understanding of growth in soil environments, and examine whether Pf0-1 uses general or soil type-specific mechanisms for success in soil environments.ResultsTwenty six genes were identified. Consistent with previous studies, these genes cluster in metabolism, information storage/processing, regulation, and ‘hypothetical’, but there was no overlap with Pf0-1 genes induced during growth in loam soil. Mutation of both a putative glutamine synthetase gene (Pfl01_2143) and a gene predicted to specify a component of a type VI secretion system (Pfl01_5595) resulted in a decline in arid soil persistence. When examined in sterile loam soil, mutation of Pfl01_5595 had no discernible impact. In contrast, the Pfl01_2143 mutant was not impaired in persistence in sterile soil, but showed a significant reduction in competitive fitness.ConclusionsThese data support the conclusion that numerous genes are specifically important for survival and fitness in natural environments, and will only be identified using in vivo approaches. Furthermore, we suggest that a subset of soil-induced genes is generally important in different soils, while others may contribute to success in specific types of soil. The importance of glutamine synthetase highlights a critical role for nitrogen metabolism in soil fitness. The implication of Type 6 secretion underscores the importance of microbial interactions in natural environments. Understanding the general and soil-specific genes will greatly improve the persistence of designed biocontrol and bioremediation strains within the target environment.
Highlights
Pseudomonas fluorescens is a common inhabitant of soil and the rhizosphere environment
in vivo expression technology (IVET) selection of Pf0-1 promoters induced in arid Nevada desert soil A library of DNA fragments, covering 94% of the P. fluorescens genome, was used to trap promoters induced during growth in arid Nevada desert soil, a non-native soil for Pf0-1, essentially as described previously in IVET studies of agricultural soil [11]
The pIVETdap-based plasmids excise from the Pf0-1 genome at a low frequency, allowing recovery from the 30 strains of interest by plasmid isolation and subsequent transformation of E. coli
Summary
Pseudomonas fluorescens is a common inhabitant of soil and the rhizosphere environment. A previous study using in vivo expression technology (IVET) identified 22 genes in P. fluorescens Pf0-1 which are up-regulated during growth in Massachusetts loam soil, a subset of which are important for fitness in soil. Despite this and other information on adaptation to soil, downstream applications such as biocontrol or bioremediation in diverse soils remain underdeveloped. Pseudomonads are often closely associated with animals and plants, but are found living free in bulk soil Apart from their probable ecological importance, several P. fluorescens strains are of interest as potential biological control agents. Determining mechanisms by which pseudomonads persist and compete in soil would be of use in improving biocontrol strategies as well as in deepening the understanding of microbial success within natural environments
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