dMicrobial adaptation to environmental conditions is a complex process, including acquisition of positive traits through horizontal gene transfer or the modification of existing genes through duplication and/or mutation. In this study, we examined the adaptation of a Pseudomonas fluorescens isolate (R124) from the nutrient-limited mineral environment of a silica cave in comparison with P. fluorescens isolates from surface soil and the rhizosphere. Examination of metal homeostasis gene pathways demonstrated a high degree of conservation, suggesting that such systems remain functionally similar across chemical environments. The examination of genomic islands unique to our strain revealed the presence of genes involved in carbohydrate metabolism, aromatic carbon metabolism, and carbon turnover, confirmed through phenotypic assays, suggesting the acquisition of potentially novel mechanisms for energy metabolism in this strain. We also identified a twitching motility phenotype active at low-nutrient concentrations that may allow alternative exploratory mechanisms for this organism in a geochemical environment. Two sets of candidate twitching motility genes are present within the genome, one on the chromosome and one on a plasmid; however, a plasmid knockout identified the functional gene as being present on the chromosome. This work highlights the plasticity of the Pseudomonas genome, allowing the acquisition of novel nutrient-scavenging pathways across diverse geochemical environments while maintaining a core of functional stress response genes.
Genomics has revolutionized the way we study microorganisms in the environment; in the postgenomic era, it is possible to describe the enzymatic pathway corresponding to metabolic pathways that are only hypothesized (1) or to predict the environmental function of uncultivated bacterial phyla based on singlecell isolation and genomic amplification (2, 3). The result has been a profound change in our understanding of microbial interactions and processes; however, not all environments have benefited from this revolution. At the intersection of microbiology and geology, comparative genomics has yet to examine how the interaction between microbes and minerals leads to genomic adaptation (4). As a result, numerous fundamental questions remain to be answered, such as what is the role of microorganisms in mineral precipitation and weathering (5, 6).In this study we examined the genome of an organism isolated from a predominantly mineral environment, using a cave-isolated Pseudomonas strain as a model. Due to their ubiquitous distribution in terrestrial environments and association with opportunistic infections, pseudomonads have been studied for many years, and a large number of representative genomes exist: 37 completed projects within the genus Pseudomonas. Among the hundreds of bacterial species we have isolated from cave environments, we decided to examine the genomic adaptations of Pseudomonas fluorescens to this mineral environment. P. fluorescens is an advantageous organism f...