Genome variations between rhizosphere and bulk soil ecotypes of a Pseudomonas koreensis population

Abstract

Bulk soil and rhizosphere are soil compartments selecting different microbial communities. However, it is unknown whether this selection also can change the genome content of specific bacterial taxa, splitting a population in distinct ecotypes. To answer this question we compared the genome sequences of 53 isolates obtained from sugarcane rhizosphere (28) and bulk soil (25). These isolates were previously classified in the Pseudomonas koreensis subgroup of the P. fluorescens complex. Phylogenomics showed a trend of separation between bulk soil and rhizosphere isolates. Discriminant analysis of principal components (DAPC) identified differences in the accessory genome of rhizosphere and bulk soil sub-populations. We found significant changes in gene frequencies distinguishing rhizosphere from bulk soil ecotypes, for example, enrichment of phosphatases and xylose utilization (xut) genes, respectively. Phenotypic assays and deletion of xutA gene indicated that accumulation of xut genes in the bulk soil sub-population provided a higher growth capacity in a d-xylose medium, supporting the corresponding genomic differences. Despite the clear differences distinguishing the two ecotypes, all 53 isolates were classified in a single 16S rRNA gene OTU. Collectively, our results revealed that the gene pool and ecological behavior of a bacterial population can be different for ecotypes living in neighbouring soil habitats.

Engineering Pseudomonas protegens Pf‐5 to improve its antifungal activity and nitrogen fixation

“…Pseudomonas fluorescens is well‐characterized PGPR known for its production of a broad spectrum of secondary metabolites and root colonization of wide range of hosts (Table S1; Budzikiewicz, ; Lopes et al ., , ; Khalid et al ., , ; Weber et al ., ). Pseudomonas protegens Pf‐5 (formerly Pseudomonas fluorescens Pf‐5) was isolated from the cotton rhizosphere, which typically protects plants from diseases caused by plant pathogens (Howell and Stipanovic, , ; Xu and Gross, ; Rodriguez and Pfender, ; Sexton et al ., ).…”

Genomic and metabolic differences between Pseudomonas putida populations inhabiting sugarcane rhizosphere or bulk soil

“…Therefore, this is a different case compared to previous results reported by our group for a P . koreensis population, where the isolates from rhizosphere and bulk soil were not in distinct populations, but in different ecotypes within a common population [29]. The rhizosphere and bulk soil ecotypes of P .…”

“…The rhizosphere and bulk soil ecotypes of P . koreensis do not have a clear phylogenetic distinction and showed only slight differences in genome content [29]. Results also indicated that a P .…”

“…We previously showed that the sugarcane rhizosphere and bulk soil select ecotypes differing in genome content within a P . koreensis population [29]. However, distinctions between sugarcane rhizosphere and bulk soil populations are unclear for other bacteria such as P .…”

Draft genome sequence of the strain 16-537536, isolated from a patient with bronchiectasis and its relationship to the Pseudomonas koreensis group of the Pseudomonas fluorescens complex

“…P. koreensis was first isolated from Korean agricultural soils. Subsequently, it has been isolated from rhizospheres, other agricultural soils [4,5], and from yak milk [6]. It has also been found as a pathogen in freshwater fish [7].…”