Tropical soils are a reservoir for fluorescent Pseudomonas spp. biodiversity

Abstract

Summary Fluorescent Pseudomonas spp. are widely studied for their beneficial activities to plants. To explore the genetic diversity of Pseudomonas spp. in tropical regions, we collected 76 isolates from a Brazilian soil. Genomes were sequenced and compared to known strains, mostly collected from temperate regions. Phylogenetic analyses classified the isolates in the P. fluorescens (57) and P. putida (19) groups. Among the isolates in the P. fluorescens group, most (37) were classified in the P. koreensis subgroup and two in the P. jessenii subgroup. The remaining 18 isolates fell into two phylogenetic subclades distinct from currently recognized P. fluorescens subgroups, and probably represent new subgroups. Consistent with their phylogenetic distance from described subgroups, the genome sequences of strains in these subclades are asyntenous to the genome sequences of members of their neighbour subgroups. The tropical isolates have several functional genes also present in known fluorescent Pseudomonas spp. strains. However, members of the new subclades share exclusive genes not detected in other subgroups, pointing to the potential for novel functions. Additionally, we identified 12 potential new species among the 76 isolates from the tropical soil. The unexplored diversity found in the tropical soil is possibly related to biogeographical patterns.

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

“…Interestingly, one of the main limitations for plant productivity in the tropical soils cropped with sugarcane is phosphate deficiency – promoted by the chemical properties of such acidic soils (Cherubin et al ., ). The low pH where phosphate is unavailable to plants is a characteristic of the soil used in our study (pH = 5.0), which was previously described in Lopes and colleagues ().…”

“…has genome variations according to the soil habitat, indicative of niche partitioning between sub‐populations. Then, we focused on the analysis of genome sequences of 53 fluorescent Pseudomonas strains cultured from the same soil samples addressed in the previous section (Lopes et al ., ). Genomic sequences of these strains isolated from sugarcane rhizosphere (28 isolates) and bulk soil (25 isolates) were compared to 41 reference genomes of the genus Pseudomonas , including phylogenetically close (from the P. fluorescens group) and distant species (e.g., Pseudomonas putida , Pseudomonas syringae and Pseudomonas aeruginosa ).…”

“…The phylogenomic tree clustered the 53 isolates to references of the P. koreensis subgroup of the P. fluorescens complex (Fig. ), corroborating a previously published multilocus sequence analysis (MLSA) (Lopes et al ., ). Neither approach (MLSA and phylogenomics) placed the bulk soil and rhizosphere isolates in distinct clades.…”

“…The 53 isolates analysed here are closely related, composing a population of P. koreensis , which was classified in a single community OTU. Average nucleotide identity (ANI) was previously calculated for each of these isolates (Lopes et al ., ). The values ranged from 84% to 99% ANI (Supporting Information Table S1).…”

“…in that study to check whether the community of this important and large group of bacteria is also distinct in sugarcane rhizosphere compared to bulk soil. Then, we focused in a collection of 53 P. koreensis strains previously isolated from the same sugarcane rhizosphere and bulk soil samples (Lopes et al ., ), to test the hypothesis that a bacterial population can harbour different ecotypes in neighbouring soil habitats, differing in genome content and enriched in niche‐specific genes/functions.…”