Abstract
Pseudomonas putida is one of 13 major groups of Pseudomonas spp. and contains numerous species occupying diverse niches and performing many functions such as plant growth promotion and bioremediation. Here we compared a set of 19 P. putida isolates obtained from sugarcane rhizosphere or bulk soil using a population genomics approach aiming to assess genomic and metabolic differences between populations from these habitats. Phylogenomics placed rhizosphere versus bulk soil strains in separate clades clustering with different type strains of the P. putida group. Multivariate analyses indicated that the rhizosphere and bulk soil isolates form distinct populations. Comparative genomics identified several genetic functions (GO-terms) significantly different between populations, including some exclusively present in the rhizosphere or bulk soil strains, such as D-galactonic acid catabolism and cellulose biosynthesis, respectively. The metabolic profiles of rhizosphere and bulk soil populations analyzed by Biolog Ecoplates also differ significantly, most notably by the higher oxidation of D-galactonic/D-galacturonic acid by the rhizosphere population. Accordingly, D-galactonate catabolism operon (dgo) was present in all rhizosphere isolates and absent in the bulk soil population. This study showed that sugarcane rhizosphere and bulk soil harbor different populations of P. putida and identified genes and functions potentially associated with their soil niches.
Highlights
Rhizosphere is a soil compartment in close contact with plant roots and highly influenced by its rhizodeposits, such as exudates, lysates, mucilage, etc [1]
The multi-locus sequence analysis (MLSA) tree using this higher set of gene markers (99) separated the rhizosphere and bulk soil isolates into distinct phylogenetic clades within the P. putida group (Fig 1B), confirming previous MLSA that used a few gene markers [30]
Two type strains classified in the P. putida group were not included in this analysis (P. donghuensis and P. coleopterum), but previous studies showed that they cluster to P. rhizosphaerae and P. vranovensis [14], which are very distant to the species clustering to our 19 isolates (Fig 1B)
Summary
Rhizosphere is a soil compartment in close contact with plant roots and highly influenced by its rhizodeposits, such as exudates, lysates, mucilage, etc [1]. These compounds are scarce or absent in the bulk soil, i.e. the root-free soil [1]. Bulk soil is characterized by the accumulation of complex and recalcitrant C-sources present in decaying plant biomass and soil organic matter [2]. Microbial abundance and activity is typically higher in the rhizosphere than in bulk. Ecology of Pseudomonas putida populations in soil habitats
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
