Metabolic and Genomic Traits of Phytobeneficial Phenazine-ProducingPseudomonasspp. Are Linked to Rhizosphere Colonization inArabidopsis thalianaandSolanum tuberosum

Abstract

Bacterial rhizosphere colonization is critical for phytobeneficial rhizobacteria such as phenazine-producing Pseudomonas spp. To better understand this colonization process, potential metabolic and genomic determinants required for rhizosphere colonization were identified using a collection of 60 phenazine-producing Pseudomonas strains isolated from multiple plant species and representative of the worldwide diversity. Arabidopsis thaliana and Solanum tuberosum (potato) were used as host plants. Bacterial rhizosphere colonization was measured by quantitative PCR using a newly designed primer pair and TaqMan probe targeting a conserved region of the phenazine biosynthetic operon. The metabolic abilities of the strains were assessed on 758 substrates using Biolog phenotype microarray technology. These data, along with available genomic sequences for all strains, were analyzed in light of rhizosphere colonization. Strains belonging to the P. chlororaphis subgroup colonized the rhizospheres of both plants more efficiently than strains belonging to the P. fluorescens subgroup. Metabolic results indicated that the ability to use amines and amino acids was associated with an increase in rhizosphere colonization capability in A. thaliana and/or in S. tuberosum. The presence of multiple genetic determinants in the genomes of the different strains involved in catabolic pathways and plant-microbe and microbe-microbe interactions correlated with increased or decreased rhizosphere colonization capabilities in both plants. These results suggest that the metabolic and genomic traits found in different phenazine-producing Pseudomonas strains reflect their rhizosphere competence in A. thaliana and S. tuberosum. Interestingly, most of these traits are associated with similar rhizosphere colonizing capabilities in both plant species. IMPORTANCE Rhizosphere colonization is crucial for plant growth promotion and biocontrol by antibiotic-producing Pseudomonas spp. This colonization process relies on different bacterial determinants which partly remain to be uncovered. In this study, we combined a metabolic and a genomic approach to decipher new rhizosphere colonization determinants which could improve our understanding of this process in Pseudomonas spp. Using 60 distinct strains of phenazine-producing Pseudomonas spp., we show that rhizosphere colonization abilities correlated with both metabolic and genomic traits when these bacteria were inoculated on two distant plants, Arabidopsis thaliana and Solanum tuberosum. Key metabolic and genomic determinants presumably required for efficient colonization of both plant species were identified. Upon further validation, these targets could lead to the development of simple screening tests to rapidly identify efficient rhizosphere colonizers.

Auxins of microbial origin and their use in agriculture

“…These genes are located on the chromosome, since no plasmids were detected in the sequenced genomes (Biessy et al 2019). IAA biosynthesis genes or gene clusters benefit phenazine-producing Pseudomonas spp., which colonized the rhizosphere of Arabidopsis thaliana and Solanum tuberosum, since their presence increases the growth of the plants up to 65 % and 31 %, respectively, more than strains not harboring them (Zboralski et al 2020).…”

In Tuber Biocontrol of Potato Late Blight by a Collection of Phenazine-1-Carboxylic Acid-Producing Pseudomonas spp.

“…This can be explained by the fact that phenazines are secondary metabolites, whose production represents a considerable cost for the cell [10]. Phenazines are also involved in colonization and competitiveness [14,39], but because there were no other microorganisms inoculated inside the potato tubers in the Pseudomonas spp. only treatments, phenazine production might not be necessary under these conditions.…”

Exploiting Beneficial Pseudomonas spp. for Cannabis Production

“…Specific in vitro assays are commonly used to quickly screen promising microorganisms for their plant growth-promoting characteristics. For examples, phosphate solubilization abilities can be assessed by growing bacteria on Pikovskaya's (PVK) agar, nitrogen fixation by using N-free medium, siderophore production with chrome azurol S (CAS) agar, IAA and other phytohormones production with Salkowski reagent and colorimetric methods, ACC deaminase activity with Dworkin and Foster's (DF) salts medium (Afzal et al, 2015;Ngalimat et al, 2021), biofilm formation with crystal violet staining (Selin et al, 2009), and metabolic capabilities with Biolog microarrays (Gómez-Lama Cabanás et al, 2018;Zboralski et al, 2020). For screening of biocontrol determinants, in vitro confrontational assays are commonly used to assess the growth inhibition of culturable pathogens (Afzal et al, 2015;Kusari et al, 2017;Balthazar et al, 2021), Mueller Hinton (MH) media are used for antibiotic diffusion assays, Cyantesmo paper for HCN production, UV-visible spectroscopy for phenazines and pyoverdine detection, and gas and/or liquid chromatography methods for quantification of volatile compounds (VOCs) and soluble antibiotics (Selin et al, 2009;Gómez-Lama Cabanás et al, 2018;Ngalimat et al, 2021).…”