Integrated Genomic and Greenhouse Assessment of a Novel Plant Growth-Promoting Rhizobacterium for Tomato Plant

Abstract

Plant growth promoting rhizobacteria (PGPR) can display several plant-beneficial properties, including support to plant nutrition, regulation of plant growth, and biocontrol of pests. Mechanisms behind these effects are directly related to the presence and expression of specific genes, and different PGPR strains can be differentiated by the presence of different genes. In this study we reported a comprehensive evaluation of a novel PGPR Klebsiella variicola UC4115 from the field to the lab, and from the lab to the plant. The isolate from tomato field was screened in-vitro for different activities related to plant nutrition and growth regulation as well as for antifungal traits. We performed a functional annotation of genes contributing to plant-beneficial functions previously tested in-vitro. Furthermore, the in-vitro characterization, the whole genome sequencing and annotation of K. variicola UC4115, were compared with the well-known PGPR Azospirillum brasilense strain Sp7. This novel comparative analysis revealed different accumulation of plant-beneficial functions contributing genes, and the presence of different genes that accomplished the same functions. Greenhouse assays on tomato seedlings from BBCH 11–12 to BBCH > 14 were performed under either organic or conventional management. In each of them, three PGPR inoculations (control, K. variicola UC4115, A. brasilense Sp7) were applied at either seed-, root-, and seed plus root level. Results confirmed the PGP potential of K. variicola UC4115; in particular, its high value potential as indole-3-acetic acid producer was observed in increasing of root length density and diameter class length parameters. While, in general, A. brasilense Sp7 had a greater effect on biomass, probably due to its high ability as nitrogen-fixing bacteria. For K. variicola UC4115, the most consistent data were noticed under organic management, with application at seed level. While, A. brasilense Sp7 showed the greatest performance under conventional management. Our data highlight the necessity to tailor the selected PGPR, with the mode of inoculation and the crop-soil combination.

Effect of endophytic bacterium, Stenotrophomonas maltophilia JVB5 on sunflowers

“…Several siderophore genes mediating the plant response against osmotic stress and pathogens have been identified in Pseudomonas species (Kang et al 2020). The detection of siderophore genes, entABCFH, in the genome of S. maltophilia JVB5 agrees with Guerrieri et al (2021) and Hubrich et al (2021), who reported similar genes in the genome of the endophytic bacterium Klebsiella variicola UC4115, with functions in deriving enterobactin from chorismate.…”

Plant growth‐promoting and antibacterial activities of cultivable bacteria alive in tobacco field against Ralstonia solanacearum

“…Some strains produced higher concentration of IAA than the same species in other reports. For example, Klebsiella variicola SSI‐2 produced 152.31 μg ml −1 IAA that was much higher than K. variicola strain UC4115 (68.32 μg ml −1 IAA) (Guerrieri et al ., 2021). Pseudomonas entomophila SSX‐5 produced more IAA (126.98 μg ml −1 ) than P. entomophila CN11 (23.26 μg ml −1 IAA) (Li et al ., 2017).…”

Genome insights into the plant growth-promoting bacterium Saccharibacillus brassicae ATSA2T

“…We used whole-genome sequencing and annotation to provide useful insights into the mechanisms governing plant growth. In a previous study, many plant growth-promoting bacteria were analyzed at the whole-genome level to gain an in-depth understanding of PGP mechanisms in bacteria such as Bacillus pumilus strain SF-4 (Iqbal et al 2021a ), B. subtilis BS87 and B. megaterium BM89 (Chandra et al 2021 ), Pseudomonas aeruginosa B18 (Singh et al 2021 ), Klebsiella variicola UC4115 (Guerrieri et al 2021 ), and Streptomyces (Subramaniam et al 2020 ). Many genes have been identified by whole-genome sequencing and have been implicated in direct mechanisms of plant growth (e.g., chitinase, phosphate solubilization, auxin production, iron acquisition, and nitrogen fixation) (Iqbal et al 2021a ; Chandra et al 2021 ; Singh et al 2021 ; Guerrieri et al 2021 ; Subramaniam et al 2020 ).…”