Deciphering the complex interaction of microbial inoculants with plants

Abstract

Plant growth promoting microorganisms (PGPM) have been proven as an efficient and environmentally friendly alternative of agrochemicals. PGPM interact with roots, affect plant growth and nutrient acquisition. Combined cultivation-dependent and independent methods to monitor PGPM and to investigate the microbial communities in the rhizosphere led to better understanding of the complex interactions in the rhizosphere. Pseudomonas sp. RU47 is a rhizosphere-competent strain showing plant growth-promoting and biocontrol activities. The genome sequence of plant beneficial strain RU47 was analyzed and revealed that the strain belongs to the P. koreensis cluster and likely represents a novel distinct species. Several genes contributing to the plant growth-promoting and biocontrol activities were also identified. Based on the genome sequence data of RU47, primers targeting four different genes potentially involved in plant-bacteria interaction were designed and used for detection and quantification of RU47 in total community DNA from the rhizosphere of tomato and maize plants grown in soils with reduced P-fertilization. RU47 could be detected in the rhizosphere of tomato and maize six weeks after planting. The influence of four PGPM (Trichoderma harzianum T-22, Pseudomonas sp. DSMZ 13134, Bacillus amyloliquefaciens FZB42 and Pseudomonas sp. RU47) on the growth of tomato and maize plants as well as on the rhizosphere microbial community under reduced P supply conditions were tested. High rhizocompetence of bacterial inoculants was observed on tomato roots and positively correlated with plant growth and shoot nutrient accumulation. Furthermore, the bacterial inoculants stimulated the plant growth and overlapping rhizosphere community changes of tomato plants. All the inoculants colonized the maize roots and beneficially changed the rhizosphere bacterial community which led to increased maize plant mass. This study supports potential use of RU47 in agriculture, which might contribute to a reduced application of pesticide and mineral fertilizer. Moreover, this research showed the successful ability of PGPM to colonize the plant roots, leading to a massive increase in the plant growth which might be also due to the shifts in the rhizosphere microbiome detected.

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