Wheat rhizosphere microbiome: response to application of the Plant Growth Promoting Rhizobacterium Bacillus subtilis T29 and Fusarium pseudograminearum

Abstract

Soil microbial communities have demonstrated enormous potential for promotion of plant health and productivity. In particular, the diversity of the soil community may play an important role in promoting plant growth and health. However, previous research has focused on profiling both fungal and bacterial communities and neglected the role that pathogen presence and plant growth promoting rhizobacteria (PGPR) inoculation play in influencing plant growth. The objectives of this study were i) to determine the structure and composition of wheat root-associated microbial communities in different wheat growing regions of South Africa (SA); ii) to determine the variations in colonization and survival potential of Bacillus subtilis T29 in the rhizosphere of different wheat cultivars following artificial inoculation for growth promotion; iii) to determine the effect of B. subtilis T29 and the wheat pathogen, Fusarium pseudograminearum’s presence and on the structure and composition of the resident microbiome. To achieve this, metagenomic sequencing targeting the 16S rRNA was employed to decipher soil microbial diversity while droplet digital PCR (ddPCR) was used to identify and quantify B. subtilis T29 in wheat rhizosphere soils. Microbial community analysis revealed structural and compositional differences between rhizosphere and non-rhizosphere soils. Findings of the study indicated that non-rhizosphere soil had a higher diversity compared to cultivated rhizosphere soils. Cultivar and soil properties also had an effect on composition and distribution of microbial populations. For the first time, this study revealed that B. subtilis T29 can successfully colonize the rhizosphere of different wheat cultivars grown in South Africa and increase wheat growth. Most importantly, correlation analysis of colonization and plant growth revealed that higher levels of B. subtilis T29 colonization do not always result in the highest plant mass increase. Comparison of taxonomic community profiles revealed major changes in fungal populations after introduction of B. subtilis T29 and/or F. pseudograminearum to the wheat rhizosphere soil. Marginal changes were however observed on bacterial populations after introduction of B. subtilis T29 and/or F. pseudograminearum. The above data provide an important insight into the diversity and composition of bacterial and fungal wheat microbiomes of different wheat cultivars from different agroecological conditions. The data also provide more information on the response of native fungi and bacteria after bioinoculation with a rhizobacteria and a wheat pathogen. The application of B. subtilis T29 provides a potential alternative strategy for increasing wheat growth, while minimising damage to the natural microbiomes. Overall, the results highlight the importance of understanding how microorganisms antagonize or benefit each other, which will contribute greatly to improving plant biomass production when manipulating agricultural soil microbial communities. Data gathered in this study therefore can be useful in future crop management strategies specific to the target production region to obtain a microbial community structure favoring improved plant health and productivity.