Plant Health Status Affects the Functional Diversity of the Rhizosphere Microbiome Associated With Solanum lycopersicum

Abstract

The microorganisms inhabiting soil perform unique functions in the growth and development of plants. However, little is known about how plant health status affects their potential functions. We examined the functional diversity of the microbiome inhabiting the rhizosphere of powdery mildew diseased and healthy tomato plants alongside the bulk soils in South Africa's Northwest Province employing a shotgun metagenomics approach. We envisaged that the functional categories would be abundant in the healthy rhizosphere (HR) of the tomato plant. We collected soil from the rhizosphere of healthy, powdery mildew diseased tomato plants (DR), and bulk soil (BR). After that, their DNA was extracted. The extracted DNA was subjected to shotgun metagenomic sequencing. Our result using the SEED subsystem revealed that a total of fifteen (15) functional categories dominated the healthy rhizosphere, seven (7) functional categories dominated the diseased rhizosphere. At the same time, six (6) functions dominated the bulk soil. Alpha (α) diversity assessment did not reveal a significant difference (p > 0.05) in all the soil samples, but a considerable difference was observed for beta (β) diversity (P = 0.01). The functional categories obtained in this research were highly abundant in HR. Therefore, this study shows that the functions groups of the rhizosphere microbiomes were more abundant in HR samples as compared to others. The high prevalence of functions groups associated with rhizobiomes in the tomato rhizosphere indicates the need for more research to establish the functional genes associated with these rhizosphere microbiomes.