Plant health is essential for food security, and constitutes a major predictor to safe and sustainable food systems. Over 40% of the global crops' productions are lost to pests, insects, diseases, and weeds, while the routinely used chemical-based pesticides to manage the menace also have detrimental effects on the microbial communities and ecosystem functioning. The rhizosphere serves as the microbial seed bank where microorganisms transform organic and inorganic substances in the rhizosphere into accessible plant nutrients as plants harbor diverse microorganisms such as fungi, bacteria, nematodes, viruses, and protists among others. Although, the pathogenic microbes initiate diseases by infiltrating the protective microbial barrier and plants' natural defense systems in the rhizosphere. Whereas, the process is often circumvented by the beneficial microorganisms which antagonize the pathogens to instill disease resistance. The management of plant health through approaches focused on disease prevention is instrumental to attaining sustainable food security, and safety. Therefore, an in-depth understanding of the evolving and succession of root microbiomes in response to crop development as discussed in this review opens up new-fangled possibilities for reaping the profit of beneficial root–microbiomes' interactions toward attaining sustainable plant health.

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The effective functioning of the rhizosphere microbiome significantly contributes to plant development, disease resistance, and agricultural sustainability. Hence, it is a major predictor of plant health. This study evaluated the microbial diversities and functions associated with healthy and diseased maize rhizosphere at selected farms in North West Province, South Africa.

Metagenomics is a scientific breakthrough that can reveal the variations in the microbial diversities and functions between the healthy and diseased plants, towards a productive deployment in diverse biotechnological processes and agricultural activities. This study investigated the possible functional diversity in the rhizosphere microbiome of both healthy and Northern Corn Leaf Blight (NCLB) infected maize growing at farms in the Lichtenburg (LI) and Mafikeng (MA) areas of the North West Province, South Africa. We hypothesized variations in the abundance and diversities of microbial functions in the healthy (LI and MA) and diseased (LID and MAD) maize plants. Hence, we extracted DNA from the healthy and diseased maize rhizosphere in the two maize farms and sequenced using a shotgun approach. Using the SEED subsystem, we discovered that the healthy rhizosphere maize plant was dominated by 24 functional categories, while the NCLB infected rhizosphere maize plant was dominated by 4 functional categories. Alpha diversity analysis showed no significant (p > 0.05) difference between the healthy and diseased maize rhizosphere. However, the analysis of beta diversity showed a significant difference. The substantial abundance of functional groups detected especially in LI indicates that presence of plant diseases altered the functions of soil microbiomes. The significant abundance of the unknown role of rhizosphere microbiomes in disease management suggests the presence of some undiscovered functional genes associated with the microbiome of the healthy maize rhizosphere. Hence, further investigation is needed to explore the roles of these functional genes for their agricultural or biotechnological relevance.