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The rhizosphere is a narrow and dynamic region of plant root-soil interfaces, and it's considered one of the most intricate and functionally active ecosystems on the Earth, which boosts plant health and alleviates the impact of biotic and abiotic stresses. Improving the key functions of the microbiome via engineering the rhizosphere microbiome is an emerging tool for improving plant growth, resilience, and soil-borne diseases. Recently, the advent of omics tools, gene-editing techniques, and sequencing technology has allowed us to unravel the entangled webs of plant-microbes interactions, enhancing plant fitness and tolerance to biotic and abiotic challenges. Plants secrete signaling compounds with low molecular weight into the rhizosphere, that engage various species to generate a massive deep complex array. The underlying principle governing the multitrophic interactions of the rhizosphere microbiome is yet unknown, however, some efforts have been made for disease management and agricultural sustainability. This review discussed the intra- and inter- microbe-microbe and microbe-animal interactions and their multifunctional roles in rhizosphere microbiome engineering for plant health and soil-borne disease management. Simultaneously, it investigates the significant impact of immunity utilizing PGPR and cover crop strategy in increasing rhizosphere microbiome functions for plant development and protection using omics techniques. The ecological engineering of rhizosphere plant interactions could be used as a potential alternative technology for plant growth improvement, sustainable disease control management, and increased production of economically significant crops.

There is a need to develop more biological control agents to fulfil the increasing demand for biological crop protection. Testing for consistent efficacy in disease control under the relevant range of environmental conditions is one of the most demanding steps during screening programs. Bioassays were conducted to target three major diseases of tomato, stem canker caused by Botrytis cinerea, leaf spot caused by B. cinerea, and bacterial spot caused by Pseudomonas syringae pv. tomato, and to assess possible growth promotion of tomato seedlings. Nine quantitative screening approaches were analyzed for a test panel of approximately 100 isolates of bacteria and fungi, all obtained from tomato, and several known antagonists as reference isolates. Even with such a limited number of isolates promising antagonists, partly not yet described as antagonists, could be selected for control of the targeted diseases when labor and resource demanding in planta bioassays had been applied. Also some promising isolates enhancing seedling development could be identified. Independent screening assays for the different traits were needed since no correlation between the different traits were found. Attempts to simplify screening assays to high-throughput systems failed since there were no positive correlations with in planta bioassays. In conclusion, the often suggested first screening rounds using in vitro tests for huge numbers of isolates followed by in planta testing of a selected group of candidates, e.g. those with high in vitro production of certain secondary metabolites or biosurfactants, may not exploit the entire potential of antagonists. Especially antagonists combining various modes of action may be excluded by in vitro screening with a bias on a specific mode of action. Therefore, independent in planta assays are proposed to screen against different pathogens and for growth promotion.