Advancing Plant Microbiome Engineering: Recent Innovations in Bioinoculant-Based and Host-Mediated Strategies

The plant microbiome plays a pivotal role in maintaining plant and soil health and is considered the cornerstone of sustainable agriculture. Plant-associated microbial communities display considerable structural and functional plasticity in response to environmental conditions and to agronomic practices. This dynamic nature is the basis for rhizoengineering approaches aimed at enhancing plant health, stress tolerance, nutrient uptake efficiency, and pathogen biocontrol. The application of bioinoculants containing beneficial microorganisms is regarded as a promising strategy for establishing resilient microbiomes that enhance crop productivity while reducing the dependence on chemical inputs. Although inconsistent efficacy across diverse environmental conditions has long been a significant barrier to the widespread adoption of bioinoculants, rapid advances in plant microbiome research are opening new avenues for innovative bioinoculant design and rhizoengineering strategies. This review explores modern approaches to plant microbiome optimization, with particular emphasis on bioinoculant design and host-mediated strategies that enhance plant nutrient uptake, stress tolerance, and biocontrol of pathogens. It presents examples of improving single-strain bioinoculants using genetic engineering, precise gene editing, and adaptive acclimation. This chapter covers the principles for the rational design of multistrain synthetic microbial consortia and discusses natural community transplantation and host-mediated microbiome engineering approaches. The rapid progress in the strategies outlined in this review holds strong potential for practical application in sustainable agriculture.