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Editorial: Microbiome-driven strategies for alleviation of biotic and abiotic stresses in agriculture

Year: 2026

Type: editorial

Abstract: Over recent decades, advances in plant microbiome research have transformed our understanding of plants as complex biological systems integrated with diverse microbial communities, whose interactions shape the functioning and fitness of the plant holobiont (Berg et al., 2016). This conceptual shift is reinforced by evidence that plant-associated microbiomes are shaped by host, environmental, and management factors, including biotic and abiotic stresses, and, in turn, influence plant performance through nutrient acquisition, phytohormone regulation, pathogen suppression, stress signaling, and host physiological responses (Trivedi et al., 2020). Building on these advances, plant-microbe research is moving beyond taxonomic profiling toward understanding microbiome assembly and function, while exploring synthetic communities and targeted microbiome manipulation for predictable, persistent field benefits. In this context, this Research Topic brings together 11 contributions that provide complementary perspectives on how plant-associated microbial communities respond to biotic and abiotic stresses, how their assembly and functions are shaped by the host and its environment, and how a deeper understanding of these interactions may help harness beneficial microbiome functions for crop resilience.Among the themes explored in this Research Topic, the relationship between resident microbial communities and plant disease offers compelling evidence of the plant microbiome's functional importance. The capacity of indigenous microbiota to suppress pathogen establishment and disease development was recognized through the phenomenon of disease-suppressive soils (Cook & Rovira, 1976), with subsequent community-level analyses identifying microbial taxa and interactions associated with such suppression (Mendes et al., 2011). Extending this concept, Jobert et al. (2025) demonstrated that plant health status in rice can leave a persistent rhizosphere microbial legacy influencing growth and disease response in the subsequent generation.Rice grown in rhizosphere mixes derived from diseased plants (DRM) exhibited 30% shorter shoots but developed 44% shorter lesions following challenge with Xanthomonas oryzae pv. oryzae (Xoo), compared with plants grown in healthy rhizosphere mixes (HRM). These findings are consistent with the "cry for help" framework, whereby pathogen-stressed plants may recruit protective microbiota (Rolfe et al., 2019), potentially contributing to persistent disease-suppressive microbial states.Beyond plant-soil feedbacks, understanding microbial sources and assembly across cropping seasons and plant development is crucial to explaining disease-associated microbiome dynamics. Whitaker et al. (2026) examined the spatial and temporal dynamics of microbiome assembly in the wheat-Fusarium head blight (FHB) pathosystem by tracking fungal communities in maize debris, wheat leaves, and heads across five developmental stages, from pre-winter tillering to dough filling, at two locations. Microbial source tracking revealed that preceding-season maize debris contributed approximately 70% of the early wheat-leaf mycobiome, whereas wheat leaves contributed only a small proportion to wheat-head fungal communities.Together, these findings suggest that disease-associated microbiome states reflect not only pathogen pressure but also microbial sources, developmental timing, and tissue- Collectively, these contributions advance ecological and functional understanding of plant microbiomes while revealing key gaps. Amplicon-based profiling still predominates, underscoring the need for greater integration of shotgun metagenomics and functional multi-omics to resolve underlying mechanisms. Hibatullah et al. (2026) similarly emphasized integrating multi-omics-guided rhizobiome engineering with regenerative soil management, while highlighting the need for long-term field validation. Crucially, associations between microbial taxa and biotic or abiotic stress resistance do not establish causality, nor do co-occurrence networks confirm direct microbial interactions. Zhao et al. (2026) highlighted microbiome steering and synthetic communities as emerging strategies, while emphasizing the need for stable establishment and field validation. Longitudinal studies across host genotypes, cropping cycles, environments, and management regimes are needed to establish the stability and context dependence of microbiome functions. Cross-kingdom interactions among bacteria, fungi, archaea, protists, and viruses remain underexplored, particularly their collective roles in pathogen suppression, nutrient cycling, and functional resilience. Bridging these gaps requires integrating community profiling with microbial isolation, re-inoculation, gnotobiotic models, synthetic communities, and functional assays to validate microbial interactions and develop predictable, field-reproducible strategies for crop resilience.

Source: Frontiers in Microbiology

DOI: 10.3389/fmicb.2026.2004577

Authors: Satish Kumar, Kamlesh K. Meena, Ajay M. Sorty, Goraksha C. Wakchaure, Mahesh Kumar