Plant–Microbiome Interactions under Climate Change: Ecological Mechanisms, Evidence Gaps and Prospects for Crop Stress Resilience
Aparna Sinha *
Department of Botany, Dr. Shyama Prasad Mukherjee University, Ranchi, India.
*Author to whom correspondence should be addressed.
Abstract
Climate change alters the frequency, intensity and concurrence of drought, heat, salinity and flooding, while changing the soil conditions in which crop-associated microorganisms assemble. Because microbial communities can modify plant water relations, nutrient acquisition, immunity and stress signalling, their management is increasingly proposed as a route to more resilient agriculture. Yet a stress-associated microbial shift is not necessarily protective, and promising pot experiments do not by themselves establish reliable field-level benefits. This critical narrative review evaluates the processes linking climatic exposure, host selection, community assembly, microbial functions and crop performance, with attention to the strength of causal evidence and translational uncertainty.
Peer-reviewed research published from 2012 to 11 August 2026 was considered, alongside methodologically important studies, using accessible scholarly indexes and linked primary literature. The synthesis integrates observational microbiome surveys, isotope and metabolite studies, gnotobiotic and synthetic-community experiments, long-term climate manipulations, inoculation trials and quantitative reviews. Across crops, drought commonly changes root-associated bacterial communities in a compartment- and developmental-stage-dependent manner; effects of heat, chronic warming, salinity and waterlogging are less uniform. Host metabolites, nutrient–immunity coordination, microbial hormone turnover and specialised stress-response traits provide experimentally supported causal routes, although the level of corroboration differs sharply among mechanisms. Arbuscular mycorrhizal associations frequently improve measured plant traits under controlled stress, but response heterogeneity and uncertain field-yield translation are substantive constraints. Recent experiments show that climate-conditioned microbiomes can also reduce plant performance, while some field studies detect modest microbiome restructuring despite appreciable water limitation.
The central argument is that successful microbiome-enabled resilience requires demonstrable, context-stable functions rather than the mere enrichment of particular taxa. Future progress depends on factorial and multi-season field experiments, absolute microbial quantification, strain-level functional verification, host-genotype comparisons and assessment of agronomic outcomes and unintended ecological effects. Microbial interventions are most defensible as complements to soil, water and crop management, not substitutes for adaptation to climatic extremes.
Keywords: Rhizosphere, synthetic microbial communities, drought adaptation, root exudates, arbuscular mycorrhiza, heat stress, microbial inoculants, causal inference