Harnessing the Phytobiome: A Critical Review of Beneficial Plant–Microbe Interactions for Mitigating Climate-Driven Abiotic Stress
Nirmal Kumar Prajapat *
Department of Agronomy, School of Agricultural Sciences, Career Point University, Alaniya, Kota, Rajasthan, India.
Jaya Sharma
Department of Soil Science, School of Agricultural Sciences, Suresh Gyan Vihar University, Jaipur, Rajasthan, India.
Kiran Meena
Department of Entomology, School of Agricultural Sciences, Career Point University, Alaniya, Kota, Rajasthan, India.
Kashifa Khan
Department of Agronomy, School of Agricultural Sciences, Career Point University, Alaniya, Kota, Rajasthan, India.
*Author to whom correspondence should be addressed.
Abstract
Rising temperatures, increasingly erratic precipitation and expanding soil salinisation are converging to constrain crop productivity across major production regions, intensifying scientific interest in the phytobiome, defined as a plant together with its associated bacterial, fungal, archaeal and viral communities, as a lever for climate adaptation. This critical narrative review synthesises the accessible peer-reviewed evidence on how beneficial plant-microbe interactions, encompassing plant growth-promoting rhizobacteria (PGPR), arbuscular mycorrhizal fungi (AMF) and fungal and bacterial endophytes, modify plant physiological and biochemical responses to drought, salinity, elevated temperature, waterlogging and their combinations. Evidence was drawn from multidisciplinary and agriculture-specific scholarly indexes together with backward and forward citation tracking of recent reviews and primary studies, without reliance on subscription-only databases that were not directly accessible during preparation. The synthesis indicates that mechanisms such as 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, exopolysaccharide-mediated biofilm formation, osmolyte induction and volatile-mediated priming are mechanistically well characterised and consistently demonstrated under controlled conditions, whereas translation into reproducible field-level yield benefit remains considerably less certain. Meta-analytic evidence for arbuscular mycorrhizal fungi under drought and for halotolerant bacterial consortia under salinity shows generally positive average effects, but with substantial heterogeneity attributable to host genotype, indigenous microbial competition, soil edaphic conditions and inoculant formulation. Thermotolerance conferred through fungal and virus-fungus-plant symbioses is mechanistically striking yet has been documented in a comparatively narrow range of plant systems. Evidence concerning waterlogging and multifactorial stress combinations is sparser and rarely field-validated. Across the literature, a persistent gap separates mechanistic and pot-scale demonstration from consistent agronomic performance, reflecting formulation instability, strain-environment mismatch and inadequate long-term, multi-site testing. The review argues that realising the climate-adaptive potential of the phytobiome requires closer integration of host genetics, community-level microbiome engineering and rigorously designed multi-season field trials, rather than continued reliance on single-strain, short-duration experimentation confined to controlled environments.
Keywords: Arbuscular mycorrhizal fungi, drought tolerance, halotolerant bacteria, induced systemic tolerance, microbiome engineering, plant growth-promoting rhizobacteria, thermotolerance