Soils and their microbiota are highly susceptible to climatic disruption, and a large-scale metagenomics study has revealed how the global distribution of bacterial plant pathogens is shaped by environmental conditions. Warm ecosystems and intensively managed agricultural soils favour pathogen prevalence, while colder climates, higher soil organic carbon content, and greater microbial diversity are associated with lower pathogen abundance. The study identified 32 globally dominant phytopathogens, including species from genera such as Agrobacterium, Clavibacter, Ralstonia, Burkholderia, Pseudomonas, and Xanthomonas. These dominant pathogens carry enriched genes related to plant interaction processes, including signalling, sugar transport, energy production, and carbohydrate metabolism, evidence of a deeply adapted plant-associated lifestyle. Crucially, the research reinforces the idea that the capacity of soils to suppress disease is not an intrinsic property of soil itself but is driven by key microbial constituents, including arbuscular mycorrhizal fungi and members of the Actinomycetota and Bacillota phyla, whose genetic potential to produce bioactive secondary metabolites plays an important protective role. Predictive models built on these data suggest that climate change may accelerate the global spread of important bacterial phytopathogens, making surveillance and targeted biocontrol deployment increasingly urgent.

The consequences of a changing climate extend far beyond crop pathogens. Drought, in particular, has emerged as a powerful selective pressure with surprising effects. By 2050, an estimated 5 billion people are expected to live in water-scarce regions as agricultural water demand doubles and freshwater availability may decline by up to half. New research examining drought across different land uses and geographic regions shows that reduced soil water content can increase the concentrations of naturally occurring antibiotics in the soil matrix, independent of the expression of antibiotic biosynthetic genes. Under severe drought, this is associated with a higher abundance of microbial genes involved in both antibiotic biosynthesis and resistance, shifting the functional composition of soil communities toward more resistant phenotypes. Projections indicate that climate change is likely to drive increased antibiotic resistance across all inhabited continents, linking agricultural and public health challenges in ways that scientists are only beginning to appreciate.

Amid this backdrop, agricultural management practices emerge as critical modulators of plant resilience. Long-term comparisons between conventional farming, characterised by high agrochemical inputs, intensive soil disturbance, and simplified rotations, and integrated management, which incorporates reduced tillage, biostimulants, and plant-derived extracts, show that integrated practices can improve key soil properties such as phosphorus availability, water content, and carbon-to-nitrogen ratios. These practices also reshape microbial communities toward taxa with stress-adaptive traits, including an enrichment of spore-forming Bacillaceae bacteria that alleviate plant drought stress under greenhouse conditions. The findings support the ‘cry for help’ hypothesis, whereby plants actively recruit beneficial microbes in response to biotic and abiotic stresses to enhance their own resilience. However, evidence from controlled experimental systems still requires validation under more realistic field conditions before broad generalisation.

One of the most promising frontiers is the rational design of synthetic microbial communities, or SynComs. These engineered consortia are being developed to help plants cope with salinity, heat, nutrient limitations, heavy metals, and even nanoplastic phytotoxicity. Recent work drew on desert plants as a source of drought-adapted microbiomes, constructing SynComs of up to 15 functionally distinct drought-tolerant strains. Applied to major crops under drought stress, these consortia promoted growth more effectively than individual isolates in both sterile and non-sterilised field soils. Their application induced compositional shifts in rhizosphere communities and activated plant physiological responses, including signalling, antioxidant defence, and osmotic adjustment pathways. Yet significant questions remain about the long-term stability of SynComs, their integration with native microbial communities, and their ecological impacts after repeated application, particularly under the increasingly variable conditions imposed by climate change.

Biocontrol agents, living organisms deployed against pathogens, offer distinct advantages over synthetic pesticides. They leave no persistent residues in soil, water, or food, have a lower energy footprint, and are generally highly specific, preserving beneficial soil microbiota that underpin resilience to drought and salinity. Bacteriophage applications, including phage cocktails, are well documented as synergistic tools against bacterial plant diseases, while emerging research explores hypovirulence-associated mycoviruses for fungal pathogen control. Soil microbes themselves are a treasure trove of bioactivity: a literature review covering 2018 to 2025 identified more than 320 natural products from soil-associated taxa, and comparative metabolomic and genomic profiling of approximately 60 actinomycete strains has linked specific bioactive metabolites to disruptions in the mycelial growth and zoospore germination of Phytophthora infestans, the causal agent of potato late blight. Equally striking, the mycoparasitic fungus Paraphaeosphaeria minitans, isolated from sclerotia, produced antifungal compounds and reduced cabbage head rot incidence under field conditions to levels comparable with fungicide treatments.

Engineering microbes to enhance biocontrol is a delicate balancing act, however. One recent study modified a plant-associated Bacillus subtilis strain to overproduce surfactin, an antimicrobial lipopeptide, to combat Fusarium banana wilt. The result was instructive: surfactin overproduction caused pleiotropic effects on the bacterium, impairing motility and biofilm formation, which ultimately reduced plant colonisation and biocontrol efficacy. A moderate increase in surfactin promoted kin-selective recruitment of helpful microbes, but hyperproduction reduced community diversity and disease suppression. The lesson is clear, biocontrol strategies must consider not only pathogen suppression but also dosage-dependent ecological effects on the wider microbial community.

Perhaps the most futuristic of the emerging technologies involves extracellular vesicles, tiny membrane-bound packets that microbes and plants alike use for communication and warfare. Phytophthora infestans deploys EVs to deliver effector proteins into host cells, while plants produce EVs as part of their defence responses. Researchers have now engineered beneficial B. subtilis and Pseudomonas putida strains to produce EVs encapsulating antifungal double-stranded RNAs targeting Botrytis cinerea and Verticillium dahliae. These vesicles were transported into fungal cells, and treatment with either purified vesicles or the engineered bacteria significantly reduced infections in both model and crop plant systems. This cross-kingdom RNA delivery offers a promising route to overcome the nucleic acid degradation challenges that have limited RNA-based antifungal approaches, although the diverse cargo carried by bacterial EVs implies broad ecological functions that must be carefully evaluated before responsible deployment.

The road from laboratory to field remains challenging. Extreme climate events have already caused an estimated US$4.3 trillion in global economic losses over recent decades, with staple crops such as maize, wheat, potato, and rice showing up to 27% of observed yield variability attributable to extremes. The biofertiliser market, currently valued between US$2.9 billion and US$3.72 billion and growing at more than 10% annually, reflects commercial momentum, with databases listing over 280 microbial biostimulant products. Yet regulatory bottlenecks persist, particularly in the European Union, where living products are governed by fragmented frameworks and RNA interference-based crop protection faces divergent rules across countries. From technology readiness perspectives, microbial inoculants are the most mature, phage applications and SynComs are evolving, while extracellular vesicles, RNA delivery systems, and nano-enabled microbiomes remain at the proof-of-concept stage. With supportive policies such as the European Green Deal aiming to halve chemical pesticide use by 2030, researchers argue that integrated microbial technologies, deployed under coherent regulatory frameworks, could transform agriculture into a more resilient, climate-adaptive system aligned with the United Nations Sustainable Development Goals.

Subject of Research: Climate change impacts on plant-microbe interactions and emerging biocontrol and microbiome engineering strategies for sustainable crop production

Article Title: Toward Sustainable Crop Production in a Changing Climate: Microbiomes, Pathogens, Biostimulants and Biocontrol Innovations

Article References: Holmes, A., & Matilla, M. A. (2026). Toward Sustainable Crop Production in a Changing Climate: Microbiomes, Pathogens, Biostimulants and Biocontrol Innovations. Microbial Biotechnology, 19(9), Article e70442. https://doi.org/10.1111/1751-7915.70442

Image Credits: AI Generated

DOI: 10.1111/1751-7915.70442

Keywords: climate change, plant microbiomes, phytopathogens, biocontrol, synthetic microbial communities, extracellular vesicles, antibiotic resistance, biostimulants, drought stress, soil health, sustainable agriculture, bacteriophages