A New Frontier for Plant-Microbe Interaction Under Changing Climate Conditions

The plant-associated soil and root microbiome, collectively known as the phytomicrobiome, forms a holobiont with the plant, engaging in symbiotic, competitive, or neutral interactions. These microbes, including rhizobacteria, plant growth-promoting fungi, mycorrhizal fungi, and endophytes, play crucial roles in maintaining plant health, growth, and stress resilience. Rhizobacteria, which are plant growth-promoting bacteria, reside in the rhizosphere or within root cells (Chauhan et al. 2023). They constitute ~2%–5% of rhizobacteria, promoting plant development through 1-aminocyclopropane-1-carboxylic acid deaminase production, nutrient absorption, root expansion, phytohormone and siderophore production, nitrogen fixation, phosphorus solubilization, and up-regulation of systemic tolerance genes. They also enhance stress tolerance by boosting the production of metabolites like glycine betaine, poly-sugars, proline, and volatile organic compounds, as well as upregulating antioxidants.

Mycorrhizal fungi (ectomycorrhizae, endomycorrhizae, ericoid, and orchidaceous mycorrhizae) form symbiotic relationships with plant roots, residing on root surfaces, within root cortex cells, or surrounding epidermal cells. They improve plant growth, innate immunity, enhance secondary metabolite accumulation, and aid in nutrient uptake (phosphates, nitrates). They induce systemic resistance and act as biocontrol agents against phytopathogens via nutrient solubilization, enzyme synthesis, and phytohormone-mediated defense mechanisms. Endophytes are microorganisms living within plant tissues without causing harm. They can be systemic (mutualistic) or non-systemic (facultative and transient) and may shift to parasitism under stress. Endophytes improve plant health via nutrient acquisition, phytohormone and siderophore production, and stress protection (Chauhan et al. 2023).

The review article published in Global Change Biology by Muhammad et al. (2025) presents the alteration of climate change on microbial diversity, community composition, and their roles in agroecosystems. In this commentary, I highlight their findings and discuss the broader implications for sustainable crop production under climate stress. Climate change, including temperature changes, altered precipitation, and high CO₂ levels, significantly disrupts microbial communities, diversity, composition, performances, and interactions. Elevated CO₂ levels shift the balance between positive and negative microbial-plant interactions (Tariq et al. 2024). Alterations in soil pH, moisture, and precipitation modify microbial community structures, such that prolonged dry conditions favor drought-resistant microbes, whereas flooding bolsters anaerobic bacteria that alter nutrient cycling. Warmer temperatures enhance microbial metabolism and organic matter decay, increasing nutrient release but negatively affecting microbial community balance. Conversely, lower temperatures change microbial activity, impacting soil fertility. Climate change weakens plant health and defense mechanisms, making them more prone to disease and pest infestations, hence impacting diseases and pests as well as plant health and resilience. These disruptions show a main challenge to world food security, with global food projections indicating that reduced microbiome performance could decrease crop yields by 30% by 2050. The global population is expected to reach 9.7 billion by 2050; consequently, the demand for more food will intensify by 70% (Muhammad et al. 2025). Understanding climate-driven changes in plant-microbe interactions is essential for developing sustainable, resilient agriculture systems and ensuring food security through improved microbial diversity.

An important illustration of the study by Muhammad et al. (2025) employs the diverse survival strategies of microorganisms to cope with extreme conditions. These microbes dynamically adjust energy production, gene expression, and population dynamics in response to climate change, underscoring their essential role in plant resilience. Some microbes produce resilient spores or cysts to endure drought, thereby maintaining ecological stability and nutrient cycling. Symbiotic associations such as those with nitrogen-fixing bacteria and mycorrhizal fungi are also modified by climate-induced stress. Mycorrhizae modulate phosphorus absorption and up-regulate spore production in response to changes in temperature and moisture content, thereby improving plant resistance. Furthermore, root exudates influence microbial communities, facilitating symbiotic relationships with mycorrhizal fungi and nitrogen-fixing bacteria. These interactions promote resource sharing and stress resistance among plants (Taylor and Bhatnagar 2024).

The review article of Muhammad et al. (2025) denoted that microbes induce key biochemical processes in soil, such as facilitating nitrogen fixation by converting ammonia to nitrite, then oxidizing nitrite to nitrate. Similarly, Rhizobium leguminosarum forms nitrogen-fixing symbiosis with legumes, enhancing soil fertility under climate stress. Decomposer fungi, such as Aspergillus and Penicillium, break down organic matter, enriching soil nutrient availability and promoting plant nutrient uptake. Pseudomonas fluorescens produces antibiotics and antifungal compounds against phytopathogens. Mycorrhizae not only facilitate nutrient absorption but also strengthen microbial networks for prohibiting pathogens. Streptococcus thermophilus and Clostridium acetobutylicum affect carbon sequestration by decomposing organic matter, partially keeping carbon levels in soil while regulating CO₂ fluxes (Raza et al. 2023). Moreover, Bacillus subtilis and Trichoderma harzianum produce extracellular products that aggregate soil and prevent soil erosion induced by wind and water. Erosion diminishes soil fertility by depleting organic matter, negatively impacting plant productivity (Muhammad et al. 2025).

The paper by Muhammad et al. (2025) displayed that climate stress reshapes morpho-physiological changes and stress tolerance of crops in addition to the plant-microbe interactions. Changing precipitation may induce drought or waterlogging stress that adversely impacts nutrient uptake and plant resilience. Higher temperatures intensify transpiration, leading to drought stress and reduced photosynthetic efficiency, disrupt protein function and metabolic pathways, while oxidative stress further disrupts plant health. Elevated CO₂ targets photosynthesis and growth, initially stimulates carbon assimilation but later disrupts nutrient homeostasis, favors invasive species, and alters crop nutritional quality. Studying these responses is a crucial aspect in balancing agricultural productivity with ecosystem sustainability (Raza et al. 2023). These plant responses to climate stress could be short- and long-term adaptive strategies. Immediate or short-term responses include shifts in phenology, stomatal regulation, and modifications in metabolism reported in plants. Long-term adaptations include genetic and evolutionary modifications, like natural selection for drought and heat tolerance, accompanied by shifts in species distribution to more favorable conditions. Innovative breeding and sustainable agricultural practices, including crop rotation and optimized irrigation, are important techniques that promote crop resistance (Muhammad et al. 2025). These responses give insights into developing sustainable agricultural strategies to acclimatize plants to harsh conditions.

The findings of Muhammad et al. (2025) are timely and vital. They underscore the urgent need to incorporate microbiome considerations into climate-resilient farming strategies. The role of beneficial microbes—such as nitrogen-fixing bacteria, mycorrhizal fungi, and decomposer fungi—is not only to support plant growth and nutrient uptake but also to buffer plants against abiotic/biotic stress. Microbial resilience strategies, such as spore formation and metabolic reprogramming, enable them to survive extreme conditions and maintain soil function. Moreover, the authors stress the potential of microbiome engineering, including microbial inoculants and biotechnological tools, to stabilize agroecosystems. A diverse and resilient microbial community is crucial for ecosystem stability, facilitating the adaptation of plants to extreme weather events and land use shifts. As climate change continues to affect ecosystems, understanding the functions of soil microbes becomes urgently needed for managing agricultural practices, enhancing soil health, and ameliorating climate impacts. Various practices like crop rotation, agroforestry, and cover cropping promote biodiversity, attenuate chemical fertilizers, and ensure resistance in agricultural systems (Muhammad et al. 2025). Microbial communities adjust through enzyme efficiency and population shifts, influencing nutrient cycling and disease suppression. Plants mediate soil microbiomes through root exudates, flourishing beneficial microbes in favor of soil health and adaptation. Promoting resilient crops and microbial diversity through sustainable practices like crop rotation and reduced tillage strengthens ecosystem stability. An adaptive strategy is essential as climate extremes intensify (Khoshru et al. 2024). Thus, climate resilience involves the anticipation of ecological and agricultural systems to withstand and recover from climate stress. Mitigating climate change impacts on ecosystems can be achieved via sustainable soil management, climate-resilient crops, and conservation efforts. Applying contour plowing, cover cropping, and organic farming is important soil management that improves health and water retention. Traditional breeding and genetic tools like CRISPR-Cas9 develop climate-resilient crops against biotic/abiotic stresses and improve crop yield. In this regard, CIMMYT and CGIAR programs develop heat- and drought-resistant varieties. Conservation initiatives restore degraded landscapes, enhance biodiversity, and sequester carbon, and projects like the Florida Everglades Restoration and coral reef restoration are directed toward ecosystem resilience. Sustainable land use and soil microbial diversity further support climate adaptation (Twomey et al. 2024).

Emerging technologies are crucial innovations for understanding the impact of climate change on plant–soil microbiomes. High-throughput sequencing and omics approaches—metagenomics, meta-transcriptomics, and metabolomics—enhance our understanding of microbial functions and interactions. Biotechnological approaches, including microbial inoculants and genetically engineered plants, help regulate nutrient absorption, stress tolerance, and disease resistance (Tilgam et al. 2024). Muhammad et al. (2025) reported that integrating these techniques can guide sustainable agricultural practices and ecosystem resilience against climate stress.

Despite growing knowledge, several gaps remain uncovered. A significant proportion of microbial communities in the soil ecosystems remain unidentified. Advanced metagenomic tools are needed to illustrate their ecological functions and associations. Long-term field investigations are needed to unravel the adaptation of microorganisms to dynamic climatic conditions. Recent studies should focus on identifying major microbial taxa shared in nutrient cycling and stress tolerance, deepening our understanding of plant-microbe-environment feedback, and evaluating the socioeconomic effects of microbiome shifts, especially in resource-limited settings. Furthermore, merging microbial research into breeding programs and climate-smart agriculture is crucial to improving soil health, food security, and ecosystem stability. Overall, Muhammad et al. (2025) advocate for international collaboration to adapt these innovations and incorporate them into practical, evidence-based solutions.

Mona F. A. Dawood: conceptualization, resources, visualization, writing – original draft, writing – review and editing.

The author declares no conflicts of interest.

This article is a Invited Commentary on Muhammad et al. https://onlinelibrary.wiley.com/doi/10.1111/gcb.70057.