Climatic trends show a significant increase in global mean temperature since 1970s, coupled with shift in precipitation patterns, and the frequency of extreme weather events (Capua and Rahmstorf, 2023). Agriculture sector is directly affected by climatic factors, experiencing a significant reduction in farm productivity. In addition, climate change could expand the range of pathogens and pests, leading to more frequent and severe disease outbreaks (De Wolf and Isard, 2007; Garrett et al., 2021). Recent findings has shown that global agricultural production is highly vulnerable to abiotic stresses (Bowerman et al., 2023). Furthermore, to meet the demand of growing human population, about 50% increase in agricultural production is needed by 2029 (Nawaz et al., 2024b). Consequently, a significant increase in deforestation and loss of natural habitats is occurring to acquire more land for cultivation (Foucher et al., 2024). To ensure food security with a limited expansion of agricultural land, a sustainable strategy involves improving the resilience of plants to climate change. Therefore, plant growth-promoting microorganisms represents one of the valuable resources to explore for increasing farm productivity (Bender et al., 2016).

Plants are associated with a diverse group of microorganisms, responsible for many essential functions e.g., plant growth, root development, nutrient use efficiency, and promoting resistance to abiotic and biotic stresses (Ojuederie et al., 2019). The rhizosphere serves as the central hub for the interactions among plant roots, soil, microorganisms, and environment (Trivedi et al., 2020). It is a specialized layer of soil around the root system, and the microbes in the soil are referred to as rhizosphere microorganisms (Rout and Southworth, 2013). Macro-nutrients such as nitrogen, phosphorous, and potassium, are assimilated by plants through the rhizosphere, enabling their integration into the nutrient cycle (Thepbandit and Athinuwat, 2024). Plants establish beneficial associations with various microorganisms in the rhizosphere to shape their community composition through rhizosphere deposition (Toju et al., 2018). Several important symbiotic microorganisms have been identified to promote plant growth by reducing the occurrence of different plant diseases, the regulation of phytohormones, and enhancing nutrient acquisition (Kuypers et al., 2018; Hu et al., 2020; Lopes et al., 2021). Plant growth-promoting rhizobacteria (PGPR) act as biofertilizers by enhancing the availability of both macro and micronutrients, thereby improving crop yield and soil fertility (Lopes et al., 2021). Therefore, a critical understanding of plant-microbe interactions in the rhizosphere, steered by hormonal crosstalk and root exudation, and their combined application for improving crop productivity is required.

Abiotic stresses impact not only plant physiology and metabolism but also soil microorganism activities. However, the impact of stress varies depending on the time, host plants, intensity, and other environmental factors (Georgieva and Vassileva, 2023). For instance, a significant reduction in growth and grain yield was observed in wheat grown under drought conditions, primarily due to the negative impact on photosynthesis, leaf area, seed set and weight (Rahimi-Moghaddam et al., 2023). In contrast, Thymus serphyllum exhibits increased production of osmolytes, such as proline, sorbitol, mannitol, and other amino acids, which confer tolerance to drought stress (Moradi et al., 2017). Furthermore, under salt stress, the rhizosphere of groundnuts exhibited a notable presence of Acidobacteria and Cyanobacteria, enhancing their salt tolerance (Xu et al., 2020). On the other hand, rice plants revealed significant yield penalties, including reduced growth, germination, and tillering which in turn affected plant biomass and height (Fang et al., 2023). Thus, interactions between plants and microbes during abiotic stress conditions are dynamic and complex. In order to harness the potential of plant microbiota in agriculture, it is essential to understand the impact of abiotic stressors on plants, microorganisms, and plant-microbe interactions (Fadiji et al., 2023). In the present review, we have summarized the effects of changing climatic conditions on plant-microbe interactions and highlighted the positive roles of plant associated microbes in enhancing agricultural production. Additionally, we discuss recent advancements in mitigating different stressors and their significance for achieving key objectives in future research.

Plants are associated with a varied and taxonomically organized community of microbiomes i.e., viruses, fungi, bacteria, and archaea that co-exist with plants in the rhizosphere (root-surrounding soil), endosphere (internal tissue), and phyllosphere (above-ground parts) to perform important activities regulating host health and fitness (Afridi et al., 2022). Among these micro-environments, rhizosphere is one of the most complex and diverse habitats for microbial communities. Plant-associated microorganisms may come from different sources, including soil, seeds, water, and other neighboring organisms i.e., insects and animals. Some of these organisms can develop a complex symbiotic relationship with plants (Fitzpatrick et al., 2018). Specifically, plant-associated microbiome form a symbiotic unit known as “holobiont” which can be influenced by environmental factors (Trivedi et al., 2020). A holobiont is a complex and interconnected system of organisms, living together in a close association in all types of ecosystems (Matthews, 2024). These microorganisms within the holobiont can significantly improve plant health by enhancing mineral solubility (Lemanceau et al., 2017), altering the signaling of phytohormones such as auxin (IAA), gibberellin (GA), and cytokinin (CK) (Spaepen and Vanderleyden, 2011), and directly providing nutrients (Saleem et al., 2024), alongside strengthening resistance against phytopathogens (Jin et al., 2024).

Plant-microbe crosstalk initiates with the release of chemical signals i.e., flavonoids and amino acids, establishing a favorable environment where microbes ultimately reside and assist plants in coping with stress and regulating growth (Stefan et al., 2018) ( Figure 1 ). Therefore, plants recognize signals created by beneficial microbes during the early phases of symbiosis (Ravelo-Ortega et al., 2023). According to Fadiji et al. (2023), when plants receive adequate water and nutrient supply, rhizosphere microorganisms consistently aid in helping plants adapt to abiotic stresses, thereby potentially enhancing crop yield. At present, there are several studies on the isolation, identification, and application of useful symbiotic microorganisms as an alternative to chemical fertilizers, that are hazardous to humans, animals, aquatic lives, and environment (Kumar et al., 2022; Shahwar et al., 2023). Abdelaziz et al. (2019) demonstrated significant improvements in tomato growth and yield by introducing the root endophytic fungus (Piriformospora indica) into the soil. The interactions between plants and rhizobia are very specific and exist at a level of species and genotype, leading to the formation of effective symbiotic relationships (Wang et al., 2018). Overall, the rhizobia are the key members in the soil to produce and fix nitrogen compounds that help plants to grow and survive under unfavorable circumstances for better ecosystem productivity.

Plants are consistently exposed to the external environment that constantly changes in many ways (Nawaz et al., 2024a). Certain regions of the world are already facing extreme climatic shifts, such as drought, salinity, and extreme temperatures. These climatic stresses have detrimental effects on plant-associated microbial communities, which in turn influence plant growth and development (Afridi et al., 2022). In response to unfavorable conditions, plants induce a wide range of physiological and morphological modifications to adapt to these abrupt changes thus, experiencing significant growth and yield penalties (Xu et al., 2023). Abiotic stresses can affect rhizosphere microbial communities in various ways including the alteration in composition and function of microbial population in the rhizosphere. For instance, prolonged exposure to drought stress can lead to an increase in the abundance of Actinobacteria and Firmicutes (Vescio et al., 2021). Additionally, a proportionate rise in the abundance of Acidobacteria and Cyanobacteria was observed in the peanut rhizosphere, when exposed to salt stress (Xu et al., 2020). Recently, Dollete et al. (2024) revealed a reduction in symbiotic nitrogen fixation in forage legumes, thereby effecting plant growth and development. Furthermore, altered phosphate solubilizing efficiency of the biocontrol fungus Trichoderma sp. was observed under abiotic stress conditions such as pH, temperature, and heavy metals (Rawat and Tewari, 2011).

Plant growth promoting microorganisms (PGPMs) have been frequently investigated to mitigate certain abiotic stresses while enhancing plants adaptation under unfavorable conditions (Chieb and Gachomo, 2023; Kibret et al., 2024). To sustain their growth under stressed conditions, plants employ various strategies i.e., induction of chemical signaling and regulation of phytohormones (biochemical adaptation), stomatal closure (physiological adaptation), changes in growth pattern (morphological adaptation) (Naamala and Smith, 2020) ( Table 1 ). Climate-associated abiotic stresses may influence plants in different ways and at different growth stages, limiting plant performance (Lata et al., 2018). These abiotic stresses are discussed in detail to further elaborate their detrimental effects on plant adaptation, which may hinder the development of a sustainable ecosystem and reduce agricultural production.

Plants in their natural habitat engage in dynamic crosstalk with various environmental signals, facilitating the integration of microbial communities. In such communicatory networks, plants possess the ability to efficiently sense and respond to interactive stimuli. However, upon recognizing of microbial substances, they have the potential to establish symbiosis or develop immune responses. Overlooking this complicated web of communication networks, the significance of chemical signaling in perception and modulation is highly pivotal for stationary organisms like plants (Afridi et al., 2022). Plants utilize chemical signals as stimuli to establish beneficial relationships with surrounding microorganisms, either aboveground (trunk, shoots, leaves) or belowground (roots). This sophisticated communicatory network is steered by hormonal crosstalk and root exudation, regulating the intricate interactions between plants and their diverse biotic and abiotic environments.

The enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase is present in many PGPR, regulating plant growth by reducing the ethylene level produced in response to stress signals (Ali and Kim, 2018). Ethylene is a gaseous phytohormone that regulates plant growth at optimal concentrations; however, at higher concentrations, it affects various plant developmental processes, including root growth, nodulation, fruit ripening, flowering, and leaf senescence (Vanderstraeten et al., 2019). Prolonged exposure to various stresses can lead to increased accumulation of ethylene, which can significantly impact plant developmental processes (Dubois et al., 2018). IAA may elicit ACC synthesis, which severs as an intermediate precursor to ethylene biosynthesis and act as a key milestone in the regulation of ethylene production in plants.

When ACC is secreted by plant roots in the presence of high concentrations of ethylene, ACC deaminase-producing bacteria catalyze the breakdown of α-ketobutyrate and ammonia rather than ethylene, thereby reducing plant growth-inhibitory ethylene levels in developing or stressed plants (Ratnaningsih et al., 2023). Furthermore, IAA synthesis by these bacteria enhances root development and nutrient uptake, further supporting plant resilience against several abiotic stresses ( Figure 4 ) (Etesami and Glick, 2024). Specifically, the role of IAA in promoting root and shoot growth significantly enhances plant adaptation to heavy metal stress (Shah et al., 2024). For instance, the availability of IAA has been shown to improve plant growth under heavy metal stress by increasing the phytoextraction of Pb, Zn, and Cd (Sytar et al., 2019). Similarly, the application of IAA can enhance plant growth in metal contaminated soil by mitigating the hazardous effects of heavy metals on plants (Sharif et al., 2022). Another study reported that the application of IAA-producing fungal endophyte Penicillium roqueforti greatly reduced the uptake of heavy metals by wheat plants (Ikram et al., 2018). Altogether, the synthesis of IAA by microbes plays significant role in enhancing plant growth and resilience, particularly in metal-contaminated soils.

Inoculating plants with ACC deaminase-producing bacteria provides protection against various stresses (Herpell et al., 2023; Roy Choudhury et al., 2023). Notably, Trichoderma strains containing ACC deaminase have been found to show phytopathogenic biocontrol and plant growth regulation activity in mangrove seedlings (Saravanakumar et al., 2018). Additionally, Increased ACC deaminase activity and IAA production was observed in the presence of Serratia K120 bacterium under heavy metal stress (Carlos et al., 2016). Similarly, it has been reported that Paraburkholderia dioscoreae Msb3, a novel bacterium designated strain, interacts with other symbionts, enhancing plant growth in tomato through ACC deaminase activity (Herpell et al., 2023). While the importance of ACC deaminase in plant growth promotion and abiotic stress resilience have been demonstrated, there is a lack of comprehensive studies on the plant root ACC exudation and microbial ACC deaminase activity under various abiotic stresses. In-depth investigation of the plant responses following the utilization of IAA- and ACC deaminase-producing bacteria would be rewarding, especially to reveal the best strategy for PGPR application in crop production, leading to more sustainable practices that reduce reliance on chemical fertilizers for better ecological safety.

Plants have been significantly affected due to the abrupt changes in climatic conditions, resulting in severe impacts on cellular homeostasis. These impacts eventually lead to stunted plant growth and development, highlighting the emerging need to shift from conventional breeding to more advanced and sustainable approaches. To address these challenges genetic engineering has emerged as a promising solution for developing microbial strains that are effective and possess extended lifespans to achieve crop yield under drought conditions. Recent developments in microbiology, molecular biology, and biotechnology have led to the discovery of novel genes linked to drought tolerance (Salvi et al., 2022). The integration of microbiotechnology concepts in agriculture should be leveraged to isolate microbial strains from the stress-affected soils, and further evaluation of these strains based on their stress tolerance may be useful in the process of bio-inoculation of crops cultivated in drylands (Kaushal and Wani, 2016).

Exploring diverse microbial communities poses a significant challenge in plant-microbe interaction research, as it is difficult to address important questions like the basic characteristics of a specific microbial community, the complex interplay among different community members, and how these members contribute to the survival of plants under such circumstances. It is now well-recognized that plants can regulate the recruitment of various root-associated microorganisms for required purposes (Bag et al., 2022). Moreover, the mechanisms of various signaling pathways in the rhizosphere that lead to the assembly and stability of intrinsic microbiome require investigation. Recent research breakthroughs in the area of plant-microbe interactions may have a significant impact on agricultural productivity. Research on these beneficial plant-microbe interactions in the rhizosphere will further elucidate how these microbes impact the nutritional composition of plant materials. However, it remains a challenging and demanding area of research to systematically exploit and utilize these beneficial microbial species living in the plant rhizosphere. Therefore, there is an urgent need to develop new and advanced scientific approaches to comprehend the complex interplay between plants and the microbiome under changing environmental conditions.

The rhizosphere is an ever-changing environment, offering diverse and intriguing aspects to researchers. The advent of highly sophisticated molecular biology techniques has brought a new era for thoroughly investigating the complex plant-microbe crosstalk for green efficient production. The emergence and continuous updating of omics, gene-editing techniques, and high-throughput sequencing technology have opened up new ideas for studying the complex networks of plant-microbe interactions and plant resilience to different biotic and abiotic stresses (Kimotho and Maina, 2024). Genomics has proven to be an efficient tool in investigating and predicting plant-microbe interactions, as well as enhancing plant resilience to different stresses (Frantzeskakis et al., 2020). Multiple sequencing technologies, including prokaryotic 16S amplicon sequencing (Qin et al., 2024), fungal internal transcribed spacer (ITS) regions sequencing (Labouyrie et al., 2023), and metagenomics (Masuda et al., 2024) have been employed to analyze the extensive genetic variability present within the soil microbiome.

Next generation sequencing (NGS)-based transcriptomics is the most comprehensive and efficient approach to uncover the molecular background of plant-microbe interactions (Katara et al., 2024). It is mostly employed to evaluate plant performance under various stress conditions, revealing the physiological responses of plants to pathogens and elucidating the signaling mechanisms occurring in the rhizosphere (Roy et al., 2024). NGS has paved the way to investigate beneficial plant-microbe interactions and plant performance under abiotic stresses (Rehman et al., 2024). For instance, enhanced drought tolerance in wild soybean (Kim et al., 2024), the cold tolerance response in upland cotton (Wang et al., 2024), the impact of short-term flooding on the expression profile of orchard grass genes (Qiao et al., 2020), and altered gene expression level in Arabidopsis under cold stress (Zhang et al., 2024), have been revealed through NGS. Metagenome sequencing using oxford nanopore technologies (ONT) is currently the most effective strategy for pathogen detection (Yu et al., 2023). It is a robust and direct method of long-read sequencing without the need for an amplification step (Wang et al., 2021b). Due to its ability to directly detect pathogens except RNA viruses, it can be used without prior knowledge of pathogens (Javaran et al., 2023). The MinONTM technology has already been used for metagenome sequencing of bacteria, fungi, and viruses, affecting various crops (Jongman et al., 2020; Mechan Llontop et al., 2020). Overall, these modern molecular techniques have greatly improved agricultural productivity and sustainability with enhanced resilience to various ongoing climatic challenges.

Plants, and specifically the rhizosphere are bustling with microorganisms. When plants encounter unfavorable conditions, they can recruit beneficial microbes to help mitigate these stresses by releasing a range of chemical signals, which is known as the ‘cry for help’ strategy (Bai et al., 2022). To understand the mechanistic background of ‘cry for help’ strategy of plants, it is important to investigate these molecular aspects of plant-microbe interactions in the rhizosphere (Zancarini et al., 2021). Identifying genes with specific functions is mandatory for understanding the signaling cascades that regulate plant growth and stress responses (Depuydt and Vandepoele, 2021). Understanding the interplay between plant functional genes and rhizosphere microbes will be essential for regulating plant growth and development processes, including root architecture, microbial abundance, phytohormones, secondary metabolites, nutrient acquisition, and plant immune responses (Liu et al., 2023). For instance, the MYB72 transcription factor in Arabidopsis, recognized for its prominent role in the induced systematic response (ISR) mediated by beneficial microbes, represents a promising area for further investigation (Vlot et al., 2021). Additionally, the roles of members of the plant multidrug and toxic compound extrusion (MATE) family in transporting phytohormones and secondary metabolites require further exploration (Wang et al., 2022). Moreover, the co-expression of the Arabidopsis gene AVP1, the rice gene OsSIZ1, and the cyanobacterium flavodoxin gene FId revealed their important contributions to plant growth and resilience to multiple environmental adversities through delicately fine-tuned their genetic and epigenetic regulation (Zhao et al., 2024).

Innovations in plant-microbe interactions at the molecular level offer a new direction for genetic breeding (Nerva et al., 2022). Exploring this relationship will help us develop crop varieties with enhanced adaptability to various stresses. Future research using cutting-edge technologies such as multi-omics, NGS, and imaging techniques as discussed in section 7, will enhance our understanding of the microbes that mutually interact with host genes is expected to provide new germplasm resources. Furthermore, the molecular and mechanistic background of microbial ACC deaminase activity in response to root-exuded ACC under various abiotic stresses is still at a preliminary stage. In-depth investigation of plant responses to IAA- and ACC deaminase-producing bacteria would be rewarding, especially in revealing the best strategies for PGPR application in crop production, leading to more sustainable practices that reduce reliance on chemical fertilizers for better ecological safety.

Climate change, with increased adversity, is a concurrent global concern that leads to implications for worldwide food security, negatively impacting both plant and microbial growth. Identifying innovative approaches to meet the growing demand for food in a changing climate is challenging, particularly as plant stresses and diseases greatly affect crop production and sustainability. Improving plant adaptations to these stressors while increasing agricultural production is one of the potential demands. In this context, the current review explores comprehensive insights into how plants and their microbiomes enhance resilience to stresses like drought, salinity, and temperature variations. We highlight key microbial strategies that mediate plant tolerance, including ROS scavenging, antioxidant regulation, and IAA synthesis. Additionally, we emphasize the role of ACC deaminase-producing bacteria in regulating ethylene levels, suggesting that future research should focus on the interaction between plant root ACC exudation and microbial ACC deaminase activity for effective ethylene mitigation during stress. Recent advancements in molecular techniques, such as next-generation sequencing and multi-omics approaches, are discussed to optimize these interactions, along with the chemotactic movement of microbes driven by hormonal crosstalk and root exudation.