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Review

Improving Crop Resilience in Drought-Prone Agroecosystems: Bioinoculants and Biocontrol Strategies from Climate-Adaptive Microorganisms

by
Dulanjalee L. Harishchandra
1,2,
Anuruddha Karunarathna
1,2,
Sukanya Haituk
1,2,
Sirikanlaya Sittihan
2,
Thitima Wongwan
2 and
Ratchadawan Cheewangkoon
2,*
1
Office of Research Administration, Chiang Mai University, Mueang Chiang Mai District, Chiang Mai 50200, Thailand
2
Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Mueang Chiang Mai District, Chiang Mai 50200, Thailand
*
Author to whom correspondence should be addressed.
Agriculture 2025, 15(23), 2479; https://doi.org/10.3390/agriculture15232479
Submission received: 20 October 2025 / Revised: 27 November 2025 / Accepted: 27 November 2025 / Published: 28 November 2025
(This article belongs to the Special Issue Biocontrol Agents for Plant Pest Management)
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Abstract

Agricultural production is becoming increasingly difficult due to various environmental fluctuations brought on by climate change. Overall increase in atmospheric temperatures due to greenhouse gases, changing rainfall patterns leading to severe water shortages, and deforestation have led to many areas facing drought conditions, causing more stress for producing enough food crops to fulfil increasing global demand. This is also exacerbated by emerging phytopathogens causing severe disease outbreaks, making it difficult to control them without drastic measures. Excessive use of agrochemicals in these areas could lead to more ecological displacements and therefore, sustainable agricultural practices are required to avoid causing more harm. Microorganisms with climate-adaptive characteristics and qualities that would be helpful in acting as bioinoculants and biological control, could prove to be more successful in sustainably controlling emerging pathogens as well as improving the overall plant immunity and health in drought affected areas. We discuss how climate change driven changes in farming areas have made them vulnerable towards emerging pathogens, and highlight how biological control agents can be successfully utilized to possibly overcome this without causing more environmental damage. This review provides a background for future research by linking the climate adaptive characteristics of microorganisms with biocontrol and plant health improving capabilities and how they can effectively be used for eco-friendly agricultural practices in agroecosystems impacted by climate change.

1. Introduction

The adverse effects of climate change are observed and felt in various aspects of human society, with agriculture and food production being the most important and immediate sectors impacted. Not only food security, but also the livelihoods and economic stability of sections in the society most vulnerable to environmental and economic stress are also highly affected. The highly productive agricultural areas are shifting, and this could, in turn, leave developing countries facing low crop yields that cannot fulfil the increasing food demand [1]. Drastic temperature increases causing heat stress, changes in precipitation patterns leading to droughts and floods, extreme weather events causing damages to crops, livestock and infrastructure, climate zone shifts leading to traditional crops declining in production, higher CO2 level affecting the food quality and nutrition and warmer temperatures and altered rainfall expanding the range and breeding cycles of pests and pathogens leading to the emergence of new pathogens and diseases are some of the effects of climate change that severely affect agriculture and food production [2].
Among them, the emergence of new phytopathogens causing new or more intense infestations due to the absence of natural controls in the disrupted ecosystems poses a significant threat to food production, thus requiring immediate and thorough attention. As natural enemies of pests also face adverse effects of climate change, the disease severity could increase with the loss of biocontrol activity within the ecosystem [3]. Emergence of new pathogens could also be highly impacted by the weakened plant health due to the low availability of essential nutrients and minerals in drought-affected soil [4]. Additionally, overuse of pesticides could do more harm to the soil microbiome and affect crop health due to the adverse effect on the naturally occurring beneficial microbes [5]. Therefore, it is extremely important to adopt agricultural practices that can counteract climate change-related issues brought on to agriculture and food production [6].
Any plant pathogen or pest, such as fungi, bacteria, viruses, oomycetes, insects, rodents, or plant parasitic nematodes, can suddenly emerge as a new threat to an ecosystem, causing problems not only to agricultural production and food security but also destabilizing the ecosystem while threatening biodiversity. This could be a sudden increase in the incidence, severity, or geographic range of a known pathogen or a previously unknown organism suddenly acting as a pathogen. These emerging pathogens are mainly introduced to the ecosystem due to changes brought on by climate change. Among them, microbial plant pathogens, including fungi, bacteria, viruses, and oomycetes, may cause increasingly severe damage under climate change, partially due to their rapid life cycles and high evolutionary rates, which facilitate quick adaptation to shifting environmental conditions [7]. These biological traits, such as high adaptability, host-switching ability, or a wide host range, acquiring resistance to available control measures, and long latent or asymptomatic infection periods going unnoticed, further facilitate their establishment and spread [8,9].
The effects of climate change on soil health are an important factor involved in crop resilience. The soil microbiome is directly involved in the biogeochemical cycles of essential sources of carbon, nitrogen, phosphorus, and other minerals important for plant health [10]. Expansion and elongation of the root system, prompting induced systemic resistance or systemic acquired resistance against phytopathogens, adequate water and nutrient availability, phytohormone production, and adaptability to environmental stressors are directly controlled by the soil microbiome, composed of Arbuscular mycorrhizal fungi (AMF), cyanobacteria, and beneficial nematodes [11,12]. Therefore, the use of climate-adaptive bioinoculants can be important in drought-affected cultivation areas. Furthermore, a disrupted soil microbiome can directly affect the emergence of new soil pathogens.
Direct influences of climate change can affect pathogen biology and the dynamics of pathogen growth, survival, reproduction, and life cycles. Both Rapid-Onset Climate Events (ROCEs), such as flash floods, tropical storms, heat waves, and wildfires, and Slow-Onset Climate Events (SOEs), such as rising average temperatures, prolonged drought, changing rainfall patterns, and soil salinization [13] are becoming prevalent due to climate change, which can help the introduction of pathogens to new ecosystems. These effects, leading to fluctuations in temperature, humidity, and precipitation, can increase proliferation, propagation, and infection rates. ROCEs can be directly responsible for new pathogen emergence by delivering pathogenic spores over long distances through storm winds, natural plant immunity being reduced due to adverse environmental conditions, and the disruption of the soil microbiome, allowing aggressive opportunistic pathogens to dominate. On the other hand, SOEs can affect the emergence of new pathogens through geographic range expansion of tropical and subtropical pathogens into temperate regions, causing changes to growth timing, creating new opportunities for pathogen attacks, and favouring the natural selection and evolution of more virulent or stress-adapted pathogen strains. Warmer temperatures and elevated CO2 levels, exacerbated by climate change, can increase the disease severity by inducing pathogen virulence factors, thus affecting their physiology and host–pathogen interactions [14].
The rise in atmospheric temperatures has caused pathogens to shift and expand their ranges and adapt to regions previously unsuitable as their habitats [15,16]. Furthermore, climate change stressors do not act in isolation. The synergistic interaction of these stressors leaves plants vulnerable. This trend has left vulnerable and previously unexposed ecologies, even in higher elevations, to new pathogens. This has caused previously localized threats to become widespread, sometimes even global issues for agriculture, food production, and biodiversity. These emerging pathogens can be hard to control with conventional control practices due to their high adaptability to harsh conditions, therefore requiring both higher doses of chemical pesticides, leading to more environmental crises [17]. Therefore, it is important to implement sustainable control measures such as biological control agents (BCAs) to prevent more ecological disruption in already vulnerable climate change-affected cultivation areas [18,19].
Biological control agents (BCAs) are microbes (viruses, bacteria, protozoa, and fungi), animals (nematodes, mites, spiders, and insects), and plants (companion, repellent, barrier, indicator, trap, insectary, and banker plants grown secondary to crops as co-cultures) with the ability to improve plant health both directly and indirectly [20,21]. Among them, microbial BCAs have the capability to protect plants by inducing systemic resistance in plants and control pathogenic infection via nutrient competition or production of antibiotic secondary metabolites without causing diseases in humans [22]. Biocontrol strategies with microbial BCAs are widely adopted in sustainable agricultural practices to overcome the negative and serious consequences on the environment and human health caused by the prolonged use of chemical and synthetic pesticides [23]. The demand for food is on the rise along with the global population increase, and there is a higher demand for clean food production as consumers and other business ventures prefer organic and sustainably sourced and produced food, free of agrochemicals [24]. Many advances in BCAs for sustainable biocontrol practices have been developed and implemented over the years, with specific research being conducted for product formulation towards direct and specific disease control [25]. The discovery of biocontrol agents is based on certain characteristics of microorganisms that have the ability to produce enzymes and metabolites that could aid in pathogen control. Chitinolytic microorganisms are one such group of microorganisms, of which the biocontrol potential can be highly effective [26,27].
This subset of microbial BCAs, known as chitinolytic microorganisms, can produce chitinases, which can degrade chitin present in the fungal cell wall, the exoskeletons of insects, and other arthropods [28]. The main role of these microorganisms in the natural ecosystem is nutrient recycling and degradation of organic matter, but this same characteristic can be useful as a potential biocontrol agent for sustainable agricultural practices. They have been extensively studied for their biocontrol abilities, bioremediation, and biofertilizers due to their efficiency in degrading chitin-based pollutants and enhancing plant growth indirectly by improving nutrient availability and soil structure [29,30,31]. The enzymatic or chemical deacetylation of chitin produces chitosan, which by itself, has biocontrol and plant growth-promoting capabilities [32,33]. These microorganisms can be successfully utilized for biocontrol of pathogens affecting crops grown in climates where conditions such as soil texture, water availability may widely vary due to the effects of climate change [34,35]. Therefore, exploring the potential of climate-adaptable biocontrol agents has become extremely important for maintaining sustainable agricultural practices in farmlands facing the effects of climate change (Figure 1). The main focus of this review was to investigate which microbial bioinoculants and biocontrol agents have demonstrated the ability to enhance crop performance under drought stress, through which functional traits, how their natural adaptability to climate change enhances their biocontrol and bioinoculant capabilities, and in which crop or environmental contexts.

2. Drought-Prone Agroecosystems and Their Susceptibility Towards Emerging Pathogens and Crop Failure

Agricultural systems are increasingly being affected by insufficient or irregular rainfall, leading to prolonged dry periods due to the effects of climate change [36]. These systems are highly vulnerable to crop failure, soil degradation, and pathogen emergence. Geographical shifts in climate zones, such as the expansion of semi-arid zones (drylands) into moderate climate regions due to delayed or shortened monsoon seasons and irregular rainfall distribution, cause previously fertile cultivation areas to become drought-prone regions. Plant health is severely affected in these areas as low precipitation and high rates of evaporation lead to limited water availability and degraded soil with low nutrients and water retention capabilities [37]. Abiotic stress factors such as higher temperatures, high soil salinity, and low water availability in these ecosystems can adversely affect plant-pathogen interactions, leading to suppression of plant defence responses, making the plants more vulnerable to existing and new pathogens alike [38]. Additionally, the environmental changes brought on by drought can affect the natural life cycle of plant pathogens, shift the pathogen ranges, and even affect the rate of genetic mutation or changes in different microbial populations, leading to the emergence of new pathogens [39] (Table 1).
These stress factors can alter the plant physiology and affect the beneficial soil microbiome, increasing vulnerability towards soilborne and drought-adapted pathogens [40]. A considerable number of severe disease outbreaks around the world are due to emerging fungal diseases [41]. Relatively shorter and milder winters have allowed for longer phases of the infectious stages of pathogenic fungi and their movements towards areas with warmer climates [42]. Additionally, plant pathogenic thermophilic or mesophilic fungi show higher disease severity at higher temperatures [43]. These factors, combined with the reduced ability of the host to respond to infections due to abiotic stress faced in a drought-prone ecosystems, cause higher disease severity [44].
Studies have even shown that new pathogens emerge when plants face water stress and high atmospheric temperatures [45]. Emergence of new fungal pathogens and the disease incidence of existing pathogens are on the rise globally [43]. Several studies have shown that drought stress factors favour pathogens establishment and increase disease severity. For example, the disease severity of dry root rot (DRR) of chick pea caused by Rhizoctonia bataticola, black root rot (BRR) of chick pea caused by Fusarium solani [46,47], seed- and soil-borne pathogenic fungus Macrophomina phaseolina causing stem and root rot, charcoal rot, and seedling blight in soybean, sorghum, and groundnut [48,49]. Blueberry stem blight and dieback caused by Neofusicoccum parvum [50], Holm oak decline caused by Phytophthora cinnamomi [51] are all found to be causing severe symptoms in drought-prone agroecosystems compared to other areas.
Table 1. Emerging pathogens due to drought effects and their current prevention strategies.
Table 1. Emerging pathogens due to drought effects and their current prevention strategies.
Pathogen (Type)How Drought/Prone Conditions Change Disease DynamicsTypical Crops AffectedEmerging/Climate-Change NoteCurrently Available Control Agents (Examples)References
Xylella fastidiosa (xylem-limited bacterium)Drought-stressed plants change xylem flow, increased symptom severity, and vector (xylem-sap feeding insects) transmission; drought can intensify outbreaksOlive, grapevine, citrus, almond, many ornamentals.Rapid geographic expansion in Europe & elsewhere; considered an emergent, high-impact pathogen whose impact is amplified by warmer/drier conditions and vector spreadNo broadly effective curative bactericide in field. Management: vector control (insecticides, habitat/vector management), removal of infected trees, use of tolerant/resistant cultivars/rootstocks where available, regulatory (quarantine) measures; experimental chemical approaches[52,53,54]
Fusarium spp. (soil-borne fungi causing Fusarium wilts/root rot)Drought weakens roots and alters the rhizosphere; some Fusarium species cause worse wilting under water stress (plant defence reduced). Drought can favour root colonizationTomato, banana, cotton, legumes, many horticultural crops.Disease severity and range are increasing in some regions with warming and water stress; emergence of new aggressive strains reported locally.Chemical soil treatments limited; soil fumigation in some systems (where allowed). Biological control: Trichoderma spp., Bacillus subtilis/Bacillus amyloliquefaciens products (commercial biocontrols) Crop rotations, resistant varieties, grafting (horticulture), and improved irrigation management to reduce stress[55,56,57]
Verticillium dahliae (soil-borne vascular fungus)Causes persistent vascular wilts that are often worse when plants are water-stressed; survives long in soil (microsclerotia), and drought reduces plant compensatory growth Olive, potato, cotton, many vegetables, and ornamentals.Historically widespread; drought increases outbreak severity and economic losses in perennial cropsCrop rotation limited effectiveness; soil amendments (organic matter), resistant/tolerant cultivars where available; some bio-agents and anaerobic soil disinfestation are used; long-term integrated management required.[58,59]
Magnaporthe oryzae pathotype TriticumEpisodic drought alternating with warm/humid conditions can drive severe epidemic windows; stress in plants may influence susceptibilityWheat and grasses.Listed as an emerging and highly destructive disease—originally in South America, spread to South Asia (Bangladesh) and new regions; climate change is predicted to expand its suitable range and increase risk under some scenarios.Integrated management: quarantine and surveillance, resistant cultivars (limited durability), seed health standards, adjusted planting dates, fungicides (azoles/strobilurins-resistance concerns), cultural measures; research on improved genetics and forecasts ongoing.[60,61,62]
Puccinia spp. (wheat rusts- stem/stripe/leaf rust) (biotrophic fungi)Shifts in temperature and rainfall patterns alter pathogen life cycles and migratory ranges; drought can reduce crop vigour and increase yield loss from rust when infection timing aligns with stressWheatNew virulent races (e.g., Ug99 lineage and derivatives) continue to emerge and spread; climate change is changing the range and seasonality of rust outbreaks and threatens resistance durabilityMajor tools: resistant cultivars (gene stacking, adult-plant resistance), fungicides (triazoles), monitoring/early warning systems and global surveillance, and agronomic practices. Breeding advancements.[63,64]
Botryosphaeriaceae & other canker/wood-decay fungi (necrotrophs causing dieback)Drought predisposes trees and woody crops to opportunistic canker pathogens; repeated droughts increase mortality and chronic diebackOrchard and forest trees (olive, grapevine trunks, almonds, hardwoods).Increased tree dieback and mortality observed in many regions as drought frequency/severity rises; opportunistic pathogens become more damaging when hosts are drought-stressed.Sanitation (prune/remove infected wood), irrigation management to reduce host stress, fungicidal wound protection in some systems, biological wound treatments under study; long-term resilience via species/cultivar choice.[45,65]
Ralstonia solanacearum (soil-borne bacterial wilt)Warmer temperatures and drought episodes can interact to increase disease pressure in some cropping systems; water management changes (irrigation reuse) affect pathogen spreadTomato, potato, banana, solanaceous crops and many others.Several tropical/temperate strains are shifting ranges with warming; complex subspecies show variable responses to environmentPhytosanitary measures (clean seed), soil sanitation, crop rotation, tolerant varieties, bio-controls (e.g., antagonistic bacteria) and grafting; chemical control generally ineffective in soil. Integrated management[40,66]
Therefore, to control the drought-induced disease occurrences, strategies to either control the disease severity of existing phytopathogens, control diseases caused by emerging phytopathogens, or induce a better plant defence response, studies on establishing proper control measures and increasing plant disease resistance are significant research areas. The use of microbial BCAs for this purpose is a better alternative, as drought-prone agroecosystems are already disrupted and therefore more vulnerable to ecological displacements [67,68,69]. Further research related to this area is warranted as climate change scenarios are predicting increased drought events in the future, and sustainable agricultural practices are also much needed to avoid disrupting ecosystems further [70].

3. Biocontrol Strategies for Emerging Pathogens

Microbial biological control agents (BCAs), including species from both bacteria and fungi, offer an eco-friendly alternative to managing plant diseases and maintaining the health of crops [71]. Various mechanism dictates their mode of action, including competition for resources and space, producing antimicrobial compounds as secondary metabolites, and lytic enzymes such as chitinases, helping to degrade chitin in pathogens’ cell walls, and activating different host plant immune responses known as Induced Systemic Resistance (ISR) [72].
The ever-changing nature of farming practices, with an increase in global food demand, climate change, and concerns regarding the overuse of pesticides, have caused setbacks in agricultural production while maintaining sustainability goals. This situation is exacerbated by the emergence of new pathogens resistant to existing control measures with high adaptability to changing environmental conditions [73,74]. Therefore, traditional biological control practices have undergone drastic changes to bridge this gap to become more effective in pathogen control and plant health promotion. This has also pushed the use of BCAs for control strategies in agriculture as an important aspect of fulfilling global food production while reducing the adverse effects caused by traditional control methods using agrochemicals.
Even though disease control using biological control agents has been a prevalent concept in sustainable agricultural practices, they have several limitations that reduce their effectiveness compared to other management methods [75]. Biocontrol agents such as predators, parasitoids, or microbial antagonists have a relatively slower response time compared to chemical pesticides. BCAs require time to establish a population and effectively control the pests and pathogens, while chemical control agents can immediately suppress the causative organism, which can be highly important in controlling acute infestations [76]. Additionally, due to the high sensitivity of certain BCAs towards environmental factors such as temperature, humidity, and soil composition, they can reduce their efficiency over time, causing the recurrence of pathogens [77]. Furthermore, while BCAs can perform relatively well under controlled conditions, their effectiveness in fields can decline due to ecological competition, variable pathogen sensitivity, and unstable product formulations [77,78]. In order to establish biocontrol strategies for emerging phytopathogens, the focus should move towards overcoming these limitations to establish better control strategies.
To overcome the limitations of biocontrol procedures, research is being conducted in many different areas related to increasing their efficiency, accurate understanding of their metabolic pathways and gene expression, better formulation of end products for lasting long in field conditions, and many more study areas. Genome-related studies of these biocontrol agents can provide great insights into this, as selective gene expression is highly important in understanding the biocontrol capabilities of an organism. Genetic engineering using CRISPR/Cas9 technology in certain BCAs has shown that it is possible to enhance their precision by improving the antimicrobial compound production [23,79]. Also, genome shuffling has been successfully utilized with enhanced biocontrol against certain pathogens [80]. Apart from that, targeting the genetic expression of certain antagonistic characteristics, such as mycoparasitism, antibiosis, the ability to produce lipopeptides working as surfactants, and siderophores, allows for broad-spectrum activity against bacteria and fungi [81].
The use of climate-adaptive microorganisms as bioinoculants and biocontrol agents is an interesting area of study when focusing on increasing crop resilience in drought-prone areas. Their natural ability to survive and function under stressful environmental conditions makes them the ideal candidates to be used to improve drought-prone agroecosystems [82]. Microbes isolated from harsh or dry environments, such as deserts, semi-arid regions, or saline habitats, where they have co-evolved with plants under stress, have a better adaptation when used for the fortification of drought-prone ecosystems and show more robust and consistent beneficial effects [83,84,85]. Certain survival strategies are inherent in these microorganisms, such as the ability to produce stress-resistant endospores [86,87,88], fungi evolving with thick cell walls with melanin for drought tolerance [89], the ability to produce osmo protectants (trehalose, proline, and other sugars/amino acids) [90], adaptations secrete exopolysaccharides (EPS) to retain soil moisture [91] can prove to be highly beneficial when designing strategies to use bioinoculants in drought-stressed cultivation areas.

4. Climate-Adaptive Biocontrol Agents and Their Mode of Action to Control Pathogens

Ongoing environmental and ecological disturbances brought on by climate change can negatively impact the efficiency and stability of traditional BCAs in field applications [92]. Even small changes in the temperature and UV radiation can affect microbial concentration and the virulence of pathogens [14]. Therefore, the ability of BCAs should be adaptable to local conditions to control current and emerging pathogens in the fields effectively.
The benefit of biocontrol agents effectively adaptable to harsh environmental conditions can be important aspect of sustainable agriculture due to this factor. Climate-adaptive biocontrol organisms can be defined as biological control agents (BCAs) that are capable of maintaining their effectiveness and beneficial functions for controlling plant pathogens under the environmental stresses exacerbated by climate change [93,94]. They have the necessary traits to withstand the environmental challenges or can modify themselves to function effectively even under harsh conditions [14].
Different yeast species act as BCAs using various modes of action, including competition for nutrition and space, which is facilitated by their ability to grow rapidly. Therefore, in drought-stressed environments, the ability to efficiently colonize and multiply at a faster pace can be a favourable characteristic as a biocontrol agent [95]. Particularly under stress conditions such as extreme temperatures, lack of nutrients, adverse pH, and low water availability, yeast biocontrol agents tend to show a lower efficiency [96,97]. Therefore, stress-adapted yeast species collected from suitable environments could be much more useful when used as biocontrol agents. For example, Rhodosporidium paludigenum identified from the East China Sea exhibited a higher osmo tolerance in its natural habitat, thus showing a higher viability under low water activity (aw ≈ 0.95) and freezing stress [98]. Pre-exposure to low pH also improved the survival of Rh. paludigenum and improved its biocontrol efficacy. The biocontrol activity against Penicillium expansum on pear fruit and Alternaria alternata on Chinese winter jujube was also comparatively higher in stress-exposed Rh. paludigenum compared to other biocontrol agents [99]. Another halotolerant yeast, Debaryomyces hansenii has shown efficient biocontrol activity against various postharvest fungal pathogens on apple, grapefruit, and papaya, and the efficiency increased furthermore when cells were pretreated with mannitol and sorbitol, showing a greater ability to control postharvest blue mould (Penicillium expansum) and grey mould (Botrytis cinerea) infections [100].
Pseudomonas fluorescens, a bacterial species highly studied as a potential BCA, is effective against a range of fungal pathogens. A study conducted by Chen et al. showed that although it has poor heat-tolerant capabilities under natural conditions, an oxidative stress-adapted strain of P. fluorescens SN15-2 showed superior heat tolerance compared to the control [101]. This shows that certain characteristics adapted to stress tolerance not only increase the biocontrol potential but also ensure stability during formulation. Some microorganisms, such as different Bacillus species, can be effective biocontrol agents over a wide temperature range. The ability to produce thermostable enzymes, like chitinases, can remain active even under high temperatures [102]. Furthermore, genetic engineering approaches such as the use of CRISPR/Cas9 technology for gene knockouts or regulatory gene manipulations have shown that enhanced production of antimicrobial compounds, such as bacillomycin D to improve pest control [103].
Not only naturally occurring characteristics, but modern genetic engineering approaches can also be used to enhance microbial stress tolerance, such as the overexpression of heat shock proteins for improved antifungal activity under heat stress [104]. This concept has been used for the genetic modification of Trichoderma species used for biocontrol to obtain better antifungal activity [105,106,107].
Symbiont engineering using horizontal gene transfer can also be an important study area for producing climate-adaptive BCAs. In Bacillus thurigiensis, insecticidal crystalline protoxin or Cry protein production can increase its potency. It has been shown that recombinant cry genes, specifically parasporal crystal proteins—Cry and Cyt improved insecticidal potency by 50% against Lepidoptera, improved crop persistence, and expanded the spectrum of action [108,109].
Genomic studies in Trichoderma species have shown that the genome structure is highly relevant in understanding the expression of genes related to enzyme and secondary metabolite production [110]. Additionally, it has been shown that valuable information related to the efficiency and behaviour of BCAs can be understood via studies related to their evolution and trait inheritance [111]. Studies related to this area are relatively lacking due to the main focus of biological control being on the direct and indirect ecological interactions between the target pests and their natural enemies. Therefore, in-depth genomic studies of native soil microbiome and their natural evolution in the native environment could provide highly important data for the establishment of targeted and efficient BCAs for better plant health.
In order to retain the efficacy of BCAs such as Trichoderma species for a prolonged period, different methodologies and formulations, such as encapsulation, have been successfully used. For example, in one study, to enhance the stability and efficacy of Trichoderma spores in high UV and high temperature environments, layer-by-layer (LbL) encapsulation method using biobased lignin derivatives has been successfully tested [112]. This is a highly important research area, as a major drawback in BCAs is their inability to establish well in natural ecosystems for a prolonged period of time to effectively improve plant health.

5. Bioinoculants to Improve Plant Health in Drought Conditions

The plant health can not only be protected through the control of pathogens but also via supporting plant resilience. Bioinoculants are living or dormant cells of efficient microbial strains that can help in plant growth and induce tolerance to various abiotic and biotic stress factors [88,113]. Not only do drought-prone agricultural areas face high temperature ranges, but the relatively low availability of water and low humidity, and altered moisture conditions can also adversely affect the health of the cultivated crops. Stress-adaptive microorganisms can be a valuable resource for alleviating these stress conditions [114]. This could be achieved through different modes of action that help the crops withstand the harsh environmental conditions (Table 2). Microbial bioinoculants can assist plants to tolerate drought conditions through many functional traits that collectively influence root development, water relations, nutrient acquisition, and stress signalling (Figure 2). Beneficial microorganisms can help plants tolerate abiotic stresses, including the adverse effects of drought-related water scarcity [73,115]. These could include the formation of resilient structures, such as biofilms, that can enhance resistance to environmental stress caused by heat [116,117]. Plant growth-promoting microorganisms (PGPM) in the soil rhizosphere collected from arid zones also have a better tolerance towards high temperatures and drought conditions, with the ability to induce plant resistance against soil phytopathogens [118]. Various studies have also shown that bio-inoculants based on mycorrhizal fungi (MF) and endophytic filamentous fungi (EFF) can significantly improve a plant’s ability to handle strong abiotic stress conditions [119,120].
Some climate-adaptive microorganisms can promote plant growth and support plants in tolerating abiotic stresses, therefore protecting them from attacks from emerging pathogens [104,114,121]. Genetic engineering of different crops is also used to create abiotic stress tolerance, such as salinity, drought, and many more [122]. Bioinoculants using drought-adapted rhizosphere soil microorganisms have been shown to improve plant growth in water- and P-deficient soils, with the possibility of reducing the use of fertilizers [123]. Additionally, nutrient deficiencies occurring due to disrupted soil in drought-prone areas could be overcome with bioinoculants such as Azospirillum species, increasing nutrient uptake [124].
Many Bacillus species produce endospores, which enable them to survive in harsh abiotic conditions such as extreme temperatures, pH, radiation, low water availability, UV radiation, and pesticide contamination [125]. They can help in alleviating drought stress by secreting various metabolites, modulating plant hormone levels, and increasing the water uptake capabilities through improving the soil microbiome and the plant root system [126]. Bacterial species such as B. paralicheniformis and B. subtilis (P1), identified from sandy soil, were used as bioinoculants on wheat, showing that the shoot weight significantly increased under drought conditions [70]. Additionally, B. paralicheniformis and T. asperellum showed the ability to protect maize from drought, cadmium, or combined stresses [127]. In another study, Nocardioides sp. abundantly found in desert habitats and drought-stressed cowpea rhizospheres [85,128] can be utilized to identify drought stress as they can act as a biomarker [129,130].
Table 2. Different characteristics of climate-adaptive microorganisms that help in drought tolerance. ↑ indicate an increase in the mentioned characteristics.
Table 2. Different characteristics of climate-adaptive microorganisms that help in drought tolerance. ↑ indicate an increase in the mentioned characteristics.
Category & Expected OutcomeDrought-Resilient Trait(s)Representative Microbial ExamplesTarget Crop(s)Suitable EnvironmentDocumented Field Performance
1. Enhanced Root Architecture & Soil Exploration
Greater root length, branching, and root hair density leading to improved water uptake.		ACC-deaminase activity; IAA (Indole-3-acetic acid) production; auxin modulationBacillus amyloliquefaciens [131], Azospirillum brasilense [132,133], Pseudomonas fluorescens [134]Wheat, maize, sorghum, soybean, pearl milletArid & semi-arid; low organic matter soils↑ Root length; ↑ grain yield
2. Soil Moisture Retention & Rhizosphere Stabilization
Better soil aggregation leading to reduced water loss and improved microbial persistence.		Exopolysaccharide (EPS) production; biofilm formationPseudomonas putida [135], Bacillus megaterium [136]Wheat, maize, legumesArid, sandy soils; degraded lands↑ Soil moisture; ↑ biomass
3. Enhanced Water & Nutrient Foraging
Boosted water uptake and nutrient mobilization when root access is limited.		Mycorrhizal hyphal extension; P-mobilization; improved osmotic balanceAMF (Rhizophagus irregularis, Rhizophagus clarus [137,138,139,140]
, Funneliformis mosseae [141,142])		Maize, soybean, vegetablesArid & nutrient-poor soils↑ Water-use efficiency; ↑ yield
4. Stress Priming & Physiological Buffering
Greater antioxidant activity and improved resilience of leaves and reproductive structures.		Induced systemic resistance (ISR); ROS detoxification; phytohormone modulationTrichoderma spp. [143,144,145,146], Bacillus subtilis [147]Tomato, pepper, grapevine, sunflowerSemi-arid climates; high temperature + drought↑ Fruit set; reduced oxidative damage
5. Improved Nitrogen Fixation Under Water Deficit
Stable nodulation and maintained N-fixation under moderate to severe drought.		ACC–ethylene balance; osmolyte production; nodulation-enhancing metabolitesBradyrhizobium japonicum [148] (often with PGPR co-inoculants)Soybean, chickpea, cowpeaSemi-arid; variable rainfall↑ Pod number; ↑ tissue N
6. Multi-Mechanistic Synergy for Severe Drought
Combination of water retention, root growth, nutrient uptake, and stress priming.		ACC-deaminase + EPS + osmolyte production + AMF symbiosisPGPR–AMF consortia (e.g., Pseudomonas + Bacillus + AMF) [57,149]Cereals, legumes, vegetablesArid & semi-arid; severe drought↑ Survival during >50% water reduction; ↑ biomass and yield
Yeasts have the ability to synthesize plant hormones and other bioactive substances that can promote drought tolerance [150,151]. Some yeast species, such as Aureobasidium pullulans and Pseudozyma flocculosa can produce biofilms, osmoprotectants and pigmentation leading to better survival in the phyllosphere in low humidity which helps in maintaining foliar protection through drought [152,153,154,155,156]. Additionally, yeasts found in extreme cold, dry, saline, and acidic environments can potentially promote plant growth under drought stress, as species like Rhodotorula mucilaginosa, Candida tropicalis HY and Naganishia albida have shown positive effects on wheat and rice [91,157,158].
Endophytic fungi isolated from wheat with drought-tolerant capabilities, such as Talaromyces purpureogenus and Penicillium citrinum, showed the ability to enhance physio-biochemical growth parameters when the plant is faced with stress conditions [159,160]. Not only individually, but when applied in combinations, microbial consortia of AMF (Arbuscular mycorrhizal fungi), PGPR (Plant Growth-Promoting Rhizobacteria), and yeasts have shown synergistic effects with a significant improvement in plant tolerance, biomass, and physiological attributes, even under severe drought [158]. The co-inoculation of Claroideoglomus claroideum (AMF), Naganishia albida (yeast), and Burkholderia caledonica (PGPR) showed significant ability to tolerate drought conditions in strawberry [158]. Furthermore, co-inoculation of Bradyrhizobium liaoningense and Ambispora leptoticha showed improved morphological, physiological, nutritional, and yield characteristics in soybean cultivars, both drought-susceptible and drought-tolerant [161].

6. Research Gaps and Future Directions

The study of biocontrol agents and bioinoculants has been a very popular research area for decades. But even though there is an abundance of preliminary studies conducted to check and establish the potential of microorganisms for disease control and improvement of overall plant health, the majority of them are successful under laboratory conditions but lose their efficiency and efficacy under field conditions. Particularly promising yeast BCAs, such as Meyerozyma guilliermondii, have both biocontrol capabilities as well as abiotic stress tolerance, but are only established at the greenhouse or laboratory level [162]. Specifically, when addressing drought-prone areas facing high abiotic and biotic stress alike, it is very important to identify the problems to utilize the BCAs appropriately.
For example, studies frequently fail to track microbial communities beyond single growing seasons, thus limiting the understanding of long-term microbial persistence and its long-lasting impact [113]. When utilizing beneficial microorganisms, their establishment, stability, and benefits provided to the resident soil microbiome should be studied to better understand their long-term effects. Additionally, how these BCAs interact with the indigenous soil microbiome under recurrent drought cycles, and how they retain their functional benefits in dormant periods, and can the same benefits be observed in rotational cropping systems should also be studied, as this is a persistent gap related to the use of beneficial microbes. Also, studies related to the synergistic effects of multiple microorganisms are lacking, as most research only focuses on single-strain inoculants. The effectiveness of native microbiome vs. introduced microbial communities, or how their interactions elicit drought tolerance and pathogen resistance, can provide interesting insights into the activity of BCAs. In the study conducted by Barriga-Medina et al. to control invasive Rubus niveus (Hill raspberry) introduced due to human interventions to the ecosystems in the Galapagos Islands, it was shown that pathogenic fungal species in the native microbiome can be successfully utilized as control agents [163]. Therefore, choosing control agents from the native environment adaptable to harsh conditions could be more beneficial than the general selection of microbial control agents.
Even though there is an abundance of studies related to identifying beneficial secondary metabolites and enzymes, there is a lack of insights linking these molecular pathways to plant drought responses. To address this issue, a better understanding of their metabolic pathways and gene expression could provide critical insights towards efficient product formulation. Transcriptomic profiling across diverse crop-microbiome systems to understand stress response and the influence of volatile organic compounds (VOCs) in acquired drought tolerance could be highly important for an accurate understanding.
Despite proven efficacy and environmental benefits, there are also socioeconomic and regulatory barriers to convince the farming community of the profits in using microbial agents in cultivation areas to improve crop production. Therefore, knowledge sharing and guidance regarding the use should be broadly implemented to better establish these beneficial microorganisms for sustainable farming practices. In the current timeline, the best use of BCAs can be obtained mainly through IPM (Integrated Pest Management) strategies, while deeper studies focusing on accurate screening, adaptive deployment, and better understanding of non-target effects should be conducted to improve efficiency [164].
When formulating products that are successful in any ecosystem, the conditions and the formulation method should be properly implemented [165,166]. Seed coating is best suitable for ACC-deaminase and IAA producing PGPR while granular or pelleted formulations are effective for AMF [167]. Also, the timing of the application is very important for the efficiency of the product. Early root colonization can be achieved through seed inoculation, and soil inoculation should be performed before a high level of water stress is present. Also, co-application with agrochemicals should be avoided as some high-salt fertilizers and low-toxicity pesticides could negatively affect the colonization of the BCAs [168].
The practical path forward in using climate adaptive BCAs should include defining the specificity of the system, while using the BCA; the cultivations would respond differently depending on factors such as the type of crops, pathogens, the drought intensity or frequency, and current pesticide practices [169]. Another approach would be to combine traits to improve the efficiency of two BCAs, with one establishing drought tolerance and the other with the superior pathogen-controlling ability [170]. This efficiency could be further enhanced through the use of stress protective formulations that would increase the shelf life as well as the field persistence under harsh environments in the drought-prone ecosystem [171].

7. Conclusions

Microbial BCAs are an important component of sustainable agricultural practices as the world is moving towards more environmentally friendly approaches for disease control and plant health improvement. Effects of climate change on agricultural practices are becoming more evident than before, as global food production has become a critical issue that needs practical and implementable solutions. As the global community is moving towards environmentally conscious, sustainable farming practices, the potential of microbial BCAs is becoming more relevant than ever. Therefore, the focus of research on microbial BCAs should shift towards establishing methodologies for their practical applications in drought-affected farming areas.

Author Contributions

Conceptualization, D.L.H.; investigation, D.L.H. and A.K.; writing—original draft preparation, D.L.H.; writing—review and editing, A.K., S.H., S.S., T.W. and R.C.; supervision, R.C. All authors have read and agreed to the published version of the manuscript.

Funding

This research received no external funding.

Data Availability Statement

No new data were created or analyzed in this study. Data sharing is not applicable to this article.

Acknowledgments

Dulanjalee Lakmali Harishchandra (EX010075), Anuruddha Karunarathna (EX010177), and Sukanya Haituk (EX010024), would like to thank the CMU Proactive Researcher Postdoctoral Program, Chiang Mai University, Thailand, for the support. The authors have reviewed and edited the output and take full responsibility for the content of this publication.

Conflicts of Interest

The authors declare no conflicts of interest.

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Figure 1. How the climate-adaptive organisms could be useful in improving crop health in drought-affected ecosystems- Stock images were taken from BioRender.com to represent concepts and edited to suit the figure.
Figure 1. How the climate-adaptive organisms could be useful in improving crop health in drought-affected ecosystems- Stock images were taken from BioRender.com to represent concepts and edited to suit the figure.
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Figure 2. Conceptual model linking microbial functional traits with crop drought-resilience mechanisms. Microbial traits such as ACC-deaminase, EPS, phytohormone modulation, osmolyte production, nutrient mobilization, ISR, and mycorrhizal associations induce plant physiological responses (enhanced root growth, antioxidant capacity, water uptake, stomatal regulation), leading to improved crop performance under drought.
Figure 2. Conceptual model linking microbial functional traits with crop drought-resilience mechanisms. Microbial traits such as ACC-deaminase, EPS, phytohormone modulation, osmolyte production, nutrient mobilization, ISR, and mycorrhizal associations induce plant physiological responses (enhanced root growth, antioxidant capacity, water uptake, stomatal regulation), leading to improved crop performance under drought.
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MDPI and ACS Style

Harishchandra, D.L.; Karunarathna, A.; Haituk, S.; Sittihan, S.; Wongwan, T.; Cheewangkoon, R. Improving Crop Resilience in Drought-Prone Agroecosystems: Bioinoculants and Biocontrol Strategies from Climate-Adaptive Microorganisms. Agriculture 2025, 15, 2479. https://doi.org/10.3390/agriculture15232479

AMA Style

Harishchandra DL, Karunarathna A, Haituk S, Sittihan S, Wongwan T, Cheewangkoon R. Improving Crop Resilience in Drought-Prone Agroecosystems: Bioinoculants and Biocontrol Strategies from Climate-Adaptive Microorganisms. Agriculture. 2025; 15(23):2479. https://doi.org/10.3390/agriculture15232479

Chicago/Turabian Style

Harishchandra, Dulanjalee L., Anuruddha Karunarathna, Sukanya Haituk, Sirikanlaya Sittihan, Thitima Wongwan, and Ratchadawan Cheewangkoon. 2025. "Improving Crop Resilience in Drought-Prone Agroecosystems: Bioinoculants and Biocontrol Strategies from Climate-Adaptive Microorganisms" Agriculture 15, no. 23: 2479. https://doi.org/10.3390/agriculture15232479

APA Style

Harishchandra, D. L., Karunarathna, A., Haituk, S., Sittihan, S., Wongwan, T., & Cheewangkoon, R. (2025). Improving Crop Resilience in Drought-Prone Agroecosystems: Bioinoculants and Biocontrol Strategies from Climate-Adaptive Microorganisms. Agriculture, 15(23), 2479. https://doi.org/10.3390/agriculture15232479

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