Mechanisms and Impact of Rhizosphere Microbial Metabolites on Crop Health, Traits, Functional Components: A Comprehensive Review


6.1. Microbial Inoculants and Biofertilizers

The use of microbial inoculants, including biofertilizers and biostimulants, represents a promising approach for enhancing crop performance and soil health in sustainable agriculture. Microbial inoculants introduce beneficial microorganisms into the soil, which helps improve nutrient availability, boost plant growth, and provide resilience against environmental stress [323]. Advances in microbial technologies are making these tools more accessible for farmers seeking sustainable alternatives to chemical fertilizers and pesticides.
Biofertilizers are one of the most widely used forms of microbial inoculants [324]. These products utilize specific microorganisms to convert unavailable nutrients into forms that plants can readily absorb, thereby enhancing soil fertility and promoting plant growth. For instance, nitrogen-fixing bacteria such as Rhizobium, Azotobacter, and Azospirillum are capable of converting atmospheric nitrogen into ammonia, making it available for plant uptake [325]. In leguminous crops, Rhizobium forms a symbiotic relationship with plant roots, producing root nodules where nitrogen is fixed and converted into proteins and other nitrogen-containing compounds essential for plant growth [326].
Biofertilizers also include phosphate-solubilizing microorganisms such as Bacillus and Aspergillus, which produce organic acids to solubilize insoluble phosphates in the soil [327]. This increases phosphorus availability, a critical nutrient for root development and overall plant health. Potassium-solubilizing bacteria and photosynthetic bacteria are also part of the biofertilizer portfolio, offering solutions to mobilize potassium and enhance photosynthetic efficiency, respectively.
Mycorrhizal fungi are another vital component of biofertilizers. These fungi form mutualistic relationships with plant roots, extending the root network and improving water and nutrient absorption, particularly phosphorus [328]. Mycorrhizal inoculants have been effectively used to enhance crop resilience in nutrient-poor soils, making them a valuable tool in sustainable farming practices [329].
Biopesticides represent another application of microbial metabolites in agriculture, helping to reduce the reliance on chemical pesticides. Certain microorganisms produce toxins, antibiotics, or antifungal compounds that target specific pests and pathogens while being harmless to beneficial organisms and humans [330]. For example, Bacillus thuringiensis (Bt) produces insecticidal proteins that target a range of insect pests, making it a popular choice for integrated pest management [331]. Actinomycetes, such as Streptomyces, produce antifungal compounds that are effective against plant pathogens like those causing tomato blight and cucumber wilt, offering a natural means of disease control [332].
Microbial metabolites are also employed as biostimulants, which promote plant growth by enhancing nutrient uptake, root growth, and stress tolerance. Compounds like auxins, gibberellins, and cytokinins produced by rhizobacteria stimulate plant hormone pathways, leading to enhanced root and shoot development [333]. These biostimulants also improve crop resilience to abiotic stresses, such as drought and salinity, by modulating physiological responses, including osmotic adjustment and antioxidant activity.
In practice, microbial fertilizers can be categorized based on the type of microorganisms they contain—bacterial fertilizers, fungal fertilizers, and actinomycete fertilizers. Bacterial fertilizers, for example, include nitrogen-fixing and phosphate-solubilizing strains that improve nutrient availability [334,335]. Actinomycetes are particularly important, as they are responsible for producing approximately 70% of microbial secondary metabolites, many of which play a role in plant growth promotion and disease control. Fungal fertilizers, such as mycorrhizal inoculants, help improve plant hormone production and nutrient uptake, further supporting sustainable crop production [336,337].

6.2. Challenges and Future Perspectives

Despite the numerous benefits offered by microbial inoculants and biofertilizers, several challenges must be addressed to ensure their widespread adoption and effectiveness in sustainable agriculture. One major challenge is the variability in field conditions, which can significantly affect the performance of microbial inoculants. Factors such as soil type, pH, temperature, moisture, and nutrient availability influence the activity and survival of introduced microorganisms. Therefore, field-specific trials are essential to determine the efficacy of microbial products under different conditions, ensuring optimal results.

Another challenge is the sensitivity of microbial metabolites to environmental conditions. Microbial metabolites are biologically active substances that require suitable environmental conditions—including appropriate levels of water, nutrients, temperature, and aeration—to function effectively. Environmental stressors such as high temperatures, low moisture, or the presence of competing microorganisms can limit the effectiveness of microbial inoculants. Therefore, careful management of soil conditions and adherence to best practices for microbial application are critical for success.

Additionally, some microbial secondary metabolites can have adverse or even toxic effects on plants when applied improperly or in excess. For instance, metabolites that alter hormone levels must be carefully regulated to avoid unintended effects such as stunted growth or premature flowering. The need for proper application techniques and adherence to recommended dosages cannot be overstated, as misuse may lead to reduced efficacy or unintended negative impacts on crop health.

In the production and use of microbial metabolites, the following considerations are crucial:

Tailored Application: The selection of suitable microbial inoculants must be based on the specific requirements of the crop, soil characteristics, and environmental conditions. Applying the right microbial product for a particular crop and condition is key to maximizing benefits and avoiding potential negative effects.

Optimal Application Practices: It is essential to apply microbial products under conditions that support their activity. For example, soil moisture should be adequate to support microbial survival, and care should be taken to avoid co-application with incompatible substances, such as fungicides or unprocessed organic manure, which may inhibit microbial activity.

Product Information and Awareness: Farmers and agricultural practitioners must be informed about the specific characteristics and requirements of microbial products. Clear product information, including application guidelines and environmental requirements, will help ensure that these products are used effectively to achieve the desired results.

Future Perspectives: To overcome the challenges of variability and environmental sensitivity, future research should focus on the development of robust microbial strains that can withstand a range of environmental stresses, including extreme temperatures, pH variations, and soil salinity. The development of microbial consortia—combinations of complementary microbial species that work synergistically—presents an exciting opportunity to improve the resilience and efficacy of microbial inoculants. Such consortia could provide more consistent performance across diverse field conditions, reducing the variability in outcomes.

The integration of advanced technologies, such as metagenomics and synthetic biology, offers promising avenues for optimizing microbial inoculants. Metagenomics can help identify beneficial microbial communities present in specific soil environments, while synthetic biology can be used to engineer microbial strains with enhanced traits, such as increased metabolite production or improved environmental tolerance.

Ultimately, the successful application of microbial metabolites and inoculants in sustainable agriculture requires a holistic approach that considers soil health, crop requirements, environmental conditions, and the characteristics of the microbial products. By addressing these challenges and advancing our understanding of microbial–plant interactions, microbial inoculants have the potential to transform agriculture, making it more productive, sustainable, and resilient to future challenges.



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Qingxia Chen www.mdpi.com