Microbial secondary metabolites play a vital role in improving soil structure, enhancing soil fertility, increasing crop yield, and improving crop quality. This article provides an overview of the concept, sources, and functions of microbial secondary metabolites, and introduces their applications in bacterial fertilizers, actinomycete fertilizers, and fungal fertilizers. Key considerations for the production and application of compound fertilizers containing microbial secondary metabolites are analyzed. Challenges in the development, promotion, and application of microbial functional fertilizers are addressed, and actionable solutions are proposed. Finally, the future prospects of the novel functional fertilizer industry are discussed.
1. Introduction
Chemical fertilizers have been fundamental to ensuring global food security by improving soil nutrient conditions and increasing crop yields. However, issues such as irrational fertilization practices, excessive fertilizer use, low nutrient utilization efficiency, and severe water pollution have hindered sustainable agricultural development. Under China’s “Zero Growth in Fertilizer Use” policy, the development and application of novel functional fertilizers—particularly those utilizing microbial secondary metabolites—have emerged as effective strategies to ensure food security while promoting environmental sustainability.
2. Overview of Microbial Secondary Metabolites
2.1 Definition and Characteristics
Microbial secondary metabolites are complex organic compounds synthesized from primary metabolites during the stationary phase of microbial growth. Unlike primary metabolites, they are not essential for basic cellular functions but play critical roles in ecological interactions, such as competition, symbiosis, and stress resistance. Key features include:
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Structural diversity: Varies by microbial species and cultivation conditions.
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Extracellular secretion: Often released into the environment to mediate microbial interactions.
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Broad applications: Used in agriculture, medicine, and food industries.
2.2 Sources of Microbial Secondary Metabolites
Microbial secondary metabolites are primarily derived from bacteria, fungi, and actinomycetes.
2.2.1 Bacteria
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Bacillus spp.: Produce antimicrobial metabolites (e.g., bacillomycin, surfactin) and γ-polyglutamic acid (γ-PGA), which enhance stress tolerance and nutrient uptake.
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Pseudomonas spp.: Synthesize biocontrol agents like 2,4-diacetylphloroglucinol (2,4-DAPG) and pyrrolnitrin.
2.2.2 Fungi
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Trichoderma spp.: Generate antifungal compounds (e.g., trichothecenes) and plant growth-promoting metabolites.
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Fusarium spp.: Produce secondary metabolites that suppress peanut rust pathogens.
2.2.3 Actinomycetes
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Streptomyces spp.: Account for ~70% of known microbial bioactive metabolites, including antibiotics (e.g., streptomycin, tetracycline) and herbicides (e.g., phthoxazolin).
3. Roles of Microbial Secondary Metabolites in Agriculture
3.1 Enhancing Crop Growth and Stress Resistance
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Phytohormone production: Auxins and cytokinins from rhizobacteria (e.g., Azospirillum) stimulate root development and cell division.
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Abiotic stress mitigation: Pseudomonas putida improves salt tolerance in cotton by modulating ion uptake (K⁺, Ca²⁺ vs. Na⁺).
3.2 Improving Soil Health and Nutrient Availability
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Organic matter decomposition: Accelerates breakdown of plant residues, increasing soil porosity and organic carbon.
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Nutrient solubilization:
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Phosphate-solubilizing microbes (e.g., Penicillium oxalicum) secrete organic acids to release bound phosphorus.
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Potassium-mobilizing bacteria (e.g., Bacillus mucilaginosus) dissolve silicate minerals.
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3.3 Biocontrol of Plant Pathogens
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Antibiotic production: Streptomycetes inhibit fungal pathogens (e.g., Fusarium oxysporum) via metabolites like actinomycin.
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Induced systemic resistance (ISR): Trichoderma metabolites activate plant defense pathways.
4. Applications in Fertilizer Formulations
4.1 Bacterial Fertilizers
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Nitrogen-fixing fertilizers: Rhizobium spp. increase soybean yields by 15–25% via biological N₂ fixation.
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Phosphate-solubilizing biofertilizers (PSB): Pseudomonas and Bacillus strains improve phosphorus availability by 30–50%.
4.2 Actinomycete Fertilizers
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Streptomyces-based products: Strain S-101 reduces cucumber wilt incidence by 70% through antifungal metabolites.
4.3 Fungal Fertilizers
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Mycorrhizal inoculants: Glomus spp. enhance water and nutrient uptake via extended hyphal networks.
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Fungal PSB: Aspergillus niger outperforms bacterial PSB in acidic soils.
5. Key Considerations for Compound Fertilizer Production and Use
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Crop-specific formulations: Tailor metabolites to crop needs (e.g., Azotobacter for cereals, Trichoderma for vegetables).
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Environmental optimization: Maintain soil pH 6.5–7.5; avoid co-application with fungicides.
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Quality control: Ensure viable cell counts (>10⁸ CFU/g) and proper storage (≤25°C, dry conditions).
6. Challenges and Future Perspectives
6.1 Current Limitations
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Production challenges: Metabolite instability, high purification costs.
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Field variability: Efficacy depends on soil microbiota and climate conditions.
6.2 Strategic Solutions
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Standardization: Establish ISO protocols for metabolite quantification and formulation.
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Public-private partnerships: Accelerate R&D through academia-industry collaboration (e.g., CRISPR-engineered Bacillus strains).
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Farmer education: Demonstrate benefits via on-farm trials and extension services.
6.3 Emerging Trends
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Synthetic biology: Engineered microbes for scalable metabolite production.
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Nano-formulations: Encapsulated metabolites for controlled release.
7. Conclusion
Microbial secondary metabolites offer a sustainable alternative to chemical fertilizers, addressing both productivity and environmental concerns. By overcoming technical and adoption barriers, these bio-based inputs can revolutionize modern agriculture. Collaborative efforts among researchers, industries, and policymakers are essential to unlock their full potential.
