Bacillus subtilis and Trichoderma harzianum are the two core microbial strains most widely applied and extensively studied in agricultural microbial products. However, they differ fundamentally in their primary modes of action and characteristics. Bacillus subtilis is a bacterium that excels in disease prevention, growth promotion, and soil improvement, whereas Trichoderma is a fungus renowned for its parasitic fungicidal activity and potent growth-promoting capabilities.
Bacillus subtilis: A Versatile Agent Centered on “Microbial Community Regulation”
The primary agricultural applications of Bacillus subtilis can be understood through three dimensions: its disease-control spectrum, growth-promotion mechanisms, and regulation of the soil microenvironment.
1.It possesses a broad disease-control spectrum, targeting both fungal and bacterial diseases. According to pesticide registration data in my country, Bacillus subtilis is registered to control a wide range of diseases, including Panax notoginseng root rot, cotton verticillium wilt, rice blast, rice sheath blight, tobacco brown spot, tobacco black shank, sugar beet leaf spot, and chili pepper wilt. Its mode of action involves the rapid proliferation of spores using nutrients and moisture from leaf surfaces or the rhizosphere to quickly occupy ecological niches; simultaneously, it secretes bioactive substances with bactericidal properties that exclude and inhibit the invasion of pathogens. Bacillus subtilis produces a diverse array of antimicrobial substances—such as lipopeptide antibiotics (e.g., surfactin, fengycin), polyene antibiotics, and catechol-type siderophores—which suppress pathogens through mechanisms including the inhibition of protein synthesis, competition for iron ions, and cell lysis. Notably, Bacillus subtilis is also effective against bacterial diseases (such as tomato bacterial wilt), a capability generally lacking in Trichoderma harzianum.
2.Its growth-promotion mechanisms focus on nutrient mobilization and hormonal regulation. Bacillus subtilis can solubilize insoluble soil phosphorus, converting it into forms that plants can absorb, and some strains also possess nitrogen-fixing capabilities. Furthermore, it produces phytohormone-like substances or utilizes volatile organic compounds (such as 3-hydroxy-2-butanone and 2,3-butanediol) to modulate the balance of cytokinins and ethylene within the plant, thereby stimulating cell division and overall plant growth. A strain of Bacillus subtilis capable of solubilizing phosphorus and producing high yields of γ-polyglutamic acid has been shown to reduce the required application of nitrogen and phosphorus fertilizers by approximately half, while simultaneously delivering significant yield increases.
3.Its ability to modulate the soil microenvironment sets it apart from Trichoderma harzianum. In a study on cotton cultivation in mildly saline-alkali soil, the application of Bacillus subtilis increased the relative abundance of the Bacillus genus in the soil by 16.85% to 54.40%. Extracellular polymers secreted by the strain enhanced soil water retention—increasing root-zone soil water content by approximately 0.02 cm³/cm³—and promoted the migration of salts to deeper soil layers, thereby reducing salt accumulation by 2–3 g/kg; this contributed between 0.35% and 26.64% to the total cotton yield. This “microbe-mediated soil improvement” effect gives Bacillus subtilis unique value in ameliorating soils under stress conditions.（1）
Trichoderma harzianum: A root specialist wielding “mycoparasitism” as its primary weapon
The core strength of Trichoderma harzianum lies in its ability to directly parasitize and kill soil-borne pathogenic fungi, as well as the potent root-growth-promoting effects derived from this interaction.
1.Mycoparasitism is Trichoderma harzianum’s unique “killer move.” It rapidly colonizes crop root surfaces and rhizosphere soil, parasitizing pathogens through hyphal coiling and the secretion of cell-wall-degrading enzymes. Simultaneously, it competes for rhizosphere niches and nutrients, effectively blocking pathogen infection. This direct parasitic mechanism enables targeted, potent inhibition of soil-borne pathogens such as Fusarium, Rhizoctonia, and Pythium. Its metabolites also activate the plant root’s innate immunity, systematically enhancing the crop’s disease resistance.
2.It demonstrates outstanding growth-promoting capabilities, offering significant advantages particularly in root system development. Research by Academician Shen Qirong’s team demonstrates that applying a Trichoderma harzianum agent to rice crops resulted in plants approximately 10 cm taller than the control group, with panicles 2–3 cm longer and an increase of about 20–30 grains per panicle; actual yield measurements reached 802 kg per mu, representing a 23% increase. （2）During the seedling stage, T. harzianum showed the most pronounced growth-promoting effects on tomato seedlings, outperforming Bacillus subtilis treatments in terms of root length, plant height, and whole-plant fresh weight. A study published in Cell in 2025 further revealed the underlying molecular mechanism: the expansin protein ThSWO, secreted by T. harzianum, penetrates the plant cell wall and precisely anchors the auxin transporter AtABCB5, mediating auxin efflux and thereby inducing changes in root system development. Rice lines heterologously expressing this protein showed a 41.3% increase in grain yield, while yields for maize, wheat, bok choy, and radish increased by 7.9%, 6.7%, 13.5%, and 35.2%, respectively.
3.It also outperformed Bacillus subtilis in improving rice quality. A comparative study showed that T. harzianum treatment reduced the chalky grain rate by 7.7%–12.0% and the degree of chalkiness by 10.3%–12.5%, whereas B. subtilis treatment failed to achieve a statistically significant improvement in chalkiness. Regarding eating quality scores, T. harzianum treatment increased the score to varying degrees, whereas B. subtilis treatment actually reduced it.
Similarities: Convergent logic for disease control and growth promotion
Despite their distinct biological identities, the two agents share significant common ground regarding their mechanisms of action and functional roles.
1.Competition serves as a fundamental strategy for both. Both can rapidly colonize the rhizosphere or leaf surface, preemptively occupying spatial niches and nutrient resources, thereby restricting the survival space available to pathogens. Bacillus subtilis spores rapidly multiply by utilizing nutrients and moisture on the leaf surface, quickly colonizing the entire leaf area, whereas Trichoderma harzianum aggressively colonizes the crop rhizosphere, competing for ecological niches and nutrients.
2.Inducing systemic resistance in plants is a shared strategy for “immune activation.” Both organisms can prime plants—placing them in a state of “alertness”—by activating defense-related genes and metabolic processes, thereby enabling a faster and more robust defense response against subsequent pathogen infections. Bacillus subtilis induces secondary defenses by activating plant genes and triggering metabolic pathways involving plant-derived compounds, while the metabolites of Trichoderma harzianum similarly activate the innate immunity of plant roots.
3.Functional overlap is evident in their shared ability to control disease and promote growth, as well as their suitability for combined application. In trials controlling root rot in Astragalus membranaceus, a root-dipping treatment using a consortium of Bacillus subtilis, Trichoderma harzianum, and Bacillus amyloliquefaciens yielded the best results regarding seedling emergence, soil enzyme activity, and disease control efficacy. Similarly, in the control of wheat powdery mildew, a microbial agent combining Bacillus subtilis and Trichoderma harzianum demonstrated superior growth-promoting effects compared to the application of either agent alone.
Key Differences: From Biological Nature to Application Strategies
| Comparison Dimension | Bacillus subtilis | Trichoderma harzianum |
| Biological Identity | Bacterium (Gram-positive) | Fungus (filamentous ascomycete) |
| Core Disease Control Mechanism | Primarily via secretion of antagonistic substances and niche competition | Unique advantage of mycoparasitism (hyphal coiling + enzymatic lysis) |
| Disease Control Focus | Excels against foliar and bacterial diseases | Highly effective and specific against soil-borne fungal diseases (root rot, damping-off, seedling blight, wilt) |
| Growth-Promoting Focus | Nutrient activation (phosphorus solubilization, nitrogen fixation) and hormonal regulation; stable yield increases during the growing season | Strong root-promoting ability; distinct advantages during the seedling stage; significantly expands root system size |
| Impact on Rice Quality | Eating quality score may decrease | Significantly improves chalkiness and enhances eating quality score |
| Soil Improvement Characteristics | Secretes extracellular polymers to improve water retention and salt distribution; suitable for ameliorating soils under stress | Improves the root zone environment primarily through rhizosphere colonization and organic matter decomposition |
| Colonization & Spread | Does not produce hyphae; reproduces via cell division; spreads relatively slowly | Produces hyphae; capable of rapid spread and expansion within the soil |
| Environmental Adaptability | Spore structure confers strong stress resistance; stable during storage | Environmentally sensitive; field efficacy is significantly influenced by conditions |
Apply strategy recommendations
Bacillus subtilis is more suitable for “full-cycle integrated management”: soil treatment or seed dressing can be carried out before planting, and continuous supplementation through root irrigation or foliar spraying during the growth period. It is especially preferred when dealing with leaf diseases and bacterial diseases.
Trichoderma is more suitable for “directional root strengthening”: it can be used in the seedling stage to cultivate strong seedlings, dipped in the roots or applied in holes during transplanting can quickly establish a rhizosphere protection circle, and can be used as a “weapon” in areas with serious soil-borne diseases or repeated cropping.