Bacillus species and related genera, such as Paenibacillus and Priestia, combine several useful traits, including phosphorus solubilization, nitrogen fixation, production of growth hormones, enzyme release, and generation of antimicrobial compounds. These abilities improve nutrient use, protect plants from pathogens, and increase stress tolerance. Applied as single strains or in microbial consortia, they have consistently increased yields, improved soil health, and reduced reliance on synthetic agrochemicals.
The rapid increase in the world population has led to an intense demand for both high quality and quantity of agricultural products. Consequently, in the last 40 years the use of chemical fertilizers and pesticides has increased about tenfold. As critical tools for food security, they are used globally in agriculture to prevent damage from plant pathogenic microorganisms, insects, and nematodes, with the goal of minimizing crop losses and preserving its quality.
On the other hand, chemical fertilizers and pesticides have many undesirable aspects that cannot be overlooked (Figure 1). They tend to persist in the soil and environment for a long time, affecting soil vitality, moisture retention capacity, soil organisms, and both environmental and human health. In addition, there is a growing percentage of pest resistance to various conventionally used chemical pesticides. The undesirable properties of agrochemicals have led to numerous studies seeking new solutions based on beneficial microorganisms for use in integrated pest management. Although the effects of these chemicals on plants have been studied for decades, there is limited knowledge about their impact on soil microbial communities. This is of particular concern, as numerically rare taxa have been shown to play a key role in many soil biogeochemical processes, including nitrification, denitrification, and methanogenesis. This results in biotic homogenization, which can undermine soil health and resilience. Soil health is considered the capacity of soil to function as a dynamic ecosystem that supports biological productivity by promoting plant, animal, and human health. Thus, protecting the soil microbiome is now recognized as a critical component of ecosystem conservation and soil health, because soil microbes directly affect soil fertility, crop yield, carbon storage, and even climate regulation.
Widespread anthropogenic activities have caused numerous soil degradation issues, including desertification, loss of biodiversity, nutrient depletion, and the breakdown of soil structure. In response, it has become essential to restore and maintain soil health and productivity. Current efforts focus on rehabilitating degraded lands through reforestation, the addition of organic amendments, and the reintroduction of native plants, soil fauna, and beneficial microbes. One promising approach is the use of rhizobacteria as indigenous organisms that can restore soil health, control plant pathogens, and promote plant growth through various mechanisms. Among these microorganisms, Bacillus spp. and related genera have emerged as promising biocontrol agents that enhance soil health and crop productivity. Bacillus is a large genus comprising more than 280 species and was previously considered as highly heterogeneous group of bacteria because of the loose criteria for adding new species to this taxon. Revision of the genus based on 16S rRNA studies subsequently reclassified certain phylogenetic groups and identified several clusters, including Bacillus sensu stricto, Brevibacillus spp., Geobacillus spp., Lysinibacillus spp., and Paenibacillus spp. Someone proposed the reclassification of 17 clades containing species previously classified as Bacillus into new genera such as Ectobacillus, Gottfriedia, Priestia, and others. For more comprehensive phylogenetic and comparative genetic sequence analyses, Patel and others used core and other conserved proteins to determine the constituents of subtilis and cereus clades, as well as additional genera, i.e. Alkalihalobacillus, Cytobacillus, Neobacillus, Mesobacillus, Metabacillus, and Peribacillus.
Besides evident heterogeneity, many strains of Bacillus and related genera possess multiple beneficial traits and can exhibit almost all biocontrol and biostimulation mechanisms, making them a top priority for sustainable agriculture research. Integrating Bacillus spp. as biofertilizers into agricultural practices can reduce cultivation costs while ensuring sustainable yields. Furthermore, they have the potential to mitigate the adverse effects of climate change and excessive agrochemical use, thereby fostering resilient and sustainable agricultural systems.
Bacillus spp. for sustainable agriculture
Why Bacillus for sustainable agriculture? Bacillus spp. are the most dominant Gram-positive bacteria colonizing the plant rhizosphere. Their ability to secrete enzymes that degrade a wide range of substrates gives them an advantage in dynamic environments. Additionally, the formation of resilient spores that withstand abiotic stresses, including salinity, temperature fluctuations, drought, and nutrient deficiency, enables long-term survival in agroecosystems. Through metabolic activities, Bacillus spp. actively maintain soil quality and health by increasing humus and carbon content, as well as reducing toxic metal concentrations in soil by bioremediation processes. Furthermore, nitrogen fixation and phosphate solubilization provide essential micronutrients to plants and accelerate their growth by producing phytohormones such as cytokinins, auxins, and gibberellins. Bacillus spp. produce a wide range of secondary metabolites with antimicrobial activity, which are the main source of their antagonistic potential against pathogens in plant tissue, giving them an advantage in colonizing new habitats. Such compounds include cyclic lipopeptides (CLPs) and volatile organic compounds (VOCs), known for their antagonistic roles. CLPs are nonribosomally-synthesized molecules that fall into several main families including surfactins, iturins, kurstakins, and fengycins; all of which may be involved in biocontrol. They directly inhibit phytopathogens by forming pores and disrupting membranes, and indirectly by inducing systemic resistance and promoting root colonization through biofilm formation. CLPs are part of a larger group of bioactive lipopeptides produced not only by Bacillus spp. but also by related genera such as Paenibacillus, highlighting the potential for further research. Several studies emphasize species such as Bacillus subtilis, Bacillus velezensis, Bacillus thuringiensis (Bt), Bacillus amyloliquefaciens, Priestia megaterium, and Paenibacillus polymyxa, which possess powerful traits and are recognized as efficient biofertilizers and biocontrol agents.
Soil microbiomes are rich in Bacillus spp., but several species are identified as optimal solutions for sustainable agriculture and soil health. One of the most studied rhizobacteria is B. velezensis, which is widely used for its plant growth-promoting and antifungal activities. Different strains are obtained from diverse sources, including water and soil. Various studies have reported numerous genes in the B. velezensis genome involved in the synthesis of indole-3-acetic acid (IAA), spermidine, and other polyamines, which have been shown to improve plant growth and salt tolerance. Bacillus velezensis isolates have been reported to produce xylanase, cellulase, pectinase, alpha-amylase, and other lignocellulose-degrading enzymes, as well as arabinogalactanase, and pectate lyase. Furthermore, the guaB gene, which encode an IMP dehydrogenase, an enzyme predicted to be involved in the nodulation process in conjunction with rhizobia has been identified in their genome. Bacillus velezensis thrives in various nutrient-deficient media, as observed in nitrogen-free cultures, NBRIP, and potassium bacteria medium, and also exhibits good biofilm production. Many of its strains are associated with the secretion of secondary metabolites with antifungal activities, which have been used to produce biocontrol products exhibiting a variety of antagonistic properties against phytopathogenic agents. Among these gene clusters, srf, bmy, fen, nrs, and dhb (covering a total of 137 kb), and many others, are responsible for synthesizing CLPs and other molecules, including surfactin, iturin, bacillomycin-D, fengycin, the iron-siderophore bacillibactin, macrolactin H, difficidin, bacillaene, bacilysin, butirosin A/B, andalusicin A/B, and certain unidentified peptides.
Bacillus subtilis also demonstrates diverse antifungal potential, as well as the production of EPS, siderophores, abscisic acid, zeatin, gibberellic acid, iturins, fengycins, phosphorus solubilization, and sulfur-oxidation. This species produces a plethora of enzymes, including alpha-amylase, cellulase, chitinase, and glucanase. Bacillus subtilis is known to activate defence response including induced systemic resistance in plant hosts, which increases their resistance to plant pathogens. For instance, B. subtilis induces host resistance to pathogens by activating jasmonate- and salicylic acid-dependent defense responses, leading to ultrastructural and cytochemical changes in host cells, such as the production of reactive oxygen species and cell wall reinforcement.
Bt is a soil bacterium that produces insecticidal crystal proteins (Cry and/or Cyt proteins) and spores during sporulation in the stationary phase of its growth cycle. Different strains are characterized by distinct types of these toxins, each targeting a narrow taxonomic group of insects. Bt toxins have been used as topical biopesticides to protect crops, and recent studies have shown that these proteins have been expressed in transgenic plants to confer inherent pest resistance. Such crops have reported higher yields with reduced use of chemical pesticides and fossil fuels. Bt has also been reported to produce exoenzymes, reduce the growth of phytopathogenic bacteria in co-culture conditions, and exert quorum quenching activity. In addition, Bt has several desirable PGP traits, such as the production of IAA, siderophores, and ACC deaminase, and phosphate solubilization. Moreover, recent studies have confirmed that Bt can efficiently degrade certain toxic pollutants, including arsenic, lead, zinc, copper, cadmium, mercury, chromium, and uranium. Besides these heavy metals some Bt strains can degrade persistent herbicides and pesticides, such as imidacloprid, phenanthrene, fipronil, cyhalothrin, triphenyltin, diphenyltin, monophenyltin, chlorpyrifos, and phenoxybenzoic acid.
Bacillus amyloliquefaciens strains also possess number of traits that improve soil and plant health. They increase the availability of minerals by enhancing bioavailable nitrogen (through N-fixation), solubilizing potassium and phosphates, and producing siderophores. Plant resistance to biotic stresses is boosted by CLPs, polyketides, phytohormones, and VOCs, which underlie both direct and indirect activity against pathogens. Their effects extend further by inducing systemic tolerance to abiotic stresses, leading to genetic, chemical, and physical changes in the plant host.
Besides Bacillus, related genera such as Paenibacillus, Lysinibacillus, and Priestia exhibit comparable PGP and biocontrol traits, offering additional options for sustainable agriculture. Bacillus-related genera constitute a diverse group of mostly aerobic bacteria, widely distributed in the environment, especially in the rhizosphere (e.g. Paenibacillus, Lysinibacillus, Priestia, Brevibacillus, and Metabacillus). Their highest abundance is recorded in soil fertilized with manure, where they play an important role as cellulolytic bacteria. Complete cellulose degradation requires three cellulases, all of which are produced by Bacillus related genera (BRG) (endoglucanase, exoglucanase, and beta-glucosidase). In addition to their significant potential in biodegradation, BRG are rich in metabolites involved in PGP activities, such as IAA, cytokinins, gibberellins, fungal cell wall-degrading enzymes, and nitrogenase, which is essential for transforming atmospheric nitrogen into forms available to plants. Many species from the genus Paenibacillus possess PGP traits, including P. polymyxa, Paenibacillus elgii, Paenibacillus alvei, and Paenibacillus brasilensis. For instance, P. polymyxa has demonstrated capabilities such as methane consumption and PGP activities, including solubilization of essential nutrients like phosphorus, zinc, and potassium, atmospheric nitrogen fixation, IAA and siderophore production. Its strong antifungal effects have been shown against a wide range of fungi, including Sclerotinia spp., Rhizoctonia spp., and Fusarium spp. Furthermore, P. megaterium solubilizes phosphates and produces antifungal enzymes. Root colonization has also been reported in other tea plants infected by Fomes lamaoensis (brown root rot disease). Priestia megaterium greatly reduces pathogen presence, and following subsequent inoculation with the pathogen, it produces polyphenolics, peroxidase, chitinase, glucanase, and phenylalanine ammonia-lyase. PGP tests have shown that P. megaterium can also produce IAA, siderophores and other antifungal metabolites. Each strain of P. megaterium produces a large number of enzymes with hydrolyzing, oxidizing, reducing, and metabolic functions. This demonstrates the effectiveness of this group as dominant species in biotechnological applications, as well as industrial products and processes. In addition to its known mosquitocidal and bioremediation activity, Lysinibacillus is a bacterial genus that has generated considerable interest in recent years, with recent reports indicating its importance as a PGP rhizobacteria. Several strains have been reported to produce IAA, ammonia, and siderophore, solubilize phosphorus, and produce metabolites with antifungal properties. Another promising genus is Brevibacillus, with numerous recent reports highlighting its plant growth-promoting traits, such as phosphate solubilization, acetylene reduction, IAA production, and antifungal activity. Strains like B. brevis SVC(II)14 can survive and exhibit these traits at higher temperatures, making it a suitable inoculant for crops in harsh environments.
Several Bacillus species and related genera are widely commercialized as biofertilizers, biostimulants, and biopesticides due to their dual roles in nutrient mobilization and plant protection (Table 1). Priestia megaterium (formerly B. megaterium) is a key phosphate-solubilizing bacterium, found in solo products such as P Sol B—BM (AgriLife, India), Applied Biotech Industries P-solubilizer (ABI, USA), as well as in consortia like Bio-NPK Powder S (Nando, Lithuania). These formulations enhance phosphorus availability, improves rooting performance, root length, and dry root matter content across diverse crops. This species is a widely used biofertilizer that was first introduced to the agricultural industry over 50 years ago. Paenibacillus polymyxa is already used as a biocontrol agent, with several strains commercialized for managing fungal diseases and other pests. This species can protect many crops, such as pepper, cucumber, cauliflower, peanut, chickpea, ginseng, soybean and many others from pathogens. Paenibacillus polymyxa, which combines nitrogen fixation, phosphate solubilization, and antimicrobial activity, is included in targeted biocontrol products like Phosfert+ (Kan Biosys, India) and in multi-strain biofertilizers, where it is often paired with P. megaterium and B. subtilis (TeamBio 2, Kan Biosys, India). Bacillus subtilis is a key active ingredient in broad-spectrum biofungicides such as Nutri-Life B.Sub (Nutri Tech Solutions, Australia) and Companion (Growth Products, USA). Bacillus amyloliquefaciens is featured in Aveo EZ Nematicide (Valent BioSciences, USA), Taegro 2-US (Novozymes, Denmark), and Serifel (BASF, Germany), while B. velezensis is represented by LALRISE START SC (Lallemand, Canada). These products combine pathogen suppression with plant growth promotion. Bt remains the leading microbial insecticide globally, with products such as DiPel (Valent BioSciences, USA), LiPel (AgriLife, India). Commercial consortia, including Corteva Agriscience Silica B, Bio-NPK (Nando, Lithuania; Kribhco, India; Jiangsu Provincial Bioengineering Institute, China), and European Bio-NPK blends, integrate complementary species to enhance nutrient use efficiency and disease resistance, with documented yield gains of 15–20% over conventional fertilization. These Bacillus-based solutions, produced by multinationals (Bayer, BASF, Valent) and regional specialists (Indogulf, Kan Biosys, AgriLife, ABiTEP), have an established role in sustainable agriculture and are increasingly adopted in integrated nutrient and pest management programs.
| Bacterial species/consortia | Product Name | Producer | Country |
| P. megaterium | P Sol B®—BM | AgriLife | India |
| Applied Biotech Industries P-solubilizer | ABI | USA | |
| Speed for Seed Mega | Agromarket | Serbia | |
| P. polymyxa | Phosfert+ | Kan Biosys | India |
| P Sol B®—BP | AgriLife | India | |
| B. subtilis | Biotilis | AgriLife | India |
| Nutri-Life B.Sub | Nutri Tech Solutions | Australia | |
| Companion | Growth Products | USA | |
| B. amyloliquefaciens | Aveo® EZ Nematicide | Valent BioSciences | USA |
| Taegro® 2- US | Novozymes | Denmark | |
| Serifel MBI600 | BASF | Germany | |
| B. velezensis | LALRISE® START SC | Lallemand | Canada |
| B. thuringiensis | DiPel (subsp. kurstaki) | Valent BioSciences | USA |
| Lipel (subsp. kurstaki) | AgriLife | India | |
| B. licheniformis, B. safensis, B. pumilus, B. velezensis | Silica B | Corteva Agriscience | USA |
| B. licheniformis, P. polymyxa | TeamBio 2 | Kan Biosys | India |
| P. azotofixans, B. megaterium, B. mucilaginosus, B. licheniformis, B. mycoides, B. subtilis, Trichoderma viride, mycorrhizal fungus | Bio-NPK Powder S | Nando | Lithuania |
SynCom-based biofertilizers and perspectives
Microbial consortia, or synthetic microbial communities (SynComs), are deliberately assembled groups of two or more microorganisms designed to mimic beneficial plant-associated microbiomes and enhance plant performance. SynComs are rationally designed consortia of well-characterized microorganisms that collectively promote plant growth through various mechanisms and complementary functions, including pathogen biocontrol. SynCom-based biofertilizers show promise for enhancing nutrient cycling and crop productivity while reducing reliance on chemical fertilizers. In recent years, there has been an interest in combining microbial species that do not naturally occupy the same ecological niche. In agriculture, the use of multiple microorganisms has received attention due to their capacity to provide environmentally friendly tools, including soil bioremediation, plant growth promotion, and pest and disease suppression. These microorganisms are often referred to as the plant’s second genome, extending the plant’s genetic and metabolic capabilities. SynComs can be built using bottom-up strategies, selecting well-characterized strains for specific functions, or top-down approaches, simplifying natural microbiomes while retaining key taxa. Well-designed consortia can outperform single strains in promoting yield stability, improving stress resilience, and enhancing nutrient efficiency across diverse crops, making them a promising component of sustainable agriculture. Therefore, SynComs can provide greater consistency, predictability, and adaptability across diverse soils and crop systems.
Future advances integrating genomics, metabolomics, and synthetic biology will enable optimized community design, stability, and host specificity. Developments in synthetic biology and AI-driven modeling may allow precise tailoring of microbial consortia to specific crops and environmental conditions. However, significant challenges remain in large-scale production, consistent field performance, regulatory approval, and understanding microbe–microbe–plant interactions under variable conditions.
Conclusions
Bacillus species and related genera have progressed from promising laboratory isolates to reliable components of modern crop production. Their ability to solubilize nutrients, fix nitrogen, produce hormones, and suppress pathogens makes them effective tools for improving crop yields while reducing chemical inputs. Field results confirm benefits for soil health, plant performance, and resilience in diverse cropping systems. Future research should focus on selecting strains tailored to specific crops and environments, understanding interactions within microbial consortia, and developing formulations that enhance survival and activity in the field. Expanding genomic and metabolomic studies will also help uncover new bioactive compounds and mechanisms, paving the way for more targeted and durable bioinoculant solutions.
Dora Agri is the leading biocontrol agents company in China, we concentrate on using bio solutions to prevent plant diseases and soil problems.
Biocontrol agents are widely used in soil improvement, biological insecticide & sterilization, and compost decomposition. With the research of biological science, it has developed many species: Trichoderma spp, Bacillus. spp, Beauveria bassiana, Paecilomyces lilacinus, Penicillium bilaii, etc.