Deep Dive: Bacillus as a Multitool for Modern Ag

Introduction: The genius in the soil

If the Bacillus genus were a machine, it would be a multi-tool: rugged, versatile, and always ready. If it were a colleague, it would be the one who shows up early, stays late, and knows how to fix everything from the copy machine to the HR drama. And if it were a software platform? It’d be open-source, constantly updated, and integrated with every system you use.

Bacillus bacteria are famous, not only in Ag, but also across industries where many Bacillus species and strains exhibit multifunctional biological performance. We’ll spend most of this post thinking about Ag, but it is good to know that the capability of the Bacillus genus extends far beyond the field. These species are industrial workhorses woven into the fabric of global biotechnology. They are used many, many contexts, but here are just a few:

Detergents & enzymes: Bacillus licheniformis and B. amyloliquefaciens (among other species) are used industrially to produce enzymes like proteases, amylases, and lipases, essential for cleaning agents and textile processing. 

Human and animal probiotics: Strains like B. coagulans and B. subtilis are widely found in gut health supplements, known for their ability to form spores that survive the digestive tract.

Fermented foods: In Japan, B. subtilis natto is responsible for the sticky, savory soybean dish natto, prized for its cardiovascular and digestive benefits, B. subtilis is found in various kombucha brews.

Bioremediation & bioplastics: Species like B. megaterium can degrade pollutants and even produce biodegradable plastics like polyhydroxybutyrate (PHB).

While the genus Bacillus has a storied legacy in industrial biotechnology, its role in agriculture began with a much narrower focus:

The origin story: Bacillus thuringiensis and pest control

The first major agricultural deployment of a Bacillus species came in the 1930s with the use of Bacillus thuringiensis (Bt)—a soil-dwelling bacterium that produces crystal (Cry) proteins toxic to certain insect larvae. Initially sprayed as a microbial insecticide, Bt became one of the earliest success stories in biological crop protection. 

By the 1990s, the genes of this Bacillus species had even been integrated into genetically modified crops like Bt corn and cotton, offering season-long protection from pests like corn borers and bollworms. Relative to other biologicals of the era, these products were also stable: Bacillus species form resilient endospores—tough, dormant structures that can survive heat, desiccation, UV radiation, and long storage. The stability of Bacillus has always given it an advantage in an industry that struggles with “snake oil” claims. That is, there is a reason that Bacillus has endured and is still favored by growers– but biocontrol and the incredible durability is only part of the strength of this genus. 

The biological pivot toward plant health

While Bt stole the spotlight for insect control, researchers began noticing that other Bacillus species could colonize the rhizosphere, outcompete soilborne pathogens, produce antibiotics and antifungals, prime plant immune responses, and solubilize essential nutrients like phosphorus and potassium. This led to a second wave of Bacillus-based ag inputs—focused not just on killing pests, but on enhancing plant performance and resilience. These weren’t just pest managers—they were plant partners, offering inherent multiple modes of action. 

Why Bacillus took off: practical advantages

The reasons for Bacillus’ continued rise in ag are both biological and logistical:

As we’ve said: spore-forming durability: Spores survive processing, formulation, shelf storage, and field conditions.

Colonization competence: Certain strains form biofilms and establish robust populations on roots and leaf surfaces, establishing both nutrient-based functions and physical barriers against biotic and abiotic stresses.

Functional redundancy: Multiple strains might solubilize phosphorus or fix nitrogen, but not under all conditions; having multiple strains that perform the same function can insure against system dysfunction. In a multiple species product, functional redundancy supports plant growth across environments and under stress.

Compatibility: Most Bacillus species play well with others: mixing well with other species in products, with other inputs in tanks, and synergizing with fungi, bacteria, and even mycorrhizae in the rhizosphere.

All of these factors made Bacillus a near-perfect fit for both traditional agriculture and the emerging biologicals market. And as sequencing and screening technologies have improved, more strains with unique properties have been identified—leading to today’s proliferation of Bacillus-based products.

The modern Bacillus toolbox: Five (and more) common species, infinite possibilities

As is clear by now, the genus Bacillus isn’t a one-trick microbe. It’s a genetic and metabolic goldmine, offering growers a menu of functions from disease suppression to abiotic stress mitigation to nutrient cycling. Below are a few of the most relevant species in modern agriculture, their mechanisms, and where they shine, but as you’ll see in the subsequent section there are many more possibilities than just these five. A couple of important things to keep in mind: Microbes are incredibly adaptive, which means that what particular benefit or benefits they confer to crops can often change based on the environment and the needs of the plant. Also important to note: even a single species has multiple genetic variants known as “strains” that can have vastly different properties that depend on small genetic differences– it is important to understand the specific strain to understand what a particular product is capable of.

1. Bacillus subtilis

Strengths of certain strains include:

• Phosphorus solubilization and contribution to N-fixation

• Immune priming through induced systemic resistance (ISR)

• Anti-fungal compound production (iturin, fengycin, surfactin)

• Biofilm formation on roots and leaves through the sensing of root exudates

• Nutrient cycling and organic matter decomposition

Example applications of certain strains:

Reduction of Fusarium, Botrytis, and Rhizoctonia infections in tomatoes, peppers, and cucurbits; increase of plant tolerance to drought and other stresses by stabilizing root zone interactions; Enhances fruit firmness and shelf life in strawberries and grapes.

 2. Bacillus amyloliquefaciens

Strengths of certain strains include:

• High production of secondary metabolites (e.g. difficidin, bacillaene)

• Solubilizes phosphorus and potassium

• Excellent rhizosphere colonizer

Example applications of certain strains:

In lettuce, reduces damping-off and boosts leaf turgor; In brassicas and cucurbits, Improves root growth and shoot biomass; in seedlings, enhances nutrient uptake and early vigor, especially in organic systems. In all crops, it produces siderophores and organic acids, and mobilizes nutrients, particularly in low-phosphorus soils.

3. Bacillus velezensis

Strengths of certain strains include:

• Is also sometimes considered B. amyloliquefaciens and B. subtilis. (This might be a confusing sentence for those not versed in microbial classification, but bacterial taxonomies are often uncertain and hotly debated. Perhaps, some day I will write a blog about these murky waters!)

• Multifunctional: antifungal, growth-promoting, stress-mitigating

• Produces plant hormone analogs (IAA, gibberellins)
  
  

Example applications of certain strains:

In grapes, suppresses Botrytis cinerea and increases anthocyanin levels; in tomatoes and cucurbits, it enhances salt and drought stress tolerance; in legumes and corn it is used as a seed treatment to improve stand and vigor; and for many crops: activates multiple metabolic pathways like ROS scavenging, cell wall strengthening, stomatal regulation and occupies the rhizosphere with dense, beneficial, competitive colonies.

4. Bacillus pumilus

Strengths of certain strains include:

• Stress tolerance enhancer—especially salinity and drought

• Produces catalases and peroxidases that scavenge ROS (reactive oxygen species)

• Forms durable spores and stable formulations

Example applications of certain strains:

Boosts germination and seedling establishment in arid-zone crops; Protects leafy greens from oxidative stress and wilting under high heat/light; In turfgrass, it is used to reduce abiotic leaf stress and improve color and in many crops, neutralizes harmful ROS produced during stress events and stabilizes chlorophyll and membrane integrity under heat and drought.

5. Paenibacillus polymyxa and Paenibacillus chitinolyticus

These ex-Bacillus species also deserve a mention! The word “Paenibacillus” is Latin for “almost a Bacillus”. While these species were historically grouped within the Bacillus genus (again, that murky bacterial classification issue), Paenibacillus have since been recognized as a distinct genus, and are gaining renewed attention due to their nitrogen-fixing and phosphate-solubilizing abilities, not to mention their ability to interact and degrade the and make available the beneficial polysaccharides that make up compounds such as chitin.

Strengths of certain strains include:

• Biological nitrogen fixation (BNF)

• Produces antimicrobial peptides and volatile organic compounds (VOCs)

• Stimulates root branching and elongation

• Stimulation of ISR in plants

• Solubilization of nutrients and organic matter like chitin

Example applications of certain strains:

In cereals, improves early-season vigor under nutrient-limited conditions; In tomatoes, reduces wilt incidence and enhances calcium uptake; Often co-inoculated with mycorrhizae for synergistic nutrient mobilization; and, in many crops, colonizes the root cortex, fixes atmospheric nitrogen, and produces growth-regulating hormones like IAA.

Just the tip of the rhizosphere…

I want to be clear, that although these are some of the most commonly used and well-known Bacillus species and provide a good list of some of the most valuable capabilities of Bacillus strains, it is by no means a comprehensive list of their capabilities in agriculture, nor is it even remotely a comprehensive list of the species that make an appearance in fields. If you are curious, here is an overview of some of the strains we discussed above and many, many more:

 

Table: Agricultural Applications of Bacillus Species

The one-strain mindset: Why are we still using Bacillus like a chemical?

Amazing, right? But I have to editorialize just a little: Given everything Bacillus can do—colonize roots, fix nitrogen, suppress pathogens, scavenge ROS, solubilize nutrients—it’s surprising how often agricultural products treat it as a single-function tool. But is this the best possible use case for microbes? I think you can guess how I feel. ;-)

The chemical mentality, useful for chemicals. Useful for microbes?

For decades, agricultural input design followed a chemical model, that is: one input, one outcome; a model in which a specific molecule targets a specific pathogen or symptom. Then, the approach has been, if it doesn’t work, change the dose—or add another product. Unfortunately, this mindset carried over to early biologicals and still widely endures today. Products were often built around a single strain—chosen for one trait, grown in pure culture and applied to fields to solve one problem: kill a pathogen, release some phosphorus, suppress a wilt. But biology doesn’t often work like that.

Microbial communities are not single notes—they're orchestras. And when we simplify them too far, we lose most of their richness. Most Bacillus products today are essentially used like chemicals which completely ignores the adaptive, synergistic potential we explored earlier. It feels a little like buying a Swiss Army knife and refusing to use anything but the corkscrew.

What we lose when we oversimplify

When we limit Bacillus to one function: We ignore functional redundancy (e.g. multiple strains that can boost calcium uptake, each in slightly different ways, so they can work better across different environments). We miss metabolic synergy (what transpires when multiple species or strains work together). We reduce resilience (a single genetic type of anything, is more vulnerable to failure under stress or field variability). And finally, we give up the chance for stacked performance—biocontrol and stress tolerance and nutrient solubilization all in one. Perhaps most ironically, we treat a living, responsive organism as if it were inert.

Multimodal microbes: Using Bacillus as a platform, not a pill

If the first wave of biologicals treated Bacillus like a biological pesticide, and the second treated it as a biostimulant, then the third wave—already emerging—is starting to see Bacillus as a biological platform. One that is intelligent, adaptive, and inherently multifunctional. In this next generation of tools, instead of asking: “What’s the one strain that solves this problem?” We are instead asking: What blend of Bacillus strains will support root growth, displace pathogens, buffer against salinity, and enhance nutrient uptake—and build in the adaptability so that these benefits manifest across local soil and climate variation? The bottom line is that a multi-strain product that is curated both for benefits and for functional redundancy should not only solve multiple issues at once, but be able to do it across many environments. While the technologies to support such complex, multi-benefit consortia are relatively new, these current and future biologicals won’t just be more resilient; because of their multiple uses, they’ll be more economical in the long term.

Closing the Loop

We started this story with an industrial powerhouse of a genus—Bacillus—used everywhere from soap to soy sauce to science labs. But in agriculture, we’ve only just begun to unlock its full capacity. Not by isolating it. But by embracing its complexity, its adaptability, and its ability to operate in concert both with other living organisms, but also in synergy with traditional agricultural inputs.

If we use Bacillus as a chemical, we’ll get certain results. But if we treat it like biology as well, —we’ll also get life. And the yield and productivity that comes with it.

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