Revolutionizing agriculture with microbial biopesticides

The world of agriculture is evolving, with farmers, researchers and manufacturers all looking for smarter and safer ways to protect crops and support a thriving crop microbiome without harming the environment. Enter biopesticides: nature’s answer to sustainable agriculture. Biopesticides – sometimes called biological pesticides – are a specific category of natural pest control products that includes microbial agents like bacteria, fungi and viruses, as well as biochemicals like plant extracts and plant-incorporated protectants. In this context, we focus on microbial biopesticides, which harness beneficial microbes to target pests with precision.

As the demand for organic, residue-free produce rises and concerns about the impact of chemical pesticides grow, microbial biopesticides are stepping into the spotlight and making a remarkable impact on both commercial agriculture and the environment. They are also being increasingly used as natural pest control for garden settings, helping home gardeners protect their plants in a safe, eco-friendly way without endangering children, pets or beneficial insects.

A growing need for natural crop protection and bio pest control

For decades, farmers have relied on chemical pesticides to protect their crops against pest damage. But we now know this approach has been degrading the soil, contaminating our water sources and threatening beneficial insects like bees. These days, there is a growing trend toward sustainable agriculture, and biopesticides are stepping in and offering effective, eco-friendly alternatives to chemical pesticides that protect crops and support the environment

One of the advantages of biopesticides is that, unlike their chemical counterparts, biopesticides control pests in a targeted way. This selectivity makes them safer for crops and spares vital insect pollinators as well as the microorganisms that comprise the crop microbiome. Some biopesticides also form symbiotic relationships with plants and boost their natural defenses and resiliency.

While the upfront investment can be higher with biopesticides, they often help farmers reduce costs in the long run. As pests have become resistant to treatment with traditional chemical pesticides, the cost of control has skyrocketed, because multiple, rotating treatments are needed to remain effective. Biopesticides often work through multiple modes of action, so pests are less likely become resistant. For farmers committed to sustainable agriculture, the use of bio pesticides in organic farming offers an advantage.

The specificity of microbial pesticides: How they protect plants

The defining feature of biopesticides is specificity. Unlike synthetic chemicals, biopesticides are highly targeted, attacking specific pests while minimizing harm to non-target species. This ensures that beneficial insects and microorganisms in the environment remain intact – a crucial advantage in today’s agricultural landscape.

Biopesticides take advantage of the natural defenses of organisms like bacteria, fungi, viruses and even other plants to protect crops. In their natural environments, these organisms often combat pests or competitors using highly specialized mechanisms. Biopesticide products adapt and amplify these processes, such as producing toxins or disrupting pest lifecycles, to effectively target agricultural pests.

For example, one commonly used biopesticide is Bacillus thuringiensis (Bt), a bacterium that produces Cry proteins that are toxic to the larvae of some insect pests. When they eat plants that have been treated with Bt pesticide, the larvae ingest these toxins, which paralyze their digestive systems and ultimately kill them. A key advantage of Bt is its specificity: It only affects the insects that ingest it, leaving beneficial organisms unharmed.

Biopesticides are natural defenders, each with its own unique mode of action. Whether they’re producing toxins, outcompeting harmful microbes or directly parasitizing pests, these organisms work with specificity and efficiency.

Toxin-producing bacterial biopesticides

Some microbes can produce powerful toxins that specifically target and kill pests or pathogens, playing a significant role in biocontrol strategies. Here are some examples of toxin-producing bacteria and the mechanisms by which they function.

• Bacillus thuringiensis (Bt): These bacteria are widely used as natural pest control for garden environments, offering an eco-friendly solution to managing common insect pests without harming beneficial organisms. B. thuringiensis produces toxic Cry proteins, which paralyze the digestive systems of insect larvae, including caterpillars and beetle grubs, eventually killing them.
• Bacillus pumilus: These bacteria produce antifungal compounds that stop soilborne pathogens in their tracks. It works particularly well against fungi like Fusarium and Rhizoctonia. Related species like Bacillus subtilis, Bacillus amyloliquefaciens and Bacillus licheniformis also produce toxins that defend against various fungal and bacterial pathogens.
• Cytobacillus firmus: These bacteria produce cytobacillin toxins that disrupt the life cycles of harmful nematodes by inhibiting their growth, impairing movement and causing cellular damage. This mode of action protects plant roots while preserving beneficial nematodes that contribute to good soil health.
• Lysinibacillus sphaericus: This bacterium produces antifungal compounds that suppress the growth of Rhizoctonia solani, the pathogen responsible for sheath blight in rice. By targeting the fungus directly, it helps reduce the severity of this damaging disease. 
• Paenibacillus popilliae and Paenibacillus lentimorbus: These bacteria are effective biocontrol agents against beetle larvae, particularly scarab beetles like Japanese beetles (Popillia japonica) and May/June beetles (Phyllophaga species). They infect and kill the larvae by releasing toxins that disrupt internal processes, preventing the grubs from damaging plant roots. The spores of these bacteria can persist in the soil, providing long-term protection against beetle infestations and helping to safeguard crops and ornamental plants from root-feeding pests.

Biological competitors: Outcompeting pathogenic organisms

Competition for nutrients and space among the microorganisms living in the soil is important for keeping plants healthy and protecting them from harmful pathogens. Beneficial microbes like bacteria and fungi outcompete pathogens by reducing their access to essential resources and keeping them from getting established. The result is a balanced soil ecosystem that favors organisms that support plants over those that cause disease.

• Pseudomonas fluorescens: These beneficial bacteria thrive in the rhizosphere, the region of soil surrounding plant roots, where they compete with harmful microbes for nutrients and space. By doing so, they prevent disease and enhance plant health by boosting nutrient uptake. Other related species, such as Pseudomonas chlororaphis and Pseudomonas syringae, also contribute to bio pest control and plant growth by producing antifungal compounds and growth-promoting substances.
• Pantoea agglomerans: This bacterial species is able to outcompete harmful bacteria on plant surfaces and prevent diseases from taking root, particularly in fruits like apples and pears. For example, its antibiotic compounds inhibit Erwinia amylovora, the causative agent of fire blight, and by occupying space and resources that would otherwise support pathogen growth.
• Streptomyces griseoviridis and Streptomyces lydicus: These soil-dwelling bacteria are experts at colonizing plant roots, where they outcompete pathogens and produce natural antifungals to stop fungi like Fusarium, Pythium, Rhizoctonia and Phytophthora in their tracks. They’re particularly effective at suppressing Fusarium wilt, damping-off, root rot and other soilborne diseases that can devastate root systems.

Fungal biopesticides that target and suppress pathogens

Some microbes have evolved mechanisms that let them directly target and neutralize specific pests or pathogens by parasitizing them or inhibiting their growth.  

• Beauveria bassiana: This fungus infects insect pests by attaching to their exoskeletons, penetrating their bodies and then slowly killing them from within. It’s especially effective against soft-bodied insects like aphids and whiteflies.
• Metarhizium anisopliae: This fungal pathogen targets insects like grasshoppers and termites and kills them by breaking down their exoskeletons.
• Clonostachys rosea: This fungus is a mycoparasite that targets plant pathogens such as Botrytis cinerea and Sclerotinia sclerotiorum, which cause destructive mold diseases. It is able to attach to the hyphae of the target fungus, penetrate the cell wall and grow inside, where it secretes enzymes that degrade the cell wall and eventually consumes the fungal contents for nutrients.
•  Ampelomyces quisqualis: This parasitic fungus specializes in controlling powdery mildew by infecting and breaking down the mildew colonies and preventing their spread.
• Cordyceps fumosorosea: This fungus parasitizes insect pests like whiteflies and kills them by penetrating their bodies and growing inside them.

Microbes to control nematodes

Nematodes are microscopic roundworms that affect the soil ecosystem in several ways. Some types of nematodes break down organic matter and improve the soil health, while others can be used as natural biopesticides. However, some species are harmful, feeding on plant roots, stunting plant growth and reducing crop yields. Certain fungi and bacteria have developed strategies to target these harmful nematodes: They parasitize nematode eggs and larvae, penetrate their bodies and disrupt their life cycles, effectively reducing nematode populations and protecting crops.

• Purpureocillium lilacinum: This fungus parasitizes the eggs and larvae of various nematodes, such as root-knot nematodes (Meloidogyne species), cyst nematodes (Heterodera and Globodera species) and reniform nematodes (Rotylenchulus reniformis). It penetrates the nematode's protective layers, preventing reproduction and limiting their ability to damage plant roots.
• Pasteuria nishizawae: A nematode-specific bacterium that parasitizes root-knot nematodes by attaching to their cuticle, eventually penetrating and inhibiting their ability to reproduce. This can help protect crops like tomatoes and soybeans from root damage.

Fungal pathogen suppressors

Fungal pathogens can wreak havoc on crops, causing problems like root rot and wilting diseases, which are difficult to manage once they get established. However, other beneficial fungi can be used as natural biopesticides that defend against the harmful organisms. Incorporating beneficial fungi into integrated pest management strategies can help growers reduce their reliance on synthetic fungicides and support a more sustainable approach to crop protection.

• Trichoderma asperellum, Trichoderma atroviride, Trichoderma gamsii, Trichoderma hamatum, Trichoderma harzianum, Trichoderma polysporum, Trichoderma virens, and Trichoderma viride: These beneficial fungi are useful in biocontrol because they colonize plant roots and break down the cell walls of disease-causing fungi like Fusarium (Fusarium wilt), Rhizoctonia solani (root rot), Pythium (damping-off) and Phytophthora (root and stem rot).
• Aureobasidium pullulans: This yeast-like fungus colonizes plant surfaces, where it produces antifungal compounds such as pullulan and siderophores that prevent postharvest diseases in fruits.
• Chondrostereum purpureum: This fungal pathogen of hardwood trees is used in forestry management to control the regrowth of undesirable tree species, such as birch and maple. It infects freshly cut stumps by colonizing the wood and causing a disease called silver leaf, which disrupts the tree's vascular system and prevents sprouting.

Other biopesticide powerhouses

Several other biopesticides offer unique modes of action that make them valuable tools in pest and disease management. Each of these organisms brings a distinct approach to controlling pests and pathogens, enhancing the arsenal of natural defenses available for sustainable agriculture.

• Chromobacterium subtsugae: This insecticidal bacterium targets caterpillars, beetles and more, making it a broad-spectrum tool for pest control. It produces a range of bioactive compounds, including violacein and cyanogenic compounds, which disrupt the metabolism of insect pests and deter feeding.
• Metschnikowia pulcherrima: This yeast is particularly good at controlling fungal diseases in fruit crops, especially after harvest. It produces pulcherriminic acid, which chelates iron from the environment, making this essential nutrient unavailable to competing fungal pathogens.
• Pseudozyma flocculosa: This fungal species is used to control powdery mildew, particularly in crops like grapes and cucumbers. It produces antifungal glycolipids, such as flocculosin, which directly inhibit the growth of mildew spores and reduce the spread of infection.

Biopesticides hold tremendous promise for sustainable agriculture, but their success isn’t always guaranteed. Farmers, researchers and manufacturers all face a variety of challenges. From maintaining product consistency to combating pest resistance and applying biopesticides at just the right time, overcoming these hurdles is key to ensuring biopesticides live up to their promise.

Making sure every application of biological pesticides is consistent and reliable

When it comes to biopesticides, consistency is everything, and manufacturers rely on stringent quality control to create products that deliver the same level of efficacy across different batches. Microbial biopesticides are living organisms, which means their effectiveness can vary based on factors like production conditions, storage and even how they’re applied in the field.

Imagine that a farmer applies a biopesticide they’ve used before, expecting it to work as in the past. If the new batch contains slight variations in microbial concentrations or perhaps some form of contamination, it could underperform. This type of inconsistency can affect the crop yield and also the farmer’s trust in the product.

Maintaining stable microbial populations and the ideal levels of active organisms from batch to batch requires rigorous quality control. Continuous monitoring and precision throughout production are essential, and without it, even the most promising biopesticides can disappoint in the field.

Staying one step ahead in the fight against pest resistance

Pests and pathogens are resilient, and over time – just like with chemical pesticides – they can become resistant to biopesticides. Resistance develops when a small number of pests survive biopesticide applications and pass on their resistant traits to the next generation. Eventually, entire populations will be less affected by the biopesticide, making it less effective over time.

Insects, fungi and bacteria are constantly evolving, and without the ability to track these changes, manufacturers and researchers are left playing catch-up. This presents a two-fold challenge: first, how can researchers track genetic changes that lead to resistance in pest populations? And second, how can manufacturers adapt their products quickly enough to outpace these evolving pests?

Early detection of crop pests in the field is critical to success

In farming, timing is everything, and this is also the case with biopesticides: Applying them too early or too late can drastically reduce their effectiveness.  While some farmers rely on preventative pesticide applications, this approach can be costly and not necessarily in line with sustainable farming principles. Knowing when to apply a biopesticide is crucial for getting the best results, but how do we determine when that right moment is?

Early detection is key. Traditional pest detection methods like visual inspection or trap monitoring often miss the early stages of a pest’s life cycle. And many pests and pathogens can cause considerable damage before they’re even visible to the naked eye. Once a farmer realizes there is a problem, it could already be too late to act.

Biopesticides must be applied at just the right time, when pest levels start to increase, but before they have increased so much to cause irreversible damage. Without a clear way to detect pests early, even the best biopesticides may not perform to their full potential.

Precision with dPCR: Absolute quantification of beneficial microbes

With dPCR, manufacturers can precisely quantify microbial concentrations down to a single DNA copy, ensuring that each batch contains the correct amounts of beneficial microbes. This level of precision is critical for maintaining consistent product performance: insufficient microbial concentrations may reduce efficacy, while excessive concentrations could lead to over-application, wasting resources or potentially disrupting the crop ecosystem.

By providing such high accuracy in microbial quantification, dPCR supports quality control and regulatory compliance and helps manufacturers produce microbial biopesticides that fit seamlessly into integrated pest management programs.

Profiling microbial communities and detecting contaminants with NGS

One key application of NGS is profiling microbial communities in soil or around crops. By analyzing these communities, researchers can uncover valuable insights into how beneficial microbes interact with pests, pathogens and their environment. This information enables more targeted pest control strategies tailored to specific environmental conditions, enhancing both efficacy and sustainability.

NGS also offers a powerful solution for detecting contaminants or unwanted genetic changes in biopesticide cultures. By sequencing microbial populations, manufacturers can identify potential issues, such as contamination or genetic drift, early in the production process. While genetic drift is generally less of a concern under controlled manufacturing conditions, NGS provides an extra layer of assurance for maintaining the integrity of microbial strains.

Combining NGS and dPCR to address resistance challenges

The combination of NGS and dPCR provides a comprehensive approach to tackling resistance development in crop pest populations. NGS enables researchers to sequence pest genomes and monitor genetic changes that signal emerging resistance to biopesticides. This information allows manufacturers to proactively adjust formulations to target resistant strains before they become widespread.

dPCR complements this application, by quantifying resistant pest populations in real time, providing actionable data for decision-making. Together, these technologies empower researchers and manufacturers to respond swiftly to resistance challenges, protecting crops and ensuring the long-term viability of pest control strategies.