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.

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.