Written by S. Ryaan Ligon, Research Associate II, and Thomas Williams PhD, Senior Director, Microbiology and Bioinformatics
Microbial discovery in agriculture has traditionally relied on large-scale screening approaches to identify beneficial organisms. While high-throughput screening methods allow for a diverse set of potential microbial candidates, these screening methods are time-consuming, costly, and do not consistently predict field performance. As expectations for biological products continue to increase, this limitation has become more pronounced. Growers and partners require consistent, reliable performance across variable field environments, increasing the focus and the challenge of discovery. It is no longer sufficient to identify microbes with beneficial traits. It is necessary to select organisms that can consistently function within complex plant and soil systems.
The Challenge: How best to discover beneficial microorganisms that perform in the field?
At BioConsortia, this challenge has driven the development of an integrated discovery approach that combines selection under relevant conditions, in-planta validation, and genetic insight to improve the predictability of performance and reduce the gap between early-stage discovery and field outcomes. To meet this challenge, we utilize a suite of in-house microbial genetic and phenotypic screening assays to efficiently, accurately, and precisely predict optimal microbial products.
This article introduces our integrated discovery approach at a high level, outlining how each component contributes to improving the predictability of microbial performance. Subsequent articles will examine these components in greater detail, as well as the broader systems they enable, including their role in improving development efficiency, supporting more reliable field outcomes, and advancing the application of biologicals in modern agricultural systems.
AMS™ Pipeline
Figure 1: BioConsortia's Advanced Microbial Selection (AMS™) pipeline allows us to preferentially select the most robust, beneficial plant-associated microbes from diverse soil environments.
The Advanced Microbial Selection (AMS™) science employed at BioConsortia allows us to selectively enrich spore-forming bacteria from soil that support crop yield and health.
How it works:
The AMS™ process is an iterative approach that evolves the soil microbiome of a given crop by growing that crop in the presence or absence of an abiotic or biotic stress. We collect diverse soil samples from both agricultural lands and from other environments. Into these soils, we plant crop seeds. Depending on our discovery target, we may introduce a stressor, like nitrogen shortage. Some plants thrive; many plants flounder. When a plant displays a beneficial phenotype, growing healthy and vigorous under stress, it is telling us something: it has recruited a community of beneficial microbes that gave it an advantage over the plants that struggled. That microbiome is the reason it thrived, so it is exactly what we want to capture. These high‑performing, plant‑associated microbes are then isolated and incorporated into our discovery library for further evaluation.
Why it matters:
AMS™ ensures that every isolate in our library has already demonstrated a mutually beneficial relationship with its target crop. This approach increases biological relevance early in discovery and improves the likelihood of consistent field performance. AMS™ is also highly flexible, enabling discovery across multiple crops, stress conditions, and production environments. Over the past decade, BioConsortia has continuously refined this platform to build a diverse, high-quality microbial portfolio designed for real agricultural systems.
GenExpress™ and GenePro™
At BioConsortia, we have a best-in-class bioinformatics and synthetic biology team that supercharges our discovery pipeline. Our scientists design broadly applicable transformation protocols to deliver DNA to a wide range of bacteria at high success rates. Meanwhile, bioinformatic analysis of the whole genome sequences of our strain library allows us to locate genes that confer beneficial stress resistance, produce beneficial metabolites, and confirm candidate strains comply with global regulatory standards.
Modifying our bacterial strains begins with our gene delivery pipeline, GenExpress™. We have optimized our proprietary protocols, known as GenExpress™, to work with a wide range of environmental Gram-negative bacteria and the typically recalcitrant Gram-positive bacteria, giving us a uniquely high success rate moving DNA into wild-type microbes. For example, we’ve used GenExpress™ to generate a large number of fluorescently tagged strains that are employed in our discovery research to observe plant colonization, a critical success factor in microbial seed treatment products, early in our discovery pipeline.
Our gene editing platform, GenePro™, allows us to leverage gene delivery through GenExpress™ to create targeted, seamless edits in our strains, allowing us to design wild type microorganisms with enhanced beneficial properties. As the agricultural markets move towards reducing reliance on chemical additives, the ability to increase performance in a microbial strain for a target biochemical system is becoming increasingly valuable. For example, some microbes have long been understood to fix nitrogen in some crops, but this is a metabolically expensive endeavor. Since it is energy-intensive, microbes have developed a strong regulatory system to ensure they aren’t “wasting” energy by producing nitrogen when it isn’t needed by the cell. Our GenePro™ method allows us to determine which genes most directly regulate that pathway and ensure they can’t “turn off” the nitrogen production, ultimately making more nitrogen available to crops. Additionally, GenePro™ allows us to insert and combine multiple genes into the target microbe’s genome. In doing this, we are able to boost the performance of our microbes above their wild type capabilities.
By combining these tools with our AMS™ pipeline and acetylene reduction (ARA) assays, we can confidently determine which strains, and which genes are most beneficial to the plant.
Conclusion
BioConsortia’s integrated approach shifts microbial discovery from a broad screening exercise to a more structured and predictive system. By combining selection under relevant conditions, in-planta validation, and genetic insight, it becomes possible to more efficiently identify microbes with a higher likelihood of consistent field performance. As the biologicals sector continues to mature, the ability to translate discovery into reliable outcomes will remain a key differentiator. Discovery is no longer defined by the number of candidates generated, but by the consistency and scalability of the results delivered in real agricultural systems. Subsequent articles will examine components of this approach in greater detail, as well as the broader systems they enable, with a focus on how BioConsortia supports more reliable and scalable biological solutions.
ABOUT BIOCONSORTIA
BioConsortia, Inc. develops transformative microbial products in agriculture, pioneering the use of directed selection and advanced genomics techniques within microbial communities. BioConsortia’s microbial products deliver superior efficacy, higher consistency, and easier grower adoption because of their focus on microbes that deliver extended shelf- and on-seed life. The company’s rich biological pipeline includes nitrogen fixation microbes to replace or reduce synthetic nitrogen fertilizers; nutrient use efficiency and biostimulants to increase crop yields; and bionematicides and biofungicides to protect crops from pests and diseases. BioConsortia’s patented Advanced Microbial Selection (AMS) process and cutting-edge GenePro platform enable the company to predict, design, and unleash the natural power of microbes.
For further information, please contact info@bioconsortia.com.