Microbial fermentation: from strain to product

November 10, 2023

In the world of science and industry, a silent revolution is brewing, one driven by the power of tiny, seemingly inconspicuous organisms. Microbial fermentation, the age-old process by which microbes are cultivated and utilized in a myriad of ways, has emerged as a cornerstone of modern biotechnology. It is a powerful tool opening a rich source of novel, more sustainable solutions for numerous industries. One of the prime industries ready for disruption through advancements in fermentation is agriculture, where the demand for more sustainable inputs is already surging.

Living microbes as ag input products

Farmers across the globe are witnessing an evolution in agricultural practices, where microbes are harnessed to improve crop yields, enhance soil health, and control pests. Living microbes, previously often overlooked in the grand tapestry of agriculture, are now stepping into the spotlight as not just tools, but as prized products themselves. The increasing importance of living microbes as agricultural inputs is changing the way we approach crop production, paving the road to a more sustainable food production. So, what are the key microbial products at the forefront of this change?


Microbial biopesticides encompass a diverse group of microbes that share the ability to control agricultural pests and pathogens. The five key modes of action they employ are competition for space and nutrients, parasitism, predation, induced resistance of the host plant, and antibiosis – the production of secondary metabolites that limit the growth of other organisms. The most common examples of these microbes include:

  • Bacillus thuringiensis (Bt) – a soilborne bacterium that produces insecticidal proteins effective against many economically important agricultural pests. Bt products are among the most widespread biopesticides globally.
  • Agrobacterium radiobacter (strains K84 & K1026) – another soilborne bacterium, effective against crown gall disease in stone fruits, nuts and ornamental plants.
  • Trichoderma spp. – natural fungal antagonists of various plant pathogens, including fungi and nematodes. They inhibit the growth and activity of these pathogens through mechanisms like mycoparasitism, competition for space and food, and production of antifungal substances.
  • Beauveria bassiana – a soilborne fungus and an effective natural insecticide that acts as a parasite of a wide range of significant insect pests. Its isolates display high host specificity, ensuring that non-target and beneficial insects are not harmed.
  • Metarhizium spp. – akin to B. bassiana, they are fungal insect pathogens that target a wide range of economically relevant crop pests.


Biostimulants are agri inputs that stimulate natural processes to enhance/benefit nutrient uptake, nutrient efficiency, abiotic stress tolerance, and crop quality, independent of their nutrient content [1]. Beneficial bacteria, fungi, or organic compounds can qualify as biostimulants. To mention a few, here some of the commercially most relevant examples:

  • Rhizobium and Bradyrhizobium spp. – Gram-negative soil bacteria that establish symbiotic relationships with plants, forming structures on their roots that facilitate nitrogen fixation. They transform atmospheric nitrogen (N2) into plant-available ammonia (NH3), leading to increased crop yield and improved nutrient utilization.
  • Azospirillum spp. – similar to previous genera, Azospirillum species are nitrogen-fixing bacteria. However, they do not form symbiotic relationships with plants, but rather associations that have greater impact in promoting plant growth through the production of growth hormones (e.g. auxins). Their activity enhances plant growth, nutrient utilization and uptake, and stress resistance.
  • Pseudomonas spp. – bacteria known for their versatile metabolic capabilities that offer wide-ranging agricultural and environmental services: suppression of soil and foliar pathogens, nutrient cycling in the soil, production of substances that promote plant growth and stress resistance, and detoxification of soil pollutants.
  • Mycorrhizal fungi – they form symbiotic relationships with plant roots, enhancing nutrient uptake, particularly phosphorus and micronutrients. They improve soil fertility both structurally and chemically, which leads to improved nutrient cycling and water availability. However, it is important to note that Mycorrhizal fungi can establish relationships with many different plants, but they will only deliver the benefits to plant species they are compatible with. Matching the right strain with the right plant is essential!

(Don’t miss our article on the benefits and challenges of Arbuscular Mycorrhizal Fungi: https://evologic.at/BenefitsAndChallengesOfAMF/)

  • Saccharomyces cerevisiae – a yeast with a very long history in the production of fermented foods, today is also used for producing biostimulants. In addition to these applications, S. cerevisiae can ferment crop residues, converting them into nutrient-rich organic fertilizers.

Note: Since we are talking about living organisms that perform multiple functions, there are overlaps between these three groups. And, of course, some microbes offer services beyond these specific product groups, offering a broader ecological and applicative value. What this practically means is that even though a microbial strain or a product may be designated as, for example, a biostimulant, it can also deliver other effects like suppression of weeds and pathogens, or sequestering carbon (in the case of arbuscular mycorrhizal fungi).

From strain to product

Microbes have their wants and needs, as all living things do. Meeting those needs, and adequately transforming microbes into effective, safe and stable products through fermentation and formulation development is quite a challenge for several reasons:


Working with living organisms always comes with a chance that other, undesired microbes find a way into the end product. These contaminations negatively affect reproducibility and product performance, and in the worst case, they are harmful to crops. Maintaining aseptic working conditions and systematic monitoring are pivotal in reducing contamination risks, as well as in achieving desired product purity and bioactive potential.

Regulatory compliance

Getting any microbial product from the production facility to the market includes meeting certain regulatory requirements and quality standards. Conducting trials and gathering data for the product registration process often requires considerable financial investments, and extensive documentation and validation processes that differ between countries.

Cost of goods

The oldest conundrum for any manufacturing process. Delivering effective, quality products is the primary goal in microbial manufacturing, but the end result is always a compromise between product quality and the cost of goods. The prime example of this type of technology is freeze-drying – while it is certainly one of the best and most sensitive drying approaches, the current costs make its use on a wider scale almost impossible. Industries with lower price points, like agriculture, are highly affected by the cost of goods, leaving ag-input producers with limited technological opportunities.

Fermentation development

Microbial fermentation development represents a critical step in the production of microbial products, as it enables the mass production of beneficial microbes, turning them into potent tools for sustainable agriculture. The choice of the proper fermentation process and its development dictates the success of the entire production endeavor.

Guided by data gathered during the screening trials, microbial fermentation engineers fine-tune the conditions within bioreactors to yield as much microbial biomass with optimal bioactive properties as possible. Since microbes are highly variable when it comes to favorable growth conditions and secondary metabolite production, the fine-tuning process requires engineering savviness of fermentation process developers. The three key aspects they are focused on include:

  • Medium development – Medium development is a fundamental step in microbial fermentation development, as the media provides the nutrients and structure for microbial growth. Properly designed media is essential for achieving the desired product quality and cost-effectiveness of the production process.
  • Bioreactor design – Bioreactors are the places where fermentation magic happens, providing a controlled environment and favorable conditions for microbial growth. Looking from the outside, all bioreactors are pretty much the same – stainless steel or glass cylindric tanks that come in various sizes. However, the design and the properties of their components can vary significantly, which impacts productivity, scalability, control, and reproducibility of the fermentation process.
  • Growth conditions – Meeting the growing requirements of the selected microbes and maintaining them during the entire production process in a consistent, reproducible, and resource-efficient way, is vital for successful and cost-effective production of microbial agricultural inputs. However, microbial species can have quite different growing requirements and conditions in which they produce desired secondary metabolites. This is why discovering optimal settings for microbial fermentation takes quite a lot of engineering savviness, and has a central role in bioprocess control.

Formulation development

Microbial product quality is largely defined by fermentation, however, microbes need to be stabilized to survive the journey from bioreactor to the field. Formulation development aims to bridge this gap and transform living organisms into user-friendly, high-performance products. However, turning fermentation broth into a stable, safe and effective product can be quite complex and expensive. The development of efficient formulation process is crucial for yielding concentrated, pure products that retain biological activity over time and are easily packed, stored, distributed, and applied. The choice of appropriate formulation method is a paramount step in product delivery, as it directly affects product performance and adoption.


The path from strain to product is rocky and curvy, full of engineering challenges, strict trials and market limitations. However, overcoming those challenges unlocks the vast power of microbes – nature’s greatest chemical engineers, opening up a whole new world of solutions to some of the greatest challenges in modern food production.


[1] EBIC

Let's get in touch!
Please enable JavaScript in your browser to complete this form.