Understanding How Microorganisms Thrive in Nature, Labs, and Asymmetry Products with Jordan Russell
Microbes have evolved to occupy nearly every conceivable ecological niche. Soil, aquatic environments, and plant- and animal-associated environments are among the most biologically active habitats, hosting dense and diverse microbial communities. Yet, life doesn’t stop there — bacteria and fungi have also been discovered living within deep rock pores, floating in the upper atmosphere, and even in manmade environments like sewage treatment facilities or acidic mining runoff.
To persist in such varied and often extreme settings, microorganisms must be adapted to handle wide-ranging nutrient availability, temperatures, pH levels, oxygen concentrations, salinity, barometric pressures, and radiation exposure. On top of that, microbes constantly face competition from other organisms, dealing with antimicrobial compounds, predation, and even immune responses from host organisms. These adaptations shape not only where microbes live, but how we grow them in the lab and use them in industry.
Cultivating Microbes in the Lab and at Scale
When researchers or product developers cultivate microorganisms, the conditions used are informed by the environments from which those microbes were originally isolated. Some microbes are generalists — they’ll grow easily in a variety of conditions — but others are highly specialized, and mimicking their natural habitat is key to getting them to grow. It’s important to note that despite the ubiquity of microbes in nature, only a tiny fraction of microbial species can currently be cultured in the lab. This is due to complex dependencies on environmental conditions or microbial partners that we don’t yet fully understand.
Ultimately, the goal in any lab or industrial culture is to optimize the conditions for consistent, high-yield, contaminant-free growth. By manipulating parameters such as nutrient composition, pH, agitation, and oxygen concentration in controlled settings, we can often grow pure cultures of bacteria and fungi to much higher densities than in nature. Selecting a culture medium that provides the required nutrients (sugars, amino acids, vitamins, minerals, etc), starting pH, and salt concentration is the first step towards growing a desired organism. Depending on the organism and purpose, researchers may use liquid broths (e.g., shaking flasks or fermenters) or solid media (e.g., agar plates). Some microorganisms grow better stationary on solid surfaces, while others prefer liquid mediaaerated by shaking.
Predictable and high yield microbial growth generally requires a pure culture of only the target organism. An undesired contaminant can drastically reduce the yield by consuming finite nutrients and releasing inhibitory compounds. To avoid this, culturing containers and media are sterilized – usually with an autoclave – before inoculation, ensuring the target organism is the only species present. Tailoring the growth media and conditions to favor the unique needs and resistances of the target organism is also a key means of biological selection. For instance, if the target organism is a thermophilic bacterium, incubating the culture at a high temperature will selectively exclude heat-sensitive contaminants. Other selective strategies include providing only a particular nutrient that the target organism is uniquely able to metabolize or including an antibiotic compound that the target is resistant to. It’s common to include antibacterial agents in fungal cultures to prevent faster-growing bacteria from outcompeting slower-growing fungi.
Sometimes, it is necessary to grow two or more organisms together in the same culture. This process, called co-culturing, is often used for organisms exhibiting some form of symbiosis, but still requires careful engineering to meet the unique needs of both organisms and achieve the desired yield ratio.
A growing microbial culture is not a static system. As microorganisms consume nutrients and replicate, they transform their environment – excreting waste products (often organic acids), producing heat, and depleting dissolved oxygen in liquid cultures. If unregulated, these changes can severely limit yield, especially at industrial scale volumes and densities. While shake flasks are adequate to grow microorganisms for many applications, bioreactors – vessels that tightly control temperature, pH, and oxygen – are essential for processes demanding the highest microbial output.
While most cultures are maintained at optimal conditions throughout the growth cycle, sometimes it is advantageous to introduce environmental changes at specific stages. Microbes have evolved response mechanisms to such changes in their environment, and sometimes those responses can be industrially useful. In a process called induction, microbes are grown under ideal conditions until they reach a target density, then exposed to changes such as temperature shock, pH alteration, or nutrient shift to trigger a desired response. This might include the production of high-value proteins or the formation of spores.
Many bacteria and fungi produce spores either as a part of their reproductive cycle or as a response to stress. These small, hardened, and metabolically dormant cell forms are more resistant to environmental stressors such as heat, desiccation, starvation, and radiation. Spores formed by organisms such as Bacillus are especially valuable in industrial applications due to their long shelf life and ability to survive harsh environments upon application.
Understanding how to grow microorganisms effectively in the lab is just the beginning. The next challenge is ensuring these organisms can perform reliably and competitively when introduced into real-world environments. At Asymmetry, we bridge this gap by translating controlled lab success into consistent field performance.
Optimized Growth for Real-World Applications at Asymmetry
Our team specializes in culturing and characterizing a wide range of bacteria and fungi, from familiar industrial and agricultural strains to novel environmental isolates. Our culture bank includes microbes from ecologically and agriculturally important genera such as Aspergillus, Bacillus, Penicillium, Rhizobium, Streptomyces, Trichoderma, and many others. These organisms have often co-evolved alongside plants and play beneficial roles – from improving nutrient uptake in roots to deterring pest and pathogens.
For our microbial products, we grow organisms like Bacillus and Trichoderma to high densities, tailoring the conditions to match the specific needs of each strain. These microbes are then formulated into products designed for soil or plant surface application where they must compete with complex native microbial communities. That’s why we don’t just grow the microbes — we engineer the delivery environment too.
Our formulations include carriers and supplemental nutrients specifically chosen to selectively help our strains establish and thrive where they land. We account for competitive inhibition and environmental stress — both of which influence microbial performance in the field.
Thanks to our team’s experience with challenging bacterial species and complex fungi, we have developed fine-tune growth protocols for both in-depth laboratory analysis and full-scale production of diverse microorganisms. We understand that what works in a petri dish may not translate directly to the field, and that’s where our scientific precision meets practical innovation.
Interested in how Asymmetry’s microbial solutions can enhance your agricultural or environmental systems? Contact us to learn more about our custom-formulated microbial products and how they’re designed to work with — not against — nature.
