Microbial Teamwork: Ecological Principles for Next-Generation Agricultural Solutions
At least once, we have read those exciting headlines about miracle microbes that will revolutionize agriculture overnight. "New Bacteria Removes The Need for Fertilizer!" or "Microscopic Fungi Could End Crop Disease Forever!"
And we all had the temptation to get swept up in the enthusiasm. However, deep down, you know that nature is much more complex than that.
One thing is true: microorganisms are essential for soil health and ecosystem functioning. Microbial communities take part in many processes, like nutrient cycling and pest protection. Their crucial functions, coupled with their cost-effectiveness and sustainability, make them a very promising market for nature-based solutions. This explains why microbial-based tools are attracting the attention of investors and researchers worldwide and beginning to challenge traditional fertilizer and pesticide markets.
But it is precisely in its promising functions that we can find a clue to the challenges of this industry. Microbial communities are included in complex ecosystems where multiple interactions are happening, while several environmental variables fluctuate! Many of these interactions are still unknown, making microbes-based products far from being mastered.
Still, progress is happening. One of the most exciting developments in this field is the creation of "SynComs" or synthetic communities. Instead of applying a single-microbe product, scientists are designing formulations with multiple microorganisms that can perform different functions and improve colonization in a new environment.
So before you lose all hope, let’s take a closer look at the fascinating world of microbial applications — and why they’re both full of potential and still challenging!
Why Aren't Microbial Products Perfect Yet?
The main challenge for these products is the difficulty of replicating laboratory results into complex agricultural settings. The reason behind is a lack of deep understanding of how microbial communities interact within them and with other components of the ecosystem. Though it may sound generic, this idea includes many levels of knowledge that still need to be understood. Some of these are:
Plant-microorganism interaction. Microbial inoculates are tested in up to a few plant species. However, the interaction with microorganisms is highly dependent on the plant. Upon different environmental factors or developmental stages (flowering, fruiting…), plants produce compounds that are realised to the soil, affecting the microbial community interacting with them. The mechanisms underlying these interactions, what compounds are involved and how microbes respond to them, are still far from being fully understood.
Competition with native microbial communities. When a SynCom is applied to the plant or soil, microorganisms need to compete with a complex and established microbial community. Though ecological interactions have been widely studied for other organisms, less is known about their functioning in microbial communities.
Microbe response to soil type and environmental factors. Soil gives microorganisms an environment where they can thrive. Soil characteristics (porosity, composition, pH…) determine how water and nutrients, the main building blocks for microbial life, are dispersed. But soil is not a closed setting, it is exposed to multiple environmental variables that can affect its composition, and thus, the microorganisms’ success. Though multiple research has been carried out on this topic, integrating this on a community level (different organisms are differently affected by these variables) is still challenging.
As you can imagine, it is difficult to test these variables before launching a product to the market, so the success of microbial products relies far too often on trial and error. But what if we could move beyond trial and error? This is where established scientific frameworks can help us navigate the complexity.
How Ecology and Evolution Can Help
When dealing with complex topics, one of the best tools we humans have are theories. Theories give us a structure and starting point to study intricate systems. And this is exactly what the authors of a recent review published in The New Phytologist discuss. Their idea is to integrate the knowledge of ecological and evolutionary theories already studied in other organisms into microbial communities. By understanding how microorganisms interact with each other and their environment (ecology) and how they have adapted to their environment (evolution), we can design SynComs that establish themselves successfully and function as expected.
Follow me in understanding some key theories that could transform our approach to microorganisms-based products!
Biodiversity Powers Performance: The Biodiversity-Ecosystem Function Theory
The Biodiversity-Ecosystem Function (BEF) theory suggests that biodiversity influences how an ecosystem functions. The assumption is that increased diversity in a community improves ecosystem functioning and stability. While this has been extensively studied in plants, research on microbial communities is catching up and showing similar benefits.
But what exactly is "ecosystem functioning"? It includes all processes involved in maintaining an ecosystem and helping it respond to changes. Some of these processes could be nutrient cycling (where nutrients are used, transformed and used by different organisms) or plants converting sunlight and inorganic matter into biological tissue.
Biodiversity can be involved in ecosystem functioning in various ways. If a community has a high diversity of organisms, a few of them likely perform the same functions. When a stressful situation happens, such as a drought or flooding, the species that survive can replace a vulnerable one in its ecological role. This is what ecologists call complementary effects. Another way biodiversity helps ecosystem functioning is through selection effects. The idea is pretty simple: with more species in your community, there is a higher likelihood of having a microbe with a crucial role in plant health. By increasing biodiversity, you’re more likely to accidentally “select” a species that turns out to be especially beneficial.
But how does this apply to microbial inoculation? Well, this is one of the ideas behind using SynComs instead of single-microbe products. Introducing a variety of microorganisms in our product can make it more stable to changes, as different microorganisms can perform a similar function (complementary effects) or even have unexpected benefits for plant health (selection effects).
So let’s randomly increase the biodiversity of our Syncoms to make them more resilient, right? Unfortunately, it’s not that simple: we need to understand the functions of the members and the proportion of them.
Including many different microbes can look like increasing biodiversity, but if they are closely related, the functional range of SynCom can be limited.
Moreover, it’s important to understand the process we want to tackle. In some cases, a few specialized microbes might be enough to drive a specific function like denitrification, while other processes, like organic matter decomposition, require more diverse microbial cooperation.
Lastly, the proportion of the individuals is also a key component of the community. A community where all microbes are equally abundant may function differently than one where key species dominate. These design choices—how many species to include, how functionally different they are, and in what proportion—are practical extensions of the biodiversity-ecosystem function theory, and are essential for developing more reliable, resilient microbial tools for agriculture.
Will a SynCom Thrive? Metacommunity Theory
We have learned about BEF theory and how to design a microbial community in terms of function. But one key aspect is still to be answered, will a syncom successfully establish itself in the environment? It needs to survive interactions with the much larger existing community in soil or plants!
This issue can be seen from the point of view of the metacommunity theory. This theory helps predict how community composition changes over time by considering two main factors:
Immigration ability. How easily can SynCom members spread and colonize? This mainly depends on the mobility and growth rate of SynCom members.
Local adaptation. Can SynCom members compete with the local community that's already adapted to the ecosystem? Here comes into play the composition and functions of the local community and the interactions happening between them, SynCom members, plants and other members of the ecosystem.
Understanding these dynamics is crucial for predicting whether a SynCom will establish successfully and deliver the intended benefits.
Theory in action: designing better SynComs
The BEF and metacommunity theories give us a strong conceptual foundation—but how do we translate these ideas into actual SynComs that work in real fields, with real plants, and under real environmental conditions?
To do this, we need to look at additional ecological principles and emerging research that shed light on how SynComs functions in practice:
The Role of Dominant Taxa. Research shows that most ecosystems are dominated by just a few hundred microbial groups. These can translate into superior colonization abilities, competition with other microorganisms and even multiple interactions, giving structure to the ecosystem. Understanding these microorganisms and how to select them could highly benefit the efficacy of SynComs.
Home-based advantage. If the environment and local communities significantly impact SynCom's effectiveness, why not design them specifically for the local environment? For instance, fast-growing microorganisms would hardly establish in soils poor in nutrients.
Plant-Microbe coevolution. Plants and microbes have coevolved over millions of years, forming context-dependent relationships. A microbe beneficial in one environment may be harmful in another. For instance, some microorganisms help plants access some nutrients, like nitrogen or phosphorus, getting carbon sources from the plant in exchange. If the soil is rich in nutrients, microbes may still demand carbon without providing benefits to the plant. Timing also matters—plant growth stages affect metabolite production, which influences microbial interactions. Applying SynComs at the right moment ensures microbes help when plants need them most. These interactions are complex and not yet fully understood, highlighting the need for more research to optimize SynCom design and application in real-world conditions.
Colonization. Although the establishment of a SynCom is important for it to work, research has shown that SynComs may not need to persist in the microbiome to have a long-term effect. This would reduce the potential long-term effects on local biodiversity while still providing the desired benefits.
Ecological networks. There is an increasing interest in studying the interaction of the members of a community. This tool allows researchers to simplify the study into groups of members with a certain type of interaction. The potential applications ranges from community design and tracking changes in soil microbiomes in response to the addition of SynComs. However, this line of research is still very much in its infancy.
Final Thoughts
After so much information, I hope you agree with me that microbial-based products represent a fascinating field in sustainable agriculture. While we're still far from perfectly designing microbial solutions, combining ecological and evolutionary perspectives with cutting-edge molecular techniques can help us advance our understanding. The journey from simplistic "miracle microbe" narratives to sophisticated ecological engineering reveals both the challenges and the immense potential in this field.
So the next time you see a headline about miracle microbes, remember: the reality is even more fascinating than the hype, and the journey to harnessing these microscopic allies is a scientific adventure worth following!
Share it on your social media!
References
Delgado‐Baquerizo, M., Singh, B. K., Liu, Y. R., Sáez‐Sandino, T., Coleine, C., Muñoz‐Rojas, M., ... & Trivedi, P. (2024). Integrating ecological and evolutionary frameworks for SynCom success. New Phytologist.
French, E., Kaplan, I., Iyer-Pascuzzi, A., Nakatsu, C. H., & Enders, L. (2021). Emerging strategies for precision microbiome management in diverse agroecosystems. Nature plants, 7(3), 256-267.
