I am so excited to welcome Dr. Tuesday Simmons to Metal Dog Labs and SFTW for a new monthly series focused on the soil microbiome. The series will run for a few months. Please do not hesitate to send me your feedback -Rhishi
Over the next few months, Dr. Tuesday Simmons will be sharing her perspective on the importance of the soil microbiome to agriculture and the development of new technologies. Starting off with an introduction to the microscopic life inhabiting cropland soils, together we’ll explore the integral role these creatures play in nutrient cycling and soil structure, the relationships they have with plants, how they impact soil health, and what this all means for farming practices and the rapidly growing biological product market.
Bio: Dr. Tuesday Simmons earned a PhD in microbiology from the University of California, Berkeley for research into the effects of drought on cereal crop microbiomes. Post-graduate school, she has worked for start-up companies in R&D, sales, and marketing roles with the goal of effectively communicating the value of cutting-edge biotechnology. As an Application Scientist at Isolation Bio, she worked with leading gut microbiome researchers to improve high-throughput microbial isolation for academic and pharmaceutical purposes. At Root Applied Sciences and Trace Genomics, she has worked to leverage microbiome research for farmers and agronomists. Since 2024, she has worked as a freelance science writer and consultant.
Soil Microbes are Feeding the World
Every ecosystem on our planet is impacted by microorganisms (aka microbes), and the soil in which we grow our food is no exception. The role microbes play in crop growth is exceedingly underappreciated, and I hope to bolster awareness and appreciation for our microscopic allies in my series of posts here on Software is Feeding the World.
Over the next few months, we’ll dig into (pun intended) the soil microbiome, its importance in nutrient cycling and soil structure, the relationships between microbes and plants, and the role microbes are playing in today’s agricultural product market.
Soil microbiome: the diverse community of microorganisms that live in the soil.
Soil: The Final Frontier
Contrary to statements made by a certain multibillion dollar media franchise, it is this microbiologist’s opinion that soil is the final frontier, not space. In the past decade, we have just begun to scratch the surface into the importance of the soil microbiome. While the individual components of soil (minerals, water, air, organic matter, and microorganisms) might seem simple on the surface, the interactions between each of these components and with soil-dwelling macroorganisms like plants and insects are incredibly convoluted.
Like our gut microbiome, the soil environment is teeming with microbial life. Unlike our guts, the complexity of the soil microbiome is largely undiscovered.
While your gut microbiome might contain ~3,000 bacterial species (1), a teaspoon of soil can have 50,000 species (or more) (2). Additionally, around 90% of gut microbes can be cultured (grown in a lab) (1), while (at best) less than 3% of soil microbes can be cultured (3). The remaining ~97% of soil microbes are referred to as “microbial dark matter”.
Historically, the field of microbiology has been dependent on growing microbes in a lab in order to study and identify them, but the development of sequencing technologies has opened up a new window into the soil ecosystem.
How do we ID what we can’t see?
Individual microorganisms may be invisible to the naked eye, but many of them form visible structures when they grow together (like mold you see growing on that old loaf of bread). In the 1800s, pioneering microbiologists started growing microbes in laboratories to study them. In the 2010s, I cultured hundreds of different microbes while working in research labs, so it’s still a great way to learn about these creatures.
Some microbes can be accurately identified by growing them in a lab and testing whether they grow with certain types of food or produce certain byproducts. Other microbes that can’t be convinced to grow in a lab might be identifiable under a microscope using special stains. However, the vast majority of soil microbes can’t be cultured, and most microbial cells can’t be differentiated under a microscope.
Since DNA sequencing came onto the scene in the 1980s, our ability to ID microbes in different environments has exploded. We can separate the DNA in a soil sample from all the other “junk” (minerals, organic material), sequence the DNA, and compare it to a database to identify what species are there. Our biggest issue now? There is so much unknown diversity in the soil microbiome, we can generally only identify (at best) 20% of the DNA.
If you’re looking for something specific in a sample, you can do targeted DNA tests (like the PCR test for COVID). When studying the soil microbiome, scientists generally use two different types of non-targeted tests: amplicon sequencing and shotgun metagenomics.
- Amplicon sequencing - sequences a “fingerprint” gene
- Shotgun metagenomics - sequences all DNA in a sample
There are pros and cons to each method, but when it comes to using the data for informed soil management, you can’t beat shotgun metagenomics. It is much more reliable at identification at a species level, whereas the best you can hope for in amplicon sequencing is a genus level ID (that is, Fusarium compared to Fusarium oxysporum.) Metagenomics also directly measures functional genes (like nitrogen cycling), where functional analyses based on amplicon sequencing are, at best, an educated guess.
So, who are these bugs?
As if the field of microbiology wasn’t complicated enough, many microbiologists lovingly refer to these critters as “bugs”, despite the word already being a source of pain for both entomologists and engineers. The soil microbiome is made up of bacteria, fungi, archaea (another type of single-celled organism), and viruses, and each of these contains a dazzling array of diversity.
Not just pathogens–important roles of soil microbes
Despite claiming most microbiological headlines, pathogens make up a small percentage of the soil microbiome, with most microbes playing a beneficial role. We’ll explore more about the relationship between soil microbes and crop plants in a later article, but here are some examples of how these tiny organisms impact the soil:
Nutrient cycling
All living things need nutrients to survive and grow. Crops rely on the macronutrients (macro because they need a lot) N, P, and K - Nitrogen, Phosphorus, and Potassium. Although plants can pull carbon out of the atmosphere (CO2) to build biomass, they aren’t able to use the form of nitrogen that’s in the air. But microbes can!
Before Fritz Haber and Carl Bosch figured out how to turn atmospheric N into ammonia in the early 1900s, microbes were responsible for all the N fixation on the planet. Bacteria and archaea transform the gas N2 into ammonia, either as free-living organisms in the soil or symbiotic partners to plants like legumes, living happily within their roots.
Soil microbes are also critical for phosphorus cycling; they can pull P out of organic matter as well as surrounding minerals. The same can be said about potassium. This is essential for turning P and K into forms that plants can use.
Organic matter breakdown
Without microbes, dead organic matter in the soil would pile up, and the “circle of life”, so to speak, would be broken. All the nutrients accumulated in previously living organisms would be trapped, unable to be freed and used by future generations. Like invisible engines beneath our feet, bacteria, fungi, and archaea power the decomposition of organic matter, turning yesterday’s life into tomorrow’s crops.
Tiny organisms–big structural impact
Microbes exude different chemicals for a variety of reasons, and some of them can be sticky. These sticky substances can impact soil structure, forming soil aggregates. This in turn improves soil structure, changes spaces between aggregates for air and water (and roots) to move through, and also improves the amount of water the soil can hold. All these changes help reduce erosion and can help crops withstand drought.
Bonus: bioremediation
In my opinion, one of the coolest things about microbes is the incredible diversity of metabolisms. In other words: they can respire and eat some pretty extravagant things. While we use oxygen to break down our food into energy, some microbes can use heavy metals! There are also some that can consume pollutants like oil.
While this list isn’t comprehensive (I didn’t even mention that soil microbes are an important source for new antibiotic discovery), I hope to have shed some light on just how amazing these tiny organisms are.
Soil is a living commodity. Treat it that way.
If you take nothing else away from this article, take this: soil is a living, breathing ecosystem that has a major impact on farming operations. Understanding the microbes living in your soil can help inform pathogen and nutrient management, provide insight into overall soil health, and ultimately allow us to better care for this precious resource.
References
- Rosenberg, E. Diversity of bacteria within the human gut and its contribution to the functional unity of holobionts. npj Biofilms and Microbiomes 10, (2024).
- Raynaud, X. & Nunan, N. Spatial Ecology of Bacteria at the Microscale in Soil. PLoS ONE 9, e87217 (2014).
- Youseif, S. H. et al. Comparative Analysis of the Cultured and Total Bacterial Community in the Wheat Rhizosphere Microbiome Using Culture-Dependent and Culture-Independent Approaches. Microbiology Spectrum 9, (2021).