How the microbiome is affecting agriculture


What the heck is a microbiome? That’s what I said when I read the word the first time. A microbiome is like a small community of bacteria that work together for a common goal. Much like how the combine operator, the combine, the trucks, the people unloading the corn, the dryer, and other key players in harvesting shelled corn work together to get the corn from the field to storage, the bacteria in a microbiome work together to achieve their goal.

What is tricky is that there are trillions of microbiomes in the world — and since the turn of the century, the study and sequencing of microbiomes all around us has intensified. Just like a how a harvesting crew for corn silage has different people and equipment than a harvesting crew for peanuts, we understand that each microbiome has its own job, own staff, and unique equipment to get the job done.

Some of the most well known microbiomes are in the human gut. The Atlas Microbiome Test allows you to test out what microbiomes you have in your gut, and how they benefit you.

A 3D rendering of the human gut microbiome. (Image by Alpha Tauri 3D Graphics, Shutterstock)

If there are over 100 trillion microbes in the human gut alone, imagine how many microbes are in fields helping crops to grow. Rhizobia are a close friend of crop farmers, as rhizobia are the nitrogen-fixing bacteria found in soil. These bacteria go to work when legumes such as alfalfa or peas are planted. Their roots have tiny nodules where the rhizobia claim a seat and get to work converting atmospheric nitrogen into ammonia.

Pluton Biosciences is a company that is working to identify the microbes in and functions of previously undiscovered microbiomes. Pluton Biosciences has created a micromining innovation engine that allows them to pinpoint new microbes in short periods of time.

They are now conducting a case study on carbon sequestering soil. The goal is to identify all the microbes in soil that store carbon and nitrogen. After the microbes are identified, they can be grown in a lab, then added into the soil. If the population of carbon and nitrogen storing microbes are higher in the soil, then any soil has the potential be an even better sponge for these gases than they already are.

One of Pluton Biosciences’ founders, Barry Goldman, spent decades of his life leading the microbial testing pipeline for Indigo Ag, and led microbial discovery for Monsanto. Pluton Bioscience focuses its efforts on agriculture, attempting to find a way to combat climate change and be able to effectively minimize pesticide use.

Likewise, the University of Florida is using the microbiome inside orange trees to fight citrus canker. Citrus canker is caused by a bacteria, and it causes the fruit and leaves of citrus trees such as oranges, limes, and grapefruit to have lesions.

University of Florida’s Nian Wang and Chris Oswalt are working toward a solution. They explain that the microbes are either epiphytic or endophytic. The endophytic microbes are where the secret lay (hopefully). Wang and Oswalt hope that when they find microbes that fight citrus canker, they will be able to engineer a synthetic microbiome in order to save Florida’s citrus economy.

While the various microbiomes affecting agriculture are largely undiscovered, we know that they are there. As more companies work to identify the microbiomes, agriculture practices will become more sustainable and even more productive.


Elizabeth Maslyn is a Cornell University student pursuing a career in the dairy industry. Her passion for agriculture has driven her desire to learn more, and let the voices of our farmers be heard.

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