Why is testing for soil microbes important?

 Soil microbes like bacteria, fungi and actinomycetes are important for many reasons. They help move nutrients to and from the soil. They help with plant growth. They even help make substances that hold soil particles in aggregates, which helps the stability of soil.

These microbes are small but exist in large numbers in soil. Soil microbes’ population varies depending on different conditions. Bacteria and actinomycetes dominate fungus in tilled soil, but fungal populations are higher in no-till soils.

While soil microbes get energy from carbon present in soil, they also contribute to soil health. Bacteria have multiple functions such as decomposition of complex organic residues from plants or animals. They help break up these “leftovers” into simpler plant-available forms. Some microbes that live in the root nodules of legumes, rhizobia, pull nitrogen from the air and make it available to plants. Other microbes convert organic nitrogen to plant available nitrate and ammonium forms.

Actinomycetes are spore-forming bacteria. They form thread-like structures in soil and are responsible for producing the earthy smell of soil. They have various roles in soil. They decompose organic matter, inhibit the growth of plant pathogens in the root zones of plants and improve plant nutrient availability.

Although most of us have seen the fruiting bodies of mushrooms, most of their mass lives underground. Shown here is a fungus that has one of the largest underground networks, Armillaria solipipes. It’s important to test for different soil microbes through testing, like that of our blog author. Credit: Arterra Picture Library

Similarly, fungi help to decompose organic molecules to simpler molecules. Mycorrhizal fungi colonize plant roots and help transform phosphorus into a plant-usable form, and transport nutrients to the plant.

Just like humans have skin to protect us from “outsiders,” soil microbes have a cell membrane. This membrane separates the interior of cell from the outside environment while allowing selected ions and molecules in and out of cell. Sometimes the membrane can protect from harm; other times molecules that are toxic get in. This is actually how antibiotics work, such as streptomycin.

It’s this cell membrane of soil microbes that my research focuses on. Measuring the amount microbes in a soil sample is important for several reasons. Usually, a healthy soil has a good mixture of different types of soil microbes, as well as adequate numbers of microbes.

Distinct layers of soil and fatty acids after centrifugation in a test tube. This work is done to measure fatty acids in fresh soil samples that can provide important information regarding soil microbial communities. Credit: Dwarika Bhattarai

My research focuses on detecting the total biomass of soil microbes. And, I’m helping to detect these in fresh soil samples. This is a faster and less expensive way to get important information for researchers and growers. I do this by measuring the fatty acid profile in the soil.

The cell membrane is made up of proteins and fatty acids. One type, phospholipid fatty acid, is the major component of the soil microbe membrane. These fatty acids have similar structure to that of edible oil like canola oil or peanut oil. A major difference is that majority of soil microbe membranes’ fatty acids have a phosphate molecule.

These type of fatty acids in a cell membrane are often different among different organisms. Hence, these fatty acids can be used as ways to identify different groups of soil microbes including bacteria and fungi. When microbes die, these fatty acids of their cell membrane are rapidly degraded. Working with fresh samples helps us get accurate measurements, swiftly.

Unlike DNA testing extracted from dead soil microbe cells, fatty acids analysis of fresh samples is faster. Analysis and identification of fatty acids from soil can provide the information about the living microbes that enhance soil health. It provides the knowledge of composition of microbes in soil that can help to increase crop production, in different ecosystems and at different temporal variations.

Answered by Dwarika Bhattarai, South Dakota State University

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