The Importance of Soil Microbes in Carbon Sequestration and Long-term Soil Accrual

by CRARS staff member Sheryl Karas. M.A.

Supporting and enhancing soil health is the driving force behind regenerative agriculture, and nothing has turned out to be more important to this goal than supporting the microscopic creatures we never think about that are present in the soil. A teaspoon of topsoil can contain between 0 – several billion microorganisms and potentially thousands of different species depending on the soil’s health, location and climate. These include multiple species of bacteria, fungi, protozoa, actinomycetes, and nematodes, all of which interact in a variety of complex ways with each other, plants and the soil itself. For example, scientists used to think that the carbon in the soil came mostly from the decomposition of plant residue; but now these microorganisms are increasingly seen as playing a crucial role(opens in new window) in photosynthesis, in the creation of soil organic carbon, in carbon sequestration, and how that interacts with climate change. Therefore, the decisions we make for our collective future may very well hinge on learning how to work most effectively with this mostly unseen life beneath our feet. Let’s take a closer look. 

How Soil Microbes Enhance Carbon Sequestration

Soil microbes enhance carbon sequestration through several interconnected mechanisms. When combined with appropriate soil health practices, these processes significantly contribute to the stabilization and long-term storage of carbon in soils. Here are a few of the most important ones we know about today:

Decomposition and Formation of Soil Organic Matter

Soil microbes break down dead animals and plants for their own energy needs, growth, and survival. Through the release of enzymes and other biochemical processes they decompose complex organic substances into simple inorganic ones such as water, carbon dioxide, nitrogen, phosphorus and calcium. These are both nutrients plants need as well as those needed by the microorganisms themselves. Easily degraded organic material tends to be broken down by bacteria early in the process, while actinomycetes and fungi break down tougher or more complex substances. During decomposition, some of the carbon becomes part of the body of the growing microbes, particularly fungal biomass, and is later stabilized as soil organic carbon (SOC) through the creation of humus which contributes to long-term carbon sequestration.

Nutrient Cycling, Photosynthesis, and Plant Growth

Photosynthesis in plants is the main process by which carbon dioxide from the atmosphere is transformed into a useable organic (sugar) form. Evidence suggests that plants gained this ability through endosymbiosis with photosynthetic microbes similar to Cyanobacteria. These ancient photosynthetic microbes evolved in plant cells to form the chloroplast organelle responsible for photosynthesis.

The plant takes what it needs from photosynthesis products (sugars) and then exudes organic compounds through its roots. This root exudate provides carbon for other microbes in the soil—in particular, mycorrhizal fungi—and helps form soil organic matter. The fungi and bacteria, in turn, release nutrients from the organic matter and make them available to the plant. This nutrient cycle supports healthy plant growth and increased photosynthesis, making carbon cycling one of the fundamental components of life on earth and a significant component of natural carbon sequestration in undisturbed soil.

Soil Aggregation

Soil aggregates are collections of soil particles that bind together in clumps that are resistant to external pressures such as water and wind erosion. This is an essential aspect of soil health. Fungi, especially mycorrhizal fungi, produce hyphae that help bind the soil particles together. They also release exudates such as glomalin (PDF) that are resistant to microbial decay and water, and act somewhat like a glue to stick the soil particles to each other and protect them from erosion. This also contributes to keeping soil carbon in the soil while creating spaces with less microbial activity that assist with water infiltration and water retention near plant roots. Soil bacteria can also assist in the creation of aggregates (opens in new window)through the release of decay-resistant polysaccharides.

In soils with enough minerals, such as clay, microbial exudates can bind with those minerals. Organic carbon can be bound to these mineral surfaces as well as remain protected in the aggregates(opens in new window).

Formation of Microbial-Derived Organic Matter

Microbial-Derived Organic Matter (MDOM) includes both living microbial biomass and the remains of dead microbes (necromass). The MDOM contributes to the soil organic matter pool and can be more resistant to decomposition compared to plant-derived organic matter. Microbial necromass is thought to be the main component of soil organic carbon sequestration(opens in new window), with fungal dominant soils showing the highest concentration of soil carbon in most studies. Fungal biomass is generally more resistant to decomposition than bacterial biomass, contributing to the stabilization of organic carbon in soils. One study estimates that two-thirds of microbial necromass originates from fungi(opens in new window).

Dan Naylor, Natalie Sadler, Arunima Bhattacharjee, Emily B. Graham, Christopher R. Anderton, Ryan McClure, Mary Lipton, Kirsten S. Hofmockel and Janet K. Jansson, CC BY-SA 4.0 <https://creativecommons.org/licenses/by-sa/4.0>, via Wikimedia Commons

Impact of Fungal-to-Bacterial Ratios and Agricultural Practices

Higher fungal-to-bacterial ratios are often associated with enhanced carbon sequestration. In undisturbed soils, fungi play key roles in every aspect of carbon sequestration as mentioned above. However, in conventionally managed cropland the fungal to bacterial ratio in soils is reversed, with bacteria being most dominant. That has led researchers to suggest that regenerative farming practices that preserve and support a higher fungal to bacterial ratio would likely be beneficial for improved carbon sequestration.

Some caveats need to be mentioned, however, as studies have indicated that these benefits can vary depending on soil type, climate, other environmental conditions, and specific land management decisions. Also, soil microbial communities are dynamic and complex. So it may not be possible to come up with a solution. Yet, the evidence is promising, so much so that more research is currently underway to quantify how fungal to bacterial ratios might influence carbon sequestration under different conditions.

So far, several studies(opens in new window) indicate that agricultural practices that focus on creating optimal conditions for higher fungal to bacterial ratios have potential for improving soil carbon sequestration. While the specific mix of practices may vary depending on the conditions and requirements of each farming operation, the most effective practices appear to be:

No-tillage or reduced tillage

Tillage disrupts soil structure and can decrease fungal biomass while promoting bacterial growth. By reducing or eliminating tillage, you maintain soil structure, which supports fungal networks and mycelial growth.

Increased Organic Matter Inputs

Adding organic matter such as compost or manure increases food sources for fungi, promoting their growth and activity.

Multi-Species Cover Cropping

Cover crops provide continuous ground cover that protects the soil from sun and water erosion. They also provide organic material input, and help maintain soil structure and moisture, which benefits fungal networks. Using multiple species seems to be most effective.

Diverse Crop Rotations

Crop rotations that include a wide variety of plant species supports more diverse microbial communities, including fungi.

Avoidance of Excessive Synthetic Fertilization

High levels of synthetic fertilizers, especially those high in nitrogen, can favor bacterial growth over fungi. Balancing nutrient inputs can help maintain a more favorable fungal-to-bacterial ratio. In many cases, maintaining healthy soil biology can reduce the need for such inputs or eliminate them completely.

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Soil microbes are indispensable to agriculture that works with nature instead of against it. In terms of carbon sequestration, they are essential through their roles in decomposing organic matter, forming stable soil organic matter and aggregates, and supporting plant growth and nutrient cycling. Fungal-to-bacterial ratio and microbial diversity further influence these processes and are well-worth supporting.