Boosting Beneficial Microbes in Soil

Growers don’t need to fret about soil microbe depletion; instead, focus on creating work for these beneficial organisms. Maintaining a balanced microbial community and minimizing soil disturbance are crucial for a healthy soil microbiome. By fostering the right environment with organic matter and smart farming practices, farmers can unlock the full potential of beneficial soil microbes, improving nutrient availability and boosting crop yields.

Written by Rachel Sim, with expertise provided by Erin Doran, Technical Agronomist, and Celeste Artiga, Research Associate.

The good news? Most growers don’t need to worry about completely depleting their soil of beneficial microbes.

“Microbes exist where there’s work to do and a need for that work to be done,” says Celeste Artiga, Research Associate at Sound Agriculture.

Why Microbes Go Dormant

Beneficial soil microbes, like phosphorus-solubilizers and nitrogen-fixers, often take a back seat when easy-access nutrients are already available. ​“It’s hard for beneficial microbes to actively mobilize nutrients locked in the soil when more accessible options are present,” says Artiga. ​“Everyone feeds on the low-hanging fruit. That means P‑solubilizers and N‑fixers may be outcompeted by less active microbes.”

In other words, when nutrients are spoon-fed through high fertilizer use, soil microbes don’t have much to do — and when there’s no job to do, they go quiet.

Feed the Soil, Not Just the Crop

To encourage microbial activity, growers should focus on practices that create work for microbes — like using more complex or bound forms of nutrients. This activates phosphorus-solubilizers and nitrogen-fixers and helps maintain a diverse, functional microbial population. ​“If you build it, they will come.”

Testing Soil Microbes Is Tricky

Soil microbial levels are dynamic and influenced by variables like temperature, moisture, and recent management practices. ​“Testing microbial counts isn’t always reliable because levels change daily,” says Erin Dornan, Technical Agronomist at Sound. ​“What’s more important is understanding the balance of microbial communities in the soil.”

Diversity is the Real Power

When one microbial group — like bacteria or fungi — dominates, growers can face issues like nutrient lock-up or disease. A diverse soil microbiome that includes bacteria, fungi, protozoa, and nematodes offers natural checks and balances. These beneficial microbes compete with harmful ones for food and space, helping reduce disease pressure and improving long-term soil health.

Different types of beneficial microbes play distinct roles in supporting soil health and plant performance. Here are a few key players:

• Mycorrhizal Fungi: Expand the root system through hyphal networks, increasing access to water and nutrients — especially phosphorus — in exchange for plant-produced carbohydrates.
• Azospirillum: Promote lateral root development and improve plant stress tolerance, enhancing nutrient and water uptake under challenging conditions.
• Rhizobium: Form nodules on legume roots to fix atmospheric nitrogen into a plant-available form, reducing the need for synthetic nitrogen fertilizers.
• Trichoderma: Suppress soil-borne pathogens while promoting root growth and nutrient availability through enzyme production.
• Bacillus subtilis: Compete with harmful microbes and produce natural antibiotics that protect plants, while also improving nutrient cycling in the rhizosphere.

Each of these microbial allies contributes to a more resilient, efficient soil ecosystem — helping crops grow stronger with fewer inputs.

Beneficial microorganisms play a vital role in building and maintaining healthy soil. They:

• Improve Nutrient Cycling: Microbes break down organic matter and convert nutrients like nitrogen and phosphorus into forms plants can absorb.
• Enhance Soil Structure: Fungal hyphae and microbial byproducts help bind soil particles, improving aeration, drainage, and root penetration.
• Suppress Harmful Pathogens: A diverse microbial community competes with or inhibits disease-causing organisms, reducing the risk of crop loss.
• Boost Plant Resilience: Microbes can help plants tolerate drought, disease, and other stressors by supporting root development and signaling defense responses.

In short, healthy microbial activity supports fertile, productive soil — naturally.

There’s no one-size-fits-all approach to supporting soil microbes. The right steps depend on your location, climate, soil type, and farm management style. Every operation is different — and growers know their land best.

“Growers in parts of the United States might have very bioactive soil — that’s soil with characteristics that create a favorable environment for biological processes like nutrient solubilization to take place,” says Celeste Artiga, Research Associate at Sound. ​“There are other parts of the US where soil types may not be as amenable to being bioactive.”

What Microbes Need to Thrive

Like all living organisms, microbes require food and water to survive. But balance is critical — too much or too little water can be harmful, and a lack of organic matter means microbes will compete for scarce resources.

“If there are really low organic matter levels in the soil, there’s not enough food for all the microbes to feed on, and then they’ll start fighting over it,” says Erin Dornan, Technical Agronomist at Sound. ​“Some of the bad microbes will win out over the good.”

Avoiding Soil Disturbance

Soil structure plays a huge role in microbial health. Below the surface, microbes live in different microclimates — from the topsoil, through the root zone, and even deeper. Each layer supports a unique microbial community.

“Microbes’ biological processes happen in very specific types of conditions; the microbes in the top layer of soil can be completely different from those found closer to plant roots, and those are different from the ones below the root system,” explains Celeste. ​“Disturbing the soil also disturbs these microclimates, creating a constant reshuffling of the microbial community across the soil. Sometimes that redistribution isn’t favorable for what we want the microbes to do for the plant.”

One example is arbuscular mycorrhizal fungi (AMF), which form thin, thread-like hyphae that transfer nutrients and water between plants and microbes. These networks — and their relationships with key bacteria like phosphorus solubilizers — can be easily disrupted by tillage.

“When we run tillage across that field or anhydrous — anything that knifes into the ground — it’s going to impact those good microbial levels,” says Erin. ​“Practices like no-till and strip tilling not only minimize soil disturbance, they also leave organic matter on the soil.”

Supporting Microbes with Smart Inputs

Stalks and other organic matter left on the soil surface act like protective blankets during winter, preserving microbial populations. If breakdown seems too slow, there are options to accelerate the process — without disrupting the soil.

“When we add digesters to the system that help break down organic matter quicker without tillage, you’re actually feeding the microbes rather than disturbing them,” she adds.

In bioactive soil, plants and microbes communicate constantly with each other. In exchange for carbohydrates that plants create through photosynthesis, microbes provide the crop with plant-available forms of a variety of nutrients, including nitrogen, phosphorus, potassium, and even micronutrients. Microbes also interact with each other; AMF, for example, act as bridges between micro-pockets of microbial activity in the soil, providing water and transporting nutrients.

“Microbial communities create a sort of hum. Close to plant roots, the hum is louder, but it persists beyond that,” says Celeste. ​“When microbes find pockets of soil with favorable conditions where there are either freely-available nutrients or nutrient-processing to be done, they’re vocal about it. They’re constantly sending and receiving signals, so when one kind of microbe finds a good spot, everyone around will know.”

Nitrogen-fixing and phosphorus-solubilizing microbes are closely associated with roots, which either trade carbohydrates or are otherwise creating an environment where nitrogen fixation is possible. Other microbes that don’t fix nitrogen but may help those that do or provide other benefits will also hang out nearby.

“One microbe can attract a different type of microbe until they daisy-chain themselves into a microbial community. They’re all working together and competing against each other in order to survive and thrive,” says Celeste.

For many growers, nitrogen and phosphorus are abundant in the environment, but without access to the phosphorus tied up in the soil or atmospheric nitrogen, growers rely on the fertilizers they purchase each year. When all of a crop’s nutrition needs are met through fertilizer, the plants stop signaling to soil microbes and the microbes stop providing nutrition to the plant.

“The root zone is often where the most disturbance occurs and the most synthetic fertilizer is placed, both of which will slow down microbial activity,” says Erin.

A healthy soil microbiome offers free access to many of the nutrients that are commonly applied in synthetic form.

“If you give plants synthetic fertilizers, they’ll soak some of it up, but those fertilizers take money and resources to produce, transport and apply. In some cases, there can be plenty of nitrogen, phosphorus and potassium in the soil and the environment, but they’re just not freely available yet,” says Celeste. ​“A microbial community will process those unavailable nutrients into their more biologically-available forms, and growers may not have to apply that costly nutrition to the same degree.”

One way to support a more balanced microbial community is with SOURCEⓇ, Sound’s microbiome activator. SOURCE is a molecule that mimics the plant-to-microbe signal to attract microbes already present in the soil and increase crops’ access to key soil nutrients.

“SOURCE helps to bring balance back to the microbiome and to plant nutrition,” says Erin. ​“When we look at in-season tissue and soil samples, we see nutrients balancing out, rather than huge spikes or lows in various nutrients throughout the season. That’s because SOURCE is activating beneficial microbes that were depleted.”

For Celeste, it’s ultimately about creating an environment where microbes can do their work, and actively want to. ​“If you have low microbe activity, there’s a reason. You could apply a microbial product, but if the environment itself isn’t conducive to supporting an active microbial community, they won’t survive long-term,” she explains. It’s essential to start with an understanding of what you have.

“You can’t improve something you haven’t measured,” says Celeste. ​“We like to make decisions based on our gut, but keeping a detailed record of practices gives us data to back those decisions up.”