Short read
Missing piece of the puzzle

Soil biology is the least understood of the trilogy of properties that influence soil health. Functional genomic soil testing is set to change this and could aid both crop management and the targeting of biologicals.

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Lucy de la Pasture
by Lucy de la Pasture

The biome of the human gut is now known to be the driver of many aspects of human health. This brain-gut superhighway not only influences how our bodies function but also affects how we see the world.

The soil microbiome works in much the same way, says Montana-based agroecologist Nicole Masters, Founder of Integrity Soils. “The best way to describe it is through the understanding that in the human gut, the microbial system really is the primary brain. The plant’s gut system is effectively outside of its body, so it’s the plant’s interface with microbiology that acts as its “primary brain”.

“This means that it’s what is going on beneath the ground that is dictating plant responses. The plant’s sensing system, in terms of temperature, water, nutrients, stress, disease and insect attack, is microbiology. It’s this vital network that enables a plant to be resilient and nutrient dense,” she adds.

Meri Mullins explains functional analysis of soil biology can help us understand where there is a biological limitation to the crop.

Source: Biome Makers Inc

It’s this link between healthy soil, healthy plants and healthy people that really excites Meri Lillia Mullins, Technical Lead at Biome Makers, a global agtech company on a mission to empower farmers and recover soil health worldwide through understanding the function of the soil microbiome. She says microbes in the human gut serve a lot of the same purposes as they do in soil – nutrient mobilization, growth hormone production, abiotic stress adaptation and biotic stress management.

There is a delicate balance as biology can switch from being beneficial to opportunistic and becoming a pathogen. Mullins says those synergies also play into our food system.


When we talk about the low nutrient density of food, the assumption is often that the soil has been depleted of nutrients. While this is sometimes the case, from the hundreds of thousands of soil samples my team has analyzed, we’ve learned that soils are often biologically deficient in the organisms that make nutrients available.”

Meri Lillia Mullins

This realization in itself provides a huge opportunity for global agriculture to become more sustainable, she says. “Soil biology is very resilient, and it is already there. It just needs nurturing to unlock the nutrients already in the soil.”

Evolutions in testing

While soil biology has been a recognized indicator of soil health for some time, it’s only recently that soil analysis has been able to supply information about the function of biology present.

“We’ve had an evolution in testing, from measuring biological respiration to give an indication of microbial biomass to measuring phospholipid fatty acid (PLFA), which estimates the total microbial biomass and community composition of the living microbiota in soils. Now we can use genomics, where the function of the soil microbiome can be understood through its DNA.”



An evolution in soil testing means it’s now possible to analyze the DNA present to identify the biological species present and their function in the soil.

Source: Biome Makers Inc

So what’s the value in having this better understanding of the microbial communities within the soil and their function? As functional genomic data builds up, this can be used to better inform management decisions, believes Mullins.

“The three critical components of the soil – physics, chemistry and biology – are intertwined. We’ve understood the soil physics and chemistry for some time and now we can start to understand the biological component.

“The aim is to understand where there is a biological bottleneck limiting the crop. For example, if there is low biological nitrogen mobilization then that will limit the yield potential, no matter how much nitrogen is applied to the crop.”

Farmers and agronomists will recognize the conundrum presented by an area of a field that consistently underperforms, despite soil physics and chemistry tests not revealing any particular issues. Mullins suggests that
where problems arise without clear physical or chemical explanations, it has been a case of taking an educated guess to best manage the crop. At least, until very recently…

Advancements in technology now allow us to better understand soil biology so we can solve problems like this with a more holistic diagnosis.”

Meri Lillia Mullins


Going back to her example of nitrogen mobilization, Mullins points out that there are many ways to improve nitrogen cycling once the problem is identified. Although the specifics will depend on the farming operation, measures may include bringing in a biological stimulant in season and considering changes in management. This may include the incorporation of practices such as growing cover crops to maintain living roots, promoting microbial diversity and keeping the soil covered, as well as reducing tillage.

“Biological information can help give much quicker insights and enable quicker decision-making when faced with questions that historically haven’t had easy answers. Knowing the direction to head is probably the most critical action that we haven’t necessarily been sure of before.”

It’s fair to say that using genomic information in this way is very much in its infancy. While having a biological diagnosis is fascinating, knowing how to use it is still a developing area.

A growing market

The global agricultural biologicals market is set to double in the next five years, reaching $27.9 billion in 2028, up from $14.6 billion in 2023, according to research by MarketsandMarkets. Genomics can also help tailor the use of products to specific situations and validate their mode of action, something Mullins believes will be necessary as a flood of biologicals become available to growers.

“The direction the industry is heading is to continue to better understand how exactly different management practices and biological products are influencing soil biology and crop production. This information can be used to address the issues that come up in the field so that a very tailored recommendation can be made, like with fertilizer today.”

Mullins says that functional biological databases are growing. This information will soon enable crop management software to adopt biological information and help design more holistic agronomy programs that will include both chemistry and biological insights.

“Artificial intelligence and machine learning have the power to interpret millions of datasets, more than generations of farmers could collect on one farm, and then use that data to empower decisions,” she concludes.

The View: Now, Next and Beyond


Functional genomic soil analysis is economically available and can be interpreted to aid crop management


As databases build over the next 3-5 years, genomic data will enable growers to target biological inputs and soil management practices more effectively


AI and machine learning will empower crop management software to adopt biological information and help design more holistic agronomy programs that will include both chemistry and biological insights