Underground Genomes and Crop Health: Reconnecting Agriculture with Soil Biodiversity

Guest Author: Dr Pushplata Singh, Senior Fellow & Director, Sustainable Agriculture, TERI

15 October 2026, New Delhi: For thousands of years, farmers understood that a productive field was more than just soil. They used farmyard manure, compost, crop residues, green manure, animal waste and nutrient-rich silt to maintain fertility. These practices supplied nutrients to crops while also returning organic matter to the soil and supporting its biological life.

In traditional farming systems, therefore, soil was not simply treated as a medium in which crops were planted. It was, in many ways, understood as a living resource.

Modern agriculture changed this relationship dramatically.

The Green Revolution brought high-yielding varieties, improved irrigation, fertilizers, pesticides and better crop-management practices. In India, these technologies transformed food production and played a major role in strengthening national food security. The Indian Council of Agricultural Research (ICAR) notes that food-grain production increased more than six-fold between 1950–51 and 2021–22.

This achievement was essential. India moved from a period of food scarcity towards greater food security and became capable of producing substantial surpluses. There is little doubt that modern agricultural science changed the country’s food-production landscape.

But agriculture now faces a new question:

Can we maintain high productivity without compromising the biological foundation on which agriculture ultimately depends?

That foundation lies partly beneath our feet.

The hidden world beneath a crop

Every handful of healthy soil contains an enormous community of living organisms—bacteria, fungi, archaea, protozoa and other microorganisms. Together, their genetic information forms what we can think of as an “underground genome.”

The term is not a single genome belonging to one organism. Rather, it is a useful way of describing the enormous genetic and functional diversity present in the soil microbiome.

One of the most important places where this underground life interacts with agriculture is the rhizosphere—the narrow region of soil surrounding plant roots.

The rhizosphere is far from being an inert zone. Plant roots release sugars, amino acids, organic acids and other compounds into the surrounding soil. These substances provide food and signals for microorganisms, while microbes, in turn, influence nutrient availability, plant growth and plant health.

Some microorganisms help make nutrients available to plants. Others participate in nitrogen and carbon cycling. Some can suppress disease-causing organisms, while others can help plants tolerate drought, salinity and other stresses. Mycorrhizal fungi form associations with plant roots and can contribute to nutrient and water acquisition.

In other words, the crop and its microbial partners are part of the same biological system.

This changes the way we should think about crop nutrition.

A plant does not obtain all of its nutrition simply by taking chemicals from the soil. Its roots interact continuously with a living microbial community that helps determine what nutrients are available, when they become available and how efficiently they can be used.

Fertilizer changes the underground community

When we apply fertilizers, we are not feeding the crop alone. We are also changing the environment in which soil microorganisms live.

Nitrogen, phosphorus and potassium fertilizers increase the availability of nutrients, while repeated fertilizer application can also influence soil acidity and other soil properties. These changes can alter the composition and functioning of microbial communities. Recent research confirms that fertilization can reshape rhizosphere microbial communities, although the direction and magnitude of these changes depend on soil, crop, climate and management conditions.

A useful example comes from cropping systems such as Rice–Maize and Wheat–Maize.

When soils receive little or no external fertilizer, microorganisms adapted to relatively low nutrient availability can become more prominent. Groups such as Acidobacteriota, Myxococcota, Chloroflexi, Planctomycetes and Actinobacteriaare commonly found in soil microbial communities, although their abundance varies considerably with soil and environmental conditions.

Rice creates another interesting microbial environment. Periodic flooding can reduce oxygen availability in the soil and encourage microorganisms adapted to low-oxygen conditions. Microbial groups involved in nitrogen fixation, iron reduction and other nutrient transformations may therefore become important.

Wheat–Maize systems can show a different microbial pattern because the crop, soil conditions and nutrient availability are different.

The important point is not that one bacterial group is universally “good” and another is “bad.”

The important point is that agricultural management changes the underground biological community.

From low-nutrient specialists to fast-growing microbes

When nutrients become more readily available, the microbial community can shift towards organisms that grow rapidly when resources are abundant. These are often described as copiotrophic microorganisms.

Groups within Proteobacteria and Bacteroidota, for example, can become more prominent under nutrient-rich conditions, although the exact response varies between soils and cropping systems.

This is similar to what happens in many ecosystems: changing the availability of resources changes which organisms have a competitive advantage. 

The same principle operates below the soil surface.

A fertilizer application can therefore have effects that extend beyond the immediate nutrient requirement of a crop. It can alter the microbial community surrounding the roots and, consequently, the biological processes taking place there.

This is why the question should not simply be:

“How much fertilizer does the crop need?”

We should also ask:

“What kind of soil microbial community does this crop need?”

When more fertilizer is not necessarily better

The challenge is not fertilizer itself.

Modern agriculture cannot simply abandon fertilizers. Crops remove nutrients from the soil, and those nutrients must be replenished through appropriate sources. Chemical fertilizers, when used according to soil and crop requirements, remain important tools for maintaining productivity.

The problem arises when fertilizer application becomes excessive, imbalanced or disconnected from the actual needs of the crop and soil.

Excess nitrogen can increase nitrogen losses through processes such as leaching, volatilization and denitrification. Some of these pathways can contribute to emissions of nitrous oxide (N₂O), an important greenhouse gas.

Long-term nutrient imbalance can also contribute to soil acidification, nutrient deficiencies or other changes in soil properties. At the same time, intensive agricultural practices can influence the diversity and functioning of soil microbial communities.

This does not mean that every fertilizer application damages soil biodiversity. The response is much more complex.

Soil type, crop variety, climate, fertilizer source, application rate, timing, irrigation, organic matter and previous management all matter.

The objective, therefore, should be neither “chemical fertilizer versus biological agriculture” nor “traditional agriculture versus modern agriculture.”

The real opportunity lies in better integration.

What happens when we look at the soil as a living system?

Imagine two fields growing the same crop.

On the surface, both may look identical. The plants may have similar height, colour and yield.

But below ground, their microbial communities may be very different.

In one field, a diverse microbial community may be actively cycling nutrients, decomposing organic matter and interacting with roots. In another, repeated nutrient inputs, pesticide exposure, low organic matter or intensive tillage may have created a different microbial environment.

The difference may not immediately be visible.

This is where modern science can provide a new window into agriculture.

Technologies such as metagenomics, microbiome profiling, DNA sequencing, transcriptomics and functional genomics allow scientists to investigate not only which microorganisms are present, but also what genes and functions are represented within the community.

This is a major shift in thinking.

Earlier, soil microbiology often focused on isolating and studying individual microorganisms. Today, scientists can increasingly study the whole microbial community and its interactions with the plant.

This matters because a soil microorganism rarely works alone.

The rhizosphere is a complex network in which hundreds or even thousands of microbial groups interact with one another and with the plant. Research on plant microbiomes increasingly focuses on these community-level interactions rather than only individual microbial species.

Can we manage the underground genome?

This is perhaps the most exciting question for the future.

If the underground microbial community influences nutrient availability, plant growth and resilience, can we deliberately manage it?

The answer may increasingly be yes—but with an important qualification.

We cannot simply introduce a microorganism into soil and assume that it will automatically establish itself and produce the desired result. Field performance of microbial products can vary because microbial survival and activity depend strongly on soil, climate, crop and the existing microbial community. Recent reviews highlight this gap between promising laboratory results and consistent field performance.

This is why the future may lie not only in individual microbial inoculants, but in microbial consortia, biofertilizers, mycorrhizae, biostimulants and integrated soil-management systems designed for particular crops and environments.

Recent research also suggests that microbial inoculants can influence native soil microbial communities, demonstrating that introducing one microbial population can have broader effects on the soil ecosystem.

The next generation of agriculture may therefore need to move from simply supplying nutrients to managing nutrient flows through biological systems.

Bringing the old and the new together

This does not mean going backwards.

Traditional farmers did not have DNA sequencing, metagenomics or precision nutrient-management tools. But many traditional practices—returning organic matter to the soil, recycling crop residues, using farmyard manure, green manuring and diversifying crops—recognized the importance of maintaining soil fertility over time.

Modern science can now help us understand why some of these practices work and how they can be improved.

At the same time, modern technologies such as soil testing, precision fertilization, improved crop varieties, biological inputs, nanotechnology, remote sensing and microbiome analysis can make agricultural management more efficient.

The future may therefore be a meeting point between traditional knowledge and modern science.

Organic matter recycling can be combined with balanced fertilizer use. Crop residues can be returned to the soil where appropriate. Crop diversification can be encouraged. Beneficial microorganisms and microbial consortia can complement conventional nutrient management. Precision agriculture can help deliver nutrients where and when crops need them.

The goal is not to eliminate one technology in favour of another.

The goal is to use every appropriate technology more intelligently.

Looking below the surface

Agriculture has spent centuries learning how to improve what happens above the ground.

We selected better seeds. We developed fertilizers and pesticides. We improved irrigation. We mechanized farming. We developed biotechnology and precision agriculture.

Now we have an opportunity to look in the other direction.

Downwards.

The soil beneath a crop contains an extraordinary biological system that we are only beginning to understand. Its microorganisms carry genes that influence nutrient cycling, decomposition, plant interactions and ecosystem functioning.

These underground genomes may hold important clues for improving nutrient-use efficiency, strengthening crop resilience, reducing nutrient losses and rebuilding degraded soils.

The challenge for agricultural science is to translate this knowledge into practical solutions that work in real fields and benefit farmers.

The future of crop productivity may therefore depend not simply on how much we put into the soil, but on how well we understand what is already living there.

Because ultimately, healthy crops begin with healthy soils—and healthy soils are living systems.

If agriculture can learn to work with those underground biological communities rather than treating soil only as a physical growing medium, we may be able to build farming systems that are simultaneously productive, resource-efficient and more resilient.

The next agricultural revolution may not be visible from the roadside.

It may be happening beneath our feet.

Also Read: Bayer to Distribute INERA’s Biological Crop Nutrition Products in India

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