Good soil, bad soil

In a living lab, sunflower stalks stood intact two months after the crop was harvested. The stalks kept root systems alive and supported microbial life underground. Elsewhere in the same field, stalks were uprooted after the March harvest, but spread as mulch to cool the soil, retain moisture, and boost microbial activity.

The living labs at the International Crop Research Institute for the Semi-Arid Tropics (ICRISAT) in Hyderabad are researchers' playgrounds for testing new agricultural practices. The experiments with sunflowers and other practices are part of regenerative agriculture techniques that ICRISAT researchers are trying to perfect. 

A key focus area for them is keeping the soil healthy. Healthy soil is alive with microorganisms — bacteria, fungi, earthworms, and insects — that work together to cycle nutrients to plants, suppress diseases and pests, and provide other ecosystem services. Because of the benefits the microbes offer, they are also used as external agri-inputs to enhance soil productivity and health. In recent decades, many such products have become available to farmers: Trichoderma spp. to control fungal pathogens, Bacillus thuringiensis for pest control, Azotobacter for nitrogen fixation, and so on. The ICRISAT researchers also used a variety of microbes, such as nitrogen fixers, phosphate solubilisers, and potassium mobilisers, to improve soil health in the living labs. "We use microbial granules on which a consortium of (two or more) microbes is immobilised," explains Rajesh Pasumarthi, Scientist, Microbiology, ICRISAT. 

In recent years, microbial consortia have become increasingly common in agriculture labs and farmer markets. "Consortia are being marketed across the country," says Appa Rao Podile, former Senior Professor of Plant Biology and former Vice Chancellor of the University of Hyderabad. Podile, who recently retired from the University, has spent over three decades studying soil microbes. He explains that to develop these consortia, researchers study microbes that are associated with or grow around the roots of a crop and identify as many beneficial microbes as possible. They then select compatible ones to create a consortium of three to eight different microbes. These consortia are called synthetic microbial communities (SynComs). Podile has developed SynComs that show promising results in peanuts and rice.

The challenge with using consortia and SynComs, however, is ensuring they get established in the soil environment. "If you change the soil, if you change the plant, everything changes for the microorganism," says Shilpi Sharma, Professor of Biochemical Engineering and Biotechnology at the Indian Institute of Technology Delhi. It is recommended that SynComs be designed with the native microbes from the soil.

To overcome these challenges, Sharma works with the microbiome associated with a plant in soil instead of using a curated collection of microbes. She is trying to tailor the microbiome to mitigate different kinds of abiotic and biotic stresses. This is a more "robust" approach, she says, as the interactions between microbes are intact and they are better adjusted to the environment.

Instead of the conventional approach of acclimatising a plant to a specific stress, Sharma and her colleagues try to acclimatise the microbiome to stress. In a 2025 study (bit.ly/salt-tomato), Sharma and her colleagues report that they acclimatised a salt-susceptible tomato variety to high salt concentration through microbiome adaptation. The root microbiome was acclimatised over 12 consecutive plant growth cycles with increasing salt stresses. In each cycle, the root microbiome of the best-grown plant under salinity stress was transferred as inoculum to the next cycle of plants. After 12 growth cycles, "stress markers were reduced in plants inoculated with an acclimatised microbiome, while the root architecture was enhanced, indicating salt tolerance," note the researchers in the paper.

In the last few years, Sharma has worked on other plants, too, to get their microbiome adapted to certain stresses and observed that microbiomes adapted for a particular selection pressure were also efficient in withstanding other kinds of stresses. "It seems that there is a set of universal stress busters that get enriched over these growth cycles, and they tend to stick together and also be efficient for other stresses," she says.

Microbiomes generated for salinity, for instance, work equally well to withstand drought. "This is a very encouraging recent result in my lab," she adds.

In Hyderabad, Podile and his colleagues wanted to see which of the two — genetics of the plant or the soil condition — had a bigger impact on what kind of microbes thrived around the root of a plant. They studied the soil microorganisms associated with the roots of the pigeonpea plant (Cajanus cajan, also called toor dal) and compared three different cultivated varieties and a wild variety of pigeonpea, Cajanus scarabaeoides, in a recent paper (bit.ly/pigeonpea-soil) published in Environmental Microbiome. "What we see is the diversity of organisms, and the presence of beneficial organisms is more influenced by the soil type than the genetics of the plant variety," says Podile. "The plant's genetics plays some role, but it plays a secondary role compared to the soil type" (in shaping the root microbiome).

The soil helps the plants in diverse ways. For example, in overused, chemical fertiliser-laden soils, minerals, such as phosphorus, zinc, and iron, become immobilised in the soil. Microbes help solubilise these minerals and facilitate their acquisition by the plant roots. Some microbes produce plant hormones like the Indole-3-acetic acid (IAA) that promote plant growth. Then, some microbes produce antibacterial and antifungal substances to stop the growth of unwanted microbes. Soils rich in such microbes are called disease-suppressive soils.

Podile's research journey as a PhD candidate started with identifying the microbes that made certain soils disease-suppressive. In a single field, there may be areas where a disease never develops. "It works on similar lines to our immune system, where not all individuals are affected similarly by the same infection," says Sharma. Researchers have tried identifying the microbial component contributing to this. Although some microbes have been identified, capturing the entire gamut of microbes that underlie the suppressive quality of soils has proved hard.

Researchers have sought to transfer the suppressive abilities of soil by simply transplanting suppressive soil into unhealthy soil. The idea is analogous to faecal microbiota transplant (FMT), a procedure where faecal matter from a healthy donor is transplanted to a recipient to restore a dysfunctional gut microbiome. The scale of transplant, however, is much smaller in FMT compared to field-level transplantation.

"It is a herculean task," says Podile. Converting several hundred tonnes of surface soil into beneficial soil demands repeated microbial inoculations, increasing organic matter content in the soil and much more, he explains. Sharma points out that there is still no means of storing a good microbiome in the matrix, which is the soil in this case. Although she has done some small-scale field trials, she is still developing the tools to conduct this on a large scale. That cannot happen until there is an effective way of storing the soil with microbes while retaining their functionality.

Despite the challenges, soil transplantation is the goal of many soil researchers. Sharma is working on an Indian map of suppressive soils. In the initial phase, her team took samples from over 150 sites that have suppressive soils in six Indian States. They found that Bacillus and Pseudomonas were richer in suppressive soil than in non-suppressive soil. The different species of the two genera may have contributed to the superiority of the suppressive soils. "My long-term goal is to simply have a method in place wherein we could ask the farmers to identify good soil, and just sprinkle it onto bad soil." It may sound simplistic and even idealistic, she reckons, but it is still a goal she is chasing.