Scientist roots for microbes to counter plant diseases

Nature India: What is microbiome engineering?

Shilpi Sharma: Microbiome engineering involves changing the composition or function of microbial populations in a habitat. Microbiomes, or microbial communities, can be engineered to have desirable features that benefit human health, plant well-being, and restore the environment.

Traditionally, humans tinkered with the environment to reshape microbial communities for a specific purpose. A classic example is the recommended intake of fibrous diet, which enriches human gut microbiota. Current microbiome engineering involves strategic manipulation of specific members/functionality. With advanced techniques, we can dissect microbial communities in different environments and predict their functions.

NI: How does microbial engineering benefit agriculture?

SS: Microbiome engineering is commonly applied to the rhizosphere, the zone of soil exposed to and impacted by the roots. This portion is a hotspot of microbes selected by the plant from the soil. Plant roots produce certain chemicals (exudates) to communicate with and govern these microbes for their own benefit, such as enhancing nutrient uptake, and by naturally defending the plants against pathogens such as bacteria, fungi and viruses.

In plant-based rhizosphere engineering, we tweak the plants to create a unique soil microbiome. We select cultivars or genetically engineered plants whose roots produce exudates, influencing and shaping a distinct set of microorganisms in the rhizosphere. Microbiome-based rhizosphere engineering, in which the soil microbiome is modified, is still evolving in terms of large-scale application.

NI: How do you tweak the rhizosphere microbiome?

SS: My group has been working to reduce the severity of environmental stresses like salinity and drought in legumes and tomato through rhizosphere engineering.

We use two approaches — the top-down approach, by growing plants under repeated stress cycles of drought and salinity to get robust microbiomes that improves stress tolerance; and the bottom-up strategy to generate synthetic microbial communities (SMCs or SynComs), which are robust culture banks of potent microbial strains that can control plant pathogens.

We identify microbes that show promising plant growth properties, compatibility with one another, and ability to establish themselves in soil and plant roots. SynComs are simplified versions of natural communities with a smaller number of microbes, but more robust and efficient when compared to individual bioinoculants or their consortia.

We are far from putting together a ‘universal SynCom’, hence we attempt ‘custom-made’ SynComs for specific agroclimatic zones.

NI: Do farming practices impact the soil microbiome?

SS: Intensive agricultural practices undermine soil microbiome diversity and adversely affect various soil processes. Sustainable practices like organic farming can enrich soil microbiome, both in terms of abundance and composition. In organic fields of Delhi NCR, Himachal Pradesh, and Uttar Pradesh, we have observed that soils with enhanced microbiomes exhibit better resistance to plant diseases compared to conventional fields in their agro-climatic zones. This means these soils have a strong potential to suppress diseases.

NI: How are you engineering microbiomes in India's soils?

SS: We want to transform soil — from an environment where pathogens thrive and infect plants (conducive soil) to one that suppresses them. We will build SynComs to counter a range of plant pathogens such as those causing wilt, diseases responsible for major cash crop losses and farmers’ distress in India.

With a project called BIOTRANSFORM, we will map the microbiomes that help soil suppress plant pathogens in six Indian states. We will catalogue agricultural management practices, crop history, agro-climatic conditions and other features. We will then profile the potential of suppressiveness of soil samples against a range of bacterial and fungal plant pathogens. Eventually we intend to extend our study to other Indian states to generate a soil suppressiveness map for different states, which will be in line with the Soil Health Card, a soil nutrient status advisory for farmers.

NI: Should soil microbiomes be considered in WHO’s One Health initiative that unifies approaches to optimize the health of people, animals, and the environment?

SS: There is a strong link between soil microbiomes and gut microbiome. While soil microbiome is already a part of environmental health in a subtle way, it must be brought to the forefront in the One Health framework. Any disturbance to the soil microbiome will affect the entire ecosystem's health.