Under the Lens: Plant microbiomes could cut agriculture’s dependence on chemicals, says Davide Bulgarelli

The microscopic organisms living around plant roots may hold the key to reducing agriculture’s reliance on chemical fertilisers and other non-renewable inputs, according to plant microbiome researcher Dr Davide Bulgarelli.

Speaking in the latest episode of Under the Lens, a video series from Applied Microbiology International (AMI) and The Microbiologist, Dr Bulgarelli explained how plants actively shape the microbial communities that surround their roots – known as the rhizosphere – and how understanding these interactions could transform crop production.

Hosted by Professor Emmanuel Adukwu, Professor of Applied Microbiology and AMI Trustee, the interview explores how advances in plant microbiome research could improve crop resilience while helping agriculture meet ambitious sustainability goals.

Incredibly dynamic

Dr Bulgarelli, a Reader at the University of Dundee and recipient of AMI’s Dorothy Jones Prize in 2022, described the rhizosphere as one of nature’s most complex ecosystems.

“The rhizosphere is an incredibly dynamic environment,” he explained. “Plants don’t simply grow in soil – they actively recruit and interact with microorganisms that can influence their health, nutrition and resilience.”

These microbial communities help plants acquire nutrients, defend themselves against disease and respond to environmental stresses. By understanding these natural partnerships, researchers hope to develop agricultural systems that rely less on synthetic fertilisers and chemical inputs.

A route to more sustainable farming

Modern agriculture faces the challenge of producing more food while reducing its environmental footprint. Dr Bulgarelli believes plant microbiome research could play an important role in achieving that balance.

Rather than replacing conventional farming overnight, he envisages microbiome-based approaches complementing existing agricultural practices to improve nutrient use efficiency and enhance crop performance naturally.

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The long-term goal, he said, is to help decouple agriculture from chemical inputs by harnessing beneficial microbes that already exist in nature.

However, he cautioned that translating laboratory discoveries into practical farming solutions requires a detailed understanding of the complex relationships between plants, microbes and their environment.

Every root tells a different story

One of the most exciting developments in the field, according to Dr Bulgarelli, is the ability to study microbial communities at increasingly fine spatial resolution.

Researchers once analysed the microbes associated with an entire root system as a single sample. New techniques are revealing that different sections of a plant’s roots can host distinct microbial communities, each with its own unique characteristics.

This detailed picture is opening new avenues of research and helping scientists understand how plants shape their microbial partners with remarkable precision.

Dr Bulgarelli also highlighted growing links between plant microbiome research and discoveries in human microbiome science, with advances in one field often inspiring progress in the other.

The importance of long-term investment

While scientific understanding of plant-associated microbes has expanded rapidly in recent years, Dr Bulgarelli said continued investment will be essential if the field is to deliver practical benefits.

He called for sustained support for research aimed at improving the sustainability of crop production, reducing dependence on non-renewable agricultural inputs and helping to decarbonise farming.

“If these are the goals society wants to achieve, they need to be reflected in long-term research priorities,” he suggested.

As researchers continue to uncover the “secret life beneath the roots”, the tiny organisms living in the soil could become powerful allies in building a more resilient and sustainable food system.

The full interview with Dr Davide Bulgarelli is available as the latest in the Under the Lens series from The Microbiologist.

This Under the Lens conversation is available to subscribers of The Microbiologist and to AMI members.