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Víctor Carrión Bravo

Plants do much better in some soils than in others, thanks to a bacterial community that helps fight soil plant pathogens. Bacteria settle on plant roots and form the first line of defence. Some of them move into plant roots, and Víctor Carrión Bravo discovered how they contribute to additional defence when a pathogenic fungus manages to penetrate roots.

Unlocking the secrets of disease-suppressive bacteria

Although plants are threatened by many pathogens, they often survive. Not only do they possess their own immune system to combat any attacks, they also get help from micro-organisms that live in and around plant roots. Some soils are called suppressive, as they harbour a microbial community that protects plants against soil pathogens. ‘This can be utilised to develop sustainable and environmentally friendly crop production systems’, Víctor Carrión Bravo states.

Earlier research of suppressive soils revealed that certain bacteria settle on plant roots, forming a so-called rhizomicrobiome. As a first line of defence, many of these bacteria were shown to help keep out pathogens. Some of them are able to enter root tissue, forming an endophytic microbiome, and Carrión wanted to know if these endophytic bacteria help destroy pathogens that resisted the first line of defence and invaded the roots, and to what extent they contribute.

To find out, he grew sugar beet seedlings in plastic trays on soils that were either suppressive against the root pathogens or conducive to them. ‘We sampled these soils on sugar beet fields. On spots where plants flourished, we collected suppressive soils. On spots where they withered, we took conducive soil samples.’ In half of the trays, he inoculated the soil with the soil pathogenic fungus Rhizoctonia solani, a common pest for sugar beet. When the pathogen was added, plants did well in suppressive soils, just as he expected; in conducive soils with fungus, plants languished and most of them died.

‘I hope that our results will form a new basis in agriculture, changing the predominantly chemical-based practices towards organic and sustainable farming, avoiding the extensive use of pesticides.’

After four weeks, Carrión analysed the root endophytic microbiome in plants grown in conducive soils without the fungus, suppressive soils without the fungus and suppressive soils to which the fungus was added. He sequenced DNA extracts from the roots and identified and quantified the bacterial DNA. Plants grown in suppressive soil to which the pathogen had been added turned out to contain much more bacteria than plants from either suppressive or conducive soils without the pathogen; in particular Chitinophaga and Flavobacterium strains were enriched.

He also analysed which genes these bacteria expressed in plants in the presence of the pathogen. It turned out that the endophytic Chitinophaga bacteria produced among others chitinase, an enzyme capable to help break down chitin, which is a major compound of fungal cell walls; Flavobacterium bacteria produced several metabolites that may have an antibiotic effect.

To confirm the role of Chitinophaga and Flavobacterium bacteria in plant defence, Carrión added seven strains to sterile soils - either alone or in combination - and inoculated the soils with the pathogenic fungus. Sure enough, sugar beet plants grew well in these soils; they did best when strains of both bacterial groups were combined. Apparently, the combination acts as a consortium, whereby Chitinophaga destroys the chitin layer on fungi, which induces the production of an antifungal compound by Flavobacterium. Finally, when he induced a mutation in one of the relevant genes in Flavobacterium, its disease-suppressive effect disappeared.

‘Our results highlight that endophytic root microbiomes harbour a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out’, Carrión concludes in a Science publication of November this year, presenting his results. He says: ‘I hope that our results will set a new basis in agriculture, changing the predominantly chemical-based practices towards organic and sustainable farming, avoiding the extensive use of pesticides.’


Víctor Carrión Bravo (Málaga, 1983) dedicated most of his time in education and as a research scientist investigating microbial-mediated defence mechanisms involved in plant protection against pathogens. His PhD research in Málaga brought him to Wageningen University in the Netherlands in 2011. After obtaining his PhD, he returned to the Netherlands as a postdoctoral researcher. Since 2018, Carrion is an assistant professor in Leiden.

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