Charting a pathway to plant probiotics

Combining metagenomics, genomics and bacterial cultivation provides evidence for a role of rhizosphere bacteria in defence against disease.
Published in Microbiology
Charting a pathway to plant probiotics

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Human microbiome research over the past 15 or so years has shone a light on microbiology that shows no signs of dimming. Researchers continue to report rosters of human microbiomes, and are working out the mechanisms  that underpin community contributions  to health, physiology and disease.  Biotech-relevant microbiomes from farm animals including pigs and ruminants are now in the literature.  And biotech companies are  developing and marketing a vast array of microbiome-related products for humans and animals.  

But  what about plants?  

 Plant roots and leaves have long been known to be colonized with commensal microbial communities that contribute to crucial plant functions. Curation of microbial communities has been reported in model plants and crops, and reported links between defined communities, nutrition and defence (PMID:28297714) have bolstered the notion that microbiome products to improve plant growth and defence against disease might actually be feasible. Further more, salicylate signalling (defence hormone) has been shown to modulate membership of the root microbiomes in model plant Arabidopsis (PMID:26184915).  

Reporting in Nature Biotechnology, Jihyun Kim and colleagues use culture independent metagenomic sequencing to detect tomato rhizosphere microbiome alterations that contribute to bacterial wilt resistance. Using a combination of sequencing, microbiome transplantation experiments, and bacterial cultivation informed by metagenomics, they investigate the role of the rhizosphere bacteria in bacterial wilt resistance.  They hypothesize that 'disease-resistant tomatoes may recruit bacterial allies to protect themselves from infection'.  Piece by piece the evidence base for using microbiome members in products to improve crop yields is growing and funders are taking note (see Breakthrough Energy Ventures funding for Pivot Bio). Exciting times are on the horizon for those working at the interface between microbiology and plants. 

Image: Artist's representation of a healthy tomato plant (right) with ‘bodyguard’ bacteria in its rhizosphere and a wilted tomato (left) infected by the pathogen Ralstonia solanacearum. Courtesy of Irin M. Kim, Seoul Women's University, and Jihyun F. Kim. Plant photo by Seon-Woo Lee.

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