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Pathogens can’t hide under the covers

Research published in Phytobiomes shows that cover crops could help improve the health of crops.

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Not all crops are grown for cash. After the harvest, many farmers grow cover crops to protect the soil or increase nutrients in their fields. New research by Rémi Maglione and colleagues shows that in addition to these benefits, cover crops could also help fight pathogens.

While there are many known benefits to cover cropping, there may also be hazards. Cover crops are known to alter the microbial communities in the soil. But is the same true above ground? Could cover crops pass on pathogens to the main crop? Maglione and colleagues examined how Secale cereale, ryegrass, affected microbes in the phyllosphere, the part of plants above the ground. 

They examined how rye affected the prevalence of Pseudomonas syringae, a common bacterial pathogen that affects many important agricultural crops. If rye could foster helpful bacteria, it may reduce the damage done by P. syringae.

A rainbow of pumpkins and squashes, if your idea of a rainbow starts at orange and ends at green.
Pumpkins and squashes. Image: Canva.

The team grew P. syringae-inoculated squash in fields that were over-wintered under four different conditions: winter rye cover crop, chemically-terminated winter rye cover crop, plastic cover, and bare soil. They compared the pathogen loads on the squash plants by culturing P. syringae from their leaves. The team also characterized the microbiomes of over 2,200 leaf samples to examine how cover cropping affects the microbial community aboveground. They found that cover cropping reduced populations of P. syringae and increased the abundance of genera such as Sphingomonas and Methylobacterium, which have been used as biocontrol agents against pathogens.

It isn’t known for sure how rye prevents infection by P. syringae, but the authors have some ideas. One possibility is that rye is an awful host. In their paper, Maglione and colleagues state: “The greatest effect of cover cropping on both the phyllosphere community and P. syringae abundance was observed early in the growing season. P. syringae begins life on leaves as an epiphyte but then must colonize host tissue through stomata or wounds… Disease severity could be lowered if the early establishment and survival of P. syringae is compromised.”

Other suggestions include cover crops preventing harmful microbes from establishing themselves by altering soil moisture or temperature.

“To our knowledge, our study is the first to explore the importance of the phyllosphere microbiome in the context of cover cropping practices. Our results suggest that cover cropping treatments can be used to manipulate biological interactions to protect plants against pathogens,” said co-author Martin Laforest in a press release.


Maglione, Rémi, Marie Ciotola, Mélanie Cadieux, Vicky Toussaint, Martin Laforest, and Steven Kembel. 2021. “Winter Rye Cover Cropping Changes Squash (Cucurbita Pepo) Phyllosphere Microbiota and Reduces Pseudomonas Syringae Symptoms.” Phytobiomes Journal. https://doi.org/10.1094/pbiomes-04-21-0029-r

Dale Maylea

Dale Maylea was a system for adding value to press releases. Then he was a manual algorithm for blogging any papers that Alun Salt thinks are interesting. Now he's an AI-assisted pen name. The idea being telling people about an interesting paper NOW beats telling people about an interesting paper at some time in the future, when there's time to sit down and take things slowly. We use the pen name to keep track of what is being written and how. You can read more about our relationship with AI.

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