Plants don’t grow in isolation. Their roots and leaves play host to thriving microbial communities. And just like the bacteria in our guts many of these microscopic organisms are beneficial to plants. They provide nutrients, help plants survive extreme drought, and even boost plant defenses. In exchange, plants provide a food source—carbon—for the microbes. Many plant immunologists, including HHMI-GBMF investigators Jeff Dangl and Sheng Yang He, are beginning to explore these relationships.
Dangl’s lab group at the University of North Carolina at Chapel Hill is studying how a plant encourages the beneficial community of microbes that live in and around its roots. In August 2012, his team published a paper in Nature describing their analysis of the hundreds of types of bacteria that mingle with the roots of the plant Arabidopsis thaliana. They compared the microbes in and around the roots of Arabidopsis plants with different genetic backgrounds grown in different soils. The team discovered that the soil close to the roots contained only a small subset of all soil bacteria. Inside the roots, the effect was amplified: even fewer bacterial species had settled in and concentrated their numbers inside the plants’ root cells. This suggests that certain types of bacteria may be actively excluded by a plant’s immune system, while others might be ignored or even encouraged to grow.
Dangl has a group of about 10 people in his lab working on the Arabidopsis root microbiome. They’ve isolated more than 500 microbes from the inside of surface-sterilized roots grown in wild soils so far. In addition to sequencing and classifying these bacteria, they are studying how individual microbes influence characteristics such as root length, root branching, and leaf size; how the microbes interact with each other; and the roles played by individual bacteria. Ultimately, Dangl would like to understand how plants assemble a population of beneficial microbes that can provide them with nutrients and protection from pathogens.
Sheng Yang He is focusing on how a plant’s microbiome affects how well its leaves respond to pathogens. His team at Michigan State University has created microbe-free Arabidopsis plants and is looking at changes in growth and disease susceptibility. They’ve noticed that the microbe-free plants tend to have weakened immune systems and are hypersensitive to infection. Without a microbiome, plant genes related to immune response in the leaves appear to be less highly expressed. “You need the microbiome to train the immune system,” He says. In concept, the idea parallels how the gut bacterial population in humans benefits the immune system.
Eventually, both Dangl and He hope their work will lead to a probiotic cocktail for crops. A dose would create a stable, beneficial bacterial community that promotes plant growth and immunity. Not unlike an Activia yogurt for plants.
-- Nicole Kresge
HHMI Bulletin, Winter 2014