Unlocking the potential of the plant microbiome

MSU microbial ecologist Ashley Shade is seeking to learn more about how microbes positively affect plant health and adapt to environmental pressures.

Ashley Shade

In recent years, there has been a lot of information published about the importance of gut bacteria and the various ways they influence human health. From eating a nutritious diet to taking probiotic supplements, the ideas revolve around boosting the body’s natural community of microorganisms to more efficiently do their jobs — digestion of food and uptake of nutrients, as well as optimizing immune system function.

Much like the human gut microbiome, plants rely on their surrounding microbial communities. Several thousand types of microorganisms reside within the plant and soil. But beyond comprehending the massive volume of microbes and some of the ecosystem services they provide, scientists know very little.

Ashley Shade, a microbial ecologist and assistant professor in the Michigan State University Department of Microbiology and Molecular Genetics, is seeking to learn more about how these microbes positively affect plant health and adapt to environmental pressures.

“The majority of these microorganisms are good,” said Shade, who is also a faculty member in the Department of Plant, Soil and Microbial Sciences. “We know that not all of them are serving an essential function for plant health, but some are helping to cycle nutrients, activate plant defense mechanisms and respond to stresses.”

In 2018, Shade joined the Plant Resilience Institute (PRI) at MSU, an initiative that launched in 2016 as a part of the Global Impact Initiative. Its mission is to enhance the ability of plants, particularly agricultural food crops, to cope with climate change. Within PRI, Shade focuses on understanding the stress response of the plant’s microbiome.

With funding from the U.S. Department of Agriculture’s National Institute of Food and Agriculture, Shade is studying how the seed microbiome of common bean, an important food crop for people around the world, reacts to stress.

Her team includes Chad Neiderhuth, an assistant professor in the MSU Department of Plant Biology, and Matthieu Barret, a research scientist with the French National Institute for Agricultural Research. They are investigating whether there are significant implications of the seed microbiome’s changes as a response to drought or excess nitrogen. She wants to know if those alterations will help or hurt future generations of the plants.

The principle objective is to identify beneficial microbes that can possibly be added to seeds before planting, allowing the next generation of plants to weather climate disturbances more easily.

“We know that common beans attract microbes that fix nitrogen, which is important for healthy soils and productive plants,” Shade said. “We want to leverage the microbiome to do that in the most efficient way possible. But if the seed microbiomes changes in a negative way, it is possible that ecosystem services won’t be as effective.

“For agriculture to be sustainable in the future, we need resilient plants that can deal with increasing pressures. Managing the plant microbiome is one approach that we can use to promote resilient, productive plants on a changing planet.”

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