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Seed Microbiome May Hold Uncommon Ability to Benefit Next Generation of Plants

Seed microbiome may hold uncommon ability to benefit next generation of plants

At the conclusion of a pilot study for Michigan State University’s Plant Resilience Institute, or PRI, microbial ecologist Ashley Shade had a hunch that started a chain reaction of exciting interdisciplinary and international collaboration and landed Shade and her team a three-year, $750,000 USDA National Institute of Food and Agriculture grant to investigate the seed microbiome of the common bean.

“I ran a pilot project to look at the microbiome associated with the roots of the common bean during stress, but the plant set seeds during the study,” said Shade, an assistant professor in the Department of Microbiology and Molecular Genetics in the MSU College of Natural Science and PRI faculty member. “So I thought, why not? Let’s look at the seed microbiome, too, and what we saw was something really interesting: it looked like stress contributed to an alteration of the microbiome in the seed.”

Shade took her pilot data to MSU plant biologist Chad Niederhuth, assistant professor in NatSci’s Department of Plant Biology and BioMolecular Science, and Matthieu Barret, a research scientist at the French National Institute for Agricultural Research, or INRA. The team of scientists wrote a research narrative based on her hunch: that the seed microbiome directly effects the next generation of plant.

This summer, the team will embark on the exploration of the microbiome of Phaseolus vulgaris, or common bean, an important crop for food security in developing nations and for sustainable agriculture in the United States and around the world.

“There are so many questions,” said Shade, who, along with Barret and Marie-Agnes Jacques also from the INRA, recently published a review about the lack of knowledge regarding seed microbiota in the scientific journal Current Opinion in Microbiology. “We know that there are beneficial and pathogenic microbes that can be passed from generation to generation via the seed but, compared to other parts of the plant, we know very little about it.”

Shade and her team will test several hypotheses. Does it matter if the seed microbiome is altered during stress? Will the alteration provide the next generation of plants with microbes that help it respond to stress with more resilience, or will it be detrimental to the plant, especially if the next generation is not exposed to the same stress?

“Whenever you have a complex set of interactions, it can be tough to dissect the role of any one component,” said Niederhuth. “In helping to plan this project, my goal was to design experiments that allow us to alter one of the components and see how it changes the whole in order to determine if the epigenome contributes in any way to the inheritance of the microbiome.”

A seed microbiome includes the community of bacteria, archaea and fungi found on both the surface and inner parts of the seed. The team will focus on the inner-seed microbiome, surface sterilizing the seed and soaking it to extract the microbial DNA for high-throughput DNA sequencing techniques.

Barret, an expert in seed microbiota who has been investigating seed transmission of microbial assemblages for the last five years, will be conducting parallel experiments at the Research Institute of Horticulture and Seeds in Angers, France. “The international aspect of the grant is crucial to help advance phytobiome science and its translation into sustainable crop production practices,” said Barret. “Indeed, multi-site experiments are essential to generate knowledge that is greater than just the sum of separate studies.”

If Shade’s team is able to pinpoint common bean’s beneficial microbes, they may be able to isolate and add them back to ready-to-plant seeds, leaving the next generation better off: more resilient to changes in climate and more able to handle drought and nutrient saturation.

“This could be really important because manipulating a microbiome in the field is hard,” said Shade. “There are already techniques developed for biological seed treatments, so it is an interesting avenue to find isolates that are potentially beneficial.

“We definitely have our eye towards translational applications,” Shade said. “The possibilities for improving common bean’s resilience to climate change are extremely exciting for the future of sustainable agriculture, but there is a lot of work before that.”

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