Plants select which microbes have the chance to live with them

It is common knowledge that microbes live inside plants but new research from Michigan State University has shown that plant genes actually select which microbes get to live inside to help the plant remain healthy.

Just like humans need a balanced gut bacteria community for a healthy digestive system, plants need a well-balanced microbiome community in their leaves, flowers and stem, the above-ground portion of plants known as the phyllosphere.

This is the first study to show a relationship between plant health and the balanced nature of the microbial community strategically selected by the plant’s genes. The discovery came about by accident.

“Although we have always been fascinated by the question of whether and how plants control their microbiomes to benefit health, the discovery of the particular plant genes reported in our study was by accident,” said professor Sheng Yang He at the university’s Department of Energy Plant Research Laboratory.

He said the lab was working on understanding how common bacterial pathogens work. Researchers found pathogens such as Pseudomonas syringae use toxic proteins to lower plant immune responses and disrupt homeostasis in leaves.

“In these experiments, we noticed a strange phenomenon,” He said.

The plants used in the experiments displayed spontaneous disease-like symptoms even in the absence of pathogen infection, he said.

That led to the current study that showed the disease-like symptoms were caused by the plant’s own leaf microbiome that were improperly assembled.

In the absence of plant immunity and proper water control in leaves, plants cannot assemble a normal, healthy leaf microbiome, resulting in dysbiosis, or an imbalance of microbes, a situation that resembles gut dysbiosis in humans.

He said in nature plants are bombarded by millions of microbes. He suspected that there was a balanced composition of microbes and that the number and types of microbes mattered.

The question became, “Do plants have a genetic system to host and nurture the right microbiome?”

Apparently, yes. The research team discovered two genetic networks in the plant. One involved the immune system and the other controlled hydration levels inside the leaves. Both networks work together to select which microbes survive inside plant leaves.

“When we remove both networks from a plant, the microbiome composition inside the leaves changes,” He said in a news release. “The numbers and mix of bacteria types are abnormal and our team sees symptoms of tissue damage in plants.”

Those symptoms are conceptually similar to those associated with inflammatory bowel disease in humans and, according to the scientists in He’s lab, this could be the first time a ‘sickness’ based on an imbalance of microbes is formerly described in the plant kingdom.

“This is a good example in which plants and animals use similar strategies to communicate with and regulate their microbiomes for health,” said He. “In this sense, discoveries in plant microbiome research could benefit not only plant health, but also potentially animal and human health.”

In the experiments, microbes were introduced to plants one or two at a time. The researchers extracted a community of bacteria from sick plants and inserted them in healthy plants. They also transplanted them from healthy to sick plants.

Researchers found that for plant health, both a diverse microbiome composition and a healthy genetic systems were required.

A plant with defective genetics could not take advantage of bacteria from a healthy plant and a healthy plant exposed to a sick plant’s microbiome suffered because the necessary microbes were limited or abnormal, and its genetic tools couldn’t select the right ones. The otherwise healthy plant could not fix the problem.

Compared to healthy plants, the sick plants had 100 times more microbes in a leaf, but the population was less diverse. The researchers carried out thousands of one-on-one bacterium face-offs to see which strains were more aggressive. In the sick plants, harmful bacteria strains jumped from two-thirds of a healthy microbiome to 96 percent in the abnormal bacterial population. Helpful bacteria strains went down in number.

“It was a surprise for us because it shows the importance of these plant genes correctly selecting the right microbiome for health,” said He.

It also showed that the driver for a healthy plant is microbe diversity.

He said that when the population of microbiome is abnormally higher in a sick plant, the microbes could be physically too close to each other.

“Suddenly, they fight over resources, and the aggressive, or harmful, ones unfortunately win. Healthy plants seem to prevent this takeover from happening.”

He said that microbial diversity may be part of a long-term solution to solving climate-related global issues.

“A major effort in future research should be to assemble a better and climate-resilient microbiome to help plants cope with climate stresses to endure health and productivity of crop fields and natural plant ecosystems.”

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