Genetics of host plants determine which microbes they attract, study finds

Plant roots often form microbial communities, which can affect plant health and development. Although recruitment of these microorganisms is determined by multiple factors, it is unclear whether genetic variation in the host plant plays a role. In a new study, researchers at the University of Illinois at Urbana-Champaign explore this question, and their work could help improve agricultural productivity.

“Previously, researchers have only studied the types of microorganisms associated with plants, but not the factors that may drive the formation of these communities and how we can control these drivers through plant breeding,” said CABBI’s Angela Kent. ), professor of natural resources and environmental sciences.

Microorganisms form complex communities in and around plant roots, called the microbiome. Host plants can use chemical signals to determine which microorganisms are invited into their roots. These microorganisms are called endophytes. They can also change soil properties around the roots to influence which microorganisms can grow on the root surface or around the rhizosphere.

However, in order to cultivate plants based on which microbes are associated with them, researchers first need to understand the extent to which the plant genome influences the rhizosphere microbiota.

To answer this question, the researchers studied two native Miscanthus species—Miscanthus pumila and Miscanthus minor. These plants are considered potential bioenergy crops because they require lower nutrient concentrations to achieve higher growth than conventional crops.

The study was conducted at 16 locations in Taiwan, covering a range of environmental conditions such as hot springs, mountain peaks and valleys to represent all possible extreme environments. The researchers collected 236 rhizosphere soil samples from randomly selected Miscanthus plants and isolated the microbiome within the roots.

“While the scale of this study is unprecedented, we were mindful of plant protection and quarantine regulations. We processed the samples in Taiwan, extracted the endophytic microbial community and collected the rhizosphere microbiome,” Kent said.

The researchers used two DNA sequencing techniques in their study. used DNA sequences of bacterial and fungal rRNA genes to identify the microbiome in and around roots and focus on portions of the genome unique to each species. Variation in plant genomes is measured through microsatellites, small stretches of repetitive DNA that can distinguish even closely related plant groups.

“These samples were collected 15 years ago in a project that was too big for the sequencing capabilities of the time. As the cost of sequencing has come down, it has allowed us to revisit the data and take a closer look at the microbiome during sample processing. , we also inadvertently extracted plant DNA, which we were able to use as a resource for genotyping miscanthus populations,” Kent said.

“We screened host genome sequences to understand how they affect the microbiome,” said Niuniu Ji, a postdoctoral researcher in the Kent lab. “I found that these plants affect the core microbiome, which is exciting.”

Although plant microbiomes are very diverse, the core microbiome is the collection of microorganisms found in most samples of a given group of plants. These microorganisms are thought to play an important role in organizing other microorganisms associated with the plant and aiding host growth.

The core microbiome the researchers found in miscanthus includes nitrogen-fixing bacteria found in rice and barley in other studies. All of these microorganisms play a role in helping plants obtain nitrogen, an important nutrient for plant growth. Recruiting nitrogen-fixing microorganisms may help plants adapt to different environments, but importantly, this ability contributes to the grass’s sustainability as a potential bioenergy crop.

On the other hand, genetic variation among plants has less impact on the rhizosphere microbiome, which is more affected by the soil environment. Even so, these plants place greater emphasis on recruiting fungi than other microorganisms.

Researchers are interested in dissecting which genes play a role in influencing the microbiome. “These microsatellites have no biological function and cannot represent the entire genome. It would be great if we could sequence the entire miscanthus genome and figure out how these genes affect nitrogen fixation,” Ji said.

“Crop breeding is based on yield. However, we need to look more broadly and consider how microbes contribute to crop sustainability,” Kent said. “The appeal of working with wild plants is that there is huge genetic variation to look at. We can identify which variations are good at recruiting nitrogen-fixing microorganisms because we can use less fertilizer on these crops. When we started our study, this was An exciting possibility is to use these plants for bioenergy purposes.”

The study, “Host genetic variation drives divergence of ecological roles in native miscanthus root-associated microbiomes,” was published in microbiome.