Let’s dig for the root of the plant microbiome

Researchers seek more knowledge about the micro-organisms that live in and around the plant. Scientists aim to use their findings to help farmers improve their crops.

by Taryn Milton

Perhaps paradoxically, we can think of the plant microbiome – or the microbial community in and around the plant – as both an old and a recent field of study.

Researchers have studied aspects of the plant microbiome for hundreds of years. In fact, over 200 years ago, people realized the nodules on legumes play a role in how plants grow, says Dr. George Lazarovits. He is the research director at A&L Biologicals in London, Ont.

Early scientists “discovered that those nodules fix nitrogen for beans and related species. Believe it or not, (these scientists) actually moved tons of earth from fields where these rhizobia live to fields where they didn't so (farmers) could grow beans, soybeans and white beans,” he says. Rhizobia are soil bacteria that fix nitrogen in legume root nodules.

The term microbiome has a much more recent history, as researchers first defined it in the late 1980s, says a June 2020 article by biologist Gabriele Berg and others in the journal Microbiome.

Today, many scientists across the country and around the world study the micro-organisms (also known as microbes) in the plant microbiome. These researchers seek to understand how micro-organisms work together to protect the plant and help it thrive. Scientists have made some intriguing discoveries, but their work underscores the fact that we still have much to learn.

So, this month, we talk to Canadian researchers about the plant microbiome. We learn about their studies and the next steps in scientific discovery. Ultimately, the advances in this scientific field could help producers improve their sustainability and yields in their farm fields.

The basics

The plant microbiome has a few important spheres.

wheat plant rhizosphere
This photo shows an uprooted wheat plant and its associated rhizosphere. This zone of soil is influenced by the roots. Microbes are highly abundant and active in this area, and they interact closely with the plant. - Dr. Étienne Yergeau photo

The rhizosphere encompasses all the micro-organisms that live in close association with the plant’s roots. The spermosphere “is a microbiologically active zone of soil surrounding a germinating seed,” says Dr. Vladimir Vujanovic. This sphere is “of vital importance for the improved plant vigour and early establishment.”

Vujanovic is a professor and an agri-food innovation chair in agricultural microbiology and bioproducts at the University of Saskatchewan (USask) in Saskatoon.

The microbiome extends above the ground too. The phyllosphere exists on the surface of the above-ground parts of the plant, such as the leaves and stems. Finally, the semosphere “is the aerial or above-ground zone surrounding plant fruits or wheat heads. This sphere harbours air and seed microbiomes to maximize crop yield and transgenerational grain quality,” Vujanovic says.

Vujanovic and Dr. James Germida, another researcher at USask, named the semosphere in 2016. The Canadian Journal of Plant Science published their findings in February 2017.

The microbiome and crops

Now that we have a better lay of the microbiome land, we can turn to a discussion of the relationship between the plant and its microbiome.

The microbiome “interacts with the plants. The microbiome can give the plant all kinds of services. … There are microbes associated with plant roots, for instance, that can access nutrients in the soil that the plant cannot access itself,” Dr. Étienne Yergeau tells Better Farming. He is an associate professor of microbial ecology at the University of Quebec in Laval.

The micro-organisms also help the plant fight off pathogens.

Although different than the immune system of mammals, plants do “have some kind of immune system,” Yergeau says. “The good microbes in the microbiome compete with pathogens. So, the (good microbes) might occupy the space and use the resources, which would prevent a pathogen from infecting a plant.”

Basically, the micro-organisms in the plant microbiome help determine if a crop will do well or not.

Research tools

“The ability to study the plant microbiome has only more recently been available to us,” says Dr. Ivan Oresnik. The way we study it “now, I could not have even imagined when I was doing my PhD.” He completed his graduate research in the late 1980s and early 1990s.

Oresnik is an associate professor in the department of microbiology at the University of Manitoba in Winnipeg.

When Oresnik started studying the plant microbiome, it was difficult for scientists to perform DNA sequencing So, researchers did not use this technology often. But, within the last 10 years, scientists have developed the technology to support more in-depth research.

Soil Sample close to plant
Dr. Ivan Oresnik and his team pull soil samples from locations very close to the plants. - Dr. Ivan Oresnik photo

Scientists use DNA sequencing technology to study the chemical building blocks that comprise the DNA molecule. The cost associated with using this technology has decreased, while the research capabilities have expanded, Dr. Jennifer Town tells Better Farming. She’s an Agriculture and Agri-Food Canada (AAFC) research scientist in Saskatoon who specializes in soil microbiology.

“Around 2010, you could do tens of samples. Now, you can do hundreds of samples. You can deeply characterize the microbiome. You can get down to almost complete coverage of the microbiome. So, that makes a huge difference,” she says.

“That technology has really changed the way that we can look at the microbiome and the size of the studies that we can do.”

Current research

Despite these scientific advances, “we still don't know what the majority of microbes in the soil do and how they interact with plants,” says Dr. Antoine Pagé. He is a research officer in Montréal with the National Research Council as well as an adjunct professor at McGill University.

So, scientists across Canada are hard at work to fill in some of these gaps in knowledge and advance the industry.

Vujanovic, for example, focuses on the earliest stages in plant life by studying plant prenatal care.

He sees this subfield as “offering unique opportunities for integrating microbiome tools in a plant breeding program, thus maximizing performance of crops under changing environmental conditions,” he tells Better Farming.

Vujanovic wants to find micro-organisms that are in the plant from the beginning to the end of its growth and help them thrive. He also wants to try to get farmers more involved in research projects.

“Plant microbiologists are in dire need of farmers’ feedback since our future farming system and bioeconomy are greatly dependent on a beneficial seed microbiome,” he says.

Yergeau is also interested in helping crops thrive – particularly under difficult growing conditions. He studies the wheat microbiome and how it responds to drought. His team wants to “engineer the microbiome to have plants that would be more resilient to drought,” he says.

In addition, Yergeau studies how a wheat plant competes with its microbiome for nitrogen.

“In the lab, I first try to understand. Then, I try to manipulate the microbiome,” he says.

Pagé shares this interest in the wheat microbiome and how it affects the plant’s access to nutrients. He studied micro-organisms that could help wheat acquire more nitrogen and phosphorus when the soil it’s grown in is deficient in these nutrients.

bioreactor to culture microbes
Dr. Antoine Pagé and his team use this bioreactor to culture beneficial microbes. - Dr. Antoine Pagé photo

In this study, Pagé and other researchers identified a list of microbes that could help the plant. Ultimately, the scientists hope others can build on their findings to use these microbes to improve commercial production.

Pagé’s work on the microbiome branches into other agricultural crops. In his latest project, he aims to develop a sustainable protein production program that will focus on the pulse – and specifically the field pea – microbiome.

Lazarovits has extensive experience in the study of the plant microbiome, having conducted research in this area for over 32 years. In his most recent project, he aims to take bacteria that are present in healthy corn fields, but absent in poor ones, and create a fertilizer with the bacteria.

test tubes potato
In this project, Dr. George Lazarovits and his team looked at potato nodal explants inoculated with a single bacterium species called Paraburkholderia phytofirmans (PsJN). The control plants have less developed roots. - Dr. George Lazarovits photo

“Every country in the world looks to reduce the amount of chemical inputs in its agricultural (production) and use more of the natural processes,” he tells Better Farming. “This will be a fairly inexpensive technology. You can grow these microbes relatively cheaply and apply them to the soil with the technology we have already for the application of fertilizers.”

Crop rotations also influence the ability of a plant to thrive.

Oresnik and Town are both conducting research in this field. Oresnik studies how crop rotations that include soybeans affect the soil microbiology.

Soil Sample microbiomes
Dr. Ivan Oresnik studies the top three inches (eight centimetres) of soil to look at the microbiomes. - Dr. Ivan Oresnik photo

“The goal is to find what bacteria should be present to benefit the plant,” he tells Better Farming. “Many people are looking to plant-growth-promoting rhizosphere bacteria. However, having a strong, stable bacterial community could also thwart pathogenic microbes from becoming part of the soil population.”

Town focuses her research on wheat, canola and corn production. She wants to determine how crop rotations affect the plant and soil microbiomes.

“Is the microbiome more diverse or less diverse with crop rotation? Do those changes in diversity correlate to things like better nitrogen availability, better phosphorus availability, and better carbon cycling in the soil? How efficient is the community at decomposing plants’ material?” asks Town.

She also studies the effects of tillage on the plant and soil microbiomes. Fields with little or no tillage generally show more efficient microbiomes in the soil, says Town.

Micro-organisms form networks and work in close association with one another. “Tillage can physically break up those networks and then they have to re-establish themselves,” she says.

Look to the future

As scientists across Canada study the plant microbiome, the agricultural research community and industry will benefit from having all this information available in one place. So, the Government of Canada's Genomics Research and Development Initiative (GRDI) launched the Ecobiomics Project in 2016.

Lori Phillips and James Macklin are AAFC researchers who are helping to create this national database, says Town.

“It’s a database for researchers to share their soil microbiome data,” she says. “Once we get this database established, it can be a real resource for researchers to look at national trends.”

Scientists still have a lot to discover about the plant microbiome, Pagé says.

“This is only the beginning. There will be more that we can achieve in the next years and decades. Even for microbiologist, there are a lot of unknowns as to the systems that (microbiomes) constitute. Untangling all the parts and understanding how they interact will affect farmers for sure,” he says. BF

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