Rhizosphere Research Part 2: Getting to the Root of Plant-Soil Interaction

Posted on July 17, 2019


Part 2 of 2: Getting to the Root of Plant-Soil Interaction

In the first installation on rhizosphere research, we shared the story of researchers who are working on sequencing the DNA of microbial communities, better understanding the physical structure of soil, and applying new technologies and knowledge to farming practices and innovative products.

In the second installation, we will explore the teams of Saskatchewan researchers who are using emerging technologies, new imaging tools, and the DNA-based tools discussed in the previous article to better understand root systems in relation to nutrient uptake, plant health and breeding for adaptations to difficult environmental conditions.

Just as communities of microbes and roots are closely interrelated, each rhizosphere research team is working on a different aspect of the same body of knowledge. Some focus on nutrient uptake and others study the connection between root architecture and plant success, sharing their findings within their networks to build a greater understanding of the complex world under our feet and improving agricultural practices at the same time.

“Microbes are critical to life, not to mention soil productivity in general. We tamper with soil so much, and we need to sustain critical functions such as good nitrogen cycling—regardless of what is happening in the environment—whether it’s wet, dry, hot, or cold,” says rhizosphere bio-geochemist Melissa Arcand.

Bobbi Helgason, soil scientist at the University of Saskatchewan (U of S) and Project Co-Lead of the U of S Plant Phenotyping and Imaging Research Centre (P2IRC) says, “It’s an interesting time to be a soil scientist, because we’ve been thinking about this for decades, and now the rest of society is beginning to notice. People can relate to the idea that healthy soil is a good thing.”

“We hear a lot about how we’re 10 per cent human and 90 per cent microbiome. Plants are the same. We’ve started thinking of a plant and its microbes as a meta-organism that functions as one biological entity.”

Arcand and Helgason are part of a team of researchers studying nitrogen and carbon cycles in agricultural systems. “Natural systems are incredibly efficient, and agricultural systems have been historically more leaky. Leaky systems can put the environment at risk and cost farmers money. We want to look at how we can get what we can out of the inputs that need to go into a field, and ultimately use fewer inputs. We know where the leaks happen—we just need to tighten them up,” says Arcand.

This research has immediate implications for the control of greenhouse gasses, such as nitrous oxide and carbon dioxide in crops and pastures. Root systems in agricultural fields contribute to the huge soil carbon sink that needs to be better understood. If plants don’t absorb nitrogen fertilizer it can end up as nitrous oxide in the atmosphere where it captures 300 times more heat than CO2.

Within P2IRC Helgason and Arcand work closely with Leon Kochian, the Canada Excellence Chair in Global Food Security and Associate Director of the Global Institute for Food Security, as well as Steven Siciliano, NSERC/COOP Industrial Research Chair in Risk Assessment and Remediation. Kochian is trying to identify which areas of plants’ genomes affect root development and interact with the microbiome. Siciliano explores how the plant-microbiome stabilizes critical soil ecosystem services such as water purification, climate regulation and food production.

In studying how plants affect the soil microbiome, and how the soil microbiome in turn affects plants, Kochian’s ultimate goal is to understand how plant roots improve production, and how to breed for that outcome. “We want to get better at translating crop improvements related to root structure and nutrient acquisition so we can help breeders select for better root traits,” he says.

Saskatoon is the right place and now is the right time to be doing root and rhizosphere research. With the support of Western Economic Diversification Canada (WD) and Innovation Saskatchewan, the Sylvia Fedoruk Canadian Centre for Nuclear Innovation at the U of S, in partnership the University of Regina, developed the world’s only root imager that can observe root function in intact soils. Steve Siciliano says “With Positron Emission Tomography (PET), we can simultaneously look at root structure and function within soils.”


Developing technologies and PET imaging will allow researchers to:

  • monitor microbes in the soil;
  • watch how nitrogen is fixed by microbes and made available to plants;
  • observe how microbes solubilize phosphorous and make it available to plants;
  • observe how carbon in the atmosphere is absorbed by plants and turned to sugar;
  • identify which microbes offer plants support in suppressing diseases.


“These new tools and technologies will help us understand the biological processes in soil much better. We can nuance our questions in ways we’ve never been able to before,” says Arcand.

The research team is excited about combining technologies, such as imaging using stable isotopes and microbial community profiling. “With new imaging technologies, we can watch a nutrient go into a microbial community and identify who is using it or taking it up. It’s like the microscope resolution went up 100,000 times.”

By understanding what factors create thriving root and microbial relationships, breeders will be able to select for those traits. “Can we breed plants robust enough to recruit beneficial microbes and create these networks across multiple environments and soil types?” says Siciliano.

While the potential for discoveries that will change the face of agriculture grows daily, so does the need to expand the diversity of research teams working to find answers to increasingly complex questions.

Kochian says “Agriculture is becoming big science. It is truly interdisciplinary, across biological, physical and mathematical sciences. The team we’re building includes a computer scientist specializing in computational biology, physicists who are experts in using X-rays and neutrons to image roots, engineers who build phenotyping systems with sensors and imaging, as well as soil microbiologists.”

He adds, “Agriculture in the future is going to look a lot different than it does now. Plant breeding, too. And having tools for precision agriculture that take into account what is going on below ground is part of that evolution.”

Read Rhizosphere Research Part 1: Digging into Soil

by Noelle Chorney