Rhizosphere Research Part 1: Digging into Soil

Posted on June 19, 2019

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Half of plants’ physiology is underground and most of their functions and interactions with the soil are unseen—until now. A network of researchers is working to understand several aspects of the rhizosphere, the area of the soil where plant roots and microbes interact.

As technology continues to evolve in leaps and bounds, soil scientists are finally able to see the interactions between plants and the microbiome that surrounds them. In the first of two installations on the rhizosphere, we’ll explore emerging research aimed at understanding the content and structure of the soil microbiome, and how that understanding can improve agricultural management.

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Feature 1 of 2: Digging into Soil

In Pursuit of Microbial DNA
The scope of what we don’t know about the rhizosphere far outweighs what we do. Sean Hemmingsen, a scientist at the National Research Council specializing in DNA sequencing of microbial communities, is quick to point out that a full 30% of life on earth, bacteria of the Candidate Phyla Radiation (CPR), weren’t even known to exist until 2016.

“CPRs are extra small, so often get filtered when we’re profiling a community. They are obligate symbionts that live in association with other things. They are extremely closely adapted to the plants they are associated with,” says Hemmingsen.

Hemmingsen and his colleagues are exploring the use of Polymerase Chain Reactions (PCR) to amplify genes for DNA profiling. They’re looking for ways to separate clusters from individual microbes and track biologically distinct strains to identify their interactions with plants.

“This field is young—we and others are working on the next generation of microbial community profiling, developing quantitative methods that are comprehensive,” says Hemmingsen.

There is still a long way to go. “A complete description of a microbial community that is quantitative and includes all the different organisms, where they are in three dimensional space, how they interact with nematodes, and other soil inhabitants, which ones are active in which situation (dry, wet, anaerobic), would be difficult, but extremely useful,” he says.

“A farmer that uses technology wants to know macro- and micro-nutrient levels in their soil. They ship them off for analysis and get information on pH, nutrient content and so on. What we’re looking for is the next generation where the biome is included. Micro- and macro-nutrients can help with your decisions. Another question would be: is this a good crop to put in this year, considering the microbiome? Or would a different crop be a better choice?”

The Long Term Effects of Agriculture on Soil Health
Long term research programs like the “Historical ABC Rotation” in Lethbridge has a full century of data showing how bulk soil changes and crops respond to varying rotations. Newton Lupwayi is part of AAFC Lethbridge’s soil microbiology team. “We’re trying to answer two questions: How are agricultural practices affecting soil microbiology? And, how can we manipulate soil micro-organisms to benefit agriculture?”

The research team has confirmed that microbial diversity is affected by crop rotations. In Rotation ABC, continuous wheat cropping with added fertilizer has been maintained indefinitely, with a very well established microbiome thriving in the soil. Fallow years and tillage have a negative impact on the microbiome and crop performance, while organic carbon and regular crop rotation have a positive impact.

“Diverse above-ground communities make diverse soil communities. This isn’t just about nutrient uptake, but also biological pest control for root rots and other disease fungi. In a diverse environment, some soil microbes attack disease fungi,” says Lupwayi.

Understanding Soil Structure
Other researchers are studying the structure of that soil—and how different soils behave as aggregates—because soil structure creates spaces for air pockets and water uptake.

“The better soil holds together, the better air and water move through it,” says Angela Bedard-Haughn, a soil scientist with the College of Agriculture and Bioresources at the University of Saskatchewan. “Healthy soil is good for plant nutrition because of water movement as well as biology. It must be well drained but have enough medium sized pores to retain the water and nutrients in solution to support plant growth.”

Root-soil relationships have an impact on soil fertility and stability, as well as salinity and water uptake. Understanding these relationships can inform the development of precision management approaches for nutrient management and irrigation.

Novozymes’ “One-Acre Study”
The scale of the potential for putting biological inputs to work for agriculture is just beginning to be understood. Novozymes’ Agriculture and Biofuels Division conducted a “One-Acre Study” to test the impact of added enzymes and microbes to various aspects of the feed corn-to-poultry agricultural chain.

They discovered that using enzymes and microbial additives at each phase of production, such as adding a microbe to corn seed that increases phosphorous availability, increased corn production on one acre to the extent that they could feed 900 chickens and use the excess corn and waste products to make ethanol and biodiesel. The use of enzymes and microbes reduced the addition of phosphorous fertilizer, produced protein-rich animal feed, and saved over a metric ton of greenhouse gasses per acre.

The Rhizosphere and the Future of Sustainable Agriculture
With several research teams making new discoveries in their areas of expertise, our knowledge of this previously unknown realm will grow. Researchers agree that biology has an important place alongside chemistry in agricultural practices.

Research organizations are taking steps to increase their capacity for soil health studies. “Agriculture Canada has recruited a lot of soil microbiologists lately,” confirms Lupwayi. The invisible world beneath our feet may be the key to long-term sustainable agriculture and feeding the planet.

Watch for Feature 2 of 2: Getting to the Root of Plant-Soil Interaction- continuing the exploration of soil and root interactions through imaging, tracing the movement of nutrients and phenotyping root architecture.

by Noelle Chorney