Soil microorganisms are at the heart of the new green revolution

An interview with researcher Chantal Hamel

Organic Agriculture Centre of Canada

Chantal Hamel, a soil microbiologist who works at Swift Current, Saskatchewan, for Agriculture and Agri-Food Canada (AAFC), is clear: "We must innovate. The nitrogen in synthetic fertilizers is derived from expensive processes. Reserves of phosphorus are measured in decades; the mines will be empty someday.  In addition, the cultivation of biofuels is now competing with food crops and mobilizing soils and inputs. And there will be 8 billion people on Earth in fifteen years!" The alternative is to develop farming practices based on the properties and activities of soil microorganisms to allow crops to feed effectively.

The concept behind Hamel’s work is simple. It is based on the association of soil fungi and bacteria with plants to ensure their mutual survival. The plant captures carbon from the air to produce energy, in the form of sugars, through photosynthesis. Fungi and bacteria, which cannot photosynthesize, need this energy. So, they settle on the roots of plants, absorbing sugars provided by the plant in exchange for minerals that they draw out of the air and soil. This process is free, natural, requires no human intervention and allows both the plants and microorganisms to gain access to the materials that they need to survive.

"The nitrogen supplied by microorganisms does not cost anything, while it is very expensive to industrially capture nitrogen from the air in the form available to plants,” says Hamel.  The Haber-Bosch process, used to fix nitrogen from using extreme pressure applied at very high temperatures is very energy intensive. The energy required for this operation represents 70% of the cost of the generated nitrogen fertilizer. Yet, soil microorganisms can perform this role for free, and merit closer examination than what they currently enjoy.

Chantal Hamel became interested in mushrooms, a larger fungus than those she currently studies, while walking in the countryside of Rivière à Pierre, north of Quebec City where, as a child, she spent the summer at the cottage of her grandparents.  More attracted by the beauty of the natural world than by mathematics in the academic setting, she headed towards the 'big city' of Montreal. After several years on the job market, she resumed her studies, this time in agronomy at McGill, allowing her to pursue her interest in nature and the food needs of the planet. Her first session was a challenge: she had to learn the language of Shakespeare along with the basics of agronomy, but she prevailed.  She then enthusiastically began a Master’s degree on mycorrhizal fungi with a grant from the Research Council Natural Sciences and Engineering Research Council of Canada (NSERC). This was the beginning of a long scientific quest to discover more about the role of fungi in the soil, those tiny microbes that are difficult to count and often associated with disease rather than soil health. Her subsequent doctoral thesis dealt with the transfer of nitrogen from nitrogen-fixing legumes and associated grasses with mycorrhizal fungi.

Unlike animals, plants do not have the ability to move to survive. Instead, their strategy is to change their environment, attracting beneficial organisms such as rhizobia and mycorrhizal fungi with which they partner. This symbiosis is very effective: the plant is an almost infinite source of energy as it feeds on the sun's rays, all the while nourishing the fungi and rhizobia housed in its roots that continuously extract nutrients from the soil and air to support their host.  But, this symbiosis does not develop when high amounts of nitrogen or phosphorus fertilizers are applied to the soil. With a plentiful supply of nutrients, the plant does not need to depend on this symbiosis and so represses it. The result: the plant loses the benefits of this association, and the now free beneficial soil fungi do not grow and may even disappear.

Organic farming relies heavily on the development of a rich soil to ensure fertility. The living soil is home to billions of microorganisms that live in symbiosis with plants. Chantal Hamel has a research project with the Organic Science Cluster, the goal of which is to define “Predictive tools for characterizing mycorrhizal contributions to phosphorus uptake by organic crops”. She explains the project: "You start at the base and identify fungi in the soils of wheat fields on different sites (SK, NS, MB, AB, ON). The goal is to understand what is growing in organic soils. We need the cooperation of producers to gather information about the farming methods that are used. Since organic farmers keep extensive records as part of their organic certification, we used the directory of organic farmers and seed producers to choose our sample sites, distributing the sampling on various types of soil whose description was already documented in the federal databases. We then study the fungi content of these soil types and models are made to predict the likely contribution of fungi in a given site based on indicators."

Knowing what's in a field is expensive, because the biotrophic fungi do not grow in laboratory dishes, only on live plants. They are microscopic and hard to identify. Samples will be screened, centrifuged, separated according to the weight of the constituents and examined microscopically. Analysis of nucleic DNA to identify fungal species is not possible, due to the numerous copies of unique genes inside fungi.  Instead, researchers examine mitrochondrial DNA, which is unique.  
Some rhizobia bacteria, associated with nitrogen fixation, are also very interesting and valuable, as they stimulate plant growth. Research will confirm the potential of these bacteria as legume inoculants and will help in selecting the most rewarding legumes for the soil and crops.

The fungus-plant symbiosis is essential for organic production, where plants feed naturally in the absence of the ecological imbalances that may result when synthetic fertilizers are applied. "It remains to convince industry to invest in this type of research. There is a lot of outreach to do to promote innovative projects whose scope is the medium to long term," says Chantal Hamel, observing the current prevalence of short-term views in many programs.

Hamel also observes that many people do not make the connection between the meals they eat and agriculture. Food in grocery stores is almost all imported from California, China or New Zealand, a tendency which cannot be described as sustainable consumption. Canola has become the second most prevalent cultivated crop in Saskatchewan, where Hamel works, second only to wheat.  This prevalence is due in large part to the rising demand for canola oil.  Low crop diversification has resulted.  Canola is a plant that does not "mycorrhize", or form associations with soil fungi.  As a result, canola production becomes increasingly dependent on synthetic fertilizers.  Without active fungi that access and alter soil phosphorus, which is characteristically poorly soluble and slowly available, the soil's ability to provide phosphorus is reduced. Soil fungi solubilize phosphorus and make it available to allow targeted, clean and efficient use of this precious resource, which is why they are necessary to maintain the biodiversity of soils.

In the summer, Chantal admires the flowers in her native plant garden that requires no care. She observes the minks, ducks and pelicans during her morning jog along the river when getting to work, and finds that life in Swift Current is very nice. The morning of her interview, she discovered an effective biochemical marker for quantifying mycorrhizal fungi, a marker so perfect that she felt much emotion. "Sometimes we find!" she says happily.

This article was written by Nicole Boudreau, Organic Federation of Canada, on behalf of the OACC with funding provided by Canada’s Organic Science Cluster (a part of the Canadian Agri-Science Clusters Initiative of Agriculture and Agri-Food Canada's Growing Forward Policy Framework).  The Organic Science Cluster is a collaborative effort led jointly by the OACC, the Organic Federation of Canada and industry partners. For more information: or 902-893-7256.

Posted June 2012