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From crops to livestock, the diversity of Canada’s agriculture plays a critical role in not only national food security but the sustainability of food systems worldwide. In the face of climate change, we stand to lose a lot. Extreme weather, shifting precipitation, and increasing incidents of crop diseases highlight threats to our food production systems. Yet, the agriculture sector itself is a contributor to the problem, generating about eight per cent of Canada’s overall greenhouse gas emissions annually. The calls for ambitious action to develop new technologies, products, and approaches to reduce emissions in the agriculture sector and to help Canada achieve net zero by 2050.

In response to this major challenge, launched Climate Action Genomics and through its  they are investing $25.7 million in novel genomic research and innovation to reduce greenhouse gas emissions and the carbon footprint of Canada’s food production systems. Today, the Honourable Greg Fergus, Parliamentary Secretary to the Prime Minister and to the President of the Treasury Board, announced that Queen’s researcher (Biology) and co-project lead (University of Manitoba) will receive $3 million in funding from this initiative. With in-kind contributions, the team has secured more than $6 million to advance their research in developing alternative microbial fertilizers.

"Genomics is driving innovation across many strategic economic sectors in Canada, from agriculture and energy to fisheries and forestry," says the Honourable Greg Fergus. "The Government of Canada is proud to support these Interdisciplinary Challenge Teams, which are building resilience in Canada’s food production systems, creating more secure and sustainable food for Canadians and people around the world." 

Finding alternatives

For over 50 years, industrial chemical fertilizers have been the go-to solution for plant nutrition in commercial agriculture, leading to a dramatic rise in crop yields. However, they also account for up to 20 per cent of GHG emissions associated with all plant and animal agriculture in Canada. Because they are imported, chemical fertilizers are not custom formulated for the diverse Canadian climate and they are also a major economic cost to our farmers. In 2022, the government specifically identified use of chemical fertilizers as an area of focus in its , with aims to reduce GHG emissions associated with fertilizers by 30 per cent compared to 2020 levels. But a reduction or discontinuation of chemical fertilizers is risky: reducing crop yields can affect our national food security.

With the funding from Genome Canada, diCenzo and team will be examining alternative ways to promote crop nutrition, and their focus is microbial inoculants, tiny organisms like bacteria, found within the soil itself.

"Microbes can be found all around us, with a single gram of soil potentially containing more microbes than the number of humans on earth," says Dr. diCenzo. "Microbes have interacted and evolved with plants for hundreds of millions of years and have developed many ways of helping plants grow and survive, such as by providing plants with important nutrients of protecting them from pathogens. Increasing the abundance in agricultural soils of microbes naturally adapted to Canadian soils and able to support crop health, could improve their benefits to plants and promote sustainable Canadian agriculture."

Produced for outdoor agriculture since the 1800s, microbial inoculants have shown encouraging results in laboratory conditions and in the field with certain legume crops. Microbes promote plant nutrition by providing a sustainable source of nitrogen, converting insoluble phosphorous in the soil, and promoting the development of root systems. They can also improve plant resiliency against environmental threats including drought, salt, and heat stress, particularly critical in the face of unexpected weather events.

While promising, microbial products need improvement. They can be unpredictable, there is limited jurisdictional regulation on use or effectiveness, and the past sale of poor-quality products has led to distrust from farmers. Realizing the full potential of microbial inoculants to complement chemical fertilizer means developing both the biotechnological innovations and a social framework, where trust can be rebuilt with farmers, and governments can establish regulations and incentives.

Canadian-focused solutions

Drs. diCenzo and Oresnik aim to generate new microbial inoculants for Canadian agriculture. To do this, the team will isolate microbes from Canadian soils, analyze how microbes survive in different soils and plant-associated environments across the country, using metagenomic sequencing, and study interactions using Canadian crop varieties. This will generate a collection of diverse microbes from Canadian soils that can be further developed into commercial products. They will also identify plant-functional traits improving the benefit plants derive from microbes, for use by plant breeders developing climate-smart crop varieties.

The genomics data will help build predictive models that will facilitate "informed inoculation" in Canada, where farmers are given an inoculant most likely to be successful in their field, based on routine tests of soil quality and microbial composition.

Within 10 years of the project ending, the team projects the application of their research could reduce chemical fertilizer use by 30 per cent for cereal and brassica (cabbage and mustard family, like canola) crops. It could also potentially eliminate the need for nitrogen fertilizers in bean crops, of which only 40-50 per cent is assimilated by plants, removing powerful GHGs created in the runoff.  

Their research will also form the basis for the Canadian Collection of Agricultural Soil Microbes at Queen’s, a first of its kind in Canada, which will host an open access, publicly available, culture collection to facilitate sharing of microbial and genomics resources across the country. The approach supports a twofold benefit, ensuring the research dissemination is widespread and accelerated, while further motivating the inoculant industry in Canada to tap into the billion-dollar global biofertilizer market, spurring economic growth.

"By putting all project deliverables in the public domain, the open science approach leads to an advanced technical starting point for all entrepreneurs and companies interested in commercializing microbial products for agriculture," says Dr. diCenzo. "This allows for more players to attempt solving downstream issues, increasing the likelihood that a commercial product will ultimately reach the market."

Building trust

However, the research team is keenly aware that, for microbial inoculants to curtail agricultural GHGs, there needs to be widespread adoption of the technology. Rehabilitating relationships in the industry goes hand in hand with their research to eliminate the current unpredictability of microbial inoculants.

Drs diCenzo and Oresnik are collaborating with the major Canadian grower organizations to understand their perspective on inoculants and hurdles to adoption. Through continual engagement with these advocacy groups and with farmers, they aim to ensure the community’s concerns are heard and used to update research directions, build trust through data sharing, and ultimately lead to widespread adoption for producers looking for alternative fertilizers. Public awareness of the role of microbes in food production and their potential to lower GHG emissions is also critical. As consumers, the team recognizes the public’s influence on market forces and hopes they can also leverage it to build consciousness of GHGs and a desire to purchase food produced using lower emission systems.

"While we are realistic and do not expect our microbial products to be able to fully replace chemical fertilizers at this point, we hope for them to be used synergistically, and for us to do this in partnership with the farming community," says Dr. diCenzo. "Ideally, microbial products can allow for a significant reduction of chemical fertilizers, and thus GHG emissions, without sacrificing yield. Microbes hold exciting possibilities for the future of Canadian agriculture and farming."

To learn more about the project and the Climate-Smart Agriculture and Food Systems initiative, visit .