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BENEFIT: How soil microbes hold a key in reducing GhG emissions

They’re Invisible. They’re Everywhere. And They May Be the Next Big Thing in Farming.

Microbes. They’re tiny. They are entirely invisible to the human eye and everywhere on Earth. Microbes cover every surface and flourish in the most inhospitable environments, ranging from many kilometres beneath the Earth’s crust to the deepest depths of the Pacific Ocean to atmospheres just below outer space.

Close to Earth’s habitable surface, countless microbes are floating around. About 40 trillion microbes have been identified as living on or in an individual human body. Scientists estimate there are at least millions of different species of microbes, possibly as much as a trillion, although only about 24,000 have been named to date.

Microbes include bacteria, archaea, fungi, viruses, and protozoa. They are the planet’s most extraordinary ecosystem. Whereas microbes are often thought of as the root cause of infections and diseases, the vast majority sustain a huge portion of life on our planet. If microbes were to vanish suddenly, so too would most other life.

The interdependent relationship life shares with microbes is a significant avenue of curiosity and innovation within science. Now more than ever, researchers are looking closely at the interactions between microbes and plants and how they promote growth. Now, researchers from Queen’s University in Kingston, Ontario, and the University of Manitoba and other research institutions, via a recently announced genomics project, are examining the possibilities of leveraging microbes as a possible replacement technology for industrially produced fertilizers.

“The BENEFIT project is focused on identifying and developing new microbial inoculants for agriculture in Canada as well as understanding how plants respond to these inoculants,” said Dr. George diCenzo, project co-lead and Assistant Professor at Queen’s. “We want to use genomics to help drive our selection of microbes that will be developed into inoculants. We will be generating a large collection of microbes collected from Canadian soils, and genomics will help prioritize which strains are most likely to be useful.”

The microbial bioinoculants produced would act as substitutes for conventionally used fertilizers, which can be expensive to buy and apply and contribute to greenhouse gas emissions.

Interest in microbes was a significant factor in making the BENEFIT project a reality. In 2023, Genome Canada, in collaboration with Genome Prairie, granted major project funding to BENEFIT via the Climate-Smart Agriculture and Food Systems initiative. BENEFIT (short for “Bio-inoculants for the promotion of nutrient use efficiency and crop resiliency in Canadian agriculture”) has secured more than $6 million in funding support, including $3 million from Genome Canada and additional support from several Canadian commodity organizations, Queen’s University, and the University of Manitoba, among others.

“The main goal of the BENEFIT project is to develop inoculants that would maintain current crop yields with reduced nutrient input, essentially allowing farmers to decrease the amount of fertilizer they have to apply,” said diCenzo. “The project will focus on nitrogen fertilizer, but we are also interested in phosphorus and other chemical inputs.”

“Of the different fertilizers, nitrogen is the one that has the biggest impact in terms of greenhouse gas emissions, so the project’s primary focus is trying to reduce the application of nitrogen fertilizers without adversely affecting crop production.

“But it’s also important to remember that industrial fertilizers are important to agriculture as they play a key role in growing our crops.”

Fertilizers are essential in modern agriculture, bolstering crop yields to feed a growing global population. Among these fertilizers, nitrogen-based fertilizers occupy a prominent position. Using nitrogen fertilizers has revolutionized agriculture, enhancing crop production and global food security. According to Statista, the use of nitrogen-based fertilizers has exploded over the past half-century. From an estimated 46 million metric tons in the 1960s to nearly 200 million metric tons today. In Canada alone, almost 3 million metric tons were used by crop growers in the year 2021.

Nitrogen fertilizers are a relatively new agricultural advancement. It wasn’t until the early 1900s that mass production of nitrogen fertilizers was revolutionized. The Haber-Bosch process, invented by German chemists Fritz Haber and Carl Bosch, made it possible to convert atmospheric nitrogen into ammonia, providing a reliable source of nitrogen for agriculture. More than 100 years on, their process is still used today.

The production and use of nitrogen fertilizers using the Haber-Bosch process is not without its downside. The process is energy-intensive and consumes significant amounts of natural gas, releasing carbon dioxide into the atmosphere during production.

“It takes a lot of energy. The Haber-Bosch process uses natural gas to produce H2 and heat nitrogen gas to over 400 degrees Celsius at 200 to 400 times atmospheric pressure to create ammonia. It is estimated that about 1 to 2% of the global energy supply is used specifically for this process.”

Moreover, said diCenzo, nitrogen fertilizer use in the field can lead to nitrous oxide emissions, a potent greenhouse gas.

“When these industrial fertilizers are applied to the soil, about 50% are used by targeted plants, and the other 50% becomes runoff, or it’s converted to nitrous oxide by microbes in the soil, which has about 300 times the warming potential compared to carbon dioxide.”

The urgent danger posed by climate change and a heating planet has created momentum to provide food producers with alternative fertilizer options with less greenhouse gas emissions. diCenzo said microbial inoculants not only hold the potential to reduce carbon emissions, but they could also hold the potential to reduce artificial fertilizer use.

“There’s a lot of potential in microbes. When we look at these microbes in labs, we’ve found they have a lot of abilities that are useful for plants, like nitrogen fixation, which means they can essentially produce nitrogen fertilizer themselves.”

Even with the drawbacks of using synthesized nitrogen, diCenzo recognizes why their usage is widespread, because, unlike many inoculants, industrial fertilizers play a powerful card at the table: dependability.

“One farmer may use an inoculant, and it works, and their neighbour might use the same inoculant, and it doesn’t work. Why is that so? It could mean there are differences in soil properties and other possibilities because, in nature, there’s incredible variability.

“You know what you’re getting with chemical fertilizer, and in many cases, inoculants right now are more unpredictable. As a farmer using an inoculant instead of a nitrogen fertilizer, you have a risk that it won’t work. So, I can understand there being hesitation to make a switch.”

Still, diCenzo is upbeat the BENEFIT project will make significant strides in its attempt to develop more effective and, thereby, dependable inoculants.

“We will be generating an extensive collection of microbes taken from Canadian soils, and genomics will help prioritize which strains are most likely helpful. Genomics will help us to understand the molecular responses between plants and inoculants, which can help breeders in the future. Suppose we find out which genes or pathways are essential to benefit from inoculants. That information might be useful for breeders to guide the future development of climate-smart crop varieties best able to capitalize on these particular inoculants.”

Ultimately, diCenzo is very upbeat about how the BENEFIT project will significantly impact how food is grown.

“We also want to use genomics to understand the inoculants better and help guide their development. We want to use different methods to try and naturally improve their ability to interact with plants or survive dry conditions.

“There’s a lot that still needs to be researched, but I believe that microbes could be a huge part of the future of food in Canada.”


For more information about this article, the Climate Smart Agriculture and Food Systems initiative, or to get more information about any Genome Prairie managed projects, please contact the Genome Prairie communications office:


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