Exploration of the canola root microbiome discovered that an abundance of Serratia bacteria in canola roots relates positively to canola yield. Could this bacteria become a yield-boosting inoculant?

Above: A map of canola’s core microbiome.

Jean-Baptiste Floc’h with Agriculture and Agri-Food Canada created this map of fungal species interaction in the canola rhizosphere. Size of the circle represents the relative abundance of the fungus species. The darker the green, the more significant its interactions with other fungi. Pink arrows indicate a negative interaction; green is a positive interaction.

Otu1 is Olpidium brassicae. While abundant, the light green colour of its node suggests that it does not respond to environmental influences the same way as others do.

The interaction between Otu3 and Otu6 (Humicola grisea spp.) is strong because these are two variants of the same species.

Otu56 (Exophiala spp.) is a small but dark circle, indicating low abundance but high interaction. Exophiala produces exophillic acid, an anti-viral compound, and other secondary metabolites that could antagonize microorganisms detrimental to canola.

“We should do more research on this,” says AAFC research scientist Chantal Hamel.

Root bacteria relates to higher canola yield

Billions of microorganisms live in every gram of healthy soil. In this world exist those things we know a bit about – such as mycorrhizae fungi and clubroot spores – but also so many more that researchers are just starting to discover. Since plant roots work through and around those microorganisms, it makes sense to explore this crowded mini-frontier to find other species that are potentially beneficial or pathogenic to crops.

Chantal Hamel, research scientist with Agriculture and Agri-Food Canada in Quebec City, is working to identify the “core microbiome” for canola – which are microorganisms “always associated with the plant.” She has been involved in two recent microbial discoveries that could help with canola productivity.

Serratia bacteria

Hamel worked with Marc St-Arnaud and Chih-Ying Lay, researchers at the University of Montreal, on a field project that demonstrated how the abundance of Serratia bacteria on roots relates to canola yield. The research was based on DNA sequencing data from replicated plots at Lacombe, Alberta, Beaverlodge, Alberta and Brandon, Manitoba.

The fact this bacteria correlates with yield and inhabits canola roots is significant. “When a yield-enhancing bacteria is more comfortable inside the plant, it is more reliable and we can manipulate it,” Hamel says. “It could become an inoculant.”

When beneficial bacteria exist in the soil but not on or in the root, their beneficial performance for the crop can be hampered by factors in the soil environment. These factors can include soil pH, organic matter and other microorganisms, Hamel says. That could be the case for Penicillium bilaii, for example, which is commercially available for its ability to dissolve phosphorus in the soil and make it more available for crop uptake.

“We don’t yet know how Serratia works to increase canola yield,” Hamel says. It could solubilize phosphorus, act as growth hormone, protect canola from pathogens, promote beneficial rhizobacteria or something else, she says, adding: “Bacteria can promote growth in many ways.” As researchers continue this work, they will isolate Serratia to test it directly on canola to see if it promotes growth.

Parasitic fungi of canola

Researchers have known about the virus-carrying fungus Olpidium for a long time. To prep for a new Prairies-based study, Chih-Ying Lay had to dig up and analyze the literature from 1878 to 2017. “There was a lot of confusion,” Hamel says, “but with this study, we cleared out much of it.”

For one thing, molecular genetics can now differentiate two common species among the genus: O. brassicae and O. virulentus. In non-brassica hosts, Olpidium infection is more likely due to O. virulentus, which is a carrier for several important disease-causing viruses, Hamel says. Good news for canola, so far, Olpidium brassicae was not found to carry viruses.

The study also demonstrated how large these populations can be. In 2014, when Prairie soils were moist at the time of sampling, 70 per cent of the microbial population in canola roots was O. brassicae. Interestingly, only 10 per cent of the microbial population in pea and wheat roots was O. brassicae. In 2013, when soil conditions were comparatively dry at sampling, numbers were not so high. What this means is that O. brassicae is a very canola-specific microorganism and it likes moisture.

Canola plants with high levels of O. brassicae don’t seem to be sick, Hamel says, but research hints that there may be some mild growth depression. “So far, no literature can prove O. brassicae is good for canola growth, but research is too sparse to conclude anything,” Hamel says. “With such abundance, Olpidium could be displacing detrimental microorganisms.”
What further research on Olpidium, Serratia and canola’s core microbiome could produce, Hamel says, are “inoculants containing the most influential microorganisms to create a beneficial root environment and canola bred for beneficial root associations.”