Industrially-produced fertilizers play an important role in agriculture, and are partially responsible for large increases in global crop yields since the 1970s. Despite their benefits, these fertilizers have limits. Using them accounts for up to 20% of all greenhouse gas emissions in Canadian agriculture, with production of nitrogen fertilizer estimated to be the largest consumer of fossil fuels in agriculture. In addition, a major portion of chemical fertilizers used in Canada are imported, exposing Canada's food production systems to risks from unstable political situations abroad. Moreover, chemical fertilizers are a major economic cost for farmers, especially with the rapid price increases in the past few years. A different method of promoting crop nutrition would therefore have environmental, economic, and food security benefits for Canadians. Bacteria and eukaryotic microbes are a potential alternative to fertilizers. Plant-associated microbes can support crop productivity with reduced nutrient inputs [1-7]. However, aside from rhizobia that form tight N-fixing symbiotic interactions with legumes [1], microbial inoculants for other crops have largely failed to reach their potential outside controlled lab conditions [8]. Together with our collaborators and industrial supporters, we are working to identify Canadian microbes with plant-growth promotion abilities, and to develop them into effective microbial inoculant products for use by Canadian growers.
Rhizobial inoculants for legumes
Legumes (e.g., bean, peas, chickpea, soybean, lentils, alfalfa, clover) are unique in their ability to associate with rhizobia to form root nodules that can satisfy the complete nitrogen demands of the plants thereby eliminating the need for synthetic N fertilizer. Effective commercial rhizobial inoculants are available for several legumes. For example, commercial soybean inoculants have resulted in growers being able to produce soybean without nitrogen fertilizer. However, this is not the case for all legumes. A notable example is Phaseolus vulgaris, better known as common bean. Green beans, kidney beans, and navy beans are just some of the examples of the types of beans produced by P. vulgaris plants. Although bean plants can establish nitrogen-fixing associations with various rhizobial species, it is considered a poor nitrogen-fixing plant, and effective nitrogen-fixing rhizobium inoculants do not exist [9]. We are interested in isolating novel rhizobia from Canadian soils and screening them for their abilities to support the growth of legumes in Canada, with a current focus on common bean, adzuki bean, and peas. Specifically, we aim to:
- Generate a collection of rhizobial isolates derived from Canadian soils. We are using nodule trapping experiments to isolate rhizobia from geographically diverse areas in Canada, with a focus on Ontario. All strains will be genome sequenced to allow for an understanding of the genetic determinants that contribute to rhizobia being effective legume symbionts in Canada.
- Identify and evolve rhizobia with superior symbiotic properties in the Canadian context. Not all rhizobia are equally effective at competing for interaction with a given legume species, or at fixing nitrogen during the symbiosis. It is therefore important that new rhizobial isolates be screened for their nodulation and nitrogen fixation capacities to identify those with potential for development into commercial inoculant products for Canadian fields. We are also using laboratory methods to improve the efficacy of our rhizobial isolates.
- Evaluate rhizobium strain x plant cultivar interactions. The effectiveness of the symbiosis is influenced by the genotypes of both the plant host and the bacterial symbiont. To ensure that newly identifies rhizobia are effective with bean and pea cultivars grown in Canada, we will screen our top performing rhizobia with plant cultivars routinely grown in Canada to identify the best plant - rhizobium combinations. Incorporating screenings into plant breeding programs will also help to maximize the nitrogen-fixing efficiency of future bean and pea cultivars for Canadians.
Microbial inoculants for cereals and brassicas
In the Canadian market, there are currently few live inoculant products available to support the nutrition of non-leguminous crops like cereals (e.g., wheat, barley) or brassicas (e.g., canola). One notable exception is Delftia acidovorans sold by Lallemand Plant Care that was isolated from the rhizosphere of Manitoban canola [10]. The lack of products is largely a result of microbial inoculants often performing unpredictably in the field [8]. Together with our collaborators, we aim to use novel approaches to develop new microbial products to support Canadian growers, as well as tools to support growers and inoculant producers in the application and development of new products. Specifically, we hope to:
- Generate a genome-sequenced library of Canadian plant-associated microbes. To support us and others in identifying promising new microbes for development as inoculants, we are working to produce a large and publicly-available library of plant-associated soil microbes (bacteria and fungi) from across Canada. All microbes in this collection will be genome-sequenced.
- Characterize and improve the plant-growth promoting abilities and other industrially-relevant phenotypes of promising microbes. In collaboration with others, we are screening our microbial isolates for their ability to support crop nutrition, as well as for other industrially-relevant properties like growth in bioreactors and desiccation tolerance; microbes that lack these properties are unlikely to be commercializable. Our consortium is also using laboratory methods to improve the relevant properties of our prospective inoculants.
- Characterize the soil microbiomes of Canadian agricultural fields. We are using shotgun metagenomics and metatranscriptomics, as well as amplicon sequencing, to better understand the microbial communities of Canadian agricultural fields, and to understand how they might interact with novel microbial inoculants.
- Develop models to support inoculant production and application. We aim to develop new models to support the development of the inoculant industry in Canada. With our collaborators, we hope to produce economic and environmental models to determine when the production or application of an inoculant is environmentally beneficial and economically feasible. We also aim to develop machine learning models to help predict whether a new microbial isolate has potential for development into an inoculant product, and to predict which inoculants are likely to be effective in a given field on a given crop.
Funding
Support for this research has been provided by Genome Canada, Genome Prairie, Ontario Genomics, Manitoba Crop Alliance, Manitoba Pulse and Soybean Growers, Western Grain Research Foundation, Sask Wheat, and the Ontario Bean Growers.
[1] Poole P, Ramachandran V, Terpolilli J. (2018) Rhizobia: from saprophytes to endosymbionts. Nature Reviews Microbiology. 16: 291–303. HTML
[2] Alori ET, Glick BR, Babalola OO. (2017) Microbial phosphorus solubilization and its potential for use in sustainable agriculture. Frontiers in Microbiology. 8: 971. HTML
[3] Haskett TL, Tkacz A, Poole PS. (2021) Engineering rhizobacteria for sustainable agriculture. The ISME Journal. 15: 949–964. HTML
[4] Kuan KB, Othman R, Abdul Rahim K, Shamsuddin ZH. (2016) Plant growth-promoting rhizobacteria inoculation to enhance vegetative growth, nitrogen fixation and nitrogen remobilisation of maize under greenhouse conditions. PLOS ONE. 11: e0152478. HTML
[5] Vyas P & Kaur R. (2021) Culturable endophytic Pseudomonas fluorescens Z1B4 isolated from Zanthoxylum alatum Roxb. with stress-tolerance and plant growth-promoting potential. BioTechnologia. 102: 285–295. HTML
[6] Leigh J, Hodge A, Fitter AH. (2009) Arbuscular mycorrhizal fungi can transfer substantial amounts of nitrogen to their host plant from organic material. New Phytologist. 181: 199–207. HTML
[7] Faber BA, Zasoski RJ, Munns DN, Shackel K. (1991) A method for measuring hyphal nutrient and water uptake in mycorrhizal plants. Canadian Journal of Botany. 69: 87–94. HTML
[8] Kaminsky LM, Trexler RV, Malik RJ, Hockett KL, Bell TH. (2019) The inherent conflicts in developing soil microbial inoculants. Trends in Biotechnology. 37: 140–151. HTML
[9] Wilker J, Navabi A, Rajcan I, Marsolais F, Hill B, Torkamaneh D, Pauls KP. (2019) Agronomic performance and nitrogen fixation of heirloom and conventional dry bean varieties under low-nitrogen field conditions. Frontiers in Plant Sciences. 10: 952. HTML
[10] Perry BJ, Bergsveinson J, Tambalo DD, Yost CK. (2017) Complete genome sequence of Delft acidovorans RAY209, a plant growth-promoting rhizobacterium for canola and soybean. Microbiology Resource Announcements. 5. HTML
[2] Alori ET, Glick BR, Babalola OO. (2017) Microbial phosphorus solubilization and its potential for use in sustainable agriculture. Frontiers in Microbiology. 8: 971. HTML
[3] Haskett TL, Tkacz A, Poole PS. (2021) Engineering rhizobacteria for sustainable agriculture. The ISME Journal. 15: 949–964. HTML
[4] Kuan KB, Othman R, Abdul Rahim K, Shamsuddin ZH. (2016) Plant growth-promoting rhizobacteria inoculation to enhance vegetative growth, nitrogen fixation and nitrogen remobilisation of maize under greenhouse conditions. PLOS ONE. 11: e0152478. HTML
[5] Vyas P & Kaur R. (2021) Culturable endophytic Pseudomonas fluorescens Z1B4 isolated from Zanthoxylum alatum Roxb. with stress-tolerance and plant growth-promoting potential. BioTechnologia. 102: 285–295. HTML
[6] Leigh J, Hodge A, Fitter AH. (2009) Arbuscular mycorrhizal fungi can transfer substantial amounts of nitrogen to their host plant from organic material. New Phytologist. 181: 199–207. HTML
[7] Faber BA, Zasoski RJ, Munns DN, Shackel K. (1991) A method for measuring hyphal nutrient and water uptake in mycorrhizal plants. Canadian Journal of Botany. 69: 87–94. HTML
[8] Kaminsky LM, Trexler RV, Malik RJ, Hockett KL, Bell TH. (2019) The inherent conflicts in developing soil microbial inoculants. Trends in Biotechnology. 37: 140–151. HTML
[9] Wilker J, Navabi A, Rajcan I, Marsolais F, Hill B, Torkamaneh D, Pauls KP. (2019) Agronomic performance and nitrogen fixation of heirloom and conventional dry bean varieties under low-nitrogen field conditions. Frontiers in Plant Sciences. 10: 952. HTML
[10] Perry BJ, Bergsveinson J, Tambalo DD, Yost CK. (2017) Complete genome sequence of Delft acidovorans RAY209, a plant growth-promoting rhizobacterium for canola and soybean. Microbiology Resource Announcements. 5. HTML