Dunfield’s team explored how agricultural management practices—such as cover cropping, crop rotation, and nitrogen fertilization—shape soil microbial communities and influence key ecosystem functions like nutrient cycling and carbon storage. Using advanced molecular techniques, her team has linked microbial diversity to soil health and crop productivity, emphasizing the need to consider biological factors in sustainable farming.
Diverse soil microbial communities are essential to soil health, driving key functions like biogeochemical cycling, soil fertility, water quality, and climate resilience. However, measuring soil health remains challenging, as commonly used indicators overlook the complexity of microbial interactions. While molecular tools provide insights into microbial diversity and activity, linking this information to ecosystem functions is still difficult. To better predict how agricultural soils respond to management practices such as cover cropping and crop rotation, a clearer understanding is needed of how soil’s physical and chemical properties in turn influence microbial activity. Research shows that soil bacterial and fungal communities shift in response to these practices, impacting nutrient cycling, but a key question remains: how do these changes affect soil function and plant health? This study aims to bridge that gap by exploring the connections between above-ground biodiversity, below-ground microbial communities, and ecosystem resilience in sustainable farming systems.
Dr. Kari Dunfield and her team focused on refining best practices for maintaining soil microbial and functional diversity on farms. The research explored how agricultural management influences soil biodiversity and the critical ecosystem services soils provide, such as nutrient cycling and organic matter formation. Through long-term field trials, Dunfield’s team established baseline measurements of soil health and microbial diversity, linking these factors to key soil functions. Using molecular techniques to analyze bacterial and fungal communities alongside soil chemical and physical properties, their research provides insights into the relationships between microbial diversity, crop productivity, and sustainable farming. By integrating genomic tools and statistical analysis, Dunfield’s team highlighted the importance of considering biological factors in agricultural management decisions using advanced techniques in next-generation sequencing, including metagenomics and meta-transcriptomics to analyze microbial communities and establish functional diversity.
Dunfield’s project provided key insights into how agricultural management practices influence soil microbial communities, soil organic matter dynamics, and overall agroecosystem function. Long-term studies demonstrated that management practices such as nitrogen fertilization, cover cropping, and crop rotation diversity can significantly alter microbial communities, with cascading effects on carbon storage, nutrient cycling, and plant-soil interactions. One study found that the amount of nitrogen fertilizer used affected the makeup of soil organic matter. Higher levels of fertilizer led to more breakdown of plant-based compounds by microbes and increased the amount of lignin, a tough organic material, from crop residues in the soil. Similarly, the team’s findings revealed that cover crops shape fungal and bacterial communities, potentially influencing crop productivity, while also changing the responses of mycorrhizal fungi to water levels. These findings highlight the intricate relationships between management practices, microbial diversity, and ecosystem functions, emphasizing the need to consider biological factors in sustainable farming strategies. Additionally, Dunfield’s team identified manure acidification as a promising approach to reducing carbon emissions from stored cattle manure. Manure acidification is the process of lowering the pH of manure before it is applied to fields, which subsequently lowers the amount of ammonia emissions from manure as ammonia is converted into a more stable compound that is less likely to leach into the air.
This research highlights the critical role of soil microbial ecology in agricultural decision-making, advancing sustainable practices like nutrient management, cover cropping, and manure acidification to enhance soil health, biodiversity, and resilience. Dunfield’s team established soil organic matter and microbial diversity as key indicators of soil function, providing insights into how microbiomes support essential ecosystem services such as nutrient cycling, water quality, and climate resilience. These findings will inform best management practices, influence policy on soil sustainability, and equip farmers with science-based tools to balance productivity with environmental stewardship. Ultimately, this research underscores the need to protect soil as a non-renewable resource and develop resilient agroecosystems capable of withstanding climate change and environmental stress.
Arias, D. E., Veluchamy, C., Dunfield, K. E., Habash, M. B., & Gilroyed, B. H. (2020). Hygienization and microbial metabolic adaptation during anaerobic co-digestion of swine manure and corn stover. Bioresource Technology, 306, 123168. https://doi.org/10.1016/j.biortech.2020.123168
Baril, X., Durand, A.-A., Srei, N., Lamothe, S., Provost, C., Martineau, C., Dunfield, K., & Constant, P. (2022). The biological sink of atmospheric H2 is more sensitive to spatial variation of microbial diversity than N2O and CO2 emissions in a winter cover crop field trial. Science of The Total Environment, 821, 153420. https://doi.org/10.1016/j.scitotenv.2022.153420
BenIsrael, M., Wanner, P., Fernandes, J., Burken, J. G., Aravena, R., Parker, B. L., Haack, E. A., Tsao, D. T., & Dunfield, K. E. (2020). Quantification of toluene phytoextraction rates and microbial biodegradation functional profiles at a fractured bedrock phytoremediation site. Science of The Total Environment, 707, 135890. https://doi.org/10.1016/j.scitotenv.2019.135890
Chen, X., Condron, L. M., Dunfield, K. E., Wakelin, S. A., & Chen, L. (2021). Impact of grassland afforestation with contrasting tree species on soil phosphorus fractions and alkaline phosphatase gene communities. Soil Biology and Biochemistry, 159, 108274. https://doi.org/10.1016/j.soilbio.2021.108274
Chen, X. D., Dunfield, K. E., Fraser, T. D., Wakelin, S. A., Richardson, A. E., & Condron, L. M. (2020). Soil biodiversity and biogeochemical function in managed ecosystems. Soil Research, 58(1), 1. https://doi.org/10.1071/SR19067
Chen, X., Jiang, N., Condron, L. M., Dunfield, K. E., Chen, Z., Wang, J., & Chen, L. (2019a). Impact of long-term phosphorus fertilizer inputs on bacterial phoD gene community in a maize field, Northeast China. Science of The Total Environment, 669, 1011–1018. https://doi.org/10.1016/j.scitotenv.2019.03.172
Chen, X., Jiang, N., Condron, L. M., Dunfield, K. E., Chen, Z., Wang, J., & Chen, L. (2019b). Soil alkaline phosphatase activity and bacterial phoD gene abundance and diversity under long-term nitrogen and manure inputs. Geoderma, 349, 36–44. https://doi.org/10.1016/j.geoderma.2019.04.039
Day, N. J., Dunfield, K. E., Johnstone, J. F., Mack, M. C., Turetsky, M. R., Walker, X. J., White, A. L., & Baltzer, J. L. (2019). Wildfire severity reduces richness and alters composition of soil fungal communities in boreal forests of western Canada. Global Change Biology, 25(7), 2310–2324. https://doi.org/10.1111/gcb.14641
Dukes, A. E., Koyama, A., Dunfield, K. E., & Antunes, P. M. (2019). Enemy of my enemy: Evidence for variable soil biota feedbacks of Vincetoxicum rossicum on native plants. Biological Invasions, 21(1), 67–83. https://doi.org/10.1007/s10530-018-1804-2
Fahey, C., Koyama, A., Antunes, P. M., Dunfield, K., & Flory, S. L. (2020). Plant communities mediate the interactive effects of invasion and drought on soil microbial communities. The ISME Journal, 14(6), 1396–1409. https://doi.org/10.1038/s41396-020-0614-6
Fraser, T. D., Lynch, D. H., O’Halloran, I. P., Voroney, R. P., Entz, M. H., & Dunfield, K. E. (2019). Soil phosphorus bioavailability as influenced by long-term management and applied phosphorus source. Canadian Journal of Soil Science, 99(3), 292–304. https://doi.org/10.1139/cjss-2018-0075
Gaiero, J. R., Bent, E., Boitt, G., Condron, L. M., & Dunfield, K. E. (2020). Effect of long-term plant biomass management on phosphatase-producing bacterial populations in soils under temperate grassland. Applied Soil Ecology, 151, 103583. https://doi.org/10.1016/j.apsoil.2020.103583
Gaiero, J. R., Tosi, M., Bent, E., Boitt, G., Khosla, K., Turner, B. L., Richardson, A. E., Condron, L. M., & Dunfield, K. E. (2021). Soil microbial communities influencing organic phosphorus mineralization in a coastal dune chronosequence in New Zealand. FEMS Microbiology Ecology, 97(4), fiab034. https://doi.org/10.1093/femsec/fiab034
King, A. E., Congreves, K. A., Deen, B., Dunfield, K. E., Simpson, M. J., Voroney, R. P., & Wagner-Riddle, C. (2020). Crop rotations differ in soil carbon stabilization efficiency, but the response to quality of structural plant inputs is ambiguous. Plant and Soil, 457(1–2), 207–224. https://doi.org/10.1007/s11104-020-04728-5
King, A. E., Congreves, K. A., Deen, B., Dunfield, K. E., Voroney, R. P., & Wagner-Riddle, C. (2019). Quantifying the relationships between soil fraction mass, fraction carbon, and total soil carbon to assess mechanisms of physical protection. Soil Biology and Biochemistry, 135, 95–107. https://doi.org/10.1016/j.soilbio.2019.04.019
Linton, N. F., Ferrari Machado, P. V., Deen, B., Wagner-Riddle, C., & Dunfield, K. E. (2020). Long-term diverse rotation alters nitrogen cycling bacterial groups and nitrous oxide emissions after nitrogen fertilization. Soil Biology and Biochemistry, 149, 107917. https://doi.org/10.1016/j.soilbio.2020.107917
Mafa-Attoye, T. G., Baskerville, M. A., Ofosu, E., Oelbermann, M., Thevathasan, N. V., & Dunfield, K. E. (2020). Riparian land-use systems impact soil microbial communities and nitrous oxide emissions in an agro-ecosystem. Science of The Total Environment, 724, 138148. https://doi.org/10.1016/j.scitotenv.2020.138148
Man, M., Deen, B., Dunfield, K. E., Wagner-Riddle, C., & Simpson, M. J. (2021). Altered soil organic matter composition and degradation after a decade of nitrogen fertilization in a temperate agroecosystem. Agriculture, Ecosystems & Environment, 310, 107305. https://doi.org/10.1016/j.agee.2021.107305
Man, M., Wagner-Riddle, C., Dunfield, K. E., Deen, B., & Simpson, M. J. (2021). Long-term crop rotation and different tillage practices alter soil organic matter composition and degradation. Soil and Tillage Research, 209, 104960. https://doi.org/10.1016/j.still.2021.104960
Mitter, E. K., Tosi, M., Obregón, D., Dunfield, K. E., & Germida, J. J. (2021). Rethinking Crop Nutrition in Times of Modern Microbiology: Innovative Biofertilizer Technologies. Frontiers in Sustainable Food Systems, 5, 606815. https://doi.org/10.3389/fsufs.2021.606815
Mooshammer, M., Grandy, A. S., Calderón, F., Culman, S., Deen, B., Drijber, R. A., Dunfield, K., Jin, V. L., Lehman, R. M., Osborne, S. L., Schmer, M., & Bowles, T. M. (2022). Microbial feedbacks on soil organic matter dynamics underlying the legacy effect of diversified cropping systems. Soil Biology and Biochemistry, 167, 108584. https://doi.org/10.1016/j.soilbio.2022.108584
Sokolov, V. K., VanderZaag, A., Habtewold, J., Dunfield, K., Wagner-Riddle, C., Venkiteswaran, J. J., Crolla, A., & Gordon, R. (2021). Dairy manure acidification reduces CH4 emissions over short and long-term. Environmental Technology, 42(18), 2797–2804. https://doi.org/10.1080/09593330.2020.1714744
Sokolov, V., VanderZaag, A., Habtewold, J., Dunfield, K., Wagner-Riddle, C., Venkiteswaran, J., & Gordon, R. (2019). Greenhouse gas emissions from gradually-filled liquid dairy manure storages with different levels of inoculant. Nutrient Cycling in Agroecosystems, 115(3), 455–467. https://doi.org/10.1007/s10705-019-10023-2
Sokolov, V., VanderZaag, A., Habtewold, J., Dunfield, K., Wagner‐Riddle, C., Venkiteswaran, J. J., & Gordon, R. (2019). Greenhouse Gas Mitigation through Dairy Manure Acidification. Journal of Environmental Quality, 48(5), 1435–1443. https://doi.org/10.2134/jeq2018.10.0355
Tosi, M., Brown, S., Ferrari Machado, P. V., Wagner-Riddle, C., & Dunfield, K. (2020). Short-term response of soil N-cycling genes and transcripts to fertilization with nitrification and urease inhibitors, and relationship with field-scale N2O emissions. Soil Biology and Biochemistry, 142, 107703. https://doi.org/10.1016/j.soilbio.2019.107703
Tosi, M., Drummelsmith, J., Obregón, D., Chahal, I., Van Eerd, L. L., & Dunfield, K. E. (2022). Cover crop-driven shifts in soil microbial communities could modulate early tomato biomass via plant-soil feedbacks. Scientific Reports, 12(1), 9140. https://doi.org/10.1038/s41598-022-11845-x
Tosi, M., Mitter, E. K., Gaiero, J., & Dunfield, K. (2020). It takes three to tango: The importance of microbes, host plant, and soil management to elucidate manipulation strategies for the plant microbiome. Canadian Journal of Microbiology, 66(7), 413–433. https://doi.org/10.1139/cjm-2020-0085
Tosi, M., Ogilvie, C. M., Spagnoletti, F. N., Fournier, S., Martin, R. C., & Dunfield, K. E. (2023). Cover Crops Modulate the Response of Arbuscular Mycorrhizal Fungi to Water Supply: A Field Study in Corn. Plants, 12(5), 1015. https://doi.org/10.3390/plants12051015
VanderZaag, A. C., Baldé, H., Habtewold, J., Le Riche, E. L., Burtt, S., Dunfield, K., Gordon, R. J., Jenson, E., & Desjardins, R. L. (2019). Intermittent agitation of liquid manure: Effects on methane, microbial activity, and temperature in a farm-scale study. Journal of the Air & Waste Management Association, 69(9), 1096–1106. https://doi.org/10.1080/10962247.2019.1629359
Dr. Laura Van Eerd, Dr. Bill Deen, Dr. Claudia Wagner-Riddle, Dr. Leo Condron, Dr. Bob Hanner, Dr. Leo Condron, Dr. Amanda Black, Dr. Alan Richardson, Dr. Peter Bolo, Dr. Gustavo Boitt, Dr. Simpson Myrna, Dr. Jon Gaiero, Dr. Dasiel Obregon, Dr. Kamini Khosla, Dr. Elizabeth Bent
Travis Mazurek, John Drummelsmith, Marcus Johnson, Jessie Loranger, Brittany Haines, Linsey Van Koppen, Sarah Fournier, William Milson, Anibal Castillo, Jordenne Cain, Travis Mazurek, Mica Tosi, Nicola Linton, Anibal Castillo, Tolu Mafa-Attoye, Evan Mayer
Grain Farmers of Ontario, GFO, Biomemakers
