Updated Aug. 11, 2020
This article is the final instalment of a three-part series highlighting lessons learned from two long-term crop rotation experiments at the Ontario Crops Research Centres at Elora and Ridgetown.
Soil is teeming with life. And despite their size, fungi, bacteria, and other micro-organisms play an enormous role in soil processes, from carbon and nitrogen cycling to the formation of soil structure, to the spread and development of infections and resistance.
They’re also very picky about where they live, both in the soil and the lab.
Part of the reason that soil biology has been all the rage in the past decade is because advances in genetic and molecular techniques have made it possible to study these microscopic critters.
“DNA analysis of microbial communities from soil has been around since before I did my PhD, long, long ago,” says Kari Dunfield, professor of microbial ecology at the University of Guelph. “But the methods were still under development, and the expense prevented our ability to replicate our analysis at a level required to understand the variability in soil.”
With the success of the Human Genome Project, DNA sequencing became quicker, more accurate, and more cost effective.
“Our challenge now is to predict how all of these communities are impacted on a field scale, by asking questions like: ‘How do crop rotations shift the microbiome?’ and, ‘Does this relate to plant and soil health?’”
Several years ago, Nicola Linton, a PhD student of Dunfield’s, set out to investigate how crop rotation affected bacteria and fungi using the long-term experiment at Elora as a study site.
In theory, Linton expected diverse crop rotations to support greater bacterial and fungal diversity than simple rotations because “you’re providing very different food sources for what’s living there.” And different microbes would likely prefer the exudates and organic material created by some crops more than others.
Comparing among the corn-based crop rotations she was studying – continuous corn, to corn-soybean, to corn-soybean-wheat, with and without red clover – she found this theory was accurate.
“As we increase crop diversity, we see different levels of overall diversity in our bacteria and fungi, but also different groups that are promoted by the different crop rotations.”
Having a diverse microbial community is critical for agricultural resilience, Linton explains.
“The more diversity you have, the more organisms you have to carry out different functions,” such as nitrogen cycling, for example.
Drought and soil compaction can sometimes knock out a group of microbes and prevent them from functioning. If the microbial community isn’t diverse, losing some microbes could mean this function is lost also.
With a diverse system where several different groups carry out the same function, losing one or two means that the function won’t necessarily be lost — a concept known as functional redundancy.
Tillage also had an impact on bacteria and fungi.
“In the tilled systems, we see lower diversity of both bacteria and fungi, especially fungi. And that makes a lot of sense: fungi form networks in the soil, and tillage disrupts those networks,” says Linton.
Not only was microbial diversity in no-till soils greater, but the microbial community was also more responsive to changes in crop rotation.
In other words, the impact of a good crop rotation was greater in a no-till system.
In diverse rotations with no-tillage, Linton found more bacterial and fungal nitrifiers, indicating that nitrogen cycling was more efficient in this system. While this can be a good thing for soil health, it can cause problems if this benefit isn’t accounted for.
In collaboration with Pedro Machado, a PhD student in Claudia Wagner Riddle’s agrometeorology lab, Linton found that there were higher nitrous oxide (N2O) emissions in the complex rotation with wheat and red clover, fueled by these bacterial and fungal nitrifiers.
At first blush this may appear as a knock against this rotation. But according to Machado, the whole system must be considered.
“If we just compare the total N2O emissions over the four years of our diverse (corn-soybean-wheat with red clover) or simple rotation (corn-soybean), then the diverse rotation emits more, but that’s because it only has one year of soybean.” Corn and wheat have much higher annual emissions because they require nitrogen fertilization.
“If you scale the emissions by the nitrogen rate used over the four years of the rotations, they are the same. Diversified continues to be the way to go.”
Machado’s research supports the need to apply a nitrogen credit to diversified corn-based rotations with cover crops. In this way, soil health improvements should lead to reduced fertilizer rates, similar crop yields, and a smaller environmental footprint.
“I had no idea that soils were so rich before I started my graduate studies,” says Linton. “It’s an unknown and untapped frontier, and the more research we can do to understand it, the more we can do to make changes for the better.”
This research was funded by Grain Farmers of Ontario, the Natural Sciences and Engineering Research Council of Canada, and the Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA), through the Ontario Agri-Food Innovation Alliance. The Ontario Crops Research Centres in Elora and Ridgetown are owned by the Agricultural Research Institute of Ontario and managed by the University of Guelph through the Ontario Agri-Food Innovation Alliance, a collaboration between the Ontario Government and the University of Guelph.
Updated Aug. 11 to include more funding sources.