Soil microbes are the epicenter of a soil’s health. If these microorganisms are in poor health, the crop will be too. The living, working organisms are responsible for turning atmospheric nitrogen into forms plants can use, and for releasing nitrogen back into the air. Farm management decisions undoubtedly affect these microscopic workhorses, but until now, scientists didn’t have a full picture of how crop rotation and tillage influence the soil microbiome. 

Now, a new 20-year study out of the University of Illinois at Urbana-Champaign has shown that continuous corn-on-corn rotations have proven detrimental to these microscopic barometers of soil health.

“Most research on soil microbial health has been done in a lab or greenhouse setting, or in short-term field experiments,” says Maria Villamil, associate professor in the Department of Crop Sciences at the University of Illinois and co-author on a new study published in Science of the Total Environment.  “Here in Illinois, we have a fantastic opportunity to look at what long-term farm management does to the soil.” 

Illinois crop scientists first planted corn and soybean at the experimental site in 1996, with some fields in continuous corn, others in continuous soybean, and others rotating annually between the crops. Within each cropping system, fields were either not tilled or chisel-tilled each year. Samples were then taken from each field in 2015 and 2016, after which the DNA was extracted and its physical and chemical properties measured.

“The DNA analysis was important because a lot of problems are related to the nitrogen cycle, whether that’s nitrous oxide emissions, nitrate leaching to water bodies, or just a toxic build-up of nitrogen in the soil,” said Gevan Behnke, lead author on the UI study and postdoctoral researcher in crop sciences. “Therefore, we studied genes and microbial groups associated with fixation, nitrification, and denitrification.” 

There are five types of soil microbes — bacteria, actinomycetes, fungi, algae and protozoa — and just a single gram of soil can contain billions of these microbes. The most numerous microbes in soil are the bacteria, where up to 10 billion cells can inhabit each gram of soil in and around the plant roots. Actinomycetes, fungi, soil algae and soil protozoa follow in decreasing numerical values.

Nakian Kim, doctoral student in the Department of Crop Sciences at the UI and lead author on a new paper in Soil Biology and Biochemistry says the use of burndown herbicides as a cover crop termination method had a strong moderating effect on the microbial community. “The results were very interesting. With chemical termination, the effect sizes were consistently smaller compared to mechanical termination. In other words, the benefits from the cover crops are diminished somehow from the herbicides. I think that’s one big takeaway.”

Tillage also made a difference. Kim said he expected conventional tillage to reduce the effect of cover crops on the soil microbes, but instead, conservation tillage did that. “My guess is that because conservation tillage included not tilling at all, that allowed weeds to grow on the land. The weeds could have mimicked what the cover crops do. So the difference between the control treatment and the cover crop may decrease because of the weeds.”

“For me, it was surprising to see the consistent, positive effect of cover crops - surprising but good...I’ve been researching cover crops in our typical corn-soybean rotations in Illinois since 2001, yet in these high-fertility environments, it has proven difficult to show any effects beyond cereal and annual rye capturing nitrogen,” says Villamil. “Changes in chemical and physical properties related to cover crop use are difficult to see. But the microbiome, that’s where it’s at. That’s how everything is related. Thanks to this work, I have something to look forward to when I put in cover crops, and have generated many more questions in need of research.”