Impacts of cover crops and nitrogen fertilization on agricultural soil fungal and bacterial communities

Sarah C. Castle, Deborah A. Samac, Jessica L. Gutknecht, Michael J. Sadowsky, Carl J. Rosen, Dan C Schlatter, Linda L Kinkel

Research output: Contribution to journalArticlepeer-review


Aims: Soil microbiomes and their interactions with crop plants are important drivers of agricultural health and productivity. Our objective was to examine short-term responses of soil microbiota to agricultural management (i.e. cover cropping and nitrogen fertilization). Methods: Following three years of cropping, soil samples were collected from replicated field plots at two southern Minnesota field sites (Lamberton and Waseca). We used amplicon-based gene sequencing (ITS2 and 16S rRNA V4) to investigate short-term soil fungal and bacterial community responses to cover crops and urea-nitrogen (N) fertilization (0, 80, 100, and 120% of recommended rates) in a corn (Zea mays)-soybean (Glycine max) cropping system planted with and without cover crops. Results: We found that rates of N-fertilizer applied, more than cover crops, significantly impacted soil chemical properties at both sites. Different cropping or N fertilization treatments did not lead to strong differences in fungal or bacterial alpha (local) diversity. At both sites, cover crop was a significant predictor of fungal community compositions and specific fungal and bacterial taxa were significantly impacted by cover crops. While, N fertilization was not a strong predictor of community compositions, urea-N additions, at any rate, resulted in changes in the relative abundances of the fungal phyla Glomeromycota in addition to a number of bacterial phyla. Conclusions: Our findings suggest that after three years of cropping, fungal communities respond to cover crops, while bacterial community responses may depend on soil chemical conditions.

Original languageEnglish (US)
JournalPlant and Soil
StatePublished - Jun 18 2021

Bibliographical note

Funding Information:
This research was supported by an internal grant awarded to CJR, DAS, JLG, LLK, and MJS by the University of Minnesota LTARN and by a USDA-NIFA postdoctoral fellowship awarded to SCC. We thank Matt Bickell and Kara Anderson for LTARN plot support, Mindy Dornbusch, Peter Lenz, Susan Miller, and Ted Jeo for field assistance, and The University of Minnesota Genomics Center for conducting all molecular sequencing. Sequence data were processed and analyzed by using the resources of the Minnesota Supercomputing Institute ( ).

Publisher Copyright:
© 2021, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.


  • Corn
  • Cover crop
  • Fertilization
  • Nitrogen application rate
  • Soil microbiota
  • Soybean


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