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

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Abstract

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.

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Acknowledgements

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 (https://www.msi.umn.edu/).

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Authors and Affiliations

  1. Plant Science Research Unit, USDA-ARS, 439 Borlaug Hall, 1991 Upper Buford Circle, Saint Paul, MN, 55108, USA

    Sarah C. Castle, Deborah A. Samac & Daniel Schlatter

  2. Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, MN, USA

    Sarah C. Castle, Jessica L. Gutknecht, Michael J. Sadowsky & Carl J. Rosen

  3. Department of Plant Pathology, University of Minnesota, MN, Saint Paul, USA

    Deborah A. Samac & Linda L. Kinkel

  4. Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA

    Michael J. Sadowsky

  5. Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA

    Michael J. Sadowsky & Linda L. Kinkel

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  1. Sarah C. Castle
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  2. Deborah A. Samac
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Contributions

SCC, CJR, DAS, JLG, LLK, and MJS conceived of the study. SCC conducted the laboratory work, data analysis, and wrote the manuscript. DS and all co-authors gave significant feedback, contributed to data interpretations, and manuscript writing.

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Correspondence to Sarah C. Castle.

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The authors declare no conflicts of interest associated with the presented research. Mention of any trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U. S. Department of Agriculture. USDA is an equal opportunity provider and employer. This paper is a joint contribution from the USDA-ARS-Plant Science Research Unit and the University of Minnesota.

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Supplementary Information

Fig. S1

Experimental design for two agricultural sites located in Lamberton and Waseca, Minnesota, USA. Different colors within sites indicate different phases of cropping sequences for crop sequence is indicated as follows: Corn-Soybean (CS), Corn-Soybean preceded by a winter rye cover crop in each phase (CSrye), Silage corn followed by pennycress-Soybean (CSpc). Different numbers (1–4) represent subplots of different N-application rate treatments of 0, 80. 100, and 120% based on the best management practice (BMP) recommendations for each crop. (PNG 2390 kb)

High Resolution Image (TIF 512 kb)

Fig. S2

Soil microbial community metrics for agricultural sites at Lamberton and Waseca, Minnesota, USA. (a) Differences in microbial community compositions among sites based on NMDS ordination of Hellinger transformed Bray-Curtis dissimilarities of bacterial and fungal OTU counts. Plotted arrows represent significant correlations among community compositions and relative abundances of dominant microbial phyla. (b) Boxplots show significant differences among sites for bacterial, but not fungal, OTU richness and Shannon H′ Diversity Index. Actual data points are shown, and box centerlines represent medians with ±95% confidence intervals. (PNG 128815 kb)

High Resolution Image (TIF 856 kb)

Fig. S3

Within-site variation in microbial community composition for two agricultural sites in southern Minnesota. NMDS shows significant differences in microbial community compositions among experimental blocks based on Hellinger transformed Bray-Curtis dissimilarities of bacterial and fungal OTU counts. Colors indicate experimental blocks (n = 4) within each agricultural field for (a,b) Lamberton and (c,d) Waseca. Significance of block-effects, assessed using permutational analysis of variance on distance matrices (PERMANOVA), are indicated in each panel. NMDS stress values were < 0.20 in all cases. (PNG 129415 kb)

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Castle, S.C., Samac, D.A., Gutknecht, J.L. et al. Impacts of cover crops and nitrogen fertilization on agricultural soil fungal and bacterial communities. Plant Soil 466, 139–150 (2021). https://doi.org/10.1007/s11104-021-04976-z

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