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

Authors: Castle, Sarah; Samac, Deborah - Debby; GUTKNECHT, JESSICA - University Of Minnesota; SADOWSKY, MICHAEL - University Of Minnesota; ROSEN, CARL - University Of Minnesota; Schlatter, Daniel; KINKEL, LINDA - University Of Minnesota

Submitted to: Plant and Soil
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/20/2021
Publication Date: 6/18/2021
Citation: Castle, S.C., Samac, D.A., Gutknecht, J.L., Sadowsky, M.J., Rosen, C.J., Schlatter, D.C., Kinkel, L.L. 2021. Impacts of cover crops and nitrogen fertilization on agricultural soil fungal and bacterial communities. Plant and Soil. https://doi.org/10.1007/s11104-021-04976-z.
DOI: https://doi.org/10.1007/s11104-021-04976-z

Interpretive Summary: The communities of bacteria and fungi in soil influence crop productivity through nutrient cycling, decomposition of organic matter, and plant health, but little is known about how communities respond to agricultural practices. We evaluated short-term responses of soil fungal and bacterial communities to crop sequence and nitrogen fertilization at two field sites located in southern Minnesota. The soils at the two sites varied for chemical properties, which influenced the composition of bacterial and fungal communities. At both sites, cropping sequence significantly influenced communities as a whole in addition to which specific fungal groups were present. Bacterial communities were influenced more strongly by soil chemistry than crop sequence. While nitrogen fertilization did not have a strong effect on overall microbial community composition, urea additions resulted in changes in the abundance of specific fungal and bacterial groups. Nitrogen fertilization had a strong negative impact on abundance of mycorrhizal fungi, which are important in phosphate acquisition by plant roots. The findings suggest that fungal communities respond quickly to changes in the cropping sequence, while bacterial community responses may develop slowly over time depending on site-specific soil properties. There is a growing interest in agricultural management strategies that both improve crop yields and enhance soil biological function. These results will be useful to those developing predictive models of agricultural management impacts of soil biology and quality.

Technical Abstract: Agricultural management is composed of many factors including the composition of cropping rotations and fertility management, both of which may have site-specific influences on soil chemistry and microbial communities. We used amplicon-based gene sequencing (ITS2 and 16S rRNAV4) to investigate short-term responses of soil fungal and bacterial communities to cropping sequence and nitrogen (N) management at two field sites in southern Minnesota (Lamberton and Waseca). Following three years of cropping, soil samples were collected from plots planted in five different cropping sequences that varied in annual crop composition (two or three crops) and inclusion of cover crops. Subplots of each cropping sequence were treated with varying amounts of synthetic urea-N fertilizer, representing 0, 80, 100, and 120% of the regionally-recommended rate for each crop species. The N application rate, but not cropping sequence, significantly impacted soil chemical properties at both agricultural sites. N fertilizer, at any application rate, led to significantly greater N availability and organic matter content at the Lamberton site and led to significantly lower P availability and increased soil pH at the Waseca site. Different cropping or N fertilization treatments did not lead to strong differences in fungal or bacterial alpha (local) diversity. At both sites, cropping sequence was a significant predictor of overall fungal community compositions, and specific fungal and bacterial taxa were significantly impacted by cropping sequence composition and/or crop identity. While N fertilization was not a strong predictor of overall microbial community compositions, urea additions resulted in changes in abundances of specific fungal and bacterial OTUs and the relative abundances of the fungal phyla Glomeromycota in addition to a number of bacterial phyla. Taken together, these findings suggest that fungal communities respond quickly to changes in the cropping sequence composition, while bacterial community responses may depend more on legacy conditions of soil chemistry and site history.