Biology and Fertility of Soils

, Volume 54, Issue 6, pp 769–781 | Cite as

Spatial patterns of microbial denitrification genes change in response to poultry litter placement and cover crop species in an agricultural soil

  • Holly Bowen
  • Jude E. MaulEmail author
  • Hanna Poffenbarger
  • Steven Mirsky
  • Michel Cavigelli
  • Stephanie YarwoodEmail author
Original Paper


Subsurface-banding manure and winter cover cropping are farming techniques designed to reduce N loss. Little is known, however, about the effects of these management tools on denitrifying microbial communities and the greenhouse gases they produce. Abundances of bacterial (16S), fungal (ITS), and denitrification genes (nirK, nirS, nosZ-I, and nosZ-II) were measured in soil samples collected from a field experiment testing the combination of cereal rye and hairy vetch cover cropping with either surface-broadcasted or subsurface-banded poultry litter. The spatial distribution of genes was mapped to identify potential denitrifier hotspots. Spatial distribution maps showed increased 16S rRNA genes around the manure band, but no denitrifier hotspots. Soil depth and nitrate concentration were the strongest drivers of gene abundance, but bacterial gene abundance also differed by gene, soil characteristics, and management methods. Gene copy number of nirK was higher under cereal rye than hairy vetch and positively associated with soil moisture, while nirS gene copies did not differ between cover crop species. The nirS gene copies increased when manure was surface broadcasted compared to subsurface banded and was positively associated with pH. Soil moisture and pH were positively correlated to nosZ-II but not to nosZ-I gene copy numbers. We observed stronger correlations between nosZ-I and nirS, and nosZ-II and nirK gene copies compared to the reverse pairings. Agricultural management practices differentially affect spatial distributions of genes coding for denitrification enzymes, leading to changes in the composition of the denitrifying community.


Denitrification Cover cropping Poultry litter Subsurface-banding Hotspot Spatial variability Functional genes 



The authors would like to acknowledge the collaborative work by all the students and employees of the Microbial Ecology and Biogeochemistry Lab at University of Maryland and the Sustainable Agricultural System Lab at USDA-ARS. We would like to acknowledge Chris Horton and Alexandra Knight at North Carolina State University for their work on the nosZ-II standards.

Funding information

This research was funded by the National Institute of Food and Agriculture, Organic Transitions Grant No. 2012-51106-20026.

Supplementary material

374_2018_1301_MOESM1_ESM.docx (1.2 mb)
ESM 1 (DOCX 1257 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Holly Bowen
    • 1
  • Jude E. Maul
    • 2
    Email author
  • Hanna Poffenbarger
    • 3
  • Steven Mirsky
    • 2
  • Michel Cavigelli
    • 2
  • Stephanie Yarwood
    • 1
    Email author
  1. 1.Department of Environmental Science and TechnologyUniversity of MarylandCollege ParkUSA
  2. 2.Sustainable Agricultural Systems LaboratoryBeltsville Agricultural Research Center USDA-ARSBeltsvilleUSA
  3. 3.Department of Plant and Soil SciencesUniversity of KentuckyLexingtonUSA

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