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

Authors: BOWEN, HOLLY - University Of Maryland; Maul, Jude; POFFENBERGER, HANNA - University Of Maryland; Mirsky, Steven; Cavigelli, Michel; YARWOOD, STEPHANIE - University Of Maryland

Submitted to: Biology and Fertility of Soils
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/4/2018
Publication Date: 7/13/2018
Citation: Bowen, H., Maul, J.E., Poffenberger, H., Mirsky, S.B., Cavigelli, M.A., Yarwood, S. 2018. Spatial patterns of microbial denitrification genes change in response to poultry litter placement and cover crop species in an agricultural soil. Biology and Fertility of Soils. 54:769-781.
DOI: https://doi.org/10.1007/s00374-018-1301-x

Interpretive Summary: Interpretative Summary One of the greatest impacts of farming on the environment is the loss of unused fertilizer into waterways and the atmosphere via leaching and volatilization of greenhouse gases, respectively. In recent years technological advances have enabled farmers to minimize fertilizer loss by optimizing the timing and physical placement of the fertilizer relative to the crop plant. For example, a current best management practice calls for splitting fertilizer application between two time points that are synchronized with crop demand and using a tractor powered implement to bury the fertilizer within 24 hours of application. These approaches have been met with great success in conventional production systems but still face challenges in Organic systems which have different timing regimens than conventional systems. Organic systems also use manure or poultry litter which do not flow like liquid fertilizer making sub-surface placement a challenge. In this study we compared indicators of soil nitrogen cycling in conventional and Organic systems that receive fertilizer in a traditional method or via a new method, which involves a newly designed implement for sub-surface delivery of poultry litter. We measured indicators of microbially mediated soil nitrogen cycling by monitoring abundances of bacterial (16S) ribosomal genes, fungal (ITS) ribosomal genes, and denitrification genes (nirK, nirS, and nosZ). Soil samples were 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 these genes was mapped to identify potential denitrification hotspots of gene abundances which may indicate locations of potential nitrogen transformations and loss to the environment. We found our approach could detect “hotspots” of 16S genes around the sub-surfaced fertilizer band and around the root system of the developing crop plant, both results indicating that the general microbial community is responding to different disturbances within the soil profile. We did not detect major “hotspots” for the denitrification genes nirK, nirS, and nosZ around the sub-surface band. This initial attempt to monitor the quantity of soil microbe derived genes, as an indicator for microbial activity, was partially successful. Although we detected a “hotspot” for 16S genes but did not detect major “hotspots” for the denitrification genes around the band, we still are encouraged by our results. We suspect that the microbial community response time for a specific function such as denitrification may take longer than the general growth response of the whole microbial community as indicated by the 16S gene. This work will contribute to the development and refining of greenhouse gas emission models by contributing to the understanding of how the soil microbial community responds to ecosystem disturbances necessitated by environmentally sound farming management decisions.

Technical Abstract: ABSTRACT Soil subsurface-banding of manure and winter cover cropping are farming techniques designed to increase nitrogen use efficiency. Little is known, however, about the effects of these management tools on denitrifying microbial communities in the soil and the greenhouse gases they produce. Abundances of bacterial (16S), fungal (ITS) ribosomal genes, and denitrification genes (nirK, nirS, and nosZ) 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 denitrification hotspots. Spatial distribution maps showed increased 16S rRNA genes around the manure band, but no denitrifier hotspots were observed. Bacteria carrying nirK versus nirS genes were found to be sensitive to different soil characteristics and management methods. Gene copies of nirK were higher under cereal rye than hairy vetch, 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. Soil depth and nitrate concentration were the strongest drivers of gene abundance. Agricultural management differentially affects spatial distributions of genes coding for denitrification enzymes, leading to changes in the structure of the denitrifying community.