Soil microbial communities as potential regulators of in situ N2O fluxes in annual and perennial cropping systems

Abstract

Significant reductions in nitrous oxide (N2O) fluxes have been observed with perennial cropping systems compared to annual crops. However, it is unclear if this reduction in N2O flux is linked to soil microbial communities due to plant-specific characteristics stimulating changes in microbial community structure. The response of microbial communities involved in N2O production to liquid dairy manure (LDM) application and tillage in annual and perennial systems has also not been assessed. Our objectives were to contrast changes in the population sizes and community structures of ammonia oxidizer (represented by amoA and crenamoA gene targets) and denitrifier (nirK, nirS, and nosZ gene targets) communities in differently managed annual and perennial fields, and to determine if differences in these microbial communities were related to observed variation in N2O fluxes. Soil was sampled in 2012 and in 2014 in a 4-ha spring-applied LDM grass-legume (perennial) field and two 4-ha corn (annual) fields under fall or spring LDM application. Soil DNA was extracted and used to target N-cycling genes via qPCR (n = 6) and for next-generation sequencing (Illumina Miseq) (n = 3). Significantly higher field-scale N2O fluxes were observed in the annual fields compared to the perennial system; however N2O fluxes increased 10-fold after plough down of the perennial field. Nonmetric multidimensional scaling (NMS) and multi-response permutation procedure (MRPP) indicated statistical differences in N-cycling communities between annual and perennial cropping systems, and in some cases, communities became indistinct in ordination space between annual and perennial fields after ploughing. Indicator species analysis was used to identify sequences clustered into operational taxonomic units (OTUs) most responsible for community shifts related to management. The abundance of N2O-reducing soil microbial communities (nosZ gene copies) and specific nirK, nirS and nosZ OTUs were proposed as important with respect to the production and consumption of N2O in these soils. Our results illustrate that ammonia oxidizer and denitrifier soil bacterial communities are sensitive to agricultural management (annual or perennial crop type, LDM management, and ploughing), highlighting their significance for the development of effective N2O mitigation strategies.