Distinct N-cycling microbial communities contribute to microtopographic variation in soil N2O emissions

Climate change is increasing the frequency and intensity of large precipitation events that flood soils and establish anoxic conditions that promote microbial denitrification, a predominant source of atmospheric nitrous oxide (N2O, a strong greenhouse gas). Denitrification may be favored within topographic depressions in otherwise flat fields that are prone to ponding, establishing “hotspots” of N2O emissions. The location of N2O hotspots may also depend on the distribution of soil microbial communities that are responsible for the production and consumption of N2O in soils. Yet, relating soil microbial community composition to N2O emissions remains challenging. To assess how spatial variation in soil microbial communities affects N2O emissions, we measured the community composition of active microorganisms using amplicon-based sequencing of cDNA generated from mRNA transcripts associated with N-cycling processes in response to experimentally flooding and draining soils in the lab. We also used stable isotope tracers to relate microbial communities to process rates. Consistent with the hypothesis that denitrifying microbial communities are not functionally redundant, we found that the diversity of microbial taxa expressing nitrite reduction genes (nirK) and N2O reduction genes (Clade I nosZ) were correlated with denitrifier-derived N2O emissions. Depressional soils had more diverse active N2O consuming communities (assessed using Clade I nosZ) under flooded conditions, limiting net N2O emissions compared to upslope soils. Furthermore, non-flooded depressional soils maintained higher rates of dissimilatory nitrate reduction to ammonia (DNRA), limiting nitrate available to denitrifiers. Our results show that depressional soils maintain distinct microbial communities that likely promote higher rates of N2O reduction and DNRA compared to upslope soils. Soil microtopography can, therefore, select for distinct microbial communities that emit different amount of N2O in response to large precipitation events.

Methods
Please see the methods in the associated publication for detailed methods. Briefy, we collected soil cores from depressional and upslops soils within three agricultural fields in central Illinois. We used stable isotopes to emasure dentirifciation and ntirification derived N2O emissions as well as rates of dissimilary nitrate reductionto ammonium. We also sequenced mRNA transcrips from genes involved in various steps of dentirification and DNRA. We used these data to link microbial community composition to microbial process rates.