Microbial community structure from southern High Plains beef cattle feedyard manure and relationship with nitrous oxide emissions

Modern molecular techniques enable characterization of the microbial biome in livestock manure, from which there is particular concern over emission of greenhouse gases. This study evaluated how sampling depth, time, temperature, and artificial rainfall affected microbial community structure in feedyard manure, and relationships between the manure biome and known parameters related to nitrous oxide (N2O) emissions. In three large incubation chambers, maintained at different temperatures that received two applications of artificial rainfall, we evaluated manure microbiome composition and abundance of N2O‐producing enzymes (nirK and nirS) using quantitative polymerase chain reaction (qPCR). These data were used with previously published data from the same study on N2O emissions and assessment of manure physicochemical properties, denitrification enzyme activity (DEA), and nitrification activity (NA). Microbiome composition was Firmicutes (50%), followed by 32% Actinobacteria, 11% Proteobacteria, 5% Bacteroidetes, 1% Chloroflexi, and small populations ( Actinobacteria > Proteobacteria > Bacteroidetes > Chloroflexi > others. Average microbial populations varied with sampling depth and time. Increases in Firmicutes coincided with nitrous oxide emissions. Copy numbers of nirK and nirS differed with date and among chambers, indicating sensitivity of denitrifying e