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 (<0.5%) of Planctomycetes, Deinococcus-Thermus, Gemmatimonadetes, Verrucomicrobia, Tenericutes, and other organisms. Average bacterial populations varied largely as a function of sampling depth and time. Firmicutes increases tended to coincide with high N2O emissions. Overall, the largest change observed was increased Proteobacteria at 5-10 cm, where relative abundance increased from 10% (17.2 degrees C) to 24% (46.2 degrees C) over time and with increased temperature. Firmicutes and Actinobacteria predominated the microbial community of manure, but favorable conditions may lead to increases in Bacteroidetes, Proteobacteria, and Chloroflexi, which could influence N cycling and N2O emissions from feedyards. Copy numbers of nirS at the beginning of the experiment were higher than nirK. Differences in concentrations of nirK and nirS indicated that denitrifying enzymes in feedyard manure, particularly nirS, were sensitive to environmental changes.