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

Authors

Heidi Waldrip, USDA, Agricultural Research Service
David Parker, West Texas A&M University
Sierra Miller, University of Texas Medical Branch
Lisa M. Durso, USDA, Agricultural Research Service
Byeng R. Min, Tuskegee University
Daniel N. Miller, USDA, Agricultural Research Service
Kenneth Casey, Texas A&M AgriLife Research and Extension
Bryan Woodbury, USDA, Agricultural Research Service
Mindy J. Spiehs, USDA, Agricultural Research Service

Document Type

Article

Citation

Waldrip, H., Parker, D., Miller, S., Durso, L. M., Min, B. R., Miller, D. N., Casey, K., Woodbury, B., & Spiehs, M. J. (2022). Microbial community structure from southern High Plains beef cattle feedyard manure and relationship with nitrous oxide emissions. Agrosystems, Geosciences & Environment, 5, e20292. https://doi.org/10.1002/agg2.20292

Comments

Open access

Abstract

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 °C) to 24% (46.2 °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.