How management practices within a poultry house during successive flock rotations change the structure of the soil microbiome

Authors: Crippen, Tawni - Tc; SHEFFIELD, CYNTHIA - Retired ARS Employee; SINGH, BANESHWAR - Virginia Commonwealth University; Byrd Ii, James - Allen; Beier, Ross

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/26/2019
Publication Date: 9/13/2019
Citation: Crippen, T.L., Sheffield, C.L., Singh, B., Byrd, J.A., Beier, R.C. 2019. How management practices within a poultry house during successive flock rotations change the structure of the soil microbiome. Frontiers in Microbiology. 10:2100. https://doi.org/10.3389/fmicb.2019.02100.
DOI: https://doi.org/10.3389/fmicb.2019.02100

Interpretive Summary: The community of microbes within a poultry house influences the health of the birds. Yet, little is known about these communities, such as what microbes are present, their functions, or the effects of management practices on their populations. Therefore, studies of these communities are the first steps to guiding management practices to influence the microbes to obtain the best production results. This study demonstrated major shifts in soil bacteria, at the taxonomic class level, related to the introduction of bedding and birds into the house. Bacteriodia, Erysipelotrichis, Negativicutes, Spriochetes, and Proteobacteria populations decreased, while Actinobacteria and Bacilli increased after the introduction of bedding and birds on top of the soil. The partial clean-out of litter did not change the bacterial community in any substantial way, only spurring a temporary increase in the genera Subdoliganulum, Clostridium XI, Tepidmicrobium, and Pseudomonas. However, the total litter clean-out had a larger effect, causing an increase in Actinobacteria. Overall, management practices could be used to affect the class structure of the poultry house soil bacterial community for beneficial outcomes.

Technical Abstract: The microbiome within a poultry production house influences the attainment of physiologically strong birds. Yet, little is known about the microbial communities within the house and the effects on the soil microbes onto which the houses are placed, nor the effects of management practices on their equilibrium. This study looked at the soil bacterial microbiome before a broiler house was constructed, then through 11 flock rotations that included a partial clean-out and a total clean-out within the management regimen. It demonstrated major shifts, occurring at the taxonomic class level, related to the introduction of bedding and birds on top of the soil. The partial clean-out of litter did not change the soil bacterial community in any substantial way, only spurring a temporary increase in some genera; however, the total litter clean-out caused a major increase in a cohort of Actinobacteria. The underlying soil contained bacteria beneficial for poultry metabolism, such as Lactobacillus, Faecalibacterium, Bacteriodes, and Ruminococcus. Therefore, the Native and Pad soil could be a source of some important intestinal bacteria and thus, could be looked at as a possible management tool for seeding the poult digestive system with beneficial bacteria, as well ones that possibly mitigate the more pathogenic species. Additionally, management practices affected the class structure of the soil bacterial community beneath the poultry house. The scheduling of these practices should be leveraged to exploit maintenance of beneficial bacteria that maximize microbiome contributions to bird production processes, while minimizing environmental effects.