Air, Soil and Water Research

Confinement is the predominant method of producing poultry and eggs for consumption in the US. Because of its high-density approach, the potential health threats regarding pathogenesis in animals and humans have raised concerns. Although there best management practices exist to control the persistence and proliferation of pathogenic bacteria in poultry houses, very little is known about the bacterial communities, and poultry houses are potential pathogen sinks. We assessed the contribution of industrial poultry production to the structure and composition of bacterial communities in the soils at a poultry production site. Soil samples were collected from under poultry housing areas, litter storage areas, and an accompanying pasture adjacent to the production area; and environmental DNA was extracted from the samples. Following validation and amplification, DNA was sequenced using bacterial-tag encoded pyrosequencing. Bioinformatics analysis showed that the bacterial communities in the soils showed no significant differences in species richness according to observed and estimated operational taxonomic units (Chao1 and rarefaction). Proteobacteria were the major phyla present in all samples ranging from 37.1% in the soils under poultry houses to 53.4% of the sequences identified under pasture soils. Significant shifts in specific taxa were observed, including drops in the abundance of Acidobacteria observed from the poultry house to litter storage soils (P < 0.05) α-Proteobacteria increased from poultry house soil (10.9%) to pasture soils (32.8%, P < 0.01) and soils under litter storage (22.3%, P < 0.05). The phyla Bacteroidetes, which were observed between poultry house and pasture soils, dropped significantly from 21.8% to 7.2% (P < 0.05). Clustering exhibited a closer relationship between the soils under pasture and litter storage, while those under the poultry houses were unique. Pathogenic genera were also found in greater abundance under the poultry houses, which raises the question of persistence and re-colonization of bedding material even in the presence of mitigation attempts.