Assessing the Structure and Membership of Soil Microbial Communities Cultivated Under An Industrial Poultry Production System.

Poultry production systems allow for the cultivation of unique soil microbial communities which play important roles in the status of the larger ecosystem.  Soil communities harboring species that affect the health of animals, humans, and the soil are poorly understood given the modern advances in molecular technologies.  It was the objective of this study to assess and describe the structure and composition, as well as the phylogeny of microbial communities cultivated in soils under industrial poultry production.  Replicate soil samples were collected from an industrial poultry production site in which three areas of the production site were sampled (poultry houses, pasture, and litter storage) in Bullock County, Alabama.  Bacterial-tag encoded FLX amplicon pyrosequencing was used to generate genomic libraries targeting 16S rDNA.  The different sampling areas also showed distinction in the structure of their microbial communities with respect to the differences detected in cluster analysis.  Specific taxa (most notably Acidobacteria, Bacteroidetes, Chloroflexi, and classes of Proteobacteria) showed significant shifts across the land-use strata.  Selected soil properties (soil organic carbon [SOC], total nitrogen (TN), and pH) also differed significantly amongst sampling areas.  Also of note were the pathogenic genera detected in soils under the poultry houses (Brevibacterium, Clostridium, Mycobacterium, and Staphylcoccus).  Together these results suggest that pyrosequencing along with traditional analysis of soil properties may be able to provide insight into the ecology of microbial communities with respect to poultry production.