Identification of Thermophilic Aerobic Sporeformers in Bedding Material of Compost-Bedded Dairy Cows Using Microbial and Molecular Methods

SIMPLE SUMMARY: Compost-bedded pack barns (CBP) reflect a novel dairy cattle housing system with favourable effects on animal health and animal behavior but can promote the growth of thermophilic aerobic sporeformers (TAS) in the composting lying surface. In our study, we determined a medium–high mean TAS concentration across all bedding samples of four different CBP groups. Six different TAS species were identified based on their 16S rRNA-gene sequence, with Bacillus licheniformis being the predominant species. Season, the moisture content of the bedding material and the relative humidity above the bedding material had significant influences on the amount of TAS in the bedding material of the CBP. In addition, the moisture content and the relative humidity above the bedding material significantly influenced the concentration of TAS species each. Other characteristics such as the bedding temperature, the bedded area/cow and the usage time of the bedding material had slight effects on the TAS species occurrence. Due to the negative effect of TAS on milk product quality, considering all identified farm characteristics to optimise TAS contents will contribute to sustainable CBP farming. ABSTRACT: Compost-bedded pack barns (CBP) are of increasing interest in dairy farming due to their positive effect on animal welfare. The temperature and the moisture content of the bedding material characterising the composting process can promote the growth of thermophilic aerobic sporeformers (TAS). Therefore, the aim of this study was to determine CBP bedding material characteristics, such as moisture content and temperature, and to determine TAS species. The dilution, the heat inactivation of all non-TAS species and the incubation of 13 bedding samples from four CBP groups resulted in a mean TAS amount over all samples of 4.11 log10 cfu/g bedding material. Based on the subsequent sequencing of parts of the 16S rRNA-gene of 99 TAS colonies, the TAS species Aneurinibacillus thermoaerophilus, Bacillus licheniformis, Geobacillus thermodenitrificans, Laceyella sacchari, Thermoactinomyces vulgaris and Ureibacillus thermosphaericus were identified. The moisture content of the bedding material, the relative humidity above the bedding material and the sampling season significantly affected the amount of TAS. The moisture content or relative humidity above the bedding material significantly influenced the concentration of Ureibacillus thermophaericus or Laceyella sacchari. Consequently, an optimal CBP management including a dry lying surface and an optimal composting process will contribute to a moderate microbial, especially TAS amount, and TAS species distribution.