Assessment of microbial composition across the Quebec dairy farm-scape

Abstract

Aims: The aim of this preliminary study was to evaluate the shared composition and structure of the microbiome between cow feces, milk, manure, and soil samples across dairy farms in Quebec.

Methods and results: Analysis of the prokaryotic 16S, eukaryotic 18S, and fungal ITS rRNA genes was used to detect community structures, diversities, and spatial compositions, alongside potential contamination routes. Community structures of prokaryotic, eukaryotic, and fungal microbiomes were significantly different between niches and could be separated based on mean temperature. Bacteria and eukaryotes showed the highest diversity in fecal samples, whereas fungi were most diverse in soil. Percent of amplicon sequence variants (ASVs) shared between feces, manure, and the other matrices varied among microbial markers, with the highest values for fungi. The contamination route prediction also identified the highest probability of transmission of fungi using the ITS marker.

Conclusions: Sample type had the greatest influence on microbiome structure, although temperature had an impact on microbial composition of soil and manure samples. Results elucidate interactions at the animal-environment interface, informing the need for a better understanding of fungal transfer and seasonal variability.

Keywords: 16S; 18S; ITS; manure; milk; soil.