Exploring the depths of viral diversity in cow faeces and slurry

Abstract: Viruses are the most abundant biological entities on Earth, known to be crucial components of microbial ecosystems. However, there is little information on the viral community within agricultural waste.

There are currently ~ 2.7 million dairy cattle in the UK producing 7–8% of their own bodyweight in manure daily, and 28 million tonnes annually. The cow faeces and other farm waste must be stored and spread in accordance with guidelines set by DEFRA, prior to use as a fertiliser.

While manure is widely used as a fertiliser and spread over crop fields, very little is known about the microbial composition, in particular the viral component. Using a combination of short and long read sequencing, along with culture-based approaches, we have begun to characterise the community of viruses found within cow faeces and resultant slurry.

We assembled, > 30 000 vOTUs, including~1200 complete viral genomes that represent new viral families. Furthermore, we are able to show the communities of viruses in slurry are stable over timescales. However, the viral community in cows changes rapidly during the life cycle of a cow and alters the diversity of the bacterial community.