Biochar supplementation affects the microbiome of recycled manure solids for cow bedding: a metagenomic analysis

Abstract

The widespread use of Recycled Manure Solids (RMS) as cow bedding material is not without risks, since cattle manure may act as a vehicle for pathogenic and antimicrobial resistant bacteria dissemination. Thus, our aim was to evaluate RMS-supplemented with a pine biochar produced in Portugal as a new cow bedding material, since the use of biochar has been shown to have the potential to mitigate the impact of relevant bacterial species when added to animal manure microbiota. Our experimental setup consisted on fresh RMS samples that were collected on a commercial dairy farm and placed in naturally-ventilated containers for a total of 4 groups: 1–non-supplemented RMS; 2-RMS supplemented with 2.5% (wt/wt) of biochar; 3-RMS supplemented with 5% (wt/wt) of biochar; and 4-RMS supplemented with 10% (wt/wt) of biochar. Sampling was performed at 4 different incubation times (0, 5, 15 and 30 d) and in 2 distinct seasons: April–May (humid season) and June–July (dry season). The resulting 32 samples were subjected to DNA extraction and their microbiome profile determined through complete 16S rDNA gene sequencing using Nanopore next-generation sequencing. We observed that biochar supplementation clearly altered the microbiome of RMS, which was reflected in changes in populations' diversity and their relative abundance of relevant pathogenic bacteria. In particular, we found that long-term storage (30 d) was more beneficial than short-term storage, an effect that was more evident for samples supplemented with 2.5% or 5% biochar. In both seasons, those concentrations of biochar led to a decrease in the levels of several mastitis-causing agents (Enterobacteriaceae, streptococci, enterococci and staphylococci). In addition, we also observed a reduction in the levels of Salmonella spp. and Gram-positive bacilli in the biochar-supplemented samples. Unexpectedly, however, those same conditions yielded an increase in the abundance of Brucella spp., a group which includes important infectious agents, highlighting the need for a deeper evaluation of the impact of biochar supplementation of RMS to ensure the future safe and sustainable use of this environmental-friendly resource in animal production.