Influence of agroecology practices on rumen microbiota associated with methane emission in dairy cattle

Moving from intensive farming to agroecology to support farm sustainability means changing feeding practices. In practical terms, this means increasing the botanical diversity and delaying mowing of the grasslands to favor fauna diversity and associated ecosystem services. However, it is unknown whether these feeding practices alter rumen microbiota and its association with methane (CH₄) emission, a potent greenhouse gas. The objective of this study was to assess CH₄ emission and rumen microbiota of several dairy breeds fed agroecology diets. Three dairy cattle breeds (Holstein Friesian, Groninger Blaarkop and Jersey) (N = 10 for each breed) were fed three grass silage-based diets that included a proportion of a control silage, an experimental silage composed of late mown grass, and an experimental silage composed of diverse botanical species. Cows were fed for 13 weeks with gradual adjustment of the proportion of each silage. Rumen fluid was sampled during the weeks that corresponded to the highest proportion of each silage in the diet. Rumen microbiota was characterized through 16 s rRNA gene amplicon sequencing for its richness and diversity, as well as its compositions according to diet type and breed. Production performances and CH₄ emission were also measured. Methane production (g/d) was similar between the control and the agroecological diets. Cows fed the experimental diets had a different rumen microbiota composition than cows fed control diet. The cows fed the agroecological diets presented reduced relative abundances of Rumminoccocaeae, and higher relative abundances of Chirstensenellaceae and Methanobrevibacter than cows fed the control diet. Besides, the cows fed the agroecological diets presented a richer (P < 0.01) and more diverse (P < 0.01) rumen microbiota. Overall, this study highlights how feeding practices that comply with agroecology principles, and applied under practical conditions, shaped the rumen microbiota of specialized and dual-purpose cattle breeds.