Contrasting Fecal Methanogenic and Bacterial Profiles of Organic Dairy Cows Located in Northwest Washington Receiving Either a Mixed Diet of Pasture and TMR or Solely TMR

SIMPLE SUMMARY: Methane is a by-product of the microbial fermentation process from a group of archaea known as methanogens. Ruminants harbor methanogens as a component of their normal gastrointestinal microbiota. In this study, we assessed the fecal microbiome of organic dairy cows across different time points receiving a mixed diet of pasture and TMR or TMR only. Our aim was to compare the archaea and bacterial fecal microbial structure, diversity and their interactions across diets. Cluster analysis based on the cows’ fecal microbial community identified four clusters. We found little difference in the relative abundance of methanogens across clusters. However, there was evidence of differences in diversity between pasture associated communities and those associated with TMR only. The cluster associated with cows receiving high-quality pasture and TMR, had higher diversity and a less robust co-occurrence network than those in TMR only or lower-quality pasture communities. The overall good pasture and TMR quality, combined with the organic allowance for feeding high levels of TMR, might have contributed to the lack of differences in the fecal archaeal community. The development of novel strategies that are independent of pasture management could have a greater impact in helping to reduce enteric CH(4) emissions on organic dairies. ABSTRACT: Currently, little is known regarding fecal microbial populations and their associations with methanogenic archaea in pasture-based dairy cattle. In this study, we assessed the fecal microbiome of organic dairy cows across different time points receiving a mixed diet of pasture and total mixed ration (TMR) or TMR only. We hypothesized that the fecal methanogenic community, as well as co-occurrence patterns with bacteria, change across diets. To test these hypotheses, we analyzed TMR and pasture samples, as well as the V3-V4 region of 16S rRNA of fecal samples collected over the course of a one-year study period from 209 cows located on an organic dairy in Northwest Washington. The inherent variability in pasture quality, quantity, availability, and animal preference can lead to diverse dietary intakes. Therefore, we conducted a k-means clustering analysis to identify samples from cows that were associated with either a pasture-based diet or a solely TMR diet. A total of 4 clusters were identified. Clusters 1 and 3 were mainly associated with samples primarily collected from cows with access to pasture of varying quality and TMR, cluster 2 was formed by samples from cows receiving only TMR, and cluster 4 was a mix of samples from cows receiving high-quality pasture and TMR or TMR only. Interestingly, we found little difference in the relative abundance of methanogens between the community clusters. There was evidence of differences in diversity between pasture associated bacterial communities and those associated with TMR. Cluster 4 had higher diversity and a less robust co-occurrence network based on Spearman correlations than communities representing TMR only or lower-quality pasture samples. These findings indicate that varied bacterial communities are correlated with the metabolic characteristics of different diets. The overall good pasture and TMR quality in this study, combined with the organic allowance for feeding high levels of TMR even during the grazing season, might have contributed to the lack of differences in the fecal archaeal community from samples associated with a mixed pasture and TMR diet, and a TMR only diet. Mitigation strategies to decrease methane emissions such as increasing concentrate to forage ratio, decreasing pasture maturity and adopting grazing systems targeting high quality pasture have been shown to be efficient for pasture-based systems. However, the allowance for organic dairy producers to provide up to an average of 70% of a ruminant’s dry matter demand from dry matter fed (e.g., TMR), suggests that reducing enteric methane emissions may require the development of novel dietary strategies independent of pasture management.