LB 21-217 - Microbiome in different habitats within a dairy farm is connected

Background/Question/Methods:

Microbial communities have important roles in many habitats, such as driving soil biogeochemical cycling and supporting plant growth and host gut health. Microbial composition varies depending on habitat types, yet it is still unclear the extent to which each habitat shares microbial taxa and how important these microbes are for functioning within each habitat. In dairy farms, cows can take in microbes from the air or by eating grasses, and their feces are composted and supplied to soils with the associated microbes, which would enable microbes to cycle among different habitats within a farm. In this study, we hypothesized that (1) a farm has unique microbes appearing in several habitats of the farm, and their number and species depend on the farm management such as cleaning frequency and manure fermentation level and that (2) the important microbes including keystone taxa in a place can appear in other habitats. To test these hypotheses, we collected grasses, cow feces, manures, soils, and sheets that wiped walls, as different habitats of microbes, in 15 dairy farms over three areas, then analyzed the fungal and bacterial communities.

Results/Conclusions:

Farms had different communities of both fungi and bacteria, though the difference in the habitat had a much stronger impact on the communities. Multidimensional scaling (MDS) analysis showed a clear separation between the sampling area in fungal communities using the 5^th and 6^th axes, which would suggest there are unique fungal communities in the area regardless of the habitat. In addition, as we expected, the farm management cause differences in the shared microbes between several habitats, since the less-composted and well-composted manures tended to share many microbes with cow feces and soils, respectively. Network analysis for each farm showed that the microbial species bridging the communities in different habitats vary by farm. Furthermore, based on the network analysis for each habitat, the keystone taxa (i.e., taxa having many connections with others) in the soil appeared in different habitats such as manure and cow feces, sometimes with higher relative abundance than that in soils, which may suggest that other environments provide some key microbes in soils. Overall, our study suggests some microbes are shared in several habitats, farm management can affect the connection between the habitats, and shared microbes can be keystone taxa in a habitat.