Microbiota in Dung and Milk Differ Between Organic and Conventional Dairy Farms

Abstract

Organic farming is increasingly promoted as a means to reduce the environmental impact of artificial fertilizers, pesticides, herbicides, and antibiotics in conventional dairy systems. These factors potentially affect the microbial communities of the production stages (soil, silage, dung, and milk) of the entire farm cycle. However, understanding whether the microbiota representative of different production stages reflects different agricultural practices-such as conventional versus organic farming-is unknown. Furthermore, the translocation of the microbial community across production stages is scarcely studied. We sequenced the microbial communities of soil, silage, dung, and milk samples from organic and conventional dairy farms in the Netherlands. We found that community structure of soil fungi and bacteria significantly differed among soil types, but not between organic versus conventional farming systems. The microbial communities of silage also did not differ among conventional and organic systems. Nevertheless, the dung microbiota of cows and the fungal communities in the milk were significantly structured by agricultural practice. We conclude that, while the production stages of dairy farms seem to be disconnected in terms of microbial transfer, certain practices specific for each agricultural system, such as the content of diet and the use of antibiotics, are potential drivers of shifts in the cow's microbiota, including the milk produced. This may reflect differences in farm animal health and quality of dairy products depending on farming practices.

Soil Microbial Indicators within Rotations and Tillage Systems

“…Micropepsaceae (F) information is scarce but has been found in acidic soils and is involved with carbon cycling [58]. Tepidisphaerales (O) has little information available except for an association with conventional farming [59], and WD2101(F) is polysaccharide degraders found in raised bogs and eutrophic fens [60]. Similarly, Ktedonobacterales (O) is relatively unknown but have been found to inhabit forests, gardens, and sand in low numbers, as well as extreme environments, such as volcanoes and geothermal areas [61].…”

Production, Composition and Nutritional Properties of Organic Milk: A Critical Review

“…Previous studies have shown that diet has a direct impact on the gut, rumen, and milk microbiota of bovines [87][88][89]. To our knowledge, only one study has compared the microbiota of dairy cows from conventional and organic farming [27]. This study demonstrated that the microbiome of the cow's gut and milk was significantly different between agricultural management systems, while no differences were found in the microbial communities of soil and silage [27].…”

“…To our knowledge, only one study has compared the microbiota of dairy cows from conventional and organic farming [27]. This study demonstrated that the microbiome of the cow's gut and milk was significantly different between agricultural management systems, while no differences were found in the microbial communities of soil and silage [27]. Milk samples from organic farms were significantly associated with the family Rhodobacteraceae and elevated levels of Ruminococcaceae.…”

“…For instance, organic milk has consistently been reported to contain significantly higher levels of whey proteins, total polyunsaturated fatty acids (PUFA), n-3 PUFA and vitamin E (α-tocopherol) [25,26]. Organic milk production has also been reported to influence the microbial content of milk [27]. Compositional differences have been linked to conditions associated with organic production such as breed, environment, health status, and feeding regime [25].…”