REVIEW published: 16 July 2019 doi: 10.3389/fnut.2019.00107 Applications of the Soil, Plant and Rumen Microbiomes in Pastoral Agriculture Graeme T. Attwood 1, Steve A. Wakelin 2†, Sinead C. Leahy 1, Suzanne Rowe 3, Shannon Clarke 3, David F. Chapman 4, Richard Muirhead 5 and Jeanne M. E. Jacobs 2* 1 Animal Science, AgResearch, Palmerston North, New Zealand, 2 Forage Science, AgResearch, Lincoln, New Zealand, 3 Animal Science, AgResearch, Invermay, New Zealand, 4 DairyNZ, Lincoln, New Zealand, 5 Farm Systems and Environment, AgResearch, Invermay, New Zealand The production of dairy, meat, and fiber by ruminant animals relies on the biological processes occurring in soils, forage plants, and the animals’ rumens. Each of these components has an associated microbiome, and these have traditionally been viewed Edited by: as distinct ecosystems. However, these microbiomes operate under similar ecological Rossana Coda, University of Helsinki, Finland principles and are connected via water, energy flows, and the carbon and nitrogen Reviewed by: nutrient cycles. Here, we summarize the microbiome research that has been done in Jeffrey Firkins, each of these three environments (soils, forage plants, animals’ rumen) and investigate The Ohio State University, what additional benefits may be possible through understanding the interactions between United States Sergiy Smetana, the various microbiomes. The challenge for future research is to enhance microbiome German Institute of Food function by appropriate matching of plant and animal genotypes with the environment to Technologies, Germany improve the output and environmental sustainability of pastoral agriculture. *Correspondence: Jeanne M. E. Jacobs Keywords: genomics, metagenomics, pasture, ecosystems, food, soil
[email protected] †Present Address: INTRODUCTION Steve A.