IAM_GenomicsThinkPiece_fnut-06-00107.pdf (809.08 kB)

Applications of the Soil, Plant and Rumen Microbiomes in Pastoral Agriculture

Download (809.08 kB)
journal contribution
posted on 2024-06-21, 03:55 authored by Graeme AttwoodGraeme Attwood, David Chapman, Shannon ClarkeShannon Clarke, Jeanne Jacobs, Sinead LeahySinead Leahy, Richard MuirheadRichard Muirhead, Suzanne RoweSuzanne Rowe, Steve Wakelin
This paper was commissioned by Our Land and Water to test the hypothesis: 'Significant additional gains in soil, plant, and animal productivity, coupled with reduced environmental footprint can be realised through appropriate matching of functional genotypes (plant and animal) and understanding the interactions among soil, plant and animal microbiomes.' Producing dairy, meat and fibre products relies on the biological processes occurring in soils, plants and animals. Each of these biological components have their own microbiome, viewed previously as distinct entities. However, these microbiomes operate under similar ecological principles and are physically connected via water, carbon and nutrient cycles. These microbiomes can be considered a meta-community (farm system biome). While opportunities through manipulating individual microbiomes are being investigated (eg rumen methanogenesis), there may be opportunities for system-wide gains by looking across two or more microbiomes. We reviewed the work done in soil, plant and animal microbiomes and explore what additional benefits may be possible through understanding their interactions, and matching soil, plant and animal genotypes to increase productivity and reduce environmental footprint. This paper considers the recent developments in genomics that provide new tools to understand the microbiome along the soil-plant-animal continuum within the pastoral production system. Within the soil-plant-animal it looks at the animal and farm management opportunities arising from advanced understanding of microbial diversity and ecosystem function and how that can be used to improve soil processes, forage growth and pasture utilization and help withstand the challenges of diseases and climate change. These opportunities are summarized via three case studies. The potential for interdependencies, interplay and interactions between the microbiomes of the ecosystems along this continuum are considered along with other downstream impacts. The paper proposes how an 'ecological genomics' approach can contribute to improved understanding of these microbiomes to improve the performance of the pastoral sector. Originally published as a think piece for Our Land and Water (October 2016)


Funded by the New Zealand Ministry for Business, Innovation and Employment's Our Land and Water National Science Challenge (Toitū te Whenua, Toiora te Wai) as part of project Innovative Agricultural Microbiomes


Publication date



  • English

Does this contain Māori information or data?

  • No

Journal title

Frontiers in Nutrition

Usage metrics


    Ref. manager