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Innovative Agricultural Microbiomes

Understanding and manipulating interactions between soil, plant and animal microbiomes to improve water quality and sustainable pastoral productivity

Agricultural microbiome cycle


Challenge funding: $1,800,000

Research duration: July 2017 – April 2020

What Are We Doing?

New Zealand dairy farm systems are strongly influenced by various sources of nitrogen: atmospheric nitrogen fixed by legumes, cow effluent, and fertilisers. These inputs must be balanced to maximise plant and animal productivity, and minimise nitrogen leaching to waterways.

The nitrogen cycle relies on the action of microbes: nitrogen-fixing bacteria in the roots of plants, bacteria in the cow rumen, and ammonifying and nitrifying bacteria in the soil. These plant, soil and animal microbiomes are usually viewed as distinct entities, but Innovative Agricultural Microbiomes research is taking the novel approach of investigating them as a meta-microbiome, or agricultural microbiome.

Our researchers are learning how agricultural microbiomes respond to increasing levels of nitrogenous fertiliser, and are identifying the soil-plant-animal microbiome interactions that mediate nitrogen in a dairy production system.

Our research aims to manipulate microbiome-driven processes in the soil, plant and animal to minimise the leaching of nitrogen, provide nutrients for forage plants, and supply the micronutrients and energy that animals need to produce foods consumed by humans.

How Can The Research Be Used?

  • An animal trial has been completed in a ryegrass-white clover dairy production system, utilising the dairy farm facilities at the Lincoln University Ashley Dene Research and Development Station (ADRDS). The work involves the characterisation of soil, plant and animal microbiomes under an external nitrogen (in the form of urea) treatment regime.
  • DNA and RNA from the soil, plant and animal microbiomes will be sequenced and correlated with metabolites, nitrogen leaching, pasture production and composition, and milk production data. We are identifying key microbial populations, metabolic pathways and genes associated with both enhanced production and reduced environmental impacts.
  • An assessment of microbiomes and their interactions between the animal, soil and plant environments will show how microbiomes align with the Māori concept of mauri (life force).
  • The microbiome marker genes that are correlated with productivity and/or sustainable practices will be useful as supporting evidence for product verification schemes to show that NZ’s pastoral farming systems are natural and sustainable.
  • Our research will support New Zealand’s competitive advantage in researching novel endophytic microorganism for existing and future crop species. The potential future value of novel endophytic species in assisting plants to adapt to global temperature rises and increased pest pressures will be significant. (For example, the current value to New Zealand of commercialised ryegrass endophytes AR1 and AR37 is estimated to be $155–$285 million annually.)

Team Snapshot

Research Outputs


Soil Nitrogen Treatment Alters Microbiome Networks Across Farm Niches

XinYue Wang, Kerri Reilly, Rosemary Heathcott, Ambarish Biswas, Linda J. Johnson, Suliana Teasdale, Gwen-Aëlle Grelet, Anastasija Podolyan, Pablo Gregorini, Graeme T. Attwood, Nikola Palevich and Sergio E. Morales
Frontiers in Microbiology (February 2022)

A farm is a collection of interlinked ecological habitats split by locations, including above-ground, below-ground, and animal-associated niches each harbouring unique microbiomes. We examined agricultural microbiome responses to 3 different nitrogen treatments (0, 150, and 300 kg/ha/yr) in soil and tracked linked responses in other neighbouring farm niches. Nitrogen treatment had little impact on microbiome structure or composition across niches, but drastically reduced the microbiome network connectivity in soil. Networks of 16S microbiomes were the most sensitive to nitrogen treatment across amplicons, where ITS microbiome networks were the least responsive. Nitrogen enrichment in soil altered soil and the neighbouring microbiome networks, supporting our hypotheses that nitrogen treatment in soil altered microbiomes in soil and in nearby niches. This suggested that agricultural microbiomes across farm niches are ecologically interactive. Therefore, knock-on effects on neighbouring niches should be considered when management is applied to a single agricultural niche.

Suitability of six extraction methods for isolating a large quantity of high-quality RNA from New Zealand free-draining stony soil

Anastasija Podolyan & Gwen-Aëlle Grelet
New Zealand Journal of Agricultural Research, May 2020

High-quality RNA from soil is essential for investigating the functionality of soil microbial communities. The affordability the RNA-Seq method enables innovative studies of whole ecosystems but relies on a high quality and quantity of RNA. Different types of soils have different physicochemical properties, and therefore RNA extraction methods are usually investigated for each soil type separately. This study investigated six RNA extraction methods from a free-draining Balmoral/Lismore stony silt loam soil. Four commercial RNA extraction kits and two manual RNA extraction methods were assessed for their suitability for high throughput, purity, integrity, and quantity of RNA and its suitability for RNA-Seq applications, processing time, and toxicity. Three RNA extraction methods satisfied the majority of the criteria, thus allowing large-scale functional studies of soil microbiome.

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

G. Attwood, S. Wakelin, S. Leahy, S. Rowe, S. Clarke, D. Chapman, R. Muirhead, J. Jacobs
Frontiers in Nutrition, July 2019

In this paper, we consider 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 continuum we look 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. We finally propose how an “ecological genomics” approach can contribute to improved understanding of these microbiomes to improve the performance of the pastoral sector.


Innovative Agricultural Microbiomes

Sergio Morales
Our Land and Water Symposium, August 2019


Genomics: Animal-Plant-Soil Microbiome

Graeme Attwood, Linda Johnson, Suzanne Rowe, Pablo Gregorini, Grant Edwards, Keith Cameron, Pierre Beukes, Gwen Grelet, Sergio Morales
Our Land and Water Symposium, April 2017

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