For when the chips are down — preserving UK soil microbial biodiversity for agriculture
New UK Crop Microbiome Cryobank to safeguard future research and facilitate sustainable production of UK’s six major food crops
Scientists from the UK’s foremost agricultural research institutes have teamed up to create a new UK Crop Microbiome Cyrobank (UK-CMCB) to safeguard future research and facilitate the sustainable yield improvement of the UK’s six major food crops including barley, oats, oil seed rape, potato, sugar beet and wheat.
CABI, who is leading the BBSRC project, joins researchers from Rothamsted Research, Scotland’s Rural College (SRUC) and the John Innes Centre, in developing a ‘Noah’s Ark’ of UK microbes from crop systems that will form the first publicly available resource of its kind anywhere in the world.
Scientists from the University of East Anglia (UEA) and the James Hutton Institute will also be collaborating on the initiative which will use state-of-the art cryo research techniques to preserve important crop microbiome samples from different soil types across the UK.
The UK-CMCB will provide a facility for researchers to source data and samples for their work, including living microbial material as well as genomic and metagenomic sequences (DNA) from different microbiome environments, including the rhizoplane.
Microbiomes are all the microbes present in any one ecosystem, in this case those associated with the crop plant, whether they are present in the leaves, seeds and stems or in the bulk soil around the roots. A beneficial microbiome results in a healthy plant and an improved crop yield and better-quality food.
Dr Matthew Ryan, Curator, Genetic Resource Collection at CABI, said, “By preserving these valuable crop microbial samples, from a ‘unique snapshot in time,’ we will generate a representative, very valuable and unique resource from key UK crop systems that will become a vital resource for scientific researchers for generations to come.
“We will be using UK-developed cryotechnology that uses liquid nitrogen to keep the samples secure at very cold temperatures. If you like, it is a ‘Noah’s Ark’ of UK microbes from crop systems and one that has many potential exciting uses.”
All of the project resources will be fully characterised using advanced DNA sequencing techniques in order for scientists to discover what microbes – fungi, bacteria, archaea (single-celled microorganisms with structure similar to bacteria) and viruses – are there, what they are doing in the microbiome and what role they play in enhancing crop growth. The UK-CMCB will create a curated database of sample information associated with annotated sequences, meta-data and analytical tools for end-users.
This will be the first synchronised resource covering the total microbiome of a variety of crops in standardised soil types, supported by bioinformatics, microbiologists, plant health experts and world class storage facilities.
Dr Tim Mauchline, Plant and Soil Microbiologist at Rothamsted Research, said, “Soil health is particularly important. If we can better understand the function of microbes present in our soils we can use this information to help farmers produce sustainable crops. There is a clear need to increase food production and reduce our reliance on chemical fertilizers and pesticides. It is imperative that biological solutions are found to help ensure the UK’s food security.”
Dr Nicola Holden, leading the genomics and bioinformatics team at SRUC and James Hutton Institute, said, “We are at a very exciting time in our understanding of microbiomes because of advances in deep sequencing capabilities, telling us not just about the composition of the microbiomes, but also informing on their functions. This resource will provide base-line data for how different crop types and the soils they are grown in impact the microbiome. Our ambition is to provide a comprehensive resource that will be used to optimise crop production systems.”
A further work package will be focussed on demonstrating the utility of the UK-CMCB for isolation of plant growth promoting bacteria and synthetic community construction.
This will involve characterisation of the culturable microbiota associated with crop plants and the generation of crop-associated synthetic microbial communities (SynComs) and testing for their positive impact on plant growth. The microbial consortia generated through this work package will be added to the CryoBank and made available to the public.
Dr Jacob Malone, Group Leader, Molecular Microbiology at the John Innes Centre, who will be leading the SynCom construction and testing work said, “The UK-CMCB will provide a comprehensive platform to enable research towards optimising plant yield and providing sustainable alternatives to environmentally damaging agrochemicals.”
The 5-year project starts in October 2020 and will engage with CHAP, the UK’s Agritech centre for crop health and protection, academic researches and industry.
Main image: A UK wheat crop – one of the six to have its microbiome held and curated as part of the UK Crop Microbiome Cryobank (Credit: Pixabay).
Wayne Coles, Communications Manager, CABI, Email: [email protected] Tel: 07539 424817
James Clarke, Head of Communications, Rothamsted Research, Email: [email protected] Tel: 01582 938109
Rosie Free, Press Officer, SRUC. Email: [email protected] Tel 0131 535 4219
Bernardo Rodriguez-Salcedo, Media Manager, James Hutton Institute, Email: [email protected] Tel: 07791 193918
Dr Felicity Perry, Head of Communications and Engagement, John Innes Centre, Email: [email protected] Tel: 01603 450269
Funded by UKRI BBSRC, the UK-CMCB will see plant culture and microbial isolation work take place at Rothamsted Research, biological resources held and curated in association with national collections at CABI, while SRUC and Rothamsted will manage the generation of functional data for the bioinformatic resource.
The John Innes Centre, in association with UEA, will undertake the work on synthetic community construction. Samples will undergo microbial community profiling, and all microbial isolates will undergo phylogenetic characterisation and a subset of these will undergo full genome sequencing. All meta genomes and genomes will be deposited in a freely accessible database resource after sequence annotation, and provide a microbial genome resource for the research community
CABI is an international not-for-profit organization that improves people’s lives by providing information and applying scientific expertise to solve problems in agriculture and the environment.
Through knowledge sharing and science, CABI helps address issues of global concern such as improving global food security and safeguarding the environment. We do this by helping farmers grow more and lose less of what they produce, combating threats to agriculture and the environment from pests and diseases, protecting biodiversity from invasive species, and improving access to agricultural and environmental scientific knowledge. Our 50 member countries guide and influence our core areas of work, which include development and research projects, scientific publishing and microbial services.
We gratefully acknowledge the core financial support from our member countries (and lead agencies) including the United Kingdom (Foreign, Commonwealth and Development Office), China (Chinese Ministry of Agriculture and Rural Affairs), Australia (Australian Centre for International Agricultural Research), Canada (Agriculture and Agri-Food Canada), Netherlands (Directorate-General for International Cooperation, and Switzerland (Swiss Agency for Development and Cooperation). Other sources of funding include programme/project funding from development agencies, the fees paid by our member countries and profits from our publishing activities which enable CABI to support rural development and scientific research around the world.
About Rothamsted Research
Rothamsted Research is the longest-running agricultural research institute in the world. We work from gene to field with a proud history of ground-breaking discoveries, from crop treatment to crop protection, from statistical interpretation to soils management. Our founders, in 1843, were the pioneers of modern agriculture, and through independent science and innovation, we make significant contributions to improving agri-food systems in the UK and internationally. Rothamsted is also home to three unique resources. These National Capabilities are open to researchers from all over the world: The Long-Term Experiments, Rothamsted Insect Survey and the North Wyke Farm Platform.
We are strategically funded by the Biotechnology and Biological Sciences Research Council (BBSRC), with additional support from other national and international funding streams, and from industry. We are also supported by the Lawes Agricultural Trust (LAT).
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The creation of Scotland’s Rural College (SRUC) took place in 2012 by merging SAC (the Scottish Agricultural College) with three respected partners (Barony, Elmwood and Oatridge Colleges).
SRUC exists to deliver comprehensive skills, education and business support for Scotland’s land-based industries, founded on world-class and sector-leading research, education and consultancy. The integration of these three complementary ‘knowledge exchange’ services is of significant value to all with an interest in land-based activities – be they learners, businesses, communities or policy-makers.
Competing demands and addressing new opportunities means the future for land-based industries will be extremely challenging. The next generation of business leaders and policymakers will need to be highly skilled and knowledgeable to navigate their way through a complex operating environment.
To achieve this, we will support land-based communities and industries by drawing on our accomplished history of more than a century of success. Strong in our heritage, yet stronger still as SRUC, we will strive to lead the way in delivering economic, social and environmental benefits while providing a strong voice for our rural industries.
About the John Innes Centre
The John Innes Centre is an independent, international centre of excellence in plant science, genetics and microbiology. Our mission is to generate knowledge of plants and microbes through innovative research, to train scientists for the future, to apply our knowledge of nature’s diversity to benefit agriculture, the environment, human health, and wellbeing, and engage with policy makers and the public.
We foster a creative, curiosity-driven approach to fundamental questions in bio-science, with a view to translating that into societal benefits. Over the last 100 years, we have achieved a range of fundamental breakthroughs, resulting in major societal impacts. Our new vision Healthy Plants, Healthy People, Healthy Planet (http://www.
The John Innes Centre is strategically funded by the Biotechnology and Biological Sciences Research Council (BBSRC), and is supported by the John Innes Foundation through provision of research accommodation, capital funding and long-term support of the Rotation PhD programme.
For more information about the John Innes Centre visit our website http://www.