The UK Crop Microbiome CryoBank

Lead Research Organisation: John Innes Centre
Department Name: Molecular Microbiology

Abstract

This project, The UK Crop Microbiome Cryobank (UKCMCB) will establish a total resource of microorganisms and information associated with the microbiome of the UKs major crops. It brings together four leading institutions: Rothamsted Research, CABI, the James Hutton Institute and the John Innes Centre (in association with UEA). Each has a proven track record of working with industry, working at the forefront of pure and applied Agritech research.
The plant microbiome mainly consists of fungi, bacteria and viruses that are associated with a plant and includes microbes that can be isolated and cultured and those that currently are currently not amenable to culture. Microbial consortia include members that help the plant host by providing nutrients, help prevent disease or allow a plant to tolerate environmental conditions. Driven by academic research and Agritech industry needs, it will provide a resource to underpin research on the Crop Microbiome, delivering sustainable solutions to improve plant health and crop productivity. The resource will facilitate better understanding of microbial community interactions, including the host plant and other components of the 'Phytobiome', and thereby impact plant health, from improvements in rhizosphere health through to control of biological threats.
The resource will comprise:
-A publicly available integrated Cryobank collection of samples (rhizoplane material -soils, bacterial and fungal isolates, plant material, and DNA) taken initially from 315 samples from systems significant to the UK Agritech sector. Initial focus will be on 6 crops (barley, oats, oil seed rape, potato, sugar beet and wheat ) from 9 different soil sites from across the UK. This will be supplemented with culturable material from the samples. Samples will be optimally preserved at ultra-low temperature using state-of-the-art technologies.
-A curated AgMicrobiome Base of sample information with annotated sequences and meta-data for end-users. This will be the first synchronised resource covering the total microbiome of a variety of crops in identical soil types, supported by a bioinformatics resource, microbiologists, plant and crop health experts, with world class storage facilities. Provision of material will allow research into unexplored cultural biodiversity.
- 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 UK crop plants and the generation of crop-associated synthetic microbial communities (SynComs) and testing for positive plant growth traits. The microbes generated through this work package will be added to the CryoBank and made available to the public.
The plant culture and microbial isolation work will take place at Rothamsted Research, biological resources will be held and curated in association with national collections at CABI, while JHI & Rothamsted will manage generation of functional data for the sequence resource. JIC 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
This will result in the creation of a unique, world-leading combined resource of microbiome material, microorganisms, DNA and associated data useful for both academic and commercial research with potential for deployment in sustainable Agriculture

Technical Summary

Sequencing technology has revolutionised the description of microbial communities and their interactions with other organisms. Many studies into the genetic diversity of microbiomes for a range of crops have been published, but these are fragmented and uncoordinated. It is impossible to understand the relative importance of genotypic and edaphic factors in driving crop microbiome function. Since samples are not stored adequately or publicly available, researchers cannot revisit them to add metadata as new technologies emerge or research priorities change. Existing culture collections store axenic cultures of single species. Whilst important, these provide limited scope in a 'microbiomic' age. To advance this, resources need to be developed and validated for preserving and reviving whole crop microbiomes, along with libraries of culturable strains with varying properties. We seek to create a cryopreserved 'CryoBank' of characterised plant-associated microbiomes (rhizoplane material, bacterial and fungal isolates, DNA) alongside an integrated bioinformatic database. After characterisation of the culturable microbiota associated with UK crops, synthetic microbial communities will be constructed and tested for positive plant growth traits. This will provide unique added value resources for further evaluation by industry and academia. This integrated resource will support Crop Microbiome research. Robust methodologies for collection and storage of intact microbial communities in environmental samples and extraction of total DNA will be applied. Cryopreservation will be optimised to sustainably maintain the resource in a genotypically, phenotypically and functionally stable state. Genomic tools capable of characterising samples will be used to assess microbial diversity (including symbionts, endophytes, pathogens) within the samples. Metadata will be accessed into the AgMicrobiome Base a bioinformatics information and data resource with links to EBI and sample metadata.

Planned Impact

WHO WILL BENEFIT FROM THE RESEARCH AND HOW?
PLANT PATHOLOGISTS, SOIL MICROBIOLOGISTS, AND OTHER RESEARCHERS STUDYING CROP HEALTH AND DISEASE: The UK Crop Microbiome CryoBank (UK-CMCB) will combine cryo-stored rhizoplane samples with microbial cultures integrated with accessible meta information, bioinformatic databases and tools to facilitate research into the crop microbiome. It will fill a gap in UK resource infrastructure and represents a unique, world-first biological resource that will underpin UK-led research in several key BBSRC strategic priority areas, most significantly the sustainable enhancement of agricultural production. Research based on the CMCB will have substantial implications for plant health, food security and the management of invasive species. The resource will further support efforts towards several UN sustainable goals (including Zero Hunger; Production and Life on Land; Responsible Consumption), as well as offering significant potential for future GCRF activity. The resource will strengthen existing ties and stimulate new collaborations between UK agricultural research organisations including the Centre for Crop Health and Protection, Rothamsted and FERA Ltd., The John Innes Centre/UEA, CABI, The James Hutton Institute alongside UK Universities and international organisations. Staff on the project will be trained in transferable skills including environmental and molecular microbiology, bioinformatics, and the analysis of complex datasets that are in high-demand among employers in academia and industry.
THE AGRITECH INDUSTRY AND RELATED BIOSCIENCE COMPANIES: Both the UK-CMCB resource itself, and the research it generates, will be of direct benefit to the bioeconomy supporting Agritech companies, from small start-ups to multinationals. Research areas that could directly benefit from the resource include the development of alternative pest-control/plant growth-promotion strategies, more efficient use of conventional pesticides/fertilisers, combatting of the spread of invasive species, and exploitation of soil microbiomes as a source of new bio-inoculants. The potential utility of the resource to these stakeholders is evidenced by the multiple letters of support we have received for this proposal and we will liaise with KTN and CHAP to ensure translation.
FARMERS AND THE AGRICULTURAL SECTOR: Research generated as a result of the UK-CMCB will produce substantial medium and long-term benefits for farmers in the form of novel crop treatments (both chemical and biological), new crop varieties with improved characteristics relating to soil health, advice and guidance on soil and crop management, and improved national responses to the threat of invasive species.
THE GENERAL PUBLIC: In addition to the indirect economic and agricultural benefits described above, development of the UK-CMCB will increase public understanding of the plant microbiome, and how plant/soil-associated microbiomes affect everyday life. For example, how microbes impact both agricultural ecosystems and natural environments, and their potential uses in biotechnology. As this is a publicly-funded resource, it is important that the public are both informed about the science we are doing, and are actively involved in discussions with scientists about how the resource should develop going forward. This will aid both in the dissemination and understanding of the work we do, and crucially will help to build public trust in the research. All applicants are actively involved in public outreach, and provide expert knowledge related to environmental and agricultural microbiology to the media, government and international bodies such as the OECD. As part of this project we will carry out a number of different outreach activities, and will actively communicate our science to the public.

Publications

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