The UK Crop Microbiome CryoBank

Lead Research Organisation: CAB International
Department Name: Egham Office


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

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.
Description This five-year research project is now in it's third year. The focus of the first part of the project has been the construction of the resource - this phase is now 90% complete and has involved collection of the samples and extraction of DNA by Rothamsted and biobanking of samples by CABI (detailed below). The resource is now being sequenced and characterized, before further development at the John Innes Centre. The resource will be opened for access during 2023.

There steady flow of samples into the UK Crop Microbiome Cryobank has continued with 960 soil & rhizoplane samples and 350 Micro-plates containing 33,600 bacterial isolates. Sample processing is coordinated by Rothamsted research focusing on key UK Crops (Wheat, barley, oats, oil seed rape, potato, faba beans, sugar beet). Samples are then transferred to CABI for processing for cryopreservation and long-term storage. All samples are being sequenced and characterized through partners at Scotland's Rural College and the James Hutton Institute. All protocols and data is available through the project website

Cryo-methodology: We successfully validated the Stirling Cycle Controlled Rate Cooler that will be used for cryopreserving the microbiome resources generated in the project. This has been achieved with 15 different strains of soil bacteria and 23 different strains of fungi representing diverse taxonomic groups. Each strain was subject to controlled rate cooling at a rate of -1 degree per minute in the presence of a cryoprotectant, using both the new device and, for comparison an older device. The viability and morphology of each strain was analysed before cooling and then compared after cooling. No adverse effects were seen with any of the organisms, with morphology and recovery within expected parameters when using the new controlled rate cooler. We are now confident that the new device is suitably validated for routine use in the project, as we develop standards for the cryopreservation of microbiome samples. Additional experimentation was designed to assess the impact of cooling rate on the genomic integrity of soil samples, from Rothamsted's experimental plots. The hypothesis tested, was that the application of optimised cooling rates conserves the genomic integrity of the soil samples. In brief, soil samples were subjected to optimal and sub-optimal cooling regimes using the Stirling cycle controlled rate cooler. DNA was extracted from samples before and after cryopreservation and subjected to both amplicon and metagenomic analysis. The methodology incorporated an innovative fermentation step. Initial results indicate that stability is retained post cryopreservation. We now intend to broaden this research to incorporate more samples.

We have also had a collaboration with Imperial College London, which involved assaying the functionality of Brassica napus rhizosphere microbiomes to identify a preferred method for cryogenic preservation. Three methods were investigated freeze drying, controlled rate cooling and plunge cooling and were measured against control samples Biolog Eco Plates were used for community-level physiological profiling. BacTiter-Glo™ assessed ATP levels. Fluorescently marked substrates assayed exoenzyme activity and MicroResp™ was used to compare respiration. The results showed that enzyme and ATP assays along with Biolog plates showed freeze-drying to be the least effective method for preservation. Freeze-drying had too greater impact on the microbiome. Plunge cooling in liquid nitrogen and controlled rate cooling were repeatedly found to conserve microbial functionality equally. Biolog assays suggested both preservation methods caused slight drops in functional diversity. On all other measures (ATP, enzyme activity and respiration) there were no statistically significant differences compared to the control soils. Controlled rate cooling is however safer and more convenient compared to plunge cooling.
Exploitation Route We are the first group developing and applying optimised cryopreservation procedures for agricultural microbiome samples. There are currently no internationally accepted standards or methodology, so we will be taking a proactive role to put these in place for the benefit of both the wider scientific community and industry. This will ultimately help protect key microbial resources and the investment and intellectual property involved in their generation. The UK Crop Microbiome Cryobank is a model for broader strategies for microbiome biobanking in other fields of research.

Additionally, the resources are already providing a baseline for research in third party institutions and for use for developing new project applications.
Sectors Agriculture, Food and Drink,Education,Healthcare,Pharmaceuticals and Medical Biotechnology

Description Contribution to the innovate-ktn deep dive report on 'The Human Intestinal Microbiome - Therapies and Diagnostics: The Science, Opportunities and Challenges'. With reference to the UK Crop Microbiome Cryobank, establishing a UK Microbiome Bank, akin to the UK Biobank, for conserving and preserving the biodiversity of microbiomes, with the added role of setting standards for sampling and associated analyses and storage.
Geographic Reach National 
Policy Influence Type Citation in other policy documents
Description KTN Microbiome Biobanking Group
Geographic Reach National 
Policy Influence Type Participation in a guidance/advisory committee
Description The KTN Microbiome Innovation Network Strategic Roadmap
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
Description MICRObiome Biobanking (RI) Enabler
Amount € 5,804,683 (EUR)
Funding ID 101094353 
Organisation European Union 
Sector Public
Country European Union (EU)
Start 02/2023 
End 01/2027
Title Cryopreservation protocols for microbiome samples 
Description Cryopreservation approaches for soil and microbiome samples utilising Stirling cycle cooling and encapsulation vitrification 
Type Of Material Biological samples 
Year Produced 2021 
Provided To Others? No  
Impact The methodology developed is the first application of these technologies for microbiome samples. The methods will be formally published as part of a series of protocols and procedures being developed through the cryobank project 
Title AgMicrobiomeBase 
Description 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 crop microbiome environments, including rhizoplane. AgMirobiomeBase is a curated and open access AgMicrobiome base of bioinformatic information, meta-data, annotated sequences, integrated with current sequence and microbiome databases such as MGnify - Linking data with sample provenance Full meta data sets including: Physical and chemical soil data, Microbial data sets, sample and isolation data, sequence data 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Impact As far as we are aware, this is the first database than links a physical sample, its provenance and soil chemistry, with its metadata, sequence information and links to EBI's MGnify 
Description Global Microbiota Vault 
Organisation Rutgers University
Country United States 
Sector Academic/University 
PI Contribution The Microbiota Vault is a major international initiative which aims to conserve the diverse microbiota to ensure long-term health for humanity. Led from Rutgers University, New York and with an international array of collaborators including Nobel prize winners, there are a number of synergies with the UK Crop Microbiome Cryobank. Although the prime focus is on the conservation of human microbiota, the technologies that we are utilizing and the methods we are using for cryopreservation of microbiome samples in the crop health domain is translatable to other domains. Dr Matthew Ryan has joined the consortium as a collaborating partner and will contribute to work packages on cryopreservation and lyophilisation.
Collaborator Contribution This is a developing collaboration. It will allow cross-fertilisation with scientists from the medical and veterinary domains
Impact Funding opportunities are being explored as the initiative develops. The collaboration is cross-disciplinary across Agrifood and medial / veterinary science with potential societal / socioeconomic impacts
Start Year 2021
Description Masters project study - Functionality of stored microbiome samples 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution The provision of samples from the UK Crop Microbiome Cryobank. Access to cryopreservation equipment and technologies,
Collaborator Contribution A masters project through (and supervised by) Professor Tom Bell at Imperial College, providing expertise in the functional analysis (potential) of bacterial communities.
Impact On-going
Start Year 2021
Description Community outreach event at Rothamsted Research 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact A community outreach event was held at Rothamsted Research in September 2021. The purpose of the event was to i) promote the Cryobank and raise awareness to the user community, ii) facilitates user engagement through access to resources and data, iii) Identify 'gaps' and help to improve approaches, iv) Ensure we adapt to meet the needs of users and identify opportunities for broader collaboration and the development of proposals and v) use this valuable networking opportunity to discuss broader issues of
relevance to the UK Crop, Soil and Agritech community including the UK Plant Microbiome Initiative and the KTN microbiome roadmap. The meeting was held face to face and attracted over 30 representatives from industry, policy bodies and academics from leading universities and research institutes. The main outcomes from the meeting were a better perspective on the requirements of industry, an improved awareness of user requirements and several potential areas for further project development utilising the cryobank resource and its associated expertise. The minutes of the meeting and slidedeck have been made publicly available through
Year(s) Of Engagement Activity 2021
Description Press release announcing the start of the project 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact The media release jointly by CABI, JIC, Rothamsted and the James Hutton Inst to announce the start of the project ad its aims was covered by 28 media outlets reaching an online readership of 58.1 million, with 378k coverage views and 73 social shares. These included FarmingUK, the Scottish Farmer, the Science Times, Food and Farming Futures and international outlets such as EurekaAlert
Year(s) Of Engagement Activity 2020
Description Project website and database 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact A project website, Twitter handle, database
Year(s) Of Engagement Activity 2020,2021,2022
Description There's a collection for that! Expert panel - Invited International 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact A panel based discussion organized by the American Phytopathological Society at Plant Health 2022 in Pittsburgh, USA. The discussion looked at the provision of cultures and resources to support plant pathology. The UK Crop Microbiome Cryobank was used as an example of approaches to conserve microbial consortia for eventual agricultural intervention. The audience consisted of researchers, agricultural extension workers, governmental representatives (USDA and others) and policy makers.
Year(s) Of Engagement Activity 2022