Crop microbiome bank opens for business

The construction of the UK Crop Microbiome Cryobank (UK-CMCB) – the first publicly available resource of its kind anywhere in the world – is now complete after three years of painstaking research.

Scientists from the UK’s foremost agricultural research institutes created the facility, which will safeguard future research and enable sustainable yield improvement for six major food crops including barley, oats, faba bean, oil seed rape, sugar beet and wheat.

The project, funded by UKRI BBSRC, was led by CABI (which houses the resource) and brought together experts from Rothamsted Research, Scotland’s Rural College (SRUC), James Hutton Institute  and the John Innes Centre. It uses state-of-the art cryo research techniques to preserve important crop microbiome samples obtained from different crops cultured in a range of UK soil types. The resource also includes living microbial material as well as genomic and metagenomic sequences (DNA) from the crop root environment.

Dr Tim Mauchline, plant and soil microbiologist at Rothamsted Research, said, “The UK-CMCB allows us to better understand the profile and function of microbes in our soils, which is important in advising farmers how to produce crops more sustainably.

“Advancing research on biological solutions to mitigate crop pests and diseases is also imperative to help ensure the UK’s food security at a time when chemical fertilizers and pesticides are in the spotlight amid the growing concerns of climate change.”

Mauchline and his colleagues drew on Rothamsted’s extensive experience of soil microbiome research in farming systems for their contribution to the project. 

“This is the first time the root microbiome has been studied at such great scale for such an important range of crops. It will give us unique insights into how the soil microbiome interacts with different plants in a range of soil types and generate new microbial candidates for plant inoculation.” he said. 

The new cryobank facility – likened to a “Noah’s Ark” of UK microbes – used UK-developed cryotechnology that uses liquid nitrogen to keep the valuable crop microbiome samples secure at very cold temperatures for generations to come.

All the resources were characterised using advanced DNA sequencing techniques. This allowed the scientists to discover what microbes – fungi, bacteria, archaea (single-celled microorganisms with structure like bacteria) and viruses – are present, in the root microbiome and improve understanding of their function and potential to enhance crop growth.

Microbiomes are all the microbes present in any one ecosystem. In this case, it is those associated with the roots of crop plants or in unplanted bulk soil. A beneficial microbiome should result in sustainably produced healthy plants, less dependent on agrochemical inputs and yielding better-quality food.

Dr Matthew Ryan, Curator, Genetic Resource Collection at CABI, said “these valuable crop microbial samples from a unique snapshot in time are a vital resource for scientific researchers investigating how to ensure food security amid a range of challenges, including the impact of climate change on crops.”

Dr Ryan said, “We are delighted that the construction of the UK Crop Microbiome Cryobank has now been completed.

“It is 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.

“As part of the work, we also looked at the utility of the UK-CMCB for the isolation of plant growth promoting bacteria and synthetic community construction.”

This involved the 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 are being added to the CryoBank and will soon be available to the public. The UK-CMCB has also created a curated database of sample information associated with DNA sequence data, metadata, and provision for analytical tools for end-users.