The UK Crop Microbiome Cryobank – Advancing Microbiome Research for Sustainable Agriculture

Plant microbiomes are critical to crop health, improved yields, and food quality. However, most research on this subject tends to focus on a single aspect of this complex network of interactions and ecological processes. Thus, the UK Crop Microbiome Cryobank (UKCMC) project is developing a unique, integrated, and open-access resource to enable the development of solutions to improve soil and crop health. The project objectives encompass providing accessible cryopreserved microbial isolates, samples origin datasets with complete metadata, comparing soil and crop sample communities, and establishing standardized protocols for complex soil microbiota. Six of the UK’s key crops and 11 sampling sites across the UK were targeted, and the methods and data outputs will underpin research activity both in the UK and internationally. Soils from these 11 locations (three contrasting soil types) were used to grow wheat, barley, oats, potato, Fava beans, oil seed rape crops in controlled glasshouse experiments with bare soils as controls. The rhizosphere soils from these pots were used for the isolation of micro-organisms (mostly bacteria), 16S rRNA gene and ITS metabarcoding and metagenome sequencing. All data generated will be made available on the AgMicrobiome Base website (https://agmicrobiomebase.org/). Currently, ~37,000 isolates have been collected , of these ~23,000 were tested for multiple plant-growth-promoting characteristics such as nutrient solubilization and stress resistance. Microbial communities from these samples underwent taxonomic sequencing, including bacterial (16S) and fungal (ITS - wheat only) communities. Shotgun metagenomic sequencing is in progress for wheat and fava bean communities, alongside de novo whole-genome sequencing of selected cultivable isolates. Robust data analysis pipelines were devised to handle the high-throughput data outputs. We believe that the model created is transferable to different crop and soil systems, acting not only as a mechanism to conserve biodiversity, but as a potential facilitator of sustainable agriculture systems that mitigate against climate change.