Details of Award
NERC Reference : NE/P008534/1
Developing methods for long-read marine viral metagenomics
Grant Award
- Principal Investigator:
- Dr B Temperton, University of Exeter, Biosciences
- Grant held at:
- University of Exeter, Biosciences
- Science Area:
- Marine
- Overall Classification:
- Unknown
- ENRIs:
- Biodiversity
- Environmental Risks and Hazards
- Global Change
- Science Topics:
- Virology
- Microbiology
- Environmental Genomics
- DNA sequencing
- Molecular biology
- Genomics
- Metagenomics
- Bioinformatics for genomics
- Bioinformatics
- Metagenomics
- Environmental Informatics
- Abstract:
- Everybody knows how important terrestrial plants are to the global climate, fixing atmospheric carbon and providing the oxygen that sustains life. What is less known is that marine microbes are responsible for around half of total global primary production. Seawater is teeming with microbes, with around 5 million in every teaspoon in surface water. These can be categorised as the phototrophs that fix atmospheric carbon, the heterotrophs that convert this carbon back to atmospheric CO2 and the vast number of viruses that interact with these two groups. At any given time, around 30% of marine microbes are infected by their associated viruses. Viral lysis kills 20% of bacterial standing stocks every day, releasing a soup of dissolved organic carbon that is the largest pool of available carbon on Earth. Heterotrophs rapidly convert this back into CO2, preventing it from sinking to the deep where it is locked away. Viruses can also act as agents of gene transfer, and can reconfigure host metabolism during infection, changing their metabolic inputs and outputs. Such changes then resonate throughout the community, ultimately shaping its function and composition. Traditionally, our understanding of viruses was limited to those for which we had successfully cultured the host. As >99% of microbes are uncultivated, this provided a very narrow representation of viral diversity. Recent advances in sequencing viruses directly from the environment, by preparing viral metagenomes (viromes) have revolutionised our understanding of the importance, abundance and impact of viruses on global biogeochemical cycles. However, such approaches rely on successfully assembling viral genomes from short read data, similar to reconstructing an enormous genomic jigsaw with billions of pieces. The high rates of evolution and extraordinary diversity of viruses makes this a challenge. Currently <1% of viral sequences from a metagenome can be assigned to a known viral group. This project will establish new methods to sequence viral metagenomes using the latest long-read sequencing technology. PacBio and Nanopore sequencers generate reads that are several thousand basepairs long, in some cases, sufficiently long to span an entire viral genome. This increased length makes assembly and analysis of viral genomes trivial. To date, application of long-read sequencing to viral metagenomics has been limited by a need for DNA input requirements that were orders of magnitude higher than that which can be reasonably extracted from an environmental viral sample. However, recent updates to library preparation for Nanopore and advances in DNA amplification for PacBio make it an opportune time to re-evaluate their use in viral metagenomics. As a result of long-read sequencing, extracting full length viral genomes from environmental samples will provide a step-change in the resolution with which we can perform viral ecology.
- NERC Reference:
- NE/P008534/1
- Grant Stage:
- Completed
- Scheme:
- Directed (RP) - NR1
- Grant Status:
- Closed
- Programme:
- IOF
This grant award has a total value of £39,786
FDAB - Financial Details (Award breakdown by headings)
| DI - Other Costs | Indirect - Indirect Costs | DA - Investigators | DA - Estate Costs | DI - T&S | DA - Other Directly Allocated |
|---|---|---|---|---|---|
| £14,661 | £5,096 | £6,754 | £1,792 | £8,340 | £3,142 |
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