Nanopore sequencing of ocean microbiomes

Langan, Emma (2022) Nanopore sequencing of ocean microbiomes. Doctoral thesis, University of East Anglia.

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Ocean microbiomes are responsible for the majority of global primary production, and are crucial for global biogeochemical cycles. Eukaryotic phytoplankton contribute to the carbon cycle which is important for the climate, with polar communities making a disproportionate contribution. These communities are threatened by climate change, and it is important to understand their distribution and interactions so that these impacts can be modelled and monitored.

Ocean microbiomes have not been well characterised, but nanopore sequencing could be used to study them with long-reads and in situ sequencing. This project piloted the use of nanopore sequencing for studying ocean microbes to improve our understanding of their genomes, communities, and interactions.

A genome assembly was produced for a haploid Emiliania huxleyi strain, to complement the single publicly available diploid genome assembly. The new assembly uses a hybrid approach and represents a significant improvement on the diploid assembly with contiguity and completeness comparable to other recent haptophyte genome assemblies.

In situ nanopore sequencing and real-time taxonomic classification onboard the RRS Discovery in the Southern Ocean established the utility of nanopore sequencing on polar ocean research cruises, and provided insights into polar ocean microbiomes. Additional samples were collected for land-based sequencing which identified key communities such as diatoms, and produced assembly-free functional annotations.

An improved protocol was developed to reduce sampling requirements, and reliance on toxic reagents, for potential use by citizen scientists. The improved protocol was successfully implemented in an in situ sequencing experiment with real-time analysis on the Norfolk coast, and a time-course analysis to investigate population flux.

These experiments showed the benefits of nanopore sequencing for researchers studying ocean microbiomes, and provided insights into their genomes, and communities. With constant improvements to the technology, nanopore sequencing will only become more useful for the study of ocean microbial communities.

Item Type: Thesis (Doctoral)
Faculty \ School: Faculty of Science > School of Environmental Sciences
Depositing User: Chris White
Date Deposited: 13 Dec 2023 14:55
Last Modified: 13 Dec 2023 14:55


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