Microbial diversity characterization of seawater in a pilot study using Oxford Nanopore Technologies long-read sequencing

Currently, the majority of non-culturable microbes in sea water are yet to be discovered. Nanopore sequencing offers a solution to overcome the challenge of identifying the genomes and complex composition of oceanic microbiomes.

In this study we evaluate the utility of Oxford Nanopore Technologies (ONT) sequencing to characterize microbial diversity in seawater from multiple locations. We compared the microbial species diversity of retrieved environmental samples from two different locations and time points. With only three MinION Flow Cells we were able to identify thousands of organisms, including bacteriophages, achieving species-level resolution for a large number of these.

It was possible to assemble genomes from environmental samples with Flye. In several cases this resulted in >1 Mbp contigs and in the particular case of a Thioglobus singularis species it even produced a near complete genome. K-mer analysis reveals that a large part of the data represents species of which close relatives have not yet been deposited in the database.

These results show that our approach is suitable for scalable genomic investigations, such as monitoring oceanic biodiversity, and this research provides a new platform for education in biodiversity.