Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads

Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads

Hiralal, Anwar (Universiteit Antwerpen)
Geelhoed, Jeanine S. (Universiteit Antwerpen)
Hidalgo-Martinez, Silvia (Universiteit Antwerpen)
Smets, Bent (Universiteit Antwerpen)
van Dijk, Jesper R. (Universiteit Antwerpen)
Meysman, F.J.R. (TU Delft BT/Environmental Biotechnology; Universiteit Antwerpen)

2024

Many environmentally relevant micro-organisms cannot be cultured, and even with the latest metagenomic approaches, achieving complete genomes for specific target organisms of interest remains a challenge. Cable bacteria provide a prominent example of a microbial ecosystem engineer that is currently unculturable. They occur in low abundance in natural sediments, but due to their capability for long-distance electron transport, they exert a disproportionately large impact on the biogeochemistry of their environment. Current available genomes of marine cable bacteria are highly fragmented and incomplete, hampering the elucidation of their unique electrogenic physiology. Here, we present a metagenomic pipeline that combines Nanopore long-read and Illumina short-read shotgun sequencing. Starting from a clonal enrichment of a cable bacterium, we recovered a circular metagenome-assembled genome (5.09 Mbp in size), which represents a novel cable bacterium species with the proposed name Candidatus Electrothrix scaldis. The closed genome contains 1109 novel identified genes, including key metabolic enzymes not previously described in incomplete genomes of cable bacteria. We examined in detail the factors leading to genome closure. Foremost, native, non-amplified long reads are crucial to resolve the many repetitive regions within the genome of cable bacteria, and by analysing the whole metagenomic assembly, we found that low strain diversity is key for achieving genome closure. The insights and approaches presented here could help achieve genome closure for other keystone micro-organisms present in complex environmental samples at low abundance.

cable bacteria
Candidatus Electrothrix scaldis
clonal enrichment
genome closure
hybrid sequencing
metagenomics

http://resolver.tudelft.nl/uuid:447a3d63-20f2-4454-b59c-5494c5c4f671

https://doi.org/10.1099/mgen.0.001197

2057-5858

Microbial Genomics, 10 (2)

Institutional Repository

journal article

© 2024 Anwar Hiralal, Jeanine S. Geelhoed, Silvia Hidalgo-Martinez, Bent Smets, Jesper R. van Dijk, F.J.R. Meysman