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Volume 10, Issue 2

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

Abstract

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 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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): cable bacteria , Candidatus Electrothrix scaldis , clonal enrichment , genome closure , hybrid sequencing and metagenomics
Funding
This study was supported by the:
  • Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Award 016.VICI.170.072)
    • Principle Award Recipient: FilipJ.R. Meysman
  • Fonds Wetenschappelijk Onderzoek (Award G038819N)
    • Principle Award Recipient: FilipJ.R. Meysman
  • Fonds Wetenschappelijk Onderzoek (Award 11D7822N)
    • Principle Award Recipient: AnwarAshok Hiralal
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.001197
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Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads
M Gen 10, 001197 (2024); https://doi.org/10.1099/mgen.0.001197
/content/journal/mgen/10.1099/mgen.0.001197
/content/journal/mgen/10.1099/mgen.0.001197
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