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. 2026 Mar 6;15(4):e00025-26. doi: 10.1128/mra.00025-26

Metagenome-assembled genome sequence of Candidatus Electrothrix sp. NPCB-01 from Southern California marine sediments

Sukrampal Yadav 1,#, Tingting Yang 1,#, Magdalene A MacLean 1, Mohamed Y El-Naggar 1,2,3,✉
Editor: Frank J Stewart4
PMCID: PMC13064052  PMID: 41789948

ABSTRACT

Cable bacteria conduct long-distance electron transport in sediments but are not yet isolated in pure culture. We report the metagenome-assembled genome of Candidatus Electrothrix sp. NPCB-01 from Newport Bay, California. This 3.46-Mb genome encodes sulfur oxidation, nitrogen and carbon metabolism, and nickel homeostasis genes, expanding resources for these electroactive microbes.

KEYWORDS: cable bacteria, extracellular electron transport, metagenome, nickel-dependent long-distance electron transport

ANNOUNCEMENT

Cable bacteria are filamentous, multicellular microbes capable of conducting electrons over centimeter-scale distances, coupling sulfide oxidation in anoxic sediments to oxygen reduction near the surface (1–4). This long-distance electron transport (LDET) is mediated by periplasmic conductive nanofibers recently proposed to contain nickel cofactors (5–7). The clade comprises two described genera occurring globally in diverse sedimentary environments: Candidatus Electrothrix (marine) and Candidatus Electronema (freshwater) (8–11). Here, we report the metagenome-assembled genome (MAG) of Candidatus Electrothrix sp. NPCB-01, which was not isolated in pure culture but reconstructed from metagenomic sequencing of marine sediments collected from the Upper Newport Bay State Marine Conservation Area (33° 38′52″ N, 117° 52′21″ W), Newport, California.

Total DNA was extracted from 1-month incubated sub-surface sediments (n = 2) using the DNeasy PowerSoil Pro Kit (Qiagen, Germany). DNA quantity and integrity were assessed using a Qubit fluorimeter and agarose gel electrophoresis. Paired-end libraries were prepared using the NEBNext Ultra DNA Library Prep Kit and quantified using an Agilent TapeStation High-Sensitivity D1000 ScreenTape. Shotgun metagenome sequencing was performed on an Illumina NovaSeq (2 × 250 bp 50 million) at MR DNA Lab (Shallowater, TX, USA), yielding 129.7 and 210.9 million reads.

Reads were merged into a single library using kb_ReadsUtilities (v1.2.2) (12), quality-checked with FastQC (v0.12.1) (13), and trimmed using Trimmomatic (v0.39) (14). Contigs were assembled with MEGAHIT (v1.2.9) using the meta-sensitive preset (15). Genome bins were generated using CONCOCT (v1.1.0) (16), MetaBAT2 (v1.7.0) (17), and MaxBin2 (v2.2.4) (18), assessed with CheckM (v1.0.18) (19) and refined with MetagenomeUtils (v1.1.1) (12). High-quality bins were annotated in RASTtk (v1.073) (20), taxonomically classified with GTDB-Tk (v2.3.2) (21), and placed phylogenetically using SpeciesTree analysis (v2.2.0) (22). To predict metabolic potential, genome-scale metabolic models were constructed using the ModelSEED-based Build Metabolic Model App (fba_tools v2.2.1) (23, 24). Default parameters were used unless otherwise noted.

The Ca. Electrothrix sp. NPCB-01 MAG (3,457,740 bp; 46.1% G+C content) comprises 104 contigs, 3,566 coding sequences, and 43 RNAs (Table 1). CheckM analysis with lineage-specific marker sets indicates the genome is ~95.8% complete. A phylogenetic dendrogram places NPCB-01 within the Ca. Electrothrix genus, confirming its affiliation with marine cable bacteria, while a comparative heatmap highlights its distinct metabolic features (Fig. 1). The genome encodes a near-complete sulfur metabolism module, including dissimilatory sulfite reductase (dsrABCD) and adenylylsulfate reductase (aprAB-sat), crucial in the sediment sulfur cycle. It encodes mostly complete carbon metabolism pathways, though it lacks a complete glycolysis pathway. Furthermore, the genome contains key electron transfer components and a full suite of nickel homeostasis genes (nikM/N/L/K/QDE and rcnA), along with various nickel-binding carbon monoxide dehydrogenase (CODH) maturation genes (cooC/F/J/S/T) and genes encoding FNOR and CODH/ACS (α, β, γ, and δ subunits). These features are consistent with a chemoautotrophic and electroactive lifestyle that may be driven by a nickel-dependent LDET process, as previously proposed (11, 25–27).

TABLE 1.

General features of the metagenome-assembled genome of Ca. Electrothrix sp. NPCB-01

Items Description
Project MAG of cable bacterium from Southern California
Sequencing platform Illumina NovaSeq 6000
Assembly method MEGAHIT
Genome coverage 98.5×
BioProject PRJNA1334316
Accession number GCA_053813925
Size (bp) 3,457,740
DNA G + C content (%) 46.13
CDSs 3,566
N50 value 57,709
L50 value 19
RNAs 43
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Fig 1.

Genomic matrix comparing metabolic pathways in seven Electrothrix and Electronema species. Colored blocks show genes for sulfur, nitrogen, carbon metabolism, electron transfer, and nickel homeostasis. Phylogenetic tree displays species relationships.

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Comparative metabolic potential and phylogenetic placement of Ca. Electrothrix sp. NPCB-01. The heatmap displays the presence (colored squares), absence (empty squares), and partial presence (gradient squares) of key metabolic genes across related Candidatus Electrothrix and Candidatus Electronema genomes. The phylogenetic dendrogram (right) illustrates the taxonomic placement of the NPCB-01 MAG (red) within the Ca. Electrothrix genus.

Ca. Electrothrix sp. NPCB-01 MAG expands the genomic representation of cable bacteria from the Pacific coast of Southern California and offers a resource for studying the genetic, biochemical, and bioenergetic basis of electron transport in sediment ecosystems.

ACKNOWLEDGMENTS

We thank the California Department of Fish and Wildlife staff for their assistance and permission (permit ID S-222970004-22297-001).

This work was supported by the WM Keck Foundation (award 8626) and Gordon and Betty Moore Foundation (grant 10148). Laboratory work was approved by the University of Southern California Institutional Biosafety Committee under Biohazardous Use Authorization (BUA-20-00031-AM003).

Contributor Information

Mohamed Y. El-Naggar, Email: mnaggar@usc.edu.

Frank J. Stewart, Montana State University, Bozeman, Montana, USA

DATA AVAILABILITY

The metagenome-assembled genome sequence of Candidatus Electrothrix sp. NPCB-01 has been deposited in the NCBI under PRJNA1334316 BioProject with GenBank assembly GCA_053813925 (ASM5381392v1). Raw sequencing reads are available in the Sequence Read Archive (SRA) under accession numbers SRR35613409 and SRR35613410.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The metagenome-assembled genome sequence of Candidatus Electrothrix sp. NPCB-01 has been deposited in the NCBI under PRJNA1334316 BioProject with GenBank assembly GCA_053813925 (ASM5381392v1). Raw sequencing reads are available in the Sequence Read Archive (SRA) under accession numbers SRR35613409 and SRR35613410.

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