Complete genome sequence of Litorivicinus marinus strain IMCC2782^T isolated from coastal seawater

Abstract

Objectives

Members of the genus Litorivicinus are marine heterotrophic bacteria with limited genomic representation, constraining our understanding of their taxonomic diversity, metabolic capabilities, and ecological roles. The genus currently comprises only two validly published species, with genomic data available exclusively for the type species, Litorivicinus lipolyticus. Here, we report the complete genome sequence of Litorivicinus marinus strain IMCC2782ᵀ, isolated from surface seawater of the Yellow Sea, Republic of Korea, to provide insights into its genomic features and metabolic potential.

Data description

The genome of strain IMCC2782ᵀ was sequenced using a hybrid approach combining short-read (Illumina) and long-read (PacBio) technologies. The assembly yielded a single circular chromosome of 2,204,001 bp with a G + C content of 56.07%. Genome annotation identified 2,196 protein-coding sequences, six rRNA genes, 41 tRNA genes, and one tmRNA gene. Functional annotation indicated complete central carbon metabolic pathways, including the Embden–Meyerhof–Parnas pathway, tricarboxylic acid cycle and oxidative phosphorylation, consistent with an aerobic chemoorganoheterotrophic lifestyle. The presence of a complete soxXYZABCD gene cluster suggests the potential for thiosulfate oxidation, whereas no pathways for dissimilatory nitrogen metabolism were identified. This genome expands the limited genomic resources available for the genus Litorivicinus and provides a foundation for future ecological and functional investigations.

Objective

The genus Litorivicinus (formerly Litoricola) was established following the isolation of Litorivicinus lipolyticus strain IMCC1097ᵀ from coastal seawater of the East Sea, Republic of Korea, and is currently placed within the family Litorivicinaceae, order Oceanospirillales, class Gammaproteobacteria [1, 2]. Members of this genus are Gram-negative, non-motile, short rod-shaped, chemoheterotrophic bacteria that are facultatively aerobic and require NaCl for growth, consistent with their adaptation to marine environments. The genus was originally described as Litoricola but was later renamed Litorivicinus due to nomenclatural illegitimacy under the International Code of Nomenclature of Prokaryotes [2]. According to the List of Prokaryotic Names with Standing in Nomenclature (LPSN; https://lpsn.dsmz.de), the genus currently comprises only two validly published species, L. lipolyticus and L. marinus [1–3].

Despite the increasing number of validly described bacterial taxa, genomic information for the genus Litorivicinus remains extremely limited, with a genome sequence available only for the type species, L. lipolyticus strain IMCC1097ᵀ (GenBank genome accession CP045871). In the present study, we address this research gap by reporting the complete genome sequence of L. marinus strain IMCC2782ᵀ. Strain IMCC2782ᵀ was previously isolated from surface seawater (1 m depth) of the Yellow Sea (37.4622, 126.4997), Republic of Korea, using a standard spread-plating method on Marine Agar 2216 (MA; Difco) [3]. Cells are Gram-negative, non-pigmented, non-motile, short rods that are chemoheterotrophic and facultatively aerobic. The strain grows optimally at 25 °C and pH 8.0, in the presence of 2.5–3.0% NaCl. The predominant cellular fatty acids include C_18:1ω7c and/or C_18:1ω6c, C_16:1ω7c and/or C_16:1ω6c, and C_10:0 3-OH [3].

Data description

Genomic DNA was extracted from an aerobically grown culture of strain IMCC2782ᵀ on MA at 25 °C using the DNeasy Blood & Tissue Kit (Qiagen, Germany), following the manufacturer’s instructions. DNA quantity and quality were assessed by agarose gel electrophoresis and with a Qubit 2.0 fluorometer (Life Technologies, USA). The same genomic DNA extract was subjected to both short-read sequencing on the Illumina NovaSeq 6000 platform (2 × 150 bp paired-end; Illumina, CA, USA) and long-read sequencing on the PacBio RS II platform (P6-C4 chemistry; Pacific Biosciences Inc., CA, USA). For Illumina sequencing, library was prepared using the TruSeq Nano DNA Prep Kit (insert size 550 bp; Illumina). For PacBio sequencing, a 20-kb SMRTbell library was prepared using the SMRTbell Template Prep Kit 1.0 (Pacific Biosciences) according to the manufacturer’s instructions, and fragments smaller than 20 kb were removed using the BluePippin size selection system. Sequencing was performed at DNA Link, Inc. (Seoul, Republic of Korea). Mapping of the Illumina and PacBio reads to the completed genome yielded average genome coverages of 1,260× and 483×, respectively.

Raw sequencing reads were first evaluated for quality using MultiQC v1.11 [4], followed by adapter trimming and removal of low-quality reads with BBDuk v38.71 [5]. High-quality reads were then subjected to de novo hybrid genome assembly using Unicycler v0.4.8 [6], integrating both Illumina short-read and PacBio long-read data. Assembly quality was assessed using QUAST v5.1.0 [7], while genome completeness and contamination were determined using CheckM2 v1.0.1 [8]. The genome map was generated using the Proksee web server [9]. Genome annotation was performed with Prokka v1.14.6 [10]. Functional annotation was performed by assigning KEGG Orthologs (KOs) using BlastKOALA [11] and KofamKOALA [12], and pathway completeness was evaluated using the KEGG pathways completeness tool (https://github.com/EBI-Metagenomics/kegg-pathways-completeness-tool). Comparative genome analysis based on ANI was performed using PyANI v0.3.0 [13].

Hybrid assembly of strain IMCC2782ᵀ yielded a single circular chromosome of 2,204,001 bp with G + C content of 56.07% (Table 1; Data file 1). CheckM2 analysis indicated 100% genome completeness with negligible contamination (0.01%). The genome encodes a total of 2,196 protein-coding sequences, six rRNA genes, 41 tRNA genes and one tmRNA genes (Data file 1). The circular genome structure and associated features are illustrated in Data file 2. Comparative genomic analysis revealed an ANI of 73% between strain IMCC2782ᵀ and L. lipolyticus IMCC1097ᵀ, which is well below the accepted species delineation threshold of 95% [18], thereby confirming the genomic distinctiveness of IMCC2782ᵀ as a separate species.

Table 1.

Overview of data files/data sets

Label	Name of data file/data set	File types (file extension)	Data repository and identifier (DOI or accession number)
Data file 1	Genome features of L. marinus strain IMCC2782T	Portable Document Format file (.pdf)	Figshare (10.6084/m9.figshare.32064705) [14]
Data file 2	Circular genome map of L. marinus strain IMCC2782 T	Portable Document Format file (.pdf)	Figshare (10.6084/m9.figshare.32064705) [14]
Data file 3	Functional potential of L. marinus strain IMCC2782T	MS Excel (.xlsx)	Figshare (10.6084/m9.figshare.32064705) [14]
Data set 1	Raw Illumina reads of L. marinus strain IMCC2782T genome	Fastq files (.fastq)	ENA (http://identifiers.org/ena.embl:ERR17028988) [15]
Data set 2	Complete genome sequence of L. marinus strain IMCC2782T	Fasta file (.fasta)	ENA (http://identifiers.org/ena.embl:OZ462263) [16]
Data set 3	Raw PacBio reads L. marinus strain IMCC2782 T	Fastq files (.fastq)	MoBiDIC repository (https://www.mabik.re.kr/mobidic/search/high-throughput-sequencings/MHTS01371) [17]

Functional annotation based on KEGG modules indicated that strain IMCC2782ᵀ encodes a complete Embden–Meyerhof–Parnas (EMP; M00001) pathway and a tricarboxylic acid cycle (TCA; M00009) (Data file 3), consistent with its chemoorganoheterotrophic metabolism [3]. In addition to the canonical TCA cycle, all genes required for the glyoxylate shunt (M00012) were identified, suggesting metabolic flexibility for growth on simple carbon substrates. The genome further encodes a complete oxidative phosphorylation system, including cytochrome c oxidase, supporting aerobic respiration. Notably, the presence of a high-affinity cbb₃-type cytochrome c oxidase (M00156) suggests potential adaptation to microaerobic or low-oxygen environments [19].

No pathways associated with dissimilatory nitrogen metabolism were detected. In contrast, the presence of a complete sulfur oxidation pathway (soxXYZABCD gene cluster) suggests a potential capability for thiosulfate oxidation (Data file 3), indicating a plausible role in marine sulfur cycling [20]. Overall, the complete genome sequence reported here provides a valuable foundation for future investigations into the metabolic potential, ecological role, and evolutionary adaptation of members of the genus Litorivicinus.

Limitations

This study provides a genome-level characterization of Litorivicinus marinus IMCC2782ᵀ; however, experimental validation of the predicted metabolic pathways, particularly those associated with sulfur metabolism and adaptation to low-oxygen conditions, remains beyond the scope of this work and warrants further investigation. In addition, the genus Litorivicinus is currently represented by only two validly published species with limited high-quality genomic data, which constrains robust comparative phylogenomic analyses and a comprehensive understanding of metabolic diversity within the genus.

Abbreviations

16S rRNA

16 S ribosomal ribonucleic acid

ANI

Average nucleotide identity

G + C

Guanine and cytosine content

MA

Marine Agar 2216

bp

Base pair

rRNA

Ribosomal ribonucleic acid

tRNA

Transfer ribonucleic acid

tmRNA

Transfer-messenger ribonucleic acid

ENA

European Nucleotide Archive

MoBiDIC

Marine organismal big data information center

Author contributions

M.R. drafted the manuscript, prepared the figures, and performed data submission. Y.L. maintained bacterial cultures and conducted nucleic acid extraction. I.K. designed the study and performed bioinformatics analyses. J.-C.C. conceived the study and supervised its execution. All authors reviewed and approved the final manuscript.

Funding

This research work was supported by Inha University Research Grant (to M.R.).

Data availability

All sequencing data generated in this study are publicly available in the European Nucleotide Archive (ENA) under BioProject accession number PRJEB111700. The complete genome assembly has been deposited under accession GCA_982526755, and the raw sequencing reads are available under run accession ERR17028988. The 16 S rRNA gene sequence has been submitted to GenBank under accession number FJ943234. In addition to these international repositories, the datasets are also accessible through Marine organismal big data Information center (MoBiDIC; https://www.mabik.re.kr/mobidic/), Republic of Korea, under the accession numbers MHTS01370 (Illumina reads), MHTS01371 (PacBio reads), and MASM00275 (genome assembly).

Declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.