ABSTRACT
Cellvibrio sp. strain 25HG11W-0 is a freshwater agarolytic bacterium isolated from the Namyangcheon stream in the Republic of Korea. Here, we report the draft genome sequence of this bacterium, which harbors multiple putative agarase genes belonging to glycoside hydrolase (GH) families GH16, GH50, GH86, and GH117.
KEYWORDS: genome sequence, agarolytic bacterium, Cellvibrio
ANNOUNCEMENT
Agarases are carbohydrate-active enzymes that hydrolyze agarose into neoagaro-oligosaccharides and related agar-derived sugars (1). Because agar-derived oligosaccharides have potential biotechnological and industrial applications (2–4), there is ongoing interest in agar-degrading microorganisms. Here, we report the draft genome sequence of Cellvibrio sp. strain 25HG11W-0, an agarolytic bacterium harboring multiple putative agarase genes.
Cellvibrio sp. strain 25HG11W-0 was isolated from an unconcentrated 50 mL water sample collected from the Namyangcheon stream in Gyeonggi-do, Republic of Korea (37°11′56.7″N, 126°47′57.9″E) in April 2025. The sample was serially diluted and plated on 1/10-strength marine agar (Difco, USA) and incubated aerobically at 25°C for 7 days. A colony forming a distinct depression zone, indicating extracellular agar degradation, was selected and purified to obtain strain 25HG11W-0. The 16S ribosomal RNA (rRNA) gene was amplified from the same genomic DNA extracted for whole-genome sequencing (see below), using the universal primers 27F and 1492R (95°C/5 min; 30 cycles of 95°C/30 s, 55°C/45 s, 72°C/1 min; 72°C/10 min), and sequenced by the Sanger method. BLASTN comparison against the National Center for Biotechnology Information 16S rRNA database showed the highest similarity (97.38%) to Cellvibrio gandavensis R-4069T. Based on this result, strain 25HG11W-0 was assigned to the genus Cellvibrio. Genomic DNA for whole-genome sequencing was extracted from cells cultured under the conditions described above using the DNeasy Blood & Tissue Kit (Qiagen, Germany) according to the manufacturer’s protocol. Libraries were prepared using the TruSeq Nano DNA Kit (350 bp insert; Illumina, USA) and the PacBio Microbial Library protocol (Pacific Biosciences, USA) for short- and long-read sequencing; for the latter, DNA was sheared using a Covaris g-TUBE (Covaris, USA), and fragments smaller than 5 kb were removed using an SRE kit (Pacific Biosciences, USA). Sequencing was performed at Theragen Bio (Republic of Korea) on an Illumina NovaSeq 6000 (20,296,274 reads; 3,064,737,374 bp) and a PacBio Revio (55,088 HiFi reads; 530,417,604 bp). Illumina reads were quality-filtered and adapter-trimmed with Trimmomatic v0.38, yielding 8,587,792 reads (1,296,196,450 bp). PacBio HiFi reads were used without additional filtering and assembled using Canu v2.2 (5), and the resulting assembly was polished with Pilon v1.22 (6) using the quality-filtered Illumina reads.
The draft genome assembly consists of two circular contigs (4,929,637 bp; N50, 4,901,983 bp; G + C, 49.7%) at depths of 108× (contig 1) and 30× (contig 2). Contig 2 (27,654 bp; G + C, 43.1%) is a putative plasmid, supported by its divergent GC content and depth, a conjugative transfer gene (traJ), a Hin-family recombinase, and a heavy-metal resistance cassette (Mn²+ exporter, Cd/Co/Zn antiporter, MprA, FrmR). Genome annotation used Prokka v1.14.6 (7); functional categorization used eggNOG v5.0 (8). The genome annotation predicted 4,076 coding sequences, 50 transfer RNA genes, and 15 rRNA genes.
CAZyme analysis using the dbCAN3 server (9) identified six putative agarase-related genes belonging to glycoside hydrolase families GH16, GH50, GH86, and GH117 (two GH50, two GH86, one GH16, and one GH117). Numerous CAZyme genes for cellulose, xylan, alginate, β-glucan, arabinan, and pectin degradation were also identified, indicating broad polysaccharide-utilization capability.
ACKNOWLEDGMENTS
This research was funded by a grant from the Nakdonggang National Institute of Biological Resources (NNIBR), supported by the Ministry of Environment (MOE) of the Republic of Korea (NNIBR20263103). Additional support was provided by the Korea Environment Industry and Technology Institute through the project for advancing multi-ministerial national biological research resources, also funded by the Ministry of Environment (MOE) (2021003420003).
Contributor Information
Hyangmi Kim, Email: hmkim@nnibr.re.kr.
Frank J. Stewart, Montana State University, Bozeman, Montana, USA
DATA AVAILABILITY
The whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JBYPPU000000000. The raw sequence reads have been deposited in the Sequence Read Archive (SRA) under the accession numbers SRX33891457 (Illumina) and SRX33891458 (PacBio). The associated BioProject and BioSample accession numbers are PRJNA1432500 and SAMN56344110, respectively. Strain 25HG11W-0 has also been deposited in the Freshwater Bioresources Culture Collection (FBCC) under accession no. FBCC-B25530.
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Associated Data
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Data Availability Statement
The whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JBYPPU000000000. The raw sequence reads have been deposited in the Sequence Read Archive (SRA) under the accession numbers SRX33891457 (Illumina) and SRX33891458 (PacBio). The associated BioProject and BioSample accession numbers are PRJNA1432500 and SAMN56344110, respectively. Strain 25HG11W-0 has also been deposited in the Freshwater Bioresources Culture Collection (FBCC) under accession no. FBCC-B25530.