
==== Front
Microbiol Resour Announc
Microbiol Resour Announc
mra
Microbiology Resource Announcements
2576-098X
American Society for Microbiology 1752 N St., N.W., Washington, DC

39162461
mra00616-24
10.1128/mra.00616-24
mra.00616-24
Genome Sequences
environmental-microbiologyEnvironmental MicrobiologyComplete genomic sequence of a Marinobacter species, a potential polyethylene degrader isolated from surface seawater
https://orcid.org/0000-0002-9328-5628
Iizuka Ryo 1 Conceptualization Funding acquisition Investigation Writing – original draft Writing – review and editing ryo.iizuka@bs.s.u-tokyo.ac.jp

https://orcid.org/0000-0001-9701-1803
Uemura Sotaro 1 2 Funding acquisition Supervision Writing – review and editing uemura@bs.s.u-tokyo.ac.jp

1 Department of Biological Sciences, Graduate School of Science, The University of Tokyo , Tokyo, Japan
2 Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency , Tokyo, Japan
Editor Stewart Frank J. Montana State University , Bozeman, Montana, USA

Address correspondence to Ryo Iizuka, ryo.iizuka@bs.s.u-tokyo.ac.jp
Address correspondence to Sotaro Uemura, uemura@bs.s.u-tokyo.ac.jp
The authors declare no conflict of interest.

9 2024
20 8 2024
20 8 2024
13 9 e00616-2409 6 2024
23 7 2024
Copyright © 2024 Iizuka and Uemura.
2024
Iizuka and Uemura
https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

ABSTRACT

The bacterium Marinobacter sp. RI1 was isolated from surface seawater through an enrichment culture using low-density polyethylene as the sole carbon source. Herein, we report its complete genomic sequence. Genomic annotation revealed that the strain harbors the genes encoding enzymes involved in alkane degradation, thus supporting polyethylene degradation.

KEYWORDS

Marinobacter
polyethylene
alkane
MEXT | Japan Society for the Promotion of Science (JSPS) JP22K05310 Iizuka Ryo MEXT | Japan Science and Technology Agency (JST) JPMJCR2231 Uemura Sotaro Mitsui Chemicals, Inc. Uemura Sotaro cover-dateSeptember 2024
==== Body
pmcANNOUNCEMENT

Marinobacter species are frequently found in hydrocarbon-contaminated marine environments, suggesting an important role in countering hydrocarbon pollution (1). Here, we present the complete genomic sequence of Marinobacter sp. RI1, an isolate from surface seawater with potential polyethylene degradation capability.

Surface seawater was collected at Odaiba Beach, Tokyo, Japan (35°37′50.3″N, 139°46′30.2″E) on 16 August 2023 and was inoculated into artificial seawater (GEX, Osaka, Japan) containing 0.1% NH4Cl and an untreated low-density polyethylene film (10 × 10 mm; NPS-0.5, KENIS, Tokyo, Japan). After 139 days of incubation at 25°C, the film surface was scraped with an inoculation loop, and bacterial cells were streaked onto an agar plate containing artificial seawater medium (2, 3). The plate was incubated for 2 days at 25°C, resulting in the isolation of strain RI1. Colony PCR was performed using the primers 27F (5′-AGAGTTTGATCMTGGCTCAG-3′) and 1492R (5′-TACGGYTACCTTGTTACGACTT-3′) to amplify the 16S rRNA gene. The sequence obtained (LC819396.1) had the highest similarity (99.93%) with that of Marinobacter nauticus DSM 50418T (AB021372.1) in the EzBioCloud database (4, 5). The strain was cultured aerobically in artificial seawater medium overnight at 25°C for genomic sequencing. Genomic DNA was extracted using the Genomic-tip 20/G (Qiagen), followed by purification using the Short Read Eliminator (PacBio) and DNA Clean Beads (MGI Tech Co., Ltd.). Genomic DNA was sheared into 10–20 kbp fragments using a g-TUBE (Covaris). A SMRTbell library was prepared using SMRTbell gDNA Sample Amplification Kit (PacBio) and SMRTbell Express Template Prep Kit 2.0 (PacBio), and then bound to DNA polymerase using Revio Polymerase Kit (PacBio). Sequencing was performed using the Revio system (PacBio). SMRT Link (v13.0.0.207600) (PacBio) was used to trim adapter sequences from the sequencing reads. The generated circular consensus sequences with average base quality values of <20 were removed to obtain HiFi reads. These reads were filtered using lima (v2.7.1) (https://github.com/pacificbiosciences/barcoding) and pbmarkdup (v1.0.3) (https://github.com/PacificBiosciences/pbmarkdup) to remove the ultra-low PCR adapters and PCR duplicates, respectively. Filtlong (v0.2.1) (https://github.com/rrwick/Filtlong) was used to exclude short HiFi reads (<1,000 bp). Using Flye (v2.9.2-b1786) (6), the remaining reads were assembled, and the overlapping ends on a circular contig were removed. Automatic annotation was performed using DFAST v1.3.1 (7, 8). Default settings were used for all software.

The RI1 genome was found to comprise a circular chromosome of 3,846,721 bp, harboring 3,466 protein-coding sequences, nine rRNA genes, and 51 tRNA genes (Table 1). Phylogenetic analysis suggested that the closest relative was M. nauticus DSM 50418T (GCF_003634635.1) with a pairwise average nucleotide identity of 97.7%, implying that the strain is a novel strain of M. nauticus. Genomic annotation revealed the presence of genes encoding key enzymes in alkane degradation pathways, including alkane 1-monooxygenases (MspRI1_13460 and MspRI1_15020), cytochrome P450 alkane hydroxylase (CYP153; MspRI1_05720), and flavin-binding monooxygenase (AlmA; MspRI1_05860) (9–11), which are likely responsible for polyethylene catabolism (12, 13). This genomic information provides insights into the genetic basis of the catabolic pathways for polyethylene degradation in this strain.

TABLE 1 Genomic characteristics of the sequenced isolate

	Strain RI1	
BioSample accession no.	SAMD00787955	
 No. of reads	40,328	
 Read N50 (bp)	6,570	
 Sum of length (bp)	248,538,631	
 SRA accession no.	DRR568656	
Assembly results	
 No. of contigs	1	
 Length (bp)	3,846,721	
 GC content (%)	57.6	
 Average read depth (×)	65	
 No. of protein-coding sequences	3,466	
 No. of rRNAs	9	
 No. of tRNAs	51	
 GenBank accession no.	AP031605.1	

ACKNOWLEDGMENTS

The authors would like to thank the Bioengineering Lab. Co., Ltd. (Kanagawa, Japan) for their invaluable technical assistance.

This study was supported by the collaboration between The University of Tokyo and Mitsui Chemicals, Inc. This study was also supported by JSPS KAKENHI Grant Number JP22K05310 and JST CREST Grant Number JPMJCR2231.

DATA AVAILABILITY

RI1 is associated with the BioProject accession number PRJDB18161. The accession numbers are listed in Table 1.
==== Refs
REFERENCES

1 Grimaud R. 2010. Marinobacter, p 1289–1296. In Timmis KN (ed), Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, Heidelberg.
2 Ito M, Muta M, Funatsu T, Hatada Y, Iizuka R. 2022. Complete genomic sequences of two agarolytic Vibrio species isolates from the red algae Gracilaria. Microbiol Resour Announc 11 :e0093422. doi: 10.1128/mra.00934-22 36342290
3 Muta M, Yoshida T, Funatsu T, Iizuka R. 2023. Complete genomic sequence of an agarolytic Pseudoalteromonas species isolated from deep seawater. Microbiol Resour Announc 12 :e0027823. doi:10.1128/mra.00278-23 37341607
4 Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y, Seo H, Chun J. 2017. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67 :1613–1617. doi:10.1099/ijsem.0.001755 28005526
5 Tindall BJ. 2020. Marinobacter nauticus (Baumann et al. 1972) comb. nov. arising from instances of synonymy and the incorrect interpretation of the international code of nomenclature of prokaryotes. Arch Microbiol 202 :657–663. doi:10.1007/s00203-019-01761-6 31760456
6 Kolmogorov M, Yuan J, Lin Y, Pevzner PA. 2019. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 37 :540–546. doi:10.1038/s41587-019-0072-8 30936562
7 Tanizawa Y, Fujisawa T, Kaminuma E, Nakamura Y, Arita M. 2016. DFAST and DAGA: web-based integrated genome annotation tools and resources. Biosci Microbiota Food Health 35 :173–184. doi:10.12938/bmfh.16-003 27867804
8 Tanizawa Y, Fujisawa T, Nakamura Y. 2018. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 34 :1037–1039. doi:10.1093/bioinformatics/btx713 29106469
9 Nie Y, Chi C-Q, Fang H, Liang J-L, Lu S-L, Lai G-L, Tang Y-Q, Wu X-L. 2014. Diverse alkane hydroxylase genes in microorganisms and environments. Sci Rep 4 :4968. doi:10.1038/srep04968 24829093
10 Wang W, Shao Z. 2012. Diversity of flavin-binding monooxygenase genes (almA) in marine bacteria capable of degradation long-chain alkanes. FEMS Microbiol Ecol 80 :523–533. doi:10.1111/j.1574-6941.2012.01322.x 22304419
11 Rojas-Vargas J, Castelán-Sánchez HG, Pardo-López L. 2023. HADEG: a curated hydrocarbon aerobic degradation enzymes and genes database. Comput Biol Chem 107 :107966. doi:10.1016/j.compbiolchem.2023.107966 37778093
12 Mohanan N, Montazer Z, Sharma PK, Levin DB. 2020. Microbial and enzymatic degradation of synthetic plastics. Front Microbiol 11 :580709. doi:10.3389/fmicb.2020.580709 33324366
13 Yeom S-J, Le T-K, Yun C-H. 2022. P450-driven plastic-degrading synthetic bacteria. Trends Biotechnol 40 :166–179. doi:10.1016/j.tibtech.2021.06.003 34243985
