Phenotypic and Genomic Characterization of Oceanisphaera submarina sp. nov. Isolated from the Sea of Japan Bottom Sediments
Abstract
1. Introduction
2. Materials and Methods
2.1. Bacterial Strains
2.2. Phenotypic Characterization
2.3. Polar Lipids, Fatty Acids, and Quinone Analyses
2.4. Phylogenetic Analysis of 16S rRNA Gene
2.5. Whole-Genome Sequencing and Genome-Based Phylogenetic Analysis
3. Results and Discussion
3.1. Phylogenetic and Phylogenomic Analyses
3.2. Genomic Characteristics and Pan-Genome Analysis
3.3. In Silico Analysis of Hydrolytic and Biosynthetic Potentials
3.4. Morphological, Physiological, and Biochemical Characteristics of Strain KMM 10153T
3.5. Chemotaxonomic Characteristics of Strain KMM 10153T
4. Conclusions
Description of Oceanisphaera submarina sp. nov.
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
- Lauro, F.M.; Bartlett, D.H. Prokaryotic lifestyles in deep sea habitats. Extremophiles 2008, 12, 5–25. [Google Scholar] [CrossRef] [PubMed]
- Romanenko, L.A.; Schumann, P.; Zhukova, N.V.; Rohde, M.; Mikhailov, V.V.; Stackebrandt, E. Oceanisphaera litoralis gen. nov., sp. nov., a novel halophilic bacterium from marine bottom sediments. Int. J. Syst. Evol. Microbiol. 2003, 53, 1885–1888. [Google Scholar] [CrossRef] [PubMed]
- Choi, W.C.; Kang, S.J.; Jung, Y.T.; Oh, T.K.; Yoon, J.H. Oceanisphaera ostreae sp. nov., isolated from seawater of an oyster farm, and emended description of the genus Oceanisphaera Romanenko et al. 2003. Int. J. Syst. Evol. Microbiol. 2011, 61, 2880–2884. [Google Scholar] [CrossRef] [PubMed]
- Srinivas, T.N.; Reddy, P.V.; Begum, Z.; Manasa, P.; Shivaji, S. Oceanisphaera arctica sp. nov., isolated from Arctic marine sediment, and emended description of the genus Oceanisphaera. Int. J. Syst. Evol. Microbiol. 2012, 62, 1926–1931. [Google Scholar] [CrossRef]
- Xu, Z.; Zhang, X.Y.; Su, H.N.; Yu, Z.C.; Liu, C.; Li, H.; Chen, X.L.; Song, X.Y.; Xie, B.B.; Qin, Q.L.; et al. . Oceanisphaera profunda sp. nov., a marine bacterium isolated from deep-sea sediment, and emended description of the genus Oceanisphaera. Int. J. Syst. Evol. Microbiol. 2014, 64, 1252–1256. [Google Scholar] [CrossRef] [PubMed]
- Parte, A.C.; Sardà Carbasse, J.; Meier-Kolthoff, J.P.; Reimer, L.C.; Göker, M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int. J. Syst. Evol. Microbiol. 2020, 70, 5607–5612. [Google Scholar] [CrossRef] [PubMed]
- Park, S.J.; Kang, C.H.; Nam, Y.D.; Bae, J.W.; Park, Y.H.; Quan, Z.X.; Moon, D.S.; Kim, H.J.; Roh, D.H.; Rhee, S.K. Oceanisphaera donghaensis sp. nov., a halophilic bacterium from the East Sea, Korea. Int. J. Syst. Evol. Microbiol. 2006, 56, 895–898. [Google Scholar] [CrossRef]
- Zhou, S.; Wang, H.; Wang, Y.; Ma, K.; He, M.; Chen, X.; Kong, D.; Guo, X.; Ruan, Z.; Zhao, B. Oceanisphaera psychrotolerans sp. nov., isolated from coastal sediment samples. Int. J. Syst. Evol. Microbiol. 2015, 65, 2797–2802. [Google Scholar] [CrossRef]
- Liu, J.; Sun, Y.W.; Zhang, D.D.; Li, S.N.; Zhang, D.C. Oceanisphaera marina sp. nov., isolated from a deep-sea seamount. Int. J. Syst. Evol. Microbiol. 2017, 67, 1996–2000. [Google Scholar] [CrossRef] [PubMed]
- Shin, N.R.; Whon, T.W.; Roh, S.W.; Kim, M.S.; Kim, Y.O.; Bae, J.W. Oceanisphaera sediminis sp. nov., isolated from marine sediment. Int. J. Syst. Evol. Microbiol. 2012, 62, 1552–1557. [Google Scholar] [CrossRef]
- Sung, H.; Kim, H.S.; Lee, J.Y.; Kang, W.; Kim, P.S.; Hyun, D.W.; Tak, E.J.; Jung, M.J.; Yun, J.H.; Kim, M.S.; et al. Oceanisphaera avium sp. nov., isolated from the gut of the cinereous vulture, Aegypius monachus. Int. J. Syst. Evol. Microbiol. 2018, 68, 2068–2073. [Google Scholar] [CrossRef] [PubMed]
- Xue, J.H.; Shi, L.F.; Zhang, B.N.; Wu, W.J.; Gao, Y.; Zhu, Q.; Zhao, L.H. Oceanisphaera pacifica sp. nov., isolated from the intestine of Trichiurus japonicus. Arch. Microbiol. 2022, 204, 338. [Google Scholar] [CrossRef]
- Gerhardt, P.; Murray, R.G.E.; Wood, W.A.; Krieg, N.R. (Eds.) Methods for General and Molecular Bacteriology; American Society for Microbiology: Washington, DC, USA, 1994. [Google Scholar]
- Romanenko, L.A.; Tanaka, N.; Svetashev, V.I. Devosia submarina sp. nov., isolated from deep sea surface sediments. Int. J. Syst. Evol. Microbiol. 2013, 63, 3079–3085. [Google Scholar] [CrossRef]
- Romanenko, L.A.; Kurilenko, V.V.; Guzev, K.V.; Svetashev, V.I. Characterization of Labrenzia polysiphoniae sp. nov. isolated from red alga Polysiphonia sp. Arch. Microbiol. 2019, 201, 705–712. [Google Scholar] [CrossRef] [PubMed]
- Folch, J.; Lees, M.; Sloane-Stanley, G.H. A simple method for the isolation and purification of total lipids from animal tissues. J. Biol. Chem. 1957, 226, 497–509. [Google Scholar] [CrossRef]
- Collins, M.D.; Shah, H.N. Fatty acid, menaquinone and polar lipid composition of Rothia dentosacariosa. Arch. Microbiol. 1984, 137, 247–249. [Google Scholar] [CrossRef]
- Collins, M.D.; Goodfellow, M.; Minnikin, D.E. Fatty acid, isoprenoid quinone and polar lipid composition in the classification of Curtobacterium and related taxa. J. Gen. Microbiol. 1980, 118, 29–37. [Google Scholar] [CrossRef]
- Sasser, M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101; MIDI Inc.: Newark, DE, USA, 1990. [Google Scholar]
- Svetashev, V.I. Mild method for preparation of 4,4-dimethyloxazoline derivatives of polyunsaturated fatty acids for GC-MS. Lipids 2011, 46, 463–467. [Google Scholar] [CrossRef] [PubMed]
- Hiraishi, A.; Ueda, Y.; Ishihara, J.; Mori, T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J. Gen. Appl. Microbiol. 1996, 42, 457–459. [Google Scholar] [CrossRef]
- Romanenko, L.; Bystritskaya, E.; Savicheva, Y.; Eremeev, V.; Otstavnykh, N.; Kurilenko, V.; Velansky, P.; Isaeva, M. Description and Whole-Genome Sequencing of Mariniflexile litorale sp. nov., Isolated from the Shallow Sediments of the Sea of Japan. Microorganisms 2024, 12, 1413. [Google Scholar] [CrossRef] [PubMed]
- Yoon, S.H.; Ha, S.M.; Kwon, S.; Lim, J.; Kim, Y.; Seo, H.; Chun, J. Introducing EzBioCloud: A taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol. 2017, 67, 1613. [Google Scholar] [CrossRef] [PubMed]
- Meier-Kolthoff, J.P.; Carbasse, J.S.; Peinado-Olarte, R.L.; Göker, M. TYGS and LPSN: A database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res. 2021, 7, D801–D807. [Google Scholar] [CrossRef] [PubMed]
- Meier-Kolthoff, J.P.; Hahnke, R.L.; Petersen, J.; Scheuner, C.; Michael, V.; Fiebig, A.; Rohde, C.; Rohde, M.; Fartmann, B.; Goodwin, L.A.; et al. Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand. Genom. Sci. 2014, 8, 10. [Google Scholar] [CrossRef] [PubMed]
- Stamatakis, A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014, 30, 1312–1313. [Google Scholar] [CrossRef]
- Goloboff, P.A.; Farris, J.S.; Nixon, K.C. TNT, a free program for phylogenetic analysis. Cladistics 2008, 24, 774–786. [Google Scholar] [CrossRef]
- Bolger, A.M.; Lohse, M.; Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 2014, 30, 2114–2120. [Google Scholar] [CrossRef]
- Bankevich, A.; Nurk, S.; Antipov, D.; Gurevich, A.A.; Dvorkin, M.; Kulikov, A.S.; Lesin, V.M.; Nikolenko, S.I.; Pham, S.; Prjibelski, A.D.; et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 2012, 19, 455–477. [Google Scholar] [CrossRef] [PubMed]
- Parks, D.H.; Imelfort, M.; Skennerton, C.T.; Hugenholtz, P.; Tyson, G.W. CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015, 25, 1043–1055. [Google Scholar] [CrossRef] [PubMed]
- Aziz, R.K.; Bartels, D.; Best, A.A.; DeJongh, M.; Disz, T.; Edwards, R.A.; Formsma, K.; Gerdes, S.; Glass, E.M.; Kubal, M.; et al. The RAST Server: Rapid annotations using subsystems technology. BMC Genom. 2008, 9, 75. [Google Scholar] [CrossRef] [PubMed]
- Tatusova, T.; DiCuccio, M.; Badretdin, A.; Chetvernin, V.; Nawrocki, E.P.; Zaslavsky, L.; Lomsadze, A.; Pruitt, K.D.; Borodovsky, M.; Ostell, J. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016, 44, 6614–6624. [Google Scholar] [CrossRef] [PubMed]
- Asnicar, F.; Thomas, A.M.; Beghini, F.; Mengoni, C.; Manara, S.; Manghi, P.; Zhu, Q.; Bolzan, M.; Cumbo, F.; May, U.; et al. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat. Commun. 2020, 11, 2500. [Google Scholar] [CrossRef] [PubMed]
- Eren, A.M.; Esen, O.C.; Quince, C.; Vineis, J.H.; Morrison, H.G.; Sogin, M.L.; Delmont, T.O. Anvi’o: An advanced analysis and visualization platformfor ‘omics data. PeerJ 2015, 3, e1319. [Google Scholar] [CrossRef] [PubMed]
- Rodriguez-R, L.M.; Konstantinidis, K.T. The enveomics collection: A toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Prepr. 2016, 4, e1900v1. [Google Scholar] [CrossRef]
- Meier-Kolthoff, J.P.; Göker, M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat. Commun. 2019, 10, 2182. [Google Scholar] [CrossRef] [PubMed]
- Zheng, J.; Ge, Q.; Yan, Y.; Zhang, X.; Huang, L.; Yin, Y. dbCAN3: Automated carbohydrate-active enzyme and substrate annotation. Nucleic Acids Res. 2023, 51, W115–W121. [Google Scholar] [CrossRef] [PubMed]
- Ausland, C.; Zheng, J.; Yi, H.; Yang, B.; Li, T.; Feng, X.; Zheng, B.; Yin, Y. dbCAN-PUL: A database of experimentally characterized CAZyme gene clusters and their substrates. Nucleic Acids Res. 2021, 49, D523–D528. [Google Scholar] [CrossRef]
- Blin, K.; Shaw, S.; Augustijn, H.E.; Reitz, Z.L.; Biermann, F.; Alanjary, M.; Fetter, A.; Terlouw, B.R.; Metcalf, W.W.; Helfrich, E.J.; et al. antiSMASH 7.0: New and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res. 2023, 51, W46–W50. [Google Scholar] [CrossRef] [PubMed]
- Neron, B.; Denise, R.; Coluzzi, C.; Touchon, M.; Rocha, E.P.; Abby, S.S. MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes. Peer Community J. 2023, 3, e28. [Google Scholar] [CrossRef]
- Hitch, T.C.A.; Riedel, T.; Oren, A.; Overmann, J.; Lawley, T.D.; Clavel, T. Automated Analysis of Genomic Sequences Facilitates High-Throughput and Comprehensive Description of Bacteria. ISME Commun. 2021, 1, 16. [Google Scholar] [CrossRef]
- Richter, M.; Rosselló-Móra, R. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA 2009, 106, 19126–19131. [Google Scholar] [CrossRef] [PubMed]
- Konstantinidis, K.T.; Rosselló-Móra, R. Classifying the uncultivated microbial majority: A place for metagenomic data in the Candidatus proposal. Syst. Appl. Microbiol. 2015, 38, 223–230. [Google Scholar] [CrossRef] [PubMed]
- Konstantinidis, K.T.; Rosselló-Móra, R.; Amann, R. Uncultivated microbes in need of their own taxonomy. ISME J. 2017, 11, 2399–2406. [Google Scholar] [CrossRef]
- Goris, J.; Konstantinidis, K.T.; Klappenbach, J.A.; Coenye, T.; Vandamme, P.; Tiedje, J.M. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 2007, 57, 81–91. [Google Scholar] [CrossRef] [PubMed]
- Chun, J.; Oren, A.; Ventosa, A.; Christensen, H.; Arahal, D.R.; Da Costa, M.S.; Rooney, A.P.; Yi, H.; Xu, X.W.; De Meyer, S.; et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int. J. Syst. Evol. Microbiol. 2018, 68, 461–468. [Google Scholar] [CrossRef] [PubMed]
- Riesco, R.; Trujillo, M.E. Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int. J. Syst. Evol. Microbiol. 2024, 74, 006300. [Google Scholar] [CrossRef]
- Tanabe, T.; Funahashi, T.; Nakao, H.; Miyoshi, S.; Shinoda, S.; Yamamoto, S. Identification and characterization of genes required for biosynthesis and transport of the siderophore vibrioferrin in Vibrio parahaemolyticus. J. Bacteriol. 2003, 185, 6938–6949. [Google Scholar] [CrossRef] [PubMed]
- Baars, O.; Zhang, X.; Morel, F.M.; Seyedsayamdost, M.R. The Siderophore Metabolome of Azotobacter vinelandii. Appl. Environ. Microbiol. 2015, 82, 27–39. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Di Costanzo, F.; Di Dato, V.; Romano, G. Diatom–Bacteria Interactions in the Marine Environment: Complexity, Heterogeneity, and Potential for Biotechnological Applications. Microorganisms 2023, 11, 2967. [Google Scholar] [CrossRef]
Feature | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Assembly level | contig | scaffold | scaffold | scaffold | contig |
Genome size (Mb) | 3.6 | 3.6 | 3.8 | 3.4 | 3.8 |
Number of contigs | 35 | 38 | 68 | 68 | 70 |
G + C Content (mol%) | 57.5 | 57.5 | 57.5 | 58.5 | 58.5 |
N50 (Kb) | 179.8 | 221.3 | 136.7 | 105.4 | 106.6 |
L50 | 7 | 8 | 11 | 11 | 11 |
Coverage | 92× | 100× | 526× | 337× | 20× |
Protein coding genes | 3369 | 3214 | 3459 | 3149 | 3066 |
rRNAs (5S/16S/23S) | 2/2/2 | 4/2/1 | 0/0/8 | 1/3/2 | 1/2/2 |
tRNAs | 72 | 78 | 95 | 81 | 46 |
checkM completeness (%) | 99.51 | 99.05 | 98.44 | 98.30 | 89.64 |
checkM contamination (%) | 1.35 | 2.03 | 0.85 | 0.97 | 2.03 |
WGS project | JBKGFN000000000 | JBHLZJ01 | BAABDS01 | JAFBBE01 | MDKE01 |
Genome assembly | ASM4652130v1 | ASM4243140v1 | ASM3953974v1 | ASM1690701v1 | ASM187048v1 |
Characteristic | 1 | 2 | 3 | 4 |
---|---|---|---|---|
DNA GC content (%) * | 57.5 | 58.5 | 57.5 | 55.5 |
Motility | + | + | − | − |
Growth in NaCl: | ||||
0% | + | − | + | + |
10% | + | + | − | + |
12% | (+) | − | − | − |
Growth at: | ||||
40 °C | + | + | − | + |
42 °C | (+) | + | − | − |
Hydrolysis of: | ||||
DNA | − | − | + | ND |
Tween 80 | − | − | − | + |
Nitrate reduction | + | + | − | + |
Urease | − | + | + | (+) |
Assimilation of: | ||||
D-mannitol | + | − | − | ND |
L-rhamnose | − | − | − | + |
L-arabinose | − | − | − | + |
L-fucose | − | − | − | + |
4-hydroxybenzoic acid | − | + | − | ND |
L-proline | + | − | + | ND |
L-serine | + | + | + | − |
Enzyme activity (API ZYM): | ||||
Alkaline phosphatase | + | (+) | + | + |
Esterase lipase C 4 | + | − | + | + |
Valine arylamidase | − | (+) | − | (+) |
Cystine arylamidase | − | − | − | (+) |
Trypsin | − | − | − | (+) |
β-glucuronidase | − | + | − | − |
Fatty Acid | 1 | 2 | 3 | 4 |
---|---|---|---|---|
C12:0 | 5.7 | 6.6 | 7.9 | 16.2 |
C14:0 | - | - | - | 1.6 |
C15:0 | Tr | Tr | 1.4 | - |
C16:0 | 24.0 | 16.6 | 13.0 | 15.9 |
C17:0 | 1.1 | Tr | 1.0 | 2.0 |
C18:0 | 2.6 | Tr | Tr | 2.8 |
C16:1ω7c | 33.5 | 40.3 | 41.6 | 24.5 * |
C16:1ω5c | 1.3 | Tr | Tr | - |
C17:1ω8c | Tr | 1.0 | 1.3 | 0.9 |
C18:1ω7c | 17.5 | 20.3 | 16.6 | 9.9 ** |
iso-C17:0 | - | - | - | 2.4 |
C14:0 3-OH | 7.5 | 8.0 | 9.2 | - |
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Romanenko, L.; Bystritskaya, E.; Otstavnykh, N.; Kurilenko, V.; Velansky, P.; Isaeva, M. Phenotypic and Genomic Characterization of Oceanisphaera submarina sp. nov. Isolated from the Sea of Japan Bottom Sediments. Life 2025, 15, 378. https://doi.org/10.3390/life15030378
Romanenko L, Bystritskaya E, Otstavnykh N, Kurilenko V, Velansky P, Isaeva M. Phenotypic and Genomic Characterization of Oceanisphaera submarina sp. nov. Isolated from the Sea of Japan Bottom Sediments. Life. 2025; 15(3):378. https://doi.org/10.3390/life15030378
Chicago/Turabian StyleRomanenko, Lyudmila, Evgeniya Bystritskaya, Nadezhda Otstavnykh, Valeriya Kurilenko, Peter Velansky, and Marina Isaeva. 2025. "Phenotypic and Genomic Characterization of Oceanisphaera submarina sp. nov. Isolated from the Sea of Japan Bottom Sediments" Life 15, no. 3: 378. https://doi.org/10.3390/life15030378
APA StyleRomanenko, L., Bystritskaya, E., Otstavnykh, N., Kurilenko, V., Velansky, P., & Isaeva, M. (2025). Phenotypic and Genomic Characterization of Oceanisphaera submarina sp. nov. Isolated from the Sea of Japan Bottom Sediments. Life, 15(3), 378. https://doi.org/10.3390/life15030378