Thalassotalea aquiviva sp. nov., and Thalassotalea maritima sp. nov., Isolated from Seawater of the Coast in South Korea.

Publisher: Microbiological Society Of Korea Country of Publication: Korea (South) NLM ID: 9703165 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1976-3794 (Electronic) Linking ISSN: 12258873 NLM ISO Abbreviation: J Microbiol Subsets: MEDLINE

Original Publication: Seoul : Microbiological Society Of Korea

Phylogeny* ; RNA, Ribosomal, 16S*/genetics ; Seawater*/microbiology ; Fatty Acids*/analysis ; Base Composition* ; DNA, Bacterial*/genetics ; Nucleic Acid Hybridization* ; Bacterial Typing Techniques*; Republic of Korea ; Sequence Analysis, DNA ; Phospholipids/analysis

Two novel bacterial strains, 273M-4 ^T and Sam97 ^T , were isolated from seawater in the Yellow Sea, Muan-gun, South Korea, and identified as members of the genus Thalassotalea. Both strains were Gram-stain-negative, aerobic, rod-shaped, non-motile, non-flagellated, and oxidase- and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains 273M-4 ^T and Sam97 ^T were most closely related to Thalassotalea ponticola KCTC 42155 ^T , with sequence similarities of 97.5% and 98.3%, respectively. Optimal growth for strain 273M-4 ^T occurred at 25-30 °C, pH 7.0, and 2% NaCl, while strain Sam97 ^T grew optimally at 30 °C, pH 8.0, and 2% NaCl. Genome sizes of strains 273M-4 ^T and Sam97 ^T were 3.37 and 3.31 Mb, with DNA G + C contents of 41.0 mol% and 42.9 mol%, respectively. The orthologous average nucleotide identity (OrthoANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 71.6% and 24.4%, respectively, indicating that they are distinct species. Further genomic analyses of these two strains revealed OrthoANI values of < 73.5% and dDDH values of < 26.7% within the genus Thalassotalea, suggesting their distinctiveness from other Thalassotalea species. The predominate fatty acids of strains 273M-4 ^T and Sam97 ^T were summed feature 3 (consisting of C 16:1 ω7c/C 16:1 ω6c) and C 16:0 . All strains contained phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids and ubiquinone-8 (Q-8) as the primary respiratory quinone. Based on phenotypic, phylogenetic, genotypic, and chemotaxonomic data, strains 273M-4 ^T (= KCTC 8644 ^T  = LMG 33695 ^T ) and Sam97 ^T (= KCTC 8645 ^T  = LMG 33694 ^T ) represent novel species of the genus Thalassotalea, named Thalassotalea aquiviva sp. nov. and Thalassotalea maritima sp. nov..
Competing Interests: Declarations. Conflict of interest: The authors declare that there are no conflicts of interest.
(© 2024. The Author(s), under exclusive licence to Microbiological Society of Korea.)

Arrigo, K. R. (2005). Marine microorganisms and global nutrient cycles. Nature, 437, 349–355. (PMID: 16163345)
Brettin, T., Davis, J. J., Disz, T., Edwards, R. A., Gerdes, S., Olsen, G. J., Olson, R., Overbeek, R., Parrello, B., Pusch, G. D., et al. (2015). RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Scientific Reports, 5, 8365. (PMID: 256665854322359)
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: Architecture and applications. BMC Bioinformatics, 10, 421. (PMID: 200035002803857)
Choi, S., Kim, E., Shin, S. K., & Yi, H. (2017). Thalassotalea crassostreae sp. nov., isolated from Pacific oyster. International Journal of Systematic and Evolutionary Microbiology, 67, 2195–2198. (PMID: 28691654)
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. (2018). Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. International Journal of Systematic and Evolutionary Microbiology, 68, 461–466. (PMID: 29292687)
Collins, M. D., & Jones, D. (1981). Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiological Reviews, 45, 316–354. (PMID: 7022156281511)
Felsenstein, J. (1981). Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution, 17, 368–376. (PMID: 7288891)
Fitch, W. M. (1971). Toward defining the course of evolution: Minimum change for a specific tree topology. Systematic Biology, 20, 406–416.
Fredriksson, N. J., Hermansson, M., & Wilen, B. M. (2013). The choice of PCR primers has great impact on assessments of bacterial community diversity and dynamics in a wastewater treatment plant. PLoS ONE, 8, e76431. (PMID: 240984983788133)
Hall, T. A. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95–98.
Heuer, H., Krsek, M., Baker, P., Smalla, K., & Wellington, E. M. (1997). Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Applied and Environment Microbiology, 63, 3233–3241.
Hou, T. T., Liu, Y., Zhong, Z. P., Liu, H. C., & Liu, Z. P. (2015). Thalassotalea marina sp. nov., isolated from a marine recirculating aquaculture system, reclassification of Thalassomonas eurytherma as Thalassotalea eurytherma comb. nov. and emended description of the genus Thalassotalea. International Journal of Systematic and Evolutionary Microbiology, 65, 4710–4715. (PMID: 26400666)
Hu, P., Dubinsky, E. A., Probst, A. J., Wang, J., Sieber, C. M. K., Tom, L. M., Gardinali, P. R., Banfield, J. F., Atlas, R. M., & Andersen, G. L. (2017). Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders. Proc Natl Acad Sci U S A, 114, 7432–7437. (PMID: 286523495514739)
Huerta-Cepas, J., Szklarczyk, D., Forslund, K., Cook, H., Heller, D., Walter, M. C., Rattei, T., Mende, D. R., Sunagawa, S., Kuhn, M., et al. (2016). eggNOG 4.5: A hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Research, 44, D286–D293. (PMID: 26582926)
Jean, W. D., Shieh, W. Y., & Liu, T. Y. (2006). Thalassomonas agarivorans sp. nov., a marine agarolytic bacterium isolated from shallow coastal water of An-Ping Harbour, Taiwan, and emended description of the genus Thalassomonas. International Journal of Systematic and Evolutionary Microbiology, 56, 1245–1250. (PMID: 16738099)
Jones, P., Binns, D., Chang, H. Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G., et al. (2014). InterProScan 5: Genome-scale protein function classification. Bioinformatics, 30, 1236–1240. (PMID: 244516263998142)
Jung, Y. T., Park, S., & Yoon, J. H. (2014). Thalassomonas fusca sp. nov., a novel gammaproteobacterium isolated from tidal flat sediment. Antonie Van Leeuwenhoek, 105, 81–87. (PMID: 24132729)
Kang, H., Kim, H., Nam, I. Y., Joung, Y., Jang, T. Y., & Joh, K. (2017). Thalassotalea litorea sp. nov., isolated from seashore sand. International Journal of Systematic and Evolutionary Microbiology, 67, 2268–2273. (PMID: 28699882)
Kim, D., Park, S., & Chun, J. (2021a). Introducing EzAAI: A pipeline for high throughput calculations of prokaryotic average amino acid identity. Journal of Microbiology, 59, 476–480. (PMID: 33907973)
Kim, J., Na, S. I., Kim, D., & Chun, J. (2021b). UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis. Journal of Microbiology, 59, 609–615. (PMID: 34052993)
Kim, M., Cha, I. T., Lee, K. E., Lee, E. Y., & Park, S. J. (2020). Genomics reveals the metabolic potential and functions in the redistribution of dissolved organic matter in marine environments of the genus Thalassotalea. Microorganisms, 8, 1412. (PMID: 329378267564069)
Lee, I., Ouk Kim, Y., Park, S. C., & Chun, J. (2016). OrthoANI: An improved algorithm and software for calculating average nucleotide identity. International Journal of Systematic and Evolutionary Microbiology, 66, 1100–1103. (PMID: 26585518)
Lian, F. B., Jiang, S., Ren, T. Y., Zhou, B. J., & Du, Z. J. (2021). Thalassotalea algicola sp. nov., an alginate-utilizing bacterium isolated from a red alga. Antonie Van Leeuwenhoek, 114, 835–844. (PMID: 33774759)
Liu, J., Sun, Y. W., Li, S. N., & Zhang, D. C. (2017). Thalassotalea profundi sp. nov. isolated from a deep-sea seamount. International Journal of Systematic and Evolutionary Microbiology, 67, 3739–3743. (PMID: 28884674)
Luo, C., Rodriguez, R. L., & Konstantinidis, K. T. (2014). MyTaxa: An advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Research, 42, e73. (PMID: 245895834005636)
Madsen, E. L. (2011). Microorganisms and their roles in fundamental biogeochemical cycles. Current Opinion in Biotechnology, 22, 456–464. (PMID: 21333523)
Manni, M., Berkeley, M. R., Seppey, M., Simao, F. A., & Zdobnov, E. M. (2021). BUSCO Update: Novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Molecular Biology and Evolution, 38, 4647–4654. (PMID: 343201868476166)
Meier-Kolthoff, J. P., Auch, A. F., Klenk, H. P., & Goker, M. (2013). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics, 14, 60. (PMID: 234329623665452)
MIDI. (1999). Sherlock Microbial Identification System Operating Manual, version 3.0. Newark, DE: MIDI, Inc.
Minnikin, D. E., O’Donnell, A. G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A., & Parlett, J. H. (1984). The use an integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipidsof semi-solid agar for the detection of bacterial motility. Journal of Microbiological Methods, 2, 233–241.
Park, S., Choi, W. C., Oh, T. K., & Yoon, J. H. (2011). Thalassomonas agariperforans sp. nov., an agarolytic bacterium isolated from marine sand. International Journal of Systematic and Evolutionary Microbiology, 61, 2573–2576. (PMID: 21131503)
Park, S., Jung, Y. T., Kang, C. H., Park, J. M., & Yoon, J. H. (2014). Thalassotalea ponticola sp. nov., isolated from seawater, reclassification of Thalassomonas fusca as Thalassotalea fusca comb. nov. and emended description of the genus Thalassotalea. International Journal of Systematic and Evolutionary Microbiology, 64, 3676–3682. (PMID: 25085877)
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015). CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 25, 1043–1055. (PMID: 259774774484387)
Pinhassi, J., Farnelid, H., Garcia, S. M., Teira, E., Galand, P. E., Obernosterer, I., Quince, C., Vila-Costa, M., Gasol, J. M., Lundin, D., et al. (2022). Functional responses of key marine bacteria to environmental change - toward genetic counselling for coastal waters. Frontiers in Microbiology, 13, 869093. (PMID: 365324599751014)
Saitou, N., & Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406–425. (PMID: 3447015)
Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. MIDI Inc.
Seemann, T. (2014). Prokka: Rapid prokaryotic genome annotation. Bioinformatics, 30, 2068–2069. (PMID: 24642063)
Stelling, S. C., Techtmann, S. M., Utturkar, S. M., Alshibli, N. K., Brown, S. D., & Hazen, T. C. (2014). Draft genome sequence of Thalassotalea sp. strain ND16A isolated from eastern Mediterranean Sea water collected from a depth of 1055 meters. Genome Announcements, 2(6), 10–128.
Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38, 3022–3027. (PMID: 338924918233496)
Thompson, F. L., Barash, Y., Sawabe, T., Sharon, G., Swings, J., & Rosenberg, E. (2006). Thalassomonas loyana sp. nov., a causative agent of the white plague-like disease of corals on the Eilat coral reef. International Journal of Systematic and Evolutionary Microbiology, 56, 365–368. (PMID: 16449441)
Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22, 4673–4680. (PMID: 7984417308517)
Tindall, B. J. (1990). Lipid composition of Halobacterium lacusprofundi. FEMS Microbiology Letters, 66, 199–202.
Tittsler, R. P., & Sandholzer, L. A. (1936). The Use of semi-solid agar for the detection of bacterial motility. Journal of Bacteriology, 31, 575–580. (PMID: 16559914543748)
Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C. A., Zeng, Q., Wortman, J., Young, S. K., et al. (2014). Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE, 9, e112963. (PMID: 254095094237348)
Wang, Y., Liu, T., Ming, H., Sun, P., Cao, C., Guo, M., Du, J., Zhou, C., & Zhu, W. (2018). Thalassotalea atypica sp. nov., isolated from seawater, and emended description of Thalassotalea eurytherma. International Journal of Systematic and Evolutionary Microbiology, 68, 271–276. (PMID: 29143725)
Wasmund, K., Mussmann, M., & Loy, A. (2017). The life sulfuric: Microbial ecology of sulfur cycling in marine sediments. Environ Microbiol Rep, 9, 323–344. (PMID: 28419734)
Worden, A. Z., Follows, M. J., Giovannoni, S. J., Wilken, S., Zimmerman, A. E., & Keeling, P. J. (2015). Environmental science: Rethinking the marine carbon cycle—Factoring in the multifarious lifestyles of microbes. Science, 347, 1257594. (PMID: 25678667)
Yamano, R., Yu, J., Haditomo, A. H. C., Jiang, C., Mino, S., Romalde, J. L., Kang, K., Sakai, Y., & Sawabe, T. (2023). Genome taxonomy of the genus Thalassotalea and proposal of Thalassotalea hakodatensis sp. Nov. isolated from sea cucumber larvae. PLoS ONE, 18, e0286693. (PMID: 3726730110237450)
Yi, H., Bae, K. S., & Chun, J. (2004). Thalassomonas ganghwensis sp. nov., isolated from tidal flat sediment. International Journal of Systematic and Evolutionary Microbiology, 54, 377–380. (PMID: 15023946)
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. International Journal of Systematic and Evolutionary Microbiology, 67, 1613–1617. (PMID: 280055265563544)
Zhang, Y., Tang, K., Shi, X., & Zhang, X. H. (2014). Description of Thalassotalea piscium gen. nov., sp. nov., isolated from flounder (Paralichthys olivaceus), reclassification of four species of the genus Thalassomonas as members of the genus Thalassotalea gen. nov. and emended description of the genus Thalassomonas. International Journal of Systematic and Evolutionary Microbiology, 64, 1223–1228. (PMID: 24421274)
Zheng, J., Ge, Q., Yan, Y., Zhang, X., Huang, L., & Yin, Y. (2023). dbCAN3: Automated carbohydrate-active enzyme and substrate annotation. Nucleic Acids Research, 51, W115–W121. (PMID: 3712564910320055)

Keywords: Thalassotalea; Thalassotalea aquiviva; Thalassotalea maritima; Genome

0 (RNA, Ribosomal, 16S)
0 (Fatty Acids)
0 (DNA, Bacterial)
0 (Phospholipids)

Date Created: 20241210 Date Completed: 20241217 Latest Revision: 20241217

20241217

10.1007/s12275-024-00191-4

39656424