Abstract
A Gram-stain-negative, aerobic, non-motile, yellow-pigmented rod-shaped and alginate-degrading bacterium, designated B1N29T, was isolated from the gut of the abalone Haliotis rubra obtained in Weihai, China. Strain B1N29T was found to grow at 4–35 ℃ (optimum, 25 ℃), at pH 6.5–9.0 (optimum, 7.0–7.5) and in the presence of 0.5–9% (w/v) NaCl (optimum, 2%). Cells were positive for oxidase and catalase activity. The 16S rRNA-based phylogenetic analysis revealed that the nearest phylogenetic neighbors of strain B1N29T were Tamlana carrageenivorans KCTC 62451T (98.2%) and Tamlana agarivorans KCTC 22176T (97.7%). Based on the phylogenomic analysis, the average nucleotide identity (ANI) values between strain B1N29T and the neighbor strains were 79.2 and 79.0%, respectively; the digital DNA–DNA hybridization (dDDH) values between strain B1N29T and its two closest neighbors were 22.8 and 23.0%, respectively. Menaquinone-6 (MK-6) was detected as the sole respiratory quinone. The dominant cellular fatty acids were iso-C15:0, iso-C17:0 3-OH, anteiso-C15:0 and iso-C15:1 G. The polar lipids included phosphatidylethanolamine, one aminophospholipid, seven aminolipids and five unidentified lipids. Based on the phylogenetic and phenotypic characteristics, strain B1N29T is considered to represent a novel species of the genus Tamlana, for which the name Tamlana haliotis sp. nov. is proposed. The type strain is B1N29T (= KCTC 72683T = MCCC 1H00394T).
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References
Alexandros S (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313. https://doi.org/10.1093/bioinformatics/btu033
Atlas RM (1993) Handbook of microbiological media. CRC Press, Boca Raton
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170
Bowman JP (2000) Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 50:1861–1868. https://doi.org/10.1016/S0924-8579(00)00196-5
Cao WR, Lu DC, Sun XK, Sun YY, Saren G, Yu XK, Du ZJ (2020) Seonamhaeicola maritimus sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 70:902–908. https://doi.org/10.1099/ijsem.0.003844
Chun J, Rainey FA (2014) Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 64:316. https://doi.org/10.1099/ijs.0.054171-0
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376. https://doi.org/10.1007/BF01734359
Fitch WM (1977) On the problem of discovering the most parsimonious tree. Am Nat 111:223–257. https://doi.org/10.1086/283157
Hiraishi A, Ueda YJ, Mori T (2006) Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469. https://doi.org/10.2323/jgam.42.457
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 11:119–119. https://doi.org/10.1186/1471-2105-11-119
Jeong SH, Park MS, Jin HM, Lee K, Park W, Jeon CO (2013) Aestuariibaculum suncheonense gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from a tidal flat and emended descriptions of the genera Gaetbulibacter and Tamlana. Int J Syst Evol Microbiol 63:332–338. https://doi.org/10.1099/ijs.0.037846-0
Jorgensen JH, Turnidge JD, Washington JA (1999) Antibacterial susceptibility tests: dilution and disk diffusion methods. In: Murray PR, Baron EJ, Pfaller MA, Tenover FC, Yolken RH (eds) Manual of clinical microbiology. American Society for Microbiology, Washington, DC, pp 1526–1543
Jung J, Bae SS, Chung D, Baek K (2019) Tamlana carrageenivorans sp. nov., a carrageenan-degrading bacterium isolated from seawater. Int J Syst Evol Microbiol 69:1355–1360. https://doi.org/10.1099/ijsem.0.003318
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120. https://doi.org/10.1007/BF01731581
Kroppenstedt R (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5:2359–2367. https://doi.org/10.1080/01483918208067640
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096
Lee SD (2007) Tamlana crocina gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae, isolated from beach sediment in Korea. Int J Syst Evol Microbiol 57:764–769. https://doi.org/10.1099/ijs.0.64720-0
Li J, Xu Y, Feng J, Zhong M, Xie Q, Peng T, Hu Z (2020) Tamlana fucoidanivorans sp. nov., isolated from algae collected in China. Int J Syst Evol Microbiol 70:1496–1502. https://doi.org/10.1099/ijsem.0.003850
Li R, Zhu HJ, Qian W, Fang X, Shi Z et al (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272. https://doi.org/10.1101/gr.097261.109
Liu X, Lai Q, Du Y, Li G, Sun F, Shao Z (2015) Tamlana nanhaiensis sp. nov., isolated from surface seawater collected from the South China Sea. Antonie Van Leeuwenhoek 107:1189–1196. https://doi.org/10.1007/s10482-015-0410-x
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964. https://doi.org/10.1093/nar/25.5.0955
Meier-Kolthoff JPAA, Klenk H, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and;improved distance functions. BMC Bioinform 14:60. https://doi.org/10.1186/1471-2105-14-60
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Meth 2:233–241. https://doi.org/10.1016/0167-7012(84)90018-6
Reichenbach H (1992) The order cytophagales. In: Balows ATH, Dworkin M, Harder W, Schleifer KH et al (eds) The prokaryotes. Springer, New York, pp 3631–3675
Richter M, Rossellómóra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 106:19126–19131. https://doi.org/10.1073/pnas.0906412106
Richter M, Rossellómóra R, Glöckner FO, Peplies J (2015) JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32:929. https://doi.org/10.1093/bioinformatics/btv681
Romanenko LA, Tanaka N, Kurilenko VV, Svetashev VI (2014) Tamlana sedimentorum sp. nov., isolated from shallow sand sediments of the Sea of Japan. Int J Syst Evol Microbiol 64:2891–2896. https://doi.org/10.1099/ijs.0.061812-0
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:405–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Sasser M (2001) Identification of bacteria by gas chromatography of cellular fatty acids Midi Technical Note:101
Smibert RM, Krieg NR (1994) Phenotypic characteristics. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular biology. American Society for Microbiology, Washington, DC, pp 607–654
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882. https://doi.org/10.1093/nar/25.24.4876
Tindall BJ, Sikorski J, Smibert RA, Krieg NR (2007) Phenotypic characterization and the principles of comparative systematics. Methods for general and molecular microbiology, 3rd edn. American Society for Microbiology, Washington, DC, pp 330–393
Yoon JH, Kang SJ, Lee MH, Oh TK (2008) Tamlana agarivorans sp. nov., isolated from seawater off Jeju Island in Korea. Int J Syst Evol Microbiol 58:1892–1895. https://doi.org/10.1099/ijs.0.65704-0
Yoon SH, Ha SM, Kwon S, Lim J, 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. https://doi.org/10.1099/ijsem.0.001755
Acknowledgements
Authors thank Qi-Yun Liang for the work of phylogenomic analysis.
Funding
This work was supported by the Natural Science Foundation of Shandong Province, China (No. ZR2020MD088), the Open Fund of the Key Laboratory of Marine Geology and Environment, Chinese Academy of Sciences (No. MGE2020KG14), the Strategic Priority Research Program of the Chinese Academy of Sciences (No. XDB42000000), State Key Laboratory of Microbial Technology Open Projects Fund (No. M2020-03) and the National Natural Science Foundation of China (No. 41976202).
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Strain B1N29T was isolated by BTL. Material preparation, data collection and analysis were performed by WRC, BTL, XKS, YYS and MYJ. The manuscript was written by WRC. Project guidance and critical revision of manuscripts were performed by ZJD. All authors read and approved the final manuscript.
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Communicated by Erko Stackebrandt.
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The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain B1N29T is MN519996. The GenBank/EMBL/DDBJ accession number for the genome sequences of strain B1N29T is WAAT00000000.
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Cao, WR., Liu, BT., Sun, XK. et al. Tamlana haliotis sp. nov., isolated from the gut of the abalone Haliotis rubra. Arch Microbiol 203, 2357–2364 (2021). https://doi.org/10.1007/s00203-021-02216-7
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DOI: https://doi.org/10.1007/s00203-021-02216-7