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Tropicibacter alexandrii sp. nov., a novel marine bacterium isolated from the phycosphere of a dinoflagellate, Alexandrium minutum

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Abstract

An aerobic, Gram-negative, rod-shaped, non-motile bacterium was isolated from a liquid culture of the dinoflagellate Alexandrium minutum and designated as strain LMIT003T. Analyses of 16S rRNA gene sequences revealed that this strain is affiliated with the genus Tropicibacter in the family Rhodobacteraceae of the class Alphaproteobacteria and shows high similarity (97.3%) with the type species Tropicibacter naphthalenivorans C02T. Phylogenetic analysis based on core genes showed that the isolate groups with members of the genus Tropicibacter. The G + C content of strain LMIT003T was determined to be 61.9 mol%. The major fatty acids identified included summed feature 8 (C18:1 ω7c/C18:1 ω6c), C18:0, C12:1 3-OH and C16:0. The sole respiratory lipoquinone was found to be ubiquinone-10. The major polar lipids were found to be phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids and four unidentified phospholipids. The draft genome size of strain LMIT003T was determined to be 4.8 Mbp. The average nucleotide identity values between strain LMIT003T and reference Tropicibacter species were determined to be 78.7% (T. naphthalenivorans) and 74.2% (Tropicibacter phthalicicus). Based on physiological, chemotaxonomic and phylogenetic analysis, strain LMIT003T is concluded to represent a novel species in the genus Tropicibacter, for which the name Tropicibacter alexandrii sp. nov., is proposed. The type strain is LMIT003T (= CICC 24660T = KCTC 62895T).

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Abbreviations

CICC:

China Center for Industrial Culture Collection

KCTC:

Korean Collection for Type Cultures

References

  • Buchan A, LeCleir GR, Gulvik CA, Gonzalez JM (2014) Master recyclers: features and functions of bacteria associated with phytoplankton blooms. Nat Rev Microbiol 12:686–698

    Article  CAS  Google Scholar 

  • Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, Costa MS, Rooney AP, Yi H, Xu XW, Meyer SD, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466

    Article  CAS  Google Scholar 

  • Cooper MB, Smith AG (2015) Exploring mutualistic interactions between microalgae and bacteria in the omics age. Curr Opin Plant Biol 26:147–153

    Article  Google Scholar 

  • Croft MT, Lawrence AD, Raux-Deery E, Warren MJ, Smith AG (2005) Algae acquire vitamin B12 through a symbiotic relationship with bacteria. Nature 438:90–93

    Article  CAS  Google Scholar 

  • Curson AR, Todd JD, Sullivan MJ, Johnston AW (2011) Catabolism of dimethylsulphoniopropionate: microorganisms, enzymes and genes. Nat Rev Microbiol 9:849–859

    Article  CAS  Google Scholar 

  • Emms DM, Kelly S (2018) OrthoFinder2: fast and accurate phylogenomic orthology analysis from gene sequences. bioRxiv, https://dx.doi.org/10.1101/466201

  • Field CB, Behrenfeld MJ, Randerson JT, Falkowski P (1998) Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281:237–240

    Article  CAS  Google Scholar 

  • Guillard RRL (1975) Culture of phytoplankton for feeding marine invertebrates. In: Smith WL, Chanley MH (eds) Culture of marine invertebrate animals. Plenum Press, New York, pp 29–60

    Chapter  Google Scholar 

  • Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075

    Article  CAS  Google Scholar 

  • Harwati TU, Kasai Y, Kodama Y, Susilaningsih D, Watanabe K (2009) Tropicibacter naphthalenivorans gen. nov., sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from Semarang Port in Indonesia. Int J Syst Evol Microbiol 59:392–396

    Article  CAS  Google Scholar 

  • Iwaki H, Nishimura A, Hasegawa Y (2012) Tropicibacter phthalicicus sp. nov., a phthalate-degrading bacterium from seawater. Curr Microbiol 64:392–396

    Article  CAS  Google Scholar 

  • Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066

    Article  CAS  Google Scholar 

  • Kim M-J, Jeong S-Y, Seong -J, Lee S-J (2008) Isolation, identification, and algicidal activity of marine bacteria against Cochlodinium polykrikoides. J Appl Phycol 20:1069–1078

    Article  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  Google Scholar 

  • Mayali X, Azam F (2004) Algicidal bacteria in the sea and their impact on algal blooms. J Eukaryot Microbiol 51:139–144

    Article  Google Scholar 

  • Minnikin DE, O’donell 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 Methods 2:233–241

    Article  CAS  Google Scholar 

  • Morgan NP, Paramvir SD, Adam PA (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26:1641–1650

    Article  Google Scholar 

  • Nedashkovskaya OI, Kim SB, Han SK, Rhee MS, Lysenko AM, Falsen E, Frolova GM, Mikhailov VV, Bae KS (2004) Ulvibacter litoralis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the green alga Ulva fenestrata. Int J Syst Evol Microbiol 54:119–123

    Article  CAS  Google Scholar 

  • Newton R, Griffin L, Loftis K, Meile C, Gifford S, Givens CC, Howard E, King E, Oakley C, Reisch C, Rinta-Kanto J, Sharma S, Sun S, Varaljay V, Vila-Costa M, Westrich J, Moran MA (2010) Genome characteristics of a generalist marine bacterial lineage. ISME J 4:784–798

    Article  CAS  Google Scholar 

  • Nurk S, Bankevich A, Antipov D, Gurevich AA (2013) Assembling genomes and mini-metagenomes from highly chimeric reads. In: Deng M, Jiang R, Sun F, Zhang X (eds) Research in computational molecular biology. Springer, Berlin, pp 158–170

    Chapter  Google Scholar 

  • Park S-K, Kim M-S, Jung M-J, Nam Y-D, Park E-J, Roh SW, Bae J-W (2011) Brachybacterium squillarum sp. nov., isolated from salt-fermented seafood. Int J Syst Evol Microbiol 61:1118–1122

    Article  CAS  Google Scholar 

  • Ramanan R, Kim BH, Cho DH, Oh HM, Kim HS (2016) Algae-bacteria interactions: evolution, ecology and emerging applications. Biotechnol Adv 34:14–29

    Article  CAS  Google Scholar 

  • Rodionov DA, Gelfand MS, Todd JD, Curson AR, Johnston AW (2006) Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria. PLoS Comput Biol 2:e163

    Article  Google Scholar 

  • Sasser M (2001) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc , Newark, DE

  • Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069

    Article  CAS  Google Scholar 

  • Seymour JR, Amin SA, Raina J-B, Stocker R (2017) Zooming in on the phycosphere: the ecological interface for phytoplankton-bacteria relationships. Nat Microbiol 2:17065

    Article  CAS  Google Scholar 

  • Shieh WY, Chen Y-W, Chaw S-M, Chiu H-H (2003) Vibrio ruber sp. nov., a red, facultatively anaerobic, marine bacterium isolated from sea water. Int J Syst Evol Microbiol 53:479–484

    Article  Google Scholar 

  • Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, et al. (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington DC, pp 607–654

    Google Scholar 

  • Tittsler RP, Sandholzer LA (1936) The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 31:575–580

    Article  CAS  Google Scholar 

  • Wagner-Döbler I, Ballhausen B, Berger M, Brinkhoff T, Buchholz I, Bunk B, Cypionka H, Daniel R, Drepper T, Gerdts G, Hahnke S, Han C, Jahn D, Kalhoefer D, Kiss H, Klenk H-P, Kyrpides N, Liebl W, Liesegang H, Meincke L, Pati A, Petersen J, Piekarski T, Pommerenke C, Pradella S, Pukall R, Rabus R, Stackebrandt E, Thole S, Thompson L, Tielen P, Tomasch J, Von JM, Wanphrut N, Wichels A, Zech H, Simon M (2009) The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea. ISME J 4:61–77

    Article  Google Scholar 

  • Wang X, Li ZJ, Su JQ, Tian Y, Ning XR, Hong H, Zheng T (2010) Lysis of a red-tide causing alga, Alexandrium tamarense, caused by bacteria from its phycosphere. Biol Control 52:123–130

    Article  Google Scholar 

  • Wang H, Laughinghouse HD, Anderson MA, Chen F, Willliams E, Place AR, Zmora O, Zohar Y, Zheng T, Hill R (2012) Novel bacterial isolate from Permian groundwater, capable of aggregating potential biofuel-producing microalgae Nannochloropsis oceanica IMET1. Appl Environ Microb 78:1445–1453

    Article  CAS  Google Scholar 

  • Wang X, Yang HX, Zhang YK (2015) Luteimonas soli sp. nov., isolated from farmland soil. Int J Syst Evol Microbiol 65:4809–4815

    Article  CAS  Google Scholar 

  • Wayne LG (1987) International committee on systematic bacteriology. Report of the Ad Hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  • Wirth JS, Whitman WB (2018) Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Syst Evol Microbiol 68:2393–2411

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

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Acknowledgements

We acknowledge the Marine Culture Collection of China (MCCC) for assistance in identifying the novel strain. We also thank Dr. Mary Atieno from International Centre for Tropical Agriculture (CIAT) for English language assistance during the preparation of this manuscript.

Funding

Funding for this study was provided by National Natural Science Foundation of China (41676116), SAIL Foundation for Distinguished Scholars (Hui Wang), Pearl River Scholar for Young Investigator (Hui Wang) and Innovation Projects of Universities in Guangdong Province (2017KTSCX072).

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Authors and Affiliations

  1. Biology Department, College of Science, Shantou University, Shantou, 515063, China

    Xiaoli Wang, Jianming Zhu, Jiarong Feng, Ali Sardar, Zhong Hu & Hui Wang

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  1. Xiaoli Wang
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  2. Jianming Zhu
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  3. Jiarong Feng
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  4. Ali Sardar
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  5. Zhong Hu
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  6. Hui Wang
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Contributions

HW, ZH and XW designed the experiments. XW, JZ, JF and HW performed the experiments, collected and analysed the data. XW, AS and HW wrote the draft of the article. XW, AS, ZH and HW revised the draft of the article.

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Correspondence to Hui Wang.

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Wang, X., Zhu, J., Feng, J. et al. Tropicibacter alexandrii sp. nov., a novel marine bacterium isolated from the phycosphere of a dinoflagellate, Alexandrium minutum. Antonie van Leeuwenhoek 113, 311–320 (2020). https://doi.org/10.1007/s10482-019-01339-8

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