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Metagenomic Analysis of Bacterial Communities Associated with Four Ecklonia cava Populations, Including Dokdo Island Population

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Abstract

Objective

The dynamics of the Ecklonia cava-associated microbiota in four Korean populations, Dokdo Island (DI), Ulleungdo Island (UI), Sangbaekdo Island (SI), and Seogwipo, were investigated to provide the initial data on E. cava-bacteria interactions in different localities.

Methods

A pyrosequencing 454 analysis of the bacterial 16S rRNA genes was carried out, and the obtained sequences were analyzed by bioinformatic methods.

Results

The Chao 1 index showed that the bacterial community richness was highest in the Seogwipo population, which contained more highly abundant bacteria than the other populations according to the ACE index. The Shannon diversity index showed that the UI population was highly diverse. Bacteria of the phylum Proteobacteria were most abundant in all four populations (49–94%). Fifty-two genera were identified in the four E. cava populations. The microbiota at DI was dominated by Granulosicoccus (17.33%) and HQ845450_g (10.67%); HQ845450_g (11.67%) and Rhodobacteraceae_uc (7.50%) were abundant in the UI population; HQ845450_g (25.32%), Streptococcus (11.39%), and Desulfomonile (11.39%) were dominant in the SI population; and Vibrio (44.91%) and AM259833_f_uc (16.37%) were dominant in the Seogwipo population. The genus Granulosicoccus was found in all four groups.

Conclusion

The microbiota in E. cava are largely dependent on the algal location, because only three bacterial operational taxonomic units (OTUs) were commonly found among the 850 bacterial sequences from four E. cava populations. The microbiota differences among the E. cava populations may contribute to seaweed forest conservation strategies at different locations.

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References

  1. Zehr, J. P., Jenkins, B. D., Short, S. M. & Steward, G. F. Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environ. Microbiol. 5, 539–554, doi: https://doi.org/10.1046/j.1462-2920.2003.00451.x(2003).

    Article  CAS  PubMed  Google Scholar 

  2. Stokes, R. W. et al. The glycan-rich outer layer of the cell wall of Mycobacterium tuberculosis acts as an antiphagocytic capsule limiting the association of the bacterium with macrophages. Infect. Immun. 72, 5676–5686, doi: https://doi.org/10.1128/Iai.72.10.5676-5686.2004 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Dash, H. R., Mangwani, N., Chakraborty, J., Kumari, S. & Das, S. Marine bacteria: potential candidates for enhanced bioremediation. Appl. Microbiol. Biotechnol. 97, 561–571, doi: https://doi.org/10.1007/s00253-012-4584-0 (2013).

    Article  CAS  PubMed  Google Scholar 

  4. Alderkamp, A. C., van Rijssel, M. & Bolhuis, H. Characterization of marine bacteria and the activity of their enzyme systems involved in degradation of the algal storage glucan laminarin. FEMS Microbiol. Ecol. 59, 108–117, doi: https://doi.org/10.1111/j.1574-6941.2006.00219.x (2007).

    Article  CAS  PubMed  Google Scholar 

  5. Guiry, M. D. & Guiry, G. M. AlgaeBase. World-wide electronic publication, National University of Ireland, Galway, https://doi.org/www.algaebase.org (2018).

    Google Scholar 

  6. Kim, K. C. et al. Fucodiphlorethol G Purified from Ecklonia cava suppresses ultraviolet B radiation-induced oxidative stress and cellular damage. Biomol. Ther. (Seoul) 22, 301–307, doi: https://doi.org/10.4062/biomolther.2014.044 (2014).

    Article  CAS  Google Scholar 

  7. Park, M. H. et al. 6,6′-bieckol isolated from Ecklonia cava protects oxidative stress through inhibiting expression of ROS and proinflammatory enzymes in high-glucose-induced human umbilical vein endothelial cells. Appl. Biochem. Biotechnol. 174, 632–643, doi: https://doi.org/10.1007/s12010-014-1099-4 (2014).

    Article  CAS  PubMed  Google Scholar 

  8. Jang, S. K. et al. The anti-aging properties of a human placental hydrolysate combined with dieckol isolated from Ecklonia cava. BMC Complement. Altern. Med. 15, 345, doi: https://doi.org/10.1186/s12906-015-0876-0 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  9. Choi, B. W., Lee, H. S., Shin, H. C. & Lee, B. H. Multifunctional activity of polyphenolic compounds associated with a potential for Alzheimer’s disease therapy from Ecklonia cava. Phytother. Res. 29, 549–553, doi: https://doi.org/10.1002/ptr.5282 (2015).

    Article  CAS  PubMed  Google Scholar 

  10. Park, E. Y. et al. Polyphenol-rich fraction of Ecklonia cava improves nonalcoholic fatty liver disease in high fat diet-fed mice. Mar. Drugs 13, 6866–6883, doi: https://doi.org/10.3390/md13116866 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Yamashita, H., Goto, M., Matsui-Yuasa, I. & Kojima-Yuasa, A. Ecklonia cava polyphenol has a protective effect against ethanol-induced liver injury in a cyclic AMP-dependent manner. Mar. Drugs 13, 3877–3891, doi: https://doi.org/10.3390/md13063877 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. You, H. N., Lee, H. A., Park, M. H., Lee, J. H. & Han, J. S. Phlorofucofuroeckol A isolated from Ecklonia cava alleviates postprandial hyperglycemia in diabetic mice. Eur. J. Pharmacol. 752, 92–96, doi: https://doi.org/10.1016/j.ejphar.2015.02.003 (2015).

    Article  CAS  PubMed  Google Scholar 

  13. Singh, R. P. & Reddy, C. R. Seaweed-microbial interactions: key functions of seaweed-associated bacteria. FEMS Microbiol. Ecol. 88, 213–230, doi: https://doi.org/10.1111/1574-6941.12297 (2014).

    Article  CAS  PubMed  Google Scholar 

  14. Egan, S. et al. The seaweed holobiont: understanding seaweed-bacteria interactions. FEMS Microbiol. Rev. 37, 462–476, doi: https://doi.org/10.1111/1574-6976.12011 (2013).

    Article  CAS  PubMed  Google Scholar 

  15. de Oliveira, L. S. et al. Molecular mechanisms for microbe recognition and defense by the red seaweed Laurencia dendroidea. mSphere 2, doi: https://doi.org/10.1128/mSphere.00094-17 (2017).

  16. Hughes, J. B., Hellmann, J. J., Ricketts, T. H. & Bohannan, B. J. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67, 4399–4406 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Lemos, L. N., Fulthorpe, R. R., Triplett, E. W. & Roesch, L. F. Rethinking microbial diversity analysis in the high throughput sequencing era. J. Microbiol. Methods 86, 42–51, doi: https://doi.org/10.1016/j.mimet.2011.03.014 (2011).

    Article  CAS  PubMed  Google Scholar 

  18. Lee, K., Lee, H. K., Choi, T. H., Kim, K. M. & Cho, J. C. Granulosicoccaceae fam. nov., to include Granulosicoccus antarcticus gen. nov., sp. nov., a non-phototrophic, obligately aerobic chemoheterotroph in the order Chromatiales, isolated from Antarctic seawater. J. Microbiol. Biotechnol. 17, 1483–1490 (2007).

    CAS  PubMed  Google Scholar 

  19. Imhoff, J. F. in Bergey’s Manual of Systematic Bacteriology, vol. 2 (The Proteobacteria) (eds Brenner, D. J., Krieg, N. R., Staley, J. T. & Garrity, G. M.) 1–3 (Williams & Wilkins, Baltimore, 2005).

  20. Kurilenko, V. V. et al. Granulosicoccus coccoides sp. nov., isolated from leaves of seagrass (Zostera marina). Int. J. Syst. Evol. Microbiol. 60, 972–976, doi: https://doi.org/10.1099/ijs.0.013516-0 (2010).

    Article  PubMed  Google Scholar 

  21. Romanenko, L. A., Tanaka, N., Frolova, G. M. & Mikhailov, V. V. Arenicella xantha gen. nov., sp nov., a gammaproteobacterium isolated from a marine sandy sediment. Int. J. Syst. Evol. Microbiol. 60, 1832–1836, doi: https://doi.org/10.1099/ijs.0.017194-0 (2010).

    Article  CAS  PubMed  Google Scholar 

  22. Lamas, C. C. & Eykyn, S. J. Blood culture negative endocarditis: analysis of 63 cases presenting over 25 years. Heart 89, 258–262 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Aslam, Z. et al. Methylobacterium jeotgali sp nov., a nonpigmented, facultatively methylotrophic bacterium isolated from jeotgal, a traditional Korean fermented seafood. Int. J. Syst. Evol. Microbiol. 57, 566–571, doi: https://doi.org/10.1099/ijs.0.64625-0 (2007).

    Article  CAS  PubMed  Google Scholar 

  24. Gromkova, R. C., Mottalini, T. C. & Dove, M. G. Genetic transformation in Haemophilus parainfluenzae clinical isolates. Curr. Microbiol. 37, 123–126, doi: https://doi.org/10.1007/s002849900349 (1998).

    Article  CAS  PubMed  Google Scholar 

  25. Keith, E. R., Podmore, R. G., Anderson, T. P. & Murdoch, D. R. Characteristics of Streptococcus pseudopneumoniae isolated from purulent sputum samples. J. Clin. Microbiol. 44, 923–927, doi: https://doi.org/10.1128/JCM.44.3.923-927.2006 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  26. Kawakami, H. et al. Late-onset bleb-related endophthalmitis caused by Streptococcus pseudopneumoniae. Int. J. Ophthalmol. 34, 643–646, doi: https://doi.org/10.1007/s10792-013-9835-2 (2014).

    Article  Google Scholar 

  27. Espinosa, E. et al. Taxonomic study of Marinomonas strains isolated from the seagrass Posidonia oceanica, with descriptions of Marinomonas balearica sp nov and Marinomonas pollencensis sp nov. Int. J. Syst. Evol. Microbiol. 60, 93–98, doi: https://doi.org/10.1099/ijs.0.008607-0 (2010).

    Article  CAS  PubMed  Google Scholar 

  28. Wang, G. et al. Phylogenetic analysis of epiphytic marine bacteria on Hole-Rotten diseased sporophytes of Laminaria japonica. J. Appl. Phycol. 20, 403–409, doi: https://doi.org/10.1007/s10811-007-9274-4 (2008).

    Article  CAS  Google Scholar 

  29. Voronina, O. L. et al. The variability of the order Burkholderiales representatives in the healthcare units. Biomed. Research International, doi: https://doi.org/10.1155/2015/680210 (2015).

    Google Scholar 

  30. Chun, J., Kim, K. Y., Lee, J. H. & Choi, Y. The analysis of oral microbial communities of wild-type and toll-like receptor 2-deficient mice using a 454 GS FLX Titanium pyrosequencer. BMC Microbiol. 10, 101, doi: https://doi.org/10.1186/1471-2180-10-101 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200, doi: https://doi.org/10.1093/bioinformatics/btr381 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Kim, O. S. et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int. J. Syst. Evol. Microbiol. 62, 716–721, doi: https://doi.org/10.1099/ijs.0.038075-0 (2012).

    Article  CAS  PubMed  Google Scholar 

  33. Schloss, P. D. et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537–7541, doi: https://doi.org/10.1128/AEM.01541-09 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Hamady, M., Lozupone, C. & Knight, R. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J. 4, 17–27, doi: https://doi.org/10.1038/ismej.2009.97 (2010).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This research was supported by a grant from the Ministry of Oceans and Fisheries of the Korean Government as “A sustainable research and development of Dokdo” project.

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Authors and Affiliations

  1. Ecological Risk Research Division, Korea Institute of Ocean Science and Technology (KIOST), Geoje, 53201, Republic of Korea

    Yejin Jo & Seungshic Yum

  2. Division of Life Science, Gyeongsang National University, Jinju, 53828, Republic of Korea

    Yoon Sik Oh

  3. Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology (KIOST), Busan, 49111, Republic of Korea

    Seonock Woo

  4. East Sea Research Institute, Korea Institute of Ocean Science and Technology (KIOST), Uljin, 36315, Republic of Korea

    Chan Hong Park

  5. Faculty of Marine Environmental Science, University of Science and Technology (UST), Geoje, 53201, Republic of Korea

    Seungshic Yum

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  1. Yejin Jo
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Correspondence to Seungshic Yum.

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Metagenomic Analysis of Bacterial Communities Associated with Four Ecklonia cava Populations, Including Dokdo Island Population

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Jo, Y., Oh, Y.S., Woo, S. et al. Metagenomic Analysis of Bacterial Communities Associated with Four Ecklonia cava Populations, Including Dokdo Island Population. Toxicol. Environ. Health Sci. 11, 11–18 (2019). https://doi.org/10.1007/s13530-019-0383-7

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  • DOI: https://doi.org/10.1007/s13530-019-0383-7

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