Skip to main content
SpringerLink
Log in

Isolation and genome analysis of Winogradskyella algicola sp. nov., the dominant bacterial species associated with the green alga Dunaliella tertiolecta

  • Microbial Systematics and Evolutionary Microbiology
  • Published:
Journal of Microbiology Aims and scope Submit manuscript

Abstract

Microalgae and bacteria are known to be closely associated in diverse environments. To isolate dominant bacterial species associated with a green alga, Dunaliella tertiolecta, a photoreactor culture of the microalga was investigated using culture-based and culture-independent approaches. The bacterial community structure of the algal culture showed that the most abundant bacterial species under the culture conditions was related to the genus Winogradskyella. The closely related amplicon sequences, showing ≥ 99.5% 16S rRNA gene sequence similarity to one of the isolates, designated IMCC-33238T, constituted > 49% of the bacterial community and was therefore regarded as the most dominant species in the algal culture. Strain IMCC33238T was characterized by Gramstaining-negative and orange-colored rods. Phylogenetic analyses of the 16S rRNA genes as well as whole genome sequences revealed that strain IMCC33238T belonged to Winogradskyella and shared more than 97.2% 16S rRNA gene sequence similarity with Winogradskyella species. The strain contained iso-C15:1 G, iso-C15:0, iso-C15:0 3-OH, and summed feature 3 (C16:1ω6c and/or C16:1ω7c) as major fatty acids and MK-6 as the predominant quinone. The polar lipids found in strain IMCC33238T were phosphatidylethanolamine, two unidentified aminolipids, and three unidentified lipids. The genome of strain IMCC33238T was 3.37 Mbp in size with 33.9 mol% G + C content and proteorhodopsin. Many genes encoding folate and vitamin production are considered to play an important role in the bacteria-algae interaction. On the basis of phylogenetic and phenotypic characteristics, strain IMCC33238T represents a novel species in the genus Winogradskyella, for which the name Winogradskyella algicola sp. nov. is proposed. The type strain is IMCC33238T (= KACC 21192T = NBRC 113704T).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • 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. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bernardet, J.F., Nakagawa, Y., and Holmes, B. 2002. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int. J. Syst. Evol. Microbiol. 52, 1049–1070.

    CAS  PubMed  Google Scholar 

  • Biebl, H., Tindall, B.J., Pukall, R., Lünsdorf, H., Allgaier, M., and Wagner-Döbler, I. 2006. Hoeflea phototrophica sp. nov., a novel marine aerobic alphaproteobacterium that forms bacteriochlorophyll a. Int. J. Syst. Evol. Microbiol. 56, 821–826.

    Article  CAS  PubMed  Google Scholar 

  • Buchan, A., LeCleir, G.R., Gulvik, C.A., and González, J.M. 2014. Master recyclers: features and functions of bacteria associated with phytoplankton blooms. Nat. Rev. Microbiol. 12, 686–698.

    Article  CAS  PubMed  Google Scholar 

  • Chisti, Y. 2007. Biodiesel from microalgae. Biotechnol. Adv. 25, 294–306.

    Article  CAS  PubMed  Google Scholar 

  • Cho, E.S., Cha, I.T., Choi, H.J., Roh, S.W., Nam, Y.D., Seo, S.M., and Seo, M.J. 2018. Zunongwangia flava sp. nov., belonging to the family Flavobacteriaceae, isolated from Salicornia europaea. J. Microbiol. 56, 868–873.

    Article  CAS  PubMed  Google Scholar 

  • Choo, Y.J., Lee, K., Song, J., and Cho, J.C. 2007. Puniceicoccus vermicola gen. nov., sp. nov., a novel marine bacterium, and description of Puniceicoccaceae fam. nov., Puniceicoccales ord. nov., Opitutaceae fam. nov., Opitutales ord. nov. and Opitutae classis nov. in the phylum ‘Verrucomicrobia’. Int. J. Syst. Evol. Microbiol. 57, 532–537.

    Article  CAS  PubMed  Google Scholar 

  • Collins, M., Shah, H., and Minnikin, D. 1980. A note on the separation of natural mixtures of bacterial menaquinones using reverse phase thin-layer chromatography. J. Appl. Bacteriol. 48, 277–282.

    Article  CAS  PubMed  Google Scholar 

  • Croft, M.T., Lawrence, A.D., Raux-Deery, E., Warren, M.J., and Smith, A.G. 2005. Algae acquire vitamin B12 through a symbiotic relationship with bacteria. Nature 438, 90–93.

    Article  CAS  PubMed  Google Scholar 

  • Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C., and Knight, R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fan, J., Ye, J., Kamphorst, J.J., Shlomi, T., Thompson, C.B., and Rabinowitz, J.D. 2014. Quantitative flux analysis reveals folate-dependent NADPH production. Nature 510, 298–302.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368–376.

    Article  CAS  PubMed  Google Scholar 

  • Galperin, M.Y., Makarova, K.S., Wolf, Y.I., and Koonin, E.V. 2015. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 43, D261–269.

    Article  CAS  PubMed  Google Scholar 

  • Gao, C., Wang, Y., Shen, Y., Yan, D., He, X., Dai, J., and Wu, Q. 2014. Oil accumulation mechanisms of the oleaginous microalga Chlorella protothecoides revealed through its genome, transcriptomes, and proteomes. BMC Genomics 15, 582.

    Article  PubMed  PubMed Central  Google Scholar 

  • Goris, J., Konstantinidis, K.T., Klappenbach, J.A., Coenye, T., Vandamme, P., and Tiedje, J.M. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57, 81–91.

    Article  CAS  PubMed  Google Scholar 

  • Guillard, R.R.L. 1975. Culture of phytoplankton for feeding marine invertebrates. In Smith, W.L. and Chanley, M.H. (eds.), Culture of Marine Invertebrate Animals, pp. 29–60. Plenum Press, New York, USA.

    Chapter  Google Scholar 

  • Han, S.I., Kim, S., Lee, C., and Choi, Y.E. 2019. Blue-Red LED wave-length shifting strategy for enhancing beta-carotene production from halotolerant microalga, Dunaliella salina. J. Microbiol. 57, 101–106.

    Article  CAS  PubMed  Google Scholar 

  • Han, J., Zhang, L., Wang, S., Yang, G., Zhao, L., and Pan, K. 2016. Co-culturing bacteria and microalgae in organic carbon containing medium. J. Biol. Res. (Thessalon) 23, 8.

    Article  CAS  Google Scholar 

  • Hejazi, M.A., de Lamarliere, C., Rocha, J.M., Vermue, M., Tramper, J., and Wijffels, R.H. 2002. Selective extraction of carotenoids from the microalga Dunaliella salina with retention of viability. Biotechnol. Bioeng. 79, 29–36.

    Article  CAS  PubMed  Google Scholar 

  • Ivanova, E.P., Alexeeva, Y.V., Flavier, S., Wright, J.P., Zhukova, N.V., Gorshkova, N.M., Mikhailov, V.V., Nicolau, D.V., and Christen, R. 2004. Formosa algae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae. Int. J. Syst. Evol. Microbiol. 54, 705–711.

    Article  CAS  PubMed  Google Scholar 

  • Jauffrais, T., Agogué, H., Gemin, M.P., Beaugeard, L., and Martin-Jézéquel, V. 2017. Effect of bacteria on growth and biochemical composition of two benthic diatoms Halamphora coffeaeformis and Entomoneis paludosa. J. Exp. Mar. Biol. Ecol. 495, 65–74.

    Article  CAS  Google Scholar 

  • Kakarla, R., Choi, J.W., Yun, J.H., Kim, B.H., Heo, J., Lee, S., Cho, D.H., Ramanan, R., and Kim, H.S. 2018. Application of highsalinity stress for enhancing the lipid productivity of Chlorella sorokiniana HS1 in a two-phase process. J. Microbiol. 56, 56–64.

    Article  CAS  PubMed  Google Scholar 

  • Kanehisa, M., Sato, Y., and Morishima, K. 2016. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428, 726–731.

    Article  CAS  PubMed  Google Scholar 

  • Kim, J.Y. and Oh, D.C. 2012. Winogradskyella jejuensis sp. nov., a marine bacterium isolated from a brown alga Carpopeltis affinis. J. Microbiol. 50, 888–892.

    Article  CAS  PubMed  Google Scholar 

  • Kozich, J.J., Westcott, S.L., Baxter, N.T., Highlander, S.K., and Schloss, P.D. 2013. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl. Environ. Microbiol. 79, 5112–5120.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kurilenko, V.V., Romanenko, L.A., Isaeva, M.P., Svetashev, V.I., and Mikhailov, V.V. 2019. Winogradskyella algae sp. nov., a marine bacterium isolated from the brown alga. Antonie van Leeuwenhoek 112, 731–739.

    Article  CAS  PubMed  Google Scholar 

  • Lau, S.C., Tsoi, M.M., Li, X., Plakhotnikova, I., Dobretsov, S., Lau, K.W., Wu, M., Wong, P.K., Pawlik, J.R., and Qian, P.Y. 2005. Winogradskyella poriferorum sp. nov., a novel member of the family Flavobacteriaceae isolated from a sponge in the Bahamas. Int. J. Syst. Evol. Microbiol. 55, 1589–1592.

    Article  CAS  PubMed  Google Scholar 

  • Le Chevanton, M., Garnier, M., Bougaran, G., Schreiber, N., Lukomska, E., Bérard, J.B., Fouilland, E., Bernard, O., and Cadoret, J.P. 2013. Screening and selection of growth-promoting bacteria for Dunaliella cultures. Algal Res. 2, 212–222.

    Article  Google Scholar 

  • Lee, S.Y., Park, S., Oh, T.K., and Yoon, J.H. 2012. Winogradskyella aquimaris sp. nov., isolated from seawater. Int. J. Syst. Evol. Microbiol. 62, 1814–1818.

    Article  CAS  PubMed  Google Scholar 

  • Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, Buchner, A., Lai, T., Steppi, S., Jobb, G., et al. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32, 1363–1371.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marchler-Bauer, A., Zheng, C.J., Chitsaz, F., Derbyshire, M.K., Geer, L.Y., Geer, R.C., Gonzales, N.R., Gwadz, M., Hurwitz, D.I., Lanczycki, C.J., et al. 2013. CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res. 41, D348–352.

    Article  CAS  PubMed  Google Scholar 

  • Martin, M., Barbeyron, T., Martin, R., Portetelle, D., Michel, G., and Vandenbol, M. 2015. The cultivable surface microbiota of the brown alga Ascophyllum nodosum is enriched in macroalgalpolysaccharide- degrading bacteria. Front. Microbiol. 6, 1487.

    Article  PubMed  PubMed Central  Google Scholar 

  • Meier-Kolthoff, J.P., Auch, A.F., Klenk, H.P., and Göker, M. 2013. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14, 60.

    Article  PubMed  PubMed Central  Google Scholar 

  • Mikhailov, I.S., Bukin, Y.S., Zakharova, Y.R., Usoltseva, M.V., Galachyants, Y.P., Sakirko, M.V., Blinov, V.V., and Likhoshway, Y.V. 2019. Co-occurrence patterns between phytoplankton and bacterioplankton across the pelagic zone of Lake Baikal during spring. J. Microbiol. 57, 252–262.

    Article  CAS  PubMed  Google Scholar 

  • Minnikin, D., O’donnell, A., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A., and Parlett, J. 1984. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J. Microbiol. Methods 2, 233–241.

    Article  CAS  Google Scholar 

  • Na, S.I., Kim, Y.O., Yoon, S.H., Ha, S.M., Baek, I., and Chun, J. 2018. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J. Microbiol. 56, 281–285.

    Article  CAS  Google Scholar 

  • Nedashkovskaya, O.I., Kim, S.B., Han, S.K., Lysenko, A.M., Rohde, M., Zhukova, N.V., Falsen, E., Frolova, G.M., Mikhailov, V.V., and Bae, K.S. 2003. Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kutz) Kornm. Int. J. Syst. Evol. Microbiol. 53, 1967–1971.

    Article  CAS  PubMed  Google Scholar 

  • Nedashkovskaya, O.I., Kim, S.B., Han, S.K., Snauwaert, C., Vancanneyt, M., Swings, J., Kim, K.O., Lysenko, A.M., Rohde, M., Frolova, G.M., et al. 2005. Winogradskyella thalassocola gen. nov., sp. nov., Winogradskyella epiphytica sp. nov. and Winogradskyella eximia sp. nov., marine bacteria of the family Flavobacteriaceae. Int. J. Syst. Evol. Microbiol. 55, 49–55.

    Article  CAS  PubMed  Google Scholar 

  • Parada, A.E., Needham, D.M., and Fuhrman, J.A. 2016. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ. Microbiol. 18, 1403–1414.

    Article  CAS  PubMed  Google Scholar 

  • Park, S.H., Kim, J.Y., Kim, Y.J., and Heo, M.S. 2015. Flavobacterium jejuensis sp. nov., isolated from marine brown alga Ecklonia cava. J. Microbiol. 53, 756–761.

    Article  CAS  PubMed  Google Scholar 

  • Park, S. and Yoon, J.H. 2013. Winogradskyella undariae sp. nov., a member of the family Flavobacteriaceae isolated from a brown algae reservoir. Antonie van Leeuwenhoek 104, 619–626.

    Article  CAS  PubMed  Google Scholar 

  • Pruesse, E., Peplies, J., and Glöckner, F.O. 2012. SINA: accurate highthroughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28, 1823–1829.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Richter, M. and Rossello-Mora, R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA 106, 19126–19131.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rzhetsky, A. and Nei, M. 1993. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol. Biol. Evol. 10, 1073–1095.

    CAS  PubMed  Google Scholar 

  • Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425.

    CAS  PubMed  Google Scholar 

  • Sandhya, S., Preetha, K., Nair, A.V., Antony, M.L., and Vijayan, K. 2017. Isolation, characterisation and phylogenetic diversity of culturable bacteria associated with marine microalgae from saline habitats of south India. Aquat. Microb. Ecol. 79, 21–30.

    Article  Google Scholar 

  • Sasser, M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note 101. DE: MIDI Inc, Newark.

  • Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., Lesniewski, R.A., Oakley, B.B., Parks, D.H., Robinson, C.J., et al. 2009. Introducing mothur: open-source, platformindependent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537–7541.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Shin, H., Hong, S.J., Kim, H., Yoo, C., Lee, H., Choi, H.K., Lee, C.G., and Cho, B.K. 2015. Elucidation of the growth delimitation of Dunaliella tertiolecta under nitrogen stress by integrating transcriptome and peptidome analysis. Bioresour. Technol. 194, 57–66.

    Article  CAS  PubMed  Google Scholar 

  • Sirikhachornkit, A., Vuttipongchaikij, S., Suttangkakul, A., Yokthongwattana, K., Juntawong, P., Pokethitiyook, P., Kangvansaichol, K., and Meetam, M. 2016. Increasing the triacylglycerol content in Dunaliella tertiolecta through isolation of starch-deficient mutants. J. Microbiol. Biotechnol. 26, 854–866.

    Article  CAS  PubMed  Google Scholar 

  • Song, J., Jeon, H.T., Lim, Y., Joung, Y., and Cho, J.C. 2018. Winogradskyella aurantiaca sp. nov., isolated from seawater. Int. J. Syst. Evol. Microbiol. 68, 3260–3265.

    Article  CAS  PubMed  Google Scholar 

  • Wang, C., Han, J.R., Liu, C.L., and Du, Z.J. 2018. Winogradskyella tangerina sp. nov., a member of the Flavobacteriaceae isolated from coastal sediment. Int. J. Syst. Evol. Microbiol. 68, 2832–2837.

    Article  CAS  PubMed  Google Scholar 

  • Weisburg, W.G., Barns, S.M., Pelletier, D.A., and Lane, D.J. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173, 697–703.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yao, S., Lyu, S., An, Y., Lu, J., Gjermansen, C., and Schramm, A. 2019. Microalgae–bacteria symbiosis in microalgal growth and biofuel production: a review. J. Appl. Microbiol. 126, 359–368.

    Article  CAS  PubMed  Google Scholar 

  • Yoon, S.H., Ha, S.M., Kwon, S., Lim, J., Kim, Y., Seo, H., and Chun, J. 2017a. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol. 67, 1613–1617.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yoon, S.H., Ha, S.M., Lim, J., Kwon, S., and Chun, J. 2017b. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 110, 1281–1286.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This study was supported by the Collaborative Genome Program of the Korea Institute of Marine Science and Technology Promotion (KIMST) funded by the Ministry of Oceans and Fisheries (MOF) (No. 20180430 to J-CC), and partially by basic research program (NRF-2017R1A6A3A-01076578 to JS) and Science Research Center grant (No. NRF-2018R1A5A1025077 to J-CC) through the National Research Foundation (NRF) funded by the Korean Government (MSIT).

Author information

Author notes

  1. These authors contributed equally to this work

Authors and Affiliations

  1. Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea

    Jaeho Song, Yeonjung Lim, Hye-Jin Jang, Yochan Joung, Ilnam Kang & Jang-Cheon Cho

  2. National Marine Bioenergy Research Center, Department of Biological Engineering, Inha University, Incheon, 22212, Republic of Korea

    Seong-Joo Hong & Choul-Gyun Lee

Authors
  1. Jaeho Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yeonjung Lim
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hye-Jin Jang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yochan Joung
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ilnam Kang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Seong-Joo Hong
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Choul-Gyun Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Jang-Cheon Cho
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jang-Cheon Cho.

Additional information

Supplemental material for this article may be found at http://www.springerlink.com/content/120956.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Song, J., Lim, Y., Jang, HJ. et al. Isolation and genome analysis of Winogradskyella algicola sp. nov., the dominant bacterial species associated with the green alga Dunaliella tertiolecta. J Microbiol. 57, 982–990 (2019). https://doi.org/10.1007/s12275-019-9378-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12275-019-9378-y

Keywords

Search

Navigation