Skip to main content
Log in

Preliminary analyses of cultured Symbiodinium isolated from sand in the oceanic Ogasawara Islands, Japan

  • Original paper
  • Published:
Marine Biodiversity Aims and scope Submit manuscript


The dinoflagellate genus Symbiodinium is generally found in many tropical and subtropical marine invertebrates. Recently, reports have focused on free-living types. We examined free-living Symbiodinium from the Ogasawara (Bonin) Islands, a group of oceanic islands south of Japan. Examining sand samples, seven of eight initial isolates were successfully cultured. Genetic analyses of 18S, 28S and internal transcribed spacer (ITS) ribosomal DNA regions reveal that one isolate cultured with only IMK was identical to clade A isolated from coral reef sand in Okinawa, and four additional isolates cultured with only IMK comprised a new clade A lineage. Additionally, two isolates cultured with IMK and soil extract were closely related to a little-known divergent lineage within clade D. Our results demonstrate some free-living Symbiodinium types may have very wide distributions, and that utilizing different culturing techniques will further discovery of unique Symbiodinium lineages from environmental samples.

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

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

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

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others


  • Adams LM, Cumbo VR, Takabayashi M (2009) Exposure to sediment enhances primary acquisition of Symbiodinium by asymbiotic coral larvae. Mar Ecol Prog Ser 377:149–156

    Article  Google Scholar 

  • Andersen RA, Kawachi M (2005) Traditional microalgae isolation techniques. In: Andersen RA (ed) Algal culture techniques. Academic Press, Hong Kong, pp 83–100

    Chapter  Google Scholar 

  • Baillie BK, Belda-Baillie CA, Maruyama T (2000) Conspecificity and Indo-Pacific distribution of Symbiodinium genotypes (Dinophyceae) from giant clams. J Phycol 36:1153–1161

    Article  CAS  Google Scholar 

  • Carlos AA, Baillie BK, Kawachi M, Maruyama T (1999) Phylogenetic position of Symbiodinium (Dinophyceae) isolates from tridacnids (Bivalvia), cardiids (Bivalvia), a sponge (Porifera), a soft coral (Anthozoa), and a free-living strain. J Phycol 35:1054–1062

    Article  CAS  Google Scholar 

  • Coffroth MA, Lewis CL, Santos SR, Weaver JL (2006) Environmental populations of symbiotic dinoflagellates in the genus Symbiodinium can initiate symbiosis with reef cnidarians. Curr Biol 16:R985–R988

    Article  CAS  PubMed  Google Scholar 

  • Correa AMS, Baker AC (2009) Understanding diversity in coral-algal symbiosis: a cluster-based approach to interpreting fine-scale genetic variation in the genus Symbiodinium. Coral Reefs 28:81–93

    Article  Google Scholar 

  • Garren M, Walsh SM, Caccone A, Knowlton N (2006) Patterns of association between Symbiodinium and members of the Montastraea annularis species complex on spatial scales ranging from within colonies to between geographic regions. Coral Reefs 25:503–512

    Article  Google Scholar 

  • Gou WL, Sun J, Li XQ, Zhen Y, Xin Z, Yu ZG, Li RX (2003) Phylogenetic analysis of a free-living strain of Symbiodinium isolated from Jiaozhou Bay, P.R. China. J Exp Mar Biol Ecol 296:135–144

    Article  CAS  Google Scholar 

  • Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biol 52:696–704

    Article  Google Scholar 

  • Hirose M, Reimer JD, Hidaka M, Suda S (2008) Phylogenetic analyses of potentially free-living Symbiodinium spp. from coral reef sand in Okinawa, Japan. Mar Biol 155:105–112

    Article  Google Scholar 

  • Hunter RL, LaJeunesse TC, Santos SR (2007) Structure and evolution of the rDNA internal transcribed spacer (ITS) region 2 in the symbiotic dinoflagellates (Symbiodinium, Dinophyta). J Phycol 43:120–128

    Article  CAS  Google Scholar 

  • Kasai F, Kawachi M, Erata M, Mori F, Yumoto K, Sto M, Ishimoto M (2009) NIES-collection, list of strains, 8th edn. Jpn J Phycol 57(Suppl):1–350

    Google Scholar 

  • Koike K, Yamashita H, Oh-Uchi A, Tamaki M, Hayashibara T (2007) A quantitative real-time PCR method for monitoring Symbiodinium in the water column. Galaxea JCRS 9:1–12

    Article  Google Scholar 

  • LaJeunesse TC (2001) Investigating the biodiversity, ecology, and phylogeny of endosymbiotic dinoflagellates of the genus Symbiodinium using the ITS region: in search of a ‘species’ level marker. J Phycol 37:866–880

    Article  CAS  Google Scholar 

  • LaJeunesse TC (2002) Diversity and community structure of symbiotic dinoflagellates from Caribbean coral reefs. Mar Biol 141:387–400

    Article  Google Scholar 

  • LaJeunesse TC (2005) “Species” radiations of symbiotic dinoflagellates in the Atlantic and Indo-Pacific since the Miocene-Pliocene transition. Mol Biol Evol 22:570–581

    Article  CAS  PubMed  Google Scholar 

  • LaJeunesse TC, Loh WKW, van Woesik R, Hoegh-Guldberg O, Schmidt GW, Fitt WK (2003) Low symbiont diversity in southern Great Barrier Reef corals, relative to those of the Caribbean. Limnol Oceanogr 48:2046–2054

    Article  Google Scholar 

  • LaJeunesse TC, Bhagooli R, Hidaka M, deVantier L, Done T, Schmidt GW, Fitt WK, Hoegh-Guldberg O (2004) Closely-related Symbiodinium spp. differ in relative dominance in coral reef host communities across environmental, latitudinal, and biogeographic gradients. Mar Ecol Prog Ser 284:147–161

    Article  Google Scholar 

  • Lee JJ, Wray CG, Lawrence C (1995) Could foraminiferal Symbiodinium be derived from environmental pools contributed to by different coelenterate hosts? Acta Protozool 34:75–85

    CAS  Google Scholar 

  • Littman RA, van Oppen MJH, Willis BL (2008) Methods for sampling free-living Symbiodinium (zooxanthellae) and their distribution and abundance at Lizard Island (Great Barrier Reef). J Exp Mar Biol Ecol 364:48–53

    Article  Google Scholar 

  • Manning MM, Gates RD (2008) Diversity in populations of free-living Symbiodinium from a Caribbean and Pacific reef. Limnol Oceanogr 53:1853–1861

    Google Scholar 

  • Moestrup O, Daugbjerg N (2007) On dinoflagellate phylogeny and classification. In: Brodie J, Lewis J (eds) Unravelling the algae: the past, present, and future of algae systematics. CRC Press, Boca Raton, pp 215–230

    Google Scholar 

  • Moore RB (2006) Molecular ecology and phylogeny of protistan algal symbionts from corals. Ph.D. thesis, University of Sydney, Sydney, p 390

  • Pawlowski J, Holzmann M, Fahrni JF, Pochon X, Lee JJ (2001) Molecular identification of algal endosymbionts in large miliolid Foraminifera: 2. Dinoflagellates. J Eukaryot Microbiol 48:368–373

    Article  CAS  PubMed  Google Scholar 

  • Pochon X, Pawlowski J, Zaninetti L, Rowan RG (2001) High genetic diversity and relative specificity among Symbiodinium-like endosymbiotic dinoflagellates in soritid foraminiferans. Mar Biol 139:1069–1078

    Article  Google Scholar 

  • Pochon X, LaJeunesse TC, Pawlowski J (2004) Biogeographic partitioning and host specialization among foraminiferan dinoflagellate symbionts (Symbiodinium; Dinophyta). Mar Biol 146:17–27

    Article  Google Scholar 

  • Porto I, Granados C, Restropo JC, Sanchez JA (2008) Macroalgal-associated dinoflagellates belonging to the genus Symbiodinium in Caribbean reefs. PLoS One 3:e2160

    Article  PubMed  Google Scholar 

  • Reimer JD, Todd PA (2009) Preliminary molecular examination of zooxanthellate zoanthid (Hexacorallia, Zoantharia) and associated zooxanthellae (Symbiodinium spp.) diversity in Singapore. Raffles Bull Zool Suppl 22:103–120

    Google Scholar 

  • Reimer JD, Takishita K, Ono S, Maruyama T, Tsukahara J (2006) Latitudinal and intracolony ITS-rDNA sequence variation in the symbiotic dinoflagellate genus Symbiodinium (Dinophyceae) in Zoanthus sansibaricus (Anthozoa: Hexacorallia). Phycol Res 54:122–132

    Article  CAS  Google Scholar 

  • Rodriguez F, Oliver JL, Marin A, Medina JR (1990) The general stochastic model of nucleotide substitution. J Theor Biol 142:485–501

    Article  CAS  PubMed  Google Scholar 

  • Ronquist F, Huelsenbeck JP (2003) Bayesian phylogenetic inference under mixed models. Bioinformatics (Oxford) 19:1572–1574

    Article  CAS  Google Scholar 

  • Rowan R, Knowlton N (1995) Intraspecific diversity and ecological zonation in coral-algal symbiosis. Proc Natl Acad Sci USA 92:2850–2853

    Article  CAS  PubMed  Google Scholar 

  • Ruiz Sebastian C, Sink KJ, McClanahan TR, Cowan DA (2009) Bleaching response of corals and their Symbiodinium communities in southern Africa. Mar Biol 156:2049–2062

    Article  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Santos SR, Taylor DJ, Coffroth MA (2001) Genetic comparisons of freshly isolated versus cultured symbiotic dinoflagellates: implications for extrapolating to the intact symbiosis. J Phycol 37:900–912

    Article  CAS  Google Scholar 

  • Santos SR, Taylor DJ, Kinzie RAIII, Hidaka M, Sakai K, Coffroth MA (2002) Molecular phylogeny of symbiotic dinoflagellates inferred from partial chloroplast large subunit (23S)-rDNA sequences. Mol Phylogenet Evol 23:97–111

    Article  CAS  PubMed  Google Scholar 

  • Santos SR, Kinzie RA III, Sakai K, Coffroth MA (2003) Molecular characterization of nuclear small subunit (18S)-rDNA pseudogenes in a symbiotic dinoflagellate (Symbiodinium, Dinophyta). J Eukaryot Microbiol 50:417–421

    Article  CAS  PubMed  Google Scholar 

  • Swofford D (2000) PAUP* 4.0b7a, Phylogenetic analysis using parsimony (*and other methods). Sinauer, Sunderland

  • Takano Y, Horiguchi T (2005) Acquiring scanning electron microscopical, light microscopical, and multiple gene sequence data from a single dinoflagelate cell. J Phycol 42:251–256

    Article  Google Scholar 

  • Thornhill DJ, LaJeunesse TC, Santos SR (2007) Measuring rDNA diversity in eukaryotic microbial systems: how intragenomic variation, pseudogenes, and PCR artifacts confound biodiversity estimates. Mol Ecol 16:5326–5340

    Article  CAS  PubMed  Google Scholar 

  • Toller WW, Rowan R, Knowlton N (2001) Zooxanthellae of the Montastraea annularis species complex: patterns of distribution of four taxa of Symbiodinium on different reefs and across depths. Biol Bull 201:348–359

    Article  CAS  PubMed  Google Scholar 

  • Tsuchiya M, Nadaoka K, Kayanne H, Yamano H (eds) (2004) Coral reefs of Japan. Ministry of the Environment, Tokyo

Download references


Sampling in the Ogasawara Islands was made possible by a permit for collection of aquatic organisms by scuba diving from the Government of Tokyo (no. 21–12). In Ogasawara, Mr. Tetsuro Sasaki (Institute of Boninology) greatly helped with logistics. Mr. Tadao Sato and Mr. Nobuyuki Niijima (Captain, Kaiyou Maru) of the Japan Fisheries Cooperatives, Ogasawara-jima aided in sample collection. F.S. was partially supported by a Japan Society for the Promotion of Science (JSPS) post-doctoral fellowship (P07812). J.D.R. was supported in part by the Rising Star Program at the University of the Ryukyus, and a JSPS “Wakate B” grant-in-aid. K.Y. was supported in part by a Research Institute of Marine Invertebrates Foundation (RIMI) grant. The authors thank Dr. Todd LaJeunesse and an anonymous reviewer for their constructive comments that greatly improved this manuscript.

Ethical standards and conflict of interest

All experiments in this study comply with the current laws of the country in which they were performed. The authors declare that they have no conflict of interest.

Author information

Authors and Affiliations


Corresponding author

Correspondence to James Davis Reimer.

Electronic supplementary material

Fig. S1

ML tree of 28S-rDNA sequences for Symbiodinium, including specimens from this study. Values at branches represent ML and NJ bootstrap probabilities, respectively. Monophylies with more than 95% Bayesian posterior probabilities are shown by thick branches. New isolates and sequences from this study in bold. Sequences used in the alignment for this tree are in Table 1 (JPEG 54 kb)

High resolution image. (EPS 338 kb)

Fig. S2

ML tree of the ITS-rDNA sequences for Symbiodinium, including specimens from this study. Values at branches represent ML and NJ bootstrap probabilities, respectively. Monophylies with more than 95% Bayesian posterior probabilities are shown by thick branches. New isolates and sequences from this study in bold. Sequences used in the alignment for this tree are in Table 1 (JPEG 58 kb)

High resolution image (EPS 374 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Reimer, J.D., Shah, M.M.R., Sinniger, F. et al. Preliminary analyses of cultured Symbiodinium isolated from sand in the oceanic Ogasawara Islands, Japan. Mar Biodiv 40, 237–247 (2010).

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: