Marine Biodiversity

, Volume 49, Issue 6, pp 2601–2608 | Cite as

Characterization of fungal biodiversity and communities associated with the reef macroalga Sargassum ilicifolium reveals fungal community differentiation according to geographic locality and algal structure

  • Benjamin J. WainwrightEmail author
  • Andrew G. Bauman
  • Geoffrey L. Zahn
  • Peter A. Todd
  • Danwei Huang
Original Paper


Marine environments abound with opportunities to discover new species of fungi even in relatively well-studied ecosystems such as coral reefs. Here, we investigated the fungal communities associated with the canopy forming macroalga Sargassum ilicifolium(Turner) C. Argardh (1820) in Singapore. We collected eight S. ilicifolium thalli from each of eight island locations and separated them into three structures—leaves, holdfast and vesicles. Amplicon sequencing of the fungal internal transcribed spacer 1 (ITS1) and subsequent analyses revealed weak but significant differences in fungal community composition from different structures. Fungal communities were also significantly different among sampling localities, even over relatively small spatial scales (≤ 12 km). Unsurprisingly, all structures from all localities were dominated by unclassified fungi. Our findings demonstrate the potential of marine environments to act as reservoirs of undocumented biodiversity that harbour many novel fungal taxa. These unclassified fungi highlight the need to look beyond terrestrial ecosystems in well-studied regions of the world, and to fully characterize fungal biodiversity in hotspots such as Southeast Asia for better understanding the roles they play in promoting and maintaining life on our planet.


Coral reefs Fungal ITS Marine fungi Microbiome Singapore Southeast Asia 



We thank Jack Darcy for the R script that allows sequence quality information to be ‘reattached’ to the processed ITSx data. Full script can be found at


This study was funded by the National Research Foundation, Prime Minister’s Office, Singapore, under its Marine Science R&D Programme (MSRDP-P03) and The Wildlife Reserves Singapore Conservation Fund (WRSCF). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All applicable permits, international, national and/or institutional guidelines required to perform the work were followed. All samples were collected under permit NP/RP15-009-2a.

Sampling and field studies

All necessary permits for sampling and observational field studies have been obtained by the authors from the competent authorities. The study is compliant with CBD and Nagoya protocols. All samples were collected under permit NP/RP15-009-2a.

Data availability

All sequences associated with this work have been deposited at the National Center for Biotechnology Information ( under BioProject ID: PRJNA504438.

Supplementary material

12526_2019_992_MOESM1_ESM.xlsx (794 kb)
ESM 1 (XLSX 793 kb)


  1. Agogué H, Lamy D, Neal PR, Sogin ML, Herndl GJ (2011) Water mass specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing. Mol Ecol 20:258–274. CrossRefPubMedGoogle Scholar
  2. Ainsworth TD, Thurber RV, Gates DR (2010) The future of coral reefs: a microbial perspective. Trends Ecol Evol 4:233–240. CrossRefGoogle Scholar
  3. Alker AP, Smith GW, Kiho K (2001) Characterization of Aspergillus sydowii (Thom et Church), a fungal pathogen of Caribbean Sea fan corals. Hydrobiologia 460:105–111. CrossRefGoogle Scholar
  4. Allen GR, Werner TB (2000) Coral reef fish assessment in the “coral triangle” of southeastern Asia. Environ Biol Fish 65:209–214CrossRefGoogle Scholar
  5. Amend A, Burgaud G, Cunliffe M, Edgcomb VP, Ettinger CL, Gutiérrez MH, Heitman J, Hom EFY, Ianiri G, Jones AC, Kagami M, Picard KT, Quandt CA, Raghukumar S, Riquelme M, Stajich J, Vargas-Muñiz J, Walker AK, Yarden O, Gladfelter AS (2019a) Fungi in the Marine Environment: Open Questions and Unsolved Problems. mBio Mar 10(2):e01189–18Google Scholar
  6. Amend AS, Cobian GM, Laruson AJ, Remple K, Tucker SJ, Poff KE, Antaky C, Boraks A, Jones CA, Kuehu D, Lensing BR, Pejhanmehr M, Richardson DT, Riley PP (2019b) Phytobiomes are compositionally nested from the ground up. PeerJ 7:e6609. CrossRefPubMedPubMedCentralGoogle Scholar
  7. Archer S, Lee K, Caruso T, Maki T, Lee C, Cowan D, Maestre R, Pointing S (2018) Airborne microbial transport limitation to isolated Antarctic soil habitats. Nat Microbiol. CrossRefGoogle Scholar
  8. Balabanova L, Slepchenko L, Son O, Tekutyeva L (2018) Biotechnology potential of marine Fungi degrading plant and algae polymeric substrates. Front Microbiol 9:1527. CrossRefPubMedPubMedCentralGoogle Scholar
  9. Bengtsson-Palme J et al (2013) Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol Evol.
  10. Blackwell M (2011) The fungi: 1, 2, 3...5.1 million species? Am J Bot 98:426–438. CrossRefPubMedGoogle Scholar
  11. Burgaud D, Meslet-Cladière L, Barbier G, Edgcomb VP (2014) Astonishing fungal diversity in deep-sea hydrothermal ecosystems: an untapped resource of biotechnological potential? In: Outstanding marine molecules: chemistry. Biology, Analysis, pp 85–98. CrossRefGoogle Scholar
  12. Callahan BJ et al (2016) DADA2: high resolution sample inference from Illumina amplicon data. Nat Methods 13:581–583. CrossRefPubMedPubMedCentralGoogle Scholar
  13. Chen H (2018) VennDiagram: generate high-resolution Venn and Euler Plots. R package version 1.6.20.
  14. Chou L, Huang MD, Tan KS, Toh TC, Goh BPL, Tun K (2019) Singapore. In: Sheppard CRC (ed) World seas: an environmental evaluation. Volume II: The Indian Ocean to the Pacific. Academic Press, London, pp 539–558. CrossRefGoogle Scholar
  15. Cole JR et al (2007) The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res 35(suppl 1):D169–D172. CrossRefPubMedGoogle Scholar
  16. Comeau AM, Vincent WF, Bernier L, Lovejoy C (2016) Novel chytrid lineages dominate fungal sequences in diverse marine and fresh water habitats. Sci Rep 6:30120. CrossRefPubMedPubMedCentralGoogle Scholar
  17. Davis NM, Proctor D, Holmes SP, Relman DA, Callahan BJ (2017) Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome. 6:226. CrossRefGoogle Scholar
  18. Deshmukh SK, Prakash V, Ranjan N (2018) Marine fungi: a source of potential anticancer compounds. Front Microbiol 8:2536. CrossRefPubMedPubMedCentralGoogle Scholar
  19. Egan S, Harder T, Burke C, Steinberg P, Thomas T (2013) The seaweed holobiont: understanding seaweed–bacteria interactions. FEMS Microbiol Rev 37:462. CrossRefPubMedGoogle Scholar
  20. Galand PE, Potvin M, Casamayor EO, Lovejoy C (2009) Hydrography shapes bacterial biogeography of the deep Arctic Ocean. Int Soc Microb Ecol 4(4):564–576. CrossRefGoogle Scholar
  21. García Parisi PA, Grimoldi AA, Omacini M (2014) Endophytic fungi of grasses protect other plants from aphid herbivory. Fungal Ecol 9:61–64. CrossRefGoogle Scholar
  22. Gardes M, Bruns TM (1993) ITS primers with enhanced specificity for basidiomycetes—application to the identification of mycorrhizas and rusts. Mol Ecol 2:113–118. CrossRefPubMedPubMedCentralGoogle Scholar
  23. Gin KYH, Lin X, Zhang S (2000) Dynamics and size structure of phytoplankton in the coastal waters of Singapore. J Plankton Res 22:1465–1485. CrossRefGoogle Scholar
  24. Gleason FH, Gadd GM, Pitt JI, Larkum AWD (2017) The roles of endolithic fungi in bioerosion and disease in marine ecosystems. II. Potential facultatively parasitic anamorphic ascomycetes can cause disease in corals and molluscsGoogle Scholar
  25. Gloor GB, Macklaim JM, Pawlowsky-Glahn V, Egozcue JJ (2017) Microbiome datasets are compositional: and this is not optional. Front Microbiol 8.
  26. Gnavi G, Ercole E, Panno L, Vizzini A, Varese GC (2014) Dothideomycetes and Leotiomycetes sterile mycelia isolated from the Italian seagrass Posidonia oceanica based on rDNA data. Springerplus 3:508 CrossRefGoogle Scholar
  27. Gonçalves VN et al (2016) Fungi associated with rocks of the Atacama Desert: taxonomy, distribution, diversity, ecology and bioprospection for bioactive compounds. Environ Microbiol 18:232–235. CrossRefPubMedGoogle Scholar
  28. Haas AF et al (2011) Effects of coral reef benthic primary producers on dissolved organic carbon and microbial activity. PLoS One 6:e27973. CrossRefPubMedPubMedCentralGoogle Scholar
  29. Hernandez-Agreda A, Leggat W, Bongaerts P, Herrera C, Ainsworth TD (2018) Rethinking the coral microbiome: simplicity exists within a diverse microbial biosphere. mBio 9:e00812–e00818. CrossRefPubMedPubMedCentralGoogle Scholar
  30. Huang D, Tun K, Chou LM, Todd PA (2009) An inventory of zooxanthellate scleractinian corals in Singapore including 33 new records. Raffles Bull Zool Sup 22:69–80Google Scholar
  31. Hughes TP, Bellwood DR, Connolly SR (2002) Biodiversity hotspots, centres of endemicity, and the conservation of coral reefs. Ecol Lett 5:775–784. CrossRefGoogle Scholar
  32. Ishino M, Kamauchi H, Takatori K, Kinoshita K (2016) Three novel phomactin-type diterpenes from a marine-derived fungus. Tetrahedron Lett 57:4341–4344. CrossRefGoogle Scholar
  33. Jompa J, McCook LJ (2003) Coral–algal competition: macroalgae with different properties have different effects on corals. Mar Ecol Prog Ser 258:87–95. CrossRefGoogle Scholar
  34. Junker RR, Keller A (2015) Microhabitat heterogeneity across leaves and flower organs promotes bacterial diversity. FEMS Microbiol Ecol 91:1–9. CrossRefGoogle Scholar
  35. Kawaroe M, Sunuddin A, Hwangbo B, Shaumi A (2015) Characteristics and selulotic activities of endophytic fungi in macroalgae (Sargassum sp., Gracilaria sp., Gelidium sp., and Caulerpa sp.) from seagrass habitat in Pari Island, Thousand Islands, Jakarta. International Journal of Sciences: basic and applied research. pp 149-160Google Scholar
  36. Kim JY (2016) Human fungal pathogens: why should we learn? J Microbiol 54:145–148. CrossRefPubMedGoogle Scholar
  37. Kohlmeyer J (1971) Fungi from the Sargasso Sea. Mar Biol 8:344–350CrossRefGoogle Scholar
  38. Leong RC et al (2018) Effect of coral-algal interactions on early life history processes in Pocillopora acuta in a highly disturbed coral reef system. Front Mar Sci.
  39. Loffler Z et al (2018) Holdfasts of Sargassum swartzii are resistant to herbivory and resilient to damage. Coral Reefs 37:1075–1084. CrossRefGoogle Scholar
  40. Low JKY (2015) Sargassum on Singapore’s reefs. PhD Thesis, National University of Singapore. Singapore. Accessed 08/03/2019
  41. Low JKY, Chou LM (1994) Coral reef fish in a sediment stressed environment. Accessed 08 Nov 2018
  42. Low JKY, Fong J, Todd PA, Chou LM, Bauman AG (2019) Seasonal variation of Sargassum ilicifolium (Phaeophyceae) growth on equatorial coral reefs. J Phycol 55:289–296. CrossRefPubMedGoogle Scholar
  43. McCook LJ (2001) Competition between coral and algal turfs along a gradient of terrestrial influence in the nearshorecentral Great Barrier Reef. Coral Reefs 19:419–425CrossRefGoogle Scholar
  44. McMurdie PJ, Holmes S (2013) Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8(4):e61217. CrossRefPubMedPubMedCentralGoogle Scholar
  45. Moree WJ et al (2014) Microbiota of healthy corals are active against fungi in a light-dependent manner. ACS Chem Biol:2300–2308. CrossRefGoogle Scholar
  46. Morrow KM, Paul VJ, Liles MR, Chadwick NE (2011) Allelochemicals produced by Caribbean macroalgae and cyanobacteria have species-specific effects on reef coral microorganisms. Coral Reefs 30:309–320. CrossRefGoogle Scholar
  47. Mortensen B (2013) Plant resistance against herbivory. Nat Educ Knowl 4:5Google Scholar
  48. Nature ecology and evolution (2018) Fungus focus. Nat Ecol Evol 2:1675. CrossRefGoogle Scholar
  49. Nugues M, Smith GW, van Hooidonk RJ (2004) Algal contact as a trigger for coral disease. Ecol Lett 7:919–923. CrossRefGoogle Scholar
  50. Okansen J et al (2016) Vegan: community ecology package. (version 2.4-0). Retrieved from Scholar
  51. Ottesen AR, Peña AG, White JR, Pettengill JB, Li C, Allard S et al (2013) Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato). BMC Microbiol 13:114. CrossRefPubMedPubMedCentralGoogle Scholar
  52. Oyesiku OO, Egunyomi A (2015) Identification and chemical studies of pelagic masses of Sargassum natans (Linnaeus) Gaillon and S. fluitans (Borgessen) Borgesen (brown algae), found offshore in Ondo State, Nigeria. Afr J Biotechnol 13:1188–1193Google Scholar
  53. Pauvert C, Buée M, Laval V, Edel-Hermann V, Fauchery L, Gautier A, Lesur I, Vallance J, Vacher C (2019) Bioinformatics matters: the accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline. Fungal Ecol 41:23–33. CrossRefGoogle Scholar
  54. Peay KG (2016) Dimensions of biodiversity in the earth mycobiome. Nat Rev Microbiol 14:434–447. CrossRefPubMedGoogle Scholar
  55. Picard KT (2017) Coastal marine habitats harbor novel early-diverging fungal diversity. Fungal Ecol 23:1–13. CrossRefGoogle Scholar
  56. Prasannarai K, Sridhar KR (2001) Diversity and abundance of higher marine fungi on woody substrates along the west coast of India. Curr Sci India 81:304–311Google Scholar
  57. Pratte ZA, Longo GO, Burns AS, Hay ME, Stewart FJ (2017) Contact with turf algae alters the coral microbiome: contact versus systemic impacts. Coral Reefs 37:1–13. CrossRefGoogle Scholar
  58. Rasher DB, Stout P, Engel S, Kubanek J, Hay ME (2011) Macroalgal terpenes function as allelopathic agents against reef corals. Proc Natl Acad Sci U S A 108:17726–17731CrossRefGoogle Scholar
  59. Rédou V, Navarri M, Meslet-Cladière L, Barbier G, Burgaud G (2015) Species richness and adaptation of marine fungi from deep-subseafloor sediments. Appl Environ Microbiol 81:3571–3583. CrossRefPubMedPubMedCentralGoogle Scholar
  60. Richards TA, Jones DMM, Leonard G, Bass D (2012) Marine fungi: their ecology and molecular diversity. Annu Rev Mar Sci 4:495–522. CrossRefGoogle Scholar
  61. Robinson CH (2001) Cold adaptation in Arctic and Antarctic fungi. New Phytol 151:341–353. CrossRefGoogle Scholar
  62. Russell JR et al (2011) Biodegradation of polyester polyurethane by endophytic fungi. Appl Environ Microbiol 17:6076–6084. CrossRefGoogle Scholar
  63. Rützler K, Santavy DL (1983) The black band disease of Atlantic corals. Mar Ecol. CrossRefGoogle Scholar
  64. Smith DP, Peay KG (2014) Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing. PLoS One 9:e90234. CrossRefGoogle Scholar
  65. Széchy MTM, Guedes PM, Baeta-Neves MH, Oliveira EN (2012) Verification of Sargassum natans (Linnaeus) Gaillon (Heterokontophyta: Phaeophyceae) from the Sargasso Sea off the coast of Brazil, western Atlantic Ocean. Checklist 8:638–641. CrossRefGoogle Scholar
  66. Tanentzap AJ, Vicari M, Bazely DR (2014) Ungulate saliva inhibits a grass–endophyte mutualism. Biol Lett 10:20140460. CrossRefPubMedPubMedCentralGoogle Scholar
  67. Tanzil JTI, Goodkin NF, Sin TM, Chen MT, Fabbro GN, Boyle EA, Lee AC, Toh KB (2019) Multi-colony coral skeletal Ba/Ca from Singapore’s turbid urban reefs: relationship with contemporaneous in-situ seawater parameters. Geochim Cosmochim Acta 250:191–208. CrossRefGoogle Scholar
  68. Tedersoo L, Toomin-Klunderud A, Anslan S (2018) PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives. New Phytol 217:1370–1385. CrossRefPubMedGoogle Scholar
  69. Tun KPP (2012) Optimisation of reef survey methods and application of reef metrics and biocriteria for the monitoring of sediment-impacted reefs. PhD Thesis, Department of Biological Sciences, National University of SingaporeGoogle Scholar
  70. Vijaykrishna D, Jeewon R, Hyde KD (2006) Molecular taxonomy, origins and evolution of freshwater Ascomycetes. Fungal Divers 23:351–390Google Scholar
  71. Wainwright BJ et al (2017) Fungi associated with mesophotic macroalgae from the ‘Au‘au Channel, west Maui are differentiated by host and overlap terrestrial communities. PeerJ 5:e3532. CrossRefPubMedPubMedCentralGoogle Scholar
  72. Wainwright BJ et al (2018) Seagrass-associated fungal communities follow Wallace’s line, but host genotype does not structure fungal community. J Biogeograpy:1–9. CrossRefGoogle Scholar
  73. Wang M, Hu C (2016a) Mapping and quantifying Sargassum distribution and coverage in the Central West Atlantic using MODIS observations. Remote Sens Environ 183:350–367. CrossRefGoogle Scholar
  74. Wang M, Hu C (2016b) Predicting Sargassum blooms in the Caribbean Sea from MODIS observations. Geophys Res Lettv 44:3265–3273. CrossRefGoogle Scholar
  75. Weldon C, du Preez LH, Hyatt AD, Muller R, Speare R (2004) Origin of the amphibian chytrid fungus. Emerg Infect Dis 10:2100–2105. CrossRefPubMedPubMedCentralGoogle Scholar
  76. White TJ, Bruns TD, Lee SB, Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH (eds) PCR protocols: a guide to methods and applications. Academic Press, London, pp 315–322Google Scholar
  77. Yip ZT et al (2018) Diversity and phylogeny of Sargassum (Fucales, Phaeophyceae) in Singapore. Phytotaxa. CrossRefGoogle Scholar

Copyright information

© Senckenberg Gesellschaft für Naturforschung 2019

Authors and Affiliations

  • Benjamin J. Wainwright
    • 1
    Email author
  • Andrew G. Bauman
    • 1
  • Geoffrey L. Zahn
    • 2
  • Peter A. Todd
    • 1
  • Danwei Huang
    • 1
    • 3
  1. 1.Department of Biological SciencesNational University of SingaporeSingaporeSingapore
  2. 2.Biology DepartmentUtah Valley UniversityOremUSA
  3. 3.Tropical Marine Science InstituteNational University of SingaporeSingaporeSingapore

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