Abstract
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.
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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. https://doi.org/10.1111/j.1365-294X.2010.04932.x
Ainsworth TD, Thurber RV, Gates DR (2010) The future of coral reefs: a microbial perspective. Trends Ecol Evol 4:233–240. https://doi.org/10.1016/j.tree.2009.11.001
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. https://doi.org/10.1023/A:1013145524136
Allen GR, Werner TB (2000) Coral reef fish assessment in the “coral triangle” of southeastern Asia. Environ Biol Fish 65:209–214
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):e01189–18
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. https://doi.org/10.7717/peerj.6609
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. https://doi.org/10.1038/s41564-019-0370-4
Balabanova L, Slepchenko L, Son O, Tekutyeva L (2018) Biotechnology potential of marine Fungi degrading plant and algae polymeric substrates. Front Microbiol 9:1527. https://doi.org/10.3389/fmicb.2018.01527
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. https://doi.org/10.1111/2041-210X.12073
Blackwell M (2011) The fungi: 1, 2, 3...5.1 million species? Am J Bot 98:426–438. https://doi.org/10.3732/ajb.1000298
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. https://doi.org/10.1002/9783527681501.ch04
Callahan BJ et al (2016) DADA2: high resolution sample inference from Illumina amplicon data. Nat Methods 13:581–583. https://doi.org/10.1038/nmeth.3869
Chen H (2018) VennDiagram: generate high-resolution Venn and Euler Plots. R package version 1.6.20. https://CRAN.R-project.org/package=VennDiagram
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. https://doi.org/10.1016/B978-0-08-100853-9.00031-2
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. https://doi.org/10.1093/nar/gkl889
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. https://doi.org/10.1038/srep30120
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. https://doi.org/10.1186/s40168-018-0605-2
Deshmukh SK, Prakash V, Ranjan N (2018) Marine fungi: a source of potential anticancer compounds. Front Microbiol 8:2536. https://doi.org/10.3389/fmicb.2017.02536
Egan S, Harder T, Burke C, Steinberg P, Thomas T (2013) The seaweed holobiont: understanding seaweed–bacteria interactions. FEMS Microbiol Rev 37:462. https://doi.org/10.1111/1574-6976.12011
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. https://doi.org/10.1038/ismej.2009.134
García Parisi PA, Grimoldi AA, Omacini M (2014) Endophytic fungi of grasses protect other plants from aphid herbivory. Fungal Ecol 9:61–64. https://doi.org/10.1016/j.funeco.2014.01.004
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. https://doi.org/10.1111/j.1365-294X.1993.tb00005.x
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. https://doi.org/10.1093/plankt/22.8.1465
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 molluscs
Gloor GB, Macklaim JM, Pawlowsky-Glahn V, Egozcue JJ (2017) Microbiome datasets are compositional: and this is not optional. Front Microbiol 8. https://doi.org/10.3389/fmicb.2017.02224
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 http://www.springerplus.com/content/3/1/508
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. https://doi.org/10.1111/1462-2920.13005
Haas AF et al (2011) Effects of coral reef benthic primary producers on dissolved organic carbon and microbial activity. PLoS One 6:e27973. https://doi.org/10.1371/journal.pone.0027973
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. https://doi.org/10.1128/mBio.00812-18
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 22:69–80
Hughes TP, Bellwood DR, Connolly SR (2002) Biodiversity hotspots, centres of endemicity, and the conservation of coral reefs. Ecol Lett 5:775–784. https://doi.org/10.1046/j.1461-0248.2002.00383.x
Ishino M, Kamauchi H, Takatori K, Kinoshita K (2016) Three novel phomactin-type diterpenes from a marine-derived fungus. Tetrahedron Lett 57:4341–4344. https://doi.org/10.1016/j.tetlet.2016.08.016
Jompa J, McCook LJ (2003) Coral–algal competition: macroalgae with different properties have different effects on corals. Mar Ecol Prog Ser 258:87–95. https://doi.org/10.3354/meps258087
Junker RR, Keller A (2015) Microhabitat heterogeneity across leaves and flower organs promotes bacterial diversity. FEMS Microbiol Ecol 91:1–9. https://doi.org/10.1093/femsec/fiv097
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 149-160
Kim JY (2016) Human fungal pathogens: why should we learn? J Microbiol 54:145–148. https://doi.org/10.1007/s12275-016-0647-8
Kohlmeyer J (1971) Fungi from the Sargasso Sea. Mar Biol 8:344–350
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. https://doi.org/10.3389/fmars.2018.00385
Loffler Z et al (2018) Holdfasts of Sargassum swartzii are resistant to herbivory and resilient to damage. Coral Reefs 37:1075–1084. https://doi.org/10.1007/s00338-018-01745-w
Low JKY (2015) Sargassum on Singapore’s reefs. PhD Thesis, National University of Singapore. Singapore. https://scholarbank.nus.edu.sg/handle/10635/118571. Accessed 08/03/2019
Low JKY, Chou LM (1994) Coral reef fish in a sediment stressed environment. http://coralreef.nus.edu.sg/publications/Low1994LIPI_JSPS.pdf. Accessed 08 Nov 2018
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. https://doi.org/10.1111/jpy.12818
McCook LJ (2001) Competition between coral and algal turfs along a gradient of terrestrial influence in the nearshorecentral Great Barrier Reef. Coral Reefs 19:419–425
McMurdie PJ, Holmes S (2013) Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8(4):e61217. https://doi.org/10.1371/journal.pone.0061217
Moree WJ et al (2014) Microbiota of healthy corals are active against fungi in a light-dependent manner. ACS Chem Biol:2300–2308. https://doi.org/10.1021/cb500432j
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. https://doi.org/10.1007/s00338-011-0747-1
Mortensen B (2013) Plant resistance against herbivory. Nat Educ Knowl 4:5
Nature ecology and evolution (2018) Fungus focus. Nat Ecol Evol 2:1675. https://doi.org/10.1038/s41559-018-0721-1
Nugues M, Smith GW, van Hooidonk RJ (2004) Algal contact as a trigger for coral disease. Ecol Lett 7:919–923. https://doi.org/10.1111/j.1461-0248.2004.00651.x
Okansen J et al (2016) Vegan: community ecology package. (version 2.4-0). Retrieved from https://CRAN.R-project.org/package=vegan
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. https://doi.org/10.1186/1471-2180-13-114
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 13:1188–1193
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. https://doi.org/10.1016/j.funeco.2019.03.005
Peay KG (2016) Dimensions of biodiversity in the earth mycobiome. Nat Rev Microbiol 14:434–447. https://doi.org/10.1038/nrmicro.2016.59
Picard KT (2017) Coastal marine habitats harbor novel early-diverging fungal diversity. Fungal Ecol 23:1–13. https://doi.org/10.1016/j.funeco.2016.10.006
Prasannarai K, Sridhar KR (2001) Diversity and abundance of higher marine fungi on woody substrates along the west coast of India. Curr Sci India 81:304–311
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. https://doi.org/10.1007/s00338-017-1615-4
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 108:17726–17731
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. https://doi.org/10.1128/AEM.04064-14
Richards TA, Jones DMM, Leonard G, Bass D (2012) Marine fungi: their ecology and molecular diversity. Annu Rev Mar Sci 4:495–522. https://doi.org/10.1146/annurev-marine-120710-100802
Robinson CH (2001) Cold adaptation in Arctic and Antarctic fungi. New Phytol 151:341–353. https://doi.org/10.1046/j.1469-8137.2001.00177.x
Russell JR et al (2011) Biodegradation of polyester polyurethane by endophytic fungi. Appl Environ Microbiol 17:6076–6084. https://doi.org/10.1128/AEM.00521-11
Rützler K, Santavy DL (1983) The black band disease of Atlantic corals. Mar Ecol. https://doi.org/10.1111/j.1439-0485.1983.tb00116.x
Smith DP, Peay KG (2014) Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing. PLoS One 9:e90234. https://doi.org/10.1371/journal.pone.0090234
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. https://doi.org/10.15560/8.4.638
Tanentzap AJ, Vicari M, Bazely DR (2014) Ungulate saliva inhibits a grass–endophyte mutualism. Biol Lett 10:20140460. https://doi.org/10.1098/rsbl.2014.0460
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. https://doi.org/10.1016/j.gca.2019.01.034
Tedersoo L, Toomin-Klunderud A, Anslan S (2018) PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives. New Phytol 217:1370–1385. https://doi.org/10.1111/nph.14776
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 Singapore
Vijaykrishna D, Jeewon R, Hyde KD (2006) Molecular taxonomy, origins and evolution of freshwater Ascomycetes. Fungal Divers 23:351–390
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. https://doi.org/10.7717/peerj.3532
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. https://doi.org/10.1111/jbi.13168
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. https://doi.org/10.1016/j.rse.2016.04.019
Wang M, Hu C (2016b) Predicting Sargassum blooms in the Caribbean Sea from MODIS observations. Geophys Res Lettv 44:3265–3273. https://doi.org/10.1002/2017GL072932
Weldon C, du Preez LH, Hyatt AD, Muller R, Speare R (2004) Origin of the amphibian chytrid fungus. Emerg Infect Dis 10:2100–2105. https://doi.org/10.3201/eid1012.030804
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 315–322
Yip ZT et al (2018) Diversity and phylogeny of Sargassum (Fucales, Phaeophyceae) in Singapore. Phytotaxa. https://doi.org/10.11646/phytotaxa.369.3.3
Acknowledgments
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 https://github.com/gzahn/Sargassum_Fungi/blob/master/R/itsx_fastq_extractor.r
Funding
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.
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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.
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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.
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All sequences associated with this work have been deposited at the National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov/bioproject/) under BioProject ID: PRJNA504438.
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Wainwright, B.J., Bauman, A.G., Zahn, G.L. et al. Characterization of fungal biodiversity and communities associated with the reef macroalga Sargassum ilicifolium reveals fungal community differentiation according to geographic locality and algal structure. Mar. Biodivers. 49, 2601–2608 (2019). https://doi.org/10.1007/s12526-019-00992-6
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DOI: https://doi.org/10.1007/s12526-019-00992-6