Characterization of fungal biodiversity and communities associated with the reef macroalga Sargassum ilicifolium reveals fungal community differentiation according to geographic locality and algal structure
- 107 Downloads
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.
KeywordsCoral 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 https://github.com/gzahn/Sargassum_Fungi/blob/master/R/itsx_fastq_extractor.r
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.
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.
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.
- 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
- 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 CrossRefPubMedPubMedCentralGoogle Scholar
- 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
- 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 CrossRefGoogle Scholar
- 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 CrossRefGoogle Scholar
- 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 CrossRefPubMedPubMedCentralGoogle Scholar
- 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
- 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
- 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
- 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
- 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
- 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
- Mortensen B (2013) Plant resistance against herbivory. Nat Educ Knowl 4:5Google Scholar
- Okansen J et al (2016) Vegan: community ecology package. (version 2.4-0). Retrieved from https://CRAN.R-project.org/package=veganGoogle Scholar
- 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
- 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 CrossRefGoogle Scholar
- 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
- 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 CrossRefGoogle Scholar
- 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 CrossRefGoogle Scholar
- 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 CrossRefGoogle Scholar
- 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
- Vijaykrishna D, Jeewon R, Hyde KD (2006) Molecular taxonomy, origins and evolution of freshwater Ascomycetes. Fungal Divers 23:351–390Google Scholar
- 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