Biodiversity of endolithic fungi in coral skeletons and other reef substrates revealed with 18S rDNA metabarcoding


Corals live in close association with a diverse community of eukaryotes, bacteria, archaea and viruses that, together with the coral host, form the coral holobiont. Fungi are an important component of the coral holobiont; however, knowledge about their taxonomic diversity and the ecological functions these organisms play in reef corals is still scarce. In this study, we used metabarcoding to characterize the fungal community inhabiting the skeleton of eleven coral genera, as well as samples of crustose coralline algae, from Australia and Papua New Guinea. Most of the 24 distinct fungal genera identified were assigned to the phylum Ascomycota, followed by Basidiomycota. Lulworthia and Lulwoana (Ascomycota) were the most abundant and prevalent genera detected in our study. Besides these widely distributed genera, others never associated with corals or marine environments before, such as Geranomyces (Chytriomycota), Flammulina (Basidiomycota) and Ophiosphaerella (Ascomycota), were also detected. The predicted functional groups give insights into potential lifestyles and ecological functions of the fungal community in reef ecosystems. This study provides important observational data on a group of holobiont members that has received little attention.

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The authors would like to thank the Graduate Programs in Microbiology ( and Bioinformatics ( AG–N received a productivity research grant (no. 310764/2016-5) from the National Council for Scientific and Technological Development ( VRM is supported by the Sydney Medical School Foundation. This work was supported by the Australian Biological Resources Study (RFL213-08).

Author information

VRM and HV collected the samples and performed the amplifications and sequencing experiments. FB conceptualized the study and wrote the paper. FFS performed the bioinformatic analyses. AG–N supervised the analyses and contributed in all the steps of the study. All the authors contributed with the data analyses and with the manuscript written.

Correspondence to Fernanda Badotti.

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Góes-Neto, A., Marcelino, V.R., Verbruggen, H. et al. Biodiversity of endolithic fungi in coral skeletons and other reef substrates revealed with 18S rDNA metabarcoding. Coral Reefs 39, 229–238 (2020).

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  • Fungal diversity
  • Coral
  • Reef substrates
  • Metabarcoding
  • Mycobiome
  • Endolithic