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eDNA metabarcoding illuminates species diversity and composition of three phyla (chordata, mollusca and echinodermata) across Indonesian coral reefs

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Abstract

Environmental DNA (eDNA) metabarcoding is an evolving tool that can provide broader assessments of marine biodiversity than conventional visual census methods. The outputs of this approach are, therefore, crucial to provide data for conservation priorities and to support fisheries management. We conducted a study using eDNA metabarcoding to understand the distribution of marine biodiversity across Indonesia and to investigate the abundance of three major phyla that comprise a majority of marine biodiversity. In this study, a total of 13,819,634 reads corresponding to 23,252 unique sequences belonging to the phyla Chordata, Mollusca, and Echinodermata were generated from COI amplicons obtained from 92 seawater eDNA samples collected from nine locations and 17 sites. Beta diversity differed significantly across locations (PERMANOVA: p < 0.05) based on Bray–Curtis and Jaccard indices. Taxa of interest were not distributed equally and there were no discernible patterns detected across the sampling area. This might be due to the highly variable percentage of sequenced species between families, preventing robust estimation of species richness. Overall, 45% of reads were identified to species level while 55% were classified as unidentified taxa. Interestingly, the percentage of unidentified taxa was similar between two locations with distinct characteristics representing eastern and western extremities of the sampling region. Despite a relatively poor rate of assignment to species level, our results highlight unprecedented levels of marine biodiversity and strong differences in species composition. This further supports the contention that the eDNA approach is a sensitive method that can provide useful data, in particular to detect changes in species composition. Importantly, this method is clearly advantageous to evaluate marine biodiversity on a large scale and can provide data to support region-wide coral reef management strategies. Knowing species diversity and the degree to which various taxa are distributed is a fundamental for advancing our knowledge of marine ecology and can play an important role in forecasting population dynamics and evolution as well as in refining conservation practices.

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Acknowledgements

The authors thank the Ministry of Research and Technology (Ristek/BRIN) for supporting the research entitled “Population genomics to estimate distribution pattern and larval distances of economically fish using environmental DNA to support food security and fisheries conservation”; the Institute of Research and Community Service (LPPM) IPB University for undertaking the research administration; the Laboratory of Marine Biodiversity and Biosystematics IPB University, Scientific Diving Laboratory IPB University, and Oceanogen Laboklinikum for the use of their research logistics and facilities.

Funding

This study was funded by the Ministry of Research and Technology (Ristek/BRIN) through a grant to Hawis Madduppa under Agreement No. 3988/IT3.L1/PN/2020.

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Authors and Affiliations

  1. Department of Marine Science and Technology, Faculty of Fisheries and Marine Sciences, IPB University, Jl. Agathis No. 1, Bogor, 16680, West Java, Indonesia

    Hawis Madduppa, Beginer Subhan, Dondy Arafat & Dietriech Geoffrey Bengen

  2. Yayasan Biodiversitas Indonesia (Bionesia), Jl. Tukad Balian No. 121, Denpasar, 80226, Bali, Indonesia

    Ni Kadek Dita Cahyani & Aji Wahyu Anggoro

  3. Marine Science Study Program, Department of Fisheries and Marine Science, Faculty of Agriculture, University of Mataram, Lombok, Mataram, West Nusa Tenggara, Indonesia

    Edwin Jefri

  4. Oceanogen Environmental Biotechnology Laboklinikum, Jl. Cemara III no. 34, Bogor, 16111, West Java, Indonesia

    Hawis Madduppa & Lalu M. Iqbal Sani

  5. Faculty of Fisheries and Marine Sciences, Universitas Khairun, Jl. Jusuf Abdulrahman, Ternate, 97719, North Maluku, Indonesia

    Nebuchadnezzar Akbar

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  1. Hawis Madduppa
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  2. Ni Kadek Dita Cahyani
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  3. Aji Wahyu Anggoro
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  8. Nebuchadnezzar Akbar
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  9. Dietriech Geoffrey Bengen
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Contributions

HM conceived the research idea; HM, BS and DGB designed the methodology; HM, DA, EJ, LMIS, NA and BS collected field data; HM and LMIS performed laboratorium analysis; HM, NKDC, AWA performed all statistical analyses; HM led the writing of the manuscript. DGB helped with statistical advice, edited and improved the manuscript together with NKDC, AWA, and LMIS. All authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Hawis Madduppa.

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The authors declare that they have no conflict of interest.

Ethical approval

All procedures followed the guidelines of the Ministry of Research and Technology (Ristek/BRIN) under Agreement No. 3988/IT3.L1/PN/2020. The research was approved by the ethical committee at the Institute of Research and Community Service (LPPM) IPB University prior to the research agreement.

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Communicated by Angus Jackson.

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Madduppa, H., Cahyani, N.K.D., Anggoro, A.W. et al. eDNA metabarcoding illuminates species diversity and composition of three phyla (chordata, mollusca and echinodermata) across Indonesian coral reefs. Biodivers Conserv 30, 3087–3114 (2021). https://doi.org/10.1007/s10531-021-02237-0

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