Diversity and distribution of Symbiodiniaceae detected on coral reefs of Lombok, Indonesia using environmental DNA metabarcoding
Background Dinoflagellates of family Symbiodiniaceae are important to coral reef ecosystems because of their contribution to coral health and growth; however, only a few studies have investigated the function and distribution of Symbiodiniaceae in Indonesia. Understanding the distribution of differe...
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PeerJ Inc.
2022-10-01
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| author | Arief Pratomo Dietriech G. Bengen Neviaty P. Zamani Christopher Lane Austin T. Humphries Erin Borbee Beginer Subhan Hawis Madduppa |
| author_facet | Arief Pratomo Dietriech G. Bengen Neviaty P. Zamani Christopher Lane Austin T. Humphries Erin Borbee Beginer Subhan Hawis Madduppa |
| author_sort | Arief Pratomo |
| collection | DOAJ |
| description | Background Dinoflagellates of family Symbiodiniaceae are important to coral reef ecosystems because of their contribution to coral health and growth; however, only a few studies have investigated the function and distribution of Symbiodiniaceae in Indonesia. Understanding the distribution of different kinds of Symbiodiniaceae can improve forecasting of future responses of various coral reef systems to climate change. This study aimed to determine the diversity of Symbiodiniaceae around Lombok using environmental DNA (eDNA). Methods Seawater and sediment samples were collected from 18 locations and filtered to obtain fractions of 0.4–12 and >12 µm. After extraction, molecular barcoding polymerase chain reaction was conducted to amplify the primary V9-SSU 18S rRNA gene, followed by sequencing (Illumina MiSeq). BLAST, Naïve-fit-Bayes, and maximum likelihood routines were used for classification and phylogenetic reconstruction. We compared results across sampling sites, sample types (seawater/sediment), and filter pore sizes (fraction). Results Phylogenetic analyses resolved the amplicon sequence variants into 16 subclades comprising six Symbiodiniaceae genera (or genera-equivalent clades) as follows: Symbiodinium, Breviolum, Cladocopium, Durusdinium, Foraminifera Clade G, and Halluxium. Comparative analyses showed that the three distinct lineages within Cladocopium, Durusdinium, and Foraminifera Clade G were the most common. Most of the recovered sequences appeared to be distinctive of different sampling locations, supporting the possibility that eDNA may resolve regional and local differences among Symbiodiniaceae genera and species. Conclusions eDNA surveys offer a rapid proxy for evaluating Symbiodiniaceae species on coral reefs and are a potentially useful approach to revealing diversity and relative ecological dominance of certain Symbiodiniaceae organisms. Moreover, Symbiodiniaceae eDNA analysis shows potential in monitoring the local and regional stability of coral–algal mutualisms. |
| first_indexed | 2024-03-09T07:00:09Z |
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| language | English |
| last_indexed | 2024-03-09T07:00:09Z |
| publishDate | 2022-10-01 |
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| spelling | doaj.art-79670aeaa9054fd7adbacd66389b69592023-12-03T09:53:23ZengPeerJ Inc.PeerJ2167-83592022-10-0110e1400610.7717/peerj.14006Diversity and distribution of Symbiodiniaceae detected on coral reefs of Lombok, Indonesia using environmental DNA metabarcodingArief Pratomo0Dietriech G. Bengen1Neviaty P. Zamani2Christopher Lane3Austin T. Humphries4Erin Borbee5Beginer Subhan6Hawis Madduppa7Raja Ali Haji Maritime University, Tanjungpinang, IndonesiaDepartment of Marine Science and Technology, Institut Pertanian Bogor, Bogor, IndonesiaDepartment of Marine Science and Technology, Institut Pertanian Bogor, Bogor, IndonesiaDepartment of Biological Sciences, University of Rhode Island, Rhode Island, United States of AmericaDepartment of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, Rhode Island, United States of AmericaDepartment of Biological Sciences, University of Rhode Island, Rhode Island, United States of AmericaDepartment of Marine Science and Technology, Institut Pertanian Bogor, Bogor, IndonesiaDepartment of Marine Science and Technology, Institut Pertanian Bogor, Bogor, IndonesiaBackground Dinoflagellates of family Symbiodiniaceae are important to coral reef ecosystems because of their contribution to coral health and growth; however, only a few studies have investigated the function and distribution of Symbiodiniaceae in Indonesia. Understanding the distribution of different kinds of Symbiodiniaceae can improve forecasting of future responses of various coral reef systems to climate change. This study aimed to determine the diversity of Symbiodiniaceae around Lombok using environmental DNA (eDNA). Methods Seawater and sediment samples were collected from 18 locations and filtered to obtain fractions of 0.4–12 and >12 µm. After extraction, molecular barcoding polymerase chain reaction was conducted to amplify the primary V9-SSU 18S rRNA gene, followed by sequencing (Illumina MiSeq). BLAST, Naïve-fit-Bayes, and maximum likelihood routines were used for classification and phylogenetic reconstruction. We compared results across sampling sites, sample types (seawater/sediment), and filter pore sizes (fraction). Results Phylogenetic analyses resolved the amplicon sequence variants into 16 subclades comprising six Symbiodiniaceae genera (or genera-equivalent clades) as follows: Symbiodinium, Breviolum, Cladocopium, Durusdinium, Foraminifera Clade G, and Halluxium. Comparative analyses showed that the three distinct lineages within Cladocopium, Durusdinium, and Foraminifera Clade G were the most common. Most of the recovered sequences appeared to be distinctive of different sampling locations, supporting the possibility that eDNA may resolve regional and local differences among Symbiodiniaceae genera and species. Conclusions eDNA surveys offer a rapid proxy for evaluating Symbiodiniaceae species on coral reefs and are a potentially useful approach to revealing diversity and relative ecological dominance of certain Symbiodiniaceae organisms. Moreover, Symbiodiniaceae eDNA analysis shows potential in monitoring the local and regional stability of coral–algal mutualisms.https://peerj.com/articles/14006.pdfCoral triangleCoral hostsEndosymbiotic dinoflagellateAquatic planktonBenthic periphytonNext generation biomonitoring |
| spellingShingle | Arief Pratomo Dietriech G. Bengen Neviaty P. Zamani Christopher Lane Austin T. Humphries Erin Borbee Beginer Subhan Hawis Madduppa Diversity and distribution of Symbiodiniaceae detected on coral reefs of Lombok, Indonesia using environmental DNA metabarcoding PeerJ Coral triangle Coral hosts Endosymbiotic dinoflagellate Aquatic plankton Benthic periphyton Next generation biomonitoring |
| title | Diversity and distribution of Symbiodiniaceae detected on coral reefs of Lombok, Indonesia using environmental DNA metabarcoding |
| title_full | Diversity and distribution of Symbiodiniaceae detected on coral reefs of Lombok, Indonesia using environmental DNA metabarcoding |
| title_fullStr | Diversity and distribution of Symbiodiniaceae detected on coral reefs of Lombok, Indonesia using environmental DNA metabarcoding |
| title_full_unstemmed | Diversity and distribution of Symbiodiniaceae detected on coral reefs of Lombok, Indonesia using environmental DNA metabarcoding |
| title_short | Diversity and distribution of Symbiodiniaceae detected on coral reefs of Lombok, Indonesia using environmental DNA metabarcoding |
| title_sort | diversity and distribution of symbiodiniaceae detected on coral reefs of lombok indonesia using environmental dna metabarcoding |
| topic | Coral triangle Coral hosts Endosymbiotic dinoflagellate Aquatic plankton Benthic periphyton Next generation biomonitoring |
| url | https://peerj.com/articles/14006.pdf |
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