Diversity and distribution of Symbiodiniaceae detected on coral reefs of Lombok, Indonesia using environmental DNA metabarcoding

PeerJ. 2022 Oct 24:10:e14006. doi: 10.7717/peerj.14006. eCollection 2022.

Abstract

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.

Keywords: Aquatic plankton; Benthic periphyton; Coral hosts; Coral triangle; Endosymbiotic dinoflagellate; Next generation biomonitoring.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Anthozoa* / genetics
  • Bayes Theorem
  • Coral Reefs
  • DNA Barcoding, Taxonomic
  • DNA, Environmental*
  • Dinoflagellida*
  • Ecosystem
  • Indonesia
  • Phylogeny

Substances

  • DNA, Environmental

Grants and funding

This research was supported by the BPPDN scholarship and USAID through the Sustainable Higher Education Research Alliances (SHERA) Program—Centre for Collaborative Research on Animal Biotechnology and Coral Reef Fisheries (CCR ANBIOCORE) of IPB University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.