Characterising planktonic dinoflagellate diversity in Singapore using DNA metabarcoding

Yue Sze,Danwei Huang,Lilibeth N Miranda,Tsai Min Sin

doi:10.3897/mbmg.2.25136

Abstract

Dinoflagellates are traditionally identified morphologically using microscopy, which is a time-consuming and labour-intensive process. Hence, we explored DNA metabarcoding using high-throughput sequencing as a more efficient way to study planktonic dinoflagellate diversity in Singapore’s waters. From 29 minimally pre-sorted water samples collected at four locations in western Singapore, DNA was extracted, amplified and sequenced for a 313-bp fragment of the V4–V5 region in the 18S ribosomal RNA gene. Two sequencing runs generated 2,847,170 assembled paired-end reads, corresponding to 573,176 unique sequences. Sequences were clustered at 97% similarity and analysed with stringent thresholds (≥150 bp, ≥20 reads, ≥95% match to dinoflagellates), recovering 28 dinoflagellate taxa. Dinoflagellate diversity captured includes parasitic and symbiotic groups which are difficult to identify morphologically. Richness is similar between the inner and outer West Johor Strait, but variations in community structure are apparent, likely driven by environmental differences. None of the taxa detected in a recent phytoplankton bloom along the West Johor Strait have been recovered in our samples, suggesting that background communities are distinct from bloom communities. The voluminous data obtained in this study contribute baseline information for Singapore’s phytoplankton communities and prompt future research and monitoring to adopt the approach established here.

Highlights

Dinoflagellates (Alveolata: Dinophyceae) are a diverse and abundant group of unicellular protists found in both marine and freshwater environments
None of the taxa detected in a recent phytoplankton bloom along the West Johor Strait have been recovered in our samples, suggesting that background communities are distinct from bloom communities
Along the West Johor Strait (WJS), three replicate samples per month were collected from stations at inner and outer WJS (1.45883°, 103.7202° and 1.34037°, 103.63018°, respectively; 24 samples)

Summary

Introduction

Dinoflagellates (Alveolata: Dinophyceae) are a diverse and abundant group of unicellular protists found in both marine and freshwater environments. With more than 2,000 living species described (Gómez 2012), they are one of the most functionally important organisms in a variety of aquatic ecosystems (Spector 1984; Taylor et al 2008). Dinoflagellates can be armoured or unarmoured (naked), based on the presence or absence of thecal plates respectively (Netzel and Dürr 1984). They play diverse ecological roles—as autotrophs, heterotrophs or mixotrophs—and can be endosymbionts of other organisms, notably the shallow-water reef-building corals, or host other endosymbionts themselves (Taylor et al 2008). As part of the phytoplankton community, they are primary producers that form the base of food chains and are a large constituent of the aquatic system’s food web (Spector 1984; Taylor et al 2008)

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