Phytoplankton diversity in a tropical bay, North Borneo, Malaysia as revealed by light microscopy and Next-Generation Sequencing
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Abstract: Assessments of phytoplankton diversity in Sabah waters, North Borneo, have primarily relied on morphology-based identification, which has inherent biases and can be time-consuming. Next-Generation Sequencing (NGS) technology has been shown to be capable of overcoming several limitations of morphology-based methods. Samples were collected from the Sepanggar Bay over the course of the year 2018 in different monsoon seasons. Morphology-based identification and NGS sequencing of the V8–V9 region of the 18S LSU rDNA were used to investigate the diversity of the phytoplankton community. Microscopy and NGS showed complementary results with more diatom taxa detected by microscopy whereas NGS detected smaller and rarer taxa. The harmful algal genera in the study site comprised of Skeletonema, Margalefidinium, Pyrodinium, Takayama, and Alexandrium as detected by NGS. This study showed that that an integrative approach of both morphological and molecular techniques could provide more comprehensive information about the phytoplankton community as the approach captured quantitative variability as well as the diversity of phytoplankton species.
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Key words:
- phytoplankton community /
- Next-Generation Sequencing (NGS) /
- Sabah /
- South China Sea
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Figure 3. Bar chart of relative abundances of phytoplankton based on cell counts. Total cell counts are provided in brackets above the respective bars. The group “other diatoms” include Asteromphalus, Bacteriastrum, Coscinodiscus, Cylindrotheca, Dactyliosolen, Ditylum, Eucampia, Lauderia, Leptocylindrus, Navicula, Nitzschia, Rhizosolenia, Thalassionema, and Pseudo-nitzschia. The group “other dinoflagellates” include Akashiwo, Ceratium, Dinophysis, Gymnodinium, Gyrodinium, and Prorocentrum.
Table 1. Taxonomic composition as revealed by amplicon sequencing
Group Rank Taxon Relative abundance/% NEM1 IMP2 SWM2 IMP3 NEM2 Diatom Subphylum Coscinodiscophytina 0.0 0.0 0.0 0.0 <0.1 Class Bacillariophyceae 0.9 0.0 0.0 4.3 1.0 Class Mediophyceae <0.1 <0.1 <0.1 1.4 0.5 Order Fragilariales 0.0 0.0 0.0 <0.1 <0.1 Genus Chaetoceros 17.3 22.0 2.5 55.7 87.1 Genus Corethron <0.1 0.0 0.0 <0.1 <0.1 Genus Coscinodiscus 0.0 0.0 0.0 <0.1 <0.1 Genus Cyclotella 0.9 1.0 2.5 1.4 1.0 Genus Leptocylindrus <0.1 <0.1 <0.1 1.4 <0.1 Genus Minutocellus 1.8 3.0 72.5 <0.1 1.0 Genus Navicula <0.1 0.0 0.0 <0.1 <0.1 Genus Odontella 0.0 0.0 0.0 <0.1 <0.1 Genus Rhizosolenia <0.1 <0.1 0.0 <0.1 0.0 Genus Skeletonema 63.6 14.0 2.5 7.1 1.9 Genus Thalassiosira <0.1 1.0 0.0 <0.1 <0.1 Dinoflagellate Infraphylum Dinoflagellata 2.7 12.0 5.0 4.3 1.0 Sub-class Gymnodiniphycidae <0.1 <0.1 <0.1 <0.1 <0.1 Order Dinophysiales 0.0 0.0 <0.1 <0.1 <0.1 Order Gonyaulacales 0.9 0.0 0.0 <0.1 0.0 Genus Peridiniales 0.0 0.0 0.0 <0.1 <0.1 Family Suessiaceae <0.1 <0.1 0.0 0.0 <0.1 Family Thoracosphaeraceae <0.1 0.0 0.0 <0.1 0.0 Genus Akashiwo 0.0 <0.1 0.0 0.0 0.0 Genus Alexandrium <0.1 <0.1 <0.1 1.4 <0.1 Genus Amphidiniopsis 0.0 0.0 <0.1 0.0 <0.1 Genus Amphidinium 0.9 <0.1 <0.1 <0.1 <0.1 Genus Azadinium 0.0 0.0 <0.1 0.0 0.0 Genus Blixaea <0.1 <0.1 <0.1 8.6 1.9 Genus Cochlodinium <0.1 <0.1 <0.1 2.9 0.5 Genus Diplosalis 0.0 0.0 0.0 <0.1 0.0 Genus Erythropsidinium 0.0 0.0 <0.1 2.9 <0.1 Genus Fragilidium <0.1 0.0 0.0 <0.1 <0.1 Genus Gonyaulax <0.1 1.0 <0.1 <0.1 <0.1 Genus Gymnodinium 0.9 <0.1 <0.1 <0.1 0.5 Genus Gyrodinium 1.8 0.0 <0.1 2.9 <0.1 Genus Haplozoon <0.1 1.0 <0.1 <0.1 <0.1 Genus (cyst) Islandinium 0.0 0.0 0.0 <0.1 0.0 Genus Katodinium 0.0 <0.1 0.0 <0.1 <0.1 Genus Oodinium <0.1 <0.1 5.0 0.0 <0.1 Genus Paragymnodinium 0.9 6.0 2.5 <0.1 <0.1 Genus Polykrikos 0.0 <0.1 0.0 <0.1 <0.1 Genus Posoniella 0.0 <0.1 0.0 0.0 0.0 Genus Prorocentrum 0.0 0.0 0.0 <0.1 <0.1 Genus Protoperidinium <0.1 1.0 <0.1 1.4 0.5 Genus Ptychodiscus <0.1 <0.1 <0.1 <0.1 <0.1 Genus Pyrodinium <0.1 0.0 <0.1 <0.1 0.5 Genus Sinophysis <0.1 0.0 <0.1 <0.1 <0.1 Genus Symbiodinium 0.9 1.0 <0.1 <0.1 0.5 Genus Takayama <0.1 1.0 <0.1 <0.1 <0.1 Genus Tripos 4.5 1.0 <0.1 1.4 0.5 Genus Woloszynskia <0.1 0.0 0.0 <0.1 <0.1 Clade Gymnodinium clade 1.8 <0.1 2.5 2.8 1.4 Eustigmatophyte Order Eustigmatales <0.1 <0.1 <0.1 <0.1 0.0 Ochrophyte Phylum Ochrophyta 0.9 5.0 2.5 1.4 0.5 Raphidophyte Order Chattonellales <0.1 <0.1 <0.1 <0.1 <0.1 Class Raphidophyceae <0.1 <0.1 <0.1 <0.1 <0.1 Silicoflagellate Class Dictyophyceae 0.0 <0.1 0.0 <0.1 <0.1 Stramenopile Genus Phaeomonas 0.0 1.0 0.0 0.0 0.0 Genus Pinguiochrysis 0.0 <0.1 0.0 0.0 0.0 Chrysophyte Class Chrysophyceae 0.0 <0.1 <0.1 <0.1 <0.1 Genus Ankylochrisis 0.0 0.0 0.0 0.0 <0.1 Genus Chrysowaernella 0.0 0.0 0.0 <0.1 0.0 Genus Ochromonas 0.0 0.0 0.0 0.0 <0.1 Genus Paraphysomonas 0.0 0.0 0.0 <0.1 <0.1 Cryptophyte Class Cryptophyceae <0.1 0.0 <0.1 <0.1 <0.1 Order Cryptomonadales <0.1 2.0 <0.1 <0.1 0.5 Genus Leucocryptos <0.1 1.0 <0.1 <0.1 <0.1 Genus Proteomonas 0.9 1.0 <0.1 <0.1 <0.1 Genus Teleaulax 0.0 <0.1 <0.1 0.0 <0.1 Species Leucocryptos marina <0.1 <0.1 0.0 <0.1 <0.1 Species Hemiselmis virescens 0.0 0.0 0.0 0.0 <0.1 Species Proteomonas sulcata <0.1 1.0 <0.1 <0.1 <0.1 Chlorophyte Phylum Chlorophyta 0.9 7.0 5.0 <0.1 1.0 Class Mamiellophyceae <0.1 <0.1 <0.1 0.0 <0.1 Order Chlorodendrales <0.1 2.0 7.5 1.4 <0.1 Order Mamiellales <0.1 8.0 <0.1 <0.1 <0.1 Order Ulvales <0.1 <0.1 <0.1 <0.1 <0.1 Genus Bathycoccus 0.0 0.0 0.0 <0.1 0.0 Genus Coccomyxa 0.0 <0.1 0.0 <0.1 <0.1 Genus Crustomastix 0.0 <0.1 0.0 0.0 0.0 Genus Mamiella <0.1 <0.1 <0.1 0.0 <0.1 Genus Nephroselmis <0.1 2.0 <0.1 <0.1 <0.1 Genus Prasinoderma 0.0 <0.1 0.0 0.0 <0.1 Genus Tetraselmis 0.0 <0.1 <0.1 0.0 <0.1 Total phytoplankton reads 10 046 8 363 3 869 6 331 18 745 Total reads 88 124 88 028 87 927 87 928 88 007 Unassigned reads 1 374 20 327 128 189 1 026 Note: Values with “<” indicate sequences that have at least one read. -
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