Quantitative real-time PCR detection of a harmful unarmoured dinoflagellate, Karlodinium australe (Dinophyceae)

Nyuk, Fong Kon and Lau, Winnie L.S. and Kieng, Soon Hii and Ing, Kuo Law and Sing, Tung Teng and Hong, Chang Lim and Takahashi, Kazuya and Gu, Haifeng and Po, Teen Lim and Chui, Pin Leaw (2017) Quantitative real-time PCR detection of a harmful unarmoured dinoflagellate, Karlodinium australe (Dinophyceae). Phycological Research, 65 (3). ISSN 1440-1835

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Abstract

We investigated a harmful algal bloom (HAB) associated with the massive fish kills in Johor Strait, Malaysia, which recurred a year after the first incident in 2014. This incident has urged for the need to have a rapid and precise method in HAB monitoring. In this study, we develop a SYBR green-based realtime PCR (qPCR) to detect the culpable dinoflagellate species, Karlodinium australe. Species-specific qPCR primers were designed in the gene region of the second internal transcribed spacer of the ribosomal RNA gene (rDNA). The species specificity of the primers designed was evaluated by screening on the non-target species (Karlodinium veneficum, Takayama spp., and Karenia spp.) and no cross-detection was observed. The extractable gene copies per cell of K. australe determined in this study were 19 998 � 505 (P < 0.0001). Estimation of cell densities by qPCR in the experimental spiked samples showed high correlation with data determined microscopically (R2 = 0.93). Using the qPCR assay developed in this study, we successfully detected the 2015 bloom species as K. australe. Single-cell PCR and rDNA sequencing from the field samples further confirmed the finding. With the sensitivity as low as five cells, the qPCR assay developed in this study could effectively and rapidly detect cells of K. australe in the environmental samples for monitoring purpose.

Item Type: Article
Uncontrolled Keywords: fish kill, ribosomal RNA gene, second internal transcribed spacer, research, Universiti Malaysia Sarawak, unimas, university, universiti, Borneo, Malaysia, Sarawak, Kuching, Samarahan, ipta, education
Subjects: S Agriculture > SH Aquaculture. Fisheries. Angling
Divisions: Academic Faculties, Institutes and Centres > Institute of Biodiversity and Environmental Conservation
Depositing User: Karen Kornalius
Date Deposited: 04 Aug 2017 06:33
Last Modified: 04 Aug 2017 06:33
URI: http://ir.unimas.my/id/eprint/17074

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