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Niu B, Pang J, Lundholm N, Liang C, Teng ST, Zheng Q, Guo X, Li Y. A Pseudo-nitzschia metabarcoding approach with a calibrated ITS1 reference sequence database applied in the Taiwan Strait. Harmful Algae 2024; 133:102602. [PMID: 38485439 DOI: 10.1016/j.hal.2024.102602] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 01/28/2024] [Accepted: 02/05/2024] [Indexed: 03/19/2024]
Abstract
Pseudo-nitzschia is a cosmopolitan phytoplankton genus of which some species can form blooms and produce the neurotoxin domoic acid (DA). Identification of Pseudo-nitzschia is generally based on field material or strains followed by morphological and/or molecular characterization. However, this process is time-consuming and laborious, and can not obtain a relatively complete and reliable profile of the Pseudo-nitzschia community, because species with low abundance in the field or potentially unavailable for culturing may easily be overlooked. In the present study, specific ITS primer sets were designed and evaluated using in silico matching. The primer set ITS-84F/456R involving the complete ITS1 region was found optimal. Based on matching with a Pseudo-nitzschia ITS1 reference sequence database carefully-calibrated in this study, a metabarcoding approach using annotated amplicon sequence variants (ASV) was applied in the Taiwan Strait of the East China Sea during two cruises in the spring and summer of 2019. In total, 48 Pseudo-nitzschia species/phylotypes including 36 known and 12 novel were uncovered, and verified by haplotype networks, ITS2 secondary structure comparisons and divergence analyses. Correlation analyses revealed that temperature was a key factor affecting the seasonal variation of the Pseudo-nitzschia community. This study provides an overview of the Pseudo-nitzschia community in the Taiwan Strait, with new insights into the diversity. The developed metabarcoding approach may be used elsewhere as a standard reference for accurate annotation of Pseudo-nitzschia.
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Affiliation(s)
- Biaobiao Niu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, West 55 of Zhongshan Avenue, Guangzhou 510631, China
| | - Jinxiu Pang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, West 55 of Zhongshan Avenue, Guangzhou 510631, China
| | - Nina Lundholm
- Natural History Museum of Denmark, University of Copenhagen, Øster Farimagsgade 5, 1353 Copenhagen K, Denmark
| | - Cuiwen Liang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, West 55 of Zhongshan Avenue, Guangzhou 510631, China
| | - Sing Tung Teng
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, Kota Samarahan 94300, Sarawak, Malaysia
| | - Qixiang Zheng
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, West 55 of Zhongshan Avenue, Guangzhou 510631, China
| | - Xin Guo
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, West 55 of Zhongshan Avenue, Guangzhou 510631, China
| | - Yang Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, West 55 of Zhongshan Avenue, Guangzhou 510631, China.
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