Resolving phytoplankton taxa based on high-throughput sequencing during brown tides in the Bohai Sea, China

Chen, Zhen-Fan; Zhang, Qing‐Chun; Kong, Fan‐Zhou; Liu, Yang; Zhao, Yue; Zhou, Zheng‐Xi; Geng, Hui-Xia; Dai, Lei; Zhou, Mingjiang; Yu, Rencheng

doi:10.1016/j.hal.2019.03.011

Cited by 27 publications

(14 citation statements)

References 61 publications

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“…Amplification was performed using the forward primer D514 for 18S (5′-TCCAGCTCCAATAGCGTA-3′) and the reverse primer B706R (5′-AATCCRAGAATTTCACCTCT-3′), , a pair of universal primers that were designed for eukaryotic phytoplankton. The HTS procedure for marine phytoplankton was described in ref . The library was sequenced using an Illumina HiSeq.…”

Section: Methodsmentioning

confidence: 99%

“…The read data were analyzed using several software packages, QIIME2 (version 2020.2), UPARSE (version 10.0.240), Mega (version 10.1.8), and BLAST (version +2.10.0). All of the procedures followed the manufacturers’ protocols . The Alexandrium sequences were extracted from the sequencing data for further analysis, including operational taxonomic unit (OTU) clustering, alignment, phylogenetic tree building, and taxonomic analysis.…”

Section: Methodsmentioning

confidence: 99%

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Identifying the Source Organisms Producing Paralytic Shellfish Toxins in a Subtropical Bay in the South China Sea

Yang

Chen

Gao

et al. 2021

Environ. Sci. Technol.

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Identifying the exact phytoplanktonic sources of paralytic shellfish toxins (PSTs) is crucial for monitoring and preventing the buildup of toxin pollution, especially for causative species occurring at low levels. Phytoplankton and shellfish samples were simultaneously collected from representative mariculture zones in Daya Bay, China. Low concentration/low toxicity PSTs predominated with N-sulfocarbamoyl toxins 1, 2 (C1/2) being detected in phytoplankton (≤6.25 pmol L–1) and shellfish (≤0.21 μg STXeq g–1), which pose a potential risk of seafood poisoning. High-throughput sequencing of the phytoplankton samples based on 18S rDNA V4 regions identified 93 genera in 445 operational taxonomic units (OTUs). Five OTUs were assigned to Alexandrium hiranoi, Ambicodamus leei, Alexandrium pacificum, Alexandrium minutum, and an uncertain Alexandrium sp. A. pacificum and A. minutum are candidate PST producers and observed under the light microscope with densities of 66–972 cells L–1. Three strains of toxigenic species were successfully isolated and identified as A. pacificum and A. minutum based on their 18S rDNA V4 regions. The predominant toxins in A. pacificum were C1/2 (43.9–53.6 fmol cell–1) and resembled the toxins found in field samples predominated with C1/2. A. minutum produced only gonyautoxins 2/3 (8.03 fmol cell–1). Therefore, A. pacificum was identified as the predominant PST contributor in this area. This research makes a valuable contribution to the understanding of the traceability of phycotoxins in marine waters.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Identifying the Source Organisms Producing Paralytic Shellfish Toxins in a Subtropical Bay in the South China Sea

Yang

Chen

Gao

et al. 2021

Environ. Sci. Technol.

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“…Through high‐throughput sequencing of amplicons derived from phytoplankton samples collected in the same investigation, it was found that the relative abundance of A. anophagefferens in the nano‐ and pico‐sized phytoplankton communities exhibited a similar variation pattern. Pelagophyte A. anophagefferens took the dominant position and formed a brown tide in May, and its relative abundance exceeded 60% (Chen et al ). The seasonal variation pattern of A. anophagefferens abundance were also supported by other studies in this region (Qiao et al ; Wang and Lei ), but the timing of brown tides may vary among different years (Chen et al ).…”

Section: Discussionmentioning

confidence: 99%

“…Pelagophyte A. anophagefferens took the dominant position and formed a brown tide in May, and its relative abundance exceeded 60% (Chen et al ). The seasonal variation pattern of A. anophagefferens abundance were also supported by other studies in this region (Qiao et al ; Wang and Lei ), but the timing of brown tides may vary among different years (Chen et al ). During the brown tide in May, high abundance of A. anophagefferens cells were mainly found at the surface of inshore waters along the coast of Qinhuangdao (Fig.…”

Section: Discussionmentioning

confidence: 99%

Development of a sensitive qPCR method for the detection of pelagophyte Aureococcus anophagefferens

Zhang

Chen

Zhao

et al. 2019

Limnology & Ocean Methods

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Brown tides of pelagophyte Aureococcus anophagefferens have been recorded in the coastal waters of Qinhuangdao in the Bohai Sea (BS) since 2009. Current understandings on the dynamics and mechanisms of brown tides in the BS, however, are still quite limited due to the lack of accurate methods for detecting low‐abundance of A. anophagefferens cells. In this study, a Taqman qPCR method was developed, which targeted 28S rDNA D1‐D2 domain of A. anophagefferens. The specificity of the qPCR method was tested using 25 strains of microalgae commonly present in the coastal waters, and the targeted species A. anophagefferens was the only species that had reliable positive signal. The method was highly sensitive and reproducible, and the lower detection limit could reach 0.3 cells of A. anophagefferens. A calibration curve was established for A. anophagefferens using the DNA template extracted from different number of cells, and the lower and upper limits of detection for the qPCR assay is 0.3 cells and 1.2 × 105 cells, respectively. A high recovery rate ranged from 96.5% to 107% was achieved for A. anophagefferens at different cell densities. The qPCR assay has been successfully applied to the study on spatial and temporal variations of A. anophagefferens in the coastal waters of Qinhuangdao in 2014.

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“…Genomic DNA was extracted from the microalgal samples using the cetyl trimethyl ammonium bromide (CTAB) method as previously described (Winnepenninckx et al 2002;Chen et al 2019), dissolved in 30 μL of Tris-EDTA buffer solution (TE), and stored at À20 C. Sequences of the Mit atp8 genes of six haptophyte strains, namely, Chrysochromulina parva (NC036938), Chrysochromulina sp. (KJ201908), Pavlova lutheri (HQ908424), Pavlova sp.…”

Section: Dna Preparation Pcr Amplification Sequencing and Phylogeneti...mentioning

confidence: 99%

Development of sensitive genotype‐specific quantitative polymerase chain reaction methods for detection of Phaeocystis globosa in the South China Sea

Niu

Liu

Zhang

et al. 2021

Limnology & Ocean Methods

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Since 1997, dense blooms of the alga Phaeocystis globosa have occurred in the South China Sea (SCS), and previous studies have revealed the co‐existence in this sea of two types of P. globosa cell characterized by different marker pigment profiles. However, owing to a lack of quantitative methods for the detection of different types of P. globosa cells, the dynamics of P. globosa blooms in the SCS are still poorly understood. In this study, on the basis of phylogenetic analysis of the mitochondrial atp8 (Mit atp8) gene and pigment profiles, the P. globosa strains from Pacific and Atlantic coastal waters were divided into four genotypes, of which Type I and Type IV strains co‐exist in the SCS. Furthermore, two genotype‐specific quantitative polymerase chain reaction (qPCR) methods were developed targeting the Mit atp8 gene for quantitative determinations of the densities of Type I and Type IV P. globosa cells. Both qPCR methods were reproducible, highly sensitive, and specific with a wide range of detection (from 30 to 1 × 108 cells L−1) for target P. globosa genotypes in the field, thereby facilitating the detection of low cell densities prior to bloom development, as well as high cell densities during bloom periods. Finally, the developed qPCR assays were successfully applied to determine the distribution patterns of Type I and Type IV P. globosa in the Beibu Gulf, a region of the SCS characterized by a high frequency of P. globosa blooms.

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Resolving phytoplankton taxa based on high-throughput sequencing during brown tides in the Bohai Sea, China

Cited by 27 publications

References 61 publications

Identifying the Source Organisms Producing Paralytic Shellfish Toxins in a Subtropical Bay in the South China Sea

Identifying the Source Organisms Producing Paralytic Shellfish Toxins in a Subtropical Bay in the South China Sea

Development of a sensitive qPCR method for the detection of pelagophyte Aureococcus anophagefferens

Development of sensitive genotype‐specific quantitative polymerase chain reaction methods for detection of Phaeocystis globosa in the South China Sea

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