Table 1.
Qrt-PCR applications for detection and estimation of marine harmful algal bloom species
| Taxa | Target gene copy number cell−1 | Standard curve method | Nucleic acid purification method | Target genomic region | Detection method | Reference |
|---|---|---|---|---|---|---|
| Dinoflagellates | ||||||
| Alexandrium minutum | 1,084 ± 120.3 | Plasmid | Cell lysates | ITS-5.8S | SYBR Green | Galluzzi et al. (2004) |
| Alexandrium minutum | n.d. | Cellular | Kit extraction | ITS-5.8S | Hybridization probe | Touzet et al. (2009) |
| Alexandrium catenella | n.d. | Cellular | Phenol | LSU (D1/D2) | TaqMan probe | Hosoi-Tanabe and Sako (2005) |
| Alexandrium catenella | n.d. | Cyst | Phenol/CTAB | LSU (D1/D2) | TaqMan probe | Kamikawa et al. (2007) |
| Alexandrium catenella | 2,489,800 ± 550,96–219,170 ± 25,98 | Plasmid | Cell lysates | ITS-5.8S | SYBR Green | Galluzzi et al. (2010) |
| Alexandrium catenella | n.d. | Cellular | Cell lysates | LSU (D1/D2) | TaqMan probe | Garneau et al. (2011) |
| Alexandrium catenella | 178–280 | Cellular PCR products | CTAB | sxtA4 gene | Evagreen | Murray et al. (2011) |
| Alexandrium fundyense | n.d. | Cellular | Kit extraction | LSU | SYBR Green | Dyrhmann et al. (2006) |
| Alexandrium fundyense | 28,402 ± 6152 | Cyst | Kit extraction | LSU (D1/D2) | SYBR Green | Erdner et al. (2010) |
| Alexandrium tamarense | n.d. | Cellular | Phenol | LSU (D1/D2) | TaqMan probe | Hosoi-Tanabe and Sako (2005) |
| Alexandrium tamarense | n.d. | Cyst | CTAB | LSU (D1/D2) | TaqMan probe | Kamikawa et al. (2005) |
| Alexandrium tamarense | n.d. | Cyst | Phenol/CTAB | LSU (D1/D2) | TaqMan probe | Kamikawa et al. (2007) |
| Alexandrium taylori | 1,345 ± 780–33,930 ± 4,820 | Plasmid | Cell lysates | ITS-5.8S | SYBR Green | Galluzzi et al. (2010) |
| Cochlodinium polykrikoides | n.d. | Cellular | CTAB | LSU (D1/D2) | Fluorescent hybridization probe | Kamikawa et al. (2006) |
| Cochlodinium polykrikoides | n.d. | Cellular | Phenol | ITS2 | TaqMan probe | Park et al. (2009) |
| Cryptoperidiniopsis brodyi | n.d. | Cellular | Kit extraction | ITS | TaqMan probe | Park et al. (2007) |
| Dinophysis acuta | n.d. | Plasmid | Kit extraction | LSU (D1/D2) | Fluorescent hybridization probe | Kavanagh et al. (2010) |
| Dinophysis acuminata | n.d. | Plasmid | Kit extraction | LSU (D1/D2) | Fluorescent hybridization probe | Kavanagh et al. (2010) |
| Gambierdiscus belizeanus | ||||||
| Gambierdiscus caribaeus | LSU (D1/D3) | |||||
| Gambierdiscus carpenter | n.d. | Cellular | Kit extraction | SSU | SYBR Green | |
| Gambierdiscus carolinianus | 5.8S | Vandersea et al. (2012) | ||||
| Gambierdiscus sp. 2 | ||||||
| Gambierdiscus rutzleri | ||||||
| Heterocapsa circulasquama | n.d. | Cellular | CTAB | LSU (D1/D2) | Fluorescent hybridization probe | Kamikawa et al. (2006) |
| Heterocapsa akashiwo | n.d. | Plasmid cellular | CTAB | SSU | TaqMan probe | Handy et al. (2006) |
| Heterocapsa akashiwo | n.d. | Plasmid | CTAB | LSU | TaqMan probe | Bowers et al. (2006) |
| Heterocapsa akashiwo | n.d. | Cellular | CTAB | LSU (D1/D2) | Fluorescent hybridization probe | Kamikawa et al. (2006) |
| Lingulodinium polyedrum | n.d. | Cellular | Cell lysates | SSU | Molecular beacon | Moorthi et al. (2006) |
| Karenia brevis | n.d. | Cellular | Kit extraction | rbcl transcript | Molecular beacon | Casper et al. (2004) |
| Karenia mikimotoi | n.d. | Cellular | CTAB | LSU (D1/D2) | Fluorescent Hybridization probe | Kamikawa et al. (2006) |
| Karenia mikimotoi | n.d. | Cellular | Kit extraction | rbcl transcript | Molecular beacon | Ulrich et al. (2010) |
| Karenia mikimotoi | n.d. | Cellular | Phenol | ITS-5.8S | TaqMan probe | Yuan et al. (2012) |
| Ostreopsis cf. ovata | 1,030 ± 49 | Plasmid cellular | Cell lysates | LSU (D1/D2) | SYBR Green | Perini et al. (2011) |
| Pfiesteria piscicida | n.d. | Cellular | CTAB | mt Cob, SSU | SYBR Green | Lin et al. (2006) |
| Pfiesteria shumwayae | n.d. | Cellular | CTAB | mt Cob, SSU | SYBR Green | Zhang and Lin (2005) |
| Raphidophyceae | ||||||
| Chattonella spp. | n.d. | Cellular | CTAB | LSU (D1/D2) | Fluorescent Hybridization probe | Kamikawa et al. (2006) |
| Chattonella verrucolosa | n.d. | Plasmid | CTAB | SSU | TaqMan probe | Bowers et al. (2006) |
| Chattonella cf. verrucolosa | n.d. | Plasmid cellular | CTAB | SSU | TaqMan probe | Handy et al. (2006) |
| Chattonella antiqua | n.d. | Plasmid | CTAB | ITS2 | TaqMan probe | Bowers et al. (2006) |
| Chattonella ovata | n.d. | Plasmid | CTAB | ITS2 | TaqMan probe | Bowers et al. (2006) |
| Chattonella subsalsa | n.d. | Plasmid | CTAB | ITS2 | TaqMan probe | Bowers et al. (2006) |
| Chattonella subsalsa | n.d. | Plasmid cellular | CTAB | SSU | TaqMan probe | Handy et al. (2006) |
| Fibrocapsa japonica | n.d. | Plasmid | CTAB | LSU | TaqMan probe | Bowers et al. (2006) |
| Haptophyceae | ||||||
| Prymnesium parvum | 10 ± 2.8–15.6 ± 1.6 | Plasmid | Cell lysates | ITS2 | SYBR Green | Galluzzi et al. (2008) |
| Prymnesium parvum | 11.7 ± 0.6 | Plasmid | Cell lysates | ITS2 | SYBR Green | Zamor et al. (2012) |
| Pelagophyceae | ||||||
| Aureococcus anophagefferens | n.d. | Cellular | CTAB | SSU | Hybridization probe | Popels et al. (2003) |
| Diatoms | ||||||
| Pseudo-nitzschia spp. | n.d. | Plasmid | Cell lysates | SSU | SYBR Green | Fitzpatrick et al. (2010) |
| Pseudo-nitzschia spp. | n.d. | Cellular | Kit extraction | ITS-5.8S | SYBR Green | Andrée et al. (2011) |
| Pseudo-nitzschia multiseries | 30,000 | Transcript | Kit extraction | rbcS transcript | TaqMan probe, beacon | Delaney et al. (2011) |
n.d not detected