q-PCR-based assay for the toxic dinoflagellate Karenia selliformis monitoring along the Tunisian coasts

Elleuch, Jihen; Amor, Faten Ben; Barkallah, Maher; Salah, Jihen Haj; Smith, Kirsty F.; Aleya, Lotfi; Fendri, Imen; Abdelkafi, Slim

doi:10.1007/s11356-021-14597-9

Cited by 10 publications

(3 citation statements)

References 69 publications

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“…In a situation where the morphological analysis method is the dominant method for diagnosing harmful dinoflagellates off Korean coasts, diagnosis using molecular biology is considered to be a more objective number, and the development of technology through this method can lead to the development of new monitoring techniques [ 28 ]. Moreover, if NGS technology has been developed and applied to the monitoring of marine organisms, it is possible to simultaneously analyze a large amount of mixed samples and save the effort and time of long-term monitoring and research analysis [ 29 , 30 , 31 ].…”

Section: Discussionmentioning

confidence: 99%

Metagenomic Analysis of the Species Composition and Seasonal Distribution of Marine Dinoflagellate Communities in Four Korean Coastal Regions

et al. 2022

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Biomonitoring of dinoflagellate communities in marine ecosystems is essential for efficient water quality management and limiting ecosystem disturbances. Current identification and monitoring of toxic dinoflagellates, which cause harmful algal blooms, primarily involves light or scanning electron microscopy; however, these techniques are limited in their ability to monitor dinoflagellates and plankton, leaving an incomplete analysis. In this study, we analyzed the species composition and seasonal distribution of the dinoflagellate communities in four Korean coastal regions using 18S rRNA amplicon sequencing. The results showed significantly high diversity in the dinoflagellate communities in all regions and seasons. Furthermore, we found seasonally dominant species and causative species of harmful algal blooms (Cochlodinium sp., Alexandrium sp., Dinophysis sp., and Gymnodinium sp.). Moreover, dominant species were classified by region and season according to the difference in geographical and environmental parameters. The molecular analysis of the dinoflagellate community based on metagenomics revealed more diverse species compositions that could not be identified by microscopy and revealed potentially harmful or recently introduced dinoflagellate species. In conclusion, metagenomic analysis of dinoflagellate communities was more precise and obtained results faster than microscopic analysis, and could improve the existing monitoring techniques for community analysis.

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Section: Discussionmentioning

confidence: 99%

Metagenomic Analysis of the Species Composition and Seasonal Distribution of Marine Dinoflagellate Communities in Four Korean Coastal Regions

et al. 2022

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“…The α-tubulin gene was used as a housekeeping gene ( Table 1 ). Reactions with an amplification efficiency between 95% and 105% were considered acceptable [ 39 , 40 , 41 ]. Relative mRNA expression values were determined with the 2- ΔΔCt method [ 42 , 43 ].…”

Section: Methodsmentioning

confidence: 99%

Improvement of Biomass and Phycoerythrin Production by a Strain of Rhodomonas sp. Isolated from the Tunisian Coast of Sidi Mansour

et al. 2022

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Microalgae are photoautotrophic microorganisms known as producers of a large variety of metabolites. The taxonomic diversity of these microorganisms has been poorly explored. In this study, a newly isolated strain was identified based on the 18S rRNA encoding gene. The phylogenetic analysis showed that the isolated strain was affiliated with the Rhodomonas genus. This genus has greatly attracted scientific attention according to its capacity to produce a large variety of metabolites, including phycoerythrin. Growth and phycoerythrin production conditions were optimized using a Plackett–Burman design and response surface methodology. An expression profile analysis of the cpeB gene, encoding the beta subunit of phycoerythrin, was performed by qRT-PCR under standard and optimized culture conditions. The optimization process showed that maximum cell abundance was achieved under the following conditions: CaCl2 = 2.1328 g/L, metal solution = 1 mL/L, pH = 7 and light intensity = 145 μmol photons/m2/s, whereas maximum phycoerythrin production level occurred when CaCl2 = 1.8467 g/L, metal solution = 1 mL/L, pH = 7 and light intensity = 157 μmol/m2/s. In agreement, positive transcriptional regulation of the cpeB gene was demonstrated using qRT-PCR. This study showed the successful optimization of abiotic conditions for highest growth and phycoerythrin production, making Rhodomonas sp. suitable for several biotechnological applications.

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“…All reactions were assessed using a StepOnePlus™ PCR cycler (Applied Biosystems, Foster City, USA) as previously reported by Barkallah et al ( 2020 ) and Elleuch et al ( 2021 ). Plasmid copy numbers were calculated using the following equation: Cn = (Pc × Ac)/(Mw × Pl), where Cn is the copy number, Pc is the plasmid concentration (g/µl), Ac is Avogadro’s constant = 6.022 × 10 23 mol −1 , Mw is the base pair mean molecular weight = 660 Da and Pl is the plasmid length containing the cloned sequence (bp).…”

Section: Methodsmentioning

confidence: 99%

A new TaqMan real-time PCR assay to detect Parachlamydia acanthamoebae and to monitor its co-existence with SARS-COV-2 among COVID-19 patients

Baccari

Barkallah

Elleuch

et al. 2022

Environ Sci Pollut Res

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Human respiratory infections caused by a large variety of microbial pathogens are the most common diseases responsible for hospitalization, morbidity and mortality. Parachlamydia acanthamoebae , a Chlamydia -related bacterium, has been found to be potentially associated with these diseases. An early and accurate diagnosis of this pathogen could be useful to avoid the potential respiratory complications linked especially to COVID-19 patients and to set suitable outbreak control measures. A TaqMan-PCR assay was developed to detect and quantify Parachlamydia acanthamoebae in environmental and clinical samples from patients of all ages with COVID-19. The selected hydrolysis probe displayed no cross-reaction with the closely related Chlamydia or the other tested pathogens. This q-PCR achieved good reproducibility and repeatability with a detection limit of about 5 DNA copies per reaction. Using this q-PCR assay, Parachlamydia acanthamoebae was detected in 2/78 respiratory specimens and 9/47 water samples. Only one case (1.3%) of Parachlamydia acanthamoebae and SARS-COV-2 co-infection was noticed. To our knowledge, the combination of these two respiratory pathogens has not been described yet. This new TaqMan-PCR assay represents an efficient diagnostic tool to survey Parachlamydia acanthamoebae on a large-scale screening programs and also during outbreaks.

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q-PCR-based assay for the toxic dinoflagellate Karenia selliformis monitoring along the Tunisian coasts

Cited by 10 publications

References 69 publications

Metagenomic Analysis of the Species Composition and Seasonal Distribution of Marine Dinoflagellate Communities in Four Korean Coastal Regions

Metagenomic Analysis of the Species Composition and Seasonal Distribution of Marine Dinoflagellate Communities in Four Korean Coastal Regions

Improvement of Biomass and Phycoerythrin Production by a Strain of Rhodomonas sp. Isolated from the Tunisian Coast of Sidi Mansour

A new TaqMan real-time PCR assay to detect Parachlamydia acanthamoebae and to monitor its co-existence with SARS-COV-2 among COVID-19 patients

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