New Design Strategy for Development of Specific Primer Sets for PCR-Based Detection of Chlorophyceae and Bacillariophyceae in Environmental Samples

• Published in: Applied and Environmental Microbiology Vol. 75; no. 17; pp. 5729 - 5733
• Main Authors: Valiente Moro, Claire, Crouzet, Olivier, Rasconi, Séréna, Thouvenot, Antoine, Coffe, Gérard, Batisson, Isabelle, Bohatier, Jacques
• Format: Journal Article
• Language: English
• Published: Washington, DC American Society for Microbiology 01.09.2009; American Society for Microbiology (ASM)
• Subjects: Algae; Algae, Green; Aquatic ecology; Aquatic environment; Bacillariophyceae; Biodiversity; Biological and medical sciences; Chlorophyceae; Chlorophyta - genetics; Chlorophyta - isolation & purification; Computational Biology; Computer Simulation; computer software; Development strategies; Diatoms; Diatoms - genetics; Diatoms - isolation & purification; DNA Primers; DNA Primers - genetics; DNA, Algal; DNA, Algal - chemistry; DNA, Algal - genetics; DNA, Ribosomal; DNA, Ribosomal - chemistry; DNA, Ribosomal - genetics; Ecotoxicology; Environmental Microbiology; Freshwater ecology; Fundamental and applied biological sciences. Psychology; fungi; Genes; health status; Life Sciences; limnology; Methods; Microalgae; Microbiology; Molecular Sequence Data; Phylogeny; Polymerase Chain Reaction; Polymerase Chain Reaction - methods; Ribonucleic acid; ribosomal RNA; RNA; RNA, Algal; RNA, Algal - genetics; RNA, Ribosomal, 18S; RNA, Ribosomal, 18S - genetics; Sensitivity and Specificity; Sequence Analysis, DNA; Sequence Homology; Toxicology; Water quality; Design; Polymerase chain reaction; Chlorophyta; Algae; Sample; Primer; Chlorophyceae; Detection
• ISSN: 0099-2240; 1098-5336; 1098-5336; 1098-6596
• DOI: 10.1128/AEM.00509-09

Studying aquatic microalgae is essential for monitoring biodiversity and water quality. We designed new sets of 18S rRNA PCR primers for Chlorophyceae and Bacillariophyceae by using the ARB software and implementing a virtual PCR program. The results of specificity analysis showed that most of the targeted algal families were identified and nontargeted organisms, such as fungi or ciliates, were excluded. These newly developed PCR primer sets were also able to amplify microalgal rRNA genes from environmental samples with accurate specificity. These tools could be of great interest for studying freshwater microalgal ecology and for developing bioindicators of the health status of aquatic environments.