Primers to block the amplification of symbiotic apostome ciliate 18S rRNA gene in a PCR-based copepod diet study

• Published in: Chinese journal of oceanology and limnology Vol. 32; no. 3; pp. 515 - 521
• Main Author: 衣晓燕 张寰 刘光兴
• Format: Journal Article
• Language: English
• Published: Heidelberg Springer-Verlag 01.05.2014; Science Press; Springer Nature B.V
• Subjects: 18S; Amplification; Aquatic crustaceans; Biology; Blocking; Ciliates; Ciliophora; Copepoda; Crustaceans; Diet; diet study techniques; DNA; Earth and Environmental Science; Earth Sciences; Exoskeleton; Exoskeletons; Food chains; Food webs; genes; Marine; Marine ecology; Natural environment; Nucleotide sequence; Oceanography; PCR扩增; Plankton; Polymerase chain reaction; Prey; Primers; ribosomal DNA; ribosomal RNA; rRNA 18S; rRNA基因; Symbionts; Zooplankton; 共生; 引物; 浮游桡足类; 纤毛虫; 饮食; apostome ciliate; copepod; 18S rDNA; blocking primer; PCR
• ISSN: 0254-4059; 2096-5508; 1993-5005; 2523-3521
• DOI: 10.1007/s00343-014-3129-z

Pelagic copepods play an important role in the marine food web. However, a full understanding of the ecological status of this zooplankton group depends on the careful study of their natural diets. In previous PCR-based copepod diet studies, we found many apostome ciliates that live symbiotically under the exoskeleton of the copepods, and their sequences were often over-represented in the 18S rRNA gene (18S rDNA) libraries. As a first step to address this issue, we designed three apostome ciliate 18S rDNA blocking primers, and tested their blocking efficiency against apostome ciliate 18s rDNA under various PCR conditions. Using a semi-quantitative PCR method, we optimized the conditions to efficiently amplify the 18S rDNA of the prey while simultaneously excluding the symbiotic apostome ciliates. This technique will facilitate PCR-based diet studies of copepods and other zooplankton in their natural environments.