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

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 un...

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Bibliographic Details
Published inChinese 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
LanguageEnglish
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
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ISSN0254-4059
2096-5508
1993-5005
2523-3521
DOI10.1007/s00343-014-3129-z

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Summary: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.
Bibliography:copepod; 18S rDNA; apostome ciliate; blocking primer; PCR
YI Xiaoyan ZHANG Huan , LIU Guangxing （1 College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China 2Department of Marine Sciences, Connecticut University, Groton, Connecticut 06340, USA 3 Key Laboratory of Marine Environment and Ecology （Ocean University of China）, Ministry of Education, Qingdao 266100 China）
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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.
http://dx.doi.org/10.1007/s00343-014-3129-z
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ISSN:0254-4059
2096-5508
1993-5005
2523-3521
DOI:10.1007/s00343-014-3129-z