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Development and evaluation of specific PCR primers targeting the ribosomal DNA-internal transcribed spacer (ITS) region of peritrich ciliates in environmental samples

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Abstract

Peritrich ciliates are highly diverse and can be important bacterial grazers in aquatic ecosystems. Morphological identifications of peritrich species and assemblages in the environment are time-consuming and expertise-demanding. In this study, two peritrich-specific PCR primers were newly designed to amplify a fragment including the internal transcribed spacer (ITS) region of ribosomal rDNA from environmental samples. The primers showed high specificity in silico, and in tests with peritrich isolates and environmental DNA. Application of these primers in clone library construction and sequencing yielded exclusively sequences of peritrichs for water and sediment samples. We also found the ITS1, ITS2, ITS, D1 region of 28S rDNA, and ITS+D1 region co-varied with, and generally more variable than, the V9 region of 18S rDNA in peritrichs. The newly designed specific primers thus provide additional tools to study the molecular diversity, community composition, and phylogeography of these ecologically important protists in different systems.

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Authors and Affiliations

  1. Laboratory of Microbial Ecology and Matter Cycles, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China

    Lei Su  (苏蕾), Qianqian Zhang  (张倩倩) & Jun Gong  (龚骏)

  2. University of Chinese Academy of Sciences, Beijing, 100049, China

    Lei Su  (苏蕾), Qianqian Zhang  (张倩倩) & Jun Gong  (龚骏)

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  1. Lei Su  (苏蕾)
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  2. Qianqian Zhang  (张倩倩)
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  3. Jun Gong  (龚骏)
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Correspondence to Jun Gong  (龚骏).

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Supported by the National Natural Science Foundation of China (Nos. 31572255, 41522604, 31301867), the Strategic Priority Research Program of CAS (No. XDA11020702), and the Science and Technology Development Program of Yantai (No. 2014ZH073)

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Su, L., Zhang, Q. & Gong, J. Development and evaluation of specific PCR primers targeting the ribosomal DNA-internal transcribed spacer (ITS) region of peritrich ciliates in environmental samples. J. Ocean. Limnol. 36, 818–826 (2018). https://doi.org/10.1007/s00343-018-6326-3

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  • DOI: https://doi.org/10.1007/s00343-018-6326-3

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