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Detecting In Situ Copepod Diet Diversity Using Molecular Technique: Development of a Copepod/Symbiotic Ciliate-Excluding Eukaryote-Inclusive PCR Protocol
Hu, SM; Guo, ZL; Li, T; Carpenter, EJ; Liu, S; Lin, SJ; shliu@scsio.ac.cn; senjie.lin@uconn.edu
2014
Source PublicationPLOS ONE
ISSN1932-6203
Volume9Issue:7Pages:-e103528
AbstractKnowledge of in situ copepod diet diversity is crucial for accurately describing pelagic food web structure but is challenging to achieve due to lack of an easily applicable methodology. To enable analysis with whole copepod-derived DNAs, we developed a copepod-excluding 18S rDNA-based PCR protocol. Although it is effective in depressing amplification of copepod 18S rDNA, its applicability to detect diverse eukaryotes in both mono- and mixed-species has not been demonstrated. Besides, the protocol suffers from the problem that sequences from symbiotic ciliates are overrepresented in the retrieved 18S rDNA libraries. In this study, we designed a blocking primer to make a combined primer set (copepod/symbiotic ciliate-excluding eukaryote-common: CEEC) to depress PCR amplification of symbiotic ciliate sequences while maximizing the range of eukaryotes amplified. We firstly examined the specificity and efficacy of CEEC by PCR-amplifying DNAs from 16 copepod species, 37 representative organisms that are potential prey of copepods and a natural microplankton sample, and then evaluated the efficiency in reconstructing diet composition by detecting the food of both lab-reared and field-collected copepods. Our results showed that the CEEC primer set can successfully amplify 18S rDNA from a wide range of isolated species and mixed-species samples while depressing amplification of that from copepod and targeted symbiotic ciliate, indicating the universality of CEEC in specifically detecting prey of copepods. All the predetermined food offered to copepods in the laboratory were successfully retrieved, suggesting that the CEEC-based protocol can accurately reconstruct the diets of copepods without interference of copepods and their associated ciliates present in the DNA samples. Our initial application to analyzing the food composition of field-collected copepods uncovered diverse prey species, including those currently known, and those that are unsuspected, as copepod prey. While testing is required, this protocol provides a useful strategy for depicting in situ dietary composition of copepods.
Department[Hu, Simin ; Guo, Zhiling ; Li, Tao ; Liu, Sheng] Chinese Acad Sci, South China Sea Inst Oceanol, Key Lab Trop Marine Bioresources & Ecol, Guangzhou, Guangdong, Peoples R China ; [Hu, Simin ; Guo, Zhiling] Univ Chinese Acad Sci, Beijing, Peoples R China ; [Li, Tao] Chinese Acad Sci, Trop Marine Biol Res Stn Hainan, Sanya, Peoples R China ; [Carpenter, Edward J.] San Francisco State Univ, Romberg Tiburon Ctr, San Francisco, CA 94132 USA ; [Lin, Senjie] Xiamen Univ, Marine Biodivers & Global Change Res Ctr, Xiamen, Peoples R China ; [Lin, Senjie] Univ Connecticut, Dept Marine Sci, Groton, CT 06340 USA
Subject AreaScience & Technology - Other Topics
Funding OrganizationChinese Academy of Sciences (CAS) [KZCX2-YW-JS206]; Natural Science Foundation of China [41076096, 41276160, 40828006] ; Chinese Academy of Sciences (CAS) [KZCX2-YW-JS206]; Natural Science Foundation of China [41076096, 41276160, 40828006] ; Chinese Academy of Sciences (CAS) [KZCX2-YW-JS206]; Natural Science Foundation of China [41076096, 41276160, 40828006] ; Chinese Academy of Sciences (CAS) [KZCX2-YW-JS206]; Natural Science Foundation of China [41076096, 41276160, 40828006]
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Indexed Bysci
Funding ProjectLMB
Funding OrganizationChinese Academy of Sciences (CAS) [KZCX2-YW-JS206]; Natural Science Foundation of China [41076096, 41276160, 40828006] ; Chinese Academy of Sciences (CAS) [KZCX2-YW-JS206]; Natural Science Foundation of China [41076096, 41276160, 40828006] ; Chinese Academy of Sciences (CAS) [KZCX2-YW-JS206]; Natural Science Foundation of China [41076096, 41276160, 40828006] ; Chinese Academy of Sciences (CAS) [KZCX2-YW-JS206]; Natural Science Foundation of China [41076096, 41276160, 40828006]
WOS IDWOS:000341354800104
Citation statistics
Document Type期刊论文
Identifierhttp://ir.scsio.ac.cn/handle/344004/10421
Collection中科院海洋生物资源可持续利用重点实验室
Corresponding Authorshliu@scsio.ac.cn; senjie.lin@uconn.edu
Recommended Citation
GB/T 7714
Hu, SM,Guo, ZL,Li, T,et al. Detecting In Situ Copepod Diet Diversity Using Molecular Technique: Development of a Copepod/Symbiotic Ciliate-Excluding Eukaryote-Inclusive PCR Protocol[J]. PLOS ONE,2014,9(7):-e103528.
APA Hu, SM.,Guo, ZL.,Li, T.,Carpenter, EJ.,Liu, S.,...&senjie.lin@uconn.edu.(2014).Detecting In Situ Copepod Diet Diversity Using Molecular Technique: Development of a Copepod/Symbiotic Ciliate-Excluding Eukaryote-Inclusive PCR Protocol.PLOS ONE,9(7),-e103528.
MLA Hu, SM,et al."Detecting In Situ Copepod Diet Diversity Using Molecular Technique: Development of a Copepod/Symbiotic Ciliate-Excluding Eukaryote-Inclusive PCR Protocol".PLOS ONE 9.7(2014):-e103528.
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