Development of a cost-effective metabarcoding strategy for analysis of the marine phytoplankton community
We developed a cost-effective metabarcoding strategy to analyze phytoplankton community structure using the Illumina MiSeq system. The amplicons (404–411 bp) obtained by end-pairing of two reads were sufficiently long to distinguish algal species and provided barcode data equivalent to those generat...
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| Format: | Article |
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PeerJ Inc.
2016-06-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/2115.pdf |
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| author | Tae-Ho Yoon Hye-Eun Kang Chang-Keun Kang Sang Heon Lee Do-Hwan Ahn Hyun Park Hyun-Woo Kim |
| author_facet | Tae-Ho Yoon Hye-Eun Kang Chang-Keun Kang Sang Heon Lee Do-Hwan Ahn Hyun Park Hyun-Woo Kim |
| author_sort | Tae-Ho Yoon |
| collection | DOAJ |
| description | We developed a cost-effective metabarcoding strategy to analyze phytoplankton community structure using the Illumina MiSeq system. The amplicons (404–411 bp) obtained by end-pairing of two reads were sufficiently long to distinguish algal species and provided barcode data equivalent to those generated with the Roche 454 system, but at less than 1/20th of the cost. The original universal primer sequences targeting the 23S rDNA region and the PCR strategy were both modified, and this resulted in higher numbers of eukaryotic algal sequences by excluding non-photosynthetic proteobacterial sequences supporting effectiveness of this strategy. The novel strategy was used to analyze the phytoplankton community structure of six water samples from the East/Japan Sea: surface and 50 m depths at coastal and open-sea sites, with collections in May and July 2014. In total, 345 operational taxonomic units (OTUs) were identified, which covered most of the prokaryotic and eukaryotic algal phyla, including Dinophyta, Rhodophyta, Ochrophyta, Chlorophyta, Streptophyta, Cryptophyta, Haptophyta, and Cyanophyta. This highlights the importance of plastid 23S primers, which perform better than the currently used 16S primers for phytoplankton community surveys. The findings also revealed that more efforts should be made to update 23S rDNA sequences as well as those of 16S in the databases. Analysis of algal proportions in the six samples showed that community structure differed depending on location, depth and season. Across the six samples evaluated, the numbers of OTUs in each phylum were similar but their relative proportions varied. This novel strategy would allow laboratories to analyze large numbers of samples at reasonable expense, whereas this has not been possible to date due to cost and time. In addition, we expect that this strategy will generate a large amount of novel data that could potentially change established methods and tools that are currently used in the realms of oceanography and marine ecology. |
| first_indexed | 2024-03-09T07:58:00Z |
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| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:58:00Z |
| publishDate | 2016-06-01 |
| publisher | PeerJ Inc. |
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| spelling | doaj.art-cd6a868e61474f079c6e507fa8eecaee2023-12-03T00:51:41ZengPeerJ Inc.PeerJ2167-83592016-06-014e211510.7717/peerj.2115Development of a cost-effective metabarcoding strategy for analysis of the marine phytoplankton communityTae-Ho Yoon0Hye-Eun Kang1Chang-Keun Kang2Sang Heon Lee3Do-Hwan Ahn4Hyun Park5Hyun-Woo Kim6Interdiciplinary Program of Biomedical Engineering, Pukyong National University, Busan, Republic of KoreaDepartment of Marine Biology, Pukyong National University, Busan, South KoreaSchool of Earth Science & Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, Republic of KoreaDepartment of Oceanography, Pusan National University, Busan, South KoreaDivision of Polar Life Sciences, Korea Polar Research Institute, Incheon, South KoreaKorea Polar Research Institute, Korea Ocean Research and Development Institute, Incheon, Republic of KoreaInterdiciplinary Program of Biomedical Engineering, Pukyong National University, Busan, Republic of KoreaWe developed a cost-effective metabarcoding strategy to analyze phytoplankton community structure using the Illumina MiSeq system. The amplicons (404–411 bp) obtained by end-pairing of two reads were sufficiently long to distinguish algal species and provided barcode data equivalent to those generated with the Roche 454 system, but at less than 1/20th of the cost. The original universal primer sequences targeting the 23S rDNA region and the PCR strategy were both modified, and this resulted in higher numbers of eukaryotic algal sequences by excluding non-photosynthetic proteobacterial sequences supporting effectiveness of this strategy. The novel strategy was used to analyze the phytoplankton community structure of six water samples from the East/Japan Sea: surface and 50 m depths at coastal and open-sea sites, with collections in May and July 2014. In total, 345 operational taxonomic units (OTUs) were identified, which covered most of the prokaryotic and eukaryotic algal phyla, including Dinophyta, Rhodophyta, Ochrophyta, Chlorophyta, Streptophyta, Cryptophyta, Haptophyta, and Cyanophyta. This highlights the importance of plastid 23S primers, which perform better than the currently used 16S primers for phytoplankton community surveys. The findings also revealed that more efforts should be made to update 23S rDNA sequences as well as those of 16S in the databases. Analysis of algal proportions in the six samples showed that community structure differed depending on location, depth and season. Across the six samples evaluated, the numbers of OTUs in each phylum were similar but their relative proportions varied. This novel strategy would allow laboratories to analyze large numbers of samples at reasonable expense, whereas this has not been possible to date due to cost and time. In addition, we expect that this strategy will generate a large amount of novel data that could potentially change established methods and tools that are currently used in the realms of oceanography and marine ecology.https://peerj.com/articles/2115.pdfBarcodePhytoplanktonNext-generation sequencingOceanographyGenomics |
| spellingShingle | Tae-Ho Yoon Hye-Eun Kang Chang-Keun Kang Sang Heon Lee Do-Hwan Ahn Hyun Park Hyun-Woo Kim Development of a cost-effective metabarcoding strategy for analysis of the marine phytoplankton community PeerJ Barcode Phytoplankton Next-generation sequencing Oceanography Genomics |
| title | Development of a cost-effective metabarcoding strategy for analysis of the marine phytoplankton community |
| title_full | Development of a cost-effective metabarcoding strategy for analysis of the marine phytoplankton community |
| title_fullStr | Development of a cost-effective metabarcoding strategy for analysis of the marine phytoplankton community |
| title_full_unstemmed | Development of a cost-effective metabarcoding strategy for analysis of the marine phytoplankton community |
| title_short | Development of a cost-effective metabarcoding strategy for analysis of the marine phytoplankton community |
| title_sort | development of a cost effective metabarcoding strategy for analysis of the marine phytoplankton community |
| topic | Barcode Phytoplankton Next-generation sequencing Oceanography Genomics |
| url | https://peerj.com/articles/2115.pdf |
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