An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples
Background Salmonids are native from the North Hemisphere but have been introduced for aquaculture and sport fishing in the South Hemisphere and inhabit most rivers and lakes in temperate and cold regions worldwide. Five species are included in the Global Invasive Species Database: rainbow trout Onc...
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PeerJ Inc.
2017-02-01
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| Online Access: | https://peerj.com/articles/3045.pdf |
| _version_ | 1827607271156219904 |
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| author | Laura Clusa Alba Ardura Sara Fernández Agustín A. Roca Eva García-Vázquez |
| author_facet | Laura Clusa Alba Ardura Sara Fernández Agustín A. Roca Eva García-Vázquez |
| author_sort | Laura Clusa |
| collection | DOAJ |
| description | Background Salmonids are native from the North Hemisphere but have been introduced for aquaculture and sport fishing in the South Hemisphere and inhabit most rivers and lakes in temperate and cold regions worldwide. Five species are included in the Global Invasive Species Database: rainbow trout Oncorhynchus mykiss, Atlantic salmon Salmo salar, brown trout Salmo trutta, brook trout Salvelinus fontinalis, and lake trout Salvelinus namaycush. In contrast, other salmonids are endangered in their native settings. Methods Here we have developed a method to identify salmonid species directly from water samples, focusing on the Iberian Peninsula as a case study. We have designed nested Salmonidae-specific primers within the 16S rDNA region. From these primers and a PCR-RFLP procedure the target species can be unequivocally identified from DNA extracted from water samples. Results The method was validated in aquarium experiments and in the field with water from watersheds with known salmonid populations. Finally, the method was applied to obtain a global view of the Salmonidae community in Nalón River (north coast of Spain). Discussion This new powerful, very sensitive (identifying the species down to 10 pg DNA/ml water) and economical tool can be applied for monitoring the presence of salmonids in a variety of situations, from checking upstream colonization after removal of river barriers to monitoring potential escapes from fish farms. |
| first_indexed | 2024-03-09T06:52:05Z |
| format | Article |
| id | doaj.art-69bc61937f614d13b5452e9d3a3dd915 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:52:05Z |
| publishDate | 2017-02-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
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| spelling | doaj.art-69bc61937f614d13b5452e9d3a3dd9152023-12-03T10:22:36ZengPeerJ Inc.PeerJ2167-83592017-02-015e304510.7717/peerj.3045An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samplesLaura Clusa0Alba Ardura1Sara Fernández2Agustín A. Roca3Eva García-Vázquez4Department of Functional Biology, University of Oviedo, Oviedo, Asturias, SpainUSR3278-CRIOBE-CNRS-EPHE-UPVD, Laboratoire d’Excellence “CORAIL”, Université de Perpignan, Perpignan, FranceDepartment of Functional Biology, University of Oviedo, Oviedo, Asturias, SpainDepartment of Functional Biology, University of Oviedo, Oviedo, Asturias, SpainDepartment of Functional Biology, University of Oviedo, Oviedo, Asturias, SpainBackground Salmonids are native from the North Hemisphere but have been introduced for aquaculture and sport fishing in the South Hemisphere and inhabit most rivers and lakes in temperate and cold regions worldwide. Five species are included in the Global Invasive Species Database: rainbow trout Oncorhynchus mykiss, Atlantic salmon Salmo salar, brown trout Salmo trutta, brook trout Salvelinus fontinalis, and lake trout Salvelinus namaycush. In contrast, other salmonids are endangered in their native settings. Methods Here we have developed a method to identify salmonid species directly from water samples, focusing on the Iberian Peninsula as a case study. We have designed nested Salmonidae-specific primers within the 16S rDNA region. From these primers and a PCR-RFLP procedure the target species can be unequivocally identified from DNA extracted from water samples. Results The method was validated in aquarium experiments and in the field with water from watersheds with known salmonid populations. Finally, the method was applied to obtain a global view of the Salmonidae community in Nalón River (north coast of Spain). Discussion This new powerful, very sensitive (identifying the species down to 10 pg DNA/ml water) and economical tool can be applied for monitoring the presence of salmonids in a variety of situations, from checking upstream colonization after removal of river barriers to monitoring potential escapes from fish farms.https://peerj.com/articles/3045.pdfeDNASpecies-specific RFLPFamily-specific primersSalmonids |
| spellingShingle | Laura Clusa Alba Ardura Sara Fernández Agustín A. Roca Eva García-Vázquez An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples PeerJ eDNA Species-specific RFLP Family-specific primers Salmonids |
| title | An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples |
| title_full | An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples |
| title_fullStr | An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples |
| title_full_unstemmed | An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples |
| title_short | An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples |
| title_sort | extremely sensitive nested pcr rflp mitochondrial marker for detection and identification of salmonids in edna from water samples |
| topic | eDNA Species-specific RFLP Family-specific primers Salmonids |
| url | https://peerj.com/articles/3045.pdf |
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