Metabarcoding to monitor the crustacean zooplankton of a lake improves when using a reference DNA library from local samples
Biodiversity surveys through morphology provide invaluable data to inform biological monitoring efforts, involving specialised taxonomic skills that are not always available. The revolution brought by the advent of metabarcoding associated to massive sequencing is currently seen as a potential adva...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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PAGEPress Publications
2023-02-01
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| Series: | Journal of Limnology |
| Subjects: | |
| Online Access: | https://www.jlimnol.it/index.php/jlimnol/article/view/2087 |
| _version_ | 1828038893899874304 |
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| author | Giuseppe Garlasché Giulia Borgomaneiro Roberta Piscia Marina Manca Ester M. Eckert Diego Fontaneto |
| author_facet | Giuseppe Garlasché Giulia Borgomaneiro Roberta Piscia Marina Manca Ester M. Eckert Diego Fontaneto |
| author_sort | Giuseppe Garlasché |
| collection | DOAJ |
| description |
Biodiversity surveys through morphology provide invaluable data to inform biological monitoring efforts, involving specialised taxonomic skills that are not always available. The revolution brought by the advent of metabarcoding associated to massive sequencing is currently seen as a potential advance, even if different approaches may often provide different results. Here we test if reliable results from metabarcoding can be obtained by i) basing the analyses on a detailed knowledge of the local diversity from morphology, ii) applying tools from DNA taxonomy to create a local reference library, ii) developing custom primers, taking as example the crustacean zooplankton of a subalpine lake in Northern Italy, Lake Maggiore. We support the idea that occurrences from metabarcoding can be reliable, especially with targeted primers, but we confirm that read numbers from massive sequencing could not be related to abundance of individuals in our analyses. Data from metabarcoding can thus be used to reliably monitor species occurrence in the lake, but not changes in abundance.
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| first_indexed | 2024-04-10T16:32:43Z |
| format | Article |
| id | doaj.art-b85cb49248b1498399d4382efd481af5 |
| institution | Directory Open Access Journal |
| issn | 1129-5767 1723-8633 |
| language | English |
| last_indexed | 2024-04-10T16:32:43Z |
| publishDate | 2023-02-01 |
| publisher | PAGEPress Publications |
| record_format | Article |
| series | Journal of Limnology |
| spelling | doaj.art-b85cb49248b1498399d4382efd481af52023-02-08T18:31:20ZengPAGEPress PublicationsJournal of Limnology1129-57671723-86332023-02-0182110.4081/jlimnol.2023.2087Metabarcoding to monitor the crustacean zooplankton of a lake improves when using a reference DNA library from local samplesGiuseppe Garlasché0Giulia Borgomaneiro1Roberta Piscia2Marina Manca3Ester M. Eckert4Diego Fontaneto5National Research Council, Water Research Institute (CNR-IRSA), Verbania PallanzaNational Research Council, Water Research Institute (CNR-IRSA), Verbania PallanzaNational Research Council, Water Research Institute (CNR-IRSA), Verbania PallanzaNational Research Council, Water Research Institute (CNR-IRSA), Verbania PallanzaNational Research Council, Water Research Institute (CNR-IRSA), Verbania PallanzaNational Research Council, Water Research Institute (CNR-IRSA), Verbania Pallanza Biodiversity surveys through morphology provide invaluable data to inform biological monitoring efforts, involving specialised taxonomic skills that are not always available. The revolution brought by the advent of metabarcoding associated to massive sequencing is currently seen as a potential advance, even if different approaches may often provide different results. Here we test if reliable results from metabarcoding can be obtained by i) basing the analyses on a detailed knowledge of the local diversity from morphology, ii) applying tools from DNA taxonomy to create a local reference library, ii) developing custom primers, taking as example the crustacean zooplankton of a subalpine lake in Northern Italy, Lake Maggiore. We support the idea that occurrences from metabarcoding can be reliable, especially with targeted primers, but we confirm that read numbers from massive sequencing could not be related to abundance of individuals in our analyses. Data from metabarcoding can thus be used to reliably monitor species occurrence in the lake, but not changes in abundance. https://www.jlimnol.it/index.php/jlimnol/article/view/2087CladoceraCopepodaDNA taxonomyLake Maggioremetabarcodingzooplankton |
| spellingShingle | Giuseppe Garlasché Giulia Borgomaneiro Roberta Piscia Marina Manca Ester M. Eckert Diego Fontaneto Metabarcoding to monitor the crustacean zooplankton of a lake improves when using a reference DNA library from local samples Journal of Limnology Cladocera Copepoda DNA taxonomy Lake Maggiore metabarcoding zooplankton |
| title | Metabarcoding to monitor the crustacean zooplankton of a lake improves when using a reference DNA library from local samples |
| title_full | Metabarcoding to monitor the crustacean zooplankton of a lake improves when using a reference DNA library from local samples |
| title_fullStr | Metabarcoding to monitor the crustacean zooplankton of a lake improves when using a reference DNA library from local samples |
| title_full_unstemmed | Metabarcoding to monitor the crustacean zooplankton of a lake improves when using a reference DNA library from local samples |
| title_short | Metabarcoding to monitor the crustacean zooplankton of a lake improves when using a reference DNA library from local samples |
| title_sort | metabarcoding to monitor the crustacean zooplankton of a lake improves when using a reference dna library from local samples |
| topic | Cladocera Copepoda DNA taxonomy Lake Maggiore metabarcoding zooplankton |
| url | https://www.jlimnol.it/index.php/jlimnol/article/view/2087 |
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