Advancements in DNA Metabarcoding Protocols for Monitoring Zooplankton in Marine and Brackish Environments
Over the past century, numerous studies have proposed various organisms for the biomonitoring of aquatic systems, but only recently has zooplankton emerged as a promising indicator of water quality. The traditional identification methods, however, can be inefficient in the context of monitoring effo...
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MDPI AG
2024-11-01
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| Series: | Journal of Marine Science and Engineering |
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| Online Access: | https://www.mdpi.com/2077-1312/12/11/2093 |
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| author | Jorge Moutinho Filipe O. Costa Sofia Duarte |
| author_facet | Jorge Moutinho Filipe O. Costa Sofia Duarte |
| author_sort | Jorge Moutinho |
| collection | DOAJ |
| description | Over the past century, numerous studies have proposed various organisms for the biomonitoring of aquatic systems, but only recently has zooplankton emerged as a promising indicator of water quality. The traditional identification methods, however, can be inefficient in the context of monitoring efforts, as they are often time consuming and costly. DNA metabarcoding offers a powerful alternative, providing a more efficient and reliable approach to monitor zooplankton communities. In this review, we assess the current state-of-the-art methodologies used to evaluate marine and brackish zooplankton communities through the DNA metabarcoding workflow. While several emerging approaches have been reported, no standardization has been achieved so far. The DNA extraction step has gained the most consensus, with the widespread use of commercial kits (DNeasy Blood & Tissue kit employed in ca. 25% of the studies), though there is still a significant variation in kit selection. Additionally, 18S and COI were the main molecular markers employed (ca. 61% and 54%, respectively) though the target region varied in the former. Moreover, many methodologies, particularly those used for processing zooplankton samples, lack practical validation. Some studies also fail to provide sufficient detail in their methodology descriptions hindering reproducibility. Overall, DNA metabarcoding shows great potential for the efficient monitoring of zooplankton communities, but further effort is needed to establish standardized practices and optimize the current approaches across the entire methodological pipeline. |
| format | Article |
| id | doaj-art-980ec590addd4d6aa99ea9498ba90f69 |
| institution | Kabale University |
| issn | 2077-1312 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Marine Science and Engineering |
| spelling | doaj-art-980ec590addd4d6aa99ea9498ba90f692024-11-26T18:08:35ZengMDPI AGJournal of Marine Science and Engineering2077-13122024-11-011211209310.3390/jmse12112093Advancements in DNA Metabarcoding Protocols for Monitoring Zooplankton in Marine and Brackish EnvironmentsJorge Moutinho0Filipe O. Costa1Sofia Duarte2Centre of Molecular and Environmental Biology (CBMA) and ARNET—Aquatic Research Network, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, PortugalCentre of Molecular and Environmental Biology (CBMA) and ARNET—Aquatic Research Network, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, PortugalCentre of Molecular and Environmental Biology (CBMA) and ARNET—Aquatic Research Network, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, PortugalOver the past century, numerous studies have proposed various organisms for the biomonitoring of aquatic systems, but only recently has zooplankton emerged as a promising indicator of water quality. The traditional identification methods, however, can be inefficient in the context of monitoring efforts, as they are often time consuming and costly. DNA metabarcoding offers a powerful alternative, providing a more efficient and reliable approach to monitor zooplankton communities. In this review, we assess the current state-of-the-art methodologies used to evaluate marine and brackish zooplankton communities through the DNA metabarcoding workflow. While several emerging approaches have been reported, no standardization has been achieved so far. The DNA extraction step has gained the most consensus, with the widespread use of commercial kits (DNeasy Blood & Tissue kit employed in ca. 25% of the studies), though there is still a significant variation in kit selection. Additionally, 18S and COI were the main molecular markers employed (ca. 61% and 54%, respectively) though the target region varied in the former. Moreover, many methodologies, particularly those used for processing zooplankton samples, lack practical validation. Some studies also fail to provide sufficient detail in their methodology descriptions hindering reproducibility. Overall, DNA metabarcoding shows great potential for the efficient monitoring of zooplankton communities, but further effort is needed to establish standardized practices and optimize the current approaches across the entire methodological pipeline.https://www.mdpi.com/2077-1312/12/11/2093DNA metabarcodingzooplankton communitiesmarinebrackishmonitoringstate-of-the-art methodology |
| spellingShingle | Jorge Moutinho Filipe O. Costa Sofia Duarte Advancements in DNA Metabarcoding Protocols for Monitoring Zooplankton in Marine and Brackish Environments Journal of Marine Science and Engineering DNA metabarcoding zooplankton communities marine brackish monitoring state-of-the-art methodology |
| title | Advancements in DNA Metabarcoding Protocols for Monitoring Zooplankton in Marine and Brackish Environments |
| title_full | Advancements in DNA Metabarcoding Protocols for Monitoring Zooplankton in Marine and Brackish Environments |
| title_fullStr | Advancements in DNA Metabarcoding Protocols for Monitoring Zooplankton in Marine and Brackish Environments |
| title_full_unstemmed | Advancements in DNA Metabarcoding Protocols for Monitoring Zooplankton in Marine and Brackish Environments |
| title_short | Advancements in DNA Metabarcoding Protocols for Monitoring Zooplankton in Marine and Brackish Environments |
| title_sort | advancements in dna metabarcoding protocols for monitoring zooplankton in marine and brackish environments |
| topic | DNA metabarcoding zooplankton communities marine brackish monitoring state-of-the-art methodology |
| url | https://www.mdpi.com/2077-1312/12/11/2093 |
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