Advancements in DNA Metabarcoding Protocols for Monitoring Zooplankton in Marine and Brackish Environments DOI Creative Commons
Jorge Moutinho, Filipe O. Costa, Sofia Duarte

et al.

Journal of Marine Science and Engineering, Journal Year: 2024, Volume and Issue: 12(11), P. 2093 - 2093

Published: Nov. 19, 2024

Over the past century, numerous studies have proposed various organisms for biomonitoring of aquatic systems, but only recently has zooplankton emerged as a promising indicator water quality. The traditional identification methods, however, can be inefficient in context monitoring efforts, they are often time consuming and costly. DNA metabarcoding offers powerful alternative, providing more efficient reliable approach to monitor communities. In this review, we assess current state-of-the-art methodologies used evaluate marine brackish communities through workflow. While several emerging approaches been reported, no standardization achieved so far. extraction step gained most consensus, with widespread use commercial kits (DNeasy Blood & Tissue kit employed ca. 25% studies), though there is still significant variation selection. Additionally, 18S COI were main molecular markers (ca. 61% 54%, respectively) target region varied former. Moreover, many methodologies, particularly those processing samples, lack practical validation. Some also fail provide sufficient detail their methodology descriptions hindering reproducibility. Overall, shows great potential communities, further effort needed establish standardized practices optimize across entire methodological pipeline.

Language: Английский

Eukaryotic biodiversity of sub-ice water in the marginal ice zone of the European Arctic: A multi-marker eDNA metabarcoding survey DOI Creative Commons
Ayla Murray, Simon Ramondenc, Simon F. Reifenberg

et al.

The Science of The Total Environment, Journal Year: 2025, Volume and Issue: 968, P. 178840 - 178840

Published: Feb. 21, 2025

The effects of climate change, including warming waters, loss sea ice habitat and the resulting changes in primary production, are inducing shifts marine communities across Arctic Ocean. marginal zone (MIZ) is a highly dynamic ecosystem transition between pack open ocean. It for wide range organisms, sympagic pelagic taxa, all which affected by changing physical dynamics MIZ. Here we use multi-marker (18S rRNA V1-2 COI Leray-XT) approach to investigate eukaryotic biodiversity upper water column this understudied habitat. Environmental DNA (eDNA) was sequenced from seawater samples collected directly beneath at depth 5 m, sourced floes representing different regimes. To explore abiotic factors influencing under-ice diversity, combined satellite-derived environmental data with simultaneous situ hydrographic measurements. Our analysis identified metazoans, along producers typical region, as well substantial uncharacterised diversity. Alpha diversity indices were higher immediately below ice, community composition differed depths floe stations. We show that properties meltwater stratification ocean, concentration distance edge, significantly shape composition. These findings highlight effectiveness eDNA metabarcoding monitoring sub-ice enhance our understanding

Language: Английский

Citations

0
Metazoan Diversity and Its Drivers: An eDNA Survey in the Pacific Gateway of a Changing Arctic Ocean DOI Creative Commons
Gerlien Verhaegen, Tatsuya Kawakami, Ayla Murray

et al.

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(2)

Published: March 1, 2025

ABSTRACT Climate change drives species to adapt or undergo range shifts survive. The Arctic Ocean, experiencing more drastic environmental changes than any other ocean, has two primary inflow regions that facilitate these shifts: the wide, deep Atlantic Gateway and narrow, shallow Pacific Gateway. Environmental DNA (eDNA) surveys have proven be effective in characterizing community composition understanding its ecological drivers. We conducted first COI marker‐based eDNA survey analyzed seawater samples from various geographic regions, depths, water masses across Bering Strait, Chukchi Sea, South Beaufort Sea. Metazoan taxa 15 different phyla indicator for were identified. characterized a highly diverse neritic fauna Strait aligning with known locations of benthic hotspots. On slope we observed transitions copepod‐dominated epipelagic waters cnidarian‐ sponge‐dominated deeper areas. Alpha diversity peaked near seabed coastlines was highest within warmest Alaskan Coastal Water mass. linked metazoan communities variables, being associated higher temperatures fluorescence, majority them lower salinities. This included mostly Pseudocalanus copepod verongiid sponges. While rising might enhance alpha diversity, anticipate this will primarily due influx warmer fresher masses. Several taxa, including bivalve Macoma calcarea seastar Leptasterias arctica , as well jellyfish Chrysaora melanaster Triconia borealis colder, saltier likely negatively impacted by ongoing change. Our study successfully rapidly changing Ocean.

Language: Английский

Citations

0
Advancements in DNA Metabarcoding Protocols for Monitoring Zooplankton in Marine and Brackish Environments DOI Creative Commons
Jorge Moutinho, Filipe O. Costa, Sofia Duarte

et al.

Journal of Marine Science and Engineering, Journal Year: 2024, Volume and Issue: 12(11), P. 2093 - 2093

Published: Nov. 19, 2024

Over the past century, numerous studies have proposed various organisms for biomonitoring of aquatic systems, but only recently has zooplankton emerged as a promising indicator water quality. The traditional identification methods, however, can be inefficient in context monitoring efforts, they are often time consuming and costly. DNA metabarcoding offers powerful alternative, providing more efficient reliable approach to monitor communities. In this review, we assess current state-of-the-art methodologies used evaluate marine brackish communities through workflow. While several emerging approaches been reported, no standardization achieved so far. extraction step gained most consensus, with widespread use commercial kits (DNeasy Blood & Tissue kit employed ca. 25% studies), though there is still significant variation selection. Additionally, 18S COI were main molecular markers (ca. 61% 54%, respectively) target region varied former. Moreover, many methodologies, particularly those processing samples, lack practical validation. Some also fail provide sufficient detail their methodology descriptions hindering reproducibility. Overall, shows great potential communities, further effort needed establish standardized practices optimize across entire methodological pipeline.

Language: Английский

Citations

0