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Canals O, Corell J, Villarino E, Chust G, Aylagas E, Mendibil I, Michell CT, González-Gordillo JI, Irigoien X, Rodríguez-Ezpeleta N. Global mesozooplankton communities show lower connectivity in deep oceanic layers. Mol Ecol 2024:e17286. [PMID: 38287749 DOI: 10.1111/mec.17286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/06/2023] [Accepted: 12/22/2023] [Indexed: 01/31/2024]
Abstract
Mesozooplankton is a key component of the ocean, regulating global processes such as the carbon pump, and ensuring energy transfer from lower to higher trophic levels. Yet, knowledge on mesozooplankton diversity, distribution and connectivity at global scale is still fragmented. To fill this gap, we applied DNA metabarcoding to mesozooplankton samples collected during the Malaspina-2010 circumnavigation expedition across the Atlantic, Indian and Pacific oceans from the surface to bathypelagic depths. We highlight the still scarce knowledge on global mesozooplankton diversity and identify the Indian Ocean and the deep sea as the oceanic regions with the highest proportion of hidden diversity. We report no consistent alpha-diversity patterns for mesozooplankton at a global scale, neither across vertical nor horizontal gradients. However, beta-diversity analysis suggests horizontal and vertical structuring of mesozooplankton communities mostly attributed to turnover and reveals an increase in mesozooplankton beta-diversity with depth, indicating reduced connectivity at deeper layers. Additionally, we identify a water mass type-mediated structuring of mesozooplankton bathypelagic communities instead of an oceanic basin-mediated as observed at upper layers. This suggests limited dispersal at deep ocean layers, most likely due to weaker currents and lower mixing of water mass types, thus reinforcing the importance of oceanic currents and barriers to dispersal in shaping global plankton communities.
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Affiliation(s)
- Oriol Canals
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Jon Corell
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Ernesto Villarino
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Guillem Chust
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Eva Aylagas
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Iñaki Mendibil
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Craig T Michell
- Biological and Environmental Science and Engineering Division, Red Sea Research Centre, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Juan Ignacio González-Gordillo
- Área de Ecología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Campus de Excelencia Internacional del Mar, Puerto Real, Spain
| | - Xabier Irigoien
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Naiara Rodríguez-Ezpeleta
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
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Haddock SHD, Choy CA. Life in the Midwater: The Ecology of Deep Pelagic Animals. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:383-416. [PMID: 38231738 DOI: 10.1146/annurev-marine-031623-095435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The water column of the deep ocean is dark, cold, low in food, and under crushing pressures, yet it is full of diverse life. Due to its enormous volume, this mesopelagic zone is home to some of the most abundant animals on the planet. Rather than struggling to survive, they thrive-owing to a broad set of adaptations for feeding, behavior, and physiology. Our understanding of these adaptations is constrained by the tools available for exploring the deep sea, but this tool kit is expanding along with technological advances. Each time we apply a new method to the depths, we gain surprising insights about genetics, ecology, behavior, physiology, diversity, and the dynamics of change. These discoveries show structure within the seemingly uniform habitat, limits to the seemingly inexhaustible resources, and vulnerability in the seemingly impervious environment. To understand midwater ecology, we need to reimagine the rules that govern terrestrial ecosystems. By spending more time at depth-with whatever tools are available-we can fill the knowledge gaps and better link ecology to the environment throughout the water column.
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Affiliation(s)
- Steven H D Haddock
- Monterey Bay Aquarium Research Institute, Moss Landing, California, USA;
| | - C Anela Choy
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA;
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Govender A, Singh S, Groeneveld J, Pillay S, Willows-Munro S. Metabarcoding analysis of marine zooplankton confirms the ecological role of a sheltered bight along an exposed continental shelf. Mol Ecol 2023; 32:6210-6222. [PMID: 35712991 DOI: 10.1111/mec.16567] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/17/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022]
Abstract
Zooplankton plays an essential role in marine ecosystems as the link between primary producers (phytoplankton) and higher trophic levels in food webs, and as a dynamic pool of recruits for invertebrates and fish. Zooplankton communities are diverse with a patchy distribution at different spatial scales, influenced by oceanographic processes. The continental shelf of eastern South Africa is narrow and exposed to the western-boundary Agulhas Current, with some shelter against strong directional flow provided by the broader KwaZulu-Natal Bight, a coastal offset adjacent to an estuary. We compared zooplankton species richness, diversity and relative abundance of key taxa among sheltered and exposed shelf areas using metabarcoding and community analysis, to explore the ecological role of the bight in a highly dynamic ocean region. Metabarcoding recovered higher richness and diversity at a finer resolution than could previously be achieved with traditional microscopy. Of 271 operational taxonomic units (OTUs) recovered through metabarcoding, 63% could be matched with >95% sequence similarity to reference barcodes. OTUs were dominated by malacostracan crustaceans (161 spp.), ray-finned fishes (45 spp.) and copepods (28 spp.). Species richness, diversity and the relative abundance of key taxa differed between sheltered and exposed shelf areas. Lower species richness in the bight was partly attributed to structurally homogeneous benthic habitats, and an associated reduction of meroplanktonic species originating from local benthic-pelagic exchange. High relative abundance of a ray-finned fish in the bight, as observed based on fish eggs and read counts, confirmed that the bight is an important fish spawning area. Overall, zooplankton metabarcoding outputs were congruent with findings of previous ecological research using more traditional methods of observation.
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Affiliation(s)
- Ashrenee Govender
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Oceanographic Research Institute, Durban, South Africa
| | - Sohana Singh
- Oceanographic Research Institute, Durban, South Africa
| | - Johan Groeneveld
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Oceanographic Research Institute, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sandi Willows-Munro
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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Matthews SA, Blanco‐Bercial L. Divergent patterns of zooplankton connectivity in the epipelagic and mesopelagic zones of the eastern North Pacific. Ecol Evol 2023; 13:e10664. [PMID: 37933324 PMCID: PMC10625861 DOI: 10.1002/ece3.10664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/11/2023] [Accepted: 10/13/2023] [Indexed: 11/08/2023] Open
Abstract
Due to historical under-sampling of the deep ocean, the distributional ranges of mesopelagic zooplankton are not well documented, leading to uncertainty about the mechanisms that shape midwater zooplankton community composition. Using a combination of DNA metabarcoding (18S-V4 and mtCOI) and trait-based analysis, we characterized zooplankton diversity and community composition in the upper 1000 m of the northeast Pacific Ocean. We tested whether the North Pacific Transition Zone is a biogeographic boundary region for mesopelagic zooplankton. We also tested whether zooplankton taxa occupying different vertical habitats and exhibiting different ecological traits differed in the ranges of temperature, Chl-a, and dissolved oxygen conditions inhabited. The depth of the maximum taxonomic richness deepened with increasing latitude in the North Pacific. Community similarity in the mesopelagic zone also increased in comparison with the epipelagic zone, and no evidence was found for a biogeographic boundary between previously delineated mesopelagic biogeochemical provinces. Epipelagic zooplankton exhibited broader temperature and Chl-a ranges than mesopelagic taxa. Within the epipelagic, taxa with broader temperature and Chl-a ranges also had broader distributional ranges. However, mesopelagic taxa were distributed across wider dissolved oxygen ranges, and within the mesopelagic, only oxygen ranges covaried with distributional ranges. Environmental and distributional ranges also varied among traits, both for epipelagic taxa and mesopelagic taxa. The strongest differences in both environmental and distributional ranges were observed for taxa with or without diel vertical migration behavior. Our results suggest that species traits can influence the differential effects of physical dispersal and environmental selection in shaping biogeographic distributions.
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Affiliation(s)
- Stephanie A. Matthews
- California Current Ecosystem Long‐Term Ecological Research Site, Integrative Oceanography Division, Scripps Institution of OceanographyUniversity of California San DiegoLa JollaCaliforniaUSA
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Röthig T, Trevathan-Tackett SM, Voolstra CR, Ross C, Chaffron S, Durack PJ, Warmuth LM, Sweet M. Human-induced salinity changes impact marine organisms and ecosystems. GLOBAL CHANGE BIOLOGY 2023; 29:4731-4749. [PMID: 37435759 DOI: 10.1111/gcb.16859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/06/2023] [Accepted: 06/11/2023] [Indexed: 07/13/2023]
Abstract
Climate change is fundamentally altering marine and coastal ecosystems on a global scale. While the effects of ocean warming and acidification on ecology and ecosystem functions and services are being comprehensively researched, less attention is directed toward understanding the impacts of human-driven ocean salinity changes. The global water cycle operates through water fluxes expressed as precipitation, evaporation, and freshwater runoff from land. Changes to these in turn modulate ocean salinity and shape the marine and coastal environment by affecting ocean currents, stratification, oxygen saturation, and sea level rise. Besides the direct impact on ocean physical processes, salinity changes impact ocean biological functions with the ecophysiological consequences are being poorly understood. This is surprising as salinity changes may impact diversity, ecosystem and habitat structure loss, and community shifts including trophic cascades. Climate model future projections (of end of the century salinity changes) indicate magnitudes that lead to modification of open ocean plankton community structure and habitat suitability of coral reef communities. Such salinity changes are also capable of affecting the diversity and metabolic capacity of coastal microorganisms and impairing the photosynthetic capacity of (coastal and open ocean) phytoplankton, macroalgae, and seagrass, with downstream ramifications on global biogeochemical cycling. The scarcity of comprehensive salinity data in dynamic coastal regions warrants additional attention. Such datasets are crucial to quantify salinity-based ecosystem function relationships and project such changes that ultimately link into carbon sequestration and freshwater as well as food availability to human populations around the globe. It is critical to integrate vigorous high-quality salinity data with interacting key environmental parameters (e.g., temperature, nutrients, oxygen) for a comprehensive understanding of anthropogenically induced marine changes and its impact on human health and the global economy.
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Affiliation(s)
- Till Röthig
- Department of Biology, University of Konstanz, Konstanz, Germany
- Branch of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Aquatic Research Facility, Nature-Based Solutions Research Centre, University of Derby, Derby, UK
| | - Stacey M Trevathan-Tackett
- School of Life and Environmental Science, Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia
- Deakin Marine Research and Innovation Centre, Deakin University, Geelong, Victoria, Australia
| | | | - Cliff Ross
- Department of Biology, University of North Florida, Jacksonville, Florida, USA
| | - Samuel Chaffron
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, F-75016, Paris, France
| | - Paul J Durack
- Program for Climate Model Diagnosis and Intercomparison, Lawrence Livermore National Laboratory, Livermore, California, USA
| | | | - Michael Sweet
- Aquatic Research Facility, Nature-Based Solutions Research Centre, University of Derby, Derby, UK
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Watanabe T, Hirai J, Sildever S, Tadokoro K, Hidaka K, Tanita I, Nishiuchi K, Iguchi N, Kasai H, Nishi N, Katakura S, Taniuchi Y, Kodama T, Tashiro S, Nakae M, Okazaki Y, Kitajima S, Sogawa S, Hasegawa T, Azumaya T, Hiroe Y, Ambe D, Setou T, Ito D, Kusaka A, Okunishi T, Tanaka T, Kuwata A, Hasegawa D, Kakehi S, Shimizu Y, Nagai S. Improving taxonomic classification of marine zooplankton by molecular approach: registration of taxonomically verified 18S and 28S rRNA gene sequences. PeerJ 2023; 11:e15427. [PMID: 37334134 PMCID: PMC10276563 DOI: 10.7717/peerj.15427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 04/25/2023] [Indexed: 06/20/2023] Open
Abstract
Background Zooplankton plays an important role in the marine ecosystem. A high level of taxonomic expertise is necessary for accurate species identification based on morphological characteristics. As an alternative method to morphological classification, we focused on a molecular approach using 18S and 28S ribosomal RNA (rRNA) gene sequences. This study investigates how the accuracy of species identification by metabarcoding improves when taxonomically verified sequences of dominant zooplankton species are added to the public database. The improvement was tested by using natural zooplankton samples. Methods rRNA gene sequences were obtained from dominant zooplankton species from six sea areas around Japan and registered in the public database for improving the accuracy of taxonomic classifications. Two reference databases with and without newly registered sequences were created. Comparison of detected OTUs associated with single species between the two references was done using field-collected zooplankton samples from the Sea of Okhotsk for metabarcoding analysis to verify whether or not the newly registered sequences improved the accuracy of taxonomic classifications. Results A total of 166 sequences in 96 species based on the 18S marker and 165 sequences in 95 species based on the 28S marker belonging to Arthropoda (mostly Copepoda) and Chaetognatha were registered in the public database. The newly registered sequences were mainly composed of small non-calanoid copepods, such as species belonging to Oithona and Oncaea. Based on the metabarcoding analysis of field samples, a total of 18 out of 92 OTUs were identified at the species level based on newly registered sequences in the data obtained by the 18S marker. Based on the 28S marker, 42 out of 89 OTUs were classified at the species level based on taxonomically verified sequences. Thanks to the newly registered sequences, the number of OTUs associated with a single species based on the 18S marker increased by 16% in total and by 10% per sample. Based on the 28S marker, the number of OTUs associated with a single species increased by 39% in total and by 15% per sample. The improved accuracy of species identification was confirmed by comparing different sequences obtained from the same species. The newly registered sequences had higher similarity values (mean >0.003) than the pre-existing sequences based on both rRNA genes. These OTUs were identified at the species level based on sequences not only present in the Sea of Okhotsk but also in other areas. Discussion The results of the registration of new taxonomically verified sequences and the subsequent comparison of databases based on metabarcoding data of natural zooplankton samples clearly showed an increase in accuracy in species identification. Continuous registration of sequence data covering various environmental conditions is necessary for further improvement of metabarcoding analysis of zooplankton for monitoring marine ecosystems.
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Affiliation(s)
- Tsuyoshi Watanabe
- Kushiro Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Kushiro, Japan
| | - Junya Hirai
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Sirje Sildever
- Yokohama Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shiogama, Japan
- Department of Marine Systems, Tallinn University of Technology, Tallinn, Estonia
| | - Kazuaki Tadokoro
- Shiogama Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shiogama, Japan
| | - Kiyotaka Hidaka
- Yokohama Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shiogama, Japan
| | - Iwao Tanita
- Yaeyama Field Station, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Japan
| | - Koh Nishiuchi
- Nagasaki Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Nagasaki, Japan
| | - Naoki Iguchi
- Niigata Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Niigata, Japan
| | - Hiromi Kasai
- Kushiro Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Kushiro, Japan
| | | | | | - Yukiko Taniuchi
- Kushiro Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Kushiro, Japan
| | - Taketoshi Kodama
- Yokohama Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shiogama, Japan
- Present Address: Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Satokuni Tashiro
- Yaeyama Field Station, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Japan
| | - Misato Nakae
- Niigata Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Niigata, Japan
| | - Yuji Okazaki
- Shiogama Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shiogama, Japan
| | - Satoshi Kitajima
- Nagasaki Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Nagasaki, Japan
| | - Sayaka Sogawa
- Yokohama Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shiogama, Japan
| | - Toru Hasegawa
- Nagasaki Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Nagasaki, Japan
| | - Tomonori Azumaya
- Kushiro Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Kushiro, Japan
| | - Yutaka Hiroe
- Nagasaki Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Nagasaki, Japan
| | - Daisuke Ambe
- Yokohama Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shiogama, Japan
| | - Takashi Setou
- Yokohama Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shiogama, Japan
| | - Daiki Ito
- Yokohama Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shiogama, Japan
| | - Akira Kusaka
- Yokohama Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shiogama, Japan
| | - Takeshi Okunishi
- Shiogama Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shiogama, Japan
| | - Takahiro Tanaka
- Shiogama Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shiogama, Japan
| | - Akira Kuwata
- Shiogama Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shiogama, Japan
| | - Daisuke Hasegawa
- Shiogama Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shiogama, Japan
| | - Shigeho Kakehi
- Shiogama Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shiogama, Japan
| | - Yugo Shimizu
- Shiogama Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shiogama, Japan
| | - Satoshi Nagai
- Yokohama Field Station, Fisheries Technology Institute, Fisheries Research and Education Agency, Yokohama, Japan
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Ishikawa NF, Tadokoro K, Matsubayashi J, Ohkouchi N. Biomass Pyramids of Marine Mesozooplankton Communities as Inferred From Their Integrated Trophic Positions. Ecosystems 2022. [DOI: 10.1007/s10021-022-00753-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Zooplankton diversity monitoring strategy for the urban coastal region using metabarcoding analysis. Sci Rep 2021; 11:24339. [PMID: 34934104 PMCID: PMC8692418 DOI: 10.1038/s41598-021-03656-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 11/29/2021] [Indexed: 11/12/2022] Open
Abstract
Marine ecosystems in urban coastal areas are exposed to many risks due to human activity. Thus, long-term and continuous monitoring of zooplankton diversity is necessary. High-throughput DNA metabarcoding has gained recognition as an efficient and highly sensitive approach to accurately describing the species diversity of marine zooplankton assemblages. In this study, we collected 30 zooplankton samples at about 2-week intervals for 1 year. Zooplankton diversity showing a typical four season pattern. Of the “total” and “common” zooplankton, we assigned 267 and 64 taxa. The cluster structure and seasonal diversity pattern were rough when only the “common” zooplankton was used. Our study examined how to maximize the benefits of metabarcoding for monitoring zooplankton diversity in urban coastal areas. The results suggest that to take full advantage of metabarcoding when monitoring a zooplankton community, it is necessary to carefully investigate potential ecosystem threats (non-indigenous species) through sufficient curation rather than disregarding low-abundance operational taxonomic units.
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Schroeder A, Pallavicini A, Edomi P, Pansera M, Camatti E. Suitability of a dual COI marker for marine zooplankton DNA metabarcoding. MARINE ENVIRONMENTAL RESEARCH 2021; 170:105444. [PMID: 34399186 DOI: 10.1016/j.marenvres.2021.105444] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
As DNA metabarcoding has become an emerging tool for surveying biodiversity, including its application in legally binding assessments, reliable and efficient barcodes are requested, especially for the highly diverse group of zooplankton. This study focuses on comparing the efficiency of two mitochondrial COI barcodes based on the internal primers mlCOIintF and mlCOIintR utilizing mesozooplankton samples collected in a Mediterranean lagoon. Our results indicate that after a slight adjustment, the mlCOIintR primer performs in combination with jdgLCO1490 (herein) very comparably to the much more widely used primer system mlCOIintF/jgHCO2198+dgHCO2198, in terms of level of taxonomic resolution, species detection and their relative abundance in terms of numbers of reads. As for some groups, like Ctenophora, this barcode is not suitable; a combination of them may be the best option to rely on the Folmer region in its entirety without the risk of losing information for a limited primer match.
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Affiliation(s)
- Anna Schroeder
- National Research Council, Institute of Marine Science (CNR ISMAR) Venice, Arsenale Tesa 104, Castello 2737/F, 30122, Venice, Italy; University of Trieste, Department of Life Sciences, Via Licio Giorgieri 5, 34127, Trieste, Italy.
| | - Alberto Pallavicini
- University of Trieste, Department of Life Sciences, Via Licio Giorgieri 5, 34127, Trieste, Italy; Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
| | - Paolo Edomi
- University of Trieste, Department of Life Sciences, Via Licio Giorgieri 5, 34127, Trieste, Italy.
| | - Marco Pansera
- National Research Council, Institute of Marine Science (CNR ISMAR) Venice, Arsenale Tesa 104, Castello 2737/F, 30122, Venice, Italy; Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
| | - Elisa Camatti
- National Research Council, Institute of Marine Science (CNR ISMAR) Venice, Arsenale Tesa 104, Castello 2737/F, 30122, Venice, Italy.
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