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Moutinho J, Carreira-Flores D, Gomes PT, Costa FO, Duarte S. Assessing the Seasonal and Spatial Dynamics of Zooplankton through DNA Metabarcoding in a Temperate Estuary. Animals (Basel) 2023; 13:3876. [PMID: 38136913 PMCID: PMC10740712 DOI: 10.3390/ani13243876] [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: 09/29/2023] [Revised: 12/07/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Zooplankton are key components of estuarine trophic networks. However, routine monitoring is hindered by the difficulty of morphology-based identification. DNA-based methods allow us to circumvent some of these hurdles, providing precise species identifications regardless of the taxonomic expertise of the investigator or the developmental stage of the specimens. However, the process is dependent on the completeness of the reference libraries. In this study, we sought to evaluate the potential of DNA metabarcoding to assess the seasonal (summer, autumn, and early spring) and spatial dynamics of zooplankton (four locations spanning ca. 6 km) in the Lima estuary (NW Portugal). Two genetic markers were used: the cytochrome c oxidase subunit I and the V4 hypervariable region of the ribosomal 18S rRNA genes. Overall, 327 species were recovered, and both markers displayed minute overlap (7% were detected with both markers). Species richness, composition, and taxonomic distinctness were majorly influenced by the season, with a declining tendency from summer (highest number of exclusive species, n = 74) to spring. Second to season, the taxa composition was influenced by spatial variation where the most downstream site displayed the highest number of exclusive species, n = 53. A total of 16 non-indigenous species were detected using metabarcoding, but only one (Austrominus modestus) has been documented out in the estuary. In conclusion, both the seasonal and spatial gradients influenced the recovered richness, composition, and taxonomic distinctness, confirming the great aptitude of DNA metabarcoding for providing higher density monitoring and shedding new light on the composition and dynamics of complex zooplankton communities.
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Affiliation(s)
- Jorge Moutinho
- Centre of Molecular and Environmental Biology (CBMA) and ARNET—Aquatic Research Network, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (D.C.-F.); (P.T.G.); (F.O.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Diego Carreira-Flores
- Centre of Molecular and Environmental Biology (CBMA) and ARNET—Aquatic Research Network, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (D.C.-F.); (P.T.G.); (F.O.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Pedro T. Gomes
- Centre of Molecular and Environmental Biology (CBMA) and ARNET—Aquatic Research Network, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (D.C.-F.); (P.T.G.); (F.O.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Filipe O. Costa
- Centre of Molecular and Environmental Biology (CBMA) and ARNET—Aquatic Research Network, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (D.C.-F.); (P.T.G.); (F.O.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA) and ARNET—Aquatic Research Network, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (D.C.-F.); (P.T.G.); (F.O.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
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Nascimento‐Schulze JC, Bean TP, Peñaloza C, Paris JR, Whiting JR, Simon A, Fraser BA, Houston RD, Bierne N, Ellis RP. SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP-array. Evol Appl 2023; 16:1044-1060. [PMID: 37216031 PMCID: PMC10197230 DOI: 10.1111/eva.13552] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/15/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023] Open
Abstract
Blue mussels from the genus Mytilus are an abundant component of the benthic community, found in the high latitude habitats. These foundation species are relevant to the aquaculture industry, with over 2 million tonnes produced globally each year. Mussels withstand a wide range of environmental conditions and species from the Mytilus edulis complex readily hybridize in regions where their distributions overlap. Significant effort has been made to investigate the consequences of environmental stress on mussel physiology, reproductive isolation, and local adaptation. Yet our understanding on the genomic mechanisms underlying such processes remains limited. In this study, we developed a multi species medium-density 60 K SNP-array including four species of the Mytilus genus. SNPs included in the platform were called from 138 mussels from 23 globally distributed mussel populations, sequenced using a whole-genome low coverage approach. The array contains polymorphic SNPs which capture the genetic diversity present in mussel populations thriving across a gradient of environmental conditions (~59 K SNPs) and a set of published and validated SNPs informative for species identification and for diagnosis of transmissible cancer (610 SNPs). The array will allow the consistent genotyping of individuals, facilitating the investigation of ecological and evolutionary processes in these taxa. The applications of this array extend to shellfish aquaculture, contributing to the optimization of this industry via genomic selection of blue mussels, parentage assignment, inbreeding assessment and traceability. Further applications such as genome wide association studies (GWAS) for key production traits and those related to environmental resilience are especially relevant to safeguard aquaculture production under climate change.
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Affiliation(s)
- Jennifer C. Nascimento‐Schulze
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
- Centre for Environment, Fisheries and Aquaculture ScienceWeymouth LaboratoryWeymouthUK
| | - Tim P. Bean
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Josephine R. Paris
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | - James R. Whiting
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | - Alexis Simon
- ISEMUniversity of Montpellier, CNRS, IRDMontpellierFrance
| | - Bonnie A. Fraser
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | | | - Nicolas Bierne
- ISEMUniversity of Montpellier, CNRS, IRDMontpellierFrance
| | - Robert P. Ellis
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
- Centre for Sustainable Aquaculture FuturesUniversity of ExeterExeterUK
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Boukadida K, Banni M, Romero-Ramirez A, Clerandeau C, Gourves PY, Cachot J. Metal contamination and heat stress impair swimming behavior and acetylcholinesterase activity in embryo-larval stages of the Mediterranean mussel, Mytilus galloprovincialis. MARINE ENVIRONMENTAL RESEARCH 2022; 179:105677. [PMID: 35738152 DOI: 10.1016/j.marenvres.2022.105677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/27/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Behavioral parameters are increasingly considered sensitive and early bioindicators of toxicity in aquatic organisms. A video-tracking tool was specifically developed to monitor the swimming behaviour of D-larvae of the Mediterranean mussel, Mytilus galloprovincialis, in controlled laboratory conditions. Both maximum and average swimming speeds and trajectories were recorded. We then investigated the impact of copper and silver with or without a moderate rise of temperature on swimming behavior and acetylcholinesterase (AChE) activity of mussel D-larvae and the possible mechanistic link between both biological responses. Our results showed that copper and/or silver exposure, as well as temperature increase, disrupts the swimming behavior of mussel larvae which could compromise their dispersal and survival. In addition, the combined effect of temperature and metals significantly (p < 0.05) increased AChE activity in mussel larvae. Pearson's correlation analysis was performed and results showed that the AChE activity is positively correlated with maximum speeds (r = 0.71, p < 0.01). This study demonstrates the value of behavioral analyzes of aquatic invertebrates as a sensitive and integrate marker of the effects of stressors.
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Affiliation(s)
- Khouloud Boukadida
- Laboratory of Oceanic and Continental Environments and Paleoenvironments, University of Bordeaux, EPOC, UMR 5805, F-33600, Pessac, France; Laboratory of Agrobiodiversity and Ecotoxicology, ISA, Chott-Mariem, 4042, Sousse, Tunisia.
| | - Mohamed Banni
- Laboratory of Agrobiodiversity and Ecotoxicology, ISA, Chott-Mariem, 4042, Sousse, Tunisia; Higher Institute of Biotechnology, University of Monastir, Tunisia
| | - Alicia Romero-Ramirez
- Laboratory of Oceanic and Continental Environments and Paleoenvironments, University of Bordeaux, EPOC, UMR 5805, F-33600, Pessac, France
| | - Christelle Clerandeau
- Laboratory of Oceanic and Continental Environments and Paleoenvironments, University of Bordeaux, EPOC, UMR 5805, F-33600, Pessac, France
| | - Pierre-Yves Gourves
- Laboratory of Oceanic and Continental Environments and Paleoenvironments, University of Bordeaux, EPOC, UMR 5805, F-33600, Pessac, France
| | - Jérôme Cachot
- Laboratory of Oceanic and Continental Environments and Paleoenvironments, University of Bordeaux, EPOC, UMR 5805, F-33600, Pessac, France
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Giusti A, Malloggi C, Tosi F, Boldini P, Larraín Barth MA, Araneda C, Arcangeli G, Armani A. Mislabeling assessment and species identification by PCR-RFLP of mussel-based products (Mytilus spp.) sold on the Italian market. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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