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Couëdel M, Dettai A, Guillaume MMM, Bruggemann F, Bureau S, Frattini B, Verde Ferreira A, Azie J, Bruggemann JH. New insights into the diversity of cryptobenthic Cirripectes blennies in the Mascarene Archipelago sampled using Autonomous Reef Monitoring Structures (ARMS). Ecol Evol 2023; 13:e9850. [PMID: 36937067 PMCID: PMC10019914 DOI: 10.1002/ece3.9850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 03/18/2023] Open
Abstract
Autonomous Reef Monitoring Structures (ARMS) are artificial mini-reefs designed for standardized sampling of sessile and small motile cryptobenthic organisms. ARMS are also effective for collecting small cryptobenthic fishes, such as the combtooth blennies of the genus Cirripectes. Recent studies discovered several Cirripectes species endemic to islands or archipelagos, in spite of the generally broad distributions of tropical and subtropical blennies. Thus, to evaluate the diversity and distribution of Cirripectes species in the Mascarene Archipelago, a little-studied region but an important biodiversity hotspot, complete mitochondrial genomes, and nuclear rhodopsin genes were sequenced for 39 specimens collected with ARMS deployed on outer reef slopes at Reunion and Rodrigues islands. Mitochondrial COI sequences were analyzed to integrate these specimens within the largest dataset of publicly available sequences. Three species were found in the Mascarene Archipelago, Cirripectes castaneus, Cirripectes randalli, and Cirripectes stigmaticus. C. castaneus and C. stigmaticus both have an Indo-Pacific distribution with several haplotypes shared among distant localities. In agreement with the literature, C. randalli shows a small-range endemism restricted to the Mascarenes. We confirmed the presence of C. castaneus, C. randalli, and C. stigmaticus in Rodrigues, and the presence of C. stigmaticus in Reunion. This study contributes to filling the gaps in taxonomic and molecular knowledge of the reef cryptobiome in the South-West Indian Ocean, and provides the first complete mitogenomes for the genus, a crucial step for future molecular-based inventories (e.g., eDNA).
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Affiliation(s)
- Marion Couëdel
- Université de La Réunion, UMR 9220 ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle‐Calédonie, CNRS)La RéunionSaint‐DenisFrance
| | - Agnes Dettai
- Muséum national d'Histoire naturelle (MNHN), UMR 7205 ISYEB (MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles)ParisFrance
| | - Mireille M. M. Guillaume
- Muséum national d'Histoire naturelle (MNHN)UMR 8067 BOrEA (MNHN, CNRS 2030, Sorbonne Université, IRD 207, Uni Caen‐Normandie, Université des Antilles)ParisFrance
- LabEx CORAILUniversité de PerpignanPerpignanFrance
| | - Fleur Bruggemann
- Université de La Réunion, UMR 9220 ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle‐Calédonie, CNRS)La RéunionSaint‐DenisFrance
| | - Sophie Bureau
- Université de La Réunion, UMR 9220 ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle‐Calédonie, CNRS)La RéunionSaint‐DenisFrance
| | - Baptiste Frattini
- Université de La Réunion, UMR 9220 ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle‐Calédonie, CNRS)La RéunionSaint‐DenisFrance
- Muséum national d'Histoire naturelle (MNHN)UMR 8067 BOrEA (MNHN, CNRS 2030, Sorbonne Université, IRD 207, Uni Caen‐Normandie, Université des Antilles)ParisFrance
| | - Amélie Verde Ferreira
- Muséum national d'Histoire naturelle (MNHN), UMR 7205 ISYEB (MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles)ParisFrance
| | | | - J. Henrich Bruggemann
- Université de La Réunion, UMR 9220 ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle‐Calédonie, CNRS)La RéunionSaint‐DenisFrance
- LabEx CORAILUniversité de PerpignanPerpignanFrance
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Lira NL, Tonello S, Lui RL, Traldi JB, Brandão H, Oliveira C, Blanco DR. Identifying fish eggs and larvae: from classic methodologies to DNA metabarcoding. Mol Biol Rep 2023; 50:1713-1726. [PMID: 36418775 DOI: 10.1007/s11033-022-08091-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 11/04/2022] [Indexed: 11/25/2022]
Abstract
Studies involving fish eggs and larvae date back to the end of the nineteenth century. Since then, studies with ichthyoplankton have proved to be an essential tool, generating information for the knowledge of the ichthyofauna and the environmental inventory. Most of these studies reveal the difficulty of obtaining a precise taxonomic identification of the collected materials, making research with ichthyoplankton extremely challenging. With the advent of molecular biology, the use of markers such as COI enabled greater taxonomic precision, helping to understand events involving ichthyofauna. Now we can observe the evolution of the molecular identification tool for ichthyoplankton via DNA barcoding, which has been increasingly used over the last few decades. From 2000 to 2010, we found six publications; from 2011 to 2021, 75 papers were published, and in 2022 four studies. Our survey also showed the accuracy of molecular identification when compared to the taxonomic identification of these. In this review, we show the state of the art of studies that used barcode and DNA metabarcoding to identify fish eggs and larvae in different environments and discuss their importance as the best practice for working with these organisms.
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Affiliation(s)
- Natália Lima Lira
- Programa de Pós-Graduação em Recursos Naturais e Sustentabilidade, Universidade Tecnológica Federal do Paraná, Prolongamento da Rua Cerejeira, S/N, Santa Helena, PR, 85892-000, Brazil.
| | - Sandro Tonello
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936, Aleixo, Manaus, AM, 69080-971, Brazil
| | - Roberto Laridondo Lui
- Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná, R. Universitária, 1619, Cascavel, PR, 85819-170, Brazil
| | - Josiane Baccarin Traldi
- Instituto de Ciências Biológicas, Departamento de Genética, Universidade Federal do Amazonas, Av. General Rodrigo Octavio, 6200, Manaus, AM, 69080-900, Brazil
| | - Heleno Brandão
- Programa de Pós-Graduação em Recursos Naturais e Sustentabilidade, Universidade Tecnológica Federal do Paraná, Prolongamento da Rua Cerejeira, S/N, Santa Helena, PR, 85892-000, Brazil
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, R. Prof. Dr. Antônio C. W. Zanin, 250, Botucatu, SP, 18618-689, Brazil
| | - Daniel Rodrigues Blanco
- Programa de Pós-Graduação em Recursos Naturais e Sustentabilidade, Universidade Tecnológica Federal do Paraná, Prolongamento da Rua Cerejeira, S/N, Santa Helena, PR, 85892-000, Brazil
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Nguyen XV, Phan TTH, Cao VL, Nguyen Nhat NT, Nguyen TH, Nguyen XT, Lau VK, Hoang CT, Nguyen-Thi MN, Nguyen HM, Dao VH, Teichberg M, Papenbrock J. Current advances in seagrass research: A review from Viet Nam. FRONTIERS IN PLANT SCIENCE 2022; 13:991865. [PMID: 36299785 PMCID: PMC9589349 DOI: 10.3389/fpls.2022.991865] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Seagrass meadows provide valuable ecosystem services but are fragile and threatened ecosystems all over the world. This review highlights the current advances in seagrass research from Viet Nam. One goal is to support decision makers in developing science-based conservation strategies. In recent years, several techniques were applied to estimate the size of seagrass meadows. Independent from the method used, there is an alarming decline in the seagrass area in almost all parts of Viet Nam. Since 1990, a decline of 46.5% or 13,549 ha was found. Only in a few protected and difficult-to-reach areas was an increase observed. Conditions at those sites could be investigated in more detail to make suggestions for conservation and recovery of seagrass meadows. Due to their lifestyle and morphology, seagrasses take up compounds from their environment easily. Phytoremediation processes of Thalassia hemprichii and Enhalus acoroides are described exemplarily. High accumulation of heavy metals dependent on their concentration in the environment in different organs can be observed. On the one hand, seagrasses play a role in phytoremediation processes in polluted areas; on the other hand, they might suffer at high concentrations, and pollution will contribute to their overall decline. Compared with the neighboring countries, the total C org stock from seagrass beds in Viet Nam was much lower than in the Philippines and Indonesia but higher than that of Malaysia and Myanmar. Due to an exceptionally long latitudinal coastline of 3,260 km covering cool to warm water environments, the seagrass species composition in Viet Nam shows a high diversity and a high plasticity within species boundaries. This leads to challenges in taxonomic issues, especially with the Halophila genus, which can be better deduced from genetic diversity/population structures of members of Hydrocharitaceae. Finally, the current seagrass conservation and management efforts in Viet Nam are presented and discussed. Only decisions based on the interdisciplinary cooperation of scientists from all disciplines mentioned will finally lead to conserve this valuable ecosystem for mankind and biodiversity.
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Affiliation(s)
- Xuan-Vy Nguyen
- Institute of Oceanography, Viet Nam Academy of Science and Technology, Nha Trang, Vietnam
- Faculty of Marine Science and Technology, Graduate University of Science and Technology, Ha Noi, Vietnam
| | | | - Van-Luong Cao
- Faculty of Marine Science and Technology, Graduate University of Science and Technology, Ha Noi, Vietnam
- Institute of Marine Environment and Resources, Viet Nam Academy of Science and Technology, Hai Phong, Vietnam
| | - Nhu-Thuy Nguyen Nhat
- Institute of Oceanography, Viet Nam Academy of Science and Technology, Nha Trang, Vietnam
| | - Trung-Hieu Nguyen
- Institute of Oceanography, Viet Nam Academy of Science and Technology, Nha Trang, Vietnam
| | - Xuan-Thuy Nguyen
- Institute of Oceanography, Viet Nam Academy of Science and Technology, Nha Trang, Vietnam
| | - Va-Khin Lau
- Institute of Oceanography, Viet Nam Academy of Science and Technology, Nha Trang, Vietnam
| | | | - My-Ngan Nguyen-Thi
- Institute of Oceanography, Viet Nam Academy of Science and Technology, Nha Trang, Vietnam
| | - Hung Manh Nguyen
- Dead Sea and Arava Science Center, Central Arava Branch, Hatseva, Israel
- French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Viet-Ha Dao
- Institute of Oceanography, Viet Nam Academy of Science and Technology, Nha Trang, Vietnam
- Faculty of Marine Science and Technology, Graduate University of Science and Technology, Ha Noi, Vietnam
| | - Mirta Teichberg
- Ecosystems Center, Marine Biological Laboratory (MBL), Woodshole, MA, United States
| | - Jutta Papenbrock
- Institute of Botany, Leibniz University Hannover, Hannover, Germany
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Metabarcoding of Fish Larvae in the Merbok River Reveals Species Diversity and Distribution Along its Mangrove Environment. Zool Stud 2022; 60:e76. [PMID: 35774258 DOI: 10.6620/zs.2021.60-76] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 10/11/2021] [Indexed: 01/24/2023]
Abstract
The Merbok River (north-west of Peninsular Malaysia) is a mangrove estuary that provides habitat for over 100 species of fish, which are economically and ecologically important. Threats such as habitat loss and overfishing are becoming a great concern for fisheries conservation and management. The identification of larval fish in this estuarine system is important to complement information on the adults. This is because the data could inform the spawning behaviour, reproductive biology, selection of nursery grounds and migration route of fish. Such information is invaluable for fisheries and aquatic environmental monitoring, and thus for their conservation and management. However, identifying fish larvae is a challenging task based only on morphology and even traditional DNA barcoding. To address this, DNA metabarcoding was utilised to detect the diversity of fish in the Merbok River. To complete the study, the fish larvae were collected at six sampling sites of the river. The extracted larval DNA was amplified for the Cytochrome Oxidase subunit 1 (COI) and 12S ribosomal RNA (12S rRNA) genes based on the metabarcoding approach using shotgun sequencing on the next-generation sequencing (NGS) Illumina MiSeq platform. Eighty-nine species from 65 genera and 41 families were detected, with Oryzias javanicus, Oryzias dancena, Lutjanus argentimaculatus and Lutjanus malabaricus among the most common species. The lower diversity observed from previous morphological studies is suggested to be mainly due to seasonal variation over the sampling period between the two methods and limited 12S rRNA sequences in current databases. The metabarcode data and a validation Sanger sequencing step using 15 species-specific primer pairs detected three species in common: Oryzias javanicus, Decapterus maruadsi and Pennahia macrocephalus. Several discrepancies observed between the two molecular approaches could be attributed to contaminants during sampling and DNA extraction, which could mask the presence of target species, especially when DNA from the contaminants is more abundant than the target organisms. In conclusion, this rapid and cost-effective identification method using DNA metabarcoding allowed the detection of numerous fish species from bulk larval samples in the Merbok River. This method can be applied to other sites and other organisms of interest.
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Maslakova S, Ellison CI, Hiebert TC, Conable F, Heaphy MC, Venera-Pontón DE, Norenburg JL, Schwartz ML, Moss ND, Boyle MJ, Driskell AC, Macdonald KS, Zattara EE, Collin R. Sampling multiple life stages significantly increases estimates of marine biodiversity. Biol Lett 2022; 18:20210596. [PMID: 35414224 PMCID: PMC9039783 DOI: 10.1098/rsbl.2021.0596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Biodiversity assessments are critical for setting conservation priorities, understanding ecosystem function and establishing a baseline to monitor change. Surveys of marine biodiversity that rely almost entirely on sampling adult organisms underestimate diversity because they tend to be limited to habitat types and individuals that can be easily surveyed. Many marine animals have planktonic larvae that can be sampled from the water column at shallow depths. This life stage often is overlooked in surveys but can be used to relatively rapidly document diversity, especially for the many species that are rare or live cryptically as adults. Using DNA barcode data from samples of nemertean worms collected in three biogeographical regions—Northeastern Pacific, the Caribbean Sea and Eastern Tropical Pacific—we found that most species were collected as either benthic adults or planktonic larvae but seldom in both stages. Randomization tests show that this deficit of operational taxonomic units collected as both adults and larvae is extremely unlikely if larvae and adults were drawn from the same pool of species. This effect persists even in well-studied faunas. These results suggest that sampling planktonic larvae offers access to a different subset of species and thus significantly increases estimates of biodiversity compared to sampling adults alone. Spanish abstract is available in the electronic supplementary material.
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Affiliation(s)
- Svetlana Maslakova
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | - Christina I Ellison
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | - Terra C Hiebert
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | - Frances Conable
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | - Maureen C Heaphy
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | | | - Jon L Norenburg
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Megan L Schwartz
- University of Washington, 1900 Commerce Avenue, Tacoma, WA 98420, USA
| | - Nicole D Moss
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | - Michael J Boyle
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Balboa Ancon, Panama
| | - Amy C Driskell
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Kenneth S Macdonald
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Eduardo E Zattara
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.,INIBIOMA, Universidad Nacional del Comahue-CONICET, Bariloche, Río Negro, 8400, Argentina
| | - Rachel Collin
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Balboa Ancon, Panama
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Abstract
Since their inception, DNA barcodes have become a powerful tool for understanding the biodiversity and biology of aquatic species, with multiple applications in diverse fields such as food security, fisheries, environmental DNA, conservation, and exotic species detection. Nevertheless, most aquatic ecosystems, from marine to freshwater, are understudied, with many species disappearing due to environmental stress, mostly caused by human activities. Here we highlight the progress that has been made in studying aquatic organisms with DNA barcodes, and encourage its further development in assisting sustainable use of aquatic resources and conservation.
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Tang KL, Stiassny MLJ, Mayden RL, DeSalle R. Systematics of Damselfishes. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/i2020105] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kevin L. Tang
- University of Michigan–Flint, Department of Biology, 303 East Kearsley St., Flint, Michigan 48502; . Send reprint requests to this address
| | - Melanie L. J. Stiassny
- American Museum of Natural History, Department of Ichthyology, Central Park West at 79th St., New York, New York 10024;
| | - Richard L. Mayden
- Saint Louis University, Department of Biology, 3507 Laclede Ave., St. Louis, Missouri 63103;
| | - Robert DeSalle
- American Museum of Natural History, Division of Invertebrate Zoology, Central Park West at 79th St., New York, New York 10024;
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Limmon G, Delrieu-Trottin E, Patikawa J, Rijoly F, Dahruddin H, Busson F, Steinke D, Hubert N. Assessing species diversity of Coral Triangle artisanal fisheries: A DNA barcode reference library for the shore fishes retailed at Ambon harbor (Indonesia). Ecol Evol 2020; 10:3356-3366. [PMID: 32273993 PMCID: PMC7141007 DOI: 10.1002/ece3.6128] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 01/01/2023] Open
Abstract
The Coral Triangle (CT), a region spanning across Indonesia and Philippines, is home to about 4,350 marine fish species and is among the world's most emblematic regions in terms of conservation. Threatened by overfishing and oceans warming, the CT fisheries have faced drastic declines over the last decades. Usually monitored through a biomass-based approach, fisheries trends have rarely been characterized at the species level due to the high number of taxa involved and the difficulty to accurately and routinely identify individuals to the species level. Biomass, however, is a poor proxy of species richness, and automated methods of species identification are required to move beyond biomass-based approaches. Recent meta-analyses have demonstrated that species richness peaks at intermediary levels of biomass. Consequently, preserving biomass is not equal to preserving biodiversity. We present the results of a survey to estimate the shore fish diversity retailed at the harbor of Ambon Island, an island located at the center of the CT that display exceptionally high biomass despite high levels of threat, while building a DNA barcode reference library of CT shore fishes targeted by artisanal fisheries. We sampled 1,187 specimens and successfully barcoded 696 of the 760 selected specimens that represent 202 species. Our results show that DNA barcodes were effective in capturing species boundaries for 96% of the species examined, which opens new perspectives for the routine monitoring of the CT fisheries.
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Affiliation(s)
- Gino Limmon
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Erwan Delrieu-Trottin
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
- Museum für Naturkunde Leibniz-Institut für Evolutions-und Biodiversitätsforschung an der Humboldt-Universität zu Berlin Berlin Germany
| | - Jesaya Patikawa
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Frederik Rijoly
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Hadi Dahruddin
- Division of Zoology Research Center for Biology Indonesian Institute of Sciences (LIPI) Cibinong Indonesia
| | - Frédéric Busson
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
- UMR 7208 BOREA (MNHN-CNRS-UPMC-IRD-UCBN) Muséum National d'Histoire Naturelle Paris France
| | - Dirk Steinke
- Department of Integrative Biology Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
| | - Nicolas Hubert
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
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