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Jarman S, Alexander JB, Dawkins KL, Lukehurst SS, Nester GM, Wilkinson S, Marnane MJ, McDonald JI, Elsdon TS, Harvey ES. Marine eDNA sampling from submerged surfaces with paint rollers. Mar Genomics 2024; 76:101127. [PMID: 38905943 DOI: 10.1016/j.margen.2024.101127] [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: 02/16/2024] [Revised: 06/13/2024] [Accepted: 06/16/2024] [Indexed: 06/23/2024]
Abstract
Environmental DNA (eDNA) analyses of species present in marine environments is the most effective biological diversity measurement tool currently available. eDNA sampling methods are an intrinsically important part of the eDNA biodiversity analysis process. Identification and development of eDNA sampling methods that are as rapid, affordable, versatile and practical as possible will improve rates of detection of marine species. Optimal outcomes of eDNA biodiversity surveys come from studies employing high levels of sampling replication, so any methods that make sampling faster and cheaper will improve scientific outcomes. eDNA sampling methods that can be applied more widely will also enable sampling from a greater range of marine surface micro-habitats, resulting in detection of a wider range of organisms. In this study, we compared diversity detection by several methods for sampling eDNA from submerged marine surfaces: polyurethane foam, nylon swabs, microfibre paint rollers, and sediment scoops. All of the methods produced a diverse range of species identifications, with >250 multicellular species represented by eDNA at the study site. We found that widely-available small paint rollers were an effective, readily available and affordable method for sampling eDNA from underwater marine surfaces. This approach enables the sampling of marine eDNA using extended poles, or potentially by remotely operated vehicles, where surface sampling by hand is impractical.
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Affiliation(s)
- Simon Jarman
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; eDNA Frontiers, Curtin University, Bentley, WA, Australia.
| | - Jason B Alexander
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | | | | | - Georgia M Nester
- Minderoo-UWA Deep Sea Research Centre, University of Western Australia, Crawley, WA, Australia
| | - Shaun Wilkinson
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Wilderlab, Miramar, Wellington, New Zealand
| | - Michael J Marnane
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Chevron Technical Center, Perth, Western Australia, Australia
| | - Justin I McDonald
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Sustainability and Biosecurity, Department of Primary Industries and Regional Development (DPIRD), Hillarys, 6025, Western Australia, Australia
| | - Travis S Elsdon
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Chevron Technical Center, Perth, Western Australia, Australia
| | - Euan S Harvey
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
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2
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Hamad MH, Islam SI, Jitsamai W, Chinkangsadarn T, Naraporn D, Ouisuwan S, Taweethavonsawat P. Metabarcoding study to reveal the structural community of strongylid nematodes in domesticated horses in Thailand. BMC Vet Res 2024; 20:70. [PMID: 38395874 PMCID: PMC10893705 DOI: 10.1186/s12917-024-03934-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Mixed strongylid infections significantly impact equine health and performance. Traditional microscopy-based methods exhibit limitations in accurately identifying strongylid species. Nemabiome deep amplicon sequencing approach previously succeeded in describing the strongylid communities in livestock including equids. However, there are no available studies that describe the structural communities of strongylid parasites in horses in Thailand. Therefore, this study was undertaken encompassing the ITS-2 rDNA metabarcoding assay to characterize strongylid species within horse fecal samples collected from a cohort of yearlings at the largest domesticated stud farm in Thailand. In addition, to investigate the capability of ITS-2 rDNA in assessing the phylogenetic relationships among the identified strongylid species. RESULTS The study identified 14 strongylid species in the examined equine populations, each with varying prevalence. Notably, Cylicocyclus nassatus and Cylicostephanus longibursatus were identified as the predominant species, with Strongylus spp. conspicuously absent. The phylogenetic analysis of 207 amplicon sequence variants (ASVs) displayed a complex relationship among the investigated cyathostomin species, with some species are positioned across multiple clades, demonstrating close associations with various species and genera. CONCLUSION The ITS-2 nemabiome sequencing technique provided a detailed picture of horse strongylid parasite species in the studied population. This establishes a foundation for future investigations into the resistance status of these parasites and enables efforts to mitigate their impact.
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Affiliation(s)
- Mohamed H Hamad
- The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Infectious Diseases, Department of Animal Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, 44511, Egypt
- Parasitology Unit, Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Sk Injamamul Islam
- The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Parasitology Unit, Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Wanarit Jitsamai
- Department of Parasitology and Entomology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Teerapol Chinkangsadarn
- Department of Surgery, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Darm Naraporn
- Horse Farm and Laboratory Animal Breeding Center, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Hua-Hin, Prachuap Khiri Khan Province, 77110, Thailand
| | - Suraseha Ouisuwan
- Horse Farm and Laboratory Animal Breeding Center, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Hua-Hin, Prachuap Khiri Khan Province, 77110, Thailand
| | - Piyanan Taweethavonsawat
- Parasitology Unit, Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
- Biomarkers in Animals Parasitology Research Unit, Chulalongkorn University, Bangkok, 10330, Thailand.
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Rosner A, Ballarin L, Barnay-Verdier S, Borisenko I, Drago L, Drobne D, Concetta Eliso M, Harbuzov Z, Grimaldi A, Guy-Haim T, Karahan A, Lynch I, Giulia Lionetto M, Martinez P, Mehennaoui K, Oruc Ozcan E, Pinsino A, Paz G, Rinkevich B, Spagnuolo A, Sugni M, Cambier S. A broad-taxa approach as an important concept in ecotoxicological studies and pollution monitoring. Biol Rev Camb Philos Soc 2024; 99:131-176. [PMID: 37698089 DOI: 10.1111/brv.13015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 08/23/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023]
Abstract
Aquatic invertebrates play a pivotal role in (eco)toxicological assessments because they offer ethical, cost-effective and repeatable testing options. Additionally, their significance in the food chain and their ability to represent diverse aquatic ecosystems make them valuable subjects for (eco)toxicological studies. To ensure consistency and comparability across studies, international (eco)toxicology guidelines have been used to establish standardised methods and protocols for data collection, analysis and interpretation. However, the current standardised protocols primarily focus on a limited number of aquatic invertebrate species, mainly from Arthropoda, Mollusca and Annelida. These protocols are suitable for basic toxicity screening, effectively assessing the immediate and severe effects of toxic substances on organisms. For more comprehensive and ecologically relevant assessments, particularly those addressing long-term effects and ecosystem-wide impacts, we recommended the use of a broader diversity of species, since the present choice of taxa exacerbates the limited scope of basic ecotoxicological studies. This review provides a comprehensive overview of (eco)toxicological studies, focusing on major aquatic invertebrate taxa and how they are used to assess the impact of chemicals in diverse aquatic environments. The present work supports the use of a broad-taxa approach in basic environmental assessments, as it better represents the natural populations inhabiting various ecosystems. Advances in omics and other biochemical and computational techniques make the broad-taxa approach more feasible, enabling mechanistic studies on non-model organisms. By combining these approaches with in vitro techniques together with the broad-taxa approach, researchers can gain insights into less-explored impacts of pollution, such as changes in population diversity, the development of tolerance and transgenerational inheritance of pollution responses, the impact on organism phenotypic plasticity, biological invasion outcomes, social behaviour changes, metabolome changes, regeneration phenomena, disease susceptibility and tissue pathologies. This review also emphasises the need for harmonised data-reporting standards and minimum annotation checklists to ensure that research results are findable, accessible, interoperable and reusable (FAIR), maximising the use and reusability of data. The ultimate goal is to encourage integrated and holistic problem-focused collaboration between diverse scientific disciplines, international standardisation organisations and decision-making bodies, with a focus on transdisciplinary knowledge co-production for the One-Health approach.
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Affiliation(s)
- Amalia Rosner
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Loriano Ballarin
- Department of Biology, University of Padova, via Ugo Bassi 58/B, Padova, I-35121, Italy
| | - Stéphanie Barnay-Verdier
- Sorbonne Université; CNRS, INSERM, Université Côte d'Azur, Institute for Research on Cancer and Aging Nice, 28 avenue Valombrose, Nice, F-06107, France
| | - Ilya Borisenko
- Faculty of Biology, Department of Embryology, Saint Petersburg State University, Universitetskaya embankment 7/9, Saint Petersburg, 199034, Russia
| | - Laura Drago
- Department of Biology, University of Padova, via Ugo Bassi 58/B, Padova, I-35121, Italy
| | - Damjana Drobne
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, 1111, Slovenia
| | - Maria Concetta Eliso
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, 80121, Italy
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Zoya Harbuzov
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
- Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, 199 Aba Koushy Ave., Haifa, 3498838, Israel
| | - Annalisa Grimaldi
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant, Varese, 3-21100, Italy
| | - Tamar Guy-Haim
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Arzu Karahan
- Middle East Technical University, Institute of Marine Sciences, Erdemli-Mersin, PO 28, 33731, Turkey
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Maria Giulia Lionetto
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via prov. le Lecce -Monteroni, Lecce, I-73100, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina, 61, Palermo, I-90133, Italy
| | - Pedro Martinez
- Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys, Barcelona, 08010, Spain
| | - Kahina Mehennaoui
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41, rue du Brill, Belvaux, L-4422, Luxembourg
| | - Elif Oruc Ozcan
- Faculty of Arts and Science, Department of Biology, Cukurova University, Balcali, Saricam, Adana, 01330, Turkey
| | - Annalisa Pinsino
- National Research Council, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Via Ugo La Malfa 153, Palermo, 90146, Italy
| | - Guy Paz
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Baruch Rinkevich
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Antonietta Spagnuolo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, 80121, Italy
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Via Celoria 26, Milan, 20133, Italy
| | - Sébastien Cambier
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41, rue du Brill, Belvaux, L-4422, Luxembourg
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Zarcero J, Antich A, Rius M, Wangensteen OS, Turon X. A new sampling device for metabarcoding surveillance of port communities and detection of non-indigenous species. iScience 2024; 27:108588. [PMID: 38111684 PMCID: PMC10726295 DOI: 10.1016/j.isci.2023.108588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/04/2023] [Accepted: 11/23/2023] [Indexed: 12/20/2023] Open
Abstract
Metabarcoding techniques are revolutionizing studies of marine biodiversity. They can be used for monitoring non-indigenous species (NIS) in ports and harbors. However, they are often biased by inconsistent sampling methods and incomplete reference databases. Logistic constraints in ports prompt the development of simple, easy-to-deploy samplers. We tested a new device called polyamide mesh for ports organismal monitoring (POMPOM) with a high surface-to-volume ratio. POMPOMS were deployed inside a fishing and recreational port in the Mediterranean alongside conventional settlement plates. We also compiled a curated database with cytochrome oxidase (COI) sequences of Mediterranean NIS. COI metabarcoding of the communities settled in the POMPOMs captured a similar biodiversity than settlement plates, with shared molecular operational units (MOTUs) representing ca. 99% of reads. 38 NIS were detected in the port accounting for ca. 26% of reads. POMPOMs were easy to deploy and handle and provide an efficient method for NIS surveillance.
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Affiliation(s)
- Jesús Zarcero
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB), CSIC, 17300 Blanes, Catalonia, Spain
- Department of Evolutionary Biology, Ecology and Environmental Sciences and Biodiversity Research Institute (IRBio), University of Barcelona, 08028 Barcelona, Catalonia, Spain
| | - Adrià Antich
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB), CSIC, 17300 Blanes, Catalonia, Spain
| | - Marc Rius
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB), CSIC, 17300 Blanes, Catalonia, Spain
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park Johannesburg 2006, South Africa
| | - Owen S. Wangensteen
- Department of Evolutionary Biology, Ecology and Environmental Sciences and Biodiversity Research Institute (IRBio), University of Barcelona, 08028 Barcelona, Catalonia, Spain
| | - Xavier Turon
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB), CSIC, 17300 Blanes, Catalonia, Spain
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5
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Duprey J, Gallego R, Klinger T, Kelly RP. Environmental DNA reveals patterns of biological invasion in an inland sea. PLoS One 2023; 18:e0281525. [PMID: 38150426 PMCID: PMC10752502 DOI: 10.1371/journal.pone.0281525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023] Open
Abstract
Non-native species have the potential to cause ecological and economic harm to coastal and estuarine ecosystems. Understanding which habitat types are most vulnerable to biological invasions, where invasions originate, and the vectors by which they arrive can help direct limited resources to prevent or mitigate ecological and socio-economic harm. Information about the occurrence of non-native species can help guide interventions at all stages of invasion, from first introduction, to naturalization and invasion. However, monitoring at relevant scales requires considerable investment of time, resources, and taxonomic expertise. Environmental DNA (eDNA) metabarcoding methods sample coastal ecosystems at broad spatial and temporal scales to augment established monitoring methods. We use COI mtDNA eDNA sampling to survey a diverse assemblage of species across distinct habitats in the Salish Sea in Washington State, USA, and classify each as non-native, native, or indeterminate in origin. The non-native species detected include both well-documented invaders and species not previously reported within the Salish Sea. We find a non-native assemblage dominated by shellfish and algae with native ranges in the temperate western Pacific, and find more-retentive estuarine habitats to be invaded at far higher levels than better-flushed rocky shores. Furthermore, we find an increase in invasion level with higher water temperatures in spring and summer across habitat types. This analysis contributes to a growing understanding of the biotic and abiotic factors that influence invasion level, and underscores the utility of eDNA surveys to monitor biological invasions and to better understand the factors that drive these invasions.
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Affiliation(s)
- Joe Duprey
- School of Marine and Environmental Affairs, University of Washington, Seattle, WA, United States of America
| | - Ramón Gallego
- School of Marine and Environmental Affairs, University of Washington, Seattle, WA, United States of America
- Universidad Autónoma de Madrid—Unidad de Genética, Madrid, Spain
| | - Terrie Klinger
- School of Marine and Environmental Affairs, University of Washington, Seattle, WA, United States of America
| | - Ryan P. Kelly
- School of Marine and Environmental Affairs, University of Washington, Seattle, WA, United States of America
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6
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Zhang M, Zou Y, Xiao S, Hou J. Environmental DNA metabarcoding serves as a promising method for aquatic species monitoring and management: A review focused on its workflow, applications, challenges and prospects. MARINE POLLUTION BULLETIN 2023; 194:115430. [PMID: 37647798 DOI: 10.1016/j.marpolbul.2023.115430] [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: 04/23/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023]
Abstract
Marine and freshwater biodiversity is under threat from both natural and manmade causes. Biological monitoring is currently a top priority for biodiversity protection. Given present limitations, traditional biological monitoring methods may not achieve the proposed monitoring aims. Environmental DNA metabarcoding technology reflects species information by capturing and extracting DNA from environmental samples, using molecular biology techniques to sequence and analyze the DNA, and comparing the obtained information with existing reference libraries to obtain species identification. However, its practical application has highlighted several limitations. This paper summarizes the main steps in the environmental application of eDNA metabarcoding technology in aquatic ecosystems, including the discovery of unknown species, the detection of invasive species, and evaluations of biodiversity. At present, with the rapid development of big data and artificial intelligence, certain advanced technologies and devices can be combined with environmental DNA metabarcoding technology to promote further development of aquatic species monitoring and management.
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Affiliation(s)
- Miaolian Zhang
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Yingtong Zou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shan Xiao
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Jing Hou
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
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7
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Zaiko A, Scheel M, Schattschneider J, von Ammon U, Scriver M, Pochon X, Pearman JK. Pest Alert Tool-a web-based application for flagging species of concern in metabarcoding datasets. Nucleic Acids Res 2023:7173698. [PMID: 37207328 DOI: 10.1093/nar/gkad364] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/13/2023] [Accepted: 05/18/2023] [Indexed: 05/21/2023] Open
Abstract
Advances in high-throughput sequencing (HTS) technologies and their increasing affordability have fueled environmental DNA (eDNA) metabarcoding data generation from freshwater, marine and terrestrial ecosystems. Research institutions worldwide progressively employ HTS for biodiversity assessments, new species discovery and ecological trend monitoring. Moreover, even non-scientists can now collect an eDNA sample, send it to a specialized laboratory for analysis and receive in-depth biodiversity record from a sampling site. This offers unprecedented opportunities for biodiversity assessments across wide temporal and spatial scales. The large volume of data produced by metabarcoding also enables incidental detection of species of concern, including non-indigenous and pathogenic organisms. We introduce an online app-Pest Alert Tool-for screening nuclear small subunit 18S ribosomal RNA and mitochondrial cytochrome oxidase subunit I datasets for marine non-indigenous species as well as unwanted and notifiable marine organisms in New Zealand. The output can be filtered by minimum length of the query sequence and identity match. For putative matches, a phylogenetic tree can be generated through the National Center for Biotechnology Information's BLAST Tree View tool, allowing for additional verification of the species of concern detection. The Pest Alert Tool is publicly available at https://pest-alert-tool-prod.azurewebsites.net/.
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Affiliation(s)
- Anastasija Zaiko
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
- Institute of Marine Science, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Sequench Ltd, 1/131 Hardy Street, Nelson 7010, New Zealand
| | | | | | - Ulla von Ammon
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Michelle Scriver
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
- Institute of Marine Science, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Xavier Pochon
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
- Institute of Marine Science, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - John K Pearman
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
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Aglieri G, Quattrocchi F, Mariani S, Baillie C, Spatafora D, Di Franco A, Turco G, Tolone M, Di Gerlando R, Milazzo M. Fish eDNA detections in ports mirror fishing fleet activities and highlight the spread of non-indigenous species in the Mediterranean Sea. MARINE POLLUTION BULLETIN 2023; 189:114792. [PMID: 36921451 DOI: 10.1016/j.marpolbul.2023.114792] [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: 11/10/2022] [Revised: 02/22/2023] [Accepted: 02/25/2023] [Indexed: 06/18/2023]
Abstract
Gathering comprehensive marine biodiversity data can be difficult, costly and time consuming, preventing adequate knowledge of diversity patterns in many areas worldwide. We propose fishing ports as "natural" sinks of biodiversity information collected by fishing vessels probing disparate habitats, depths, and environments. By combining rapid environmental DNA metabarcoding (eDNA) surveys and data from public registers and Automatic Identification Systems, we show significant positive relationships between fishing fleet activities (i.e. fishing effort and characteristics of the fishing grounds) and the taxonomic fish assemblage composition in eleven Mediterranean fishing ports. Overall, we identified 160 fish and 123 invertebrate OTUs, including at least seven non-indigenous species, in some instances well beyond their known distribution areas. Our findings suggest that eDNA assessments of fishing harbours' waters might offer a rapid way to monitor marine biodiversity in unknown or under-sampled areas, as well as to reconstruct fishing catches, often underreported in several regions.
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Affiliation(s)
- Giorgio Aglieri
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Palermo, Italy; NBFC, National Biodiversity Future Center, Palermo, Italy.
| | - Federico Quattrocchi
- NBFC, National Biodiversity Future Center, Palermo, Italy; University of Palermo, Department of Earth and Marine Sciences (DiSTeM), Palermo, Italy; Institute for Biological Resources and Marine Biotechnologies, National Research Council (IRBIM-CNR), Mazara del Vallo, Italy
| | - Stefano Mariani
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | | | - Davide Spatafora
- University of Palermo, Department of Earth and Marine Sciences (DiSTeM), Palermo, Italy
| | - Antonio Di Franco
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Palermo, Italy; NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Gabriele Turco
- University of Palermo, Department of Earth and Marine Sciences (DiSTeM), Palermo, Italy
| | - Marco Tolone
- University of Palermo, Department of Agricultural Food and Forest Sciences, Palermo, Italy
| | - Rosalia Di Gerlando
- University of Palermo, Department of Agricultural Food and Forest Sciences, Palermo, Italy
| | - Marco Milazzo
- NBFC, National Biodiversity Future Center, Palermo, Italy; University of Palermo, Department of Earth and Marine Sciences (DiSTeM), Palermo, Italy
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9
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Compilation, Revision, and Annotation of DNA Barcodes of Marine Invertebrate Non-Indigenous Species (NIS) Occurring in European Coastal Regions. DIVERSITY 2023. [DOI: 10.3390/d15020174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The introduction of non-indigenous species (NIS) is one of the major threats to the integrity of European coastal ecosystems. DNA-based assessments have been increasingly adopted for monitoring NIS. However, the accuracy of DNA-based taxonomic assignments is largely dependent on the completion and reliability of DNA barcode reference libraries. As such, we aimed to compile and audit a DNA barcode reference library for marine invertebrate NIS occurring in Europe. To do so, we compiled a list of NIS using three databases: the European Alien Species Information Network (EASIN), the Information System on Aquatic Non-indigenous and Cryptogenic Species (AquaNIS), and the World Register of Introduced Marine Species (WRiMS). For each species, we retrieved the available cytochrome c oxidase subunit I (COI) mitochondrial gene sequences from the Barcode of Life Data System (BOLD) and used the Barcode, Audit & Grade System (BAGS) to check congruence between morphospecies names and Barcode Index Numbers (BINs). From the 1249 species compiled, approximately 42% had records on BOLD, among which 56% were discordant. We further analyzed these cases to determine the causes of the discordances and attributed additional annotation tags. Of the 622 discordant BINs, after revision, 35% were successfully solved, which increased the number of NIS detected in metabarcoding datasets from 12 to 16. However, a fair number of BINs remained discordant. Reliability of reference barcode records is particularly critical in the case of NIS, where erroneous identification may trigger action or inaction when not required.
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Willassen E, Westgaard JI, Kongsrud JA, Hanebrekke T, Buhl-Mortensen P, Holte B. Benthic invertebrates in Svalbard fjords-when metabarcoding does not outperform traditional biodiversity assessment. PeerJ 2022; 10:e14321. [PMID: 36415859 PMCID: PMC9676020 DOI: 10.7717/peerj.14321] [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: 06/02/2022] [Accepted: 10/10/2022] [Indexed: 11/18/2022] Open
Abstract
To protect and restore ecosystems and biodiversity is one of the 10 challenges identified by the United Nations's Decade of the Ocean Science. In this study we used eDNA from sediments collected in two fjords of the Svalbard archipelago and compared the taxonomic composition with traditional methods through metabarcoding, targeting mitochondrial CO1, to survey benthos. Clustering of 21.6 mill sequence reads with a d value of 13 in swarm, returned about 25 K OTU reads. An identification search with the BOLD database returned 12,000 taxonomy annotated sequences spanning a similarity range of 50% to 100%. Using an acceptance filter of minimum 90% similarity to the CO1 reference sequence, we found that 74% of the ca 100 taxon identified sequence reads were Polychaeta and 22% Nematoda. Relatively few other benthic invertebrate species were detected. Many of the identified sequence reads were extra-organismal DNA from terrestrial, planktonic, and photic zone sources. For the species rich Polychaeta, we found that, on average, only 20.6% of the species identified from morphology were also detected with DNA. This discrepancy was not due to missing reference sequences in the search database, because 90-100% (mean 96.7%) of the visually identified species at each station were represented with barcodes in Boldsystems. The volume of DNA samples is small compared with the volume searched in visual sorting, and the replicate DNA-samples in sum covered only about 2% of the surface area of a grab. This may considerably reduce the detection rate of species that are not uniformly distributed in the sediments. Along with PCR amplification bias and primer mismatch, this may be an important reason for the limited congruence of species identified with the two approaches. However, metabarcoding also identified 69 additional species that are usually overlooked in visual sample sorting, demonstrating how metabarcoding can complement traditional methodology by detecting additional, less conspicuous groups of organisms.
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Affiliation(s)
- Endre Willassen
- Department of Natural History, University of Bergen, Bergen, Norway
| | - Jon-Ivar Westgaard
- Department of Population Genetics, Institute of Marine Research, Tromsø, Troms, Norway
| | | | - Tanja Hanebrekke
- Department of Population Genetics, Institute of Marine Research, Tromsø, Troms, Norway
| | - Pål Buhl-Mortensen
- Department of Bentic Communities, Institute of Marine Research, Bergen, Norway
| | - Børge Holte
- Department of Bentic Communities, Institute of Marine Research, Tromsø, Troms, Norway
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11
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Gold Z, Wall AR, Schweizer TM, Pentcheff ND, Curd EE, Barber PH, Meyer RS, Wayne R, Stolzenbach K, Prickett K, Luedy J, Wetzer R. A manager's guide to using eDNA metabarcoding in marine ecosystems. PeerJ 2022; 10:e14071. [PMID: 36405018 PMCID: PMC9673773 DOI: 10.7717/peerj.14071] [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: 06/24/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: (1) select genes and primers to target taxa; (2) assemble or develop comprehensive barcode reference databases; (3) apply rigorous site occupancy based decontamination pipelines; (4) conduct pilot studies to define spatial and temporal variance of eDNA; and (5) archive samples, extracts, and raw sequence data. We demonstrate the importance of each of these considerations using a case study of eDNA metabarcoding in the Ports of Los Angeles and Long Beach. eDNA metabarcoding approaches detected 94.1% (16/17) of species observed in paired trawl surveys while identifying an additional 55 native fishes, providing more comprehensive biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding results improved ecological interpretation and confidence in species detections while providing archived genetic resources for future analyses. Well designed and validated eDNA metabarcoding approaches are ideally suited for biomonitoring applications that rely on the detection of species, including mapping invasive species fronts and endangered species habitats as well as tracking range shifts in response to climate change. Incorporating these considerations will enhance the utility and efficacy of eDNA metabarcoding for routine biomonitoring applications.
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Affiliation(s)
- Zachary Gold
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Adam R. Wall
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
| | - Teia M. Schweizer
- Department of Fish and Wildlife Conservation Biology, Colorado State University, Fort Collins, CO, United States of America
| | - N. Dean Pentcheff
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
| | - Emily E. Curd
- Department of Natural Sciences, Landmark College, Putney, VT, United States of America
| | - Paul H. Barber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Rachel S. Meyer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America,Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Robert Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Kevin Stolzenbach
- Wood Environment and Infrastructure, Inc., San Diego, CA, United States of America
| | - Kat Prickett
- Port of Los Angeles, Los Angeles, CA, United States of America
| | - Justin Luedy
- Port of Long Beach, Long Beach, CA, United States of America
| | - Regina Wetzer
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
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12
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Good E, Holman LE, Pusceddu A, Russo T, Rius M, Iacono CL. Detection of community-wide impacts of bottom trawl fishing on deep-sea assemblages using environmental DNA metabarcoding. MARINE POLLUTION BULLETIN 2022; 183:114062. [PMID: 36075115 DOI: 10.1016/j.marpolbul.2022.114062] [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: 04/04/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Although considerable research progress on the effects of anthropogenic disturbance in the deep sea has been made in recent years, our understanding of these impacts at community level remains limited. Here, we studied deep-sea assemblages of Sicily (Mediterranean Sea) subject to different intensities of benthic trawling using environmental DNA (eDNA) metabarcoding and taxonomic identification of meiofauna communities. Firstly, eDNA metabarcoding data did not detect trawling impacts using alpha diversity whereas meiofauna data detected a significant effect of trawling. Secondly, both eDNA and meiofauna data detected significantly different communities across distinct levels of trawling intensity when we examined beta diversity. Taxonomic assignment of the eDNA data revealed that Bryozoa was present only at untrawled sites, highlighting their vulnerability to trawling. Our results provide evidence for community-wide impacts of trawling, with different trawling intensities leading to distinct deep-sea communities. Finally, we highlight the need for further studies to unravel understudied deep-sea biodiversity.
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Affiliation(s)
- Edward Good
- School of Ocean and Earth Science, University of Southampton, Waterfront Campus, Southampton, United Kingdom.
| | - Luke E Holman
- School of Ocean and Earth Science, University of Southampton, Waterfront Campus, Southampton, United Kingdom; Section for Molecular Ecology and Evolution, Faculty of Health and Medical Sciences, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Antonio Pusceddu
- Department of Life and Environmental Sciences, University of Cagliari, Via T. Fiorelli, 1, 09126 Cagliari, Italy
| | - Tommaso Russo
- Laboratory of Experimental Ecology and Aquaculture, Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Marc Rius
- School of Ocean and Earth Science, University of Southampton, Waterfront Campus, Southampton, United Kingdom; Centre for Advanced Studies of Blanes - Spanish National Research Council (CEAB-CSIC), Accés a la Cala Sant Francesc 14, 17300 Blanes (Girona), Spain; Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, South Africa
| | - Claudio Lo Iacono
- Marine Sciences Institute - Spanish National Research Council (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
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13
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Macher JN, Bloska DM, Holzmann M, Girard EB, Pawlowski J, Renema W. Mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding of Foraminifera communities using taxon-specific primers. PeerJ 2022; 10:e13952. [PMID: 36093332 PMCID: PMC9454970 DOI: 10.7717/peerj.13952] [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] [Received: 03/11/2022] [Accepted: 08/05/2022] [Indexed: 01/19/2023] Open
Abstract
Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in most marine environments. Molecular methods such as metabarcoding have revealed a high, yet undescribed diversity of Foraminifera. However, so far only one molecular marker, the 18S ribosomal RNA, was available for metabarcoding studies on Foraminifera. Primers that allow amplification of foraminiferal mitochondrial cytochrome oxidase I (COI) and identification of Foraminifera species were recently published. Here we test the performance of these primers for the amplification of whole foraminiferal communities, and compare their performance to that of the highly degenerate LerayXT primers, which amplify the same COI region in a wide range of eukaryotes. We applied metabarcoding to 48 samples taken along three transects spanning a North Sea beach in the Netherlands from dunes to the low tide level, and analysed both sediment samples and meiofauna samples, which contained taxa between 42 µm and 1 mm in body size obtained by decantation from sand samples. We used single-cell metabarcoding (Girard et al., 2022) to generate a COI reference library containing 32 species of Foraminifera, and used this to taxonomically annotate our community metabarcoding data. Our analyses show that the highly degenerate LerayXT primers do not amplify Foraminifera, while the Foraminifera primers are highly Foraminifera- specific, with about 90% of reads assigned to Foraminifera and amplifying taxa from all major groups, i.e., monothalamids, Globothalamea, and Tubothalamea. We identified 176 Foraminifera ASVs and found a change in Foraminifera community composition along the beach transects from high tide to low tide level, and a dominance of single-chambered monothalamid Foraminifera. Our results highlight that COI metabarcoding can be a powerful tool for assessing Foraminiferal communities.
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Affiliation(s)
- Jan-Niklas Macher
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | - Maria Holzmann
- Department of Genetics & Evolution, University of Geneva, Geneva, Switzerland
| | - Elsa B. Girard
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands,Department of Ecosystem & Landscape Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Jan Pawlowski
- Laboratory of Paleoceanography, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Willem Renema
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands,Department of Ecosystem & Landscape Dynamics, University of Amsterdam, Amsterdam, Netherlands
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14
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MacAulay S, Ellison AR, Kille P, Cable J. Moving towards improved surveillance and earlier diagnosis of aquatic pathogens: From traditional methods to emerging technologies. REVIEWS IN AQUACULTURE 2022; 14:1813-1829. [PMID: 36250037 PMCID: PMC9544729 DOI: 10.1111/raq.12674] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/21/2022] [Accepted: 03/01/2022] [Indexed: 06/16/2023]
Abstract
Early and accurate diagnosis is key to mitigating the impact of infectious diseases, along with efficient surveillance. This however is particularly challenging in aquatic environments due to hidden biodiversity and physical constraints. Traditional diagnostics, such as visual diagnosis and histopathology, are still widely used, but increasingly technological advances such as portable next generation sequencing (NGS) and artificial intelligence (AI) are being tested for early diagnosis. The most straightforward methodologies, based on visual diagnosis, rely on specialist knowledge and experience but provide a foundation for surveillance. Future computational remote sensing methods, such as AI image diagnosis and drone surveillance, will ultimately reduce labour costs whilst not compromising on sensitivity, but they require capital and infrastructural investment. Molecular techniques have advanced rapidly in the last 30 years, from standard PCR through loop-mediated isothermal amplification (LAMP) to NGS approaches, providing a range of technologies that support the currently popular eDNA diagnosis. There is now vast potential for transformative change driven by developments in human diagnostics. Here we compare current surveillance and diagnostic technologies with those that could be used or developed for use in the aquatic environment, against three gold standard ideals of high sensitivity, specificity, rapid diagnosis, and cost-effectiveness.
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Affiliation(s)
| | | | - Peter Kille
- School of Biosciences, Cardiff UniversityCardiffUK
| | - Joanne Cable
- School of Biosciences, Cardiff UniversityCardiffUK
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15
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DiBattista JD, Fowler AM, Riley IJ, Reader S, Hay A, Parkinson K, Hobbs JPA. The use of environmental DNA to monitor impacted coastal estuaries. MARINE POLLUTION BULLETIN 2022; 181:113860. [PMID: 35779383 DOI: 10.1016/j.marpolbul.2022.113860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) metabarcoding is increasingly being used to assess community composition in coastal ecosystems. In this study, we chose to examine temporal and spatial changes in the aquatic community of Manly Lagoon - one of the most heavily developed and polluted estuaries in eastern Australia. Based on metabarcoding of the 16S mitochondrial gene (for fish) and the 18S nuclear gene (for macroinvertebrates), we identified seasonal differences in fish and macroinvertebrate community composition as well as species richness, which correlated, in some cases, with the environmental parameters of sea surface temperature and freshwater input. Moreover, given the greater taxonomic resolution of fish versus macroinvertebrate assignments, we identified several known migratory fish species of management importance that contributed significantly to the overall patterns observed. Overall, our data support the use of eDNA metabarcoding to track fish assemblages shifting in response to environmental drivers in polluted estuaries with increased sampling and consultation with historical data.
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Affiliation(s)
- Joseph D DiBattista
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia.
| | - Ashley M Fowler
- New South Wales Department of Primary Industries, Sydney Institute of Marine Science, Mosman, NSW 2088, Australia
| | - Indiana J Riley
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Sydney Institute of Marine Science, Mosman, NSW 2088, Australia
| | - Sally Reader
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia
| | - Amanda Hay
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia
| | - Kerryn Parkinson
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia
| | - Jean-Paul A Hobbs
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4069, Australia
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16
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Hanson MC, Petch GM, Ottosen TB, Skjøth CA. Climate change impact on fungi in the atmospheric microbiome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154491. [PMID: 35283127 DOI: 10.1016/j.scitotenv.2022.154491] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/13/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
The atmospheric microbiome is one of the least studied microbiomes of our planet. One of the most abundant, diverse and impactful parts of this microbiome is arguably fungal spores. They can be very potent outdoor aeroallergens and pathogens, causing an enormous socio-economic burden on health services and annual damages to crops costing billions of Euros. We find through hypothesis testing that an expected warmer and drier climate has a dramatic impact on the atmospheric microbiome, conceivably through alteration of the hydrological cycle impacting agricultural systems, with significant differences in leaf wetness between years (p-value <0.05). The data were measured via high-throughput sequencing analysis using the DNA barcode marker, ITS2. This was complemented by remote sensing analysis of land cover and dry matter productivity based on the Sentinel satellites, on-site detection of atmospheric and vegetation variables, GIS analysis, harvesting analysis and footprint modelling on trajectory clusters using the atmospheric transport model HYSPLIT. We find the seasonal spore composition varies between rural and urban zones reflecting both human activities (e.g. harvest), type and status of the vegetation and the prevailing climate rather than mesoscale atmospheric transport. We find that crop harvesting governs the composition of the atmospheric microbiome through a clear distinction between harvest and post-harvest beta-diversity by PERMANOVA on Bray-Curtis dissimilarity (p-value <0.05). Land cover impacted significantly by two-way ANOVA (p-value <0.05), while there was minimal impact from air mass transport over the 3 years. The hypothesis suggests that the fungal spore composition will change dramatically due to climate change, an until now unforeseen effect affecting both food security, human health and the atmospheric hydrological cycle. Consequently the management of crop diseases and impact on human health through aeroallergen exposure need to consider the timing of crop treatments and land management, including post harvest, to minimize exposure of aeroallergens and pathogens.
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Affiliation(s)
- M C Hanson
- School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK.
| | - G M Petch
- School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK
| | - T-B Ottosen
- School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK; Department of Air and Sensor Technology, Danish Technological Institute, Kongsvang Allé 29, DK-8000 Aarhus C, Denmark
| | - C A Skjøth
- School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK.
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17
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Monitoring of benthic eukaryotic communities in two tropical coastal lagoons through eDNA metabarcoding: a spatial and temporal approximation. Sci Rep 2022; 12:10089. [PMID: 35710829 PMCID: PMC9203746 DOI: 10.1038/s41598-022-13653-9] [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: 10/12/2021] [Accepted: 05/09/2022] [Indexed: 11/14/2022] Open
Abstract
Tropical coastal lagoons are important ecosystems that support high levels of biodiversity and provide several goods and services. Monitoring of benthic biodiversity and detection of harmful or invasive species is crucial, particularly in relation to seasonal and spatial variation of environmental conditions. In this study, eDNA metabarcoding was used in two tropical coastal lagoons, Chacahua (CH) and Corralero (C) (Southern Mexican Pacific), to describe the benthic biodiversity and its spatial–temporal dynamics. The distribution of benthic diversity within the lagoons showed a very particular pattern evidencing a transition from freshwater to seawater. Although the two lagoon systems are similar in terms of the species composition of metazoans and microeukaryotes, our findings indicate that they are different in taxa richness and structure, resulting in regional partitioning of the diversity with salinity as the driving factor of community composition in CH. Harmful, invasive, non-indigenous species, bioindicators and species of commercial importance were detected, demonstrating the reach of this technique for biodiversity monitoring along with the continued efforts of building species reference libraries.
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18
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Jeunen GJ, Lipinskaya T, Gajduchenko H, Golovenchik V, Moroz M, Rizevsky V, Semenchenko V, Gemmell NJ. Environmental DNA (eDNA) metabarcoding surveys show evidence of non-indigenous freshwater species invasion to new parts of Eastern Europe. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.e68575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Active environmental DNA (eDNA) surveillance through species-specific amplification has shown increased sensitivity in the detection of non-indigenous species (NIS) compared to traditional approaches. When many NIS are of interest, however, active surveillance decreases in cost- and time-efficiency. Passive surveillance through eDNA metabarcoding takes advantage of the complex DNA signal in environmental samples and facilitates the simultaneous detection of multiple species. While passive eDNA surveillance has previously detected NIS, comparative studies are essential to determine the ability of eDNA metabarcoding to accurately describe the range of invasion for multiple NIS versus alternative approaches. Here, we surveyed twelve sites, covering nine rivers across Belarus for NIS with three different techniques, i.e. an ichthyological, hydrobiological and eDNA survey, whereby DNA was extracted from 500 ml surface water samples and amplified with two 16S rDNA primer assays targeting the fish and macroinvertebrate biodiversity. Nine non-indigenous fish and ten non-indigenous benthic macroinvertebrates were detected by traditional surveys, while seven NISeDNA signals were picked up, including four fish, one aquatic and two benthic macroinvertebrates. Passive eDNA surveillance extended the range of invasion further north for two invasive fish and identified a new NIS for Belarus, the freshwater jellyfish Craspedacusta sowerbii. False-negative detections for the eDNA survey might be attributed to: (i) preferential amplification of aquatic over benthic macroinvertebrates from surface water samples and (ii) an incomplete reference database. The evidence provided in this study recommends the implementation of both molecular-based and traditional approaches to maximise the probability of early detection of non-native organisms.
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19
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Pawlowski J, Bruce K, Panksep K, Aguirre FI, Amalfitano S, Apothéloz-Perret-Gentil L, Baussant T, Bouchez A, Carugati L, Cermakova K, Cordier T, Corinaldesi C, Costa FO, Danovaro R, Dell'Anno A, Duarte S, Eisendle U, Ferrari BJD, Frontalini F, Frühe L, Haegerbaeumer A, Kisand V, Krolicka A, Lanzén A, Leese F, Lejzerowicz F, Lyautey E, Maček I, Sagova-Marečková M, Pearman JK, Pochon X, Stoeck T, Vivien R, Weigand A, Fazi S. Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151783. [PMID: 34801504 DOI: 10.1016/j.scitotenv.2021.151783] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/06/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.
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Affiliation(s)
- J Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - K Bruce
- NatureMetrics Ltd, CABI Site, Bakeham Lane, Egham TW20 9TY, UK
| | - K Panksep
- Institute of Technology, University of Tartu, Tartu 50411, Estonia; Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia; Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Estonia
| | - F I Aguirre
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - S Amalfitano
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - L Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Baussant
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Bouchez
- INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - L Carugati
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - K Cermakova
- ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; NORCE Climate, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway
| | - C Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - F O Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - R Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - A Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - S Duarte
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - U Eisendle
- University of Salzburg, Dept. of Biosciences, 5020 Salzburg, Austria
| | - B J D Ferrari
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - F Frontalini
- Department of Pure and Applied Sciences, Urbino University, Urbino, Italy
| | - L Frühe
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - A Haegerbaeumer
- Bielefeld University, Animal Ecology, 33615 Bielefeld, Germany
| | - V Kisand
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - A Krolicka
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - F Leese
- University of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research, Germany
| | - F Lejzerowicz
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - E Lyautey
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - I Maček
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; Faculty of Mathematics, Natural Sciences and Information Technologies (FAMNIT), University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - M Sagova-Marečková
- Czech University of Life Sciences, Dept. of Microbiology, Nutrition and Dietetics, Prague, Czech Republic
| | - J K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - X Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Warkworth 0941, New Zealand
| | - T Stoeck
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - R Vivien
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - A Weigand
- National Museum of Natural History Luxembourg, 25 Rue Münster, L-2160 Luxembourg, Luxembourg
| | - S Fazi
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy.
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20
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Ellis MR, Clark ZSR, Treml EA, Brown MS, Matthews TG, Pocklington JB, Stafford-Bell RE, Bott NJ, Nai YH, Miller AD, Sherman CDH. Detecting marine pests using environmental DNA and biophysical models. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151666. [PMID: 34793806 DOI: 10.1016/j.scitotenv.2021.151666] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
The spread of marine pests is occurring at record rates due to globalisation and increasing trade. Environmental DNA (eDNA) is an emerging tool for pest surveillance, allowing for the detection of genetic material shed by organisms into the environment. However, factors influencing the spatial and temporal detection limits of eDNA in marine environments are poorly understood. In this study we use eDNA assays to assess the invasive ranges of two marine pests in south-eastern Australia, the kelp Undaria pinnatifida and the seastar Asterias amurensis. We explored the temporal and spatial detection limits of eDNA under different oceanographic conditions by combining estimates of eDNA decay with biophysical modelling. Positive eDNA detections at several new locations indicate the invasive range of both pest species is likely to be wider than currently assumed. Environmental DNA decay rates were similar for both species, with a decay rate constant of 0.035 h-1 for U. pinnatifida, and a decay rate constant of 0.041 h-1 for A. amurensis, resulting in a 57-73% decrease in eDNA concentrations in the first 24 h and decaying beyond the limits of detection after 3-4 days. Biophysical models informed by eDNA decay profiles indicate passive transport of eDNA up to a maximum of 10 to 20 km from its source, with a ~90-95% reduction in eDNA concentration within 1-3 km from the source, depending on local oceanography. These models suggest eDNA signals are likely to be highly localised, even in complex marine environments. This was confirmed with spatially replicated eDNA sampling around an established U. pinnatifida population indicating detection limits of ~750 m from the source. This study highlights the value of eDNA methods for marine pest surveillance and provides a much-needed description of the spatio-temporal detection limits of eDNA under different oceanographic conditions.
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Affiliation(s)
- Morgan R Ellis
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Zach S R Clark
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Eric A Treml
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Morgan S Brown
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Ty G Matthews
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Jacqueline B Pocklington
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Environment and Science Division, Parks Victoria, Melbourne, Victoria 3000, Australia
| | - Richard E Stafford-Bell
- Department of Jobs, Precincts and Regions, 475 Mickleham Road, Attwood, Vic. 3049, Australia
| | - Nathan J Bott
- School of Science, RMIT University, PO Box 71, Bundoora, VIC 3083, Australia
| | - Yi Heng Nai
- Centre for Regional and Rural Futures, Faculty of Science, Engineering and Built Environment, Deakin University, Geelong, Victoria, 3220, Australia
| | - Adam D Miller
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Craig D H Sherman
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia.
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21
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Couton M, Lévêque L, Daguin-Thiébaut C, Comtet T, Viard F. Water eDNA metabarcoding is effective in detecting non-native species in marinas, but detection errors still hinder its use for passive monitoring. BIOFOULING 2022; 38:367-383. [PMID: 35575060 DOI: 10.1080/08927014.2022.2075739] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/21/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Marinas are high-priority targets for marine non-indigenous species (NIS), where they compose a large portion of the biofouling communities. The practicality of water samples collection makes environmental DNA (eDNA) metabarcoding an interesting tool for routine NIS surveys. Here the effectiveness of water-eDNA-metabarcoding to identify biofouling NIS, in 10 marinas from western France, was examined. Morphological identification of specimens collected in quadrats brought out 18 sessile benthic NIS beneath floating pontoons. Water-eDNA-metabarcoding detected two thirds of them, failing to detect important NIS. However, sampling and bioinformatics filtering steps can be optimized to identify more species. In addition, this method allowed the detection of additional NIS from neighboring micro-habitats. Caution should, however, be taken when reporting putative novel NIS, because of errors in species assignment. This work highlights that water-eDNA-metabarcoding is effective for active (targeted) NIS surveys and could be significantly improved for its further use in marine NIS passive surveys.
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Affiliation(s)
- Marjorie Couton
- Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Laurent Lévêque
- Sorbonne Université, CNRS, FR 2424, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Claire Daguin-Thiébaut
- Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Thierry Comtet
- Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Frédérique Viard
- Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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22
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Holman LE, Parker-Nance S, de Bruyn M, Creer S, Carvalho G, Rius M. Managing human-mediated range shifts: understanding spatial, temporal and genetic variation in marine non-native species. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210025. [PMID: 35067092 PMCID: PMC8784926 DOI: 10.1098/rstb.2021.0025] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The use of molecular tools to manage natural resources is increasingly common. However, DNA-based methods are seldom used to understand the spatial and temporal dynamics of species' range shifts. This is important when managing range shifting species such as non-native species (NNS), which can have negative impacts on biotic communities. Here, we investigated the ascidian NNS Ciona robusta, Clavelina lepadiformis, Microcosmus squamiger and Styela plicata using a combined methodological approach. We first conducted non-molecular biodiversity surveys for these NNS along the South African coastline, and compared the results with historical surveys. We detected no consistent change in range size across species, with some displaying range stability and others showing range shifts. We then sequenced a section of cytochrome c oxidase subunit I (COI) from tissue samples and found genetic differences along the coastline but no change over recent times. Finally, we found that environmental DNA metabarcoding data showed broad congruence with both the biodiversity survey and the COI datasets, but failed to capture the complete incidence of all NNS. Overall, we demonstrated how a combined methodological approach can effectively detect spatial and temporal variation in genetic composition and range size, which is key for managing both thriving NNS and threatened species. This article is part of the theme issue ‘Species’ ranges in the face of changing environments (part I)’.
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Affiliation(s)
- Luke E Holman
- School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK
| | - Shirley Parker-Nance
- Zoology Department, Institute for Coastal and Marine Research Nelson Mandela University Ocean Sciences Campus, Gqeberha (Port Elizabeth), South Africa.,South African Environmental Observation Network (SAEON) Elwandle Coastal Node, Nelson Mandela University Ocean Sciences Campus, Gqeberha (Port Elizabeth), South Africa
| | - Mark de Bruyn
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, Australia.,Molecular Ecology and Evolution Group, School of Natural Sciences, Bangor University, Bangor, UK
| | - Simon Creer
- Molecular Ecology and Evolution Group, School of Natural Sciences, Bangor University, Bangor, UK
| | - Gary Carvalho
- Molecular Ecology and Evolution Group, School of Natural Sciences, Bangor University, Bangor, UK
| | - Marc Rius
- School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK.,Centre for Advanced Studies of Blanes (CEAB, CSIC), Accés a la Cala Sant Francesc 14, 17300 Blanes, Spain.,Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, South Africa
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23
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Cowart DA, Murphy KR, Cheng CHC. Environmental DNA from Marine Waters and Substrates: Protocols for Sampling and eDNA Extraction. Methods Mol Biol 2022; 2498:225-251. [PMID: 35727547 DOI: 10.1007/978-1-0716-2313-8_11] [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] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) analysis has emerged in recent years as a powerful tool for the detection, monitoring, and characterization of aquatic metazoan communities, including vulnerable species. The rapid rate of adopting the eDNA approach across diverse habitats and taxonomic groups attests to its value for a wide array of investigative goals, from understanding natural or changing biodiversity to informing on conservation efforts at local and global scales. Regardless of research objectives, eDNA workflows commonly include the following essential steps: environmental sample acquisition, processing and preservation of samples, and eDNA extraction, followed by eDNA sequencing library preparation, high-capacity sequencing and sequence data analysis, or other methods of genetic detection. In this chapter, we supply instructional details for the early steps in the workflow to facilitate researchers considering adopting eDNA analysis to address questions in marine environments. Specifically, we detail sampling, preservation, extraction, and quantification protocols for eDNA originating from marine water, shallow substrates, and deeper sediments. eDNA is prone to degradation and loss, and to contamination through improper handling; these factors crucially influence the outcome and validity of an eDNA study. Thus, we also provide guidance on avoiding these pitfalls. Following extraction, purified eDNA is often sequenced on massively parallel sequencing platforms for comprehensive faunal diversity assessment using a metabarcoding or metagenomic approach, or for the detection and quantification of specific taxa by qPCR methods. These components of the workflow are project-specific and thus not included in this chapter. Instead, we briefly touch on the preparation of eDNA libraries and discuss comparisons between sequencing approaches to aid considerations in project design.
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Affiliation(s)
- Dominique A Cowart
- Company for Open Ocean Observations and Logging (COOOL), Saint Leu, La Réunion, France
| | - Katherine R Murphy
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - C-H Christina Cheng
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana - Champaign, Urbana, IL, USA.
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24
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Are well-studied marine biodiversity hotspots still blackspots for animal barcoding? Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01909] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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25
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Clarke LJ, Suter L, Deagle BE, Polanowski AM, Terauds A, Johnstone GJ, Stark JS. Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems. PeerJ 2021; 9:e12458. [PMID: 34820189 PMCID: PMC8601059 DOI: 10.7717/peerj.12458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 10/18/2021] [Indexed: 01/18/2023] Open
Abstract
Antarctic benthic ecosystems support high biodiversity but their characterization is limited to a few well-studied areas, due to the extreme environment and remoteness making access and sampling difficult. Our aim was to compare water and sediment as sources of environmental DNA (eDNA) to better characterise Antarctic benthic communities and further develop practical approaches for DNA-based biodiversity assessment in remote environments. We used a cytochrome c oxidase subunit I (COI) metabarcoding approach to characterise metazoan communities in 26 nearshore sites across 12 locations in the Vestfold Hills (East Antarctica) based on DNA extracted from either sediment cores or filtered seawater. We detected a total of 99 metazoan species from 12 phyla across 26 sites, with similar numbers of species detected in sediment and water eDNA samples. However, significantly different communities were detected in the two sample types at sites where both were collected (i.e., where paired samples were available). For example, nematodes and echinoderms were more likely to be detected exclusively in sediment and water eDNA samples, respectively. eDNA from water and sediment core samples are complementary sample types, with epifauna more likely to be detected in water column samples and infauna in sediment. More reference DNA sequences are needed for infauna/meiofauna to increase the proportion of sequences and number of taxa that can be identified. Developing a better understanding of the temporal and spatial dynamics of eDNA at low temperatures would also aid interpretation of eDNA signals from polar environments. Our results provide a preliminary scan of benthic metazoan communities in the Vestfold Hills, with additional markers required to provide a comprehensive biodiversity survey. However, our study demonstrates the choice of sample type for eDNA studies of benthic ecosystems (sediment, water or both) needs to be carefully considered in light of the research or monitoring question of interest.
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Affiliation(s)
- Laurence J Clarke
- Australian Antarctic Division, Kingston, Tasmania, Australia.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Leonie Suter
- Australian Antarctic Division, Kingston, Tasmania, Australia
| | - Bruce E Deagle
- Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, Australia
| | | | - Aleks Terauds
- Australian Antarctic Division, Kingston, Tasmania, Australia
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26
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Zhao B, van Bodegom PM, Trimbos K. The particle size distribution of environmental DNA varies with species and degradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149175. [PMID: 34303977 DOI: 10.1016/j.scitotenv.2021.149175] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/15/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
Environmental DNA (eDNA) analysis is frequently used as a non-invasive method to investigate species and biodiversity in ecosystems. However, such eDNA may represent both organisms currently present as well as species that released their DNA some point in the past, thereby representing a mix of current and historic biodiversity. This may lead to a false-positive detection of organisms' presence. As the eDNA particle size distribution (PSD) changes along with the decay process, it may facilitate solving the above problem. Here, we set up tank experiments with snails, zebrafish and daphnids, respectively, to monitor the change in eDNA PSD and eDNA degradation through time after removing organisms. We found that zebrafish eDNA decays more slowly for larger particle sizes. Across all species tested, the percentage of large size ranges tended to increase over time while the smaller sizes showed relatively fast decay rates. As a result, PSD changed consistently with eDNA decay, although initial PSD varied between species. In combination, we propose that eDNA PSD can be used to assess the current prevalence of organisms at an eDNA sampling location while avoiding false-positives on the presence of species. Our findings expand the applicability of eDNA for monitoring target species in freshwater ecosystems.
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Affiliation(s)
- Beilun Zhao
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Einsteinweg 2, 2333 CC Leiden, Netherlands.
| | - Peter M van Bodegom
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Einsteinweg 2, 2333 CC Leiden, Netherlands
| | - Krijn Trimbos
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Einsteinweg 2, 2333 CC Leiden, Netherlands
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27
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Ríos-Castro R, Romero A, Aranguren R, Pallavicini A, Banchi E, Novoa B, Figueras A. High-Throughput Sequencing of Environmental DNA as a Tool for Monitoring Eukaryotic Communities and Potential Pathogens in a Coastal Upwelling Ecosystem. Front Vet Sci 2021; 8:765606. [PMID: 34805343 PMCID: PMC8595318 DOI: 10.3389/fvets.2021.765606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/08/2021] [Indexed: 12/04/2022] Open
Abstract
The marine environment includes diverse microeukaryotic organisms that play important functional roles in the ecosystem. With molecular approaches, eukaryotic taxonomy has been improved, complementing classical analysis. In this study, DNA metabarcoding was performed to describe putative pathogenic eukaryotic microorganisms in sediment and marine water fractions collected in Galicia (NW Spain) from 2016 to 2018. The composition of eukaryotic communities was distinct between sediment and water fractions. Protists were the most diverse group, with the clade TSAR (Stramenopiles, Alveolata, Rhizaria, and Telonemida) as the primary representative organisms in the environment. Harmful algae and invasive species were frequently detected. Potential pathogens, invasive pathogenic organisms as well as the causative agents of harmful phytoplanktonic blooms were identified in this marine ecosystem. Most of the identified pathogens have a crucial impact on the aquacultural sector or affect to relevant species in the marine ecosystem, such as diatoms. Moreover, pathogens with medical and veterinary importance worldwide were also found, as well as pathogens that affect diatoms. The evaluation of the health of a marine ecosystem that directly affects the aquacultural sector with a zoonotic concern was performed with the metabarcoding assay.
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Affiliation(s)
- Raquel Ríos-Castro
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
| | - Alejandro Romero
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
| | - Raquel Aranguren
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Trieste, Italy.,Division of Oceanography, National Institute of Oceanography and Applied Geophysics, Trieste, Italy
| | - Elisa Banchi
- Department of Life Sciences, University of Trieste, Trieste, Italy.,Division of Oceanography, National Institute of Oceanography and Applied Geophysics, Trieste, Italy
| | - Beatriz Novoa
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
| | - Antonio Figueras
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
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28
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Gargan LM, Brooks PR, Vye SR, Ironside JE, Jenkins SR, Crowe TP, Carlsson J. The use of environmental DNA metabarcoding and quantitative PCR for molecular detection of marine invasive non-native species associated with artificial structures. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02672-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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29
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Fernandez S, Miller DL, Holman LE, Gittenberger A, Ardura A, Rius M, Mirimin L. Environmental DNA sampling protocols for the surveillance of marine non-indigenous species in Irish coastal waters. MARINE POLLUTION BULLETIN 2021; 172:112893. [PMID: 34464822 DOI: 10.1016/j.marpolbul.2021.112893] [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: 07/02/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Understanding the spread and distribution of Non-Indigenous Species (NIS) is key when implementing legislation to maintain good ecosystem health. Environmental DNA (eDNA) has shown great potential to detect aquatic organisms in a rapid and cost-effective way, however their applicability to new environments must be validated prior to their implementation. Here, we tested different field sampling methods in combination with eDNA metabarcoding to develop a tool to detect NIS. Large and small volumes of seawater were filtered, in addition to the collection of sediment and horizontal tow net samples at 12 locations across four distinct geographic areas in Ireland. The biggest dissimilarity in the species recovered was found between sediment and town net samples. Tow nets showed to be the most efficient. A total of 357 taxa were identified, including 16 NIS. Fine mesh tow nets were identified as the most cost-efficient for large-scale monitoring and surveillance of NIS.
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Affiliation(s)
- Sara Fernandez
- Marine and Freshwater Research Centre, Dublin Road, H91 T8NW Galway, Ireland; Galway-Mayo Institute of Technology, School of Science and Computing, Department of Natural Sciences, Dublin Road, H91 T8NW Galway, Ireland.
| | - Dulaney L Miller
- Marine and Freshwater Research Centre, Dublin Road, H91 T8NW Galway, Ireland; Galway-Mayo Institute of Technology, School of Science and Computing, Department of Natural Sciences, Dublin Road, H91 T8NW Galway, Ireland
| | - Luke E Holman
- School of Ocean and Earth Science, National Oceanography Centre, European Way, Southampton SO14 3ZH, University of Southampton, United Kingdom
| | - Arjan Gittenberger
- GiMaRIS, Rijksstraatweg 75, 2171 AK Sassenheim, the Netherlands; Department of Marine Zoology, Naturalis Biodiversity Center, Pesthuislaan 7, 2333 BA Leiden, the Netherlands
| | - Alba Ardura
- Department of Functional Biology, University of Oviedo, 33006 Oviedo, Asturias, Spain
| | - Marc Rius
- School of Ocean and Earth Science, National Oceanography Centre, European Way, Southampton SO14 3ZH, University of Southampton, United Kingdom; Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, 2006 Johannesburg, South Africa
| | - Luca Mirimin
- Marine and Freshwater Research Centre, Dublin Road, H91 T8NW Galway, Ireland; Galway-Mayo Institute of Technology, School of Science and Computing, Department of Natural Sciences, Dublin Road, H91 T8NW Galway, Ireland
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30
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Stauffer S, Jucker M, Keggin T, Marques V, Andrello M, Bessudo S, Cheutin M, Borrero‐Pérez GH, Richards E, Dejean T, Hocdé R, Juhel J, Ladino F, Letessier TB, Loiseau N, Maire E, Mouillot D, Mutis Martinezguerra M, Manel S, Polanco Fernández A, Valentini A, Velez L, Albouy C, Pellissier L, Waldock C. How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs? Ecol Evol 2021; 11:14630-14643. [PMID: 34765130 PMCID: PMC8571620 DOI: 10.1002/ece3.8150] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/31/2021] [Accepted: 09/08/2021] [Indexed: 01/22/2023] Open
Abstract
Quantifying fish species diversity in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, amplification, and sequencing of DNA traces from water samples. However, because eDNA concentration is low in marine environments, the reliability of eDNA to detect species diversity can be limited. Using an eDNA metabarcoding approach to identify fish Molecular Taxonomic Units (MOTUs) with a single 12S marker, we aimed to assess how the number of sampling replicates and filtered water volume affect biodiversity estimates. We used a paired sampling design of 30 L per replicate on 68 reef transects from 8 sites in 3 tropical regions. We quantified local and regional sampling variability by comparing MOTU richness, compositional turnover, and compositional nestedness. We found strong turnover of MOTUs between replicated pairs of samples undertaken in the same location, time, and conditions. Paired samples contained non-overlapping assemblages rather than subsets of one another. As a result, non-saturated localized diversity accumulation curves suggest that even 6 replicates (180 L) in the same location can underestimate local diversity (for an area <1 km). However, sampling regional diversity using ~25 replicates in variable locations (often covering 10 s of km) often saturated biodiversity accumulation curves. Our results demonstrate variability of diversity estimates possibly arising from heterogeneous distribution of eDNA in seawater, highly skewed frequencies of eDNA traces per MOTU, in addition to variability in eDNA processing. This high compositional variability has consequences for using eDNA to monitor temporal and spatial biodiversity changes in local assemblages. Avoiding false-negative detections in future biomonitoring efforts requires increasing replicates or sampled water volume to better inform management of marine biodiversity using eDNA.
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Affiliation(s)
- Salomé Stauffer
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
| | - Meret Jucker
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
| | - Thomas Keggin
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Virginie Marques
- MARBECUniv. MontpellierCNRSIFREMERIRDMontpellierFrance
- CEFEUniv. MontpellierCNRSEPHE‐PSL UniversityIRDUniv. Paul Valéry Montpellier 3MontpellierFrance
| | - Marco Andrello
- Institute for the Study of Anthropic Impacts and Sustainability in the Marine EnvironmentNational Research CouncilRomeItaly
| | - Sandra Bessudo
- Fundación Malpelo y otros ecosistemas marinosBogotáColombia
| | | | - Giomar Helena Borrero‐Pérez
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR Museo de Historia Natural Marina de Colombia (MHNMC)Santa MartaColombia
| | - Eilísh Richards
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
| | | | - Régis Hocdé
- MARBECUniv. MontpellierCNRSIFREMERIRDMontpellierFrance
| | | | - Felipe Ladino
- Fundación Malpelo y otros ecosistemas marinosBogotáColombia
| | - Tom B. Letessier
- Institute of ZoologyZoological Society of LondonLondonUK
- Marine Futures LabUniversity of Western AustraliaCrawleyWAAustralia
| | | | - Eva Maire
- Lancaster Environment CentreLancaster UniversityLancasterUK
| | | | - Maria Mutis Martinezguerra
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR Museo de Historia Natural Marina de Colombia (MHNMC)Santa MartaColombia
| | - Stéphanie Manel
- CEFEUniv. MontpellierCNRSEPHE‐PSL UniversityIRDUniv. Paul Valéry Montpellier 3MontpellierFrance
| | - Andrea Polanco Fernández
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR Museo de Historia Natural Marina de Colombia (MHNMC)Santa MartaColombia
| | | | - Laure Velez
- MARBECUniv. MontpellierCNRSIFREMERIRDMontpellierFrance
| | - Camille Albouy
- IFREMERunité Écologie et Modèles pour l’HalieutiqueNantesFrance
| | - Loïc Pellissier
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Conor Waldock
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
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Use of environmental DNA in early detection of Mnemiopsis leidyi in UK coastal waters. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02650-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Vilizzi L, Copp GH, Hill JE, Adamovich B, Aislabie L, Akin D, Al-Faisal AJ, Almeida D, Azmai MNA, Bakiu R, Bellati A, Bernier R, Bies JM, Bilge G, Branco P, Bui TD, Canning-Clode J, Cardoso Ramos HA, Castellanos-Galindo GA, Castro N, Chaichana R, Chainho P, Chan J, Cunico AM, Curd A, Dangchana P, Dashinov D, Davison PI, de Camargo MP, Dodd JA, Durland Donahou AL, Edsman L, Ekmekçi FG, Elphinstone-Davis J, Erős T, Evangelista C, Fenwick G, Ferincz Á, Ferreira T, Feunteun E, Filiz H, Forneck SC, Gajduchenko HS, Gama Monteiro J, Gestoso I, Giannetto D, Gilles AS, Gizzi F, Glamuzina B, Glamuzina L, Goldsmit J, Gollasch S, Goulletquer P, Grabowska J, Harmer R, Haubrock PJ, He D, Hean JW, Herczeg G, Howland KL, İlhan A, Interesova E, Jakubčinová K, Jelmert A, Johnsen SI, Kakareko T, Kanongdate K, Killi N, Kim JE, Kırankaya ŞG, Kňazovická D, Kopecký O, Kostov V, Koutsikos N, Kozic S, Kuljanishvili T, Kumar B, Kumar L, Kurita Y, Kurtul I, Lazzaro L, Lee L, Lehtiniemi M, Leonardi G, Leuven RSEW, Li S, Lipinskaya T, Liu F, Lloyd L, Lorenzoni M, Luna SA, Lyons TJ, Magellan K, Malmstrøm M, Marchini A, Marr SM, Masson G, Masson L, McKenzie CH, Memedemin D, Mendoza R, Minchin D, Miossec L, Moghaddas SD, Moshobane MC, Mumladze L, Naddafi R, Najafi-Majd E, Năstase A, Năvodaru I, Neal JW, Nienhuis S, Nimtim M, Nolan ET, Occhipinti-Ambrogi A, Ojaveer H, Olenin S, Olsson K, Onikura N, O'Shaughnessy K, Paganelli D, Parretti P, Patoka J, Pavia RTB, Pellitteri-Rosa D, Pelletier-Rousseau M, Peralta EM, Perdikaris C, Pietraszewski D, Piria M, Pitois S, Pompei L, Poulet N, Preda C, Puntila-Dodd R, Qashqaei AT, Radočaj T, Rahmani H, Raj S, Reeves D, Ristovska M, Rizevsky V, Robertson DR, Robertson P, Ruykys L, Saba AO, Santos JM, Sarı HM, Segurado P, Semenchenko V, Senanan W, Simard N, Simonović P, Skóra ME, Slovák Švolíková K, Smeti E, Šmídová T, Špelić I, Srėbalienė G, Stasolla G, Stebbing P, Števove B, Suresh VR, Szajbert B, Ta KAT, Tarkan AS, Tempesti J, Therriault TW, Tidbury HJ, Top-Karakuş N, Tricarico E, Troca DFA, Tsiamis K, Tuckett QM, Tutman P, Uyan U, Uzunova E, Vardakas L, Velle G, Verreycken H, Vintsek L, Wei H, Weiperth A, Weyl OLF, Winter ER, Włodarczyk R, Wood LE, Yang R, Yapıcı S, Yeo SSB, Yoğurtçuoğlu B, Yunnie ALE, Zhu Y, Zięba G, Žitňanová K, Clarke S. A global-scale screening of non-native aquatic organisms to identify potentially invasive species under current and future climate conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 788:147868. [PMID: 34134389 DOI: 10.1016/j.scitotenv.2021.147868] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 05/22/2023]
Abstract
The threat posed by invasive non-native species worldwide requires a global approach to identify which introduced species are likely to pose an elevated risk of impact to native species and ecosystems. To inform policy, stakeholders and management decisions on global threats to aquatic ecosystems, 195 assessors representing 120 risk assessment areas across all six inhabited continents screened 819 non-native species from 15 groups of aquatic organisms (freshwater, brackish, marine plants and animals) using the Aquatic Species Invasiveness Screening Kit. This multi-lingual decision-support tool for the risk screening of aquatic organisms provides assessors with risk scores for a species under current and future climate change conditions that, following a statistically based calibration, permits the accurate classification of species into high-, medium- and low-risk categories under current and predicted climate conditions. The 1730 screenings undertaken encompassed wide geographical areas (regions, political entities, parts thereof, water bodies, river basins, lake drainage basins, and marine regions), which permitted thresholds to be identified for almost all aquatic organismal groups screened as well as for tropical, temperate and continental climate classes, and for tropical and temperate marine ecoregions. In total, 33 species were identified as posing a 'very high risk' of being or becoming invasive, and the scores of several of these species under current climate increased under future climate conditions, primarily due to their wide thermal tolerances. The risk thresholds determined for taxonomic groups and climate zones provide a basis against which area-specific or climate-based calibrated thresholds may be interpreted. In turn, the risk rankings help decision-makers identify which species require an immediate 'rapid' management action (e.g. eradication, control) to avoid or mitigate adverse impacts, which require a full risk assessment, and which are to be restricted or banned with regard to importation and/or sale as ornamental or aquarium/fishery enhancement.
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Affiliation(s)
- Lorenzo Vilizzi
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland
| | - Gordon H Copp
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland; Centre for Environment, Fisheries and Aquaculture Science, Lowestoft, Suffolk NR33 0HT, UK; Centre for Ecology, Environment and Sustainability, Bournemouth University, Poole, Dorset BH12 5BB, UK; School of the Environment, Trent University, Peterborough, Ontario K9L 0G2, Canada
| | - Jeffrey E Hill
- Tropical Aquaculture Laboratory, Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Ruskin, FL 33570, USA
| | - Boris Adamovich
- Faculty of Biology, Belarusian State University, 220030 Minsk, Belarus
| | - Luke Aislabie
- Centre for Environment, Fisheries and Aquaculture Science, Lowestoft, Suffolk NR33 0HT, UK
| | - Daniel Akin
- College of Science and Mathematics, Auburn University, Auburn, AL 36849, USA
| | - Abbas J Al-Faisal
- Marine Science Centre, University of Basrah, PO Box 49, Basrah, Iraq
| | - David Almeida
- Departamento de Ciencias Médicas Básicas, Facultad de Medicina, Universidad San Pablo CEU, 28003 Madrid, Spain
| | - M N Amal Azmai
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 Seri Kembangan, Selangor, Malaysia
| | - Rigers Bakiu
- Department of Aquaculture and Fisheries, Faculty of Agriculture and Environment, Agricultural University of Tirana, Tirana 1000, Albania; Albanian Center for Environmental Protection and Sustainable Development, Tirana 1000, Albania
| | - Adriana Bellati
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy
| | - Renée Bernier
- Fisheries and Oceans Canada, Gulf Fisheries Centre, Moncton, New Brunswick E1C 5K4, Canada
| | - Jason M Bies
- Department of Wildlife, Fisheries & Aquaculture, Mississippi State University, Mississippi State, MS 39762, USA
| | - Gökçen Bilge
- Department of Basic Sciences, Faculty of Fisheries, Muğla Sıtkı Koçman University, 48000 Menteşe, Muğla, Turkey
| | - Paulo Branco
- Forest Research Centre, School of Agriculture, University of Lisbon, Tapada da Ajuda 1349-017, Lisbon, Portugal
| | - Thuyet D Bui
- Faculty of Marine Science, Hanoi University of Natural Resources and Environment, 41A Phu Dien, Bac Tu Liem, Hanoi, Viet Nam
| | - João Canning-Clode
- MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), 9020-105 Funchal, Madeira, Portugal; Smithsonian Environmental Research Center, Edgewater, MD 21037, USA
| | - Henrique Anatole Cardoso Ramos
- Coordination of Sustainable Use of Fisheries Resources, Department of Species Conservation, Ministry of Environment, 70068-900 Brasilia, Brazil
| | - Gustavo A Castellanos-Galindo
- Leibniz Centre for Tropical Marine Research (ZMT), 28359 Bremen, Germany; Smithsonian Tropical Research Institute, Apartado 2072, Balboa, Panamá
| | - Nuno Castro
- MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), 9020-105 Funchal, Madeira, Portugal
| | - Ratcha Chaichana
- Department of Environmental Technology and Management, Faculty of Environment, Kasetsart University, Bangkok 10900, Thailand
| | - Paula Chainho
- MARE - Marine and Environmental Sciences Centre, Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal; Department of Animal Biology, Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal; Polytechnic Institute of Setúbal, 2910-761 Setúbal, Portugal
| | - Joleen Chan
- Department of Biological Sciences, National University of Singapore, 117558, Singapore
| | - Almir M Cunico
- Laboratory of Ecology, Fisheries and Ichthyology, Biodiversity Department - Palotina Sector, Federal University of Paraná (UFPR), Curitiba 80060-000, Brazil
| | - Amelia Curd
- Laboratory of Coastal Benthic Ecology, French Research Institute for Exploitation of the Sea (IFREMER), 29280 Plouzané, France
| | - Punyanuch Dangchana
- Division of Research Policy and Plan, National Research Council of Thailand, Bangkok 10900, Thailand
| | - Dimitriy Dashinov
- Department of General and Applied Hydrobiology, Faculty of Biology, Sofia University, 1164 g.k. Lozenets, Sofia, Bulgaria
| | - Phil I Davison
- Centre for Environment, Fisheries and Aquaculture Science, Lowestoft, Suffolk NR33 0HT, UK
| | - Mariele P de Camargo
- Laboratory of Ecology, Fisheries and Ichthyology, Biodiversity Department - Palotina Sector, Federal University of Paraná (UFPR), Curitiba 80060-000, Brazil
| | - Jennifer A Dodd
- Animal and Plant Sciences Group, Edinburgh Napier University, Sighthill, Edinburgh EH11 4BN, UK
| | - Allison L Durland Donahou
- Tropical Aquaculture Laboratory, Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Ruskin, FL 33570, USA; Florida Southern College, Lakeland, FL 33801, USA
| | - Lennart Edsman
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, SE-750 07 Drottningholm, Sweden
| | - F Güler Ekmekçi
- Hydrobiology section, Department of Biology, Faculty of Science, Hacettepe University, Çankaya-Ankara 06800, Turkey
| | | | - Tibor Erős
- Centre for Ecological Research, Balaton Limnological Institute, Tihany 8237, Hungary
| | - Charlotte Evangelista
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, NO-0316 Oslo, Norway
| | - Gemma Fenwick
- Lancaster Environment Centre, Lancaster University, Lancaster, Lancashire LA1 4YW, UK
| | - Árpád Ferincz
- Institute for Natural Resources Conservation, Department of Aquaculture, Faculty of Agriculture and Environmental Sciences, Szent István University, Gödöllő 2100, Hungary
| | - Teresa Ferreira
- Department of Natural Resources, Environment and Landscape, School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal
| | - Eric Feunteun
- Muséum National d'Histoire Naturelle, Laboratoire Biologie des Organismes et Ecosystèmes Aquatiques, BOREA (MNHN, CNRS, Sorbonne Université, Université de Caen, IRD, Université de Guadeloupe Antilles), Station Marine de Dinard, CRESCO, 35800 Dinard, France
| | - Halit Filiz
- Department of Basic Sciences, Faculty of Fisheries, Muğla Sıtkı Koçman University, 48000 Menteşe, Muğla, Turkey
| | - Sandra C Forneck
- Laboratory of Ecology, Fisheries and Ichthyology, Biodiversity Department - Palotina Sector, Federal University of Paraná (UFPR), Curitiba 80060-000, Brazil
| | - Helen S Gajduchenko
- Laboratory of Ichthyology, Scientific and Practical Center for Bioresources, National Academy of Sciences of Belarus, Minsk 220072, Belarus
| | - João Gama Monteiro
- MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), 9020-105 Funchal, Madeira, Portugal
| | - Ignacio Gestoso
- MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), 9020-105 Funchal, Madeira, Portugal; Smithsonian Environmental Research Center, Edgewater, MD 21037, USA
| | - Daniela Giannetto
- Department of Biology, Faculty of Science, Muğla Sıtkı Koçman University, 48000 Menteşe, Muğla, Turkey
| | - Allan S Gilles
- Department of Biological Sciences, College of Science, Research Center for the Natural and Applied Sciences, Graduate School, University of Santo Tomas, Manila, 1008, Metro Manila, Philippines
| | - Francesca Gizzi
- MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), 9020-105 Funchal, Madeira, Portugal
| | - Branko Glamuzina
- Department of Applied Ecology, University of Dubrovnik, 20000 Dubrovnik, Croatia
| | - Luka Glamuzina
- Department of Applied Ecology, University of Dubrovnik, 20000 Dubrovnik, Croatia
| | - Jesica Goldsmit
- Fisheries and Oceans Canada, Maurice Lamontagne Institute, Mont-Joli, Quebec G5H 3Z4, Canada; Arctic and Aquatic Research Division, Freshwater Institute, Fisheries and Oceans Canada, Winnipeg, Quebec MB R3T 2N6, Canada
| | | | - Philippe Goulletquer
- Scientific Direction, French Research Institute for Exploitation of the Sea (IFREMER), 44980 Nantes, France
| | - Joanna Grabowska
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland
| | - Rogan Harmer
- Centre for Environment, Fisheries and Aquaculture Science, Lowestoft, Suffolk NR33 0HT, UK
| | - Phillip J Haubrock
- Senckenberg Research Institute and Natural History Museum Frankfurt, Department of River Ecology and Conservation, 63571 Gelnhausen, Germany; Nature and Environment Management Operators s.r.l., 50121 Florence, Italy; Department of Biology, University of Florence, 50121 Florence, Italy
| | - Dekui He
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jeffrey W Hean
- DST/NRF Research Chair in Inland Fisheries and Freshwater Ecology, South African Institute for Aquatic Biodiversity, Grahamstown 6140, South Africa; GroundTruth, Water, Wetlands and Environmental Engineering, Hilton, KwaZulu-Natal 3245, South Africa
| | - Gábor Herczeg
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Kimberly L Howland
- Arctic and Aquatic Research Division, Freshwater Institute, Fisheries and Oceans Canada, Winnipeg, Quebec MB R3T 2N6, Canada
| | - Ali İlhan
- Faculty of Fisheries, Ege University, 35100 Bornova, Izmir, Turkey
| | - Elena Interesova
- Tomsk State University, Tomsk 634050, Russia; Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Novosibirsk branch of Russian Federal Research Institute of Fisheries and Oceanography, Novosibirsk 630090, Russia
| | - Katarína Jakubčinová
- Department of Ecology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia
| | - Anders Jelmert
- Institute of Marine Research, Flødevigen Research Station, NO-7485 His, Norway
| | - Stein I Johnsen
- Norwegian Institute for Nature Research, NO-7485 Trondheim, Norway
| | - Tomasz Kakareko
- Department of Ecology and Biogeography, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100 Toruń, Poland
| | - Kamalaporn Kanongdate
- Faculty of Environment and Resource Studies, Mahidol University, Salaya 73170, Thailand
| | - Nurçin Killi
- Department of Basic Sciences, Faculty of Fisheries, Muğla Sıtkı Koçman University, 48000 Menteşe, Muğla, Turkey
| | - Jeong-Eun Kim
- College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon 305-764, Republic of Korea
| | | | - Dominika Kňazovická
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Praha, Czechia
| | - Oldřich Kopecký
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Praha, Czechia
| | - Vasil Kostov
- Department of Fisheries, Institute of Animal Science, Ss Cyril and Methodius University, Skopje 1000, Macedonia
| | - Nicholas Koutsikos
- Institute of Marine Biological Resources & Inland Waters, Hellenic Centre for Marine Research, Anavissos, 19013, Attica, Greece
| | - Sebastian Kozic
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland
| | - Tatia Kuljanishvili
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Praha, Czechia
| | - Biju Kumar
- Department of Aquatic Biology & Fisheries, University of Kerala, Thiruvananthapuram, Kerala 695034, India
| | - Lohith Kumar
- REF Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal 700120, India
| | - Yoshihisa Kurita
- Fishery Research Laboratory, Kyushu University, Fukutsu, Fukuoka 811-3304, Japan
| | - Irmak Kurtul
- Faculty of Fisheries, Ege University, 35100 Bornova, Izmir, Turkey
| | - Lorenzo Lazzaro
- Department of Biology, University of Florence, 50121 Florence, Italy
| | - Laura Lee
- Department of Evolution, Ecology and Behaviour, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7TX, England, United Kingdom
| | - Maiju Lehtiniemi
- Marine Research Centre, Finnish Environment Institute, 00790 Helsinki, Finland
| | | | - Rob S E W Leuven
- Department of Animal Ecology and Physiology, Institute for Water and Wetland Research, Radboud University & Netherlands Centre of Expertise on Exotic Species, 6500 GL Nijmegen, the Netherlands
| | - Shan Li
- Natural History Research Center, Shanghai Natural History Museum, Branch of Shanghai Science & Technology Museum, Shanghai 200041, China
| | - Tatsiana Lipinskaya
- Laboratory of Hydrobiology, Scientific and Practical Center for Bioresources, National Academy of Sciences of Belarus, Minsk 220072, Belarus
| | - Fei Liu
- Aquatic Science Institute, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa 850009, China
| | - Lance Lloyd
- Lloyd Environmental Pty Ltd, Somers, Victoria 3927, Australia; School of Health and Life Sciences, Federation University Australia, Ballarat, Victoria 3350, Australia
| | - Massimo Lorenzoni
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06123 Perugia, Italy
| | - Sergio Alberto Luna
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Nuevo León 66455, Mexico
| | - Timothy J Lyons
- Tropical Aquaculture Laboratory, Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Ruskin, FL 33570, USA; New Mexico Biopark Society, Albuquerque, NM 87102, USA
| | - Kit Magellan
- South African Institute for Aquatic Biodiversity, Grahamstown 6140, South Africa; University of Battambang, 02360 Battambang, Cambodia
| | - Martin Malmstrøm
- Norwegian Scientific Committee for Food and Environment (VKM), NO-0213 Oslo, Norway
| | - Agnese Marchini
- Department of Earth and Environmental Sciences, University of Pavia, 27100 Pavia, Italy
| | - Sean M Marr
- DST/NRF Research Chair in Inland Fisheries and Freshwater Ecology, South African Institute for Aquatic Biodiversity, Grahamstown 6140, South Africa
| | - Gérard Masson
- Laboratoire interdisciplinaire des environnements continentaux, Centre national de la recherche scientifique, Université de Lorraine, 57000 Metz, France
| | - Laurence Masson
- Freshwater Fish Ecology Laboratory, Ecosystem Science and Management Program, University of Northern British Columbia, Prince George, British Columbia V2N 4Z9, Canada
| | - Cynthia H McKenzie
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador A1A 5J7, Canada
| | - Daniyar Memedemin
- Faculty of Natural and Agricultural Sciences, Ovidius University of Constanta, Constanta 900527, Romania
| | - Roberto Mendoza
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Nuevo León 66455, Mexico
| | - Dan Minchin
- Marine Organism Investigations, Marina Village, Ballina, Killaloe, Clare V94 767X, Ireland; Marine Research Institute, Klaipėda University, 92294 Klaipėda, Lithuania
| | - Laurence Miossec
- Scientific Direction, French Research Institute for Exploitation of the Sea (IFREMER), 44980 Nantes, France
| | - Seyed Daryoush Moghaddas
- Department of Biodiversity and Ecosystems Management, Environmental Sciences Research Institute, Shahid Beheshti University, 1983963113 Tehran, Iran
| | - Moleseng C Moshobane
- South African National Biodiversity Institute, Biological Invasions Directorate, Pretoria 0001, South Africa; Department of Biology, Sefako Makgatho Health Sciences University, Gauteng 0208, South Africa; Young Water Professionals, South African Chapter, Limpopo 1685, South Africa
| | - Levan Mumladze
- Institute of Zoology, Ilia State University, Tbilisi 0162, Georgia
| | - Rahmat Naddafi
- Swedish University of Agricultural Sciences, Department of Aquatic Resources, Division of Coastal Research, SE-453 30 Oregrund, Sweden
| | - Elnaz Najafi-Majd
- Department of Biology, Faculty of Sciences, Ege University, 35040 Izmir, Turkey
| | - Aurel Năstase
- Department of Biodiversity Conservation and Sustainable Use of Natural Resources, Danube Delta National Institute for Research and Development, Tulcea 820112, Romania
| | - Ion Năvodaru
- Department of Biodiversity Conservation and Sustainable Use of Natural Resources, Danube Delta National Institute for Research and Development, Tulcea 820112, Romania
| | - J Wesley Neal
- Department of Wildlife, Fisheries & Aquaculture, Mississippi State University, Mississippi State, MS 39762, USA
| | - Sarah Nienhuis
- Ontario Ministry of Natural Resources and Forestry, Peterborough, Ontario K9J 8M5, Canada
| | - Matura Nimtim
- Department of Environmental Technology and Management, Faculty of Environment, Kasetsart University, Bangkok 10900, Thailand
| | - Emma T Nolan
- Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, Talbot Campus, Poole BH12 5BB, UK
| | - Anna Occhipinti-Ambrogi
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy
| | - Henn Ojaveer
- University of Tartu, 80012 Pärnu, Estonia; National Institute of Aquatic Resources, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Sergej Olenin
- Marine Research Institute, Klaipėda University, 92294 Klaipėda, Lithuania
| | - Karin Olsson
- Centre for Environment, Fisheries and Aquaculture Science, Lowestoft, Suffolk NR33 0HT, UK; School of Zoology, Tel Aviv University, Tel Aviv 6997801, Israel; The Inter-University Institute for Marine Sciences in Eilat, Coral Beach, Eilat 8810302, Israel
| | - Norio Onikura
- Fishery Research Laboratory, Kyushu University, Fukutsu, Fukuoka 811-3304, Japan
| | - Kathryn O'Shaughnessy
- Texas Parks and Wildlife Department, Coastal Fisheries, 4200 Smith School Rd., Austin, TX 78744, USA
| | | | - Paola Parretti
- MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), 9020-105 Funchal, Madeira, Portugal; CIBIO, Research Center in Biodiversity and Genetic Resources, InBIO Associate Laboratory and Faculty of Sciences and Technologies, University of the Azores, 9500-321 Ponta Delgada, Portugal
| | - Jiří Patoka
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Praha, Czechia
| | - Richard Thomas B Pavia
- Department of Biological Sciences, College of Science, Research Center for the Natural and Applied Sciences, Graduate School, University of Santo Tomas, Manila, 1008, Metro Manila, Philippines
| | | | | | - Elfritzson M Peralta
- Department of Biological Sciences, College of Science, Research Center for the Natural and Applied Sciences, Graduate School, University of Santo Tomas, Manila, 1008, Metro Manila, Philippines
| | - Costas Perdikaris
- Department of Fisheries, Regional Unit of Thesprotia, Epirus, 46 100, Igoumenitsa, Greece
| | - Dariusz Pietraszewski
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland
| | - Marina Piria
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland; Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, University of Zagreb Faculty of Agriculture, 10000 Zagreb, Croatia.
| | - Sophie Pitois
- Centre for Environment, Fisheries and Aquaculture Science, Lowestoft, Suffolk NR33 0HT, UK
| | - Laura Pompei
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06123 Perugia, Italy
| | - Nicolas Poulet
- Pôle écohydraulique OFB-IMFT-P, French Agency for Biodiversity, 31400 Toulouse, France
| | - Cristina Preda
- Faculty of Natural and Agricultural Sciences, Ovidius University of Constanta, Constanta 900527, Romania
| | - Riikka Puntila-Dodd
- Marine Research Centre, Finnish Environment Institute, 00790 Helsinki, Finland
| | | | - Tena Radočaj
- Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, University of Zagreb Faculty of Agriculture, 10000 Zagreb, Croatia
| | - Hossein Rahmani
- Sari Agricultural Sciences and Natural Resources University, Sari, 4816118771, Mazandaran, Iran
| | - Smrithy Raj
- Department of Aquatic Biology & Fisheries, University of Kerala, Thiruvananthapuram, Kerala 695034, India; National Centre for Biological Sciences, Bangalore 560065, India
| | - David Reeves
- National Fish and Wildlife Foundation, Baton Rouge, LA 70808, USA
| | - Milica Ristovska
- Institute of Biology, Faculty of Natural Sciences and Mathematics, Ss Cyril and Methodius University, 1000 Skopje, Macedonia
| | - Viktor Rizevsky
- Laboratory of Ichthyology, Scientific and Practical Center for Bioresources, National Academy of Sciences of Belarus, Minsk 220072, Belarus
| | - D Ross Robertson
- Smithsonian Tropical Research Institute, Apartado 2072, Balboa, Panamá
| | - Peter Robertson
- Modelling, Evidence and Policy Group, School of Natural and Environmental Resources, Newcastle University, Newcastle NE1 7RU, UK
| | - Laura Ruykys
- Nature and Biodiversity Conservation Agency, Vietnam Environment Administration, Ministry of Natural Resources and Environment, 10 Ton That Thuyet, Nam Tu Liem District, Hanoi, Viet Nam; Flora and Fauna Division, Department of Environment and Natural Resources, Palmerston, Northern Territory 0828, Australia
| | - Abdulwakil O Saba
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 Seri Kembangan, Selangor, Malaysia; School of Agriculture, Lagos State University, Epe Campus, 106101 Epe, Lagos State, Nigeria
| | - José M Santos
- Forest Research Centre, School of Agriculture, University of Lisbon, Tapada da Ajuda 1349-017, Lisbon, Portugal
| | - Hasan M Sarı
- Faculty of Fisheries, Ege University, 35100 Bornova, Izmir, Turkey
| | - Pedro Segurado
- Forest Research Centre, School of Agriculture, University of Lisbon, Tapada da Ajuda 1349-017, Lisbon, Portugal
| | - Vitaliy Semenchenko
- Laboratory of Hydrobiology, Scientific and Practical Center for Bioresources, National Academy of Sciences of Belarus, Minsk 220072, Belarus
| | - Wansuk Senanan
- Department of Aquatic Science, Faculty of Science, Burapha University, Chon Buri 20130, Thailand
| | - Nathalie Simard
- Fisheries and Oceans Canada, Maurice Lamontagne Institute, Mont-Joli, Quebec G5H 3Z4, Canada
| | - Predrag Simonović
- Faculty of Biology & Institute for Biological Research "Siniša Stanković", University of Belgrade, Belgrade 11000, Serbia
| | - Michał E Skóra
- University of Gdańsk, Faculty of Oceanography and Geography, Institute of Oceanography, Professor Krzysztof Skóra Hel Marine Station, 84-150 Hel, Poland
| | - Kristína Slovák Švolíková
- Department of Ecology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia
| | - Evangelia Smeti
- Institute of Marine Biological Resources & Inland Waters, Hellenic Centre for Marine Research, Anavissos, 19013, Attica, Greece
| | - Tereza Šmídová
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Praha, Czechia
| | - Ivan Špelić
- Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, University of Zagreb Faculty of Agriculture, 10000 Zagreb, Croatia
| | - Greta Srėbalienė
- Marine Research Institute, Klaipėda University, 92294 Klaipėda, Lithuania
| | | | - Paul Stebbing
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset DT4 8UB, UK; APEM Ltd, A17 Embankment, Business Park, Heaton Mersey, Manchester, Cheshire SK4 3GN, UK
| | - Barbora Števove
- Department of Ecology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia
| | - Vettath R Suresh
- Division of Mariculture, Central Marine Fisheries Research Institute, Cochin, Kerala 682018, India
| | - Bettina Szajbert
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Kieu Anh T Ta
- Nature and Biodiversity Conservation Agency, Vietnam Environment Administration, Ministry of Natural Resources and Environment, 10 Ton That Thuyet, Nam Tu Liem District, Hanoi, Viet Nam
| | - Ali Serhan Tarkan
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland; Department of Basic Sciences, Faculty of Fisheries, Muğla Sıtkı Koçman University, 48000 Menteşe, Muğla, Turkey
| | | | - Thomas W Therriault
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia V9T 6N7, Canada
| | - Hannah J Tidbury
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset DT4 8UB, UK
| | - Nildeniz Top-Karakuş
- Department of Basic Sciences, Faculty of Fisheries, Muğla Sıtkı Koçman University, 48000 Menteşe, Muğla, Turkey
| | - Elena Tricarico
- Department of Biology, University of Florence, 50121 Florence, Italy
| | - Débora F A Troca
- Institute of Oceanography, Federal University of Rio Grande, 96203-900 Rio Grande, Brazil
| | - Konstantinos Tsiamis
- Institute of Oceanography, Hellenic Centre for Marine Research, Attica, Anavyssos 19013, Greece
| | - Quenton M Tuckett
- Tropical Aquaculture Laboratory, Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Ruskin, FL 33570, USA
| | - Pero Tutman
- Laboratory for Ichthyology and Coastal Fisheries, Institute of Oceanography and Fisheries, 21000 Split, Croatia
| | - Umut Uyan
- Skretting Turkey, Güllük Milas, 48670, Muğla, Turkey
| | - Eliza Uzunova
- Department of General and Applied Hydrobiology, Faculty of Biology, Sofia University, 1164 g.k. Lozenets, Sofia, Bulgaria
| | - Leonidas Vardakas
- Institute of Marine Biological Resources & Inland Waters, Hellenic Centre for Marine Research, Anavissos, 19013, Attica, Greece
| | - Gaute Velle
- Norwegian Research Centre, 5007 Bergen, Norway; Department of Biological Sciences, University of Bergen, 5007 Bergen, Norway
| | - Hugo Verreycken
- Research Institute for Nature and Forest (INBO), B-1630 Linkebeek, Belgium
| | - Lizaveta Vintsek
- Institute of Botany, Faculty of Biology, Jagiellonian University, 30-387 Kraków, Poland
| | - Hui Wei
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510380, China; Key Laboratory of Recreational fisheries Research, Ministry of Agriculture and Rural Affairs, Guangzhou 510380, China
| | - András Weiperth
- Institute for Natural Resources Conservation, Department of Aquaculture, Faculty of Agriculture and Environmental Sciences, Szent István University, Gödöllő 2100, Hungary
| | - Olaf L F Weyl
- Centre for Invasion Biology, South African Institute for Aquatic Biodiversity, Makhanda 6139, South Africa; DST/NRF Research Chair in Inland Fisheries and Freshwater Ecology, South African Institute for Aquatic Biodiversity, Grahamstown 6140, South Africa
| | - Emily R Winter
- Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, Talbot Campus, Poole BH12 5BB, UK
| | - Radosław Włodarczyk
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland
| | - Louisa E Wood
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset DT4 8UB, UK
| | - Ruibin Yang
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Sercan Yapıcı
- Department of Basic Sciences, Faculty of Fisheries, Muğla Sıtkı Koçman University, 48000 Menteşe, Muğla, Turkey
| | - Shayne S B Yeo
- Department of Biological Sciences, National University of Singapore, 117558, Singapore
| | - Baran Yoğurtçuoğlu
- Hydrobiology section, Department of Biology, Faculty of Science, Hacettepe University, Çankaya-Ankara 06800, Turkey
| | | | - Yunjie Zhu
- Aquaculture Technology Promotion Station of Nantong, Nantong, China
| | - Grzegorz Zięba
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland
| | - Kristína Žitňanová
- Department of Ecology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia
| | - Stacey Clarke
- Centre for Environment, Fisheries and Aquaculture Science, Lowestoft, Suffolk NR33 0HT, UK
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Ogata M, Masuda R, Harino H, Sakata MK, Hatakeyama M, Yokoyama K, Yamashita Y, Minamoto T. Environmental DNA preserved in marine sediment for detecting jellyfish blooms after a tsunami. Sci Rep 2021; 11:16830. [PMID: 34417484 PMCID: PMC8379222 DOI: 10.1038/s41598-021-94286-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 07/08/2021] [Indexed: 02/07/2023] Open
Abstract
Environmental DNA (eDNA) can be a powerful tool for detecting the distribution and abundance of target species. This study aimed to test the longevity of eDNA in marine sediment through a tank experiment and to use this information to reconstruct past faunal occurrence. In the tank experiment, juvenile jack mackerel (Trachurus japonicus) were kept in flow-through tanks with marine sediment for two weeks. Water and sediment samples from the tanks were collected after the removal of fish. In the field trial, sediment cores were collected in Moune Bay, northeast Japan, where unusual blooms of jellyfish (Aurelia sp.) occurred after a tsunami. The samples were analyzed by layers to detect the eDNA of jellyfish. The tank experiment revealed that after fish were removed, eDNA was not present in the water the next day, or subsequently, whereas eDNA was detectable in the sediment for 12 months. In the sediment core samples, jellyfish eDNA was detected at high concentrations above the layer with the highest content of polycyclic aromatic hydrocarbons, reflecting tsunami-induced oil spills. Thus, marine sediment eDNA preserves a record of target species for at least one year and can be used to reconstruct past faunal occurrence.
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Affiliation(s)
- Mizuki Ogata
- grid.258799.80000 0004 0372 2033Maizuru Fisheries Research Station, Field Science Education and Research Center, Kyoto University, Nagahama, Maizuru, Kyoto 625-0086 Japan ,Benesse Corporation, 3-7-17 Minamigata, Kitaku, Okayama 700-8686 Japan
| | - Reiji Masuda
- grid.258799.80000 0004 0372 2033Maizuru Fisheries Research Station, Field Science Education and Research Center, Kyoto University, Nagahama, Maizuru, Kyoto 625-0086 Japan
| | - Hiroya Harino
- grid.444507.60000 0001 0424 8271Department of Human Sciences, Kobe College, 4-1 Okadayama, Nishinomiya, Hyogo 662-8508 Japan
| | - Masayuki K. Sakata
- grid.31432.370000 0001 1092 3077Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe, Hyogo 657-8501 Japan
| | - Makoto Hatakeyama
- Non-Profit Organization Mori-Umi, Nishi-Moune, Karakuwa, Kesennuma, Miyagi 988-0527 Japan
| | - Katsuhide Yokoyama
- grid.265074.20000 0001 1090 2030Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 092-0397 Japan
| | - Yoh Yamashita
- grid.258799.80000 0004 0372 2033Maizuru Fisheries Research Station, Field Science Education and Research Center, Kyoto University, Nagahama, Maizuru, Kyoto 625-0086 Japan
| | - Toshifumi Minamoto
- grid.31432.370000 0001 1092 3077Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe, Hyogo 657-8501 Japan
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Faria R, Johannesson K, Stankowski S. Speciation in marine environments: Diving under the surface. J Evol Biol 2021; 34:4-15. [PMID: 33460491 DOI: 10.1111/jeb.13756] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/31/2020] [Accepted: 01/03/2021] [Indexed: 12/28/2022]
Abstract
Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we 'dive under the surface' by studying a wider range of taxa and ecosystems is necessary for a more comprehensive picture of speciation. Although studying marine evolutionary processes is often challenging, recent technological advances in different fields, from maritime engineering to genomics, are making it increasingly possible to study speciation of marine life forms across diverse ecosystems and taxa. Motivated by recent research in the field, including the 14 contributions in this issue, we highlight and discuss six axes of research that we think will deepen our understanding of speciation in the marine realm: (a) study a broader range of marine environments and organisms; (b) identify the reproductive barriers driving speciation between marine taxa; (c) understand the role of different genomic architectures underlying reproductive isolation; (d) infer the evolutionary history of divergence using model-based approaches; (e) study patterns of hybridization and introgression between marine taxa; and (f) implement highly interdisciplinary, collaborative research programmes. In outlining these goals, we hope to inspire researchers to continue filling this critical knowledge gap surrounding the origins of marine biodiversity.
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Affiliation(s)
- Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal.,CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Kerstin Johannesson
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Sean Stankowski
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.,IST Austria, Klosterneuburg, Austria
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Metabarcoding under Brine: Microbial Ecology of Five Hypersaline Lakes at Rottnest Island (WA, Australia). WATER 2021. [DOI: 10.3390/w13141899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hypersaline ecosystems—aquatic environments where concentration of salt exceeds 35 g L−1—host microbial communities that are highly specialised to cope with these extreme conditions. However, our knowledge on the taxonomic diversity and functional metabolisms characterising microbial communities in the water columns of hypersaline ecosystems is still limited, and this may compromise the future preservation of these unique environments. DNA metabarcoding provides a reliable and affordable tool to investigate environmental dynamics of aquatic ecosystems, and its use in brine can be highly informative. Here, we make use of bacterial 16S metabarcoding techniques combined with hydrochemical analyses to investigate the microbial patterns (diversity and functions) from five hypersaline lakes located at Rottnest Island (WA). Our results indicate lake-driven microbial aquatic assemblages that are characterised by taxonomically and functionally moderately to extremely halophilic groups, with TDS (total dissolved solids) and alkalinity amongst the most influential parameters driving the community patterns. Overall, our findings suggest that DNA metabarcoding allows rapid but reliable ecological assessment of the hypersaline aquatic microbial communities at Rottnest Island. Further studies involving different hypersaline lakes across multiple seasons will help elucidate the full extent of the potential of this tool in brine.
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Benthic Foraminiferal Indices and Environmental Quality Assessment of Transitional Waters: A Review of Current Challenges and Future Research Perspectives. WATER 2021. [DOI: 10.3390/w13141898] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Transitional waters straddle the interface between marine and terrestrial biomes and, among others, include fjords, bays, lagoons, and estuaries. These coastal systems are essential for transport and manufacturing industries and suffer extensive anthropogenic exploitation of their ecosystem services for aquaculture and recreational activities. These activities can have negative effects on the local biota, necessitating investigation and regulation. As a result of this, EcoQS (ecological quality status) assessment has garnered great attention as an essential aspect of governmental bodies’ legislative decision-making process. Assessing EcoQS in transitional water ecosystems is problematic because these systems experience high natural variability and organic enrichment and often lack information about their pre-human impact, baseline, or “pristine” reference conditions, knowledge of which is essential to many commonly used assessment methods. Here, foraminifera can be used as environmental sentinels, providing ecological data such as diversity and sensitivity, which can be used as the basis for EcoQS assessment indices. Fossil shells of foraminifera can also provide a temporal aspect to ecosystem assessment, making it possible to obtain reference conditions from the study site itself. These foraminifera-based indices have been shown to correlate not only with various environmental stressors but also with the most common macrofaunal-based indices currently employed by bodies such as the Water Framework Directive (WFD). In this review, we firstly discuss the development of various foraminifera-based indices and address the challenge of how best to implement these synergistically to understand and regulate human environmental impact, particularly in transitional waters, which have historically suffered disproportionate levels of human impact or are difficult to assess with standard EcoQS methods. Further, we present some case studies to exemplify key issues and discuss potential solutions for those. Such key issues include, for example, the disparate performance of multiple indices applied to the same site and a proper assignment of EcoQS class boundaries (threshold values) for each index. Disparate aptitudes of indices to specific geomorphologic and hydrological regimes can be leveraged via the development of a site characteristics catalogue, which would enable the identification of the most appropriate index to apply, and the integration of multiple indices resulting in more representative EcoQS assessment in heterogenous transitional environments. In addition, the difficulty in assigning threshold values to systems without analogous unimpacted reference sites (a common issue among many transitional waters) can be overcome by recording EcoQS as an ecological quality ratio (EQR). Lastly, we evaluate the current status and future potential of an emerging field, genetic biomonitoring, focusing on how these new techniques can be used to increase the accuracy of EcoQS assessment in transitional systems by supplementing more established morphology-based methods.
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Cordier T, Alonso‐Sáez L, Apothéloz‐Perret‐Gentil L, Aylagas E, Bohan DA, Bouchez A, Chariton A, Creer S, Frühe L, Keck F, Keeley N, Laroche O, Leese F, Pochon X, Stoeck T, Pawlowski J, Lanzén A. Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap. Mol Ecol 2021; 30:2937-2958. [PMID: 32416615 PMCID: PMC8358956 DOI: 10.1111/mec.15472] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.
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Affiliation(s)
- Tristan Cordier
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
| | - Laura Alonso‐Sáez
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
| | | | - Eva Aylagas
- Red Sea Research Center (RSRC)Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - David A. Bohan
- AgroécologieINRAEUniversity of BourgogneUniversity Bourgogne Franche‐ComtéDijonFrance
| | | | - Anthony Chariton
- Department of Biological SciencesMacquarie UniversitySydneyNSWAustralia
| | - Simon Creer
- School of Natural SciencesBangor UniversityGwyneddUK
| | - Larissa Frühe
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | | | - Nigel Keeley
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Olivier Laroche
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
| | - Xavier Pochon
- Coastal & Freshwater GroupCawthron InstituteNelsonNew Zealand
- Institute of Marine ScienceUniversity of AucklandWarkworthNew Zealand
| | - Thorsten Stoeck
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | - Jan Pawlowski
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
- ID‐Gene EcodiagnosticsGenevaSwitzerland
- Institute of OceanologyPolish Academy of SciencesSopotPoland
| | - Anders Lanzén
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
- Basque Foundation for ScienceIKERBASQUEBilbaoSpain
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Ibabe A, Miralles L, Carleos CE, Soto-López V, Menéndez-Teleña D, Bartolomé M, Montes HJ, González M, Dopico E, Garcia-Vazquez E, Borrell YJ. Building on gAMBI in ports for a challenging biological invasions scenario: Blue-gNIS as a proof of concept. MARINE ENVIRONMENTAL RESEARCH 2021; 169:105340. [PMID: 33930798 DOI: 10.1016/j.marenvres.2021.105340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/05/2021] [Accepted: 04/10/2021] [Indexed: 06/12/2023]
Abstract
The status of aquatic ecosystems has historically been monitored by the use of biotic indices. However, few biotic measures consider the presence of non-indigenous species as a sign of anthropogenic pollution and habitat disturbance even when this may seriously affect the metric scores and ecological status classifications of an environment. Today, biological invasions are currently one of the greatest threats to biodiversity and sustainable blue economies around the world. In this work, environmental assessments were conducted in the Port of Gijon, Northern Spain, using eDNA metabarcoding, and the gAMBI (genetics based AZTI Marine Biotic Index) was estimated. Results indicate a high/good ecological status within the port. However, nine non-indigenous species and five invasive species were found, and a modification of the gAMBI that includes species invasiveness was proposed: Blue-gNIS. The index was preliminary tested against existing validated indices such as gAMBI, BENTIX (based on the ecology of macroinvertebrates) and ALEX (based on the invasiveness of the species). Blue-gNIS classified the port in a good ecological status and showed its potential usefulness to achieve more complete water quality assessments of ports.
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Affiliation(s)
- A Ibabe
- Genetics, Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n, 33006, Oviedo, Spain
| | - L Miralles
- Genetics, Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n, 33006, Oviedo, Spain; Ecohydros S.L., Polígono Industrial de Cros, Edif. 5-Nave 8, 39600, Maliaño, Cantabria, Spain
| | - C E Carleos
- Department of Statistics and Operations Research and Mathematics Didactics, University of Oviedo, Facultad de Ciencias, C/ Federico García Lorca, s/n, 33007, Oviedo, Spain
| | - V Soto-López
- Department of Marine Science and Technology, University of Oviedo, Escuela Superior de Marina Civil, Campus de Gijón C/Blasco de Garay s/n, 33203, Gijón, Asturias, Spain
| | - D Menéndez-Teleña
- Department of Marine Science and Technology, University of Oviedo, Escuela Superior de Marina Civil, Campus de Gijón C/Blasco de Garay s/n, 33203, Gijón, Asturias, Spain
| | - M Bartolomé
- Department of Marine Science and Technology, University of Oviedo, Escuela Superior de Marina Civil, Campus de Gijón C/Blasco de Garay s/n, 33203, Gijón, Asturias, Spain
| | - H J Montes
- Department of Marine Science and Technology, University of Oviedo, Escuela Superior de Marina Civil, Campus de Gijón C/Blasco de Garay s/n, 33203, Gijón, Asturias, Spain
| | - M González
- CEO of Environmental Sustainability, Port Authority of Gijon, Spain
| | - E Dopico
- Department of Educational Sciences, C/ Aniceto Sela s/n, 33005, Oviedo, Spain
| | - E Garcia-Vazquez
- Genetics, Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n, 33006, Oviedo, Spain
| | - Y J Borrell
- Genetics, Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n, 33006, Oviedo, Spain.
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Vieira PE, Lavrador AS, Parente MI, Parretti P, Costa AC, Costa FO, Duarte S. Gaps in DNA sequence libraries for Macaronesian marine macroinvertebrates imply decades till completion and robust monitoring. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13305] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Pedro E. Vieira
- Centre of Molecular and Environmental Biology (CBMA) Department of Biology University of Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) University of Minho Braga Portugal
| | - Ana S. Lavrador
- Centre of Molecular and Environmental Biology (CBMA) Department of Biology University of Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) University of Minho Braga Portugal
| | - Manuela I. Parente
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Associate Laboratory University of Azores Ponta Delgada Portugal
| | - Paola Parretti
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Associate Laboratory University of Azores Ponta Delgada Portugal
- MARE – Marine and Environmental Sciences Centre Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI) Edifício Madeira Tecnopolo Funchal Portugal
| | - Ana C. Costa
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Associate Laboratory University of Azores Ponta Delgada Portugal
| | - Filipe O. Costa
- Centre of Molecular and Environmental Biology (CBMA) Department of Biology University of Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) University of Minho Braga Portugal
| | - Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA) Department of Biology University of Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) University of Minho Braga Portugal
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Watson GJ, Dyos J, Barfield P, Stebbing P, Dey KG. Evidence for self-sustaining populations of Arcuatula senhousia in the UK and a review of this species' potential impacts within Europe. Sci Rep 2021; 11:9678. [PMID: 33958602 PMCID: PMC8102542 DOI: 10.1038/s41598-021-86876-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 02/24/2021] [Indexed: 02/03/2023] Open
Abstract
The invasive Asian date mussel (Arcuatula senhousia) inhabits diverse global coastal environments, in some circumstances posing significant ecological and economic risks. Recently recorded in the Greater North Sea ecoregion, an established population has not previously been confirmed. Combining historical and field data, we provided baseline information from the UK and recorded colonisation in a variety of habitats. Gonadal development was assessed using the gonadosomatic index (GSI) to determine if an intertidal soft-sediment population is self-sustaining. Arcuatula senhousia records from subtidal muddy/mixed-sediment within a major estuarine system from 2007 to 2016 were also analysed. First detected in 2011, spatial distribution was variable across the years within the subtidal, with individuals found at 4-9 out of 25 sites, and densities per site varying from 10 to 290 individuals per m2. The intertidal population was, in part, associated with seagrass (Zostera spp.) and attached to bivalves. In marinas, individuals were attached to concrete tiles, associated with live Mytilus edulis, and to dead Ostrea edulis. Mean GSI from the intertidal population differed across months, peaking in July before declining in September/October, but with high inter-individual variability. Arcuatula senhousia is reproducing and maintaining viable populations. Using a natural capital approach, we identify the potential impacts on Europe's functionally important habitats, fisheries and aquaculture if its spread continues.
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Affiliation(s)
- Gordon James Watson
- grid.4701.20000 0001 0728 6636Institute of Marine Sciences, School of Biological Sciences, University of Portsmouth, Ferry Road, Portsmouth, PO4 9LY UK
| | - Jesie Dyos
- grid.4701.20000 0001 0728 6636Institute of Marine Sciences, School of Biological Sciences, University of Portsmouth, Ferry Road, Portsmouth, PO4 9LY UK
| | - Peter Barfield
- grid.4701.20000 0001 0728 6636Institute of Marine Sciences, School of Biological Sciences, University of Portsmouth, Ferry Road, Portsmouth, PO4 9LY UK
| | - Paul Stebbing
- APEM Ltd, A17 Embankment Business Park, Heaton Mersey, Manchester, SK4 3GN UK
| | - Kate Gabrielle Dey
- grid.4701.20000 0001 0728 6636Institute of Marine Sciences, School of Biological Sciences, University of Portsmouth, Ferry Road, Portsmouth, PO4 9LY UK
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Evans HK, Bunch AJ, Schmitt JD, Hoogakker FJ, Carlson KB. High-throughput sequencing outperforms traditional morphological methods in Blue Catfish diet analysis and reveals novel insights into diet ecology. Ecol Evol 2021; 11:5584-5597. [PMID: 34026031 PMCID: PMC8131796 DOI: 10.1002/ece3.7460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 12/27/2022] Open
Abstract
Blue Catfish Ictalurus furcatus are an invasive, yet economically important species in the Chesapeake Bay. However, their impact on the trophic ecology of this system is not well understood. In order to provide in-depth analysis of predation by Blue Catfish, we identified prey items using high-throughput DNA sequencing (HTS) of entire gastrointestinal tracts from 134 samples using two genetic markers, mitochondrial cytochrome c oxidase I (COI) and the nuclear 18S ribosomal RNA gene. We compared our HTS results to a more traditional "hybrid" approach that coupled morphological identification with DNA barcoding. The hybrid study was conducted on additional Blue Catfish samples (n = 617 stomachs) collected from the same location and season in the previous year. Taxonomic representation with HTS vastly surpassed that achieved with the hybrid methodology in Blue Catfish. Significantly, our HTS study identified several instances of at-risk and invasive species consumption not identified using the hybrid method, supporting the hypothesis that previous studies using morphological methods may greatly underestimate consumption of critical species. Finally, we report the novel finding that Blue Catfish diet diversity inversely correlates to daily flow rates, perhaps due to higher mobility and prey-seeking behaviors exhibited during lower flow.
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Affiliation(s)
- Heather K. Evans
- Genomics and Microbiology LaboratoryNorth Carolina Museum of Natural SciencesRaleighNCUSA
- North Carolina Wildlife Resources CommissionRaleighNCUSA
| | - Aaron J. Bunch
- Virginia Department of Wildlife ResourcesCharles CityVAUSA
- Department of Forestry and Environmental ConservationClemson UniversityClemsonSCUSA
| | - Joseph D. Schmitt
- Virginia Polytechnic Institute and State UniversityBlacksburgVAUSA
- U.S. Geological SurveyGreat Lakes Science CenterSanduskyOHUSA
| | - Frederick J. Hoogakker
- Virginia Department of Wildlife ResourcesCharles CityVAUSA
- Tennessee Cooperative Fishery Research UnitTennessee Tech UniversityCookevilleTNUSA
| | - Kara B. Carlson
- Genomics and Microbiology LaboratoryNorth Carolina Museum of Natural SciencesRaleighNCUSA
- Department of GeneticsNorth Carolina State UniversityRaleighNCUSA
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42
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Towards the Optimization of eDNA/eRNA Sampling Technologies for Marine Biosecurity Surveillance. WATER 2021. [DOI: 10.3390/w13081113] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The field of eDNA is growing exponentially in response to the need for detecting rare and invasive species for management and conservation decisions. Developing technologies and standard protocols within the biosecurity sector must address myriad challenges associated with marine environments, including salinity, temperature, advective and deposition processes, hydrochemistry and pH, and contaminating agents. These approaches must also provide a robust framework that meets the need for biosecurity management decisions regarding threats to human health, environmental resources, and economic interests, especially in areas with limited clean-laboratory resources and experienced personnel. This contribution aims to facilitate dialogue and innovation within this sector by reviewing current approaches for sample collection, post-sampling capture and concentration of eDNA, preservation, and extraction, all through a biosecurity monitoring lens.
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43
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Holman LE, de Bruyn M, Creer S, Carvalho G, Robidart J, Rius M. Animals, protists and bacteria share marine biogeographic patterns. Nat Ecol Evol 2021; 5:738-746. [PMID: 33859375 DOI: 10.1038/s41559-021-01439-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 03/08/2021] [Indexed: 01/22/2023]
Abstract
Over millennia, ecological and evolutionary mechanisms have shaped macroecological patterns across the tree of life. Research describing these patterns at both regional and global scales has traditionally focused on the study of metazoan species. Consequently, there is a limited understanding of cross-phylum biogeographic structuring and an escalating need to understand the macroecology of both microscopic and macroscopic organisms. Here we used environmental DNA (eDNA) metabarcoding to explore the biodiversity of marine metazoans, protists and bacteria along an extensive and highly heterogeneous coastline. Our results showed remarkably consistent biogeographic structure across the kingdoms of life despite billions of years of evolution. Analyses investigating the drivers of these patterns for each taxonomic kingdom found that environmental conditions (such as temperature) and, to a lesser extent, anthropogenic stressors (such as fishing pressure and pollution) explained some of the observed variation. Additionally, metazoans displayed biogeographic patterns that suggested regional biotic homogenization. Against the backdrop of global pervasive anthropogenic environmental change, our work highlights the importance of considering multiple domains of life to understand the maintenance and drivers of biodiversity patterns across broad taxonomic, ecological and geographical scales.
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Affiliation(s)
- Luke E Holman
- School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK.
| | - Mark de Bruyn
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia.,Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor, UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor, UK
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor, UK
| | - Julie Robidart
- Ocean Technology and Engineering Group, National Oceanography Centre Southampton, Southampton, UK
| | - Marc Rius
- School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK.,Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, South Africa
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44
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Progress on Research Regarding Ecology and Biodiversity of Coastal Fisheries and Nektonic Species and Their Habitats within Coastal Landscapes. DIVERSITY 2021. [DOI: 10.3390/d13040168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This paper aims to highlight the new research and significant advances in our understanding of links between coastal habitat quality/quantity/diversity and the diversity of fisheries species and other mobile aquatic species (hereafter nekton) that use them within coastal landscapes. This topic is quite diverse owing to the myriad of habitat types found in coastal marine waters and the variety of life history strategies fisheries species and nekton use in these environments. Thus, we focus our review on five selective but relevant topics, habitat templates, essential fish habitat, habitat mosaics/habitat connectivity, transitory/ephemeral habitat, and the emerging/maturing approaches to the study of fish-habitat systems as a roadmap to its development. We have highlighted selected important contributions in the progress made on each topic to better identify and quantify landscape scale interactions between living biota and structured habitats set within a dynamic landscape.
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45
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Mariani S, Fernandez C, Baillie C, Magalon H, Jaquemet S. Shark and ray diversity, abundance and temporal variation around an Indian Ocean Island, inferred by eDNA metabarcoding. CONSERVATION SCIENCE AND PRACTICE 2021. [DOI: 10.1111/csp2.407] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Stefano Mariani
- School of Biological & Environmental Sciences, Liverpool John Moores University Liverpool UK
| | | | - Charles Baillie
- School of Science, Engineering & Environment, University of Salford Salford UK
| | - Helene Magalon
- UMR Entropie, Université de La Réunion Saint‐Denis France
- Laboratoire d'Excellence CORAIL Perpignan France
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46
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van den Heuvel-Greve MJ, van den Brink AM, Glorius ST, de Groot GA, Laros I, Renaud PE, Pettersen R, Węsławski JM, Kuklinski P, Murk AJ. Early detection of marine non-indigenous species on Svalbard by DNA metabarcoding of sediment. Polar Biol 2021. [DOI: 10.1007/s00300-021-02822-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
AbstractNon-indigenous species (NIS) in the Arctic have an increased likelihood of arrival from ship traffic in the region, while the survival potential of the species becomes more likely in a warming environment. Monitoring is essential to detect the rate and magnitude of the establishment of NIS. In this study, a list of 123 potential marine NIS for Svalbard was drafted and the presence of marine NIS in soft sediment of Kongsfjorden in Svalbard was assessed using molecular metabarcoding techniques. For 37 species, including eight potential Arctic NIS, we generated new 18S and/or COI barcode sequences to improve the available online reference databases. In total, 299 species were identified in the sediment samples, including seven potential NIS. Three of these potential NIS have not been reported before in Svalbard: the harpacticoid copepod Euterpina acutifrons, and the ascidians Botrylloides violaceus and Molgula manhattensis. Another novel observation for Svalbard was the polychaete Chone mollis. Additional studies are needed to assess whether the NIS have been established on Svalbard and what their potential impact on the local system may be. Metabarcoding proved to be an effective monitoring tool to detect the presence of new species in Svalbard marine waters. We advise its use to set up a baseline record for the presence of NIS at points of entry, especially harbours. This approach is also valuable for biodiversity monitoring, in particular the detection of small organisms and life stages that are hard to identify using current visual techniques.
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47
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Duarte S, Vieira PE, Lavrador AS, Costa FO. Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:141729. [PMID: 32889465 DOI: 10.1016/j.scitotenv.2020.141729] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 06/11/2023]
Abstract
In coastal ecosystems, non-indigenous species (NIS) are recognized as a major threat to biodiversity, ecosystem functioning and socio-economic activities. Here we present a systematic review on the use of metabarcoding for NIS surveillance in marine and coastal ecosystems, through the analysis of 42 publications. Metabarcoding has been mainly applied to environmental DNA (eDNA) from water samples, but also to DNA extracted from bulk organismal samples. DNA extraction kits have been widely used and the 18S rRNA and the COI genes the most employed markers, but less than half of the studies targeted more than one marker loci. The Illumina MiSeq platform has been used in >50% of the publications. Current weaknesses include potential occurrence of false negatives due to the primer-biased or faulty DNA amplification and the incompleteness of reference libraries. This is particularly concerning in the case of NIS surveillance, where proficiency in species level detection is critical. Until these weaknesses are resolved, ideally NIS metabarcoding should be supported by complementary approaches, such as morphological analysis or more targeted molecular approaches (e.g. qPCR, ddPCR). Even so, metabarcoding has already proved to be a highly sensitive tool to detect small organisms or undifferentiated life stages across a wide taxonomic range. In addition, it also seems to be very effective in ballast water management and to improve the spatial and temporal sampling frequency of NIS surveillance in marine and coastal ecosystems. Although specific protocols may be required for species-specific NIS detection, for general monitoring it would be vital to settle on a standard protocol able to generate comparable results among surveillance campaigns and regions of the globe, seeking the best approach for detecting the broadest range of species, while minimizing the chances of a false positive or negative detection.
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Affiliation(s)
- Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Pedro E Vieira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Ana S Lavrador
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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48
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Gallego R, Jacobs-Palmer E, Cribari K, Kelly RP. Environmental DNA metabarcoding reveals winners and losers of global change in coastal waters. Proc Biol Sci 2020; 287:20202424. [PMID: 33290686 DOI: 10.1098/rspb.2020.2424] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Studies of the ecological effects of global change often focus on one or a few species at a time. Consequently, we know relatively little about the changes underway at real-world scales of biological communities, which typically have hundreds or thousands of interacting species. Here, we use COI mtDNA amplicons from monthly samples of environmental DNA to survey 221 planktonic taxa along a gradient of temperature, salinity, dissolved oxygen and carbonate chemistry in nearshore marine habitat. The result is a high-resolution picture of changes in ecological communities using a technique replicable across a wide variety of ecosystems. We estimate community-level differences associated with time, space and environmental variables, and use these results to forecast near-term community changes due to warming and ocean acidification. We find distinct communities in warmer and more acidified conditions, with overall reduced richness in diatom assemblages and increased richness in dinoflagellates. Individual taxa finding more suitable habitat in near-future waters are more taxonomically varied and include the ubiquitous coccolithophore Emiliania huxleyi and the harmful dinoflagellate Alexandrium sp. These results suggest foundational changes for nearshore food webs under near-future conditions.
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Affiliation(s)
- Ramón Gallego
- School of Marine and Environmental Affairs, University of Washington, 3707 Brooklyn Avenue NE, Seattle, WA 98105, USA
| | - Emily Jacobs-Palmer
- School of Marine and Environmental Affairs, University of Washington, 3707 Brooklyn Avenue NE, Seattle, WA 98105, USA
| | - Kelly Cribari
- School of Marine and Environmental Affairs, University of Washington, 3707 Brooklyn Avenue NE, Seattle, WA 98105, USA
| | - Ryan P Kelly
- School of Marine and Environmental Affairs, University of Washington, 3707 Brooklyn Avenue NE, Seattle, WA 98105, USA
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49
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Blackman RC, Ling KKS, Harper LR, Shum P, Hänfling B, Lawson‐Handley L. Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels, Dreissena rostriformis bugensis in flowing water. Ecol Evol 2020; 10:13248-13259. [PMID: 33304534 PMCID: PMC7713958 DOI: 10.1002/ece3.6921] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 09/14/2020] [Indexed: 12/29/2022] Open
Abstract
The early detection of invasive non-native species (INNS) is important for informing management actions. Established monitoring methods require the collection or observation of specimens, which is unlikely at the beginning of an invasion when densities are likely to be low. Environmental DNA (eDNA) analysis is a highly promising technique for the detection of INNS-particularly during the early stages of an invasion.Here, we compared the use of traditional kick-net sampling with two eDNA approaches (targeted detection using both conventional and quantitative PCR and passive detection via metabarcoding with conserved primers) for detection of quagga mussel, Dreissena rostriformis bugensis, a high priority INNS, along a density gradient on the River Wraysbury, UK.All three molecular tools outperformed traditional sampling in terms of detection. Conventional PCR and qPCR both had 100% detection rate in all samples and outperformed metabarcoding when the target species was at low densities. Additionally, quagga mussel DNA copy number (qPCR) and relative read count (metabarcoding) were significantly influenced by both mussel density and distance from source population, with distance being the most significant predictor. Synthesis and application. All three molecular approaches were more sensitive than traditional kick-net sampling for the detection of the quagga mussel in flowing water, and both qPCR and metabarcoding enabled estimates of relative abundance. Targeted approaches were more sensitive than metabarcoding, but metabarcoding has the advantage of providing information on the wider community and consequently the impacts of INNS.
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Affiliation(s)
- Rosetta C. Blackman
- Department of Aquatic EcologyEawagSwiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZürichSwitzerland
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
| | - Kar Keun Sean Ling
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
| | - Lynsey R. Harper
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Peter Shum
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Bernd Hänfling
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
| | - Lori Lawson‐Handley
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
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50
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Antich A, Palacín C, Cebrian E, Golo R, Wangensteen OS, Turon X. Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities? Mol Ecol 2020; 30:3175-3188. [PMID: 32974967 DOI: 10.1111/mec.15641] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/06/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
In the marine realm, biomonitoring using environmental DNA (eDNA) of benthic communities requires destructive direct sampling or the setting-up of settlement structures. Comparatively much less effort is required to sample the water column, which can be accessed remotely. In this study we assess the feasibility of obtaining information from the eukaryotic benthic communities by sampling the adjacent water layer. We studied two different rocky-substrate benthic communities with a technique based on quadrat sampling. We also took replicate water samples at four distances (0, 0.5, 1.5, and 20 m) from the benthic habitat. Using broad range primers to amplify a ca. 313 bp fragment of the cytochrome oxidase subunit I gene, we obtained a total of 3,543 molecular operational taxonomic units (MOTUs). The structure obtained in the two environments was markedly different, with Metazoa, Archaeplastida and Stramenopiles being the most diverse groups in benthic samples, and Hacrobia, Metazoa and Alveolata in the water. Only 265 MOTUs (7.5%) were shared between benthos and water samples and, of these, 180 (5.1%) were identified as benthic taxa that left their DNA in the water. Most of them were found immediately adjacent to the benthos, and their number decreased as we moved apart from the benthic habitat. It was concluded that water eDNA, even in the close vicinity of the benthos, was a poor proxy for the analysis of benthic structure, and that direct sampling methods are required for monitoring these complex communities via metabarcoding.
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Affiliation(s)
- Adrià Antich
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
| | - Cruz Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, and Research Institute of Biodiversity (IRBIO), Barcelona, Spain
| | - Emma Cebrian
- Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Raül Golo
- Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Xavier Turon
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
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