1
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Marcuk V, Piña-Ortiz A, Castillo-Guerrero JA, Masello JF, Bustamante P, Griep S, Quillfeldt P. Trophic plasticity of a tropical seabird revealed through DNA metabarcoding and stable isotope analyses. MARINE ENVIRONMENTAL RESEARCH 2024; 199:106627. [PMID: 38968803 DOI: 10.1016/j.marenvres.2024.106627] [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: 05/04/2024] [Revised: 06/19/2024] [Accepted: 06/28/2024] [Indexed: 07/07/2024]
Abstract
DNA metabarcoding and stable isotope analysis have significantly advanced our understanding of marine trophic ecology, aiding systematic research on foraging habits and species conservation. In this study, we employed these methods to analyse faecal and blood samples, respectively, to compare the trophic ecology of two Red-billed Tropicbird (Phaethonaethereus; Linnaeus, 1758) colonies on Mexican islands in the Pacific. Trophic patterns among different breeding stages were also examined at both colonies. Dietary analysis reveals a preference for epipelagic fish, cephalopods, and small crustaceans, with variations between colonies and breeding stages. Isotopic values (δ15N and δ13C) align with DNA metabarcoding results, with wider niches during incubation stages. Differences in diet are linked to environmental conditions and trophic plasticity among breeding stages, influenced by changing physiological requirements and prey availability. Variations in dietary profiles reflect contrasting environmental conditions affecting local prey availability.
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Affiliation(s)
- Vladislav Marcuk
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392, Giessen, Germany.
| | - Alberto Piña-Ortiz
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392, Giessen, Germany.
| | - José Alfredo Castillo-Guerrero
- Departamento de Estudios para el Desarrollo Sustentable de la Zona Costera, Centro Universitario de la Costa Sur, Universidad de Guadalajara, Gómez Farías 82, San Patricio-Melaque, Municipio de Cihuatlán, Jalisco, C.P. 48980, Mexico.
| | - Juan F Masello
- Department of Animal Behaviour, Bielefeld University, Germany; Department of Biological Sciences, University of Venda, Private Bag X5050, Thohoyandou, 0950, South Africa.
| | - Paco Bustamante
- LIttoral, Environnement et Societés (LIENSs), UMR 7266 CNRS - La Rochelle Université, 17000, La Rochelle, France.
| | - Sven Griep
- Institute for Bioinformatics and Systems Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 58, D-35392, Giessen, Germany.
| | - Petra Quillfeldt
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392, Giessen, Germany.
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2
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Bhendarkar M, Rodriguez-Ezpeleta N. Exploring uncharted territory: new frontiers in environmental DNA for tropical fisheries management. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:617. [PMID: 38874640 DOI: 10.1007/s10661-024-12788-8] [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: 11/07/2023] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
Tropical ecosystems host a significant share of global fish diversity contributing substantially to the global fisheries sector. Yet their sustainable management is challenging due to their complexity, diverse life history traits of tropical fishes, and varied fishing techniques involved. Traditional monitoring techniques are often costly, labour-intensive, and/or difficult to apply in inaccessible sites. These limitations call for the adoption of innovative, sensitive, and cost-effective monitoring solutions, especially in a scenario of climate change. Environmental DNA (eDNA) emerges as a potential game changer for biodiversity monitoring and conservation, especially in aquatic ecosystems. However, its utility in tropical settings remains underexplored, primarily due to a series of challenges, including the need for a comprehensive barcode reference library, an understanding of eDNA behaviour in tropical aquatic environments, standardized procedures, and supportive biomonitoring policies. Despite these challenges, the potential of eDNA for sensitive species detection across varied habitats is evident, and its global use is accelerating in biodiversity conservation efforts. This review takes an in-depth look at the current state and prospects of eDNA-based monitoring in tropical fisheries management research. Additionally, a SWOT analysis is used to underscore the opportunities and threats, with the aim of bridging the knowledge gaps and guiding the more extensive and effective use of eDNA-based monitoring in tropical fisheries management. Although the discussion applies worldwide, some specific experiences and insights from Indian tropical fisheries are shared to illustrate the practical application and challenges of employing eDNA in a tropical context.
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Affiliation(s)
- Mukesh Bhendarkar
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), 48395, Sukarrieta, Bizkaia, Spain.
- ICAR-National Institute of Abiotic Stress Management, Baramati, 413 115, Maharashtra, India.
| | - Naiara Rodriguez-Ezpeleta
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), 48395, Sukarrieta, Bizkaia, Spain
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3
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Perry WB. Limited summer palate with no colonic irrigation required: life of a migratory shark through the metabarcoding lens. JOURNAL OF FISH BIOLOGY 2023; 103:1251. [PMID: 38148282 DOI: 10.1111/jfb.15636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
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4
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Chen G, Xu W, Han D, Wang C, Ye S. Application of high-throughput sequencing to analyze the diet of black croaker (Atrobucca nibe) in southern coastal waters of Zhejiang. MARINE ENVIRONMENTAL RESEARCH 2023; 191:106153. [PMID: 37633172 DOI: 10.1016/j.marenvres.2023.106153] [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: 03/29/2023] [Revised: 07/15/2023] [Accepted: 08/16/2023] [Indexed: 08/28/2023]
Abstract
This study investigated the feeding habits of black croaker (Atrobucca nibe) to fully understand its role in the food web in southern coastal waters of Zhejiang, China. In total, 225 black croakers were collected in a bottom trawl survey, of which 195 were used for the stomach contents analysis and 30 for high-throughput sequencing (HTS). Both approaches showed that the main prey was shrimp, with Alpheus japonicus being the most predominant. In addition, black croaker also fed on other benthic species, suggesting that it was a demersal predator. Feeding intensity also varied with black croaker body length, as did prey preference, from small-sized species to larger species with increases in fish size; in addition, prey species were more diverse in the large-bodied prey group. Canonical correspondence analysis indicated that the feeding habit of black croaker was most significantly correlated with temperature and dissolved oxygen. HTS was shown to be a feasible high precision semi-quantitative analytical approach, although it must be combined with morphological methods to obtain more complete feeding data; thus, it could provide an effective scientific basis for feeding ecology studies of marine organisms.
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Affiliation(s)
- Gan Chen
- College of Marine Science, Shanghai Ocean University, Shanghai, 201306, China; National Distant-water Fisheries Engineering Research Center, Shanghai, 201306, China; National Data Centre for Distant-Water Fisheries of China, Shanghai, 201306, China
| | - Wen Xu
- College of Marine Science, Shanghai Ocean University, Shanghai, 201306, China; National Distant-water Fisheries Engineering Research Center, Shanghai, 201306, China; National Data Centre for Distant-Water Fisheries of China, Shanghai, 201306, China
| | - Dongyan Han
- College of Marine Science, Shanghai Ocean University, Shanghai, 201306, China; National Distant-water Fisheries Engineering Research Center, Shanghai, 201306, China; National Data Centre for Distant-Water Fisheries of China, Shanghai, 201306, China.
| | - Congcong Wang
- College of Marine Science, Shanghai Ocean University, Shanghai, 201306, China; National Distant-water Fisheries Engineering Research Center, Shanghai, 201306, China; National Data Centre for Distant-Water Fisheries of China, Shanghai, 201306, China.
| | - Shen Ye
- Zhejiang Maricultural Research Institute, Wenzhou, 325005, Zhejiang, China; Zhejiang Key Laboratory of Exploitation and Preservation of Offshore Bio-resource, Wenzhou, 325005, Zhejiang, China
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5
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Yue L, Wang C, Meng B, Xie B, Cao H, Su H, Zhang M. The Food Niche Overlap and Interspecific Relationship between the Sympatric Tibetan Macaque and Grey Snub-Nosed Monkey. Animals (Basel) 2023; 13:2536. [PMID: 37570344 PMCID: PMC10417265 DOI: 10.3390/ani13152536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/26/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
Assessing the trophic niche and interspecific relationships between related species and determining how the species maintain differences in nutritional niches while coexisting in the same area are important topics in ecological research. Therefore, exploring the mechanism of food resource utilization, competition and coexistence among species distributed in the same region is important. In this study, we used fecal samples and metagenome sequencing technology to study the plant feeding habits and coexistence mechanisms of Tibetan macaques (Macaca thibetana) and grey snub-nosed monkeys (Rhinopithecus brelichi) within the same area. In the winter of 2020, we collected a total of 40 fecal samples from Tibetan macaques and grey snub-nosed monkeys; of those, 29 samples were considered valid and were analyzed using DNA metabarcoding. The results showed that in winter, Tibetan macaques consumed plants from 117 families and 184 genera, whereas grey snub-nosed monkeys consumed plants from 109 families and 165 genera. Diversity analysis revealed that there was a significant difference in the food composition of Tibetan macaques and grey snub-nosed monkeys. Tibetan macaques had a broader food niche width than grey snub-nosed monkeys at the family and genus levels. In winter, the food niches of Tibetan macaques and grey snub-nosed monkeys almost entirely overlapped (0.99). Our research provides detailed dietary data for Tibetan macaques and grey snub-nosed monkeys and valuable information that can aid in conservation efforts targeting these species.
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Affiliation(s)
- Li Yue
- College of Forestry, Research Center for Biodiversity and Nature Conservation, Guizhou University, Guiyang 550025, China
| | - Cheng Wang
- Zhangjiajie Giant Salamander National Nature Reserve Affairs Center, Zhangjiajie 427400, China
| | - Bingshun Meng
- College of Forestry, Research Center for Biodiversity and Nature Conservation, Guizhou University, Guiyang 550025, China
| | - Bo Xie
- College of Forestry, Research Center for Biodiversity and Nature Conservation, Guizhou University, Guiyang 550025, China
| | - Heqin Cao
- College of Forestry, Research Center for Biodiversity and Nature Conservation, Guizhou University, Guiyang 550025, China
| | - Haijun Su
- College of Forestry, Research Center for Biodiversity and Nature Conservation, Guizhou University, Guiyang 550025, China
| | - Mingming Zhang
- College of Forestry, Research Center for Biodiversity and Nature Conservation, Guizhou University, Guiyang 550025, China
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6
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Yao M, Zhang S, Lu Q, Chen X, Zhang SY, Kong Y, Zhao J. Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward. Mol Ecol 2022; 31:5132-5164. [PMID: 35972241 DOI: 10.1111/mec.16659] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 12/15/2022]
Abstract
Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.
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Affiliation(s)
- Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Shan Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Qi Lu
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Xiaoyu Chen
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Si-Yu Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Yueqiao Kong
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Jindong Zhao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
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7
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Using DNA metabarcoding as a novel approach for analysis of platypus diet. Sci Rep 2022; 12:2247. [PMID: 35145160 PMCID: PMC8831530 DOI: 10.1038/s41598-022-06023-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 01/14/2022] [Indexed: 11/08/2022] Open
Abstract
Platypuses (Ornithorhynchus anatinus) forage for macroinvertebrate prey exclusively in freshwater habitats. Because food material in their faeces is well digested and mostly unidentifiable, previous dietary studies have relied on cheek pouch assessments and stable isotope analysis. Given DNA metabarcoding can identify species composition from only fragments of genetic material, we investigated its effectiveness in analysing the diet of platypuses, and to assess variation across seasons and sexes. Of the 18 orders and 60 families identified, Ephemeroptera and Diptera were the most prevalent orders, detected in 100% of samples, followed by Trichoptera, Pulmonata, and Odonata (86.21% of samples). Caenidae and Chironomidae were the most common families. Diptera had a high average DNA read, suggesting it is an important dietary component that may have been underestimated in previous studies. We found no variation in diet between sexes and only minimal changes between seasons. DNA metabarcoding proved to be a highly useful tool for assessing platypus diet, improving prey identification compared to cheek pouch analysis, which can underestimate soft-bodied organisms, and stable isotope analysis which cannot distinguish all taxa isotopically. This will be a useful tool for investigating how platypus prey diversity is impacted by habitat degradation as a result of anthropogenic stressors.
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8
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Wang Y, Smith HK, Goossens E, Hertzog L, Bletz MC, Bonte D, Verheyen K, Lens L, Vences M, Pasmans F, Martel A. Diet diversity and environment determine the intestinal microbiome and bacterial pathogen load of fire salamanders. Sci Rep 2021; 11:20493. [PMID: 34650115 PMCID: PMC8516891 DOI: 10.1038/s41598-021-98995-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 09/09/2021] [Indexed: 01/04/2023] Open
Abstract
Diverse communities of symbiotic microbes inhabit the digestive systems of vertebrates and play a crucial role in animal health, and host diet plays a major role in shaping the composition and diversity of these communities. Here, we characterized diet and gut microbiome of fire salamander populations from three Belgian forests. We carried out DNA metabarcoding on fecal samples, targeting eukaryotic 18S rRNA of potential dietary prey items, and bacterial 16S rRNA of the concomitant gut microbiome. Our results demonstrated an abundance of soft-bodied prey in the diet of fire salamanders, and a significant difference in the diet composition between males and females. This sex-dependent effect on diet was also reflected in the gut microbiome diversity, which is higher in males than female animals. Proximity to human activities was associated with increased intestinal pathogen loads. Collectively, the data supports a relationship between diet, environment and intestinal microbiome in fire salamanders, with potential health implications.
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Affiliation(s)
- Yu Wang
- grid.5342.00000 0001 2069 7798Wildlife Health Ghent, Department of Pathology, Bacteriology & Avian Diseases, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Hannah K. Smith
- grid.5342.00000 0001 2069 7798Wildlife Health Ghent, Department of Pathology, Bacteriology & Avian Diseases, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Evy Goossens
- grid.5342.00000 0001 2069 7798Department of Pathology, Bacteriology & Avian Diseases, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Lionel Hertzog
- grid.5342.00000 0001 2069 7798Terrestrial Ecology Unit (TEREC), Department of Biology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium ,Thünen Institute for Biodiversity, Bundesallee 68, 38116 Brunswick, Germany
| | - Molly C. Bletz
- grid.6738.a0000 0001 1090 0254Evolutionary Biology Lab, Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106 Brunswick, Germany
| | - Dries Bonte
- grid.5342.00000 0001 2069 7798Terrestrial Ecology Unit (TEREC), Department of Biology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Kris Verheyen
- grid.5342.00000 0001 2069 7798Forest & Nature Lab, Department of Environment, Ghent University, Geraardsberge Steenweg 267, 9090 Gontrode, Belgium
| | - Luc Lens
- grid.5342.00000 0001 2069 7798Terrestrial Ecology Unit (TEREC), Department of Biology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Miguel Vences
- grid.6738.a0000 0001 1090 0254Evolutionary Biology Lab, Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106 Brunswick, Germany
| | - Frank Pasmans
- grid.5342.00000 0001 2069 7798Wildlife Health Ghent, Department of Pathology, Bacteriology & Avian Diseases, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - An Martel
- grid.5342.00000 0001 2069 7798Wildlife Health Ghent, Department of Pathology, Bacteriology & Avian Diseases, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
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9
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Spoiled for Choice during Cold Season? Habitat Use and Potential Impacts of the Invasive Silurus glanis L. in a Deep, Large, and Oligotrophic Lake (Lake Maggiore, North Italy). WATER 2021. [DOI: 10.3390/w13182549] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The ecological features of invasive alien species are crucial for their effective management. However, they are often lacking in newly invaded ecosystems. This is the case of the European catfish Silurus glanis L. in Lake Maggiore, where the species is present since 1990, but no scientific information is available on its ecology. To start filling this knowledge gap, 236 catfish (67 cm to 150 cm of total length) were collected, measured, and dissected for stomach content analyses from three localities and in two habitats (littoral vs. pelagic) in late autumn/early winter. The NPUE and BPUE (individuals (N) and biomass (B, in grams) per unit effort (m2), respectively) of catfish were generally higher in littoral (NPUE > 0.01; BPUE > 96) than in pelagic habitats (NPUE < 0.009; BPUE < 114), but the catfish had, on average, larger sizes in pelagic habitats. Overall, 581 individual prey items were recorded, belonging to 12 taxa. Pelagic catfish specialized their diet exclusively on three prey fish (coregonids, shad, and roach), whilst the diet of littoral catfish was more variable and dominated by crayfish, perch, and roach. These results highlighted for the first time the interaction of larger catfish with the lake’s pelagic food web, and thus possible consequences are discussed, including the potential contrasting role S. glanis may have for the lake’s fishery.
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10
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Nzau Matondo B, Benitez JP, Dierckx A, Renardy S, Rollin X, Colson D, Baltus L, Romain VRM, Ovidio M. What are the best upland river characteristics for glass eel restocking practice? THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 784:147042. [PMID: 33895513 DOI: 10.1016/j.scitotenv.2021.147042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/18/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
The fitness of restocked European eel (Anguilla anguilla), an endangered fish species, was studied in relation to the environmental variables of habitats in six upland rivers that are typologically different in terms of their hydromorphological and physicochemical characteristics, food resources and fish communities. These rivers received a total of 76,370 imported glass eels in 2017. During a three-year period, we monitored eels with respect to total length, annual growth rate, condition factor and density using capture-mark-recapture experiments to understand the effects of the characteristics of receiving rivers on restocking success levels. Our results showed the survival of the restocked eels in the six rivers and revealed significant differences between them in terms of total length, condition factor and density. Better performance in eel yield variables was observed in a eutrophic alkaline river with greater roughness of riverbed substrates, dominant pool- and riffle-type flow facies and lower brown trout density. The variables conductivity and total hardness had higher explanatory power and were strongly associated with increased eel density. This study suggests that a well-selected habitat/river in a restocking programme can be beneficial for the species and recommends restocking practice as a management tool to achieve eel conservation goals.
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Affiliation(s)
- Billy Nzau Matondo
- Laboratory of Fish Demography and Hydroecology, Management of Aquatic Resources and Aquaculture Unit, Freshwater and Oceanic science Unit of Research-FOCUS, University of Liège, 22 Quai E. Van Beneden, B-4020 Liège, Belgium.
| | - Jean-Philippe Benitez
- Laboratory of Fish Demography and Hydroecology, Management of Aquatic Resources and Aquaculture Unit, Freshwater and Oceanic science Unit of Research-FOCUS, University of Liège, 22 Quai E. Van Beneden, B-4020 Liège, Belgium.
| | - Arnaud Dierckx
- Laboratory of Fish Demography and Hydroecology, Management of Aquatic Resources and Aquaculture Unit, Freshwater and Oceanic science Unit of Research-FOCUS, University of Liège, 22 Quai E. Van Beneden, B-4020 Liège, Belgium.
| | - Séverine Renardy
- Laboratory of Fish Demography and Hydroecology, Management of Aquatic Resources and Aquaculture Unit, Freshwater and Oceanic science Unit of Research-FOCUS, University of Liège, 22 Quai E. Van Beneden, B-4020 Liège, Belgium.
| | - Xavier Rollin
- SPWARNE-DNF-Public Service of Wallonia - Agriculture, Natural Ressources & Environnement, Wildlife & Forestry Department, 15 Avenue Prince de Liège, B-5100 Jambes, Belgium.
| | - Dylan Colson
- Laboratory of Fish Demography and Hydroecology, Management of Aquatic Resources and Aquaculture Unit, Freshwater and Oceanic science Unit of Research-FOCUS, University of Liège, 22 Quai E. Van Beneden, B-4020 Liège, Belgium
| | - Loïc Baltus
- Laboratory of Fish Demography and Hydroecology, Management of Aquatic Resources and Aquaculture Unit, Freshwater and Oceanic science Unit of Research-FOCUS, University of Liège, 22 Quai E. Van Beneden, B-4020 Liège, Belgium
| | - Vasthi Rose Myrielle Romain
- Laboratory of Fish Demography and Hydroecology, Management of Aquatic Resources and Aquaculture Unit, Freshwater and Oceanic science Unit of Research-FOCUS, University of Liège, 22 Quai E. Van Beneden, B-4020 Liège, Belgium
| | - Michaël Ovidio
- Laboratory of Fish Demography and Hydroecology, Management of Aquatic Resources and Aquaculture Unit, Freshwater and Oceanic science Unit of Research-FOCUS, University of Liège, 22 Quai E. Van Beneden, B-4020 Liège, Belgium.
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11
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Tosa MI, Dziedzic EH, Appel CL, Urbina J, Massey A, Ruprecht J, Eriksson CE, Dolliver JE, Lesmeister DB, Betts MG, Peres CA, Levi T. The Rapid Rise of Next-Generation Natural History. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.698131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many ecologists have lamented the demise of natural history and have attributed this decline to a misguided view that natural history is outdated and unscientific. Although there is a perception that the focus in ecology and conservation have shifted away from descriptive natural history research and training toward hypothetico-deductive research, we argue that natural history has entered a new phase that we call “next-generation natural history.” This renaissance of natural history is characterized by technological and statistical advances that aid in collecting detailed observations systematically over broad spatial and temporal extents. The technological advances that have increased exponentially in the last decade include electronic sensors such as camera-traps and acoustic recorders, aircraft- and satellite-based remote sensing, animal-borne biologgers, genetics and genomics methods, and community science programs. Advances in statistics and computation have aided in analyzing a growing quantity of observations to reveal patterns in nature. These robust next-generation natural history datasets have transformed the anecdotal perception of natural history observations into systematically collected observations that collectively constitute the foundation for hypothetico-deductive research and can be leveraged and applied to conservation and management. These advances are encouraging scientists to conduct and embrace detailed descriptions of nature that remain a critically important component of the scientific endeavor. Finally, these next-generation natural history observations are engaging scientists and non-scientists alike with new documentations of the wonders of nature. Thus, we celebrate next-generation natural history for encouraging people to experience nature directly.
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12
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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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13
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Vagnon C, Cattanéo F, Goulon C, Grimardias D, Guillard J, Frossard V. An allometric niche model for species interactions in temperate freshwater ecosystems. Ecosphere 2021. [DOI: 10.1002/ecs2.3420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Chloé Vagnon
- Univ. Savoie Mont‐Blanc INRAE, CARRTEL Thonon‐les‐Bains74200France
| | | | - Chloé Goulon
- Univ. Savoie Mont‐Blanc INRAE, CARRTEL Thonon‐les‐Bains74200France
| | | | - Jean Guillard
- Univ. Savoie Mont‐Blanc INRAE, CARRTEL Thonon‐les‐Bains74200France
| | - Victor Frossard
- Univ. Savoie Mont‐Blanc INRAE, CARRTEL Thonon‐les‐Bains74200France
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14
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Traugott M, Thalinger B, Wallinger C, Sint D. Fish as predators and prey: DNA-based assessment of their role in food webs. JOURNAL OF FISH BIOLOGY 2021; 98:367-382. [PMID: 32441321 PMCID: PMC7891366 DOI: 10.1111/jfb.14400] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/26/2020] [Accepted: 05/20/2020] [Indexed: 05/04/2023]
Abstract
Fish are both consumers and prey, and as such part of a dynamic trophic network. Measuring how they are trophically linked, both directly and indirectly, to other species is vital to comprehend the mechanisms driving alterations in fish communities in space and time. Moreover, this knowledge also helps to understand how fish communities respond to environmental change and delivers important information for implementing management of fish stocks. DNA-based methods have significantly widened our ability to assess trophic interactions in both marine and freshwater systems and they possess a range of advantages over other approaches in diet analysis. In this review we provide an overview of different DNA-based methods that have been used to assess trophic interactions of fish as consumers and prey. We consider the practicalities and limitations, and emphasize critical aspects when analysing molecular derived trophic data. We exemplify how molecular techniques have been employed to unravel food web interactions involving fish as consumers and prey. In addition to the exciting opportunities DNA-based approaches offer, we identify current challenges and future prospects for assessing fish food webs where DNA-based approaches will play an important role.
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Affiliation(s)
- Michael Traugott
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
| | - Bettina Thalinger
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
- Centre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Corinna Wallinger
- Institute of Interdisciplinary Mountain Research, Austrian Academy of ScienceInnsbruckAustria
| | - Daniela Sint
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
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15
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Boulêtreau S, Carry L, Meyer E, Filloux D, Menchi O, Mataix V, Santoul F. High predation of native sea lamprey during spawning migration. Sci Rep 2020; 10:6122. [PMID: 32273527 PMCID: PMC7145853 DOI: 10.1038/s41598-020-62916-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/17/2020] [Indexed: 11/09/2022] Open
Abstract
Sea lamprey (Petromyzon marinus) is a unique jawless vertebrate among the most primitive of all living vertebrates. This migratory fish is endangered in much of its native area due to dams, overfishing, pollution, and habitat loss. An introduced predator, the European catfish (Silurus glanis), is now widespread in Western and Southern European freshwaters, adding a new threat for sea lamprey migrating into freshwater to spawn. Here, we use a new prototype predation tag coupled with RFID telemetry on 49 individuals from one of the largest sea lamprey European populations (Southwestern France) to quantify the risk of predation for adult sea lampreys during its spawning migration in rivers with large populations of European catfish. We found that at least 80% of tagged sea lampreys (39 among 49) were preyed upon within one month, and that 50% of the released lampreys were rapidly consumed on average 8 days after tagging. This very high predation rate suggests that the European catfish represents a supplementary serious threat of extirpation for the native sea lamprey population we studied. This threat is likely to happen throughout most of the native lamprey distribution area, as the European catfish is becoming established almost everywhere the sea lamprey is.
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Affiliation(s)
| | | | | | | | | | - Vincent Mataix
- EDF, Développement Durable, 4 rue Claude Marie Perroud, 31096, Toulouse, France
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16
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Abstract
Biological invasions are considered to be one of the leading causes of biodiversity loss worldwide. Freshwater ecosystems are amongst the most biodiverse, containing about 50% of the world’s known fish species but, ironically, are the most invaded ecosystems. In Portuguese freshwaters, there are currently 20 identified non-native fishes, arriving at an unprecedented rate of a new species every two years. A recent non-native is the European catfish Silurus glanis, a top predator native to Central and Eastern Europe, that arrived at the Lower Tagus (Portugal) circa 2006. This study compares the dietary habits of this top predator in two different habitats of the Lower Tagus in order to evaluate its potential impact. The stomach contents of 96 individuals were analyzed, 61 from the lotic environment and 35 from the lentic systems. A total of 66 stomachs contained prey items, 38 from the lotic and 28 from the lentic. Diet varied considerably between habitats, with shrimp and crayfish being the most abundant prey items in the lentic systems and shrimp and fish the most abundant prey items in the lotic section. Tendency to piscivory was observed in large-sized individuals. Overall, the findings in this study provide the first evidence of the potential impacts of European catfish through predation on the fish communities.
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17
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Nobile AB, Freitas-Souza D, Ruiz-Ruano FJ, Nobile MLMO, Costa GO, de Lima FP, Camacho JPM, Foresti F, Oliveira C. DNA metabarcoding of Neotropical ichthyoplankton: Enabling high accuracy with lower cost. METABARCODING AND METAGENOMICS 2019. [DOI: 10.3897/mbmg.3.35060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Knowledge of ichthyoplankton dynamics is extremely important for conservation management as it can provide information about preferential spawning sites, reproductive period, migratory routes and recruitment success, which can be used to guide management and conservation efforts. However, identification of the eggs and larvae of Neotropical freshwater fish is a difficult task. DNA barcodes have emerged as an alternative and highly accurate approach for species identification, but DNA barcoding can be time-consuming and costly. To solve this problem, we aimed to develop a simple protocol based on DNA metabarcoding, to investigate whether it is possible to detect and quantify all species present in a pool of organisms. To do this, 230 larvae were cut in half, one half was sequenced by the Sanger technique and the other half was used to compose six arrays with a pool of larvae that were sequenced using a next-generation technique (NGS). The results of the Sanger sequencing allowed the identification of almost all larvae at species level, and the results from NGS showed high accuracy in species detection, ranging from 83% to 100%, with an average of 95% in all samples. No false positives were detected. The frequency of organisms in the two methods was positively correlated (Pearson), with low variation among species. In conclusion, this protocol represents a considerable advance in ichthyoplankton studies, allowing a rapid, cost-effective, quali-quantitative approach that improves the accuracy of identification.
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18
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Andriollo T, Gillet F, Michaux JR, Ruedi M. The menu varies with metabarcoding practices: A case study with the bat Plecotus auritus. PLoS One 2019; 14:e0219135. [PMID: 31276547 PMCID: PMC6611578 DOI: 10.1371/journal.pone.0219135] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/17/2019] [Indexed: 11/19/2022] Open
Abstract
Metabarcoding of feces has revolutionized the knowledge of animal diets by providing unprecedented resolution of consumed resources. However, it is still unclear how different methodological approaches influence the ecological conclusions that can be drawn from such data. Here, we propose a critical evaluation of several data treatments on the inferred diet of the bat Plecotus auritus using guano regularly collected from various colonies throughout the entire active season. First and unlike previous claims, our data indicates that DNA extracted from large amounts of fecal material issued from guano accumulates yield broader taxonomic diversity of prey than smaller numbers of pellets would do, provided that extraction buffer volumes are adapted to such increased amounts of material. Second, trophic niche analyses based on prey occurrence data uncover strong seasonality in the bat’s diet and major differences among neighboring maternity colonies. Third, while the removal of rare prey items is not always warranted as it introduces biases affecting particularly samples with greater prey species richness. Fourth, examination of distinct taxonomic depths in diet analyses highlights different aspects of food consumption providing a better understanding of the consumer’s diet. Finally, the biologically meaningful patterns recovered with presence-absence approaches are virtually lost when attempting to quantify prey consumed using relative read abundances. Even in an ideal situation where reference barcodes are available for most potential prey species, inferring realistic patterns of prey consumption remains relatively challenging. Although best practice in metabarcoding analyses will depend on the aims of the study, several previous methodological recommendations seem unwarranted for studying such diverse diets as that of brown long-eared bats.
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Affiliation(s)
- Tommy Andriollo
- Department of Mammalogy and Ornithology, Natural History Museum of Geneva, CP, CH, Geneva, Switzerland
- Section of Biology, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet, Geneva, Switzerland
| | - François Gillet
- Laboratoire de Génétique de la Conservation, Université de Liège, Institut de Botanique B22, Liège, Belgium
- Comportement et Écologie de la Faune Sauvage (CEFS), Institut National de la Recherche Agronomique, Auzeville, Castanet-Tolosan Cedex, France
| | - Johan R. Michaux
- Laboratoire de Génétique de la Conservation, Université de Liège, Institut de Botanique B22, Liège, Belgium
- CIRAD, Agirs Unit, TA C- 22/E- Campus international de Baillarguet, Montpellier Cedex, France
| | - Manuel Ruedi
- Department of Mammalogy and Ornithology, Natural History Museum of Geneva, CP, CH, Geneva, Switzerland
- * E-mail:
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Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00547] [Citation(s) in RCA: 303] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Sze Y, Miranda LN, Sin TM, Huang D. Characterising planktonic dinoflagellate diversity in Singapore using DNA metabarcoding. METABARCODING AND METAGENOMICS 2018. [DOI: 10.3897/mbmg.2.25136] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Dinoflagellates are traditionally identified morphologically using microscopy, which is a time-consuming and labour-intensive process. Hence, we explored DNA metabarcoding using high-throughput sequencing as a more efficient way to study planktonic dinoflagellate diversity in Singapore’s waters. From 29 minimally pre-sorted water samples collected at four locations in western Singapore, DNA was extracted, amplified and sequenced for a 313-bp fragment of the V4–V5 region in the 18S ribosomal RNA gene. Two sequencing runs generated 2,847,170 assembled paired-end reads, corresponding to 573,176 unique sequences. Sequences were clustered at 97% similarity and analysed with stringent thresholds (≥150 bp, ≥20 reads, ≥95% match to dinoflagellates), recovering 28 dinoflagellate taxa. Dinoflagellate diversity captured includes parasitic and symbiotic groups which are difficult to identify morphologically. Richness is similar between the inner and outer West Johor Strait, but variations in community structure are apparent, likely driven by environmental differences. None of the taxa detected in a recent phytoplankton bloom along the West Johor Strait have been recovered in our samples, suggesting that background communities are distinct from bloom communities. The voluminous data obtained in this study contribute baseline information for Singapore’s phytoplankton communities and prompt future research and monitoring to adopt the approach established here.
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Boulêtreau S, Gaillagot A, Carry L, Tétard S, De Oliveira E, Santoul F. Adult Atlantic salmon have a new freshwater predator. PLoS One 2018; 13:e0196046. [PMID: 29672636 PMCID: PMC5909622 DOI: 10.1371/journal.pone.0196046] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/05/2018] [Indexed: 11/18/2022] Open
Abstract
The Atlantic salmon (Salmo salar) is one of the world's most emblematic freshwater fish. Despite conservation and rehabilitation plans, populations of this species are dramatically declining due to human impacts such as habitat fragmentation, overfishing and water pollution. Owing to their large body size, anadromous adults were historically invulnerable to fish predation during their spawning period migration. This invulnerability has disappeared in Western Europe with the introduction of a new freshwater predator, the European catfish (Silurus glanis). Here we report how adults of Atlantic salmon are predated in the fishway of a large river of SW France, where the delayed and narrow passage created by the structure increases the probability of predator-prey encounter. We assessed predation risk by monitoring salmon and catfish in one fishway of the River Garonne, using video fish-counting from 1993 to 2016. We analysed the predation strategy of catfish using observations made with acoustic camera and RFID telemetry in 2016. Our results demonstrate a high predation rate (35%-14/39 ind.) on salmon inside the fishway during the 2016 spawning period migration. Our results suggest that a few specialized catfish individuals adapted their hunting behaviour to such prey, including their presence synchronized with that of salmon (i.e, more occurrences by the end of the day). Such results suggest that the spread of European catfish will potentially impact migration of anadromous species through anthropized systems.
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