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Canals O, Lanzén A, Mendibil I, Bachiller E, Corrales X, Andonegi E, Cotano U, Rodríguez-Ezpeleta N. Increasing marine trophic web knowledge through DNA analyses of fish stomach content: a step towards an ecosystem-based approach to fisheries research. JOURNAL OF FISH BIOLOGY 2024; 105:431-443. [PMID: 38726501 DOI: 10.1111/jfb.15754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/12/2024] [Accepted: 03/28/2024] [Indexed: 08/20/2024]
Abstract
Multispecies and ecosystem models, which are key for the implementation of ecosystem-based approaches to fisheries management, require extensive data on the trophic interactions between marine organisms, including changes over time. DNA metabarcoding, by allowing the simultaneous taxonomic identification of the community present in hundreds of samples, could be used for speeding up large-scale stomach content data collection. Yet, for DNA metabarcoding to be routinely implemented, technical challenges should be addressed, such as the potentially complicated sampling logistics, the detection of a high proportion of predator DNA, and the inability to provide reliable abundance estimations. Here, we present a DNA metabarcoding assay developed to examine the diet of five commercially important fish, which can be feasibly incorporated into routinary samplings. The method is devised to speed up the analysis process by avoiding the stomach dissection and content extraction steps, while preventing the amplification of predator DNA by using blocking primers. Tested in mock samples and in real stomach samples, the method has proven effective and shows great effectiveness discerning diet variations due to predator ecology or prey availability. Additionally, by applying our protocol to mackerel stomachs previously analyzed by visual inspection, we showcase how DNA metabarcoding could complement visually based data by detecting overlooked prey by the visual approach. We finally discuss how DNA metabarcoding-based data can contribute to trophic data collection. Our work reinforces the potential of DNA metabarcoding for the study and monitoring of fish trophic interactions and provides a basis for its incorporation into routine monitoring programs, which will be critical for the implementation of ecosystem-based approaches to fisheries management.
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Affiliation(s)
- Oriol Canals
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Anders Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
- IKERBASQUE - Basque Foundation for Science, Bilbao, Spain
| | - Iñaki Mendibil
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Eneko Bachiller
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Xavier Corrales
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Eider Andonegi
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Unai Cotano
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
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Yu TS, Lee SY, Lee J, Suman TY, Kwak IS. Insights into trophic interactions: DNA metabarcoding reveals species composition in black-tailed gull fecal samples in coastal environments of South Korea. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:761. [PMID: 39048811 DOI: 10.1007/s10661-024-12892-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 07/05/2024] [Indexed: 07/27/2024]
Abstract
This study explored the algae, zooplankton, macroinvertebrate, fish, and parasitic single-celled organism communities in Larus crassirostris (black-tailed gull) fecal samples from Baengnyeongdo, Hongdo, and Ulleungdo in South Korea. The fecal samples can identify key species consumed by black-tailed gull, providing insights into their, trophic interactions, and habitat dependencies. Using DNA metabarcoding, we identified algae, zooplankton, macroinvertebrate, fish, and intestinal and single-celled parasite species in the fecal samples. Parasitic single-celled organisms, such as Rhogostoma sp., Rhogostoma schuessleri, Eimeria furonis, and Aggregata eberthi, showed differing relative abundances at each sampling location, indicating variability in parasite diversity in the fecal DNA analysis of birds at each site. Intestinal parasites showed similar site-specific variability, though Clistobothrium sp. and Tetrabothrius sp. were common at all locations. Algae species, including Heterocapsa steinii, Heterocapsa niei, and Sargassum cristaefolium, also displayed habitat-specific patterns, as did zooplankton, with Calanus sp., Corycaeus speciosus, and Caprella californica being dominant on Baengnyeongdo, Hongdo, and Ulleungdo, respectively. In the macroinvertebrate communities, Octopus sinensis was prevalent at all locations but at varying abundances. Site-specific dominant fish species were also identified, with Ammodytes personatus, Decapterus maruadsi, and Arctoscopus japonicus highly predominant on Baengnyeongdo, Hongdo, and Ulleungdo, respectively. Other fish species, such as Ammodytes hexapterus, were detected in lower frequencies, suggesting a diverse diet for the seabirds. These results offer insights into the species composition and ecological dynamics in black-tailed gull populations across disparate Korean islands.
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Affiliation(s)
- Tae-Sik Yu
- Fisheries Science Institute, Chonnam National University, Yeosu, Republic of Korea
| | - Soo Yong Lee
- Natural Environment Research Division, National Institute of Environmental Research, Incheon, Republic of Korea
| | - Jangho Lee
- Natural Environment Research Division, National Institute of Environmental Research, Incheon, Republic of Korea
| | | | - Ihn-Sil Kwak
- Fisheries Science Institute, Chonnam National University, Yeosu, Republic of Korea.
- Department of Ocean Integrated Science, Chonnam National University, 50, Daehak-Ro, Yeosu-Si, Jeollanam-Do, 59626, Republic of Korea.
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Slimani D, Abdellaoui S, El Ouamari N, Kaddouri N, Kasmi K, Mouedden R, Layachi M, Settih J, Chaabane K. Trophic Interactions of European Hake Merluccius merluccius (Linnaeus, 1758) in Benthic Communities off the Moroccan Mediterranean Coastline: Seasonal and Ontogenetic Shifts. SCIENTIFICA 2023; 2023:8865128. [PMID: 38179147 PMCID: PMC10764652 DOI: 10.1155/2023/8865128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/03/2023] [Accepted: 12/07/2023] [Indexed: 01/06/2024]
Abstract
The European hake, Merluccius merluccius (Linnaeus, 1758), is one of the most important resources for Mediterranean fisheries. Due to its pivotal role in energy transfer from lower to higher trophic levels, this species is a crucial component of the ecosystem's functioning. The ecological role of Merluccius merluccius, off the Moroccan Mediterranean Sea (southern Alboran Sea), was investigated, exploring seasonal and ontogenetic shifts, geographical variations in prey composition, and feeding strategy. Between November 2020 and July 2022, a total of 402 hake specimens were collected by oceanographic bottom trawl surveys (MEDITS) that were carried out during warm and cold seasons to assess their diet and feeding habits. The sample was analyzed according to fish sizes and seasons, and qualitative/quantitative feeding indices were calculated. The trophic spectrum of Merluccius merluccius included 24 prey items in total, mainly belonging to Osteichthyes (12), Crustacea (10), Cephalopoda (1), and Polychaeta (1), suggesting a generalist behavior of this predator as in numerous regions of the Mediterranean Sea, with several species that occasionally occurs in its diet. In the Moroccan Mediterranean Sea, Osteichthyes proved to be the most important prey item (%IRI = 78.56) among the different zoological groups, followed by Crustacea (%IRI = 16.22). The other food items were occasionally and randomly consumed, and cannibalism was low (0.8%). Hierarchical cluster analysis and nonmetric multidimensional scaling (nMDS) showed different feeding habits of two main groups separated at 60% similarity: small specimens <10 cm TL, primarily feed on zooplanktonic prey, while medium and large specimens hold a diet based on Osteichthyes with crustaceans. Furthermore, a significant positive relationship between hake and fish prey size was confirmed. Seasonally, mesopelagic Osteichthyes were the main food prey in the summer season, while pelagic species were predominant during the autumn. SIMPER analysis revealed that the prey items contributing the most to the differences between seasons and length classes were Engraulis encrasicolus, Micromesistius poutassou, Boops boops, Macroramphosus scolopax, gobids, Gadiculus argenteus, and most of Crustacea. The diet does not appear to be influenced by sex (>0.05). A trophic level (TROPH) of 4.1 was calculated, indicating that the species is a top predator (quaternary consumers). The TROPH values ranged between 2.58 and 4.38 from juveniles to adults, increasing asymptotically with the size of specimens. In contrast to what has previously been found in other Mediterranean regions, where ichthyophagous hake feed mostly on pelagic Osteichthyes, such as Engraulis encrasicolus, Sardina pilchardus, and Micromesistius poutassou, the study points up the vital role played by Atlantic horse mackerel Trachurus trachurus for hake diet in the Moroccan Mediterranean Sea. Information on the feeding ecology of fish species as provided in this study is essential to improve ecosystem conservation in accordance with multispecies approach to fishery management, leading to a better understanding of the role of hake in the Moroccan Mediterranean Sea demersal communities.
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Affiliation(s)
- Douaa Slimani
- Laboratory for the Improvement of Agricultural Production, Biotechnology and the Environment, FSO, Mohammed First University, Oujda, Morocco
| | - Souad Abdellaoui
- Laboratory for the Improvement of Agricultural Production, Biotechnology and the Environment, FSO, Mohammed First University, Oujda, Morocco
- Regional Center of the National Institute of Fisheries Research, Fishing Laboratory, Casablanca, Morocco
| | - Najib El Ouamari
- Regional Center of the National Institute of Fisheries Research, Fishing Laboratory, Nador, Morocco
| | - Nassir Kaddouri
- Regional Center of the National Institute of Fisheries Research, Fishing Laboratory, Nador, Morocco
- Department of Biology, Biodiversity, Ecology and Genomics Laboratory, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Khaoula Kasmi
- Laboratory for the Improvement of Agricultural Production, Biotechnology and the Environment, FSO, Mohammed First University, Oujda, Morocco
| | - Rajae Mouedden
- Laboratory for the Improvement of Agricultural Production, Biotechnology and the Environment, FSO, Mohammed First University, Oujda, Morocco
| | - Mostafa Layachi
- Regional Center of the National Institute of Fisheries Research, Fishing Laboratory, Nador, Morocco
| | - Jamal Settih
- Regional Center of the National Institute of Fisheries Research, Fishing Laboratory, Nador, Morocco
| | - Khalid Chaabane
- Laboratory for the Improvement of Agricultural Production, Biotechnology and the Environment, FSO, Mohammed First University, Oujda, Morocco
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Mroue-Ruiz FH, Pacheco-Sandoval A, Lago-Lestón A, Giffard-Mena I, Abadía-Cardoso A, Chong-Robles J, Schramm Y. Metabarcoding Used for the First Time to Identify Prey of Wild Totoaba macdonaldi. Integr Comp Biol 2023; 63:276-287. [PMID: 37164934 DOI: 10.1093/icb/icad030] [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: 02/17/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/12/2023] Open
Abstract
Totoaba macdonaldi is an endangered endemic fish of the Gulf of California. Overexploitation resulted in the Mexican government banning the fishing of this species in 1975, and it being listed as endangered. However, the species is still subject to illegal fishing. Despite its conservation status, little is known about totoaba biology. The present study aimed to implement, for the first time, a metabarcoding protocol to describe the totoaba diet. Four wild totoaba individuals, seized by Mexican law enforcement agents, were dissected, and their stomach contents were collected. Three representative amplicon libraries were generated for cephalopods, chordates, and eukaryotes. After sequencing, 18 different taxa were identified, of which 11 species were recognized as prey. The totoaba were found to have consumed Pacific anchovy (Cetengraulis mysticetus), flathead grey mullet (Mugil cephalus), bigeye croaker (Micropogonias megalops), northern anchovy (Engraulis mordax), ocean whitefish (Caulolatilus princeps), milkfish (Chanos chanos), and Pacific sardine (Sardinops sagax). Members of the Euphausiidae family (krill) were also identified. This study identified up to four times more species in much fewer samples than previous studies based on morphological recognition, thus confirming metabarcoding as an effective method for studying the feeding habits of this species and one providing the tools required for further analysis of the totoaba diet.
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Affiliation(s)
- F H Mroue-Ruiz
- Facultad de Ciencias, Universidad Autónoma de Baja California, 22860 Ensenada, Baja California, Mexico
| | - A Pacheco-Sandoval
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, 22860 Ensenada, Baja California, Mexico
- Posgrado en Ciencias de la Vida, Centro de Investigación Científica y de Educación Superior de Ensenada, 22860 Ensenada, Baja California, Mexico
| | - A Lago-Lestón
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, 22860 Ensenada, Baja California, Mexico
| | - I Giffard-Mena
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, 22860 Ensenada, Baja California, Mexico
| | - A Abadía-Cardoso
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, 22860 Ensenada, Baja California, Mexico
| | - J Chong-Robles
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, 22860 Ensenada, Baja California, Mexico
| | - Y Schramm
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, 22860 Ensenada, Baja California, Mexico
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D’Iglio C, Porcino N, Savoca S, Profeta A, Perdichizzi A, Armeli Minicante E, Salvati D, Soraci F, Rinelli P, Giordano D. Ontogenetic shift and feeding habits of the European hake ( Merluccius merluccius L., 1758) in Central and Southern Tyrrhenian Sea (Western Mediterranean Sea): A comparison between past and present data. Ecol Evol 2022; 12:e8634. [PMID: 35356562 PMCID: PMC8941333 DOI: 10.1002/ece3.8634] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 11/29/2022] Open
Abstract
The present paper aims to investigate the ecological role of Merluccius merluccius, Linnaeus, 1758, in southern and central Tyrrhenian Sea (GSA 10, Resolution GFCM/33/2009/2 General Fisheries Commission for the Mediterranean), analyzing ontogenetic diet shifts, geographical variations on prey composition, and feeding habits. A total of 734 hake specimens ranging in size between 6 cm and 73 cm (Total Length, TL) were collected in 2018. In order to evaluate ontogenetic shifts in prey composition, samples were divided into five size classes and for each class the quantitative feeding indices have been calculated. The statistical analysis, based on index of relative importance percentage (%IRI), resulted in three trophic groups. The most abundant prey found in the immature hake specimens (size class I) were the Euphausiids, Stylocheiron longicorne and Mysidacea, while for samples with a total length over 10.5 cm were crustaceans and fish. Engraulis encrasicolus was the most abundant fish prey identified, followed by Boops boops and Myctophids. The high presence of Euphausiids, Mysids, Myctophidae, and Sternoptychidae in classes I, II, II, and IV (6-23 cm) showed the relevant role of mesopelagic fauna in hake diets, with an essential organic matter and energy flow from the mesopelagic to the epipelagic environment. Additionally, decapod crustaceans were found in the stomach contents of hakes belonging to class V (with size over 36 cm TL), which is notable considering that our study area includes an important decapod crustacean fishing area.
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Affiliation(s)
- Claudio D’Iglio
- Institute for Marine Biological Resources and Biotechnology (IRBIM)National Research CouncilMessinaItaly
- Department of Chemical, Biological, Pharmaceutical and Environmental SciencesUniversity of MessinaMessinaItaly
| | - Nunziatina Porcino
- Institute for Marine Biological Resources and Biotechnology (IRBIM)National Research CouncilMessinaItaly
| | - Serena Savoca
- Department of Biomedical, Dental and Morphological and Functional ImagingUniversity of MessinaMessinaItaly
| | - Adriana Profeta
- Institute for Marine Biological Resources and Biotechnology (IRBIM)National Research CouncilMessinaItaly
| | - Anna Perdichizzi
- Institute for Marine Biological Resources and Biotechnology (IRBIM)National Research CouncilMessinaItaly
| | - Enrico Armeli Minicante
- Institute for Marine Biological Resources and Biotechnology (IRBIM)National Research CouncilMessinaItaly
| | - Davide Salvati
- Institute for Marine Biological Resources and Biotechnology (IRBIM)National Research CouncilMessinaItaly
| | - Francesco Soraci
- Institute for Marine Biological Resources and Biotechnology (IRBIM)National Research CouncilMessinaItaly
| | - Paola Rinelli
- Institute for Marine Biological Resources and Biotechnology (IRBIM)National Research CouncilMessinaItaly
| | - Daniela Giordano
- Institute for Marine Biological Resources and Biotechnology (IRBIM)National Research CouncilMessinaItaly
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Riccioni G, Stagioni M, Manfredi C, Tinti F, Piccinetti C, Libralato S. DNA metabarcoding suggests dietary niche partitioning in the Adriatic European hake. Sci Rep 2022; 12:1343. [PMID: 35079081 PMCID: PMC8789918 DOI: 10.1038/s41598-022-05346-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 01/03/2022] [Indexed: 11/09/2022] Open
Abstract
The Northern Adriatic Sea (FAO Geographical Sub-Area 17) is one of the most productive fishing areas of the Mediterranean Sea and it includes a broad diversity of habitats. In the Northern Adriatic basin, the Pomo Pit (200-273 m of depth) is one of the most important areas of aggregation for some demersal stocks shared in the Adriatic Sea and it is an important spawning/nursery area of the European hake (Merluccius merluccius). Through a metabarcoding approach we investigated the feeding habits of European hake, both inside and outside the Pomo Pit, and their temporal variability comparing samples collected in 2016 and 2014. Our analyses proved the presence of an ontogenetic shift from a diet based mainly on crustaceans in juveniles to a more piscivorous feeding behaviour in adult hakes and suggested the presence of a specific niche partitioning and food preferences between hakes living inside and outside the Pomo Pit. The main differences among adult hakes refer to the presence of molluscs in the stomachs of hakes collected within the Pomo Pit and the presence of high depth prey species (i.e., Micromesistius poutassou). Metabarcoding revealed the relevant ecological role played by the Pomo Pit in M. merluccius feeding behaviour and ontogenetic development, promoting a careful ecosystem-based management of fisheries in this area through focused conservation measures.
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Affiliation(s)
- Giulia Riccioni
- Department of Biological, Geological and Environmental Sciences, Laboratory of Marine Biology and Fisheries, University of Bologna, viale Adriatico 1/n, 61032, Fano, Italy.
- BioDNA - Centro di Ricerca sulla Biodiversità e DNA Antico, Facoltà di scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, via Emilia Parmense n. 84, 29122, Piacenza, Italy.
| | - Marco Stagioni
- Department of Biological, Geological and Environmental Sciences, Laboratory of Marine Biology and Fisheries, University of Bologna, viale Adriatico 1/n, 61032, Fano, Italy
- Co.N.I.S.Ma- URL Fano, Laboratory of Marine Biology and Fisheries, viale Adriatico 1/n, 61032, Fano, Italy
| | - Chiara Manfredi
- Department of Biological, Geological and Environmental Sciences, Laboratory of Marine Biology and Fisheries, University of Bologna, viale Adriatico 1/n, 61032, Fano, Italy
- Co.N.I.S.Ma- URL Fano, Laboratory of Marine Biology and Fisheries, viale Adriatico 1/n, 61032, Fano, Italy
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Sant'Alberto 163, 48123, Ravenna, Italy
| | - Corrado Piccinetti
- Department of Biological, Geological and Environmental Sciences, Laboratory of Marine Biology and Fisheries, University of Bologna, viale Adriatico 1/n, 61032, Fano, Italy
| | - Simone Libralato
- National Institute of Oceanography and Applied Geophysics - OGS, Via Beirut 2/4 (Ex-Sissa building), 34151, Trieste, Italy
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Bachiller E, Giménez J, Albo‐Puigserver M, Pennino MG, Marí‐Mena N, Esteban A, Lloret‐Lloret E, Bellido JM, Coll M. Trophic niche overlap between round sardinella ( Sardinella aurita) and sympatric pelagic fish species in the Western Mediterranean. Ecol Evol 2021; 11:16126-16142. [PMID: 34824816 PMCID: PMC8601905 DOI: 10.1002/ece3.8293] [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: 05/17/2021] [Revised: 10/12/2021] [Accepted: 10/15/2021] [Indexed: 01/27/2023] Open
Abstract
The northward expansion of round sardinella (Sardinella aurita) in the Mediterranean Sea, together with declines and fluctuations in biomass and landings of European sardine (Sardina pilchardus) and anchovy (Engraulis encrasicolus) observed in recent decades, may suggest potential inter-specific competition in the pelagic domain. The coexistence of sympatric zooplanktivorous fish species might therefore be exposed in part to trophic niche overlap and competition for food. Combining visual diet characterization under the microscope with DNA metabarcoding from stomach contents of fish collected in spring results show that predation on relatively large krill is equally important for sardinella than for the other two niche overlapping species. Furthermore, an important overlap is found in their isotopic niche, especially with anchovy, using nitrogen (δ15N) and carbon (δ13C) stable isotopes in muscle tissue. In fact, the three fish species are able to feed effectively in the whole prey size spectrum available during the sampled season, from the smallest diatoms and copepods to the larger prey (i.e., decapods and euphausiids), including fish larvae. Moreover, effective predation upon other large prey like siphonophores, which is observed only when multi-proxy analyses in stomach contents are applied, might also be relevant in the diet of sardinella. The overlapping diet composition in spring, together with the effective use of food resource by sardinella, can be of special interest in potential future scenarios with warmer water temperature leading to lower zooplankton and/or higher jellyfish availability, where sardinella may take advantage over other species due to its feeding plasticity.
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Affiliation(s)
- Eneko Bachiller
- Marine Renewable Resources DepartmentInstitute of Marine Science (ICM‐CSIC)BarcelonaSpain
| | - Joan Giménez
- Marine Renewable Resources DepartmentInstitute of Marine Science (ICM‐CSIC)BarcelonaSpain
- MaREI CentreEnvironmental Research InstituteUniversity College CorkCorkIreland
- School of Biological, Earth, and Environmental SciencesUniversity College CorkCorkIreland
| | - Marta Albo‐Puigserver
- Marine Renewable Resources DepartmentInstitute of Marine Science (ICM‐CSIC)BarcelonaSpain
- Centro de Ciências do MarUniversidade do Algarve (CCMAR‐UAlg)FaroPortugal
| | | | | | - Antonio Esteban
- Centro Oceanográfico de MurciaInstituto Español de OceanografíaSan Pedro del PinatarSpain
| | - Elena Lloret‐Lloret
- Marine Renewable Resources DepartmentInstitute of Marine Science (ICM‐CSIC)BarcelonaSpain
| | - José María Bellido
- Centro Oceanográfico de MurciaInstituto Español de OceanografíaSan Pedro del PinatarSpain
| | - Marta Coll
- Marine Renewable Resources DepartmentInstitute of Marine Science (ICM‐CSIC)BarcelonaSpain
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Diet of the Deep-Sea Shark Galeus melastomus Rafinesque, 1810, in the Mediterranean Sea: What We Know and What We Should Know. SUSTAINABILITY 2021. [DOI: 10.3390/su13073962] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We reviewed literature on the diet of the Galeus melastomus Rafinesque, 1810, from the Mediterranean Sea. Specific keywords (“Galeus melastomus diet”, “feeding habits”, “trophic position”, “biology”, “deep environment adaptation”) in the principal data sources, such as Web of Science, PubMed, and Google Scholar were used. Seventeen studies conducted on the diet and trophic position of G. melastomus have been considered for Mediterranean Sea regions. The feeding habits have been analyzed in many areas of the western basin; instead, for the Tyrrhenian, Adriatic, and central Mediterranean Seas, information is outdated and fragmentary. In all investigated sub areas, the data showed that G. melastomus is an opportunistic demersal supra benthic predator, benthic feeder, and scavenger, that adapts its diet to the seasonal and geographical fluctuations of the prey availability. It occupies a generalist niche showing individual specialization. In all reviewed Mediterranean sub areas, the most important prey groups were crustaceans, cephalopods, and teleost fishes. Taxa percentage in its diet composition can vary depending on different habitats with ontogenetic development of individuals, depth (that is correlated with the ontogenetic development), seasonal availability, and distribution of different prey groups. Widening knowledge of G. melastomus feeding habits is a fundamental tool for better understand meso and bathy-pelagic ecosystems.
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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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Meyer JM, Leempoel K, Losapio G, Hadly EA. Molecular Ecological Network Analyses: An Effective Conservation Tool for the Assessment of Biodiversity, Trophic Interactions, and Community Structure. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.588430] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Ducotterd C, Crovadore J, Lefort F, Rubin JF, Ursenbacher S. A powerful long metabarcoding method for the determination of complex diets from faecal analysis of the European pond turtle (Emys orbicularis, L. 1758). Mol Ecol Resour 2020; 21:433-447. [PMID: 33047508 PMCID: PMC7821331 DOI: 10.1111/1755-0998.13277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 08/31/2020] [Accepted: 10/01/2020] [Indexed: 01/16/2023]
Abstract
High‐throughput sequencing has become an accurate method for the identification of species present in soil, water, faeces, gut or stomach contents. However, information at the species level is limited due to the choice of short barcodes and based on the idea that DNA is too degraded to allow longer sequences to be amplified. We have therefore developed a long DNA metabarcoding method based on the sequencing of short reads followed by de novo assembly, which can precisely identify the taxonomic groups of organisms associated with complex diets, such as omnivorous individuals. The procedure includes 11 different primer pairs targeting the COI gene, the large subunit of the ribulose‐1,5‐bisphosphate carboxylase gene, the maturase K gene, the 28S rRNA and the trnL‐trnF chloroplastic region. We validated this approach using 32 faeces samples from an omnivorous reptile, the European pond turtle (Emys orbicularis, L. 1758). This metabarcoding approach was assessed using controlled experiments including mock communities and faecal samples from captive feeding trials. The method allowed us to accurately identify prey DNA present in the diet of the European pond turtles to the species level in most of the cases (82.4%), based on the amplicon lengths of multiple markers (168–1,379 bp, average 546 bp), and produced by de novo assembly. The proposed approach can be adapted to analyse various diets, in numerous conservation and ecological applications. It is consequently appropriate for detecting fine dietary variations among individuals, populations and species as well as for the identification of rare food items.
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Affiliation(s)
- Charlotte Ducotterd
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Centre Emys, Association de Protection et Récupération des Tortues, Chavornay, Switzerland.,La Maison de la Rivière, Tolochenaz, Switzerland.,HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Jussy, Switzerland
| | - Julien Crovadore
- HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Jussy, Switzerland
| | - François Lefort
- HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Jussy, Switzerland
| | - Jean-François Rubin
- La Maison de la Rivière, Tolochenaz, Switzerland.,HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Jussy, Switzerland
| | - Sylvain Ursenbacher
- Department of Environmental Sciences, Section of Conservation Biology, University of Basel, Basel, Switzerland.,info fauna - Centre Suisse de Cartographie de la Faune (CSCF) and Centre de coordination pour les reptiles et les amphibiens de Suisse (Karch), Neuchâtel, Switzerland
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Amundsen PA, Sánchez-Hernández J. Feeding studies take guts - critical review and recommendations of methods for stomach contents analysis in fish. JOURNAL OF FISH BIOLOGY 2019; 95:1364-1373. [PMID: 31589769 DOI: 10.1111/jfb.14151] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
Studies on the feeding ecology of fish are essential for exploring and contrasting trophic interactions and population and community dynamics within and among aquatic ecosystems. In this respect, many different methods have been adopted for the analysis of fish stomach contents. No consensus has, however, been reached for a standardised methodology despite that for several decades there has been an ongoing debate about which methodical approaches that should be preferred. Here, we critically review and scrutinise methods, addressing their strengths and weaknesses and emphasising inherent problems and possible pitfalls in their use. Although our critical assessment reveals that no completely ideal approach exists, appropriate and reliable procedures can be adopted through careful considerations and implementation. In particular, we advocate that different objectives require different methodical approaches and the choice of method should therefore be closely linked to the research questions that are addressed. For a standardisation of methods, we recommend a combination of the relative-fullness and presence-absence methods as the optimal approach for the commonly applied feeding studies addressing relative dietary composition in terms of prey diversity and abundance. Additionally, we recommend the gravimetric method for objectives related to the quantification of food consumption rates and the numerical method for prey selection studies. DNA-based dietary analysis provides a new and promising complementary approach to visual examination of stomach contents, although some technical challenges still exist. The suggested method standardisation facilitates comparisons across species, ecosystems and time and will enhance the applicability and benefits of fish feeding studies in trophic ecology research.
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Affiliation(s)
- Per-Arne Amundsen
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Javier Sánchez-Hernández
- Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física yQuímica Inorgánica, Universidad Rey JuanCarlos, Móstoles, Madrid, Spain
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