1
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Denis V, Ferrier-Pagès C, Schubert N, Coppari M, Baker DM, Camp EF, Gori A, Grottoli AG, Houlbrèque F, Maier SR, Mancinelli G, Martinez S, Yalçın Özdilek Ş, Radice VZ, Ribes M, Richter C, Viladrich N, Rossi S. Heterotrophy in marine animal forests in an era of climate change. Biol Rev Camb Philos Soc 2024; 99:965-978. [PMID: 38284299 DOI: 10.1111/brv.13053] [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: 06/19/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/30/2024]
Abstract
Marine animal forests (MAFs) are benthic ecosystems characterised by biogenic three-dimensional structures formed by suspension feeders such as corals, gorgonians, sponges and bivalves. They comprise highly diversified communities among the most productive in the world's oceans. However, MAFs are in decline due to global and local stressors that threaten the survival and growth of their foundational species and associated biodiversity. Innovative and scalable interventions are needed to address the degradation of MAFs and increase their resilience under global change. Surprisingly, few studies have considered trophic interactions and heterotrophic feeding of MAF suspension feeders as an integral component of MAF conservation. Yet, trophic interactions are important for nutrient cycling, energy flow within the food web, biodiversity, carbon sequestration, and MAF stability. This comprehensive review describes trophic interactions at all levels of ecological organisation in tropical, temperate, and cold-water MAFs. It examines the strengths and weaknesses of available tools for estimating the heterotrophic capacities of the foundational species in MAFs. It then discusses the threats that climate change poses to heterotrophic processes. Finally, it presents strategies for improving trophic interactions and heterotrophy, which can help to maintain the health and resilience of MAFs.
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Affiliation(s)
- Vianney Denis
- Institute of Oceanography, National Taiwan University, No. 1, Section 4, Roosevelt Road, Da'an District, Taipei, 10617, Taiwan
| | | | - Nadine Schubert
- CCMAR-Center of Marine Sciences, University of Algarve, Campus Gambelas, Bld. 7, Faro, 8005-139, Portugal
| | - Martina Coppari
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche snc, Ancona, 60131, Italy
| | - David M Baker
- School of Biological Sciences & Swire Institute of Marine Science, The University of Hong Kong, Hong Kong
| | - Emma F Camp
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Andrea Gori
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
| | - Andréa G Grottoli
- School of Earth Sciences, The Ohio State University, 125 South Oval Mall, Columbus, OH, 43210, USA
| | - Fanny Houlbrèque
- Entropie UMR 9220, Institut de Recherche pour le Développement, Nouméa, 98848, New Caledonia
| | - Sandra R Maier
- Greenland Climate Research Centre, Greenland Institute of Natural Resources, Kivioq 2 PO Box 570, Nuuk, 3900, Greenland
| | - Giorgio Mancinelli
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Monteroni s/n, Lecce, 73100, Italy
| | - Stephane Martinez
- Graduate School of Oceanography, University of Rhode Island, 215 South Ferry Road, Narragansett, RI, 02882, USA
| | - Şükran Yalçın Özdilek
- Department of Biology, Science Faculty, Çanakkale Onsekiz Mart University, Çanakkale, 17100, Turkey
| | - Veronica Z Radice
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, 23529, USA
| | - Marta Ribes
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, 08003, Spain
| | - Claudio Richter
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Alten Hafen 26, Bremerhaven, 27568, Germany
- Department of Biology/Chemistry, University of Bremen, Leobener Str., NW 2, Bremen, 28359, Germany
| | - Nuria Viladrich
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
| | - Sergio Rossi
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Monteroni s/n, Lecce, 73100, Italy
- Universidade Federal do Ceara, Instituto de Ciencias do Mar (Labomar), Av. da Abolicao 3207, Fortaleza, Brazil
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2
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Robinson JPW, Benkwitt CE, Maire E, Morais R, Schiettekatte NMD, Skinner C, Brandl SJ. Quantifying energy and nutrient fluxes in coral reef food webs. Trends Ecol Evol 2024; 39:467-478. [PMID: 38105132 DOI: 10.1016/j.tree.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/21/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023]
Abstract
The movement of energy and nutrients through ecological communities represents the biological 'pulse' underpinning ecosystem functioning and services. However, energy and nutrient fluxes are inherently difficult to observe, particularly in high-diversity systems such as coral reefs. We review advances in the quantification of fluxes in coral reef fishes, focusing on four key frameworks: demographic modelling, bioenergetics, micronutrients, and compound-specific stable isotope analysis (CSIA). Each framework can be integrated with underwater surveys, enabling researchers to scale organismal processes to ecosystem properties. This has revealed how small fish support biomass turnover, pelagic subsidies sustain fisheries, and fisheries benefit human health. Combining frameworks, closing data gaps, and expansion to other aquatic ecosystems can advance understanding of how fishes contribute to ecosystem functions and services.
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Affiliation(s)
- James P W Robinson
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK.
| | | | - Eva Maire
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Renato Morais
- Université Paris Sciences et Lettres, École Pratique des Hautes Études, USR 3278 CRIOBE, Perpignan 66860, France
| | | | - Christina Skinner
- School of the Environment, University of Queensland, St Lucia 4072, QLD, Australia
| | - Simon J Brandl
- Department of Marine Science, The University of Texas at Austin, Marine Science Institute, Port Aransas, TX 78373, USA
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3
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Liu Y, Li X, Chen W, Feng G, Chen F, Li J, Zhou Q. High-throughput sequencing and fatty acid profile analyses of the Black Amur bream ( Megalobrama terminalis) reveal variation in dietary niche associated with geographic segregation. Ecol Evol 2024; 14:e11226. [PMID: 38628924 PMCID: PMC11019299 DOI: 10.1002/ece3.11226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/07/2024] [Accepted: 03/15/2024] [Indexed: 04/19/2024] Open
Abstract
Fish dietary niche is a core focus, and it reflects the diversity of resources, habitats, or environments occupied by a species. However, whether geographic segregation among different populations triggers dietary diversification and concomitant fish niche shift remains unknown. In the present study, we selected the Black Amur bream (Megalobrama terminalis) is a migratory fish species that plays an important role in the material transfer and energy cycling of river ecosystems, inhabiting southern China drainage with multiple geographic populations. Here, we utilized the combined analyses of 18S rDNA high-throughput sequencing in fish gut contents and fatty acid (FA) in muscle tissues to evaluate potential spatial patterns of habitat and resource use for M. terminalis in three rivers of southern China. Our results showed that prey items of the Xijiang (XR) population (Pearl River) exhibited the highest species diversity and richness among the three geographic populations. Moreover, diet composition of M. terminalis was affected by spatial differences associated with geographic segregation. Analyses of FA biomarkers indicated that the highest levels of C16:0, C18:3n-3, and C18:2n-6c were found in Wanquan (WS) population (Wanquan River). The XR population exhibited a distinct FA profile characterized by higher amounts of arachidonic acid (ARA) and docosahexaenoic acid (DHA). The Moyang (MY) population (Moyang River) acted as the linkage between WS and XR populations and consisted of middle levels of saturated FAs (SFAs) and polyunsaturated FAs (PUFAs). The XR population displayed a greater FA niche width compared with WS population. Furthermore, we observed a close positive relationship between the niche width and α-diversity indices of dietary resources for FA proflies. Our study provides valued information to develop different conservation strategies among different populations and improve fisheries management for M. terminalis and other endemic species in local rivers.
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Affiliation(s)
- Yaqiu Liu
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Areas, College of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
- Pearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and EnvironmentGuangzhouChina
| | - Xinhui Li
- Pearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and EnvironmentGuangzhouChina
| | - Weitao Chen
- Pearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and EnvironmentGuangzhouChina
| | - Guangpeng Feng
- Jiangxi Institute for Fisheries Sciences, Poyang Lake Fisheries Research Centre of Jiangxi ProvinceNanchangChina
| | - Fangchan Chen
- Guangzhou Qianjiang Water Ecology Technology Co. LtdGaungzhouChina
| | - Jie Li
- Pearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and EnvironmentGuangzhouChina
- Guangzhou Qianjiang Water Ecology Technology Co. LtdGaungzhouChina
| | - Qiong Zhou
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Areas, College of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
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Hartig F, Abrego N, Bush A, Chase JM, Guillera-Arroita G, Leibold MA, Ovaskainen O, Pellissier L, Pichler M, Poggiato G, Pollock L, Si-Moussi S, Thuiller W, Viana DS, Warton DI, Zurell D, Yu DW. Novel community data in ecology-properties and prospects. Trends Ecol Evol 2024; 39:280-293. [PMID: 37949795 DOI: 10.1016/j.tree.2023.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 11/12/2023]
Abstract
New technologies for monitoring biodiversity such as environmental (e)DNA, passive acoustic monitoring, and optical sensors promise to generate automated spatiotemporal community observations at unprecedented scales and resolutions. Here, we introduce 'novel community data' as an umbrella term for these data. We review the emerging field around novel community data, focusing on new ecological questions that could be addressed; the analytical tools available or needed to make best use of these data; and the potential implications of these developments for policy and conservation. We conclude that novel community data offer many opportunities to advance our understanding of fundamental ecological processes, including community assembly, biotic interactions, micro- and macroevolution, and overall ecosystem functioning.
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Affiliation(s)
- Florian Hartig
- Theoretical Ecology, University of Regensburg, Regensburg, Germany.
| | - Nerea Abrego
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35 (Survontie 9C), FI-40014 Jyväskylä, Finland
| | - Alex Bush
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Jonathan M Chase
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | | | | | - Otso Ovaskainen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35 (Survontie 9C), FI-40014 Jyväskylä, Finland; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, Helsinki 00014, Finland
| | - Loïc Pellissier
- Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zürich, 8092 Zurich, Switzerland; Unit of Land Change Science, Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), 8903 Birmensdorf, Switzerland
| | | | - Giovanni Poggiato
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F38000, Grenoble, France
| | - Laura Pollock
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Sara Si-Moussi
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F38000, Grenoble, France
| | - Wilfried Thuiller
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F38000, Grenoble, France
| | | | | | | | - Douglas W Yu
- Kunming Institute of Zoology; Yunnan, China; University of East Anglia, Norfolk, UK
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5
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Pérez-Pezoa K, Cárdenas CA, González-Aravena M, Gallardo P, Rivero A, Arriagada V, Demianenko K, Zabroda P, Santa Cruz F. Trophodynamics of the Antarctic toothfish (Dissostichus mawsoni) in the Antarctic Peninsula: Ontogenetic changes in diet composition and prey fatty acid profiles. PLoS One 2023; 18:e0287376. [PMID: 37796854 PMCID: PMC10553334 DOI: 10.1371/journal.pone.0287376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/04/2023] [Indexed: 10/07/2023] Open
Abstract
The Antarctic toothfish (Dissostichus mawsoni) is the largest notothenioid species in the Southern Ocean, playing a keystone role in the trophic web as a food source for marine mammals and a top predator in deep-sea ecosystems. Most ecological knowledge on this species relies on samples from areas where direct fishing is allowed, whereas in areas closed to fishing, such as the Antarctic Peninsula (AP), there are still key ecological gaps to ensure effective conservation, especially regarding our understanding of its trophic relationships within the ecosystem. Here, we present the first comprehensive study of the feeding behavior of Antarctic toothfish caught in the northern tip of the AP, during two consecutive fishing seasons (2019/20 and 2020/21). Stomach content was analyzed according to size-classes, sex and season. Macroscopic morphological analysis was used to identify prey, whereas DNA analysis was used in highly digested prey items. Fatty acid analysis was conducted to determine the prey's nutritional composition. The diet mainly consisted of Macrouridae, Cephalopoda, Anotopteridae, and Channichthyidae. Other prey items found were crustaceans and penguin remains; however, these were rare in terms of their presence in stomach samples. Sex had no effect on diet, whereas size-class and fishing season influenced prey composition. From 27 fatty acid profiles identified, we observed two different prey groups of fishes (integrated by families Anotopteridae, Macrouridae and Channichthyidae) and cephalopods. Our results revealed a narrow range of prey items typical of a generalist predator, which probably consumes the most abundant prey. Understanding the diet and trophic relationships of Antarctic toothfish is critical for a better comprehension of its role in the benthic-demersal ecosystem of the AP, key for ecosystemic fisheries management, and relevant for understanding and predicting the effect of climate change on this species.
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Affiliation(s)
- Karina Pérez-Pezoa
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - César A. Cárdenas
- Departamento Científico, Instituto Antártico Chileno, Plaza Muñoz Gamero, Punta Arenas, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
| | | | - Pablo Gallardo
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad de Magallanes, Punta Arenas, Chile
| | - Alí Rivero
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad de Magallanes, Punta Arenas, Chile
| | - Vicente Arriagada
- Departamento de Microbiología, Universidad de Concepción, Concepción, Chile
| | | | - Pavlo Zabroda
- Institute of Fisheries and Marine Ecology (IFME), Berdyansk, Ukraine
| | - Francisco Santa Cruz
- Departamento Científico, Instituto Antártico Chileno, Plaza Muñoz Gamero, Punta Arenas, Chile
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6
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DiBattista JD, Liu SYV, De Brauwer M, Wilkinson SP, West K, Koziol A, Bunce M. Gut content metabarcoding of specialized feeders is not a replacement for environmental DNA assays of seawater in reef environments. PeerJ 2023; 11:e16075. [PMID: 37790632 PMCID: PMC10542274 DOI: 10.7717/peerj.16075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/20/2023] [Indexed: 10/05/2023] Open
Abstract
In tropical marine ecosystems, the coral-based diet of benthic-feeding reef fishes provides a window into the composition and health of coral reefs. In this study, for the first time, we compare multi-assay metabarcoding sequences of environmental DNA (eDNA) isolated from seawater and partially digested gut items from an obligate corallivore butterflyfish (Chaetodon lunulatus) resident to coral reef sites in the South China Sea. We specifically tested the proportional and statistical overlap of the different approaches (seawater vs gut content metabarcoding) in characterizing eukaryotic community composition on coral reefs. Based on 18S and ITS2 sequence data, which differed in their taxonomic sensitivity, we found that gut content detections were only partially representative of the eukaryotic communities detected in the seawater based on low levels of taxonomic overlap (3 to 21%) and significant differences between the sampling approaches. Overall, our results indicate that dietary metabarcoding of specialized feeders can be complimentary to, but is no replacement for, more comprehensive environmental DNA assays of reef environments that might include the processing of different substrates (seawater, sediment, plankton) or traditional observational surveys. These molecular assays, in tandem, might be best suited to highly productive but cryptic oceanic environments (kelp forests, seagrass meadows) that contain an abundance of organisms that are often small, epiphytic, symbiotic, or cryptic.
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Affiliation(s)
- Joseph D. DiBattista
- School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Shang Yin Vanson Liu
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | | | - Shaun P. Wilkinson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Katrina West
- CSIRO Australian National Fish Collection, CSIRO, Hobart, TAS, Australia
| | - Adam Koziol
- School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
- Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
| | - Michael Bunce
- Institute of Environmental Science and Research, Kenepuru, Porirua, New Zealand
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Riaz M, Warren D, Wittwer C, Cocchiararo B, Hundertmark I, Reiners TE, Klimpel S, Pfenninger M, Khaliq I, Nowak C. Using eDNA to understand predator-prey interactions influenced by invasive species. Oecologia 2023; 202:757-767. [PMID: 37594600 PMCID: PMC10474997 DOI: 10.1007/s00442-023-05434-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/03/2023] [Indexed: 08/19/2023]
Abstract
Invasive predatory species may alter population dynamic processes of their prey and impact biological communities and ecosystem processes. Revealing biotic interactions, however, including the relationship between predator and prey, is a difficult task, in particular for species that are hard to monitor. Here, we present a case study that documents the utility of environmental DNA analysis (eDNA) to assess predator-prey interactions between two invasive fishes (Lepomis gibbosus, Pseudorasbora parva) and two potential amphibian prey species, (Triturus cristatus, Pelobates fuscus). We used species-specific TaqMan assays for quantitative assessment of eDNA concentrations from water samples collected from 89 sites across 31 ponds during three consecutive months from a local amphibian hotspot in Germany. We found a negative relationship between eDNA concentrations of the predators (fishes) and prey (amphibians) using Monte-Carlo tests. Our study highlights the potential of eDNA application to reveal predator-prey interactions and confirms the hypothesis that the observed local declines of amphibian species may be at least partly caused by recently introduced invasive fishes. Our findings have important consequences for local conservation management and highlight the usefulness of eDNA approaches to assess ecological interactions and guide targeted conservation action.
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Affiliation(s)
- Maria Riaz
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum, 63571, Frankfurt, Gelnhausen, Germany.
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany.
- Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Straße 9, 60438, Frankfurt Am Main, Germany.
| | - Dan Warren
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
| | - Claudia Wittwer
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum, 63571, Frankfurt, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
- Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Straße 9, 60438, Frankfurt Am Main, Germany
| | - Berardino Cocchiararo
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum, 63571, Frankfurt, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
| | - Inga Hundertmark
- Hessische Gesellschaft Für Ornithologie Und Naturschutz (HGON E. V.), Lindenstrasse 5, 61209, Echzell, Germany
| | - Tobias Erik Reiners
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum, 63571, Frankfurt, Gelnhausen, Germany
- Hessische Gesellschaft Für Ornithologie Und Naturschutz (HGON E. V.), Lindenstrasse 5, 61209, Echzell, Germany
| | - Sven Klimpel
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
- Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Straße 9, 60438, Frankfurt Am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
| | - Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
- Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 7, 55128, Mainz, Germany
| | - Imran Khaliq
- Department of Education, Punjab, Pakistan
- Department of Aquatic Ecology Eawag (Swiss Federal Institute of Aquatic Science and Technology) Überlandstrasse 133, 8600, Dübendorf, Switzerland
- Snow and Landscape Research (WSL), Swiss Federal Institute for Forest, Flüelastr. 11, 7260, Davos Dorf, Switzerland
| | - Carsten Nowak
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum, 63571, Frankfurt, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
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8
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Brandl SJ, Lefcheck JS, Bates AE, Rasher DB, Norin T. Can metabolic traits explain animal community assembly and functioning? Biol Rev Camb Philos Soc 2023; 98:1-18. [PMID: 36054431 DOI: 10.1111/brv.12892] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 01/12/2023]
Abstract
All animals on Earth compete for free energy, which is acquired, assimilated, and ultimately allocated to growth and reproduction. Competition is strongest within communities of sympatric, ecologically similar animals of roughly equal size (i.e. horizontal communities), which are often the focus of traditional community ecology. The replacement of taxonomic identities with functional traits has improved our ability to decipher the ecological dynamics that govern the assembly and functioning of animal communities. Yet, the use of low-resolution and taxonomically idiosyncratic traits in animals may have hampered progress to date. An animal's metabolic rate (MR) determines the costs of basic organismal processes and activities, thus linking major aspects of the multifaceted constructs of ecological niches (where, when, and how energy is obtained) and ecological fitness (how much energy is accumulated and passed on to future generations). We review evidence from organismal physiology to large-scale analyses across the tree of life to propose that MR gives rise to a group of meaningful functional traits - resting metabolic rate (RMR), maximum metabolic rate (MMR), and aerobic scope (AS) - that may permit an improved quantification of the energetic basis of species coexistence and, ultimately, the assembly and functioning of animal communities. Specifically, metabolic traits integrate across a variety of typical trait proxies for energy acquisition and allocation in animals (e.g. body size, diet, mobility, life history, habitat use), to yield a smaller suite of continuous quantities that: (1) can be precisely measured for individuals in a standardized fashion; and (2) apply to all animals regardless of their body plan, habitat, or taxonomic affiliation. While integrating metabolic traits into animal community ecology is neither a panacea to disentangling the nuanced effects of biological differences on animal community structure and functioning, nor without challenges, a small number of studies across different taxa suggest that MR may serve as a useful proxy for the energetic basis of competition in animals. Thus, the application of MR traits for animal communities can lead to a more general understanding of community assembly and functioning, enhance our ability to trace eco-evolutionary dynamics from genotypes to phenotypes (and vice versa), and help predict the responses of animal communities to environmental change. While trait-based ecology has improved our knowledge of animal communities to date, a more explicit energetic lens via the integration of metabolic traits may further strengthen the existing framework.
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Affiliation(s)
- Simon J Brandl
- Department of Marine Science, The University of Texas at Austin, Marine Science Institute, Port Aransas, TX, 78373, USA
| | - Jonathan S Lefcheck
- Tennenbaum Marine Observatories Network and MarineGEO Program, Smithsonian Environmental Research Center, Edgewater, MD, 21037, USA
| | - Amanda E Bates
- Biology Department, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8P 5C2, Canada
| | - Douglas B Rasher
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
| | - Tommy Norin
- DTU Aqua: National Institute of Aquatic Resources, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
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9
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Kavazos CRJ, Ricci F, Leggat W, Casey JM, Choat JH, Ainsworth TD. Intestinal Microbiome Richness of Coral Reef Damselfishes ( Actinopterygii: Pomacentridae). Integr Org Biol 2022; 4:obac026. [PMID: 36136736 PMCID: PMC9486986 DOI: 10.1093/iob/obac026] [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: 01/27/2021] [Revised: 06/13/2022] [Indexed: 12/03/2022] Open
Abstract
Fish gastro-intestinal system harbors diverse microbiomes that affect the host's
digestion, nutrition, and immunity. Despite the great taxonomic diversity of fish, little
is understood about fish microbiome and the factors that determine its structure and
composition. Damselfish are important coral reef species that play pivotal roles in
determining algae and coral population structures of reefs. Broadly, damselfish belong to
either of two trophic guilds based on whether they are planktivorous or algae-farming. In
this study, we used 16S rRNA gene sequencing to investigate the intestinal microbiome of 5
planktivorous and 5 algae-farming damselfish species (Pomacentridae) from
the Great Barrier Reef. We detected Gammaproteobacteria ASVs belonging to
the genus Actinobacillus in 80% of sampled individuals across the 2
trophic guilds, thus, bacteria in this genus can be considered possible core members of
pomacentrid microbiomes. Algae-farming damselfish had greater bacterial alpha-diversity, a
more diverse core microbiome and shared 35 ± 22 ASVs, whereas planktivorous species shared
7 ± 3 ASVs. Our data also highlight differences in microbiomes associated with both
trophic guilds. For instance, algae-farming damselfish were enriched in
Pasteurellaceae, whilst planktivorous damselfish in
Vibrionaceae. Finally, we show shifts in bacterial community
composition along the intestines. ASVs associated with the classes Bacteroidia,
Clostridia, and Mollicutes bacteria were predominant in the
anterior intestinal regions while Gammaproteobacteria abundance was
higher in the stomach. Our results suggest that the richness of the intestinal bacterial
communities of damselfish reflects host species diet and trophic guild.
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Affiliation(s)
- Christopher R J Kavazos
- Biological, Earth and Environmental Sciences, The University of New South Wales , Kensington, NSW 2052 , Australia
| | - Francesco Ricci
- Biological, Earth and Environmental Sciences, The University of New South Wales , Kensington, NSW 2052 , Australia
- Centre of Marine Bio-Innovation, The University of New South Wales , Kensington, NSW 2052 , Australia
| | - William Leggat
- School of Environmental and Life Sciences, The University of Newcastle , 10 Chittaway Dr, Ourimbah, NSW 2258 , Australia
| | - Jordan M Casey
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University , Townsville, QLD 4811 , Australia
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan , Perpignan 66100 , France
- Laboratoire d'Excellence “CORAIL,” Université de Perpignan , Perpignan 66100 , France
| | - J Howard Choat
- College of Science and Engineering, James Cook University , Townsville QLD 4814 , Australia
| | - Tracy D Ainsworth
- Biological, Earth and Environmental Sciences, The University of New South Wales , Kensington, NSW 2052 , Australia
- Centre of Marine Bio-Innovation, The University of New South Wales , Kensington, NSW 2052 , Australia
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10
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Gül G, Yokeş MB, Demirel N. The occurrence and feeding of a critically endangered shark species, Oxynotus centrina in the Sea of Marmara. JOURNAL OF FISH BIOLOGY 2022; 101:728-735. [PMID: 35642655 DOI: 10.1111/jfb.15119] [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: 03/04/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
The angular roughshark, Oxynotus centrina (Linnaeus, 1758), is a rarely encountered deep-sea demersal shark species. It is listed as "Critically Endangered" in the IUCN's regional assessment for the Mediterranean. Like other sharks and rays, the angular roughshark is subject to by-catch in demersal trawl and longline fisheries. This study contributes new knowledge on (a) its occurrence, size and sex information; and (b) its feeding ecology in the Sea of Marmara. Data were collected on total length (TL), total weight (TW) and sex from unpublished research survey reports performed intermittently from 1994 to 2020. According to the data, O. centrina was mainly recorded from the muddy sand bottom type in the southwest region of the Marmara Sea, which has higher biodiversity of macrobenthic species than other regions. Different methodological approaches were conducted to understand its feeding, such as DNA metabarcoding and isotope analysis to identify its prey spectra and assign a trophic level. Sampled specimens were full of liquid in their stomachs without any discernible visually identifiable prey items. The metabarcoding analyses were also unsuccessful in identifying any prey items. Trophic position calculation based on nitrogen isotope in muscles highlighted that O. centrina has the highest trophic position compared to the other sharks and rays in the Sea of Marmara. Although it was found mainly feeding on polychaetes and sipunculids species from previous studies, the δ15 N values made the authors cautious about the possibility of this species feeding on low trophic-level benthic invertebrates. Because the authors could not observe the presence of shark vitellus in the stomachs and could not succeed in DNA identification for prey, this study highlights high δ15 N values similar to top predators for O. centrina. The authors conclude that this species strategically feeds mainly on shark eggs to fulfil its nutritional requirements with minimum energy expenditure in line with its slow-moving behaviour and mouth morphology.
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Affiliation(s)
- Güzin Gül
- Institute of Marine Sciences and Management, Istanbul University, Istanbul, Turkey
| | | | - Nazli Demirel
- Institute of Marine Sciences and Management, Istanbul University, Istanbul, Turkey
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11
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Arjunwadkar CV, Tebbett SB, Bellwood DR, Bourne DG, Smith HA. Algal turf structure and composition vary with particulate loads on coral reefs. MARINE POLLUTION BULLETIN 2022; 181:113903. [PMID: 35843165 DOI: 10.1016/j.marpolbul.2022.113903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 05/10/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
Algal turfs trap and retain particulates, however, little is known about the relationship between particulate accumulation and taxonomic composition of algal turfs. We investigated how particulate mass related to algal turf structure (length and density) and community composition (taxonomic and functional) on two disparate reefs. Particulate mass was positively related to algal turf length. By contrast, the relationship between particulate mass and turf density was more complex and followed a negative parabolic shape; density increased with particulate mass before stabilising and then declining. Community analyses showed taxonomic, but not functional group compositions differed significantly between reefs and with increasing particulate mass. Our results suggest high loads of particulates accumulated in algal turfs are related to a longer, lower density turf structure, typified by filamentous forms such as Cladophora. Changes in algal turf structure and composition could have a variety of bottom-up influences on coral reef ecosystems.
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Affiliation(s)
| | - Sterling B Tebbett
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia; Research Hub for Coral Reef Ecosystem Functions, James Cook University, Townsville, QLD, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
| | - David R Bellwood
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia; Research Hub for Coral Reef Ecosystem Functions, James Cook University, Townsville, QLD, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia; Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Hillary A Smith
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia; Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, NSW, Australia.
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12
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Wyckhuys KAG, Nguyen H, Fonte SJ. Artefactual depiction of predator-prey trophic linkages in global soils. Sci Rep 2021; 11:23861. [PMID: 34903745 PMCID: PMC8668944 DOI: 10.1038/s41598-021-03234-7] [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: 03/31/2021] [Accepted: 11/30/2021] [Indexed: 11/29/2022] Open
Abstract
Soil invertebrates contribute to multiple ecosystem services, including pest control, nutrient cycling, and soil structural regulation, yet trophic interactions that determine their diversity and activity in soils remain critically understudied. Here, we systematically review literature (1966-2020) on feeding habits of soil arthropods and macrofauna and summarize empirically studied predator-prey linkages across ecosystem types, geographies and taxa. Out of 522 unique predators and 372 prey organisms (constituting 1947 predator-prey linkages), the vast majority (> 75%) are only covered in a single study. We report a mean of just 3.0 ± 4.7 documented linkages per organism, with pronounced taxonomic biases. In general, model organisms and crop pests (generally Insecta) are well-studied, while important soil-dwelling predators, fungivores and detritivores (e.g., Collembola, Chilopoda and Malacostraca) remain largely ignored. We argue that broader food-web based research approaches, considering multiple linkages per organism and targeting neglected taxa, are needed to inform science-driven management of soil communities and associated ecosystem services.
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Affiliation(s)
- Kris A G Wyckhuys
- Institute of Plant Protection, China Academy of Agricultural Sciences, Beijing, China
- Fujian Agriculture and Forestry University, Fuzhou, China
- University of Queensland, Brisbane, Australia
- Chrysalis Consulting, Hanoi, Vietnam
| | - Ha Nguyen
- Center for Agricultural Research and Ecological Studies, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Steven J Fonte
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA.
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13
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Jochum M, Barnes AD, Brose U, Gauzens B, Sünnemann M, Amyntas A, Eisenhauer N. For flux's sake: General considerations for energy-flux calculations in ecological communities. Ecol Evol 2021; 11:12948-12969. [PMID: 34646445 PMCID: PMC8495806 DOI: 10.1002/ece3.8060] [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: 02/19/2021] [Revised: 07/26/2021] [Accepted: 07/30/2021] [Indexed: 11/18/2022] Open
Abstract
Global change alters ecological communities with consequences for ecosystem processes. Such processes and functions are a central aspect of ecological research and vital to understanding and mitigating the consequences of global change, but also those of other drivers of change in organism communities. In this context, the concept of energy flux through trophic networks integrates food-web theory and biodiversity-ecosystem functioning theory and connects biodiversity to multitrophic ecosystem functioning. As such, the energy-flux approach is a strikingly effective tool to answer central questions in ecology and global-change research. This might seem straight forward, given that the theoretical background and software to efficiently calculate energy flux are readily available. However, the implementation of such calculations is not always straight forward, especially for those who are new to the topic and not familiar with concepts central to this line of research, such as food-web theory or metabolic theory. To facilitate wider use of energy flux in ecological research, we thus provide a guide to adopting energy-flux calculations for people new to the method, struggling with its implementation, or simply looking for background reading, important resources, and standard solutions to the problems everyone faces when starting to quantify energy fluxes for their community data. First, we introduce energy flux and its use in community and ecosystem ecology. Then, we provide a comprehensive explanation of the single steps towards calculating energy flux for community data. Finally, we discuss remaining challenges and exciting research frontiers for future energy-flux research.
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Affiliation(s)
- Malte Jochum
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of BiologyLeipzig UniversityLeipzigGermany
| | | | - Ulrich Brose
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of BiodiversityUniversity of JenaJenaGermany
| | - Benoit Gauzens
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of BiodiversityUniversity of JenaJenaGermany
| | - Marie Sünnemann
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of BiologyLeipzig UniversityLeipzigGermany
| | - Angelos Amyntas
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of BiodiversityUniversity of JenaJenaGermany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of BiologyLeipzig UniversityLeipzigGermany
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14
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Pozas-Schacre C, Casey JM, Brandl SJ, Kulbicki M, Harmelin-Vivien M, Strona G, Parravicini V. Congruent trophic pathways underpin global coral reef food webs. Proc Natl Acad Sci U S A 2021; 118:e2100966118. [PMID: 34544855 PMCID: PMC8488628 DOI: 10.1073/pnas.2100966118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 11/18/2022] Open
Abstract
Ecological interactions uphold ecosystem structure and functioning. However, as species richness increases, the number of possible interactions rises exponentially. More than 6,000 species of coral reef fishes exist across the world's tropical oceans, resulting in an almost innumerable array of possible trophic interactions. Distilling general patterns in these interactions across different bioregions stands to improve our understanding of the processes that govern coral reef functioning. Here, we show that across bioregions, tropical coral reef food webs exhibit a remarkable congruence in their trophic interactions. Specifically, by compiling and investigating the structure of six coral reef food webs across distinct bioregions, we show that when accounting for consumer size and resource availability, these food webs share more trophic interactions than expected by chance. In addition, coral reef food webs are dominated by dietary specialists, which makes trophic pathways vulnerable to biodiversity loss. Prey partitioning among these specialists is geographically consistent, and this pattern intensifies when weak interactions are disregarded. Our results suggest that energy flows through coral reef communities along broadly comparable trophic pathways. Yet, these critical pathways are maintained by species with narrow, specialized diets, which threatens the existence of coral reef functioning in the face of biodiversity loss.
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Affiliation(s)
- Chloé Pozas-Schacre
- Paris Sciences et Lettres Université Paris: Ecole Pratique des Hautes Etudes-Université de Perpignan Via Domitia-Centre National de la Recherche Scientifique, Unité de Service et de Recherche 3278 Centre de Recherches Insulaires et Observatoire de l'Environnement, Université de Perpignan, 66860 Perpignan, France;
- Laboratoire d'Excellence "CORAIL," 66860 Perpignan, France
| | - Jordan M Casey
- Paris Sciences et Lettres Université Paris: Ecole Pratique des Hautes Etudes-Université de Perpignan Via Domitia-Centre National de la Recherche Scientifique, Unité de Service et de Recherche 3278 Centre de Recherches Insulaires et Observatoire de l'Environnement, Université de Perpignan, 66860 Perpignan, France
- Laboratoire d'Excellence "CORAIL," 66860 Perpignan, France
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX 78373
| | - Simon J Brandl
- Paris Sciences et Lettres Université Paris: Ecole Pratique des Hautes Etudes-Université de Perpignan Via Domitia-Centre National de la Recherche Scientifique, Unité de Service et de Recherche 3278 Centre de Recherches Insulaires et Observatoire de l'Environnement, Université de Perpignan, 66860 Perpignan, France
- Laboratoire d'Excellence "CORAIL," 66860 Perpignan, France
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX 78373
- Fondation pour la Recherche sur la Biodiversité, Centre for the Synthesis and Analysis of Biodiversity, 34000 Montpellier, France
| | - Michel Kulbicki
- Unité Mixte de Recherche Entropie, Labex Corail, Institut de Recherche pour le Développement, Université de Perpignan, 66860 Perpignan, France
| | - Mireille Harmelin-Vivien
- Instititut Méditerranéen d'Océanologie, Unité Mixte 110 Aix-Marseille Université, Centre National de la Recherche Scientifique/Institut National des Sciences de l'Univers, Institut pour la Recherche et le Développement, 13288 Marseille, France
| | - Giovanni Strona
- Department of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Valeriano Parravicini
- Paris Sciences et Lettres Université Paris: Ecole Pratique des Hautes Etudes-Université de Perpignan Via Domitia-Centre National de la Recherche Scientifique, Unité de Service et de Recherche 3278 Centre de Recherches Insulaires et Observatoire de l'Environnement, Université de Perpignan, 66860 Perpignan, France;
- Laboratoire d'Excellence "CORAIL," 66860 Perpignan, France
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15
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Harnessing the Power of Metabarcoding in the Ecological Interpretation of Plant-Pollinator DNA Data: Strategies and Consequences of Filtering Approaches. DIVERSITY 2021. [DOI: 10.3390/d13090437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Although DNA metabarcoding of pollen mixtures has been increasingly used in the field of pollination biology, methodological and interpretation issues arise due to its high sensitivity. Filtering or maintaining false positives, contaminants, and rare taxa or molecular features could lead to different ecological results. Here, we reviewed how this choice has been addressed in 43 studies featuring pollen DNA metabarcoding, which highlighted a very high heterogeneity of filtering methods. We assessed how these strategies shaped pollen assemblage composition, species richness, and interaction networks. To do so, we compared four processing methods: unfiltering, filtering with a proportional 1% of sample reads, a fixed threshold of 100 reads, and the ROC approach (Receiver Operator Characteristic). The results indicated that filtering impacted species composition and reduced species richness, with ROC emerging as a conservative approach. Moreover, in contrast to unfiltered networks, filtering decreased network Connectance and Entropy, and it increased Modularity and Connectivity, indicating that using cut-off thresholds better describes interactions. Overall, unfiltering might compromise reliable ecological interpretations, unless a study targets rare species. We discuss the suitability of each filtering type, plead for justifying filtering strategies on biological or methodological bases and for developing shared approaches to make future studies more comparable.
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16
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Côté IM, Brandl SJ. Functional niches of cleanerfish species are mediated by habitat use, cleaning intensity and client selectivity. J Anim Ecol 2021; 90:2834-2847. [PMID: 34478567 DOI: 10.1111/1365-2656.13585] [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: 09/06/2020] [Accepted: 08/23/2021] [Indexed: 11/28/2022]
Abstract
An animal's functional niche is a complex, multidimensional construct, mediated by an individual's morphology, physiology and behaviour. Behavioural aspects of the niche can be difficult to quantify, as their expression is often subtle and tailored to an infinite number of different situations that involve sophisticated mechanisms such as mutualisms, species dominance or fear effects. The extreme diversity of tropical fish assemblages has led to extensive debate over the extent to which species differ in their resource use and functional role. Ectoparasite removal by cleanerfish species is considered a behaviourally complex interspecific interaction in vertebrates, but differences in the services rendered by various species of cleanerfish, and potential consequences for the range of clients (i.e. resources) they attract, have rarely been examined. Here, we quantify differences among three coexisting species of morphologically similar cleaner wrasses (Labroides bicolor, L. dimidiatus and L. pectoralis) in the global centre of marine biodiversity, the Coral Triangle. We found no clear taxonomic partitioning of clients among cleanerfishes. However, the three cleanerfish species exhibited distinct habitat preferences, and differed in their cleaning intensity: L. bicolor serviced the fewest species and clients, while L. pectoralis serviced the most clients and spent the most time cleaning. Accordingly, L. pectoralis showed no preference for clients based on client size or abundance, while both L. bicolor and L. dimidiatus had a higher likelihood of interacting with clients based on their size (larger client species in L. bicolor, smaller client species in L. dimidiatus) and abundance (more abundant client species for both). Our results suggest that the services rendered by the three species of cleanerfishes differ in their spatial availability, quality and selectivity, thus permitting the coexistence of these species despite their ecological similarity. This, in turn, creates a complex seascape of species-specific cleaning services that underpins crucial biotic interactions in the ocean's most diverse ecosystem.
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Affiliation(s)
- Isabelle M Côté
- Earth to Ocean Group, Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Simon J Brandl
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, Texas, USA
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17
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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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18
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Aubert J, Schbath S, Robin S. Model‐based biclustering for overdispersed count data with application in microbial ecology. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Julie Aubert
- Université Paris‐SaclayAgroParisTechINRAEMIA‐Paris Paris France
| | | | - Stéphane Robin
- Université Paris‐SaclayAgroParisTechINRAEMIA‐Paris Paris France
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19
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van Zinnicq Bergmann MPM, Postaire BD, Gastrich K, Heithaus MR, Hoopes LA, Lyons K, Papastamatiou YP, Schneider EVC, Strickland BA, Talwar BS, Chapman DD, Bakker J. Elucidating shark diets with DNA metabarcoding from cloacal swabs. Mol Ecol Resour 2021; 21:1056-1067. [PMID: 33527665 DOI: 10.1111/1755-0998.13315] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 12/07/2020] [Accepted: 12/18/2020] [Indexed: 12/20/2022]
Abstract
Animal dietary information provides the foundation for understanding trophic relationships, which is essential for ecosystem management. Yet, in marine systems, high-resolution diet reconstruction tools are currently under-developed. This is particularly pertinent for large marine vertebrates, for which direct foraging behaviour is difficult or impossible to observe and, due to their conservation status, the collection of stomach contents at adequate sample sizes is frequently impossible. Consequently, the diets of many groups, such as sharks, have largely remained unresolved. To address this knowledge gap, we applied metabarcoding to prey DNA in faecal residues (fDNA) collected on cotton swabs from the inside of a shark's cloaca. We used a previously published primer set targeting a small section of the 12S rRNA mitochondrial gene to amplify teleost prey species DNA. We tested the utility of this method in a controlled feeding experiment with captive juvenile lemon sharks (Negaprion brevirostris) and on free-ranging juvenile bull sharks (Carcharhinus leucas). In the captive trial, we successfully isolated and correctly identified teleost prey DNA without incurring environmental DNA contamination from the surrounding seawater. In the field, we were able to reconstruct high-resolution teleost dietary information from juvenile C. leucas fDNA that was generally consistent with expectations based on published diet studies of this species. While further investigation is needed to validate the method for larger sharks and other species, it is expected to be broadly applicable to aquatic vertebrates and provides an opportunity to advance our understanding of trophic interactions in marine and freshwater systems.
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Affiliation(s)
- Maurits P M van Zinnicq Bergmann
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA.,Bimini Biological Field Station Foundation, Bimini, The Bahamas
| | - Bautisse D Postaire
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - Kirk Gastrich
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - Michael R Heithaus
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | | | | | - Yannis P Papastamatiou
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - Eric V C Schneider
- Exuma Sound Ecosystem Research Project, Cape Eleuthera Institute, Eleuthera, The Bahamas
| | - Bradley A Strickland
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - Brendan S Talwar
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA.,Exuma Sound Ecosystem Research Project, Cape Eleuthera Institute, Eleuthera, The Bahamas
| | - Demian D Chapman
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - Judith Bakker
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
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20
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Parravicini V, Casey JM, Schiettekatte NMD, Brandl SJ, Pozas-Schacre C, Carlot J, Edgar GJ, Graham NAJ, Harmelin-Vivien M, Kulbicki M, Strona G, Stuart-Smith RD. Delineating reef fish trophic guilds with global gut content data synthesis and phylogeny. PLoS Biol 2020; 18:e3000702. [PMID: 33370276 PMCID: PMC7793298 DOI: 10.1371/journal.pbio.3000702] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 01/08/2021] [Accepted: 12/03/2020] [Indexed: 11/19/2022] Open
Abstract
Understanding species' roles in food webs requires an accurate assessment of their trophic niche. However, it is challenging to delineate potential trophic interactions across an ecosystem, and a paucity of empirical information often leads to inconsistent definitions of trophic guilds based on expert opinion, especially when applied to hyperdiverse ecosystems. Using coral reef fishes as a model group, we show that experts disagree on the assignment of broad trophic guilds for more than 20% of species, which hampers comparability across studies. Here, we propose a quantitative, unbiased, and reproducible approach to define trophic guilds and apply recent advances in machine learning to predict probabilities of pairwise trophic interactions with high accuracy. We synthesize data from community-wide gut content analyses of tropical coral reef fishes worldwide, resulting in diet information from 13,961 individuals belonging to 615 reef fish. We then use network analysis to identify 8 trophic guilds and Bayesian phylogenetic modeling to show that trophic guilds can be predicted based on phylogeny and maximum body size. Finally, we use machine learning to test whether pairwise trophic interactions can be predicted with accuracy. Our models achieved a misclassification error of less than 5%, indicating that our approach results in a quantitative and reproducible trophic categorization scheme, as well as high-resolution probabilities of trophic interactions. By applying our framework to the most diverse vertebrate consumer group, we show that it can be applied to other organismal groups to advance reproducibility in trait-based ecology. Our work thus provides a viable approach to account for the complexity of predator-prey interactions in highly diverse ecosystems.
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Affiliation(s)
- Valeriano Parravicini
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
- Laboratoire d’Excellence “CORAIL,” Perpignan, France
| | - Jordan M. Casey
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
- Laboratoire d’Excellence “CORAIL,” Perpignan, France
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, Texas, United States of America
| | - Nina M. D. Schiettekatte
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
- Laboratoire d’Excellence “CORAIL,” Perpignan, France
| | - Simon J. Brandl
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
- Laboratoire d’Excellence “CORAIL,” Perpignan, France
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, Texas, United States of America
- Centre for the Synthesis and Analysis of Biodiversity (CESAB), Institut Bouisson Bertrand, Montpellier, France
| | - Chloé Pozas-Schacre
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
- Laboratoire d’Excellence “CORAIL,” Perpignan, France
| | - Jérémy Carlot
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
- Laboratoire d’Excellence “CORAIL,” Perpignan, France
| | - Graham J. Edgar
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | | | | | - Michel Kulbicki
- UMR Entropie, LabEx Corail, IRD, Université de Perpignan, Perpignan, France
| | - Giovanni Strona
- University of Helsinki, Department of Bioscience, Helsinki, Finland
| | - Rick D. Stuart-Smith
- Centre for the Synthesis and Analysis of Biodiversity (CESAB), Institut Bouisson Bertrand, Montpellier, France
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21
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Compson ZG, McClenaghan B, Singer GAC, Fahner NA, Hajibabaei M. Metabarcoding From Microbes to Mammals: Comprehensive Bioassessment on a Global Scale. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.581835] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Global biodiversity loss is unprecedented, and threats to existing biodiversity are growing. Given pervasive global change, a major challenge facing resource managers is a lack of scalable tools to rapidly and consistently measure Earth's biodiversity. Environmental genomic tools provide some hope in the face of this crisis, and DNA metabarcoding, in particular, is a powerful approach for biodiversity assessment at large spatial scales. However, metabarcoding studies are variable in their taxonomic, temporal, or spatial scope, investigating individual species, specific taxonomic groups, or targeted communities at local or regional scales. With the advent of modern, ultra-high throughput sequencing platforms, conducting deep sequencing metabarcoding surveys with multiple DNA markers will enhance the breadth of biodiversity coverage, enabling comprehensive, rapid bioassessment of all the organisms in a sample. Here, we report on a systematic literature review of 1,563 articles published about DNA metabarcoding and summarize how this approach is rapidly revolutionizing global bioassessment efforts. Specifically, we quantify the stakeholders using DNA metabarcoding, the dominant applications of this technology, and the taxonomic groups assessed in these studies. We show that while DNA metabarcoding has reached global coverage, few studies deliver on its promise of near-comprehensive biodiversity assessment. We then outline how DNA metabarcoding can help us move toward real-time, global bioassessment, illustrating how different stakeholders could benefit from DNA metabarcoding. Next, we address barriers to widespread adoption of DNA metabarcoding, highlighting the need for standardized sampling protocols, experts and computational resources to handle the deluge of genomic data, and standardized, open-source bioinformatic pipelines. Finally, we explore how technological and scientific advances will realize the promise of total biodiversity assessment in a sample—from microbes to mammals—and unlock the rich information genomics exposes, opening new possibilities for merging whole-system DNA metabarcoding with (1) abundance and biomass quantification, (2) advanced modeling, such as species occupancy models, to improve species detection, (3) population genetics, (4) phylogenetics, and (5) food web and functional gene analysis. While many challenges need to be addressed to facilitate widespread adoption of environmental genomic approaches, concurrent scientific and technological advances will usher in methods to supplement existing bioassessment tools reliant on morphological and abiotic data. This expanded toolbox will help ensure that the best tool is used for the job and enable exciting integrative techniques that capitalize on multiple tools. Collectively, these new approaches will aid in addressing the global biodiversity crisis we now face.
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22
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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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23
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Bachiller E, Albo-Puigserver M, Giménez J, Pennino MG, Marí-Mena N, Esteban A, Lloret-Lloret E, Jadaud A, Carro B, Bellido JM, Coll M. A trophic latitudinal gradient revealed in anchovy and sardine from the Western Mediterranean Sea using a multi-proxy approach. Sci Rep 2020; 10:17598. [PMID: 33077761 PMCID: PMC7572414 DOI: 10.1038/s41598-020-74602-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 10/05/2020] [Indexed: 12/21/2022] Open
Abstract
This work combines state-of-the-art methods (DNA metabarcoding) with classic approaches (visual stomach content characterization and stable isotope analyses of nitrogen (δ15N) and carbon (δ13C)) to investigate the trophic ecology of anchovy (Engraulis encrasicolus) and sardine (Sardina pilchardus) at high taxonomic and spatial resolution in the Western Mediterranean Sea. Gut contents observed are in accordance with the dietary plasticity generally described for anchovy and sardine, suggesting a diet related to the opportunistic ingestion of available prey in a certain area and/or time. Genetic tools also showed modest inter-specific differences regarding ingested species. However, inter-specific and intra-specific differences in ingested prey frequencies and prey biomass reflected a latitudinal signal that could indicate a more effective predation on large prey like krill by anchovy versus sardine, as well as a generalized higher large prey ingestion by both species southwards. In fact, both species presented lower δ15N in the northernmost area. This latitudinal gradient indicates changes in the trophic ecology of anchovy and sardine that coincide with previously described better biological conditions for fish in the southern part of the study area as well as higher landings of both species in recent years.
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Affiliation(s)
- Eneko Bachiller
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain. .,AZTI, Sustainable Fisheries Management (Data), Basque Research and Technology Alliance (BRTA), Txatxarramendi uhartea z/g, 48395, Sukarrieta, Bizkaia (Basque Country), Spain.
| | - Marta Albo-Puigserver
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Joan Giménez
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Maria Grazia Pennino
- Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, Subida Radio Faro, 50, 36390, Vigo, Spain
| | - Neus Marí-Mena
- AllGenetics and Biology SL, Edificio CICA, Campus de Elviña, 15008, A Coruña, Spain
| | - Antonio Esteban
- Instituto Español de Oceanografía, Centro Oceanográfico de Murcia, Varadero 1 Apdo 22, 30740, San Pedro del Pinatar, Murcia, Spain
| | - Elena Lloret-Lloret
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Angelique Jadaud
- Marine Biodiversity, Exploitation and Conservation (MARBEC), Ifremer, University Montpellier, CNRS, IRD, Sète, France
| | - Belén Carro
- AllGenetics and Biology SL, Edificio CICA, Campus de Elviña, 15008, A Coruña, Spain
| | - José María Bellido
- Instituto Español de Oceanografía, Centro Oceanográfico de Murcia, Varadero 1 Apdo 22, 30740, San Pedro del Pinatar, Murcia, Spain
| | - Marta Coll
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
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24
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Uiterwaal SF, DeLong JP. Using patterns in prey DNA digestion rates to quantify predator diets. Mol Ecol Resour 2020; 20:1723-1732. [PMID: 32688451 DOI: 10.1111/1755-0998.13231] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/01/2020] [Accepted: 07/10/2020] [Indexed: 11/26/2022]
Abstract
Dietary metabarcoding-the process of taxonomic identification of food species from DNA in consumer guts or faeces-has been rapidly adopted by ecologists to gain insights into biocontrol, invasive species and the structure of food webs. However, an outstanding issue with metabarcoding is the semi-quantitative nature of the data it provides: because metabarcoding is likely to produce false negatives for some prey more often than for other prey, we cannot infer relative frequencies of prey in the diet. To correct for this, we can adjust detected prey frequencies using DNA detectability half-lives unique to each predator-prey combination. Because the feeding experiments required to deduce these half-lives are time- and resource-intensive, our ability to weight the frequency of observations using their detectability has thus far been limited to systems with just a few prey. Here, we present a meta-analysis of 24 spider prey DNA half-lives and show that these half-lives are predictable given predator and prey mass, predator family, digestion temperature and DNA amplicon length. We further provide a new technique for weighting observations with half-lives, which allows not just for the ranking of prey in the diet, but reveals the proportion of the diet each prey comprises. Lastly, we apply this method to published dietary metabarcoding data to calculate half-lives and proportion of the predator's diet for 35 prey families, demonstrating that this technique can generate improved understanding of diets in real, diverse systems.
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Affiliation(s)
- Stella F Uiterwaal
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - John P DeLong
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
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25
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Brandl SJ, Johansen JL, Casey JM, Tornabene L, Morais RA, Burt JA. Extreme environmental conditions reduce coral reef fish biodiversity and productivity. Nat Commun 2020; 11:3832. [PMID: 32737315 PMCID: PMC7395083 DOI: 10.1038/s41467-020-17731-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/10/2020] [Indexed: 12/11/2022] Open
Abstract
Tropical ectotherms are hypothesized to be vulnerable to environmental changes, but cascading effects of organismal tolerances on the assembly and functioning of reef fish communities are largely unknown. Here, we examine differences in organismal traits, assemblage structure, and productivity of cryptobenthic reef fishes between the world’s hottest, most extreme coral reefs in the southern Arabian Gulf and the nearby, but more environmentally benign, Gulf of Oman. We show that assemblages in the Arabian Gulf are half as diverse and less than 25% as abundant as in the Gulf of Oman, despite comparable benthic composition and live coral cover. This pattern appears to be driven by energetic deficiencies caused by responses to environmental extremes and distinct prey resource availability rather than absolute thermal tolerances. As a consequence, production, transfer, and replenishment of biomass through cryptobenthic fish assemblages is greatly reduced on Earth’s hottest coral reefs. Extreme environmental conditions, as predicted for the end of the 21st century, could thus disrupt the community structure and productivity of a critical functional group, independent of live coral loss. Brandl, Johansen et al. compare organismal traits, community structure, and productivity dynamics of cryptobenthic reef fishes across two locations, the Arabian Gulf and the Gulf of Oman, the former of which harbors the world’s hottest coral reefs. They show that environmental extremes in the Arabian Gulf result in dramatically less diverse, abundant, and productive cryptobenthic fish assemblages, which could foreshadow the future of coral reef biodiversity and functioning.
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Affiliation(s)
- Simon J Brandl
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada. .,CESAB-FRB, 5 Rue de l'École de Médecine, 34000, Montpellier, France. .,PSL Université Paris: CNRS-EPHE-UPVD USR3278 CRIOBE, Université de Perpignan, Perpignan, France. .,Laboratoire d'Excellence "CORAIL,", Perpignan, France.
| | - Jacob L Johansen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Manoa, Kane'ohe, HI, USA. .,Marine Biology Laboratory, Centre for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
| | - Jordan M Casey
- PSL Université Paris: CNRS-EPHE-UPVD USR3278 CRIOBE, Université de Perpignan, Perpignan, France.,Laboratoire d'Excellence "CORAIL,", Perpignan, France
| | - Luke Tornabene
- School of Aquatic and Fishery Sciences and the Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
| | - Renato A Morais
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia.,College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - John A Burt
- Marine Biology Laboratory, Centre for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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26
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Schiettekatte NMD, Barneche DR, Villéger S, Allgeier JE, Burkepile DE, Brandl SJ, Casey JM, Mercière A, Munsterman KS, Morat F, Parravicini V. Nutrient limitation, bioenergetics and stoichiometry: A new model to predict elemental fluxes mediated by fishes. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13618] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Nina M. D. Schiettekatte
- PSL Université Paris: EPHE‐UPVD‐CNRS USR 3278 CRIOBE Université de Perpignan Perpignan France
- Laboratoire d'Excellence “CORAIL” Perpignan France
| | - Diego R. Barneche
- Australian Institute of Marine Science Crawley WA Australia
- Oceans InstituteThe University of Western Australia Crawley WA Australia
- College of Life and Environmental Sciences University of Exeter Penryn UK
| | | | - Jacob E. Allgeier
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI USA
| | - Deron E. Burkepile
- Department of Ecology, Evolution, and Marine Biology University of California Santa Barbara CA USA
- Marine Science Institute University of California Santa Barbara CA USA
| | - Simon J. Brandl
- Department of Biological Sciences Simon Fraser University Burnaby BC Canada
| | - Jordan M. Casey
- PSL Université Paris: EPHE‐UPVD‐CNRS USR 3278 CRIOBE Université de Perpignan Perpignan France
- Laboratoire d'Excellence “CORAIL” Perpignan France
| | - Alexandre Mercière
- PSL Université Paris: EPHE‐UPVD‐CNRS USR 3278 CRIOBE Université de Perpignan Perpignan France
- Laboratoire d'Excellence “CORAIL” Perpignan France
| | - Katrina S. Munsterman
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI USA
| | - Fabien Morat
- PSL Université Paris: EPHE‐UPVD‐CNRS USR 3278 CRIOBE Université de Perpignan Perpignan France
- Laboratoire d'Excellence “CORAIL” Perpignan France
| | - Valeriano Parravicini
- PSL Université Paris: EPHE‐UPVD‐CNRS USR 3278 CRIOBE Université de Perpignan Perpignan France
- Laboratoire d'Excellence “CORAIL” Perpignan France
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27
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French BJ, Lim YW, Zgliczynski BJ, Edwards RA, Rohwer F, Sandin SA. Decoding diversity in a coral reef fish species complex with restricted range using metagenomic sequencing of gut contents. Ecol Evol 2020; 10:3413-3423. [PMID: 32273998 PMCID: PMC7141070 DOI: 10.1002/ece3.6138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/22/2020] [Accepted: 02/03/2020] [Indexed: 12/21/2022] Open
Abstract
AIM Identification of the processes that generate and maintain species diversity within the same region can provide insight into biogeographic patterns at broader spatiotemporal scales. Hawkfishes in the genus Paracirrhites are a unique taxon to explore with respect to niche differentiation, exhibiting diagnostic differences in coloration, and an apparent center of distribution outside of the Indo-Malay-Philippine (IMP) biodiversity hotspot for coral reef fishes. Our aim is to use next-generation sequencing methods to leverage samples of a taxon at their center of maximum diversity to explore phylogenetic relationships and a possible mechanism of coexistence. LOCATION Flint Island, Southern Line Islands, Republic of Kiribati. METHODS A comprehensive review of museum records, the primary literature, and unpublished field survey records was undertaken to determine ranges for four "arc-eye" hawkfish species in the Paracirrhites species complex and a potential hybrid. Fish from four Paracirrhites species were collected from Flint Island in the Southern Line Islands, Republic of Kiribati. Hindgut contents were sequenced, and subsequent metagenomic analyses were used to assess the phylogenetic relatedness of the host fish, the microbiome community structure, and prey remains for each species. RESULTS Phylogenetic analyses conducted with recovered mitochondrial genomes revealed clustering of P. bicolor with P. arcatus and P. xanthus with P. nisus, which were unexpected on the basis of previous morphological work in this species complex. Differences in taxonomic composition of gut microbial communities and presumed prey remains indicate likely separation of foraging niches. MAIN CONCLUSIONS Our findings point toward previously unidentified relationships in this cryptic species complex at its proposed center of distribution. The three species endemic to the Polynesian province (P. nisus, P. xanthus, and P. bicolor) cluster separately from the more broadly distributed P. arcatus on the basis of relative abundance of metazoan sequences in the gut (presumed prey remains). Discordance between gut microbial communities and phylogeny of the host fish further reinforce the hypothesis of niche separation.
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Affiliation(s)
- Beverly J. French
- Center for Marine Biodiversity and ConservationScripps Institution of OceanographyUniversity of CaliforniaSan DiegoCAUSA
| | - Yan Wei Lim
- Department of BiologySan Diego State UniversitySan DiegoCAUSA
| | - Brian J. Zgliczynski
- Center for Marine Biodiversity and ConservationScripps Institution of OceanographyUniversity of CaliforniaSan DiegoCAUSA
| | - Robert A. Edwards
- Department of BiologySan Diego State UniversitySan DiegoCAUSA
- Department of Computer ScienceSan Diego State UniversitySan DiegoCAUSA
| | - Forest Rohwer
- Department of BiologySan Diego State UniversitySan DiegoCAUSA
| | - Stuart A. Sandin
- Center for Marine Biodiversity and ConservationScripps Institution of OceanographyUniversity of CaliforniaSan DiegoCAUSA
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28
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Takahashi M, DiBattista JD, Jarman S, Newman SJ, Wakefield CB, Harvey ES, Bunce M. Partitioning of diet between species and life history stages of sympatric and cryptic snappers (Lutjanidae) based on DNA metabarcoding. Sci Rep 2020; 10:4319. [PMID: 32152406 PMCID: PMC7062689 DOI: 10.1038/s41598-020-60779-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/17/2020] [Indexed: 01/23/2023] Open
Abstract
Lutjanus erythropterus and L. malabaricus are sympatric, sister taxa that are important to fisheries throughout the Indo-Pacific. Their juveniles are morphologically indistinguishable (i.e. cryptic). A DNA metabarcoding dietary study was undertaken to assess the diet composition and partitioning between the juvenile and adult life history stages of these two lutjanids. Major prey taxa were comprised of teleosts and crustaceans for all groups except adult L. erythropterus, which instead consumed soft bodied invertebrates (e.g. tunicates, comb jellies and medusae) as well as teleosts, with crustaceans being notably absent. Diet composition was significantly different among life history stages and species, which may be associated with niche habitat partitioning or differences in mouth morphology within adult life stages. This study provides the first evidence of diet partitioning between cryptic juveniles of overlapping lutjanid species, thus providing new insights into the ecological interactions, habitat associations, and the specialised adaptations required for the coexistence of closely related species. This study has improved our understanding of the differential contributions of the juvenile and adult diets of these sympatric species within food webs. The diet partitioning reported in this study was only revealed by the taxonomic resolution provided by the DNA metabarcoding approach and highlights the potential utility of this method to refine the dietary components of reef fishes more generally.
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Affiliation(s)
- Miwa Takahashi
- School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia.
| | - Joseph D DiBattista
- School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia.,Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW, 2010, Australia
| | - Simon Jarman
- School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia.,School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Stephen J Newman
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, P.O. Box 20, North Beach, WA, 6920, Australia
| | - Corey B Wakefield
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, P.O. Box 20, North Beach, WA, 6920, Australia
| | - Euan S Harvey
- School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia
| | - Michael Bunce
- School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia.,Environmental Protection Authority, 215 Lambton Quay, Wellington, 6011, New Zealand
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