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An S, Wang L, Wang L. MINM: Marine intelligent netting monitoring using multi-scattering model and multi-space transformation. ISA TRANSACTIONS 2024; 150:278-297. [PMID: 38782640 DOI: 10.1016/j.isatra.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 03/28/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
Marine intelligent net tank aquaculture monitoring plays an important role in improving aquaculture efficiency, environmental monitoring efficiency, and environmental safety. The underwater environment has complex light, often with problems such as scattering and absorption, resulting in poor image quality, making it difficult to accurately analyze and judge the aquaculture environment. Improving marine intelligent net tank aquaculture monitoring has the following three advantages: 1) better observation and monitoring of the aquaculture process, timely detection of problems and abnormalities, to protect the benefits of aquaculture and product quality. 2) more convenient and rapid monitoring of the aquaculture environment, improving monitoring efficiency and reducing monitoring costs. 3) effective monitoring of the underwater environment around the farm, and timely detection of foreign pollution, harmful substances, and other problems, to protect the safety of the aquaculture environment. Therefore, in order to solve the two degradation problems of scattering and absorption in the process of marine smart net farm monitoring, we propose a marine smart net farm monitoring method using multiple scattering models and multiple spatial transformations, called MINM. Specifically, inspired by the image chromatic aberration correction method, we design a color correction method in the multicolor space, which is implemented by using the Lab and RGB color space by performing contrast-constrained adaptive histogram equalization and gray world assumptions, respectively, to correct color shifts in different color models. Based on this, we propose a de-scattering method using a multi-scattering model, which eliminates the effect of scattering on underwater imaging by embedding a complete multi-scattering underwater imaging model to guide the extraction of different features in the multi-scattering model. To obtain more qualified results, we also propose an efficient perceptual fusion to mix the output of the de-scattering and color correction. Thus, our method can take advantage of multiple scattering models and multiple spatial transformations to effectively improve the visual quality of underwater images, producing enhanced results that fit the complete underwater imaging model and have bio-visual characteristics. In extensive experimental demonstrations, our MINM method has shown higher performance than the state-of-the-art methods in terms of both visual quality and quantitative metrics. All experimental results and datasets in this paper are available from the following website: https://github.com/An-Shunmin/MINM.
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Affiliation(s)
- Shunmin An
- Shanghai Research Institute for Intelligent Autonomous Systems, Tongji University, Shanghai, China.
| | - Linling Wang
- Shanghai Engineering Research Center of Intelligent Maritime Search & Rescue and Underwater Vehicles, Shanghai Maritime University, Shanghai, China
| | - Le Wang
- Institute of Logistics Science and Engineering, Shanghai Maritime University, Shanghai, China
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2
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Parikh A, Pansu J, Stow A, Warne MSJ, Chivas C, Greenfield P, Boyer F, Simpson S, Smith R, Gruythuysen J, Carlin G, Caulfield N, Viard F, Chariton AA. Environmental DNA highlights the influence of salinity and agricultural run-off on coastal fish assemblages in the Great Barrier Reef region. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 349:123954. [PMID: 38604307 DOI: 10.1016/j.envpol.2024.123954] [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: 10/03/2023] [Revised: 03/14/2024] [Accepted: 04/09/2024] [Indexed: 04/13/2024]
Abstract
Agricultural run-off in Australia's Mackay-Whitsunday region is a major source of nutrient and pesticide pollution to coastal and inshore ecosystems of the Great Barrier Reef. While the effects of run-off are well documented for the region's coral and seagrass habitats, the ecological impacts on estuaries, the direct recipients of run-off, are less known. This is particularly true for fish communities, which are shaped by the physico-chemical properties of coastal waterways that vary greatly in tropical regions. To address this knowledge gap, we used environmental DNA (eDNA) metabarcoding to examine fish assemblages at four locations (three estuaries and a harbour) subjected to varying levels of agricultural run-off during a wet and dry season. Pesticide and nutrient concentrations were markedly elevated during the sampled wet season with the influx of freshwater and agricultural run-off. Fish taxa richness significantly decreased in all three estuaries (F = 164.73, P = <0.001), along with pronounced changes in community composition (F = 46.68, P = 0.001) associated with environmental variables (largely salinity: 27.48% contribution to total variance). In contrast, the nearby Mackay Harbour exhibited a far more stable community structure, with no marked changes in fish assemblages observed between the sampled seasons. Among the four sampled locations, variation in fish community composition was more pronounced within the wet season (F = 2.5, P = 0.001). Notably, variation in the wet season was significantly correlated with agricultural contaminants (phosphorus: 6.25%, pesticides: 5.22%) alongside environmental variables (salinity: 5.61%, DOC: 5.57%). Historically contaminated and relatively unimpacted estuaries each demonstrated distinct fish communities, reflecting their associated catchment use. Our findings emphasise that while seasonal effects play a key role in shaping the community structure of fish in this region, agricultural contaminants are also important contributors in estuarine systems.
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Affiliation(s)
- Aashi Parikh
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia.
| | - Johan Pansu
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia; CSIRO Environment, Lucas Heights, NSW, 2234, Australia; ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, 34095, France; Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France.
| | - Adam Stow
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia.
| | - Michael St J Warne
- Reef Catchments Science Partnership, Mackay, QLD, 4740, Australia; School of Earth and Environmental Sciences, University of Queensland, QLD, 4067, Australia; Centre for Agroecology, Water and Resilience, Coventry University, West Midlands, United Kingdom; Queensland Department of Environment and Science, Brisbane, QLD, 4179, Australia.
| | - Christine Chivas
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia.
| | - Paul Greenfield
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia; CSIRO Energy, Lindfield, NSW, 2070, Australia.
| | - Frédéric Boyer
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, 38000, France.
| | | | - Rachael Smith
- Office of the Great Barrier Reef, Queensland Department of Environment and Science, Brisbane, QLD, 4179, Australia.
| | - Jacob Gruythuysen
- Science Division, Queensland Department of Environment and Science, Brisbane, QLD, 4179, Australia.
| | - Geoffrey Carlin
- CSIRO Environment, Dutton Park, Queensland, 4102, Australia.
| | - Natalie Caulfield
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia.
| | - Frédérique Viard
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, 34095, France.
| | - Anthony A Chariton
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia.
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3
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Baptista J, van der Linden P, Martinho F, Martins R, Carneiro M, Bento EG, Pardal MÂ. The functional composition of nearshore fish communities demonstrated by trait analysis: Response to environmental gradients. MARINE POLLUTION BULLETIN 2021; 169:112562. [PMID: 34091252 DOI: 10.1016/j.marpolbul.2021.112562] [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: 02/01/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 06/12/2023]
Abstract
There is limited understanding on nearshore fish community functioning in relation to changing environmental gradients. To address this, we investigated the trait composition of fish communities in five regions along the Portuguese coast during 4 years. Northern regions were characterized by higher Chlorophyll-α and small-sized species with short lifespans. The southernmost region was characterized by warmer waters, more intense upwelling events and typical warm-water species. Higher species richness and functional redundancy at the southernmost region suggested that in case of potential species loss, community functioning would be less affected in this region, and thus, a certain level of community resilience is maintained. The central region presented lower functional redundancy and high functional richness, which indicated the presence of rare species with rare traits, suggesting a more vulnerable community. This information on the nearshore fish community distribution may be particularly important towards managing coastal ecosystems in response to changing environmental conditions.
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Affiliation(s)
- Joana Baptista
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal.
| | - Pieter van der Linden
- Department of Biology, Faculty of Sciences, University of Porto, 4150-181 Porto, Portugal; Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), 4450-208 Matosinhos, Portugal
| | - Filipe Martinho
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Rogélia Martins
- Instituto Português do Mar e da Atmosfera (IPMA), Departamento do Mar e de Recursos Marinhos (DMRM), Divisão de Modelação e Gestão de Recursos da Pesca (DivRP), 1440-006 Lisboa, Portugal
| | - Miguel Carneiro
- Instituto Português do Mar e da Atmosfera (IPMA), Departamento do Mar e de Recursos Marinhos (DMRM), Divisão de Modelação e Gestão de Recursos da Pesca (DivRP), 1440-006 Lisboa, Portugal
| | - Eduardo G Bento
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Miguel Ângelo Pardal
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
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4
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Eger AM, Best RJ, Baum JK. Dominance determines fish community biomass in a temperate seagrass ecosystem. Ecol Evol 2021; 11:10489-10501. [PMID: 34367591 PMCID: PMC8328455 DOI: 10.1002/ece3.7854] [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: 10/01/2020] [Revised: 05/31/2021] [Accepted: 06/10/2021] [Indexed: 11/07/2022] Open
Abstract
Biodiversity and ecosystem function are often correlated, but there are multiple hypotheses about the mechanisms underlying this relationship. Ecosystem functions such as primary or secondary production may be maximized by species richness, evenness in species abundances, or the presence or dominance of species with certain traits. Here, we combine surveys of natural fish communities (conducted in July and August 2016) with morphological trait data to examine relationships between biodiversity and ecosystem function (quantified as fish community biomass) across 14 subtidal eelgrass meadows in the Northeast Pacific (54°N, 130°W). We employ both taxonomic and functional trait measures of diversity to investigate whether ecosystem function is best predicted by species diversity (complementarity hypothesis) or by the presence or dominance of species with particular trait values (selection or dominance hypotheses). After controlling for environmental variation, we find that fish community biomass is maximized when taxonomic richness and functional evenness are low, and in communities dominated by species with particular trait values, specifically those associated with benthic habitats and prey capture. While previous work on fish communities has found that species richness is often positively correlated with ecosystem function, our results instead highlight the capacity for regionally prevalent and locally dominant species to drive ecosystem function in moderately diverse communities. We discuss these alternate links between community composition and ecosystem function and consider their divergent implications for ecosystem valuation and conservation prioritization.
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Affiliation(s)
- Aaron M. Eger
- Department of BiologyUniversity of VictoriaVictoriaBCCanada
- Present address:
School of Biological, Earth, and Environmental SciencesUniversity of New South WalesSydneyNSWAustralia
| | - Rebecca J. Best
- School of Earth and SustainabilityNorthern Arizona UniversityFlagstaffAZUSA
| | - Julia K. Baum
- Department of BiologyUniversity of VictoriaVictoriaBCCanada
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5
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Osathanunkul M, Minamoto T. Molecular detection of giant snakeheads, Channa micropeltes (Cuvier, 1831), one of the most troublesome fish species. Sci Rep 2021; 11:9943. [PMID: 33976284 PMCID: PMC8113229 DOI: 10.1038/s41598-021-89320-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/01/2021] [Indexed: 11/16/2022] Open
Abstract
A lack of reliable tools for determining the presence and distribution of fish species can impede understanding of predator–prey interactions and fishery management. Conventional fish survey methods are invasive, and can be size or species selective. Combining netting and electrofishing is a current method used to monitor fish species in Phayao Lake (Kwan Phayao), Thailand. However, the methods are inefficient and time-consuming. Recently, locals who rely on inland fisheries in Kwan Phayao expressed their deep concerns about the giant snakehead, Channa micropeltes (Cuvier, 1831) destroying other fish there. The giant snakehead prey on many commercially important fish species, as the prey species is reduced, negative effects on both biodiversity and the fishery sector could follow. Here, an eDNA-based survey was developed to detect the presence of the giant snakehead. Water samples were collected from six sites within Kwan Phayao and 17 sites in Ing River where water flowed into and out of Kwan Payao. The eDNA of the giant snakehead was detected in water samples from all collection sites using the developed qPCR assay with various concentrations. The eDNA was shown here to be a sensitive and reliable tool for fish surveillance so there will be a better chance for developing an effective management strategy.
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Affiliation(s)
- Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand. .,Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand.
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, Hyogo, Japan
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Murphy GE, Dunic JC, Adamczyk EM, Bittick SJ, Côté IM, Cristiani J, Geissinger EA, Gregory RS, Lotze HK, O’Connor MI, Araújo CA, Rubidge EM, Templeman ND, Wong MC. From coast to coast to coast: ecology and management of seagrass ecosystems across Canada. Facets (Ott) 2021. [DOI: 10.1139/facets-2020-0020] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Seagrass meadows are among the most productive and diverse marine ecosystems, providing essential structure, functions, and services. They are also among the most impacted by human activities and in urgent need of better management and protection. In Canada, eelgrass ( Zostera marina) meadows are found along the Atlantic, Pacific, and Arctic coasts, and thus occur across a wide range of biogeographic conditions. Here, we synthesize knowledge of eelgrass ecosystems across Canada’s coasts, highlighting commonalities and differences in environmental conditions, plant, habitat, and community structure, as well as current trends and human impacts. Across regions, eelgrass life history, phenology, and general species assemblages are similar. However, distinct regional differences occur in environmental conditions, particularly with water temperature and nutrient availability. There is considerable variation in the types and strengths of human activities among regions. The impacts of coastal development are prevalent in all regions, while other impacts are of concern for specific regions, e.g., nutrient loading in the Atlantic and impacts from the logging industry in the Pacific. In addition, climate change represents a growing threat to eelgrass meadows. We review current management and conservation efforts and discuss the implications of observed differences from coast to coast to coast.
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Affiliation(s)
- Grace E.P. Murphy
- Department of Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
| | - Jillian C. Dunic
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Emily M. Adamczyk
- Department of Zoology, Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sarah J. Bittick
- Department of Zoology, Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Isabelle M. Côté
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - John Cristiani
- Department of Zoology, Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | | | - Robert S. Gregory
- Department of Biology, Memorial University, St. John’s, NL A1C 5S7, Canada
- Fisheries and Oceans Canada, St. John’s, NL A1A 5J7, Canada
| | - Heike K. Lotze
- Department of Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Mary I. O’Connor
- Department of Zoology, Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Carlos A.S. Araújo
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, Rimouski, QC G5L 3A1, Canada
| | - Emily M. Rubidge
- Institute of Ocean Sciences, Fisheries and Oceans Canada, Sidney, BC V8L 4B2, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | | | - Melisa C. Wong
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
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7
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Hanson JM. Diet of Striped Bass in the Southern Gulf of St. Lawrence (Canada) with Emphasis on the Spring Spawning Aggregation. Northeast Nat (Steuben) 2020. [DOI: 10.1656/045.027.0301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- John Mark Hanson
- Science Branch, Gulf Fisheries Centre, PO Box 5030, Moncton, NB, E1C 9B6, Canada;
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8
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Holubová M, Blabolil P, Čech M, Vašek M, Peterka J. Species-specific schooling behaviour of fish in the freshwater pelagic habitat: an observational study. JOURNAL OF FISH BIOLOGY 2020; 97:64-74. [PMID: 32189344 DOI: 10.1111/jfb.14326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 03/12/2020] [Accepted: 03/17/2020] [Indexed: 06/10/2023]
Abstract
Social living of animals is a broadly occurring phenomenon, although poorly studied in freshwater systems, fish schooling behaviour is an excellent example. The composition of fish schools, species-specific schooling tendencies and preferences of adult fish were studied in the pelagic habitat of the Římov Reservoir, Czech Republic. Video recordings captured over a total of 34 days (16 h per day) in the clear water period of three seasons were analysed. From four species identified as school-forming species - bream, bleak, roach and perch, 40% of the individuals observed formed schools of 3-36 individuals. Although conspecific schools prevailed, 20% of individuals formed heterospecific schools, except bleak that schooled strictly with conspecifics. Schools were composed of individuals of similar body size and life strategy. Heterospecific schools were significantly larger than conspecific schools and showed uneven proportion among species, that is, one species being more abundant when the school dimension increased. Probability of encounter in bleak was lowest and proved highest inclination for schooling. Gregarianism levels depended on species morphology and body size, with larger and morphologically advanced fish tending less to sociability. This indicates that the antipredator function of schooling behaviour is intensified with increasing vulnerability of the species.
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Affiliation(s)
- Michaela Holubová
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Petr Blabolil
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Martin Čech
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Mojmír Vašek
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jiří Peterka
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
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9
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Jeunen GJ, Knapp M, Spencer HG, Lamare MD, Taylor HR, Stat M, Bunce M, Gemmell NJ. Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement. Mol Ecol Resour 2019; 19:426-438. [PMID: 30576077 DOI: 10.1111/1755-0998.12982] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 10/27/2018] [Accepted: 11/19/2018] [Indexed: 11/30/2022]
Abstract
While in recent years environmental DNA (eDNA) metabarcoding surveys have shown great promise as an alternative monitoring method, the integration into existing marine monitoring programs may be confounded by the dispersal of the eDNA signal. Currents and tidal influences could transport eDNA over great distances, inducing false-positive species detection, leading to inaccurate biodiversity assessments and, ultimately, mismanagement of marine environments. In this study, we determined the ability of eDNA metabarcoding surveys to distinguish localized signals obtained from four marine habitats within a small spatial scale (<5 km) subject to significant tidal and along-shore water flow. Our eDNA metabarcoding survey detected 86 genera, within 77 families and across 11 phyla using three established metabarcoding assays targeting fish (16S rRNA gene), crustacean (16S rRNA gene) and eukaryotic (cytochrome oxidase subunit 1) diversity. Ordination and cluster analyses for both taxonomic and OTU data sets show distinct eDNA signals between the sampled habitats, suggesting dispersal of eDNA among habitats was limited. Individual taxa with strong habitat preferences displayed localized eDNA signals in accordance with their respective habitat, whereas taxa known to be less habitat-specific generated more ubiquitous signals. Our data add to evidence that eDNA metabarcoding surveys in marine environments detect a broad range of taxa that are spatially discrete. Our work also highlights that refinement of assay choice is essential to realize the full potential of eDNA metabarcoding surveys in marine biodiversity monitoring programs.
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Affiliation(s)
- Gert-Jan Jeunen
- Department of Anatomy, University of Otago, Dunedin, New Zealand.,Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Hamish G Spencer
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Miles D Lamare
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - Helen R Taylor
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Michael Stat
- Trace and Environmental DNA (TrEnD) laboratory, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia.,Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) laboratory, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
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10
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Jeunen G, Knapp M, Spencer HG, Taylor HR, Lamare MD, Stat M, Bunce M, Gemmell NJ. Species-level biodiversity assessment using marine environmental DNA metabarcoding requires protocol optimization and standardization. Ecol Evol 2019; 9:1323-1335. [PMID: 30805162 PMCID: PMC6374651 DOI: 10.1002/ece3.4843] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/13/2018] [Accepted: 11/25/2018] [Indexed: 01/10/2023] Open
Abstract
DNA extraction from environmental samples (environmental DNA; eDNA) for metabarcoding-based biodiversity studies is gaining popularity as a noninvasive, time-efficient, and cost-effective monitoring tool. The potential benefits are promising for marine conservation, as the marine biome is frequently under-surveyed due to its inaccessibility and the consequent high costs involved. With increasing numbers of eDNA-related publications have come a wide array of capture and extraction methods. Without visual species confirmation, inconsistent use of laboratory protocols hinders comparability between studies because the efficiency of target DNA isolation may vary. We determined an optimal protocol (capture and extraction) for marine eDNA research based on total DNA yield measurements by comparing commonly employed methods of seawater filtering and DNA isolation. We compared metabarcoding results of both targeted (small taxonomic group with species-level assignment) and universal (broad taxonomic group with genus/family-level assignment) approaches obtained from replicates treated with the optimal and a low-performance capture and extraction protocol to determine the impact of protocol choice and DNA yield on biodiversity detection. Filtration through cellulose-nitrate membranes and extraction with Qiagen's DNeasy Blood & Tissue Kit outperformed other combinations of capture and extraction methods, showing a ninefold improvement in DNA yield over the poorest performing methods. Use of optimized protocols resulted in a significant increase in OTU and species richness for targeted metabarcoding assays. However, changing protocols made little difference to the OTU and taxon richness obtained using universal metabarcoding assays. Our results demonstrate an increased risk of false-negative species detection for targeted eDNA approaches when protocols with poor DNA isolation efficacy are employed. Appropriate optimization is therefore essential for eDNA monitoring to remain a powerful, efficient, and relatively cheap method for biodiversity assessments. For seawater, we advocate filtration through cellulose-nitrate membranes and extraction with Qiagen's DNeasy Blood & Tissue Kit or phenol-chloroform-isoamyl for successful implementation of eDNA multi-marker metabarcoding surveys.
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Affiliation(s)
- Gert‐Jan Jeunen
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Michael Knapp
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
| | | | | | - Miles D. Lamare
- Department of Marine ScienceUniversity of OtagoDunedinNew Zealand
| | - Michael Stat
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
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11
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Plough LV, Ogburn MB, Fitzgerald CL, Geranio R, Marafino GA, Richie KD. Environmental DNA analysis of river herring in Chesapeake Bay: A powerful tool for monitoring threatened keystone species. PLoS One 2018; 13:e0205578. [PMID: 30383750 PMCID: PMC6211659 DOI: 10.1371/journal.pone.0205578] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/27/2018] [Indexed: 11/18/2022] Open
Abstract
Environmental DNA (eDNA) sampling has emerged as a powerful tool to detect and quantify species abundance in aquatic environments. However, relatively few studies have compared the performance of eDNA-based abundance estimates to traditional catch or survey approaches in the field. Here, we have developed and field-tested a qPCR assay to detect eDNA from alewife and blueback herring (collectively known as ‘river herring’), comparing eDNA-based presence and abundance data to traditional methods of quantification (ichthyoplankton sampling and adult observations). Overall, the qPCR assay showed very high target specificity in lab trials, and was successful in detecting river herring for 11/12 Chesapeake Bay tributaries in spring 2015 and 2016, with 106 out of 445 samples exhibiting positive eDNA hits. We found a strong correlation between eDNA abundance and ichthyoplankton count data (Spearman’s Rho = 0.52), and Phi-tests (correlation of presence/absence data) showed higher correlation between eDNA and ichthyoplankton data (Phi = 0.45) than adult data (Phi = 0.35). Detection probability was significantly lower on western vs. eastern shore tributaries of Chesapeake Bay, and blueback herring and alewife were more likely detected on the western and eastern shores, respectively. Temporal patterns of eDNA abundance over the spring spawning season revealed that alewife were present in high abundances weeks ahead of blueback herring, which aligns with known differences in spawning behavior of the species. In summary, the eDNA abundance data corresponded well to other field methods and has great potential to assist future monitoring efforts of river herring abundance and habitat use.
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Affiliation(s)
- Louis V. Plough
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, United States of America
- * E-mail:
| | - Matthew B. Ogburn
- Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
| | - Catherine L. Fitzgerald
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, United States of America
| | - Rose Geranio
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, United States of America
| | - Gabriella A. Marafino
- Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
| | - Kimberly D. Richie
- Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
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12
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Bosch NE, Gonçalves JMS, Erzini K, Tuya F. "How" and "what" matters: Sampling method affects biodiversity estimates of reef fishes. Ecol Evol 2017; 7:4891-4906. [PMID: 28690817 PMCID: PMC5496540 DOI: 10.1002/ece3.2979] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 03/06/2017] [Accepted: 03/16/2017] [Indexed: 11/28/2022] Open
Abstract
Understanding changes in biodiversity requires the implementation of monitoring programs encompassing different dimensions of biodiversity through varying sampling techniques. In this work, fish assemblages associated with the “outer” and “inner” sides of four marinas, two at the Canary Islands and two at southern Portugal, were investigated using three complementary sampling techniques: underwater visual censuses (UVCs), baited cameras (BCs), and fish traps (FTs). We firstly investigated the complementarity of these sampling methods to describe species composition. Then, we investigated differences in taxonomic (TD), phylogenetic (PD) and functional diversity (FD) between sides of the marinas according to each sampling method. Finally, we explored the applicability/reproducibility of each sampling technique to characterize fish assemblages according to these metrics of diversity. UVCs and BCs provided complementary information, in terms of the number and abundances of species, while FTs sampled a particular assemblage. Patterns of TD, PD, and FD between sides of the marinas varied depending on the sampling method. UVC was the most cost‐efficient technique, in terms of personnel hours, and it is recommended for local studies. However, for large‐scale studies, BCs are recommended, as it covers greater spatio‐temporal scales by a lower cost. Our study highlights the need to implement complementary sampling techniques to monitor ecological change, at various dimensions of biodiversity. The results presented here will be useful for optimizing future monitoring programs.
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Affiliation(s)
- Néstor E Bosch
- Grupo en Biodiversidad y Conservación IU-ECOAQUA Universidad de Las Palmas de Gran Canaria Las Palmas de G.C. Canary Islands Spain.,Centro de Ciências do Mar (CCMAR) Universidade do Algarve Faro Portugal
| | | | - Karim Erzini
- Centro de Ciências do Mar (CCMAR) Universidade do Algarve Faro Portugal
| | - Fernando Tuya
- Grupo en Biodiversidad y Conservación IU-ECOAQUA Universidad de Las Palmas de Gran Canaria Las Palmas de G.C. Canary Islands Spain
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13
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Kelly RP, O'Donnell JL, Lowell NC, Shelton AO, Samhouri JF, Hennessey SM, Feist BE, Williams GD. Genetic signatures of ecological diversity along an urbanization gradient. PeerJ 2016; 4:e2444. [PMID: 27672503 PMCID: PMC5028742 DOI: 10.7717/peerj.2444] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 08/13/2016] [Indexed: 12/11/2022] Open
Abstract
Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore marine eelgrass communities and assess the relationship between these ecological communities and the degree of urbanization in the surrounding watershed. Counter to conventional wisdom, we find strongly increasing richness and decreasing beta diversity with greater urbanization, and similar trends in the diversity of life histories with urbanization. We also find evidence that urbanization influences nearshore communities at local (hundreds of meters) rather than regional (tens of km) scales. Given that different survey methods sample different components of an ecosystem, we then discuss the advantages of eDNA—which we use here to detect hundreds of taxa simultaneously—as a complement to traditional ecological sampling, particularly in the context of broad ecological assessments where exhaustive manual sampling is impractical. Genetic data are a powerful means of uncovering human-ecosystem interactions that might otherwise remain hidden; nevertheless, no sampling method reveals the whole of a biological community.
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Affiliation(s)
- Ryan P Kelly
- School of Marine and Environmental Affairs, University of Washington , Seattle , WA , United States of America
| | - James L O'Donnell
- School of Marine and Environmental Affairs, University of Washington , Seattle , WA , United States of America
| | - Natalie C Lowell
- School of Aquatic and Fishery Sciences, University of Washington , Seattle , WA , United States of America
| | - Andrew O Shelton
- Northwest Fisheries Science Center, NOAA Fisheries , Seattle , WA , United States of America
| | - Jameal F Samhouri
- Northwest Fisheries Science Center, NOAA Fisheries , Seattle , WA , United States of America
| | - Shannon M Hennessey
- Department of Integrative Biology, Oregon State University , Corvallis , OR , United States of America
| | - Blake E Feist
- Northwest Fisheries Science Center, NOAA Fisheries , Seattle , WA , United States of America
| | - Gregory D Williams
- Northwest Fisheries Science Center, NOAA Fisheries , Seattle , WA , United States of America
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