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Gold Z, Koch MQ, Schooler NK, Emery KA, Dugan JE, Miller RJ, Page HM, Schroeder DM, Hubbard DM, Madden JR, Whitaker SG, Barber PH. A comparison of biomonitoring methodologies for surf zone fish communities. PLoS One 2023; 18:e0260903. [PMID: 37314989 DOI: 10.1371/journal.pone.0260903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 04/25/2023] [Indexed: 06/16/2023] Open
Abstract
Surf zones are highly dynamic marine ecosystems that are subject to increasing anthropogenic and climatic pressures, posing multiple challenges for biomonitoring. Traditional methods such as seines and hook and line surveys are often labor intensive, taxonomically biased, and can be physically hazardous. Emerging techniques, such as baited remote underwater video (BRUV) and environmental DNA (eDNA) are promising nondestructive tools for assessing marine biodiversity in surf zones of sandy beaches. Here we compare the relative performance of beach seines, BRUV, and eDNA in characterizing community composition of bony (teleost) and cartilaginous (elasmobranch) fishes of surf zones at 18 open coast sandy beaches in southern California. Seine and BRUV surveys captured overlapping, but distinct fish communities with 50% (18/36) of detected species shared. BRUV surveys more frequently detected larger species (e.g. sharks and rays) while seines more frequently detected one of the most abundant species, barred surfperch (Amphistichus argenteus). In contrast, eDNA metabarcoding captured 88.9% (32/36) of all fishes observed in seine and BRUV surveys plus 57 additional species, including 15 that frequent surf zone habitats. On average, eDNA detected over 5 times more species than BRUVs and 8 times more species than seine surveys at a given site. eDNA approaches also showed significantly higher sensitivity than seine and BRUV methods and more consistently detected 31 of the 32 (96.9%) jointly observed species across beaches. The four species detected by BRUV/seines, but not eDNA were only resolved at higher taxonomic ranks (e.g. Embiotocidae surfperches and Sygnathidae pipefishes). In frequent co-detection of species between methods limited comparisons of richness and abundance estimates, highlighting the challenge of comparing biomonitoring approaches. Despite potential for improvement, results overall demonstrate that eDNA can provide a cost-effective tool for long-term surf zone monitoring that complements data from seine and BRUV surveys, allowing more comprehensive surveys of vertebrate diversity in surf zone habitats.
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Affiliation(s)
- Zachary Gold
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - McKenzie Q Koch
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Nicholas K Schooler
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Kyle A Emery
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Jenifer E Dugan
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Robert J Miller
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Henry M Page
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Donna M Schroeder
- Bureau of Ocean Energy Management, Camarillo, CA, United States of America
| | - David M Hubbard
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Jessica R Madden
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Stephen G Whitaker
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
- Channel Islands National Park, Ventura, CA, United States of America
| | - Paul H Barber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
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2
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Cruz MM, Hoffmann LS, de Freitas TRO. Saint Peter and Saint Paul Archipelago barcoded: Fish diversity in the remoteness and DNA barcodes reference library for metabarcoding monitoring. Genet Mol Biol 2022; 45:e20210349. [PMID: 36205729 PMCID: PMC9540803 DOI: 10.1590/1678-4685-gmb-2021-0349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 08/04/2022] [Indexed: 11/04/2022] Open
Abstract
In order to monitor the effects of anthropogenic pressures in ecosystems,
molecular techniques can be used to characterize species composition. Among
molecular markers capable of identifying species, the cytochrome c oxidase I
(COI) is the most used. However, new possibilities of
biodiversity profiling have become possible, in which molecular fragments of
medium and short-length can now be analyzed in metabarcoding studies. Here, a
survey of fishes from the Saint Peter and Saint Paul Archipelago was barcoded
using the COI marker, which allowed the identification of 21
species. This paved the way to further investigate the fish biodiversity of the
archipelago, transitioning from barcoding to metabarcoding analysis. As
preparatory steps for future metabarcoding studies, the first extensive
COI library of fishes listed for these islands was
constructed and includes new data generated in this survey as well as previously
available data, resulting in a final database with 9,183 sequences from 169
species and 63 families of fish. A new primer specifically designed for those
fishes was tested in silico to amplify a region of 262 bp. The
new approach should guarantee a reliable surveillance of the archipelago and can
be used to generate policies that will enhance the archipelago’s protection.
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Affiliation(s)
- Marcelo Merten Cruz
- Universidade Federal do Rio Grande do Sul, Programa de
Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Porto
Alegre, RS, Brazil
| | - Lilian Sander Hoffmann
- Universidade Federal do Rio Grande do Sul, Programa de
Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Porto
Alegre, RS, Brazil
| | - Thales R. O. de Freitas
- Universidade Federal do Rio Grande do Sul, Programa de
Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Porto
Alegre, RS, Brazil
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3
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Lavergne E, Kume M, Ahn H, Henmi Y, Terashima Y, Ye F, Kameyama S, Kai Y, Kadowaki K, Kobayashi S, Yamashita Y, Kasai A. Effects of forest cover on richness of threatened fish species in Japan. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13847. [PMID: 34668598 PMCID: PMC9299902 DOI: 10.1111/cobi.13849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 05/09/2023]
Abstract
Estuaries--one of the most vulnerable ecosystems globally--face anthropogenic threats, including biodiversity loss and the collapse of sustainable fisheries. Determining the factors contributing to the maintenance of estuarine biodiversity, especially that of fish, is vital for promoting estuarine conservation and sustainability. We used environmental DNA metabarcoding analysis to determine fish species composition in 22 estuaries around Japan and measured watershed-scale land-use factors (e.g., population size, urban area percentage, and forest area percentage). We sought to test the hypothesis that the richness of the most vulnerable estuarine fish species (i.e., registered by the Japanese Ministry of the Environment in the national species red-list) is determined by watershed-scale land-use factors. The richness of such species was greater, where forest cover was highest; thus, forest cover contributes to their conservation. The proportion of agriculture cover was associated with low species richness of red-listed fishes (redundancy analysis, adjusted R2 = 43.9% of total variance, df = 5, F = 5.3843, p = 0.0001). The number of red-listed species increased from 3 to 11 along a watershed land-use gradient ranging from a high proportion of agriculture cover to a large proportion of forest cover. Furthermore, the results showed that throughout Japan all the examined watersheds that were covered by >74.8% forest had more than the average (6.7 species per site) richness of red-listed fish species. This result can be attributed to the already high average forest cover in Japan of 67.2%. Our results demonstrate how the land use of watersheds can affect the coastal sea environment and its biodiversity and suggest that proper forest management in conjunction with land-use management may be of prime importance for threatened fish species and coastal ecosystems in general.
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Affiliation(s)
- Edouard Lavergne
- Field Science Education and Research Center (FSERC)Kyoto UniversityKyotoJapan
- Research and Educational Unit for Studies on Connectivity of Hills, Humans and OceansKyoto UniversityKyotoJapan
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), Institut Universitaire Européen de la Mer (IUEM)Université de Bretagne OccidentalePlouzanéFrance
- Plastic@SeaBanyuls‐sur‐MerFrance
| | - Manabu Kume
- Field Science Education and Research Center (FSERC)Kyoto UniversityKyotoJapan
- Research and Educational Unit for Studies on Connectivity of Hills, Humans and OceansKyoto UniversityKyotoJapan
| | - Hyojin Ahn
- Research and Educational Unit for Studies on Connectivity of Hills, Humans and OceansKyoto UniversityKyotoJapan
- Faculty of Fisheries SciencesHokkaido UniversityHakodateJapan
| | - Yumi Henmi
- Field Science Education and Research Center (FSERC)Kyoto UniversityKyotoJapan
- Research and Educational Unit for Studies on Connectivity of Hills, Humans and OceansKyoto UniversityKyotoJapan
| | - Yuki Terashima
- Research and Educational Unit for Studies on Connectivity of Hills, Humans and OceansKyoto UniversityKyotoJapan
| | - Feng Ye
- Research and Educational Unit for Studies on Connectivity of Hills, Humans and OceansKyoto UniversityKyotoJapan
- Biodiversity DivisionNational Institute for Environmental Studies (NIES)TsukubaJapan
| | - Satoshi Kameyama
- Biodiversity DivisionNational Institute for Environmental Studies (NIES)TsukubaJapan
| | - Yoshiaki Kai
- Field Science Education and Research Center (FSERC)Kyoto UniversityKyotoJapan
| | - Kohmei Kadowaki
- Field Science Education and Research Center (FSERC)Kyoto UniversityKyotoJapan
- The Hakubi Center for Advanced ResearchGraduate School of Agriculture, Kyoto UniversityKyotoJapan
| | - Shiho Kobayashi
- Field Science Education and Research Center (FSERC)Kyoto UniversityKyotoJapan
| | - Yoh Yamashita
- Field Science Education and Research Center (FSERC)Kyoto UniversityKyotoJapan
- Research and Educational Unit for Studies on Connectivity of Hills, Humans and OceansKyoto UniversityKyotoJapan
| | - Akihide Kasai
- Faculty of Fisheries SciencesHokkaido UniversityHakodateJapan
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Ellis MR, Clark ZSR, Treml EA, Brown MS, Matthews TG, Pocklington JB, Stafford-Bell RE, Bott NJ, Nai YH, Miller AD, Sherman CDH. Detecting marine pests using environmental DNA and biophysical models. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151666. [PMID: 34793806 DOI: 10.1016/j.scitotenv.2021.151666] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
The spread of marine pests is occurring at record rates due to globalisation and increasing trade. Environmental DNA (eDNA) is an emerging tool for pest surveillance, allowing for the detection of genetic material shed by organisms into the environment. However, factors influencing the spatial and temporal detection limits of eDNA in marine environments are poorly understood. In this study we use eDNA assays to assess the invasive ranges of two marine pests in south-eastern Australia, the kelp Undaria pinnatifida and the seastar Asterias amurensis. We explored the temporal and spatial detection limits of eDNA under different oceanographic conditions by combining estimates of eDNA decay with biophysical modelling. Positive eDNA detections at several new locations indicate the invasive range of both pest species is likely to be wider than currently assumed. Environmental DNA decay rates were similar for both species, with a decay rate constant of 0.035 h-1 for U. pinnatifida, and a decay rate constant of 0.041 h-1 for A. amurensis, resulting in a 57-73% decrease in eDNA concentrations in the first 24 h and decaying beyond the limits of detection after 3-4 days. Biophysical models informed by eDNA decay profiles indicate passive transport of eDNA up to a maximum of 10 to 20 km from its source, with a ~90-95% reduction in eDNA concentration within 1-3 km from the source, depending on local oceanography. These models suggest eDNA signals are likely to be highly localised, even in complex marine environments. This was confirmed with spatially replicated eDNA sampling around an established U. pinnatifida population indicating detection limits of ~750 m from the source. This study highlights the value of eDNA methods for marine pest surveillance and provides a much-needed description of the spatio-temporal detection limits of eDNA under different oceanographic conditions.
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Affiliation(s)
- Morgan R Ellis
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Zach S R Clark
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Eric A Treml
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Morgan S Brown
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Ty G Matthews
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Jacqueline B Pocklington
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Environment and Science Division, Parks Victoria, Melbourne, Victoria 3000, Australia
| | - Richard E Stafford-Bell
- Department of Jobs, Precincts and Regions, 475 Mickleham Road, Attwood, Vic. 3049, Australia
| | - Nathan J Bott
- School of Science, RMIT University, PO Box 71, Bundoora, VIC 3083, Australia
| | - Yi Heng Nai
- Centre for Regional and Rural Futures, Faculty of Science, Engineering and Built Environment, Deakin University, Geelong, Victoria, 3220, Australia
| | - Adam D Miller
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Craig D H Sherman
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia.
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5
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Ionescu D, Bizic M, Karnatak R, Musseau CL, Onandia G, Kasada M, Berger SA, Nejstgaard JC, Ryo M, Lischeid G, Gessner MO, Wollrab S, Grossart H. From microbes to mammals: Pond biodiversity homogenization across different land‐use types in an agricultural landscape. ECOL MONOGR 2022. [DOI: 10.1002/ecm.1523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- D. Ionescu
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - M. Bizic
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - R. Karnatak
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - C. L. Musseau
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Department of Biology, Chemistry, Pharmacy, Institute of Biology Free University of Berlin Germany
| | - G. Onandia
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
| | - M. Kasada
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
| | - S. A. Berger
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - J. C. Nejstgaard
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - M. Ryo
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
- Brandenburg University of Technology Cottbus–Senftenberg Cottbus Germany
| | - G. Lischeid
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
| | - M. O. Gessner
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Department of Ecology Berlin Institute of Technology (TU Berlin) Berlin Germany
| | - S. Wollrab
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - H.‐P. Grossart
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Institute of Biochemistry and Biology Potsdam University Potsdam Germany
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