1
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Chiquillo KL, Wong JM, Eirin-Lopez JM. Ecological forensic testing: Using multiple primers for eDNA detection of marine vertebrates in an estuarine lagoon subject to anthropogenic influences. Gene 2024; 928:148720. [PMID: 38936785 DOI: 10.1016/j.gene.2024.148720] [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: 03/01/2024] [Revised: 06/12/2024] [Accepted: 06/20/2024] [Indexed: 06/29/2024]
Abstract
Many critical aquatic habitats are in close proximity to human activity (i.e., adjacent to residences, docks, marinas, etc.), and it is vital to monitor biodiversity in these and similar areas that are subject to ongoing urbanization, pollution, and other environmental disruptions. Environmental DNA (eDNA) metabarcoding is an accessible, non-invasive genetic technique used to detect and monitor species diversity and is a particularly useful approach in areas where traditional biodiversity monitoring methods (e.g., visual surveys or video surveillance) are challenging to conduct. In this study, we implemented an eDNA approach that used a combination of three distinct PCR primer sets to detect marine vertebrates within a canal system of Biscayne Bay, Florida, an ecosystem representative of challenging sampling conditions and a myriad of impacts from urbanization. We detected fish species from aquarium, commercial, and recreational fisheries, as well as invasive, cryptobenthic, and endangered vertebrate species, including charismatic marine mammals such as the protected West Indian manatee, Trichechus manatus. Our results support the potential for eDNA analyses to supplement traditional biodiversity monitoring methods and ultimately serve as an important tool for ecosystem management. This approach minimizes stress or disturbance to organisms and removes the intrinsic risk and logical limitations of SCUBA diving, snorkeling, or deploying sensitive equipment in areas that are subject to high vessel traffic and/or low visibility. Overall, this work sets the framework to understand how biodiversity may change over different spatial and temporal scales in an aquatic ecosystem heavily influenced by urbanization and validates the use of eDNA as a complementary approach to traditional ecological monitoring methods.
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Affiliation(s)
- Kelcie L Chiquillo
- Department of Biology, University of Puerto Rico Río Piedras, P.O. Box 23360, San Juan, PR 00931 USA; Environmental Epigenetics Laboratory, Institute of Environment, Florida International University, Miami, FL, USA.
| | - Juliet M Wong
- Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University Marine Lab, Beaufort, NC, USA; Environmental Epigenetics Laboratory, Institute of Environment, Florida International University, Miami, FL, USA.
| | - Jose M Eirin-Lopez
- Environmental Epigenetics Laboratory, Institute of Environment, Florida International University, Miami, FL, USA.
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2
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Martin B, Doane MP, Henkens J, Morgan JAT, Inglis L, Peddemors VM, Dinsdale EA, Huveneers C, Meyer L. Who bit the boat? New DNA collection and genomic methods enable species identification in suspected shark-related incidents. Forensic Sci Int Genet 2024; 72:103087. [PMID: 38996566 DOI: 10.1016/j.fsigen.2024.103087] [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: 05/03/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 07/14/2024]
Abstract
Species identification following shark-related incidents is critical for effective incident management and for collecting data to inform shark-bite mitigation strategies. Witness statements are not always reliable, and species identification is often ambiguous or missing. Alternative methods for species identification include morphological assessments of bite marks, analysis of collected teeth at the scene of the incident, and genetic approaches. However, access to appropriate collection media and robust genetic assays have limited the use of genetic technologies. Here, we present a case study that facilitated a unique opportunity to compare the effectiveness of medical gauze readily available in first-aid kits, and forensic-grade swabs in collecting genetic material for shark-species identification. Sterile medical gauze and forensic-grade swabs were used to collect transfer DNA from the bite margins on a bitten surf ski which were compared to a piece of shark tissue embedded along the bite margin. Witness accounts and the characteristics of the bite mark impressions inferred the involvement of a Carcharodon carcharias (white shark). The morphology of a tooth found on the boat that picked up the surf ski, however, suggested it belonged to an Orectolobus spp. (wobbegong). Genetic analysis of DNA transferred from the shark to the surf ski included the application of a broad-target nested PCR assay followed by Sanger sequencing, with white shark contribution to the 'total sample DNA' determined with a species-specific qPCR assay. The results of the genetic analyses were congruent between sampling methods with respect to species identification and the level of activity inferred by the donor-specific DNA contribution. These data also supported the inferences drawn from the bite mark morphology. DNA from the recovered tooth was PCR amplified with a wobbegong-specific primer pair designed for this study to corroborate the tooth's morphological identification. Following the confirmation of gauze used for sampling in the case study event, two additional isolated incidents occurred and were sampled in situ using gauze, as typically found in a first-aid kit, by external personnel. DNA extracted from these gauze samples resulted in the identification of a white shark as the donor of the DNA collected from the bite marks in both instances. This study, involving three incidents separated by time and location, represents the seminal application of gauze as a sampling media after critical human-shark interactions and strongly supports the practical implementation of these methods in the field.
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Affiliation(s)
- Belinda Martin
- Flinders University, Flinders Accelerator for Microbiome Exploration, Bedford Park, SA 5042, Australia; Flinders University, College of Science and Engineering, Bedford Park, SA 5042, Australia.
| | - Michael P Doane
- Flinders University, Flinders Accelerator for Microbiome Exploration, Bedford Park, SA 5042, Australia; Flinders University, College of Science and Engineering, Bedford Park, SA 5042, Australia.
| | - Jessica Henkens
- Flinders University, College of Science and Engineering, Bedford Park, SA 5042, Australia.
| | - Jess A T Morgan
- Queensland Department of Agriculture and Fisheries, Dutton Park, QLD 4102, Australia.
| | - Laura Inglis
- Flinders University, Flinders Accelerator for Microbiome Exploration, Bedford Park, SA 5042, Australia; Flinders University, College of Science and Engineering, Bedford Park, SA 5042, Australia.
| | - Victor M Peddemors
- New South Wales Department of Primary Industries, Sydney Institute of Marine Science, Mosman, NSW 2088, Australia.
| | - Elizabeth A Dinsdale
- Flinders University, Flinders Accelerator for Microbiome Exploration, Bedford Park, SA 5042, Australia; Flinders University, College of Science and Engineering, Bedford Park, SA 5042, Australia.
| | - Charlie Huveneers
- Flinders University, College of Science and Engineering, Bedford Park, SA 5042, Australia; Flinders University, Southern Shark Ecology Group, Bedford Park, SA 5042, Australia.
| | - Lauren Meyer
- Flinders University, College of Science and Engineering, Bedford Park, SA 5042, Australia; Flinders University, Southern Shark Ecology Group, Bedford Park, SA 5042, Australia; The Georgia Aquarium, Atlanta, GA 30313, United States.
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3
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Cheng R, Zhou X, Zhang Y, Li Q, Zhang J, Luo Y, Chen Q, Liu Z, Li Y, Shen Y. eDNA reveals spatial homogenization of fish diversity in a mountain river affected by a reservoir cascade. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 361:121248. [PMID: 38820798 DOI: 10.1016/j.jenvman.2024.121248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 05/05/2024] [Accepted: 05/25/2024] [Indexed: 06/02/2024]
Abstract
One of the main reasons for the decline in global freshwater biodiversity can be attributed to alterations in hydrological conditions resulting from dam construction. However, the majority of current research has focused on single or limited numbers of dams. Here, we carried out a seasonal fish survey, using environmental DNA (eDNA) method, on the Wujiang River mainstream (Tributaries of the Yangtze River, China) to investigate the impact of large-scale cascade hydropower development on changes in fish diversity patterns. eDNA survey revealed that native fish species have decreased in contrast to alien fish. There was also a shift in fish community structure, with declines of the dominant rheophilic fish species, an increase of the small-size fish species, and homogenization of species composition across reservoirs. Additionally, environmental factors, such as temperature, dissolved oxygen and reservoir age, had a significant effect on fish community diversity. This study provides basic information for the evaluation of the impact of cascade developments on fish diversity patterns.
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Affiliation(s)
- Ruli Cheng
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Xinxin Zhou
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Yufeng Zhang
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Qinghua Li
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Jiaming Zhang
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Yang Luo
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Qiliang Chen
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Zhihao Liu
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Yingwen Li
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Yanjun Shen
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China.
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4
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Dan ME, Portner EJ, Bowman JS, Semmens BX, Owens SM, Greenwald SM, Choy CA. Using low volume eDNA methods to sample pelagic marine animal assemblages. PLoS One 2024; 19:e0303263. [PMID: 38748719 PMCID: PMC11095688 DOI: 10.1371/journal.pone.0303263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024] Open
Abstract
Environmental DNA (eDNA) is an increasingly useful method for detecting pelagic animals in the ocean but typically requires large water volumes to sample diverse assemblages. Ship-based pelagic sampling programs that could implement eDNA methods generally have restrictive water budgets. Studies that quantify how eDNA methods perform on low water volumes in the ocean are limited, especially in deep-sea habitats with low animal biomass and poorly described species assemblages. Using 12S rRNA and COI gene primers, we quantified assemblages comprised of micronekton, coastal forage fishes, and zooplankton from low volume eDNA seawater samples (n = 436, 380-1800 mL) collected at depths of 0-2200 m in the southern California Current. We compared diversity in eDNA samples to concurrently collected pelagic trawl samples (n = 27), detecting a higher diversity of vertebrate and invertebrate groups in the eDNA samples. Differences in assemblage composition could be explained by variability in size-selectivity among methods and DNA primer suitability across taxonomic groups. The number of reads and amplicon sequences variants (ASVs) did not vary substantially among shallow (<200 m) and deep samples (>600 m), but the proportion of invertebrate ASVs that could be assigned a species-level identification decreased with sampling depth. Using hierarchical clustering, we resolved horizontal and vertical variability in marine animal assemblages from samples characterized by a relatively low diversity of ecologically important species. Low volume eDNA samples will quantify greater taxonomic diversity as reference libraries, especially for deep-dwelling invertebrate species, continue to expand.
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Affiliation(s)
- Michelle E. Dan
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Elan J. Portner
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Jeff S. Bowman
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Brice X. Semmens
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Sarah M. Owens
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - Stephanie M. Greenwald
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - C. Anela Choy
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
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5
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Green ME, Hardesty BD, Deagle BE, Wilcox C. Environmental DNA as a tool to reconstruct catch composition for longline fisheries vessels. Sci Rep 2024; 14:10188. [PMID: 38702492 PMCID: PMC11068744 DOI: 10.1038/s41598-024-60917-7] [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: 12/20/2023] [Accepted: 04/29/2024] [Indexed: 05/06/2024] Open
Abstract
Global wild-capture fisheries are a large and diverse sector requiring various tools for fisheries-dependant data collection and effective Monitoring, Control and Surveillance (MCS). Here we present a novel protocol to collect eDNA from brine tanks onboard commercial longline vessels to reconstruct catch composition. We collected samples from nine vessels operating out of the Eastern Tuna Billfish Fishery, Australia, validating eDNA results with reliable catch data consisting of seven target and bycatch species. Environmental DNA was highly effective for detecting species retained on vessels without contamination or false positives. For four vessels, logbook data and eDNA were consistent with detections of all species. The remaining vessels detected all species except for rare catches of short-billed spearfish (Tetrapturus angustirostris). Similarities between rank abundance distributions of catch and eDNA reads were observed with logbook data mirrored when eDNA sequences were organised into rank order abundance. The method was effective at identifying highly abundant taxa retained in brine tanks- tuna (Thunnus spp.), swordfish (Xiphias gladius), marlin (Kajijia audax), and Atlantic Pomfret (Brama brama). Further research is required to validate how eDNA and other molecular monitoring tools can be scaled and applied to provide solutions for monitoring challenges in the fisheries sector.
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Affiliation(s)
- M E Green
- Institute for Marine and Antactic Studies, University of Tasmania, Private Bag 49, Hobart, TAS, 7001, Australia.
- Centre for Marine Socioecology, University of Tasmania, Private Bag 49, Hobart, TAS, 7001, Australia.
| | - B D Hardesty
- CSIRO Environment, Castray Esplanade, Hobart, TAS, 7001, Australia
| | - B E Deagle
- CSIRO Australian National Fish Collection, Castray Esplanade, Hobart, TAS, 7001, Australia
| | - C Wilcox
- Wilco Analytics, 93 Carlton Beach Road, Dodges Ferry, TAS, 7173, Australia
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6
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Ip YCA, Chang JJM, Tun KPP, Meier R, Huang D. Multispecies environmental DNA metabarcoding sheds light on annual coral spawning events. Mol Ecol 2023; 32:6474-6488. [PMID: 35852023 DOI: 10.1111/mec.16621] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 06/27/2022] [Accepted: 07/14/2022] [Indexed: 11/28/2022]
Abstract
Synchronous multispecific coral spawning generally occurs annually and forms an integral part of the coral life cycle. Apart from spawning times and species participation, however, much else remains unknown. Here, we applied environmental DNA (eDNA) metabarcoding to study two tropical reef sites of contrasting coral cover before, during and after coral spawning. Using coral-ITS2 and vertebrate-12S markers, we evaluated eDNA as an alternative monitoring tool by assessing its capabilities in detecting spawning species and tracking relative abundances of coral and fish eDNA. Over 3 years, elevated eDNA coral signals during the event (proportional read increase of up to five-fold) were observed, detecting a total of 38 coral and 133 fish species with all but one of the coral species visually observed to be spawning. This is also the first demonstration that eDNA metabarcoding can be used to infer the diurnal partitioning of night- and day-time spawning, spawning in coral species overlooked by visual surveys, and the associated changes in fish trophic structures as an indicator of spawning events. Our study paves the way for applied quantitative eDNA metabarcoding approaches to better study ephemeral and important biological events.
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Affiliation(s)
- Yin Cheong Aden Ip
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Jia Jin Marc Chang
- Department of Biological Sciences, National University of Singapore, Singapore
| | | | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore
- Centre for Nature-based Climate Solutions, National University of Singapore, Singapore
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore
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7
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Hoban ML, Bunce M, Bowen BW. Plumbing the depths with environmental DNA (eDNA): Metabarcoding reveals biodiversity zonation at 45-60 m on mesophotic coral reefs. Mol Ecol 2023; 32:5590-5608. [PMID: 37728237 DOI: 10.1111/mec.17140] [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: 04/15/2023] [Accepted: 09/06/2023] [Indexed: 09/21/2023]
Abstract
Mesophotic coral ecosystems (MCEs) are tropical reefs found at depths of ~30-150 m, below the region most heavily impacted by heat stress and other disturbances. Hence, MCEs may serve as potential refugia for threatened shallow reefs, but they also harbour depth-endemic fauna distinct from shallow reefs. Previous studies have characterized biodiversity patterns along depth gradients, but focussed primarily on conspicuous taxa (fishes, corals, etc.). Environmental DNA (eDNA) metabarcoding offers a more holistic approach to assess biodiversity patterns across the tree of life. Here, we use three metabarcoding assays targeting fishes (16S rRNA), eukaryotes (18S rDNA) and metazoans (COI) to assess biodiversity change from the surface to ~90 m depth across 15-m intervals at three sites within the Hawaiian Archipelago. We observed significant community differences between most depth zones, with distinct zonation centred at 45-60 m for eukaryotes and metazoans, but not for fishes. This finding may be attributable to the higher mobility of reef fishes, although methodological limitations are likely a contributing factor. The possibility for MCEs to serve as refugia is not excluded for fishes, but invertebrate communities >45 m are distinct, indicating limited connectivity for the majority of reef fauna. This study provides a new approach for surveying biodiversity on MCEs, revealing patterns in a much broader context than the limited-taxon studies that comprise the bulk of our present knowledge.
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Affiliation(s)
- Mykle L Hoban
- Hawai'i Institute of Marine Biology, Kāne'ohe, Hawai'i, USA
| | - Michael Bunce
- Department of Conservation, Wellington, New Zealand
- Trace and Environmental DNA Laboratory, Curtin University, Perth, Western Australia, Australia
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, Kāne'ohe, Hawai'i, USA
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8
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Jensen MR, Høgslund S, Knudsen SW, Nielsen J, Møller PR, Rysgaard S, Thomsen PF. Distinct latitudinal community patterns of Arctic marine vertebrates along the East Greenlandic coast detected by environmental
DNA. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
| | - Signe Høgslund
- Department of Ecoscience Aarhus University Silkeborg Denmark
| | - Steen Wilhelm Knudsen
- NIVA Denmark Water Research Copenhagen Denmark
- Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Julius Nielsen
- Department of Fish and Shellfish Greenland Institute of Natural Resources Nuuk Greenland
| | - Peter Rask Møller
- Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- Norwegian College of Fishery Science UiT – The Arctic University of Norway Tromsø Norway
| | - Søren Rysgaard
- Department of Biology, Arctic Research Centre Aarhus University Aarhus Denmark
- Centre for Earth Observation Science, CHR Faculty of Environment Earth and Resources University of Manitoba Winnipeg Manitoba Canada
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9
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Gold Z, Wall AR, Schweizer TM, Pentcheff ND, Curd EE, Barber PH, Meyer RS, Wayne R, Stolzenbach K, Prickett K, Luedy J, Wetzer R. A manager's guide to using eDNA metabarcoding in marine ecosystems. PeerJ 2022; 10:e14071. [PMID: 36405018 PMCID: PMC9673773 DOI: 10.7717/peerj.14071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: (1) select genes and primers to target taxa; (2) assemble or develop comprehensive barcode reference databases; (3) apply rigorous site occupancy based decontamination pipelines; (4) conduct pilot studies to define spatial and temporal variance of eDNA; and (5) archive samples, extracts, and raw sequence data. We demonstrate the importance of each of these considerations using a case study of eDNA metabarcoding in the Ports of Los Angeles and Long Beach. eDNA metabarcoding approaches detected 94.1% (16/17) of species observed in paired trawl surveys while identifying an additional 55 native fishes, providing more comprehensive biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding results improved ecological interpretation and confidence in species detections while providing archived genetic resources for future analyses. Well designed and validated eDNA metabarcoding approaches are ideally suited for biomonitoring applications that rely on the detection of species, including mapping invasive species fronts and endangered species habitats as well as tracking range shifts in response to climate change. Incorporating these considerations will enhance the utility and efficacy of eDNA metabarcoding for routine biomonitoring applications.
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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
| | - Adam R. Wall
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
| | - Teia M. Schweizer
- Department of Fish and Wildlife Conservation Biology, Colorado State University, Fort Collins, CO, United States of America
| | - N. Dean Pentcheff
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
| | - Emily E. Curd
- Department of Natural Sciences, Landmark College, Putney, VT, 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
| | - Rachel S. Meyer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America,Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Robert Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Kevin Stolzenbach
- Wood Environment and Infrastructure, Inc., San Diego, CA, United States of America
| | - Kat Prickett
- Port of Los Angeles, Los Angeles, CA, United States of America
| | - Justin Luedy
- Port of Long Beach, Long Beach, CA, United States of America
| | - Regina Wetzer
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
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10
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Zainal Abidin DH, Mohd Nor SA, Lavoué S, A Rahim M, Mohammed Akib NA. Assessing a megadiverse but poorly known community of fishes in a tropical mangrove estuary through environmental DNA (eDNA) metabarcoding. Sci Rep 2022; 12:16346. [PMID: 36175455 PMCID: PMC9523059 DOI: 10.1038/s41598-022-19954-3] [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: 02/11/2022] [Accepted: 09/07/2022] [Indexed: 11/18/2022] Open
Abstract
Biodiversity surveys are crucial for monitoring the status of threatened aquatic ecosystems, such as tropical estuaries and mangroves. Conventional monitoring methods are intrusive, time-consuming, substantially expensive, and often provide only rough estimates in complex habitats. An advanced monitoring approach, environmental DNA (eDNA) metabarcoding, is promising, although only few applications in tropical mangrove estuaries have been reported. In this study, we explore the advantages and limitations of an eDNA metabarcoding survey on the fish community of the Merbok Estuary (Peninsular Malaysia). COI and 12S eDNA metabarcoding assays collectively detected 178 species from 127 genera, 68 families, and 25 orders. Using this approach, significantly more species have been detected in the Merbok Estuary over the past decade (2010–2019) than in conventional surveys, including several species of conservation importance. However, we highlight three limitations: (1) in the absence of a comprehensive reference database the identities of several species are unresolved; (2) some of the previously documented specimen-based diversity was not captured by the current method, perhaps as a consequence of PCR primer specificity, and (3) the detection of non-resident species—stenohaline freshwater taxa (e.g., cyprinids, channids, osphronemids) and marine coral reef taxa (e.g., holocentrids, some syngnathids and sharks), not known to frequent estuaries, leading to the supposition that their DNA have drifted into the estuary through water movements. The community analysis revealed that fish diversity along the Merbok Estuary is not homogenous, with the upstream more diverse than further downstream. This could be due to the different landscapes or degree of anthropogenic influences along the estuary. In summary, we demonstrated the practicality of eDNA metabarcoding in assessing fish community and structure within a complex and rich tropical environment within a short sampling period. However, some limitations need to be considered and addressed to fully exploit the efficacy of this approach.
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Affiliation(s)
- Danial Hariz Zainal Abidin
- Centre for Global Sustainability Studies (CGSS), Level 5, Hamzah Sendut Library, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Siti Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia.
| | - Sébastien Lavoué
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | | | - Noor Adelyna Mohammed Akib
- Centre for Global Sustainability Studies (CGSS), Level 5, Hamzah Sendut Library, Universiti Sains Malaysia, 11800, Penang, Malaysia. .,School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
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11
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Polanco F. A, Waldock C, Keggin T, Marques V, Rozanski R, Valentini A, Dejean T, Manel S, Vermeij M, Albouy C, Pellissier L. Ecological indices from environmental
DNA
to contrast coastal reefs under different anthropogenic pressures. Ecol Evol 2022. [DOI: 10.1002/ece3.9212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Andrea Polanco F.
- Beauval Nature Association Saint Aignan sur Cher France
- Fundación Biodiversa Colombia Bogotá, D.C. Colombia
| | - Conor Waldock
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems ETH Zürich Zürich Switzerland
- Unit of Land Change Science Swiss Federal Research Institute WSL Birmensdorf Switzerland
| | - Thomas Keggin
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems ETH Zürich Zürich Switzerland
- Unit of Land Change Science Swiss Federal Research Institute WSL Birmensdorf Switzerland
| | - Virginie Marques
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3 Montpellier France
- MARBEC Univ Montpellier, CNRS, Ifremer, IRD Montpellier France
| | - Romane Rozanski
- Fundación Biodiversa Colombia Bogotá, D.C. Colombia
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems ETH Zürich Zürich Switzerland
- IFREMER Unité Ecologie et Modèles pour l'Halieutique, EMH Nantes France
| | | | | | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3 Montpellier France
| | | | - Camille Albouy
- Fundación Biodiversa Colombia Bogotá, D.C. Colombia
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems ETH Zürich Zürich Switzerland
- IFREMER Unité Ecologie et Modèles pour l'Halieutique, EMH Nantes France
| | - Loïc Pellissier
- Fundación Biodiversa Colombia Bogotá, D.C. Colombia
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems ETH Zürich Zürich Switzerland
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12
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DiBattista JD, Fowler AM, Riley IJ, Reader S, Hay A, Parkinson K, Hobbs JPA. The use of environmental DNA to monitor impacted coastal estuaries. MARINE POLLUTION BULLETIN 2022; 181:113860. [PMID: 35779383 DOI: 10.1016/j.marpolbul.2022.113860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) metabarcoding is increasingly being used to assess community composition in coastal ecosystems. In this study, we chose to examine temporal and spatial changes in the aquatic community of Manly Lagoon - one of the most heavily developed and polluted estuaries in eastern Australia. Based on metabarcoding of the 16S mitochondrial gene (for fish) and the 18S nuclear gene (for macroinvertebrates), we identified seasonal differences in fish and macroinvertebrate community composition as well as species richness, which correlated, in some cases, with the environmental parameters of sea surface temperature and freshwater input. Moreover, given the greater taxonomic resolution of fish versus macroinvertebrate assignments, we identified several known migratory fish species of management importance that contributed significantly to the overall patterns observed. Overall, our data support the use of eDNA metabarcoding to track fish assemblages shifting in response to environmental drivers in polluted estuaries with increased sampling and consultation with historical data.
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Affiliation(s)
- Joseph D DiBattista
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia.
| | - Ashley M Fowler
- New South Wales Department of Primary Industries, Sydney Institute of Marine Science, Mosman, NSW 2088, Australia
| | - Indiana J Riley
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Sydney Institute of Marine Science, Mosman, NSW 2088, Australia
| | - Sally Reader
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia
| | - Amanda Hay
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia
| | - Kerryn Parkinson
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia
| | - Jean-Paul A Hobbs
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4069, Australia
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13
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Alexander JB, Marnane MJ, Elsdon TS, Bunce M, Songploy S, Sitaworawet P, Harvey ES. Complementary molecular and visual sampling of fish on oil and gas platforms provides superior biodiversity characterisation. MARINE ENVIRONMENTAL RESEARCH 2022; 179:105692. [PMID: 35785679 DOI: 10.1016/j.marenvres.2022.105692] [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: 12/06/2021] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Offshore oil and gas platforms have the potential to provide complex refugia for fish and benthic colonisers. We compare two methods of biodiversity assessment for fish and elasmobranchs at seven decommissioned oil and gas platforms as well as five sediment sites, located 5 km from platforms, in the Gulf of Thailand. Using surveys from stereo-video ROV transects, and data from Environmental DNA (eDNA) water-column samples, we detected fish and elasmobranch taxa from 39 families and 66 genera across both platform and sediment sites with eDNA, compared with 18 families and 29 genera by stereo-ROV with platforms yielding significantly greater species richness. This study demonstrates that the combination of stereo-video ROV and eDNA provide effective, non-extractive and complementary methods to enhance data capture. This approach sets new benchmarks for evaluating fish assemblages surrounding platforms and will enhance measurements of biota to inform decisions on the fate of oil/gas infrastructure.
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Affiliation(s)
- Jason B Alexander
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia.
| | | | - Travis S Elsdon
- Chevron Technical Center, Perth, Western Australia, Australia
| | - Michael Bunce
- Institute of Environmental Science and Research, New Zealand
| | - Se Songploy
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
| | | | - Euan S Harvey
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
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14
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Flück B, Mathon L, Manel S, Valentini A, Dejean T, Albouy C, Mouillot D, Thuiller W, Murienne J, Brosse S, Pellissier L. Applying convolutional neural networks to speed up environmental DNA annotation in a highly diverse ecosystem. Sci Rep 2022; 12:10247. [PMID: 35715444 PMCID: PMC9205931 DOI: 10.1038/s41598-022-13412-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 05/24/2022] [Indexed: 01/04/2023] Open
Abstract
High-throughput DNA sequencing is becoming an increasingly important tool to monitor and better understand biodiversity responses to environmental changes in a standardized and reproducible way. Environmental DNA (eDNA) from organisms can be captured in ecosystem samples and sequenced using metabarcoding, but processing large volumes of eDNA data and annotating sequences to recognized taxa remains computationally expensive. Speed and accuracy are two major bottlenecks in this critical step. Here, we evaluated the ability of convolutional neural networks (CNNs) to process short eDNA sequences and associate them with taxonomic labels. Using a unique eDNA data set collected in highly diverse Tropical South America, we compared the speed and accuracy of CNNs with that of a well-known bioinformatic pipeline (OBITools) in processing a small region (60 bp) of the 12S ribosomal DNA targeting freshwater fishes. We found that the taxonomic labels from the CNNs were comparable to those from OBITools, with high correlation levels for the composition of the regional fish fauna. The CNNs enabled the processing of raw fastq files at a rate of approximately 1 million sequences per minute, which was about 150 times faster than with OBITools. Given the good performance of CNNs in the highly diverse ecosystem considered here, the development of more elaborate CNNs promises fast deployment for future biodiversity inventories using eDNA.
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Affiliation(s)
- Benjamin Flück
- Department of Environmental System Science, ETH Zürich, 8092, Zurich, Switzerland. .,Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland.
| | - Laëtitia Mathon
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - Stéphanie Manel
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | | | | | - Camille Albouy
- DECOD (Ecosystem Dynamics and Sustainability), IFREMER, INRAE, Institut Agro - Agrocampus Ouest, Rue de l'Ile d'Yeu, BP21105, 44311, Nantes Cedex 3, France
| | - David Mouillot
- MARBEC, Univ. Montpellier,CNRS, IRD, Ifremer, Montpellier, France.,Institut Universitaire de France, IUF, 75231, Paris, France
| | - Wilfried Thuiller
- CNRS, LECA, Laboratoire d'Écologie Alpine, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, 38000, Grenoble, France
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité Biologique (UMR5174), CNRS, IRD, Université Paul Sabatier, Toulouse, France
| | - Sébastien Brosse
- Laboratoire Evolution et Diversité Biologique (UMR5174), CNRS, IRD, Université Paul Sabatier, Toulouse, France
| | - Loïc Pellissier
- Department of Environmental System Science, ETH Zürich, 8092, Zurich, Switzerland. .,Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland.
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15
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Mathon L, Marques V, Mouillot D, Albouy C, Andrello M, Baletaud F, Borrero-Pérez GH, Dejean T, Edgar GJ, Grondin J, Guerin PE, Hocdé R, Juhel JB, Kadarusman, Maire E, Mariani G, McLean M, Polanco F. A, Pouyaud L, Stuart-Smith RD, Sugeha HY, Valentini A, Vigliola L, Vimono IB, Pellissier L, Manel S. Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding. Proc Biol Sci 2022; 289:20220162. [PMID: 35440210 PMCID: PMC9019517 DOI: 10.1098/rspb.2022.0162] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/24/2022] [Indexed: 12/11/2022] Open
Abstract
Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems.
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Affiliation(s)
- Laetitia Mathon
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
- ENTROPIE, Institut de Recherche pour le Développement (IRD), Univ. Réunion, UNC, CNRS, Q1 IFREMER, Nouméa, New Caledonia, France
| | - Virginie Marques
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | - David Mouillot
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
- Institut Universitaire de France, France
| | - Camille Albouy
- DECOD (Ecosystem Dynamics and Sustainability), IFREMER, INRAE, Institut Agro - Agrocampus Ouest, Nantes, France
| | - Marco Andrello
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
- Institute for the study of Anthropic Impacts and Sustainability in the marine environment, National Research Council (CNR-IAS), Rome, Italy
| | - Florian Baletaud
- ENTROPIE, Institut de Recherche pour le Développement (IRD), Univ. Réunion, UNC, CNRS, Q1 IFREMER, Nouméa, New Caledonia, France
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
- SOPRONER, groupe GINGER, 98000 Noumea, New Caledonia, France
| | - Giomar H. Borrero-Pérez
- Programa de Biodiversidad y Ecosistemas Marinos, Museo de Historia Natural Marina de Colombia (MHNMC), Instituto de Investigaciones Marinas y Costeras- INVEMAR, Santa Marta, Colombia
| | | | - Graham J. Edgar
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | | | | | - Régis Hocdé
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | | | - Kadarusman
- Politeknik Kelautan dan Perikanan Sorong, KKD BP Sumberdaya Genetik, Konservasi dan Domestikasi, Papua Barat, Indonesia
| | - Eva Maire
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Gael Mariani
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | - Matthew McLean
- Department of Biology, Dalhousie University, Halifax NSB3H4R2, Canada
| | - Andrea Polanco F.
- Programa de Biodiversidad y Ecosistemas Marinos, Museo de Historia Natural Marina de Colombia (MHNMC), Instituto de Investigaciones Marinas y Costeras- INVEMAR, Santa Marta, Colombia
| | - Laurent Pouyaud
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Rick D. Stuart-Smith
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Hagi Yulia Sugeha
- Research Center for Oceanography, National Research and Innovation Agency, Jl. Pasir Putih 1, Ancol Timur, Jakarta Utara 14430, Indonesia
| | | | - Laurent Vigliola
- ENTROPIE, Institut de Recherche pour le Développement (IRD), Univ. Réunion, UNC, CNRS, Q1 IFREMER, Nouméa, New Caledonia, France
| | - Indra B. Vimono
- Research Center for Oceanography, National Research and Innovation Agency, Jl. Pasir Putih 1, Ancol Timur, Jakarta Utara 14430, Indonesia
| | - Loïc Pellissier
- Landscape Ecology, Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Unit of Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Stéphanie Manel
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
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16
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Miya M. Environmental DNA Metabarcoding: A Novel Method for Biodiversity Monitoring of Marine Fish Communities. ANNUAL REVIEW OF MARINE SCIENCE 2022; 14:161-185. [PMID: 34351788 DOI: 10.1146/annurev-marine-041421-082251] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Environmental DNA (eDNA) is genetic material that has been shed from macroorganisms. It has received increased attention as an indirect marker for biodiversity monitoring. This article reviews the current status of eDNA metabarcoding (simultaneous detection of multiple species) as a noninvasive and cost-effective approach for monitoring marine fish communities and discusses the prospects for this growing field. eDNA metabarcoding coamplifies short fragments of fish eDNA across a wide variety of taxa and, coupled with high-throughput sequencing technologies, allows massively parallel sequencing to be performed simultaneously for dozens to hundreds of samples. It can predict species richness in a given area, detect habitat segregation and biogeographic patterns from small to large spatial scales, and monitor the spatiotemporal dynamics of fish communities. In addition, it can detect an anthropogenic impact on fish communities through evaluation of their functional diversity. Recognizing the strengths and limitations of eDNA metabarcoding will help ensure that continuous biodiversity monitoring at multiple sites will be useful for ecosystem conservation and sustainable use of fishery resources, possibly contributing to achieving the targets of the United Nations' Sustainable Development Goal 14 for 2030.
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Affiliation(s)
- Masaki Miya
- Natural History Museum and Institute, Chiba, Chiba 260-8682, Japan;
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17
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18
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Yang J, Zhang X, Jin X, Seymour M, Richter C, Logares R, Khim JS, Klymus K. Recent advances in environmental DNA‐based biodiversity assessment and conservation. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13415] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Jun Yang
- Aquatic EcoHealth Group Fujian Key Laboratory of Watershed Ecology Key Laboratory of Urban Environment and Health Institute of Urban Environment Chinese Academy of Sciences Xiamen China
| | - Xiaowei Zhang
- School of the Environment State Key Laboratory of Pollution Control & Resource Reuse Nanjing University Nanjing China
| | - Xiaowei Jin
- China National Environmental Monitoring CentreMinistry of Ecology and Environment of the People's Republic of China Beijing China
| | - Mathew Seymour
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Catherine Richter
- Columbia Environmental Research CenterU.S. Geological Survey Columbia MO USA
| | - Ramiro Logares
- Institute of Marine Sciences CSICPasseig Marítim de la Barceloneta Barcelona Spain
| | - Jong Seong Khim
- School of Earth & Environmental Sciences College of Natural Sciences Seoul National University Seoul Republic of Korea
| | - Katy Klymus
- Columbia Environmental Research CenterU.S. Geological Survey Columbia MO USA
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