1
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Rosner A, Ballarin L, Barnay-Verdier S, Borisenko I, Drago L, Drobne D, Concetta Eliso M, Harbuzov Z, Grimaldi A, Guy-Haim T, Karahan A, Lynch I, Giulia Lionetto M, Martinez P, Mehennaoui K, Oruc Ozcan E, Pinsino A, Paz G, Rinkevich B, Spagnuolo A, Sugni M, Cambier S. A broad-taxa approach as an important concept in ecotoxicological studies and pollution monitoring. Biol Rev Camb Philos Soc 2024; 99:131-176. [PMID: 37698089 DOI: 10.1111/brv.13015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 08/23/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023]
Abstract
Aquatic invertebrates play a pivotal role in (eco)toxicological assessments because they offer ethical, cost-effective and repeatable testing options. Additionally, their significance in the food chain and their ability to represent diverse aquatic ecosystems make them valuable subjects for (eco)toxicological studies. To ensure consistency and comparability across studies, international (eco)toxicology guidelines have been used to establish standardised methods and protocols for data collection, analysis and interpretation. However, the current standardised protocols primarily focus on a limited number of aquatic invertebrate species, mainly from Arthropoda, Mollusca and Annelida. These protocols are suitable for basic toxicity screening, effectively assessing the immediate and severe effects of toxic substances on organisms. For more comprehensive and ecologically relevant assessments, particularly those addressing long-term effects and ecosystem-wide impacts, we recommended the use of a broader diversity of species, since the present choice of taxa exacerbates the limited scope of basic ecotoxicological studies. This review provides a comprehensive overview of (eco)toxicological studies, focusing on major aquatic invertebrate taxa and how they are used to assess the impact of chemicals in diverse aquatic environments. The present work supports the use of a broad-taxa approach in basic environmental assessments, as it better represents the natural populations inhabiting various ecosystems. Advances in omics and other biochemical and computational techniques make the broad-taxa approach more feasible, enabling mechanistic studies on non-model organisms. By combining these approaches with in vitro techniques together with the broad-taxa approach, researchers can gain insights into less-explored impacts of pollution, such as changes in population diversity, the development of tolerance and transgenerational inheritance of pollution responses, the impact on organism phenotypic plasticity, biological invasion outcomes, social behaviour changes, metabolome changes, regeneration phenomena, disease susceptibility and tissue pathologies. This review also emphasises the need for harmonised data-reporting standards and minimum annotation checklists to ensure that research results are findable, accessible, interoperable and reusable (FAIR), maximising the use and reusability of data. The ultimate goal is to encourage integrated and holistic problem-focused collaboration between diverse scientific disciplines, international standardisation organisations and decision-making bodies, with a focus on transdisciplinary knowledge co-production for the One-Health approach.
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Affiliation(s)
- Amalia Rosner
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Loriano Ballarin
- Department of Biology, University of Padova, via Ugo Bassi 58/B, Padova, I-35121, Italy
| | - Stéphanie Barnay-Verdier
- Sorbonne Université; CNRS, INSERM, Université Côte d'Azur, Institute for Research on Cancer and Aging Nice, 28 avenue Valombrose, Nice, F-06107, France
| | - Ilya Borisenko
- Faculty of Biology, Department of Embryology, Saint Petersburg State University, Universitetskaya embankment 7/9, Saint Petersburg, 199034, Russia
| | - Laura Drago
- Department of Biology, University of Padova, via Ugo Bassi 58/B, Padova, I-35121, Italy
| | - Damjana Drobne
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, 1111, Slovenia
| | - Maria Concetta Eliso
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, 80121, Italy
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Zoya Harbuzov
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
- Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, 199 Aba Koushy Ave., Haifa, 3498838, Israel
| | - Annalisa Grimaldi
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant, Varese, 3-21100, Italy
| | - Tamar Guy-Haim
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Arzu Karahan
- Middle East Technical University, Institute of Marine Sciences, Erdemli-Mersin, PO 28, 33731, Turkey
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Maria Giulia Lionetto
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via prov. le Lecce -Monteroni, Lecce, I-73100, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina, 61, Palermo, I-90133, Italy
| | - Pedro Martinez
- Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys, Barcelona, 08010, Spain
| | - Kahina Mehennaoui
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41, rue du Brill, Belvaux, L-4422, Luxembourg
| | - Elif Oruc Ozcan
- Faculty of Arts and Science, Department of Biology, Cukurova University, Balcali, Saricam, Adana, 01330, Turkey
| | - Annalisa Pinsino
- National Research Council, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Via Ugo La Malfa 153, Palermo, 90146, Italy
| | - Guy Paz
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Baruch Rinkevich
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Antonietta Spagnuolo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, 80121, Italy
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Via Celoria 26, Milan, 20133, Italy
| | - Sébastien Cambier
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41, rue du Brill, Belvaux, L-4422, Luxembourg
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2
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Saenz-Agudelo P, Ramirez P, Beldade R, Campoy AN, Garmendia V, Search FV, Fernández M, Wieters EA, Navarrete SA, Landaeta MF, Pérez-Matus A. Environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: Toward a baseline for biodiversity monitoring of unexplored marine habitats. Ecol Evol 2024; 14:e10999. [PMID: 38390005 PMCID: PMC10881902 DOI: 10.1002/ece3.10999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/12/2024] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
Temperate mesophotic reef ecosystems (TMREs) are among the least known marine habitats. Information on their diversity and ecology is geographically and temporally scarce, especially in highly productive large upwelling ecosystems. Lack of information remains an obstacle to understanding the importance of TMREs as habitats, biodiversity reservoirs and their connections with better-studied shallow reefs. Here, we use environmental DNA (eDNA) from water samples to characterize the community composition of TMREs on the central Chilean coast, generating the first baseline for monitoring the biodiversity of these habitats. We analyzed samples from two depths (30 and 60 m) over four seasons (spring, summer, autumn, and winter) and at two locations approximately 16 km apart. We used a panel of three metabarcodes, two that target all eukaryotes (18S rRNA and mitochondrial COI) and one specifically targeting fishes (16S rRNA). All panels combined encompassed eDNA assigned to 42 phyla, 90 classes, 237 orders, and 402 families. The highest family richness was found for the phyla Arthropoda, Bacillariophyta, and Chordata. Overall, family richness was similar between depths but decreased during summer, a pattern consistent at both locations. Our results indicate that the structure (composition) of the mesophotic communities varied predominantly with seasons. We analyzed further the better-resolved fish assemblage and compared eDNA with other visual methods at the same locations and depths. We recovered eDNA from 19 genera of fish, six of these have also been observed on towed underwater videos, while 13 were unique to eDNA. We discuss the potential drivers of seasonal differences in community composition and richness. Our results suggest that eDNA can provide valuable insights for monitoring TMRE communities but highlight the necessity of completing reference DNA databases available for this region.
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Affiliation(s)
- Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile Valdivia Chile
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
| | - Paula Ramirez
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile Valdivia Chile
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
| | - Ricardo Beldade
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
| | - Ana N Campoy
- Center of Marine Sciences (CCMAR-CIMAR) University of the Algarve Faro Portugal
| | - Vladimir Garmendia
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
| | - Francesca V Search
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
| | - Miriam Fernández
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
| | - Evie A Wieters
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
| | - Sergio A Navarrete
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
- Center for Applied Ecology and Sustainability (CAPES) and Coastal Socio-Ecological Millennium Institute (SECOS) Pontificia Universidad Católica de Chile Santiago Chile
- Center for Oceanographic Research COASTAL-COASTAL Universidad de Concepción Concepción Chile
| | - Mauricio F Landaeta
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Laboratorio de Ictiología e Interacciones Biofísicas (LABITI) Instituto de Biología, Facultad de Ciencias, Universidad de Valparaíso Valparaíso Chile
| | - Alejandro Pérez-Matus
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
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3
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Liao Y, Miao X, Wang R, Zhang R, Li H, Lin L. First pelagic fish biodiversity assessment of Cosmonaut Sea based on environmental DNA. Mar Environ Res 2023; 192:106225. [PMID: 37866974 DOI: 10.1016/j.marenvres.2023.106225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/22/2023] [Accepted: 10/09/2023] [Indexed: 10/24/2023]
Abstract
The Cosmonaut Sea is a typical marginal sea in East Antarctica that has not yet been greatly impacted by climate change. As one of the least explored areas in the Southern Ocean, our knowledge regarding its fish taxonomy and diversity has been sparse. eDNA metabarcoding, as an emerging and promising tool for marine biodiversity research and monitoring, has been widely used across taxa and habitats. During the 38th Chinese Antarctic Research Expedition (CHINARE-38), we collected seawater and surface sediment samples from 38 stations in the Cosmonaut Sea and performed the first, to our knowledge, eDNA analysis of fish biodiversity in the Southern Ocean based on the molecular markers of 12S rRNA and 16S rRNA. There were 48 fish species detected by the two markers in total, with 30 and 34 species detected by the 12S rRNA and 16S rRNA marker, respectively. This was more than the trawling results (19 species) and historical survey records (16 species, "BROKE-West" cruise). With some nonsignificant differences between the Gunnerus Ridge and the Oceanic Area of Enderby Land, the Cosmonaut Sea had a richer fish biodiversity in this research compared with previous studies, and its overall composition and distribution patterns were consistent with what we know in East Antarctica. We also found that the eDNA composition of fish in the Cosmonaut Sea might be related to some environmental factors. Our study demonstrated that the use of the eDNA technique for Antarctic fish biodiversity research is likely to yield more information with less sampling effort than traditional methods. In the context of climate change, the eDNA approach will provide a novel and powerful tool that is complementary to traditional methods for polar ecology research.
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Affiliation(s)
- Yuzhuo Liao
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China; College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Xing Miao
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Rui Wang
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Ran Zhang
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Hai Li
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
| | - Longshan Lin
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
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4
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DiBattista JD, Liu SYV, De Brauwer M, Wilkinson SP, West K, Koziol A, Bunce M. Gut content metabarcoding of specialized feeders is not a replacement for environmental DNA assays of seawater in reef environments. PeerJ 2023; 11:e16075. [PMID: 37790632 PMCID: PMC10542274 DOI: 10.7717/peerj.16075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/20/2023] [Indexed: 10/05/2023] Open
Abstract
In tropical marine ecosystems, the coral-based diet of benthic-feeding reef fishes provides a window into the composition and health of coral reefs. In this study, for the first time, we compare multi-assay metabarcoding sequences of environmental DNA (eDNA) isolated from seawater and partially digested gut items from an obligate corallivore butterflyfish (Chaetodon lunulatus) resident to coral reef sites in the South China Sea. We specifically tested the proportional and statistical overlap of the different approaches (seawater vs gut content metabarcoding) in characterizing eukaryotic community composition on coral reefs. Based on 18S and ITS2 sequence data, which differed in their taxonomic sensitivity, we found that gut content detections were only partially representative of the eukaryotic communities detected in the seawater based on low levels of taxonomic overlap (3 to 21%) and significant differences between the sampling approaches. Overall, our results indicate that dietary metabarcoding of specialized feeders can be complimentary to, but is no replacement for, more comprehensive environmental DNA assays of reef environments that might include the processing of different substrates (seawater, sediment, plankton) or traditional observational surveys. These molecular assays, in tandem, might be best suited to highly productive but cryptic oceanic environments (kelp forests, seagrass meadows) that contain an abundance of organisms that are often small, epiphytic, symbiotic, or cryptic.
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Affiliation(s)
- Joseph D. DiBattista
- School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Shang Yin Vanson Liu
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | | | - Shaun P. Wilkinson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Katrina West
- CSIRO Australian National Fish Collection, CSIRO, Hobart, TAS, Australia
| | - Adam Koziol
- School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
- Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
| | - Michael Bunce
- Institute of Environmental Science and Research, Kenepuru, Porirua, New Zealand
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5
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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Wang Y, Li X, Zhao X, Chen J, Wang Z, Chen L, Zhang S, Wang K. Assessment of Fish Diversity in the Ma'an Archipelago Special Protected Area Using Environmental DNA. Biology (Basel) 2022; 11. [PMID: 36552340 DOI: 10.3390/biology11121832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/11/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
This study aimed to investigate the practical validity of the environmental DNA (eDNA) method for evaluating fish composition and diversity in different habitats. We evaluated the fish composition and diversity characteristics of seven different habitats in the Ma'an Archipelago Special Protected Area in April 2020. The results showed that a total of twenty-seven species of fishes belonging to six orders, eighteen families, and twenty-three genera of the Actinopterygii were detected in the marine waters of the Ma'an Archipelago Special Protected Area. The dominant species in each habitat were Larimichthys crocea, Paralichthys olivaceus, and Lateolabrax maculatus. The mussel culture area had the highest number of species, with 19 fish species, while the offshore bulk load shedding platform had the lowest number of species, with 12 fish species. The rest of the habitat was not significantly different. The results showed that the mussel culture area had the highest diversity index (average value of 2.352 ± 0.161), and the offshore bulk load shedding platform had the lowest diversity index (average value of 1.865 ± 0.127); the rest of the habitat diversity indices did not differ significantly. A comparison with historical surveys showed that the eDNA technique can detect species not collected by traditional methods such as gillnets and trawls. Our study demonstrates the role of eDNA technology in obtaining fish diversity in different habitats and provides a theoretical basis for the continuous monitoring and management of fish biodiversity in protected areas.
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Yao M, Zhang S, Lu Q, Chen X, Zhang SY, Kong Y, Zhao J. Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward. Mol Ecol 2022; 31:5132-5164. [PMID: 35972241 DOI: 10.1111/mec.16659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 12/15/2022]
Abstract
Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.
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Affiliation(s)
- Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Shan Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Qi Lu
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Xiaoyu Chen
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Si-Yu Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Yueqiao Kong
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Jindong Zhao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
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McCartin LJ, Vohsen SA, Ambrose SW, Layden M, McFadden CS, Cordes EE, McDermott JM, Herrera S. Temperature Controls eDNA Persistence across Physicochemical Conditions in Seawater. Environ Sci Technol 2022; 56:8629-8639. [PMID: 35658125 PMCID: PMC9231374 DOI: 10.1021/acs.est.2c01672] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 05/20/2023]
Abstract
Environmental DNA (eDNA) quantification and sequencing are emerging techniques for assessing biodiversity in marine ecosystems. Environmental DNA can be transported by ocean currents and may remain at detectable concentrations far from its source depending on how long it persist. Thus, predicting the persistence time of eDNA is crucial to defining the spatial context of the information derived from it. To investigate the physicochemical controls of eDNA persistence, we performed degradation experiments at temperature, pH, and oxygen conditions relevant to the open ocean and the deep sea. The eDNA degradation process was best explained by a model with two phases with different decay rate constants. During the initial phase, eDNA degraded rapidly, and the rate was independent of physicochemical factors. During the second phase, eDNA degraded slowly, and the rate was strongly controlled by temperature, weakly controlled by pH, and not controlled by dissolved oxygen concentration. We demonstrate that marine eDNA can persist at quantifiable concentrations for over 2 weeks at low temperatures (≤10 °C) but for a week or less at ≥20 °C. The relationship between temperature and eDNA persistence is independent of the source species. We propose a general temperature-dependent model to predict the maximum persistence time of eDNA detectable through single-species eDNA quantification methods.
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Affiliation(s)
- Luke J. McCartin
- Department
of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015-3027, United States
| | - Samuel A. Vohsen
- Department
of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015-3027, United States
| | - Susan W. Ambrose
- Department
of Earth and Environmental Sciences, Lehigh
University, Bethlehem, Pennsylvania 18015-3027, United States
| | - Michael Layden
- Department
of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015-3027, United States
| | - Catherine S. McFadden
- Department
of Biology, Harvey Mudd College, Claremont, California 91711, United States
| | - Erik E. Cordes
- Department
of Biology, Temple University, Philadelphia, Pennsylvania 19122-6008, United States
| | - Jill M. McDermott
- Department
of Earth and Environmental Sciences, Lehigh
University, Bethlehem, Pennsylvania 18015-3027, United States
| | - Santiago Herrera
- Department
of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015-3027, United States
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10
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Kumar G, Reaume AM, Farrell E, Gaither MR. Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary. PLoS One 2022; 17:e0266720. [PMID: 35714082 PMCID: PMC9205523 DOI: 10.1371/journal.pone.0266720] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 03/26/2022] [Indexed: 12/21/2022] Open
Abstract
Metabarcoding of environmental DNA is increasingly used for biodiversity assessments in aquatic communities. The efficiency and outcome of these efforts are dependent upon either de novo primer design or selecting an appropriate primer set from the dozens that have already been published. Unfortunately, there is a lack of studies that have directly compared the efficacy of different metabarcoding primers in marine and estuarine systems. Here we evaluate five commonly used primer sets designed to amplify rRNA barcoding genes in fishes and compare their performance using water samples collected from estuarine sites in the highly biodiverse Indian River Lagoon in Florida. Three of the five primer sets amplify a portion of the mitochondrial 12S gene (MiFish_12S, 171bp; Riaz_12S, 106 bp; Valentini_12S, 63 bp), one amplifies 219 bp of the mitochondrial 16S gene (Berry_16S), and the other amplifies 271 bp of the nuclear 18S gene (MacDonald_18S). The vast majority of the metabarcoding reads (> 99%) generated using the 18S primer set assigned to non-target (non-fish) taxa and therefore this primer set was omitted from most analyses. Using a conservative 99% similarity threshold for species level assignments, we detected a comparable number of species (55 and 49, respectively) and similarly high Shannon’s diversity values for the Riaz_12S and Berry_16S primer sets. Meanwhile, just 34 and 32 species were detected using the MiFish_12S and Valentini_12S primer sets, respectively. We were able to amplify both bony and cartilaginous fishes using the four primer sets with the vast majority of reads (>99%) assigned to the former. We detected the greatest number of elasmobranchs (six species) with the Riaz_12S primer set suggesting that it may be a suitable candidate set for the detection of sharks and rays. Of the total 76 fish species that were identified across all datasets, the combined three 12S primer sets detected 85.5% (65 species) while the combination of the Riaz_12S and Berry_16S primers detected 93.4% (71 species). These results highlight the importance of employing multiple primer sets as well as using primers that target different genomic regions. Moreover, our results suggest that the widely adopted MiFish_12S primers may not be the best choice, rather we found that the Riaz_12S primer set was the most effective for eDNA-based fish surveys in our system.
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Abstract
Environmental DNA (eDNA) metabarcoding is an increasingly important tool for surveying biodiversity in marine ecosystems. However, the scale of temporal and spatial variability in eDNA signatures, and how this variation may impact eDNA-based marine biodiversity assessments, remains uncertain. To address this question, we systematically examined variation in vertebrate eDNA signatures across depth (0 m to 10 m) and horizontal space (nearshore kelp forest and surf zone) over three successive days in Southern California. Across a broad range of teleost fish and elasmobranchs, results showed significant variation in species richness and community assemblages between surface and depth, reflecting microhabitat depth preferences of common Southern California nearshore rocky reef taxa. Community assemblages between nearshore and surf zone sampling stations at the same depth also differed significantly, consistent with known habitat preferences. Additionally, assemblages also varied across three sampling days, but 69% of habitat preferences remained consistent. Results highlight the sensitivity of eDNA in capturing fine-scale vertical, horizontal, and temporal variation in marine vertebrate communities, demonstrating the ability of eDNA to capture a highly localized snapshot of marine biodiversity in dynamic coastal environments.
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Affiliation(s)
- Keira Monuki
- Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
| | - Paul H. Barber
- Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
| | - Zachary Gold
- Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
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