1
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Hakimzadeh A, Asbun AA, Albanese D, Bernard M, Buchner D, Callahan B, Caporaso JG, Curd E, Djemiel C, Durling MB, Elbrecht V, Gold Z, Gweon HS, Hajibabaei M, Hildebrand F, Mikryukov V, Normandeau E, Özkurt E, Palmer JM, Pascal G, Porter TM, Straub D, Vasar M, Větrovský T, Zafeiropoulos H, Anslan S. A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses. Mol Ecol Resour 2024; 24:e13847. [PMID: 37548515 PMCID: PMC10847385 DOI: 10.1111/1755-0998.13847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/05/2023] [Accepted: 07/06/2023] [Indexed: 08/08/2023]
Abstract
Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high-throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon-specific primers have been developed, extending the usability of metabarcoding across archaea, bacteria and eukaryotes. Accordingly, a multitude of metabarcoding data analysis tools and pipelines have also been developed. Often, several developed workflows are designed to process the same amplicon sequencing data, making it somewhat puzzling to choose one among the plethora of existing pipelines. However, each pipeline has its own specific philosophy, strengths and limitations, which should be considered depending on the aims of any specific study, as well as the bioinformatics expertise of the user. In this review, we outline the input data requirements, supported operating systems and particular attributes of thirty-two amplicon processing pipelines with the goal of helping users to select a pipeline for their metabarcoding projects.
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Affiliation(s)
- Ali Hakimzadeh
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
| | - Alejandro Abdala Asbun
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | - Davide Albanese
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, Italy
| | - Maria Bernard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
- INRAE, SIGENAE, 78350, Jouy-en-Josas, France
| | - Dominik Buchner
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Benjamin Callahan
- Department of Population Health and Pathobiology, College of Veterinary Medicine and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - J. Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Emily Curd
- Vermont Biomedical Research Network, University of Vermont, Burlington, VT, USA
| | - Christophe Djemiel
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Mikael B. Durling
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007 Uppsala, Sweden
| | - Vasco Elbrecht
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitaetsstrasse 5, 45141, Essen, Germany
| | - Zachary Gold
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hyun S. Gweon
- UK Centre for Ecology & Hydrology, Wallingford, Oxfordshire, OX10 8BB, UK
- School of Biological Sciences, University of Reading, Reading, RG6 6EX, UK
| | - Mehrdad Hajibabaei
- Department of Integrative Biology and Centre for Biodiversity Genomics, University of Guelph, Canada
| | - Falk Hildebrand
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK
| | | | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Ezgi Özkurt
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK
| | - Jonathan M. Palmer
- Center for Forest Mycology Research, Northern Research Station, US Forest Service, Madison, WI USA (current address: Genencor Technology Center, IFF, Palo Alto, CA USA)
| | - Géraldine Pascal
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France
| | - Teresita M. Porter
- Department of Integrative Biology and Centre for Biodiversity Genomics, University of Guelph, Canada
| | - Daniel Straub
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen D-72076, Germany
| | - Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Haris Zafeiropoulos
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
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2
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Mu Y, Zhang J, Yang J, Wu J, Zhang Y, Yu H, Zhang X. Enhancing amphibian biomonitoring through eDNA metabarcoding. Mol Ecol Resour 2024; 24:e13931. [PMID: 38345249 DOI: 10.1111/1755-0998.13931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 02/17/2024]
Abstract
Surveying biodiversity has taken a quantum leap with environmental DNA (eDNA) metabarcoding, an immensely powerful approach lauded for its efficiency, sensitivity, and non-invasiveness. This approach emerges as a game-changer for the elusive realm of endangered and rare species-think nocturnal, environmentally elusive amphibians. Here, we have established a framework for constructing a reliable metabarcoding pipeline for amphibians, covering primer design, performance evaluation, laboratory validation, and field validation processes. The Am250 primer, located on the mitochondrial 16S gene, was optimal for the eDNA monitoring of amphibians, which demonstrated higher taxonomic resolution, smaller species amplification bias, and more extraordinary detection ability compared to the other primers tested. Am250 primer exhibit an 83.8% species amplification rate and 75.4% accurate species identification rate for Chinese amphibians in the in silico PCR and successfully amplified all tested species of the standard samples in the in vitro assay. Furthermore, the field-based mesocosm experiment showed that DNA can still be detected by metabarcoding even days to weeks after organisms have been removed from the mesocosm. Moreover, field mesocosm findings indicate that eDNA metabarcoding primers exhibit different read abundances, which can affect the relative biomass of species. Thus, appropriate primers should be screened and evaluated by three experimental approaches: in silico PCR simulation, target DNA amplification, and mesocosm eDNA validation. The selection of a single primer set or multiple primers' combination should be based on the monitoring groups to improve the species detection rate and the credibility of results.
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Affiliation(s)
- Yawen Mu
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing, China
- Jiangsu Provincial Environmental Monitoring Center, Nanjing, China
| | - Jingwen Zhang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing, China
| | - Jianghua Yang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing, China
- School of Marine Science and Engineering, Nanjing Normal University, Nanjing, China
| | - Jun Wu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, China
| | - Yong Zhang
- Jiangsu Provincial Environmental Monitoring Center, Nanjing, China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing, China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing, China
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3
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McGaughran A, Dhami MK, Parvizi E, Vaughan AL, Gleeson DM, Hodgins KA, Rollins LA, Tepolt CK, Turner KG, Atsawawaranunt K, Battlay P, Congrains C, Crottini A, Dennis TPW, Lange C, Liu XP, Matheson P, North HL, Popovic I, Rius M, Santure AW, Stuart KC, Tan HZ, Wang C, Wilson J. Genomic Tools in Biological Invasions: Current State and Future Frontiers. Genome Biol Evol 2024; 16:evad230. [PMID: 38109935 PMCID: PMC10776249 DOI: 10.1093/gbe/evad230] [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: 09/15/2023] [Revised: 11/16/2023] [Accepted: 12/12/2023] [Indexed: 12/20/2023] Open
Abstract
Human activities are accelerating rates of biological invasions and climate-driven range expansions globally, yet we understand little of how genomic processes facilitate the invasion process. Although most of the literature has focused on underlying phenotypic correlates of invasiveness, advances in genomic technologies are showing a strong link between genomic variation and invasion success. Here, we consider the ability of genomic tools and technologies to (i) inform mechanistic understanding of biological invasions and (ii) solve real-world issues in predicting and managing biological invasions. For both, we examine the current state of the field and discuss how genomics can be leveraged in the future. In addition, we make recommendations pertinent to broader research issues, such as data sovereignty, metadata standards, collaboration, and science communication best practices that will require concerted efforts from the global invasion genomics community.
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Affiliation(s)
- Angela McGaughran
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Manpreet K Dhami
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Elahe Parvizi
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Amy L Vaughan
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Dianne M Gleeson
- Centre for Conservation Ecology and Genomics, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Lee A Rollins
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Carolyn K Tepolt
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Kathryn G Turner
- Department of Biological Sciences, Idaho State University, Pocatello, ID, USA
| | - Kamolphat Atsawawaranunt
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Paul Battlay
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Carlos Congrains
- Entomology Section, Department of Plant and Environmental Protection Sciences, University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
- US Department of Agriculture-Agricultural Research Service, Daniel K. Inouye US Pacific Basin Agricultural Research Center, Hilo, HI 96720, USA
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto 4169–007, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - Tristan P W Dennis
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Claudia Lange
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Xiaoyue P Liu
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - Paige Matheson
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Henry L North
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Iva Popovic
- School of the Environment, University of Queensland, Brisbane, QLD, Australia
| | - Marc Rius
- Centre for Advanced Studies of Blanes (CEAB, CSIC), Accés a la Cala Sant Francesc, Blanes, Spain
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg 2006, South Africa
| | - Anna W Santure
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Katarina C Stuart
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Hui Zhen Tan
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Cui Wang
- The Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Jonathan Wilson
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
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4
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Shashank PR, Parker BM, Rananaware SR, Plotkin D, Couch C, Yang LG, Nguyen LT, Prasannakumar NR, Braswell WE, Jain PK, Kawahara AY. CRISPR-based diagnostics detects invasive insect pests. Mol Ecol Resour 2024; 24:e13881. [PMID: 37888995 PMCID: PMC10842307 DOI: 10.1111/1755-0998.13881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/24/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
Rapid identification of organisms is essential for many biological and medical disciplines, from understanding basic ecosystem processes, disease diagnosis, to the detection of invasive pests. CRISPR-based diagnostics offers a novel and rapid alternative to other identification methods and can revolutionize our ability to detect organisms with high accuracy. Here we describe a CRISPR-based diagnostic developed with the universal cytochrome-oxidase 1 gene (CO1). The CO1 gene is the most sequenced gene among Animalia, and therefore our approach can be adopted to detect nearly any animal. We tested the approach on three difficult-to-identify moth species (Keiferia lycopersicella, Phthorimaea absoluta and Scrobipalpa atriplicella) that are major invasive pests globally. We designed an assay that combines recombinase polymerase amplification (RPA) with CRISPR for signal generation. Our approach has a much higher sensitivity than real-time PCR assays and achieved 100% accuracy for identification of all three species, with a detection limit of up to 120 fM for P. absoluta and 400 fM for the other two species. Our approach does not require a sophisticated laboratory, reduces the risk of cross-contamination, and can be completed in less than 1 h. This work serves as a proof of concept that has the potential to revolutionize animal detection and monitoring.
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Affiliation(s)
- Pathour R Shashank
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Division of Entomology, ICAR-Indian Agricultural Research Institution, New Delhi, India
| | - Brandon M Parker
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
- Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Santosh R Rananaware
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - David Plotkin
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - Christian Couch
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - Lilia G Yang
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - Long T Nguyen
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - N R Prasannakumar
- Division of Crop Protection, ICAR-Indian Institute of Horticultural Research, Bengaluru, India
| | - W Evan Braswell
- Insect Management and Molecular Diagnostics Laboratory, USDA APHIS PPQ S&T, Edinburg, Texas, USA
| | - Piyush K Jain
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida, USA
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
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5
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Emerson BC, Borges PAV, Cardoso P, Convey P, deWaard JR, Economo EP, Gillespie RG, Kennedy S, Krehenwinkel H, Meier R, Roderick GK, Strasberg D, Thébaud C, Traveset A, Creedy TJ, Meramveliotakis E, Noguerales V, Overcast I, Morlon H, Papadopoulou A, Vogler AP, Arribas P, Andújar C. Collective and harmonized high throughput barcoding of insular arthropod biodiversity: Toward a Genomic Observatories Network for islands. Mol Ecol 2023; 32:6161-6176. [PMID: 36156326 DOI: 10.1111/mec.16683] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 12/01/2022]
Abstract
Current understanding of ecological and evolutionary processes underlying island biodiversity is heavily shaped by empirical data from plants and birds, although arthropods comprise the overwhelming majority of known animal species, and as such can provide key insights into processes governing biodiversity. Novel high throughput sequencing (HTS) approaches are now emerging as powerful tools to overcome limitations in the availability of arthropod biodiversity data, and hence provide insights into these processes. Here, we explored how these tools might be most effectively exploited for comprehensive and comparable inventory and monitoring of insular arthropod biodiversity. We first reviewed the strengths, limitations and potential synergies among existing approaches of high throughput barcode sequencing. We considered how this could be complemented with deep learning approaches applied to image analysis to study arthropod biodiversity. We then explored how these approaches could be implemented within the framework of an island Genomic Observatories Network (iGON) for the advancement of fundamental and applied understanding of island biodiversity. To this end, we identified seven island biology themes at the interface of ecology, evolution and conservation biology, within which collective and harmonized efforts in HTS arthropod inventory could yield significant advances in island biodiversity research.
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Affiliation(s)
- Brent C Emerson
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), San Cristóbal de la Laguna, Spain
| | - Paulo A V Borges
- Centre for Ecology, Evolution and Environmental Changes (cE3c)/Azorean Biodiversity Group, Faculty of Agricultural Sciences and Environment, CHANGE - Global Change and Sustainability Institute, University of the Azores, Angra do Heroísmo, Portugal
| | - Pedro Cardoso
- Centre for Ecology, Evolution and Environmental Changes (cE3c)/Azorean Biodiversity Group, Faculty of Agricultural Sciences and Environment, CHANGE - Global Change and Sustainability Institute, University of the Azores, Angra do Heroísmo, Portugal
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History Luomus, University of Helsinki, Helsinki, Finland
| | - Peter Convey
- British Antarctic Survey, NERC, Cambridge, UK
- Department of Zoology, University of Johannesburg, Auckland Park, South Africa
| | - Jeremy R deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
- School of Environmental Sciences, University of Guelph, Guelph, Canada
| | - Evan P Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, Massachusetts, USA
| | - Rosemary G Gillespie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, USA
| | - Susan Kennedy
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | | | - Rudolf Meier
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
- Department of Biological Sciences, National University of Singapore, Singapore City, Singapore
| | - George K Roderick
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, USA
| | | | - Christophe Thébaud
- UMR 5174 EDB Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier Toulouse III, CNRS, IRD, Toulouse, France
| | - Anna Traveset
- Global Change Research Group, Mediterranean Institut of Advanced Studies (CSIC-UIB), Mallorca, Spain
| | - Thomas J Creedy
- Department of Life Sciences, Natural History Museum, London, UK
| | | | - Víctor Noguerales
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), San Cristóbal de la Laguna, Spain
| | - Isaac Overcast
- Département de Biologie, École normale supérieure, Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Université PSL, Paris, France
| | - Hélène Morlon
- Département de Biologie, École normale supérieure, Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Université PSL, Paris, France
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Paula Arribas
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), San Cristóbal de la Laguna, Spain
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), San Cristóbal de la Laguna, Spain
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Carvalho S, Shchepanik H, Aylagas E, Berumen ML, Costa FO, Costello MJ, Duarte S, Ferrario J, Floerl O, Heinle M, Katsanevakis S, Marchini A, Olenin S, Pearman JK, Peixoto RS, Rabaoui LJ, Ruiz G, Srėbalienė G, Therriault TW, Vieira PE, Zaiko A. Hurdles and opportunities in implementing marine biosecurity systems in data-poor regions. Bioscience 2023; 73:494-512. [PMID: 37560322 PMCID: PMC10408360 DOI: 10.1093/biosci/biad056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/26/2023] [Accepted: 06/06/2023] [Indexed: 08/11/2023] Open
Abstract
Managing marine nonindigenous species (mNIS) is challenging, because marine environments are highly connected, allowing the dispersal of species across large spatial scales, including geopolitical borders. Cross-border inconsistencies in biosecurity management can promote the spread of mNIS across geopolitical borders, and incursions often go unnoticed or unreported. Collaborative surveillance programs can enhance the early detection of mNIS, when response may still be possible, and can foster capacity building around a common threat. Regional or international databases curated for mNIS can inform local monitoring programs and can foster real-time information exchange on mNIS of concern. When combined, local species reference libraries, publicly available mNIS databases, and predictive modeling can facilitate the development of biosecurity programs in regions lacking baseline data. Biosecurity programs should be practical, feasible, cost-effective, mainly focused on prevention and early detection, and be built on the collaboration and coordination of government, nongovernment organizations, stakeholders, and local citizens for a rapid response.
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Affiliation(s)
- Susana Carvalho
- King Abdullah University of Science and Technology, Red Sea Research Center, 23955-6900 Thuwal, Saudi Arabia
| | - Hailey Shchepanik
- King Abdullah University of Science and Technology, Red Sea Research Center, 23955-6900 Thuwal, Saudi Arabia
| | - Eva Aylagas
- King Abdullah University of Science and Technology, Red Sea Research Center, 23955-6900 Thuwal, Saudi Arabia
- Red Sea Global, Riyadh 12382-6726, Saudi Arabia
| | - Michael L Berumen
- King Abdullah University of Science and Technology, Red Sea Research Center, 23955-6900 Thuwal, Saudi Arabia
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA) and Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | | | - Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA) and Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Jasmine Ferrario
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
| | | | - Moritz Heinle
- Applied Research Center for Environment & Marine Studies, King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
- International Centre for Water Resources and Global Change, Federal Institute of Hydrology, Koblenz, Germany
| | | | - Agnese Marchini
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
| | - Sergej Olenin
- Marine Research Institute, Klaipeda University, Lithuania
| | | | - Raquel S Peixoto
- King Abdullah University of Science and Technology, Red Sea Research Center, 23955-6900 Thuwal, Saudi Arabia
| | - Lotfi J Rabaoui
- Applied Research Center for Environment & Marine Studies, King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
- National Center for Wildlife, Riyadh, Saudi Arabia
| | - Greg Ruiz
- Smithsonian Environmental Research Center, Edgewater, Maryland
| | | | | | - Pedro E Vieira
- Centre of Molecular and Environmental Biology (CBMA) and Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Anastasija Zaiko
- Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
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7
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Chen J, Zhang T, Sun L, Liu Y, Li D, Leng X, An S. Abundance trade-offs and dominant taxa maintain the stability of the bacterioplankton community underlying Microcystis blooms. Front Microbiol 2023; 14:1181341. [PMID: 37275174 PMCID: PMC10235547 DOI: 10.3389/fmicb.2023.1181341] [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: 03/07/2023] [Accepted: 05/09/2023] [Indexed: 06/07/2023] Open
Abstract
Microcystis blooms are an intractable global environmental problem that pollute water and compromise ecosystem functioning. Closed-lake management practices keep lakes free of sewage and harmful algae invasions and have succeeded in controlling local Microcystis blooms; however, there is little understanding of how the bacterioplankton communities associated with Microcystis have changed. Here, based on metagenomic sequencing, the phyla, genera, functional genes and metabolic functions of the bacterioplankton communities were compared between open lakes (underlying Microcystis blooms) and closed lakes (no Microcystis blooms). Water properties and zooplankton density were investigated and measured as factors influencing blooms. The results showed that (1) the water quality of closed lakes was improved, and the nitrogen and phosphorus concentrations were significantly reduced. (2) The stability of open vs. closed-managed lakes differed notably at the species and genus levels (p < 0.01), but no significant variations were identified at the phylum and functional genes levels (p > 0.05). (3) The relative abundance of Microcystis (Cyanobacteria) increased dramatically in the open lakes (proportions from 1.44 to 41.76%), whereas the relative abundance of several other dominant genera of Cyanobacteria experienced a trade-off and decreased with increasing Microcystis relative abundance. (4) The main functions of the bacterioplankton communities were primarily related to dominant genera of Proteobacteria and had no significant relationship with Microcystis. Overall, the closed-lake management practices significantly reduced nutrients and prevented Microcystis blooms, but the taxonomic and functional structures of bacterioplankton communities remained stable overall.
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Affiliation(s)
- Jun Chen
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing, China
- Nanjing University Ecology Research Institute of Changshu (NJUecoRICH), Changshu, China
| | - Tiange Zhang
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing, China
- Nanjing University Ecology Research Institute of Changshu (NJUecoRICH), Changshu, China
| | - Lingyan Sun
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing, China
- Nanjing University Ecology Research Institute of Changshu (NJUecoRICH), Changshu, China
| | - Yan Liu
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing, China
- Nanjing University Ecology Research Institute of Changshu (NJUecoRICH), Changshu, China
| | - Dianpeng Li
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing, China
- Nanjing University Ecology Research Institute of Changshu (NJUecoRICH), Changshu, China
| | - Xin Leng
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing, China
- Nanjing University Ecology Research Institute of Changshu (NJUecoRICH), Changshu, China
| | - Shuqing An
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing, China
- Nanjing University Ecology Research Institute of Changshu (NJUecoRICH), Changshu, China
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8
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Shashank PR, Parker BM, Rananaware SR, Plotkin D, Couch C, Yang LG, Nguyen LT, Prasannakumar NR, Braswell WE, Jain PK, Kawahara AY. CRISPR-based diagnostics detects invasive insect pests. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541004. [PMID: 37292907 PMCID: PMC10245733 DOI: 10.1101/2023.05.16.541004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rapid identification of organisms is essential across many biological and medical disciplines, from understanding basic ecosystem processes and how organisms respond to environmental change, to disease diagnosis and detection of invasive pests. CRISPR-based diagnostics offers a novel and rapid alternative to other identification methods and can revolutionize our ability to detect organisms with high accuracy. Here we describe a CRISPR-based diagnostic developed with the universal cytochrome-oxidase 1 gene (CO1). The CO1 gene is the most sequenced gene among Animalia, and therefore our approach can be adopted to detect nearly any animal. We tested the approach on three difficult-to-identify moth species (Keiferia lycopersicella, Phthorimaea absoluta, and Scrobipalpa atriplicella) that are major invasive pests globally. We designed an assay that combines recombinase polymerase amplification (RPA) with CRISPR for signal generation. Our approach has a much higher sensitivity than other real time-PCR assays and achieved 100% accuracy for identification of all three species, with a detection limit of up to 120 fM for P. absoluta and 400 fM for the other two species. Our approach does not require a lab setting, reduces the risk of cross-contamination, and can be completed in less than one hour. This work serves as a proof of concept that has the potential to revolutionize animal detection and monitoring.
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Affiliation(s)
- Pathour R. Shashank
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Division of Entomology, ICAR-Indian Agricultural Research Institution, New Delhi 110012, India
| | - Brandon M. Parker
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37831, USA
- U.S. Environmental Protection Agency, Office of Research and Development, RTP, NC, 27709, USA
| | - Santosh R. Rananaware
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - David Plotkin
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Christian Couch
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Lilia G. Yang
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Long T. Nguyen
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - N. R. Prasannakumar
- Division of Crop Protection, ICAR-Indian Institute of Horticultural Research, Bengaluru 560089, India
| | - W. Evan Braswell
- Insect Management and Molecular Diagnostics Laboratory, USDA APHIS PPQ S&T, 22675 North Moorefield Road, Edinburg, Texas 78541, USA
| | - Piyush K. Jain
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida, USA
| | - Akito Y. Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
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9
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Shea MM, Kuppermann J, Rogers MP, Smith DS, Edwards P, Boehm AB. Systematic review of marine environmental DNA metabarcoding studies: toward best practices for data usability and accessibility. PeerJ 2023; 11:e14993. [PMID: 36992947 PMCID: PMC10042160 DOI: 10.7717/peerj.14993] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/12/2023] [Indexed: 03/31/2023] Open
Abstract
The emerging field of environmental DNA (eDNA) research lacks universal guidelines for ensuring data produced are FAIR-findable, accessible, interoperable, and reusable-despite growing awareness of the importance of such practices. In order to better understand these data usability challenges, we systematically reviewed 60 peer reviewed articles conducting a specific subset of eDNA research: metabarcoding studies in marine environments. For each article, we characterized approximately 90 features across several categories: general article attributes and topics, methodological choices, types of metadata included, and availability and storage of sequence data. Analyzing these characteristics, we identified several barriers to data accessibility, including a lack of common context and vocabulary across the articles, missing metadata, supplementary information limitations, and a concentration of both sample collection and analysis in the United States. While some of these barriers require significant effort to address, we also found many instances where small choices made by authors and journals could have an outsized influence on the discoverability and reusability of data. Promisingly, articles also showed consistency and creativity in data storage choices as well as a strong trend toward open access publishing. Our analysis underscores the need to think critically about data accessibility and usability as marine eDNA metabarcoding studies, and eDNA projects more broadly, continue to proliferate.
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Affiliation(s)
- Meghan M. Shea
- Emmett Interdisciplinary Program in Environment & Resources (E-IPER), Stanford University, Stanford, CA, United States of America
| | - Jacob Kuppermann
- Earth Systems Program, Stanford University, Stanford, CA, United States of America
| | - Megan P. Rogers
- Program in Human Biology, Stanford University, Stanford, CA, United States of America
| | - Dustin Summer Smith
- Earth Systems Program, Stanford University, Stanford, CA, United States of America
| | - Paul Edwards
- Program in Science, Technology and Society, Stanford University, Stanford, CA, United States of America
| | - Alexandria B. Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America
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10
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Hao R, Liu Y, Shen W, Zhao R, Jiang B, Song H, Yan M, Ma H. Surveillance of emerging infectious diseases for biosecurity. SCIENCE CHINA LIFE SCIENCES 2022; 65:1504-1516. [PMID: 35287183 PMCID: PMC8918423 DOI: 10.1007/s11427-021-2071-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 01/26/2022] [Indexed: 12/03/2022]
Abstract
Emerging infectious diseases, such as COVID-19, continue to pose significant threats to human beings and their surroundings. In addition, biological warfare, bioterrorism, biological accidents, and harmful consequences arising from dual-use biotechnology also pose a challenge for global biosecurity. Improving the early surveillance capabilities is necessary for building a common biosecurity shield for the global community of health for all. Furthermore, surveillance could provide early warning and situational awareness of biosecurity risks. However, current surveillance systems face enormous challenges, including technical shortages, fragmented management, and limited international cooperation. Detecting emerging biological risks caused by unknown or novel pathogens is of particular concern. Surveillance systems must be enhanced to effectively mitigate biosecurity risks. Thus, a global strategy of meaningful cooperation based on efficient integration of surveillance at all levels, including interdisciplinary integration of techniques and interdepartmental integration for effective management, is urgently needed. In this paper, we review the biosecurity risks by analyzing potential factors at all levels globally. In addition to describing biosecurity risks and their impact on global security, we also focus on analyzing the challenges to traditional surveillance and propose suggestions on how to integrate current technologies and resources to conduct effective global surveillance.
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Affiliation(s)
- Rongzhang Hao
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, 100069, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, 100069, China
| | - Yuqi Liu
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, 100850, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, 100071, China
| | - Wanzhu Shen
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, 100069, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, 100069, China
| | - Rongtao Zhao
- Chinese PLA Center for Disease Control and Prevention, Beijing, 100071, China
| | - Bo Jiang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, 100069, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, 100069, China
| | - Hongbin Song
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, 100850, China.
- Chinese PLA Center for Disease Control and Prevention, Beijing, 100071, China.
| | - Muyang Yan
- The First Medical Center of PLA General Hospital, Beijing, 100853, China.
| | - Hui Ma
- The Nursing Department of PLA General Hospital, Beijing, 100853, China.
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11
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Haubrock PJ, Ahmed DA, Cuthbert RN, Stubbington R, Domisch S, Marquez JRG, Beidas A, Amatulli G, Kiesel J, Shen LQ, Soto I, Angeler DG, Bonada N, Cañedo-Argüelles M, Csabai Z, Datry T, de Eyto E, Dohet A, Drohan E, England J, Feio MJ, Forio MAE, Goethals P, Graf W, Heino J, Hudgins EJ, Jähnig SC, Johnson RK, Larrañaga A, Leitner P, L'Hoste L, Lizee MH, Maire A, Rasmussen JJ, Schäfer RB, Schmidt-Kloiber A, Vannevel R, Várbíró G, Wiberg-Larsen P, Haase P. Invasion impacts and dynamics of a European-wide introduced species. GLOBAL CHANGE BIOLOGY 2022; 28:4620-4632. [PMID: 35570183 DOI: 10.1111/gcb.16207] [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: 02/01/2022] [Accepted: 04/16/2022] [Indexed: 06/15/2023]
Abstract
Globalization has led to the introduction of thousands of alien species worldwide. With growing impacts by invasive species, understanding the invasion process remains critical for predicting adverse effects and informing efficient management. Theoretically, invasion dynamics have been assumed to follow an "invasion curve" (S-shaped curve of available area invaded over time), but this dynamic has lacked empirical testing using large-scale data and neglects to consider invader abundances. We propose an "impact curve" describing the impacts generated by invasive species over time based on cumulative abundances. To test this curve's large-scale applicability, we used the data-rich New Zealand mud snail Potamopyrgus antipodarum, one of the most damaging freshwater invaders that has invaded almost all of Europe. Using long-term (1979-2020) abundance and environmental data collected across 306 European sites, we observed that P. antipodarum abundance generally increased through time, with slower population growth at higher latitudes and with lower runoff depth. Fifty-nine percent of these populations followed the impact curve, characterized by first occurrence, exponential growth, then long-term saturation. This behaviour is consistent with boom-bust dynamics, as saturation occurs due to a rapid decline in abundance over time. Across sites, we estimated that impact peaked approximately two decades after first detection, but the rate of progression along the invasion process was influenced by local abiotic conditions. The S-shaped impact curve may be common among many invasive species that undergo complex invasion dynamics. This provides a potentially unifying approach to advance understanding of large-scale invasion dynamics and could inform timely management actions to mitigate impacts on ecosystems and economies.
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Affiliation(s)
- Phillip J Haubrock
- Senckenberg Research Institute and Natural History Museum Frankfurt, Department of River Ecology and Conservation, Gelnhausen, Germany
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Vodňany, Czech Republic
| | - Danish A Ahmed
- Center for Applied Mathematics and Bioinformatics (CAMB), Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Hawally, Kuwait
| | - Ross N Cuthbert
- GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Rachel Stubbington
- School of Science & Technology, Nottingham Trent University, Nottingham, UK
| | - Sami Domisch
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department Community and Ecosystem Ecology, Berlin, Germany
| | - Jaime R G Marquez
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department Community and Ecosystem Ecology, Berlin, Germany
| | - Ayah Beidas
- Center for Applied Mathematics and Bioinformatics (CAMB), Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Hawally, Kuwait
| | - Giuseppe Amatulli
- Yale University, School of the Environment, New Haven, Connecticut, USA
| | - Jens Kiesel
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department Community and Ecosystem Ecology, Berlin, Germany
- Christian-Albrechts-University Kiel, Institute for Natural Resource Conservation, Department of Hydrology and Water Resources Management, Kiel, Germany
| | - Longzhu Q Shen
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department Community and Ecosystem Ecology, Berlin, Germany
- Carnegie Mellon University, Institute for Green Science, Pittsburgh, Pennsylvania, USA
| | - Ismael Soto
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Vodňany, Czech Republic
| | - David G Angeler
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Núria Bonada
- Freshwater Ecology, Hydrology and Management, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Miguel Cañedo-Argüelles
- Freshwater Ecology, Hydrology and Management, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), Barcelona, Spain
| | - Zoltán Csabai
- Department of Hydrobiology, University of Pécs, Pécs, Hungary
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Thibault Datry
- INRAE, UR RiverLy, centre de Lyon-Villeurbanne, Villeurbanne, France
| | | | - Alain Dohet
- Environmental Research and Innovation (ERIN) Luxembourg Institute of Science and Technology (LIST), Belvaux, Luxembourg
| | - Emma Drohan
- Institute of Technology, Centre for Freshwater and Environmental Studies, Dundalk, Ireland
| | | | - Maria J Feio
- MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Marie A E Forio
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Peter Goethals
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Wolfram Graf
- University of Natural Resources and Life Sciences, Institute of Hydrobiology and Aquatic Ecosystem Management, Vienna, Austria
| | - Jani Heino
- Finnish Environment Institute, Freshwater Centre, Oulu, Finland
| | - Emma J Hudgins
- Department of Biology, Carleton University, Ottawa, Canada
| | - Sonja C Jähnig
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department Community and Ecosystem Ecology, Berlin, Germany
- Geography Department, Faculty of Mathematics and Natural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Richard K Johnson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Aitor Larrañaga
- Department of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Patrick Leitner
- University of Natural Resources and Life Sciences, Institute of Hydrobiology and Aquatic Ecosystem Management, Vienna, Austria
| | - Lionel L'Hoste
- Environmental Research and Innovation (ERIN) Luxembourg Institute of Science and Technology (LIST), Belvaux, Luxembourg
| | - Marie-Helene Lizee
- RECOVER Research Unit, National Research Institute for Agriculture, Food and Environment (INRAE), Aix-en-Provence, France
| | - Anthony Maire
- EDF R&D, Laboratoire National d'Hydraulique et Environnement (LNHE), Chatou, France
| | - Jes J Rasmussen
- Section for Nature Based Solutions, Norwegian Institute for Water Research (NIVA), Oslo, Norway
| | - Ralf B Schäfer
- University of Koblenz Landau, Institute for Environmental Sciences, Landau, Germany
| | - Astrid Schmidt-Kloiber
- University of Natural Resources and Life Sciences, Institute of Hydrobiology and Aquatic Ecosystem Management, Vienna, Austria
| | | | - Gábor Várbíró
- Department of Tisza Research, Institute of Aquatic Ecology, Centre for Ecological Research, Debrecen, Hungary
| | | | - Peter Haase
- Senckenberg Research Institute and Natural History Museum Frankfurt, Department of River Ecology and Conservation, Gelnhausen, Germany
- University of Duisburg-Essen, Faculty of Biology, Essen, Germany
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12
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Butterwort V, Dansby H, Zink FA, Tembrock LR, Gilligan TM, Godoy A, Braswell WE, Kawahara AY. A DNA Extraction Method for Insects From Sticky Traps: Targeting a Low Abundance Pest, Phthorimaea absoluta (Lepidoptera: Gelechiidae), in Mixed Species Communities. JOURNAL OF ECONOMIC ENTOMOLOGY 2022; 115:844-851. [PMID: 35391487 DOI: 10.1093/jee/toac046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Invasive insects can cause catastrophic damage to ecosystems and cost billions of dollars each year due to management expenses and lost revenue. Rapid detection is an important step to prevent invasive insects from spreading, but improvements in detection capabilities are needed for bulk collections like those from sticky traps. Here we present a bulk DNA extraction method designed for the detection of Phthorimaea absoluta Meyrick (Lepidoptera: Gelechiidae), an invasive moth that can decimate tomato crops. We test the extraction method for insect specimens on sticky traps, subjected to different temperature and humidity conditions, and among mock insect communities left in the field for up to 21 d. We find that the extraction method yielded high success (>92%) in recovering target DNA across field and lab trials, without a decline in recovery after three weeks, across all treatments. These results may have a large impact on tomato growing regions where P. absoluta is in the early stages of invasion or not yet present. The extraction method can also be used to improve detection capabilities for other bulk insect collections, especially those using sticky traps, to the benefit of pest surveys and biodiversity studies.
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Affiliation(s)
- V Butterwort
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32511, USA
| | - H Dansby
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32511, USA
| | - F A Zink
- Department of Agricultural Biology, 1177 Campus Delivery, Colorado State University, Fort Collins, CO 80523, USA
| | - L R Tembrock
- Department of Agricultural Biology, 1177 Campus Delivery, Colorado State University, Fort Collins, CO 80523, USA
| | - T M Gilligan
- USDA-APHIS-PPQ-Science & Technology, Identification Technology Program, 2301 Research Boulevard, Suite 108, Fort Collins, CO 80526, USA
| | - A Godoy
- USDA-APHIS-PPQ-Science & Technology, Insect Management and Molecular Diagnostics Laboratory, 22675 N. Moorfield Road, Building 6414, Edinburg, TX 78541, USA
| | - W E Braswell
- USDA-APHIS-PPQ-Science & Technology, Insect Management and Molecular Diagnostics Laboratory, 22675 N. Moorfield Road, Building 6414, Edinburg, TX 78541, USA
| | - A Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32511, USA
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13
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Couton M, Lévêque L, Daguin-Thiébaut C, Comtet T, Viard F. Water eDNA metabarcoding is effective in detecting non-native species in marinas, but detection errors still hinder its use for passive monitoring. BIOFOULING 2022; 38:367-383. [PMID: 35575060 DOI: 10.1080/08927014.2022.2075739] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/21/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Marinas are high-priority targets for marine non-indigenous species (NIS), where they compose a large portion of the biofouling communities. The practicality of water samples collection makes environmental DNA (eDNA) metabarcoding an interesting tool for routine NIS surveys. Here the effectiveness of water-eDNA-metabarcoding to identify biofouling NIS, in 10 marinas from western France, was examined. Morphological identification of specimens collected in quadrats brought out 18 sessile benthic NIS beneath floating pontoons. Water-eDNA-metabarcoding detected two thirds of them, failing to detect important NIS. However, sampling and bioinformatics filtering steps can be optimized to identify more species. In addition, this method allowed the detection of additional NIS from neighboring micro-habitats. Caution should, however, be taken when reporting putative novel NIS, because of errors in species assignment. This work highlights that water-eDNA-metabarcoding is effective for active (targeted) NIS surveys and could be significantly improved for its further use in marine NIS passive surveys.
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Affiliation(s)
- Marjorie Couton
- Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Laurent Lévêque
- Sorbonne Université, CNRS, FR 2424, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Claire Daguin-Thiébaut
- Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Thierry Comtet
- Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Frédérique Viard
- Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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14
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Pinho CJ, Lopes EP, Paupério J, Gomes I, Romeiras MM, Vasconcelos R. Trust your guts? The effect of gut section on diet composition and impact of
Mus musculus
on islands using metabarcoding. Ecol Evol 2022; 12:e8638. [PMID: 35309743 PMCID: PMC8901889 DOI: 10.1002/ece3.8638] [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: 08/06/2021] [Revised: 01/20/2022] [Accepted: 01/27/2022] [Indexed: 11/11/2022] Open
Abstract
DNA metabarcoding is widely used to characterize the diet of species, and it becomes very relevant for biodiversity conservation, allowing the understanding of trophic chains and the impact of invasive species. The need for cost‐effective biodiversity monitoring methods fostered advances in this technique. One question that arises is which sample type provides a better diet representation. Therefore, with this study, we intended to evaluate if there were differences in diet estimates according to the section of the gastrointestinal tract analysed and which section(s) provided the best diet representation. Additionally, we intended to infer the ecological/economic impacts of an invader as a model of the potential effects in an originally mammal‐free ecosystem. We examined the gut contents of the house mouse Mus musculus introduced to Cabo Verde, considering three sections: stomach, small intestine, and large intestine. We applied a DNA‐metabarcoding approach using two genetic markers, one specific for plants and another for invertebrates. We showed that this invader consumed 131 taxa (73 plants and 58 invertebrates). We obtained significant differences in the composition of two of the three sections, with a higher incidence of invertebrates in the stomach and plants in the intestines. This may be due to stomach inhibitors acting on plants and/or to faster absorption of soft‐body invertebrates compared to the plant fibers in the intestines. We verified that the impact of this invader in the ecosystem is predominantly negative, as at least 50% of the ingested items were native, endemic, or economically important taxa, and only 19% of the diet items were exotics. Overall, results showed the need to analyse only two gastrointestinal tract sections to obtain robust diet data, increasing the cost‐effectiveness of the method. Furthermore, by uncovering the native taxa most frequently preyed on by mice, this DNA‐metabarcoding approach allowed us to evaluate efficiently which are at the highest risk.
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Affiliation(s)
- Catarina J. Pinho
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do PortoVairão Portugal
- Departamento de Biologia Faculdade de Ciências da Universidade do Porto Porto Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning CIBIO, Campus de Vairão Vairão Portugal
| | - Evandro P. Lopes
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do PortoVairão Portugal
- Departamento de Biologia Faculdade de Ciências da Universidade do Porto Porto Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning CIBIO, Campus de Vairão Vairão Portugal
- ISECMAR‐UTA Instituto Engenharia e Ciências do Mar da Universidade Técnica do AtlânticoMindelo Cabo Verde
| | - Joana Paupério
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do PortoVairão Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning CIBIO, Campus de Vairão Vairão Portugal
| | - Isildo Gomes
- INIDA Instituto Nacional de Investigação e Desenvolvimento AgrárioSantiago Cabo Verde
| | - Maria M. Romeiras
- LEAF‐ISA Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia Universidade de Lisboa Lisboa Portugal
| | - Raquel Vasconcelos
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do PortoVairão Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning CIBIO, Campus de Vairão Vairão Portugal
- ISECMAR‐UTA Instituto Engenharia e Ciências do Mar da Universidade Técnica do AtlânticoMindelo Cabo Verde
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15
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Zhang L, Yang J, Zhang Y, Shi J, Yu H, Zhang X. eDNA biomonitoring revealed the ecological effects of water diversion projects between Yangtze River and Tai Lake. WATER RESEARCH 2022; 210:117994. [PMID: 34974345 DOI: 10.1016/j.watres.2021.117994] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
Water diversion has been widely used to address water shortages and security issues. However, its long-term ecological impacts, particularly on the biodiversity and structure of the local community, have often been neglected due to limitations of conventional biomonitoring. Taking the water diversion projects from Yangtze River to Tai Lake (WDYT) as examples, environmental DNA (eDNA) metabarcoding was used to investigate the potential ecological impact of water diversion on the connected basins. Firstly, 136 phytoplankton genera/species, including 31 cyanobacteria and 105 eukaryotic phytoplankton (Euk-phytoplankton), were identified from 26 sites by metabarcoding of 16S rDNA V3 and 18S rDNA V9 regions. eDNA metabarcoding showed an obvious advantage in detecting nano/pico-plankton (< 20 μm in size) compared with the morphological approach. Secondly, more shared taxa and higher similarity of community composition were observed in Gonghu Bay/Zhushan Bay with its connected river than with the center of Tai Lake, indicating that water diversions were accelerating the biotic homogenization between different waterbodies. Skeletonema potamos, the native species of Yangtze River (4.04% of the total Euk-phytoplankton reads) was detected in different connecting regions of Tai Lake (0.03%-0.54% of the total Euk-phytoplankton reads), where its relative abundance was consistent with the influence of water diversion from Yangtze River. Furthermore, the introduction of S. potamos significantly affected the local community compositions of phytoplankton in Tai Lake. Finally, the ecological effect (e.g., taxa richness, community composition and species invasion) of the WDYT on phytoplankton in the west of Tai Lake was more significant than that in the east, which was consistent with the scale (volume and duration) of the water diversion projects. Overall, this study highlights the value of eDNA biomonitoring in the ecological impact assessment of water transfer projects.
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Affiliation(s)
- Lijuan Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jianghua Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yong Zhang
- Jiangsu Provincial Environmental Monitoring Center, Nanjing, Jiangsu 210036, China
| | - Junzhe Shi
- Wuxi Environmental Monitoring Center of Jiangsu Province, Wuxi, Jiangsu 214121, China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China.
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16
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ITS DNA Barcoding Reveals That Halophila stipulacea Still Remains the Only Non-Indigenous Seagrass of the Mediterranean Sea. DIVERSITY 2022. [DOI: 10.3390/d14020076] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Non-indigenous species (NIS) are one of the major threats to the native marine ecosystems of the Mediterranean Sea. Halophila stipulacea was the only exotic seagrass of the Mediterranean until 2018, when small patches of a species morphologically identified as Halophila decipiens were reported in Salamina Island, Greece. Given the absence of reproductive structures during the identification and the taxonomic ambiguities known to lead to misidentifications on this genus, we reassessed the identity of this new exotic record using DNA barcoding (rbcL, matK and ITS) and the recently published taxonomic key. Despite their morphologic similarity to H. decipiens based on the new taxonomic key, the specimens showed no nucleotide differences with H. stipulacea specimens (Crete) for the three barcodes and clustered together on the ITS phylogenetic tree. Considering the high species resolution of the ITS region and the common morphological variability within the genus, the unequivocal genetic result suggests that the Halophila population found in Salamina Island most likely corresponds to a morphologically variant H. stipulacea. Our results highlight the importance of applying an integrated taxonomic approach (morphological and molecular) to taxonomically complex genera such as Halophila, in order to avoid overlooking or misreporting species range shifts, which is essential for monitoring NIS introductions.
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17
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Saito T. Monitoring and databasing nonnative species to manage establishment debt in aquatic ecosystems. Ecol Res 2022. [DOI: 10.1111/1440-1703.12295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takumi Saito
- Department of Biology, Faculty of Science Toho University Funabashi Chiba Japan
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18
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New developments in the field of genomic technologies and their relevance to conservation management. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01415-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
AbstractRecent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from the toolbox is crucial and can pose a challenging task. With this in mind, we strive to inspire, inform and illuminate managers and practitioners on how conservation efforts can benefit from the current genomic and biotechnological revolution. With inspirational case studies we show how new technologies can help resolve some of the main conservation challenges, while also informing how implementable the different technologies are. We here focus specifically on small population management, highlight the potential for genetic rescue, and discuss the opportunities in the field of gene editing to help with adaptation to changing environments. In addition, we delineate potential applications of gene drives for controlling invasive species. We illuminate that the genomic toolbox offers added benefit to conservation efforts, but also comes with limitations for the use of these novel emerging techniques.
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19
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Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates. WATER 2021. [DOI: 10.3390/w13030331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Benthic macroinvertebrates are among the most used biological quality elements for assessing the condition of all types of aquatic ecosystems worldwide (i.e., fresh water, transitional, and marine). Current morphology-based assessments have several limitations that may be circumvented by using DNA-based approaches. Here, we present a comprehensive review of 90 publications on the use of DNA metabarcoding of benthic macroinvertebrates in aquatic ecosystems bioassessments. Metabarcoding of bulk macrozoobenthos has been preferentially used in fresh waters, whereas in marine waters, environmental DNA (eDNA) from sediment and bulk communities from deployed artificial structures has been favored. DNA extraction has been done predominantly through commercial kits, and cytochrome c oxidase subunit I (COI) has been, by far, the most used marker, occasionally combined with others, namely, the 18S rRNA gene. Current limitations include the lack of standardized protocols and broad-coverage primers, the incompleteness of reference libraries, and the inability to reliably extrapolate abundance data. In addition, morphology versus DNA benchmarking of ecological status and biotic indexes are required to allow general worldwide implementation and higher end-user confidence. The increased sensitivity, high throughput, and faster execution of DNA metabarcoding can provide much higher spatial and temporal data resolution on aquatic ecological status, thereby being more responsive to immediate management needs.
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20
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Duarte S, Vieira PE, Lavrador AS, Costa FO. Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:141729. [PMID: 32889465 DOI: 10.1016/j.scitotenv.2020.141729] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 06/11/2023]
Abstract
In coastal ecosystems, non-indigenous species (NIS) are recognized as a major threat to biodiversity, ecosystem functioning and socio-economic activities. Here we present a systematic review on the use of metabarcoding for NIS surveillance in marine and coastal ecosystems, through the analysis of 42 publications. Metabarcoding has been mainly applied to environmental DNA (eDNA) from water samples, but also to DNA extracted from bulk organismal samples. DNA extraction kits have been widely used and the 18S rRNA and the COI genes the most employed markers, but less than half of the studies targeted more than one marker loci. The Illumina MiSeq platform has been used in >50% of the publications. Current weaknesses include potential occurrence of false negatives due to the primer-biased or faulty DNA amplification and the incompleteness of reference libraries. This is particularly concerning in the case of NIS surveillance, where proficiency in species level detection is critical. Until these weaknesses are resolved, ideally NIS metabarcoding should be supported by complementary approaches, such as morphological analysis or more targeted molecular approaches (e.g. qPCR, ddPCR). Even so, metabarcoding has already proved to be a highly sensitive tool to detect small organisms or undifferentiated life stages across a wide taxonomic range. In addition, it also seems to be very effective in ballast water management and to improve the spatial and temporal sampling frequency of NIS surveillance in marine and coastal ecosystems. Although specific protocols may be required for species-specific NIS detection, for general monitoring it would be vital to settle on a standard protocol able to generate comparable results among surveillance campaigns and regions of the globe, seeking the best approach for detecting the broadest range of species, while minimizing the chances of a false positive or negative detection.
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Affiliation(s)
- Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Pedro E Vieira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Ana S Lavrador
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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21
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Gleason JE, Elbrecht V, Braukmann TWA, Hanner RH, Cottenie K. Assessment of stream macroinvertebrate communities with eDNA is not congruent with tissue-based metabarcoding. Mol Ecol 2020; 30:3239-3251. [PMID: 32799390 DOI: 10.1111/mec.15597] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 07/18/2020] [Indexed: 02/06/2023]
Abstract
Freshwater biomonitoring programmes routinely sample aquatic macroinvertebrates. These samples are time-consuming to collect, as well as challenging and costly to identify reliably genus or species. Environmental DNA (eDNA) metabarcoding has emerged as a surrogate to traditional collection techniques and has been used in whole-community approaches across several taxa and ecosystems. However, the usefulness of eDNA-based detection of freshwater macroinvertebrates has not been extensively explored. Few studies have directly compared bulk sample and eDNA metabarcoding at a local scale to assess how effective each method is at characterizing aquatic macroinvertebrate communities. Here, we collected both eDNA and kicknet samples at the same sample transect locations across nine different streams in southern Ontario, Canada. We observed minimal overlap in community composition between these paired samples. Bulk tissue metabarcoding resulted in a greater proportion of sequences belonging to metazoan taxa (over 99%) than eDNA (12%) and had higher OTU richness for macroinvertebrate taxa. We suggest that degenerate primers are not effective for eDNA metabarcoding due to the high degree of nontarget amplification and subsequently low yield of target DNA. While both bulk sample and eDNA metabarcoding had the power to detect differences between stream communities, eDNA did not represent local communities. Bulk tissue metabarcoding thus provides a more accurate representation of local stream macroinvertebrate communities and is the preferred method if smaller-scale spatial resolution is an important factor in data analyses.
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Affiliation(s)
| | - Vasco Elbrecht
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany.,Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Robert H Hanner
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Karl Cottenie
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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22
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Xiong W, Huang X, Chen Y, Fu R, Du X, Chen X, Zhan A. Zooplankton biodiversity monitoring in polluted freshwater ecosystems: A technical review. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2019; 1:100008. [PMCID: PMC9488063 DOI: 10.1016/j.ese.2019.100008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 05/26/2023]
Abstract
Freshwater ecosystems harbor a vast diversity of micro-eukaryotes (rotifers, crustaceans and protists), and such diverse taxonomic groups play important roles in ecosystem functioning and services. Unfortunately, freshwater ecosystems and biodiversity therein are threatened by many environmental stressors, particularly those derived from intensive human activities such as chemical pollution. In the past several decades, significant efforts have been devoted to halting biodiversity loss to recover services and functioning of freshwater ecosystems. Biodiversity monitoring is the first and a crucial step towards diagnosing pollution impacts on ecosystems and making conservation plans. Yet, bio-monitoring of ubiquitous micro-eukaryotes is extremely challenging, owing to many technical issues associated with micro-zooplankton such as microscopic size, fuzzy morphological features, and extremely high biodiversity. Here, we review current methods used for monitoring zooplankton biodiversity to advance management of impaired freshwater ecosystems. We discuss the development of traditional morphology-based identification methods such as scanning electron microscope (SEM) and ZOOSCAN and FlowCAM automatic systems, and DNA-based strategies such as metabarcoding and real-time quantitative PCR. In addition, we summarize advantages and disadvantages of these methods when applied for monitoring impacted ecosystems, and we propose practical DNA-based monitoring workflows for studying biological consequences of environmental pollution in freshwater ecosystems. Finally, we propose possible solutions for existing technical issues to improve accuracy and efficiency of DNA-based biodiversity monitoring. Freshwater ecosystems and associated biodiversity have been highly degraded. Biodiversity monitoring is crucial for diagnosing degradation degrees. Here we review available methods for monitoring zooplankton biodiversity. We propose possible solutions for existing technical issues.
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Affiliation(s)
- Wei Xiong
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Ruiying Fu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Xun Du
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Xingyu Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
- College of Resources, Environment and Tourism, Capital Normal University, 105 West Third Ring Road, Haidian District, Beijing, 100048, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China
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