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Li X, Chen K, Wang C, Zhuo T, Li H, Wu Y, Lei X, Li M, Chen B, Chai B. Deciphering environmental factors influencing phytoplankton community structure in a polluted urban river. J Environ Sci (China) 2025; 148:375-386. [PMID: 39095172 DOI: 10.1016/j.jes.2023.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 08/04/2024]
Abstract
Tuojiang River Basin is a first-class tributary of the upper reaches of the Yangtze River-which is the longest river in China. As phytoplankton are sensitive indicators of trophic changes in water bodies, characterizing phytoplankton communities and their growth influencing factors in polluted urban rivers can provide new ideas for pollution control. Here, we used direct microscopic count and environmental DNA (eDNA) metabarcoding methods to investigate phytoplankton community structure in Tuojiang River Basin (Chengdu, Sichuan Province, China). The association between phytoplankton community structure and water environmental factors was evaluated by Mantel analysis. Additional environmental monitoring data were used to pinpoint major factors that influenced phytoplankton growth based on structural equation modeling. At the phylum level, the dominant phytoplankton taxa identified by the conventional microscopic method mainly belonged to Bacillariophyta, Chlorophyta, and Cyanophyta, in contrast with Chlorophyta, Dinophyceae, and Bacillariophyta identified by eDNA metabarcoding. In α-diversity analysis, eDNA metabarcoding detected greater species diversity and achieved higher precision than the microscopic method. Phytoplankton growth was largely limited by phosphorus based on the nitrogen-to-phosphorus ratios > 16:1 in all water samples. Redundancy analysis and structural equation modeling also confirmed that the nitrogen-to-phosphorus ratio was the principal factor influencing phytoplankton growth. The results could be useful for implementing comprehensive management of the river basin environment. It is recommended to control the discharge of point- and surface-source pollutants and the concentration of dissolved oxygen in areas with excessive nutrients (e.g., Jianyang-Ziyang). Algae monitoring techniques and removal strategies should be improved in 201 Hospital, Hongrihe Bridge and Colmar Town areas.
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Affiliation(s)
- Xiaxia Li
- School of Water Conservancy and Hydroelectric Power, Hebei University of Engineering, Handan 056038, China; Collaborative Innovation Center for Intelligent Regulation and Comprehensive Management of Water Resources, School of Water Conservancy and Hydroelectric, Hebei University of Engineering, Handan 056038, China; Hebei Key Laboratory of Intelligent Water Conservancy, Hebei University of Engineering, Handan 056038, China
| | - Kai Chen
- Tianjin Water Group Binhai Water Co., Ltd., Tianjin 300308, China
| | - Chao Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100038, China.
| | - Tianyu Zhuo
- School of Architecture and Civil Engineering, Xi'an University of Science and Technology, Xi'an 710054, China
| | - Hongtao Li
- Chengdu University of Technology, Chengdu 610059, China
| | - Yong Wu
- Chengdu University of Technology, Chengdu 610059, China
| | - Xiaohui Lei
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100038, China
| | - Ming Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Bin Chen
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Beibei Chai
- Collaborative Innovation Center for Intelligent Regulation and Comprehensive Management of Water Resources, School of Water Conservancy and Hydroelectric, Hebei University of Engineering, Handan 056038, China; Hebei Key Laboratory of Intelligent Water Conservancy, Hebei University of Engineering, Handan 056038, China.
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Lavrador AS, Amaral FG, Moutinho J, Vieira PE, Costa FO, Duarte S. Comprehensive DNA metabarcoding-based detection of non-indigenous invertebrates in recreational marinas through a multi-substrate approach. MARINE ENVIRONMENTAL RESEARCH 2024; 200:106660. [PMID: 39088889 DOI: 10.1016/j.marenvres.2024.106660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/15/2024] [Accepted: 07/29/2024] [Indexed: 08/03/2024]
Abstract
eDNA metabarcoding has been increasingly employed in the monitoring of marine invertebrate non-indigenous species (NIS), in particular using filtered seawater. However, comprehensive detection of all NIS may require a diversity of sampling substrates. To assess the effectiveness of 5 sample types (hard and artificial substrates, water, zooplankton) on the recovery of invertebrates' diversity, two marinas were monitored over three time points, using COI and 18S rRNA genes as DNA metabarcoding markers. We detected a total of 628 species and 23 NIS, with only up to 9% species and 17% of NIS detected by all sample types. Hard and artificial substrates were similar to each other but displayed the most significant difference in invertebrate recovery when compared to water eDNA and zooplankton. Five NIS are potential first records for Portugal. No NIS were detected in all sample types and seasons, highlighting the need for varied sampling approaches, and consideration of temporal variation for comprehensive marine NIS surveillance.
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Affiliation(s)
- Ana S Lavrador
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, 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.
| | - Fábio G Amaral
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, 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
| | - Jorge Moutinho
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, 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) and ARNET-Aquatic Research Network, 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) and ARNET-Aquatic Research Network, 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
| | - Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, 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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3
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Ardura A, Fernandez S, Planes S, Garcia-Vazquez E. Environmental DNA for the surveillance of biosecurity threats in Mediterranean lagoons. MARINE ENVIRONMENTAL RESEARCH 2024; 199:106601. [PMID: 38875900 DOI: 10.1016/j.marenvres.2024.106601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 06/03/2024] [Accepted: 06/07/2024] [Indexed: 06/16/2024]
Abstract
Invasive species that outcompete endemic ones and toxic harmful algae that cause algal blooms threaten marine resources like fisheries, aquaculture, and even tourism. Environmental DNA (eDNA) metabarcoding can help as a method for early alert. In this study, we have analyzed communities inhabiting six lagoons within the Gulf of Lion (northwest Mediterranean Sea) with spatial protection as RAMSAR and Natura 2000 sites. Employing the COI gene as the only metabarcode, we found 15 genera that have caused recognized algal bloom outbreaks in the studied lagoons since 2000. In addition, seven alien invasive species that can pose risks to the rich marine resources of the zone and lagoons were also found. The results found from eDNA are consistent with events of toxic algae blooms before and after the sampling moment and with reported occurrences of the invasive species in nearby Mediterranean areas. Multivariate multiple analysis showed the importance of anthropic pressure in the abundance of these nuisance species. Mitigation actions and routine eDNA metabarcoding in zones of special interest like these fragile French Mediterranean lagoons are recommended for early alert of nuisance species in order to plan timely management actions.
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Affiliation(s)
- Alba Ardura
- Department of Functional Biology, C/ Julian Claveria s/n, 33006, Oviedo, Spain; Centro Universitario para la Investigación y el Desarrollo del Agua (CUIDA), Edificio de Investigación del Campus de Mieres, University of Oviedo, C/Gonzalo Gutiérrez Quirós, s/n, 33600, Mieres, Spain.
| | - Sara Fernandez
- Department of Functional Biology, C/ Julian Claveria s/n, 33006, Oviedo, Spain
| | - Serge Planes
- USR3278 CRIOBE EPHE-CNRS-UPVD, 66860, Perpignan, France; Centre de Recherche Insulaire et Observatoire de l'Environnement, Moorea, French Polynesia
| | - Eva Garcia-Vazquez
- Department of Functional Biology, C/ Julian Claveria s/n, 33006, Oviedo, Spain; Centro Universitario para la Investigación y el Desarrollo del Agua (CUIDA), Edificio de Investigación del Campus de Mieres, University of Oviedo, C/Gonzalo Gutiérrez Quirós, s/n, 33600, Mieres, Spain
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Rishan ST, Kline RJ, Rahman MS. Exploitation of environmental DNA (eDNA) for ecotoxicological research: A critical review on eDNA metabarcoding in assessing marine pollution. CHEMOSPHERE 2024; 351:141238. [PMID: 38242519 DOI: 10.1016/j.chemosphere.2024.141238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 01/05/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
The rise in worldwide population has led to a noticeable spike in the production, consumption, and transportation of energy and food, contributing to elevated environmental pollution. Marine pollution is a significant global environmental issue with ongoing challenges, including plastic waste, oil spills, chemical pollutants, and nutrient runoff, threatening marine ecosystems, biodiversity, and human health. Pollution detection and assessment are crucial to understanding the state of marine ecosystems. Conventional approaches to pollution evaluation usually represent laborious and prolonged physical and chemical assessments, constraining their efficacy and expansion. The latest advances in environmental DNA (eDNA) are valuable methods for the detection and surveillance of pollution in the environment, offering enhanced sensibility, efficacy, and involvement. Molecular approaches allow genetic information extraction from natural resources like water, soil, or air. The application of eDNA enables an expanded evaluation of the environmental condition by detecting both identified and unidentified organisms and contaminants. eDNA methods are valuable for assessing community compositions, providing indirect insights into the intensity and quality of marine pollution through their effects on ecological communities. While eDNA itself is not direct evidence of pollution, its analysis offers a sensitive tool for monitoring changes in biodiversity, serving as an indicator of environmental health and allowing for the indirect estimation of the impact and extent of marine pollution on ecosystems. This review explores the potential of eDNA metabarcoding techniques for detecting and identifying marine pollutants. This review also provides evidence for the efficacy of eDNA assessment in identifying a diverse array of marine pollution caused by oil spills, harmful algal blooms, heavy metals, ballast water, and microplastics. In this report, scientists can expand their knowledge and incorporate eDNA methodologies into ecotoxicological research.
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Affiliation(s)
- Sakib Tahmid Rishan
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA
| | - Richard J Kline
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA; School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA
| | - Md Saydur Rahman
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA; School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA.
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Papaioannou C, Geladakis G, Kommata V, Batargias C, Lagoumintzis G. Insights in Pharmaceutical Pollution: The Prospective Role of eDNA Metabarcoding. TOXICS 2023; 11:903. [PMID: 37999555 PMCID: PMC10675236 DOI: 10.3390/toxics11110903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/25/2023]
Abstract
Environmental pollution is a growing threat to natural ecosystems and one of the world's most pressing concerns. The increasing worldwide use of pharmaceuticals has elevated their status as significant emerging contaminants. Pharmaceuticals enter aquatic environments through multiple pathways related to anthropogenic activity. Their high consumption, insufficient waste treatment, and the incapacity of organisms to completely metabolize them contribute to their accumulation in aquatic environments, posing a threat to all life forms. Various analytical methods have been used to quantify pharmaceuticals. Biotechnology advancements based on next-generation sequencing (NGS) techniques, like eDNA metabarcoding, have enabled the development of new methods for assessing and monitoring the ecotoxicological effects of pharmaceuticals. eDNA metabarcoding is a valuable biomonitoring tool for pharmaceutical pollution because it (a) provides an efficient method to assess and predict pollution status, (b) identifies pollution sources, (c) tracks changes in pharmaceutical pollution levels over time, (d) assesses the ecological impact of pharmaceutical pollution, (e) helps prioritize cleanup and mitigation efforts, and (f) offers insights into the diversity and composition of microbial and other bioindicator communities. This review highlights the issue of aquatic pharmaceutical pollution while emphasizing the importance of using modern NGS-based biomonitoring actions to assess its environmental effects more consistently and effectively.
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Affiliation(s)
- Charikleia Papaioannou
- Department of Biology, University of Patras, 26504 Patras, Greece; (C.P.); (G.G.); (V.K.)
| | - George Geladakis
- Department of Biology, University of Patras, 26504 Patras, Greece; (C.P.); (G.G.); (V.K.)
| | - Vasiliki Kommata
- Department of Biology, University of Patras, 26504 Patras, Greece; (C.P.); (G.G.); (V.K.)
| | - Costas Batargias
- Department of Biology, University of Patras, 26504 Patras, Greece; (C.P.); (G.G.); (V.K.)
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Specchia V, Zangaro F, Tzafesta E, Saccomanno B, Vadrucci MR, Pinna M. Environmental DNA detects biodiversity and ecological features of phytoplankton communities in Mediterranean transitional waters. Sci Rep 2023; 13:15192. [PMID: 37709858 PMCID: PMC10502138 DOI: 10.1038/s41598-023-42389-3] [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: 05/19/2023] [Accepted: 09/09/2023] [Indexed: 09/16/2023] Open
Abstract
Climate changes and anthropogenic pressures are causing a biodiversity decline in terms of species number and genetic diversity, reducing the adaptability and evolvability of natural communities. Transitional water ecosystems are more sensitive to habitat reduction and degradation and, thus, are more exposed to biodiversity declines requiring biodiversity monitoring programs for their conservation. Environmental DNA (eDNA) metabarcoding represents a high-throughput tool for biodiversity assessment that is facilitating data collection for biodiversity monitoring. In this study, we applied, for the first time, eDNA metabarcoding in a Mediterranean coastal lagoon to assess the ecological features of eukaryotic phytoplankton communities. We sampled water in seven different lagoon sites and amplified the extracted DNA with primers targeting the variable region 4 (V4) of the 18S rRNA gene marker. The results demonstrated the validity of eDNA studies to provide insights into lagoon phytoplankton composition, establish the structure and spatial variation of phytoplankton communities, and evaluate its correlation to abiotic factors. Finally, the genetic distances analysis suggests that the different spatial distribution of OTUs, at least for the Tetraselmis genus, reflects the genetic background.
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Affiliation(s)
- Valeria Specchia
- Department of Biological and Environmental Sciences and Technologies, DiSTeBA, University of Salento, via Monteroni 165, 73100, Lecce, Italy.
- NBFC, National Biodiversity Future Center, 90133, Palermo, Italy.
| | - Francesco Zangaro
- Department of Biological and Environmental Sciences and Technologies, DiSTeBA, University of Salento, via Monteroni 165, 73100, Lecce, Italy
| | - Eftychia Tzafesta
- Department of Biological and Environmental Sciences and Technologies, DiSTeBA, University of Salento, via Monteroni 165, 73100, Lecce, Italy
| | - Benedetta Saccomanno
- Department of Biological and Environmental Sciences and Technologies, DiSTeBA, University of Salento, via Monteroni 165, 73100, Lecce, Italy
| | - Maria Rosaria Vadrucci
- Regional Agency for the Environmental Prevention and Protection (ARPA Puglia), Corso Trieste 27, Bari, Italy
| | - Maurizio Pinna
- Department of Biological and Environmental Sciences and Technologies, DiSTeBA, University of Salento, via Monteroni 165, 73100, Lecce, Italy.
- NBFC, National Biodiversity Future Center, 90133, Palermo, Italy.
- Research Centre for Fisheries and Aquaculture of Acquatina di Frigole, DiSTeBA, University of Salento, 73100, Lecce, Italy.
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Zhang J, Ding R, Wang Y, Wen J. Experimental study on the response relationship between environmental DNA concentration and biomass of Schizothorax prenanti in still water. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.972680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The superiority of the environmental DNA (eDNA) method for estimating the biomass of aquatic species has been demonstrated. However, the relationship between eDNA concentration and biomass is difficult to clarify under the influence of complex water flow and habitat conditions. It seriously restricts the popularization and application of the eDNA method in estimating aquatic biomass. In this paper, a typical fish species of rivers in southwest China, Schizothorax prenanti, was selected as the target species. Under standardized laboratory hydrostatic conditions, two environmental factors, water pH and water temperature were firstly determined through pre-experiments. Then we investigated the correlation between eDNA concentration and biomass under different body sizes and different body size compositions. The experimental results showed that water pH and the water temperature had a great influence on eDNA concentration. Therefore, the effects of these environmental factors need to be considered simultaneously when using eDNA concentration to estimate biomass. Under the premise of consistent environmental conditions, the biomass of Schizothorax prenanti was positively correlated with the eDNA concentration when the individual body size was the same. For each 1% increase in biomass of the fish, the eDNA concentration of adult (larger size) fish increased by 0.98%, while the eDNA concentration of juvenile (smaller size) fish increased by 1.38%. The smaller the size of individual fish, the greater the increase of eDNA concentration with biomass, and the increase of juvenile fish was about 1.4 times that the adult fish. When the biomass was the same but the body size composition was different, the higher the proportion of small body size individuals in the population, the higher the eDNA concentration. Special attention needs to be paid to the body size composition of the population to avoid the biomass estimation being lower than the actual value when the smaller size fish are dominant. The experimental results provide a strong basis for a more accurate estimation of aquatic biomass in reservoirs, lakes, and other still water areas by using the eDNA method.
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Keller AG, Grason EW, McDonald PS, Ramón-Laca A, Kelly RP. Tracking an invasion front with environmental DNA. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e2561. [PMID: 35128750 DOI: 10.1002/eap.2561] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/21/2021] [Accepted: 12/14/2021] [Indexed: 05/03/2023]
Abstract
Data from environmental DNA (eDNA) may revolutionize environmental monitoring and management, providing increased detection sensitivity at reduced cost and survey effort. However, eDNA data are rarely used in decision-making contexts, mainly due to uncertainty around (1) data interpretation and (2) whether and how molecular tools dovetail with existing management efforts. We address these challenges by jointly modeling eDNA detection via qPCR and traditional trap data to estimate the density of invasive European green crab (Carcinus maenas), a species for which, historically, baited traps have been used for both detection and control. Our analytical framework simultaneously quantifies uncertainty in both detection methods and provides a robust way of integrating different data streams into management processes. Moreover, the joint model makes clear the marginal information benefit of adding eDNA (or any other) additional data type to an existing monitoring program, offering a path to optimizing sampling efforts for species of management interest. Here, we document green crab eDNA beyond the previously known invasion front and find that the value of eDNA data dramatically increases with low population densities and low traditional sampling effort, as is often the case at leading-edge locations. We also highlight the detection limits of the molecular assay used in this study, as well as scenarios under which eDNA sampling is unlikely to improve existing management efforts.
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Affiliation(s)
- Abigail G Keller
- School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA
| | - Emily W Grason
- Washington Sea Grant, University of Washington, Seattle, Washington, USA
| | - P Sean McDonald
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Ana Ramón-Laca
- CICOES, University of Washington at Northwest Fisheries Science Center, Seattle, Washington, USA
| | - Ryan P Kelly
- School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA
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9
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Mediterranean Coastal Lagoons Review: Sites to Visit before Disappearance. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10030347] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Coastal lagoons are an established priority habitat in the European environment because of the biological communities that inhabit them. Their origin is related to the transport of sediments from a nearby river or the movement of sands by the marine currents that produce the closure of a gulf. Therefore, they are recent geological formations, which also disappear quickly if environmental conditions change. The 37 coastal lagoons with a surface area greater than 10 km2 located in the Mediterranean basin have been identified. Fishing has been the traditional use of these lagoons, in addition to their use as a navigation harbor when they are open to the sea. Pollution, quality problems and their consequences are the most studied topics in recent publications. Sentinel-2 images taken in the summer of 2020 have been used to study water transparency, suspended matter and chlorophyll a concentration. The result was that only six of them are in good ecological condition, but most of them are eutrophic due to the impacts on their environment and the inflow of poor quality water. The cultural values of these lagoons must also be protected and preserved.
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Vieira PE, Lavrador AS, Parente MI, Parretti P, Costa AC, Costa FO, Duarte S. Gaps in DNA sequence libraries for Macaronesian marine macroinvertebrates imply decades till completion and robust monitoring. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13305] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Pedro E. Vieira
- Centre of Molecular and Environmental Biology (CBMA) Department of Biology University of Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) University of Minho Braga Portugal
| | - Ana S. Lavrador
- Centre of Molecular and Environmental Biology (CBMA) Department of Biology University of Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) University of Minho Braga Portugal
| | - Manuela I. Parente
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Associate Laboratory University of Azores Ponta Delgada Portugal
| | - Paola Parretti
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Associate Laboratory University of Azores Ponta Delgada Portugal
- MARE – Marine and Environmental Sciences Centre Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI) Edifício Madeira Tecnopolo Funchal Portugal
| | - Ana C. Costa
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Associate Laboratory University of Azores Ponta Delgada Portugal
| | - Filipe O. Costa
- Centre of Molecular and Environmental Biology (CBMA) Department of Biology University of Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) University of Minho Braga Portugal
| | - Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA) Department of Biology University of Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) University of Minho Braga Portugal
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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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