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Shang L, Hu Z, Deng Y, Li J, Liu Y, Song X, Zhai X, Zhan Z, Tian W, Xu J, Han Y, Shen H, Ding H, Tang YZ. Transoceanic ships as a source of alien dinoflagellate invasions of inland freshwater ecosystems. HARMFUL ALGAE 2024; 135:102630. [PMID: 38830708 DOI: 10.1016/j.hal.2024.102630] [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: 12/11/2023] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/05/2024]
Abstract
Ships' ballast water and sediments have long been linked to the global transport and expansion of invasive species and thus have become a hot research topic and administrative challenge in the past decades. The relevant concerns, however, have been mainly about the ocean-to-ocean invasion and sampling practices have been almost exclusively conducted onboard. We examined and compared the dinoflagellate cysts assemblages in 49 sediment samples collected from ballast tanks of international and domestic routes ships, washing basins associated with a ship-repair yard, Jiangyin Port (PS), and the nearby area of Yangtze River (YR) during 2017-2018. A total of 43 dinoflagellates were fully identified to species level by metabarcoding, single-cyst PCR-based sequencing, cyst germination and phylogenetic analyses, including 12 species never reported from waters of China, 14 HABs-causing, 9 toxic, and 10 not strictly marine species. Our metabarcoding and single-cyst sequencing also detected many OTUs and cysts of dinoflagellates that could not be fully identified, indicating ballast tank sediments being a risky repository of currently unrecognizable invasive species. Particularly important, 10 brackish and fresh water species of dinoflagellate cysts (such as Tyrannodinium edax) were detected from the transoceanic ships, indicating these species may function as alien species potentially invading the inland rivers and adjacent lakes if these ships conduct deballast and other practices in fresh waterbodies. Significantly higher numbers of reads and OTUs of dinoflagellates in the ballast tanks and washing basins than that in PS and YR indicate a risk of releasing cysts by ships and the associated ship-repair yards to the surrounding waters. Phylogenetic analyses revealed high intra-species genetic diversity for multiple cyst species from different ballast tanks. Our work provides novel insights into the risk of bio-invasion to fresh waters conveyed in ship's ballast tank sediments and washing basins of shipyards.
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Affiliation(s)
- Lixia Shang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yunyan Deng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jing Li
- State Key Laboratory of Ballast Water Research, Comprehensive Technical Service Center of Jiangyin Customs, Jiangyin 214431, China
| | - Yuyang Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xiaoying Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinyu Zhai
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zifeng Zhan
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Wen Tian
- State Key Laboratory of Ballast Water Research, Comprehensive Technical Service Center of Jiangyin Customs, Jiangyin 214431, China
| | - Jinxiang Xu
- State Key Laboratory of Ballast Water Research, Comprehensive Technical Service Center of Jiangyin Customs, Jiangyin 214431, China
| | - Yangchun Han
- State Key Laboratory of Ballast Water Research, Comprehensive Technical Service Center of Jiangyin Customs, Jiangyin 214431, China
| | - Hao Shen
- State Key Laboratory of Ballast Water Research, Comprehensive Technical Service Center of Jiangyin Customs, Jiangyin 214431, China
| | - Hua Ding
- State Key Laboratory of Ballast Water Research, Comprehensive Technical Service Center of Jiangyin Customs, Jiangyin 214431, China
| | - Ying Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
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2
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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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3
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Thompson LR, Anderson SR, Den Uyl PA, Patin NV, Lim SJ, Sanderson G, Goodwin KD. Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake. Gigascience 2022; 11:6651346. [PMID: 35902092 PMCID: PMC9334028 DOI: 10.1093/gigascience/giac066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 02/28/2022] [Accepted: 06/15/2022] [Indexed: 12/21/2022] Open
Abstract
Background Amplicon sequencing (metabarcoding) is a common method to survey diversity of environmental communities whereby a single genetic locus is amplified and sequenced from the DNA of whole or partial organisms, organismal traces (e.g., skin, mucus, feces), or microbes in an environmental sample. Several software packages exist for analyzing amplicon data, among which QIIME 2 has emerged as a popular option because of its broad functionality, plugin architecture, provenance tracking, and interactive visualizations. However, each new analysis requires the user to keep track of input and output file names, parameters, and commands; this lack of automation and standardization is inefficient and creates barriers to meta-analysis and sharing of results. Findings We developed Tourmaline, a Python-based workflow that implements QIIME 2 and is built using the Snakemake workflow management system. Starting from a configuration file that defines parameters and input files—a reference database, a sample metadata file, and a manifest or archive of FASTQ sequences—it uses QIIME 2 to run either the DADA2 or Deblur denoising algorithm; assigns taxonomy to the resulting representative sequences; performs analyses of taxonomic, alpha, and beta diversity; and generates an HTML report summarizing and linking to the output files. Features include support for multiple cores, automatic determination of trimming parameters using quality scores, representative sequence filtering (taxonomy, length, abundance, prevalence, or ID), support for multiple taxonomic classification and sequence alignment methods, outlier detection, and automated initialization of a new analysis using previous settings. The workflow runs natively on Linux and macOS or via a Docker container. We ran Tourmaline on a 16S ribosomal RNA amplicon data set from Lake Erie surface water, showing its utility for parameter optimization and the ability to easily view interactive visualizations through the HTML report, QIIME 2 viewer, and R- and Python-based Jupyter notebooks. Conclusion Automated workflows like Tourmaline enable rapid analysis of environmental amplicon data, decreasing the time from data generation to actionable results. Tourmaline is available for download at github.com/aomlomics/tourmaline.
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Affiliation(s)
- Luke R Thompson
- Northern Gulf Institute, Mississippi State University, Mississippi State, MS 39762, USA.,Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL 33149, USA
| | - Sean R Anderson
- Northern Gulf Institute, Mississippi State University, Mississippi State, MS 39762, USA.,Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL 33149, USA
| | - Paul A Den Uyl
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI 48108, USA
| | - Nastassia V Patin
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL 33149, USA.,Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
| | - Shen Jean Lim
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL 33149, USA.,Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
| | - Grant Sanderson
- Marine Science Department, University of Hawaii, Hilo, HI 96720, USA
| | - Kelly D Goodwin
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL 33149, USA
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Pagenkopp Lohan KM, Darling JA, Ruiz GM. International shipping as a potent vector for spreading marine parasites. DIVERS DISTRIB 2022; 28:1922-1933. [PMID: 38269301 PMCID: PMC10807284 DOI: 10.1111/ddi.13592] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/10/2022] [Indexed: 12/21/2022] Open
Abstract
Aim The global shipping fleet, the primary means of transporting goods among countries, also serves as a major dispersal mechanism for marine invasive species. To date, researchers have primarily focussed on the role of ships in transferring marine macrofauna, often overlooking transfers of associated parasites, which can have larger impacts on naïve host individuals and populations. Here, we re-examine three previously published metabarcode datasets targeting zooplankton and protists in ships' ballast water to assess the diversity of parasites across life stages arriving to three major US ports. Location Port of Hampton Roads in the Chesapeake Bay, Virginia; Ports of Texas City, Houston and Bayport in Galveston Bay, Texas; and Port of Valdez in Prince William Sound, Alaska. Methods We selected all known parasitic taxa, using sequences generated from the small subunit gene (SSU) from ribosomal RNA (rRNA) amplified from (1) zooplankton collected from plankton tows (35 and 80 μm datasets) and (2) eukaryotes collected from samples of ships' ballast water (3 μm dataset). Results In all three datasets, we found a broad range of parasitic taxa, including many protistan and metazoan parasites, that infect a wide range of hosts, from teleost fish to dinoflagellates. Parasite richness was highest in the 3 μm dataset and relatively uniform across arrival regions. Several parasite taxa were found in high relative abundance (based on number of sequences recovered) either in ships entering a single or across multiple regions. Main Conclusions The ubiquity, diversity and relative abundance of parasites detected demonstrate ships are a potent vector for spreading marine parasites across the world's oceans, potentially contributing to reported increases in outbreaks of marine diseases. Future research is urgently needed to evaluate the fate of parasites upon arrival and the efficacy of ballast water treatment systems to reduce future transfers and colonization.
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Affiliation(s)
| | - John A. Darling
- Center for Environmental Measurement and Modeling, United States Environmental Protection Agency, Durham, North Carolina, USA
| | - Gregory M. Ruiz
- Marine Invasions Research Laboratory, Smithsonian Environmental Research Center, Edgewater, Maryland, USA
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5
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Meredith C, Hoffman J, Trebitz A, Pilgrim E, Okum S, Martinson J, Cameron ES. Evaluating the performance of DNA metabarcoding for assessment of zooplankton communities in Western Lake Superior using multiple markers. METABARCODING AND METAGENOMICS 2021; 50:83-97. [PMID: 34447921 DOI: 10.3897/mbmg.5.64735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
For DNA metabarcoding to attain its potential as a community assessment tool, we need to better understand its performance versus traditional morphological identification and work to address any remaining performance gaps in incorporating DNA metabarcoding into community assessments. Using fragments of the 18S nuclear and 16S mitochondrial rRNA genes and two fragments of the mitochondrial COI marker, we examined the use of DNA metabarcoding and traditional morphological identification for understanding the diversity and composition of crustacean zooplankton at 42 sites across western Lake Superior. We identified 51 zooplankton taxa (genus or species, depending on the finest resolution of the taxon across all identification methods), of which 17 were identified using only morphological traits, 13 using only DNA and 21 using both methods. The taxa found using only DNA metabarcoding included four species and one genus-level identification not previously known to occur in Lake Superior, the presence of which still needs to be confirmed. A substantial portion of taxa that were identified to genus or species by morphological identification, but not identified using DNA metabarcoding, had zero ("no record") or ≤ 2 ("underrepresented records") reference barcodes in the BOLD or NCBI databases (63% for COI, 80% for 16S, 74% for 18S). The two COI marker fragments identified the most genus- and species-level taxa, whereas 18S was the only marker whose family-level percent sequence abundance patterns showed high correlation to composition patterns from morphological identification, based on a NMDS analysis of Bray-Curtis similarities. Multiple replicates were collected at a subset of sites and an occupancy analysis was performed, which indicated that rare taxa were more likely to be detected using DNA metabarcoding than traditional morphology. Our results support that DNA metabarcoding can augment morphological identification for estimating zooplankton diversity and composition of zooplankton over space and time, but may require use of multiple markers. Further addition of taxa to reference DNA databases will improve our ability to use DNA metabarcoding to identify zooplankton and other invertebrates in aquatic surveys.
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Affiliation(s)
- Christy Meredith
- Montana Department of Environmental Quality, 1520 E. 6th Avenue, Helena, Montana, 59601 USA
| | - Joel Hoffman
- U. S. Environmental Protection Agency, Office of Research and Development, Great Lakes Toxicology and Ecology Division, 6201 Congdon Blvd, Duluth, Minnesota, 55804 USA
| | - Anett Trebitz
- U. S. Environmental Protection Agency, Office of Research and Development, Great Lakes Toxicology and Ecology Division, 6201 Congdon Blvd, Duluth, Minnesota, 55804 USA
| | - Erik Pilgrim
- U. S. Environmental Protection Agency Office of Research and Development, Watershed and Ecosystem Characterization Division, 26 West Martin Luther King Dr., Cincinnati, Ohio, 45268, USA
| | - Sarah Okum
- U. S. Environmental Protection Agency Office of Research and Development, Watershed and Ecosystem Characterization Division, 26 West Martin Luther King Dr., Cincinnati, Ohio, 45268, USA
| | - John Martinson
- U. S. Environmental Protection Agency, Office of Research and Development, Great Lakes Toxicology and Ecology Division, 26 Martin Luther King Dr., Cincinnati, OH 45268, USA
| | - Ellen S Cameron
- Department of Biology, University of Waterloo, 200 University Ave. W, Waterloo, Ontario, Canada, N2L 3G1
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Ardura A, Martinez JL, Zaiko A, Garcia-Vazquez E. Poorer diversity but tougher species in old ballast water: Biosecurity challenges explored from visual and molecular techniques. MARINE POLLUTION BULLETIN 2021; 168:112465. [PMID: 33991987 DOI: 10.1016/j.marpolbul.2021.112465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
Millions of tons of water cross the oceans inside ships' ballast tanks every day. Planktonic species hitch-hike with water and some may pose risks to ecosystems and economies if get released and establish outside their native range. We monitored ballast water in different trans-equatorial travels, visually and using molecular techniques, and found significant increases of potential nuisance taxa over travel duration, despite evident diversity depletion. Thus, less diverse but more resistant and potentially more harmful communities persist in ballast water over long voyages. If we consider the enormous volume transported every day, the persistence of resistant species in ballast water would be threating the global marine biodiversity. This should be taken into account when modeling and assessing the bioinvasion risks associated with the ballast water and transfer considered in the future research.
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Affiliation(s)
- Alba Ardura
- Department of Functional Biology, University of Oviedo, C/ Julian Claveria s/n, 33006 Oviedo, Spain.
| | - Jose L Martinez
- Scientific-technical Services, University of Oviedo, Oviedo, Asturias, Spain
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, 7010 Nelson, New Zealand; Marine Research Institute, Klaipeda University, H. Manto 84, LT-92294 Klaipeda, Lithuania
| | - Eva Garcia-Vazquez
- Department of Functional Biology, University of Oviedo, C/ Julian Claveria s/n, 33006 Oviedo, Spain
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Garcia-Vazquez E, Georges O, Fernandez S, Ardura A. eDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters. Sci Rep 2021; 11:7224. [PMID: 33790382 PMCID: PMC8012656 DOI: 10.1038/s41598-021-86731-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/19/2021] [Indexed: 11/16/2022] Open
Abstract
Zooplankton community inventories are the basis of fisheries management for containing fish larvae and their preys; however, the visual identification of early-stage larvae (the "missing biomass") is difficult and laborious. Here, eDNA metabarcoding was employed to detect zooplankton species of interest for fisheries from open and coastal waters. High-Throughput sequencing (HTS) from environmental samples using small water volumes has been proposed to detect species of interest whose DNA is the most abundant. We analyzed 6-L water samples taken from subtropical and tropical waters using Cytochrome oxidase I (COI) gene as metabarcode. In the open ocean, several commercial fish larvae and invertebrate species important in fish diet were found from metabarcodes and confirmed from individual barcoding. Comparing Atlantic, Mediterranean, Red Sea, and Pacific samples we found a lower taxonomic depth of OTU assignments in samples from tropical waters than in those from temperate ones, suggesting large gaps in reference databases for those areas; thus a higher effort of zooplankton barcoding in tropical oceans is highly recommended. This and similar simplified sampling protocols could be applied in early detection of species important for fisheries.
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Affiliation(s)
- Eva Garcia-Vazquez
- Department of Functional Biology, University of Oviedo, C/Julian Claveria S/N, 33006, Oviedo, Spain
| | - Oriane Georges
- Department of Functional Biology, University of Oviedo, C/Julian Claveria S/N, 33006, Oviedo, Spain
| | - Sara Fernandez
- Department of Natural Sciences, School of Science and Computing, Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Dublin Road, Galway, H91 T8NW, Ireland
| | - Alba Ardura
- Department of Functional Biology, University of Oviedo, C/Julian Claveria S/N, 33006, Oviedo, Spain.
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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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9
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Darling JA, Martinson J, Pagenkopp Lohan KM, Carney KJ, Pilgrim E, Banerji A, Holzer KK, Ruiz GM. Metabarcoding quantifies differences in accumulation of ballast water borne biodiversity among three port systems in the United States. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 749:141456. [PMID: 32846346 PMCID: PMC8190815 DOI: 10.1016/j.scitotenv.2020.141456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 04/14/2023]
Abstract
Characterizing biodiversity conveyed in ships' ballast water (BW), a global driver of biological invasions, is critically important for understanding risks posed by this key vector and establishing baselines to evaluate changes associated with BW management. Here we employ high throughput sequence (HTS) metabarcoding of the 18S small subunit rRNA to test for and quantify differences in the accumulation of BW-borne biodiversity among three distinct recipient port systems in the United States. These systems were located on three different coasts (Pacific, Gulf, and Atlantic) and chosen to reflect distinct trade patterns and source port biogeography. Extensive sampling of BW tanks (n = 116) allowed detailed exploration of molecular diversity accumulation. Our results indicate that saturation of introduced zooplankton diversity may be achieved quickly, with fewer than 25 tanks needed to achieve 95% of the total extrapolated diversity, if source biogeography is relatively limited. However, as predicted, port systems with much broader source geographies require more extensive sampling to estimate diversity, which continues to accumulate after sampling >100 discharges. The ability to identify BW sources using molecular indicators was also found to depend on the breadth of source biogeography and the extent to which sources had been sampled. These findings have implications both for the effort required to fully understand introduced diversity and for projecting risks associated with future changes to maritime traffic that may increase source biogeography for many recipient ports. Our data also suggest that molecular diversity may not decline significantly with BW age, indicating either that some organisms survive longer than recognized in previous studies or that nucleic acids from dead organisms persist in BW tanks. We present evidence for detection of potentially invasive species in arriving BW but discuss important caveats that preclude strong inferences regarding the presence of living representatives of these species in BW tanks.
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Affiliation(s)
- John A Darling
- United States Environmental Protection Agency, Center for Environmental Measurement & Modeling, USA.
| | - John Martinson
- United States Environmental Protection Agency, Center for Environmental Measurement & Modeling, USA
| | | | | | - Erik Pilgrim
- United States Environmental Protection Agency, Center for Environmental Measurement & Modeling, USA
| | - Aabir Banerji
- United States Environmental Protection Agency, Center for Computational Toxicology & Exposure, USA
| | | | - Gregory M Ruiz
- Smithsonian Environmental Research Center, Edgewater, MD 21037, USA
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Blackman RC, Ling KKS, Harper LR, Shum P, Hänfling B, Lawson‐Handley L. Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels, Dreissena rostriformis bugensis in flowing water. Ecol Evol 2020; 10:13248-13259. [PMID: 33304534 PMCID: PMC7713958 DOI: 10.1002/ece3.6921] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 09/14/2020] [Indexed: 12/29/2022] Open
Abstract
The early detection of invasive non-native species (INNS) is important for informing management actions. Established monitoring methods require the collection or observation of specimens, which is unlikely at the beginning of an invasion when densities are likely to be low. Environmental DNA (eDNA) analysis is a highly promising technique for the detection of INNS-particularly during the early stages of an invasion.Here, we compared the use of traditional kick-net sampling with two eDNA approaches (targeted detection using both conventional and quantitative PCR and passive detection via metabarcoding with conserved primers) for detection of quagga mussel, Dreissena rostriformis bugensis, a high priority INNS, along a density gradient on the River Wraysbury, UK.All three molecular tools outperformed traditional sampling in terms of detection. Conventional PCR and qPCR both had 100% detection rate in all samples and outperformed metabarcoding when the target species was at low densities. Additionally, quagga mussel DNA copy number (qPCR) and relative read count (metabarcoding) were significantly influenced by both mussel density and distance from source population, with distance being the most significant predictor. Synthesis and application. All three molecular approaches were more sensitive than traditional kick-net sampling for the detection of the quagga mussel in flowing water, and both qPCR and metabarcoding enabled estimates of relative abundance. Targeted approaches were more sensitive than metabarcoding, but metabarcoding has the advantage of providing information on the wider community and consequently the impacts of INNS.
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Affiliation(s)
- Rosetta C. Blackman
- Department of Aquatic EcologyEawagSwiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZürichSwitzerland
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
| | - Kar Keun Sean Ling
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
| | - Lynsey R. Harper
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Peter Shum
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Bernd Hänfling
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
| | - Lori Lawson‐Handley
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
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11
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Ibabe A, Borrell YJ, Knobelspiess S, Dopico E. Perspectives on the marine environment and biodiversity in recreational ports: The marina of Gijon as a case study. MARINE POLLUTION BULLETIN 2020; 160:111645. [PMID: 33181927 DOI: 10.1016/j.marpolbul.2020.111645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 06/11/2023]
Abstract
Recreational ports are known to be sources of pollution to the coastal marine environment due to the pouring of pollutants or the transfer of invasive species to neighboring areas. Nonetheless, the responsibility of protecting the marine environment does not lie solely on the users of the ports, but also affects the rest of citizens. Thus, an effective communication is necessary between scientists and citizens to avoid the lack of knowledge and boost cooperation against these environmental problems. In this study, (focused on the marina of Gijon, Northwestern Spain) citizens set education and social media as the main sources of information, rarely considering science outreach. Also, their environmental knowledge showed to be based on a visual perception, rather than on a cognitive one, as marine litter was considered a great environmental problem, while invasive species and biofouling went unnoticed, remarking the lack of an effective communication from scientific sources.
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Affiliation(s)
- A Ibabe
- Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n. 33006 Oviedo, Spain.
| | - Y J Borrell
- Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n. 33006 Oviedo, Spain
| | - S Knobelspiess
- International Master in Marine Biological Resources (IMBRSea), Ghent University, Belgium
| | - E Dopico
- Department of Educational Sciences, University of Oviedo, C/ Aniceto Sela s/n. 33005 Oviedo, Spain
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12
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Duarte S, Vieira PE, Costa FO. Assessment of species gaps in DNA barcode libraries of non-indigenous species (NIS) occurring in European coastal regions. METABARCODING AND METAGENOMICS 2020. [DOI: 10.3897/mbmg.4.55162] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
DNA metabarcoding has the capacity to bolster current biodiversity assessment techniques, including the early detection and monitoring of non-indigenous species (NIS). However, the success of this approach is greatly dependent on the availability, taxonomic coverage and reliability of reference sequences in genetic databases, whose deficiencies can potentially compromise species identifications at the taxonomic assignment step. In this study we assessed lacunae in availability of DNA sequence data from four barcodes (COI, 18S, rbcL and matK) for NIS occurring in European marine and coastal environments. NIS checklists were based on EASIN and AquaNIS databases. The highest coverage was found for COI for Animalia and rbcL for Plantae (up to 63%, for both) and 18S for Chromista (up to 51%), that greatly increased when only high impact species were taken into account (up to 82 to 89%). Results show that different markers have unbalanced representations in genetic databases, implying that the parallel use of more than one marker can act complimentarily and may greatly increase NIS identification rates through DNA-based tools. Furthermore, based on the COI marker, data for approximately 30% of the species had maximum intra-specific distances higher than 3%, suggesting that many NIS may have undescribed or cryptic diversity. Although completing the gaps in reference libraries is essential to make the most of the potential of the DNA-based tools, a careful compilation, verification and annotation of available sequences is fundamental to assemble large curated and reliable reference libraries that provide support for rigorous species identifications.
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13
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Nuisance Algae in Ballast Water Facing International Conventions. Insights from DNA Metabarcoding in Ships Arriving in Bay of Biscay. WATER 2020. [DOI: 10.3390/w12082168] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ballast water is one of the main vectors of transport of nuisance species among marine ports. Neither treatment nor interchange completely reduces the risk of ballast water containing DNA from harmful species, being a signal of potential threat. However, although there are some efficient treatments, they are not available on all ships and there might be some technological/economical constrains for their active and routine usage. Understanding what routes lead to a higher risk of contamination is important for designing targeted surveillance. We analysed ballast water from seven ships arriving in Gijon port (south Bay of Biscay, Spain). DNA metabarcoding was employed for identification of exotic species and harmful algae. One ship carried DNA of 20 risk species in the ballast water. Three ships contained DNA of only one risk species, and three ships had none. Seventy two algae species were found, 22.2% are exotic to the Bay of Biscay and 11.1% are catalogued as harmful. The results demonstrated the importance of continuous surveillance of ballast water.
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14
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Thakur IS, Roy D. Environmental DNA and RNA as Records of Human Exposome, Including Biotic/Abiotic Exposures and Its Implications in the Assessment of the Role of Environment in Chronic Diseases. Int J Mol Sci 2020; 21:ijms21144879. [PMID: 32664313 PMCID: PMC7402316 DOI: 10.3390/ijms21144879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/05/2020] [Accepted: 07/08/2020] [Indexed: 12/21/2022] Open
Abstract
Most of environment-related diseases often result from multiple exposures of abiotic and/or biotic stressors across various life stages. The application of environmental DNA/RNA (eDNA/eRNA) to advance ecological understanding has been very successfully used. However, the eminent extension of eDNA/eRNA-based approaches to estimate human exposure to biotic and/or abiotic environmental stressors to understand the environmental causes of chronic diseases has yet to start. Here, we introduce the potential of eDNA/eRNA for bio-monitoring of human exposome and health effects in the real environmental or occupational settings. This review is the first of its kind to discuss how eDNA/eRNA-based approaches can be applied for assessing the human exposome. eDNA-based exposome assessment is expected to rely on our ability to capture the genome- and epigenome-wide signatures left behind by individuals in the indoor and outdoor physical spaces through shedding, excreting, etc. Records of eDNA/eRNA exposome may reflect the early appearance, persistence, and presence of biotic and/or abiotic-exposure-mediated modifications in these nucleic acid molecules. Functional genome- and epigenome-wide mapping of eDNA offer great promise to help elucidate the human exposome. Assessment of longitudinal exposure to physical, biological, and chemical agents present in the environment through eDNA/eRNA may enable the building of an integrative causal dynamic stochastic model to estimate environmental causes of human health deficits. This model is expected to incorporate key biological pathways and gene networks linking individuals, their geographic locations, and random multi-hits of environmental factors. Development and validation of monitoring of eDNA/eRNA exposome should seriously be considered to introduce into safety and risk assessment and as surrogates of chronic exposure to environmental stressors. Here we highlight that eDNA/eRNA reflecting longitudinal exposure of both biotic and abiotic environmental stressors may serve as records of human exposome and discuss its application as molecular tools for understanding the toxicogenomics basis of environment-related health deficits.
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Affiliation(s)
- Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Correspondence: (I.S.T.); (D.R.); Tel.: +91-2670-4321 (I.S.T.); +1-30-5348-1694 (D.R.)
| | - Deodutta Roy
- Department of Environmental Health Sciences, Florida International University, Miami, FL 33199, USA
- Correspondence: (I.S.T.); (D.R.); Tel.: +91-2670-4321 (I.S.T.); +1-30-5348-1694 (D.R.)
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15
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Zaiko A, Wood SA, Pochon X, Biessy L, Laroche O, Croot P, Garcia-Vazquez E. Elucidating Biodiversity Shifts in Ballast Water Tanks during a Cross-Latitudinal Transfer: Complementary Insights from Molecular Analyses. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:8443-8454. [PMID: 32436694 DOI: 10.1021/acs.est.0c01931] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this study, the evolution of ballast water (BW) assemblages across different trophic levels was characterized over a 21 day cross-latitudinal vessel transit using a combination of molecular methods. Triplicate BW samples were collected every second day and size-fractionated (<2.7, 10, >50 μm). Measurements of adenosine triphosphate (ATP) and metabarcoding of environmental nucleic acid (DNA and RNA) analyses, complemented by microscopy and flow cytometry, were performed on each sample. Measured ATP concentrations exhibited high variance between replicates and a strong negative trend in the large (≥50 μm) fraction over the voyage. In concert with microscopy, the metabarcoding data indicated a die-off of larger metazoans during the first week of study and gradual reductions in dinoflagellates and ochrophytes. The ATP and metabarcoding data signaled persistent or increased cellular activity of heterotrophic bacteria and protists in the BW, which was supported by flow cytometry. The metabarcoding showed the presence of active bacteria in all size fractions, suggesting that the sequential filtration approach does not ensure taxonomical differentiation, which has implications for BW quality assessment. Although our data show that ATP and metabarcoding have potential for indicative BW screening for BW compliance monitoring, further research and technological development is needed to improve representativeness of sampling and deliver the unequivocal response criteria required by the international Ballast Water Management Convention.
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Affiliation(s)
- Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
- Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
- Marine Research Institute, Klaipeda University, H.Manto 84, 92294 Klaipeda, Lithuania
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
- Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
| | - Laura Biessy
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Olivier Laroche
- Benthic Resources, The Norwegian Institute of Marine Research, Nordnesgaten 50, 5005 Bergen, Norway
| | - Peter Croot
- Irish Centre for Research in Applied Geoscience (iCRAG), Earth and Ocean Sciences, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Eva Garcia-Vazquez
- Department of Functional Biology, University of Oviedo, C/Julian Claveria s/n, 33006 Oviedo, Spain
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16
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Novak BJ, Fraser D, Maloney TH. Transforming Ocean Conservation: Applying the Genetic Rescue Toolkit. Genes (Basel) 2020; 11:E209. [PMID: 32085502 PMCID: PMC7074136 DOI: 10.3390/genes11020209] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/25/2020] [Accepted: 02/13/2020] [Indexed: 01/21/2023] Open
Abstract
Although oceans provide critical ecosystem services and support the most abundant populations on earth, the extent of damage impacting oceans and the diversity of strategies to protect them is disconcertingly, and disproportionately, understudied. While conventional modes of conservation have made strides in mitigating impacts of human activities on ocean ecosystems, those strategies alone cannot completely stem the tide of mounting threats. Biotechnology and genomic research should be harnessed and developed within conservation frameworks to foster the persistence of viable ocean ecosystems. This document distills the results of a targeted survey, the Ocean Genomics Horizon Scan, which assessed opportunities to bring novel genetic rescue tools to marine conservation. From this Horizon Scan, we have identified how novel approaches from synthetic biology and genomics can alleviate major marine threats. While ethical frameworks for biotechnological interventions are necessary for effective and responsible practice, here we primarily assessed technological and social factors directly affecting technical development and deployment of biotechnology interventions for marine conservation. Genetic insight can greatly enhance established conservation methods, but the severity of many threats may demand genomic intervention. While intervention is controversial, for many marine areas the cost of inaction is too high to allow controversy to be a barrier to conserving viable ecosystems. Here, we offer a set of recommendations for engagement and program development to deploy genetic rescue safely and responsibly.
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Affiliation(s)
- Ben J. Novak
- Revive & Restore, 1505 Bridgeway #203, Sausalito, CA 94965, USA;
| | - Devaughn Fraser
- Genetics Research Lab, California Department of Fish and Wildlife, Sacramento, CA 95834, USA;
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17
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Lin Y, Zhan A, Hernandez MR, Paolucci E, MacIsaac HJ, Briski E. Can chlorination of ballast water reduce biological invasions? J Appl Ecol 2019. [DOI: 10.1111/1365-2664.13528] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Yaping Lin
- GEOMAR Helmholtz‐Zentrum für Ozeanforschung Kiel Kiel Germany
- Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
| | - Aibin Zhan
- Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Marco R. Hernandez
- Great Lakes Institute for Environmental Research University of Windsor Windsor ON Canada
| | - Esteban Paolucci
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” and Consejo Nacional de Investigaciones Cientı́ficas y Técnicas Buenos Aires Argentina
| | - Hugh J. MacIsaac
- Great Lakes Institute for Environmental Research University of Windsor Windsor ON Canada
- School of Ecology and Environmental Sciences Yunnan University Kunming China
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18
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Rey A, Carney KJ, Quinones LE, Pagenkopp Lohan KM, Ruiz GM, Basurko OC, Rodríguez-Ezpeleta N. Environmental DNA Metabarcoding: A Promising Tool for Ballast Water Monitoring. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:11849-11859. [PMID: 31545591 DOI: 10.1021/acs.est.9b01855] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nonindigenous species are introduced worldwide with ballast water (BW). To prevent further introductions, oceanic BW exchange and BW treatment systems are utilized, but their performance needs to be evaluated. To that aim, characterizing BW communities is essential but usually relies on exhaustive sampling and morphological taxonomic identification, which does not always allow fine-scale taxonomic resolution. Through the analysis of BW samples from 11 vessels arriving to the Chesapeake Bay (USA), we evaluated the potential of environmental DNA (eDNA) metabarcoding for BW monitoring by assessing whether the impact of BW management type could be identified, analyzing the influence of BW sampling access locations on communities, and comparing the accuracy of eDNA for taxonomic assignment and identification of nonindigenous taxa. We found that (1) different sampling access locations of the same tank resulted in different communities, (2) communities from treated and exchanged BW differ, (3) signals of source port and of ocean exchange are observed, (4) eDNA metabarcoding results in more diversity than morphological taxonomy, and (5) the nonindigenous copepod Oithona davisae, not reported before in the Chesapeake Bay, is detected. Overall, this study highlights the potential of eDNA metabarcoding for BW monitoring, but more comprehensive sampling will be needed to optimize the approach.
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Affiliation(s)
- Anaïs Rey
- Marine Research Division , AZTI , Sukarrieta , Spain
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19
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Metagenomic Sequencing Identifies Highly Diverse Assemblages of Dinoflagellate Cysts in Sediments from Ships' Ballast Tanks. Microorganisms 2019; 7:microorganisms7080250. [PMID: 31405065 PMCID: PMC6724030 DOI: 10.3390/microorganisms7080250] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/30/2019] [Accepted: 08/06/2019] [Indexed: 11/17/2022] Open
Abstract
Ships’ ballast tanks have long been known as vectors for the introduction of organisms. We applied next-generation sequencing to detect dinoflagellates (mainly as cysts) in 32 ballast tank sediments collected during 2001–2003 from ships entering the Great Lakes or Chesapeake Bay and subsequently archived. Seventy-three dinoflagellates were fully identified to species level by this metagenomic approach and single-cell polymerase chain reaction (PCR)-based sequencing, including 19 toxic species, 36 harmful algal bloom (HAB) forming species, 22 previously unreported as producing cysts, and 55 reported from ballast tank sediments for the first time (including 13 freshwater species), plus 545 operational taxonomic units (OTUs) not fully identified due to a lack of reference sequences, indicating tank sediments are repositories of many previously undocumented taxa. Analyses indicated great heterogeneity of species composition among samples from different sources. Light and scanning electron microscopy and single-cell PCR sequencing supported and confirmed results of the metagenomic approach. This study increases the number of fully identified dinoflagellate species from ballast tank sediments to 142 (>50% increase). From the perspective of ballast water management, the high diversity and spatiotemporal heterogeneity of dinoflagellates in ballast tanks argues for continuing research and stringent adherence to procedures intended to prevent unintended introduction of non-indigenous toxic and HAB-forming species.
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20
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Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00547] [Citation(s) in RCA: 303] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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21
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Zhang GK, Chain FJJ, Abbott CL, Cristescu ME. Metabarcoding using multiplexed markers increases species detection in complex zooplankton communities. Evol Appl 2018; 11:1901-1914. [PMID: 30459837 PMCID: PMC6231476 DOI: 10.1111/eva.12694] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/02/2018] [Accepted: 08/05/2018] [Indexed: 01/13/2023] Open
Abstract
Metabarcoding combines DNA barcoding with high-throughput sequencing, often using one genetic marker to understand complex and taxonomically diverse samples. However, species-level identification depends heavily on the choice of marker and the selected primer pair, often with a trade-off between successful species amplification and taxonomic resolution. We present a versatile metabarcoding protocol for biomonitoring that involves the use of two barcode markers (COI and 18S) and four primer pairs in a single high-throughput sequencing run, via sample multiplexing. We validate the protocol using a series of 24 mock zooplanktonic communities incorporating various levels of genetic variation. With the use of a single marker and single primer pair, the highest species recovery was 77%. With all three COI fragments, we detected 62%-83% of species across the mock communities, while the use of the 18S fragment alone resulted in the detection of 73%-75% of species. The species detection level was significantly improved to 89%-93% when both markers were used. Furthermore, multiplexing did not have a negative impact on the proportion of reads assigned to each species and the total number of species detected was similar to when markers were sequenced alone. Overall, our metabarcoding approach utilizing two barcode markers and multiple primer pairs per barcode improved species detection rates over a single marker/primer pair by 14% to 35%, making it an attractive and relatively cost-effective method for biomonitoring natural zooplankton communities. We strongly recommend combining evolutionary independent markers and, when necessary, multiple primer pairs per marker to increase species detection (i.e., reduce false negatives) in metabarcoding studies.
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Affiliation(s)
- Guang K. Zhang
- Department of BiologyMcGill UniversityMontrealQuebecCanada
| | - Frédéric J. J. Chain
- Department of BiologyMcGill UniversityMontrealQuebecCanada
- Present address:
Department of Biological SciencesUniversity of Massachusetts LowellOne University AvenueLowellMA
| | - Cathryn L. Abbott
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimoBritish ColumbiaCanada
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22
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Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities. Sci Rep 2018; 8:16290. [PMID: 30389965 PMCID: PMC6215007 DOI: 10.1038/s41598-018-34541-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/19/2018] [Indexed: 11/09/2022] Open
Abstract
Marine infrastructure can favor the spread of non-indigenous marine biofouling species by providing a suitable habitat for them to proliferate. Cryptic organisms or those in early life stages can be difficult to distinguish by conventional morphological taxonomy. Molecular tools, such as metabarcoding, may improve their detection. In this study, the ability of morpho-taxonomy and metabarcoding (18S rRNA and COI) using three reference databases (PR2, BOLD and NCBI) to characterize biodiversity and detect non-indigenous species (NIS) in biofouling was compared on 60 passive samplers deployed over summer and winter in a New Zealand marina. Highest resolution of metazoan taxa was identified using 18S rRNA assigned to PR2. There were higher assignment rates to NCBI reference sequences, but poorer taxonomic identification. Using all methods, 48 potential NIS were identified. Metabarcoding detected the largest proportion of those NIS: 77% via 18S rRNA/PR2 and NCBI and 35% via COI/BOLD and NCBI. Morpho-taxonomy detected an additional 14% of all identified NIS comprising mainly of bryozoan taxa. The data highlight several on-going challenges, including: differential marker resolution, primer biases, incomplete sequence reference databases, and variations in bioinformatic pipelines. Combining morpho-taxonomy and molecular analysis methods will likely enhance the detection of NIS from complex biofouling.
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23
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Darling JA, Martinson J, Gong Y, Okum S, Pilgrim E, Lohan KMP, Carney KJ, Ruiz GM. Ballast Water Exchange and Invasion Risk Posed by Intracoastal Vessel Traffic: An Evaluation Using High Throughput Sequencing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:9926-9936. [PMID: 30059206 PMCID: PMC6944436 DOI: 10.1021/acs.est.8b02108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Ballast water remains a potent vector of non-native aquatic species introductions, despite increased global efforts to reduce risk of ballast water mediated invasions. This is particularly true of intracoastal vessel traffic, whose characteristics may limit the feasibility and efficacy of management through ballast water exchange (BWE). Here we utilize high throughput sequencing (HTS) to assess biological communities associated with ballast water being delivered to Valdez, Alaska from multiple source ports along the Pacific Coast of the United States. Our analyses indicate that BWE has a significant but modest effect on ballast water assemblages. Although overall richness was not reduced with exchange, we detected losses of some common benthic coastal taxa (e.g., decapods, mollusks, bryozoans, cnidaria) and gains of open ocean taxa (e.g., certain copepods, diatoms, and dinoflagellates), including some potentially toxic species. HTS-based metabarcoding identified significantly differentiated biodiversity signatures from individual source ports; this signal persisted, though weakened, in vessels undergoing BWE, indicating incomplete faunal turnover associated with management. Our analysis also enabled identification of taxa that may be of particular concern if established in Alaskan waters. While these results reveal a clear effect of BWE on diversity in intracoastal transit, they also indicate continued introduction risk of non-native and harmful taxa.
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Affiliation(s)
- John A Darling
- United States Environmental Protection Agency , National Exposure Research Laboratory , Research Triangle Park , North Carolina 27711 , United States
| | - John Martinson
- United States Environmental Protection Agency , National Exposure Research Laboratory , Research Triangle Park , North Carolina 27711 , United States
| | - Yunguo Gong
- United States Environmental Protection Agency , Cincinnati , Ohio 45220 , United States
| | - Sara Okum
- United States Environmental Protection Agency , Cincinnati , Ohio 45220 , United States
| | - Erik Pilgrim
- United States Environmental Protection Agency , National Exposure Research Laboratory , Research Triangle Park , North Carolina 27711 , United States
| | | | - Katharine J Carney
- Smithsonian Environmental Research Center , Edgewater , Maryland 21037 United States
| | - Gregory M Ruiz
- Smithsonian Environmental Research Center , Edgewater , Maryland 21037 United States
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24
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Ojaveer H, Galil BS, Carlton JT, Alleway H, Goulletquer P, Lehtiniemi M, Marchini A, Miller W, Occhipinti-Ambrogi A, Peharda M, Ruiz GM, Williams SL, Zaiko A. Historical baselines in marine bioinvasions: Implications for policy and management. PLoS One 2018; 13:e0202383. [PMID: 30114232 PMCID: PMC6095587 DOI: 10.1371/journal.pone.0202383] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The human-mediated introduction of marine non-indigenous species is a centuries- if not millennia-old phenomenon, but was only recently acknowledged as a potent driver of change in the sea. We provide a synopsis of key historical milestones for marine bioinvasions, including timelines of (a) discovery and understanding of the invasion process, focusing on transfer mechanisms and outcomes, (b) methodologies used for detection and monitoring, (c) approaches to ecological impacts research, and (d) management and policy responses. Early (until the mid-1900s) marine bioinvasions were given little attention, and in a number of cases actively and routinely facilitated. Beginning in the second half of the 20th century, several conspicuous non-indigenous species outbreaks with strong environmental, economic, and public health impacts raised widespread concerns and initiated shifts in public and scientific perceptions. These high-profile invasions led to policy documents and strategies to reduce the introduction and spread of non-indigenous species, although with significant time lags and limited success and focused on only a subset of transfer mechanisms. Integrated, multi-vector management within an ecosystem-based marine management context is urgently needed to address the complex interactions of natural and human pressures that drive invasions in marine ecosystems.
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Affiliation(s)
- Henn Ojaveer
- Estonian Marine Institute, University of Tartu, Pärnu, Estonia
| | - Bella S. Galil
- The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
| | - James T. Carlton
- Maritime Studies Program of Williams College and Mystic Seaport, Mystic, Connecticut, United States of America
| | - Heidi Alleway
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | | | - Maiju Lehtiniemi
- Marine Research Centre, Finnish Environment Institute, Helsinki, Finland
| | - Agnese Marchini
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
| | - Whitman Miller
- Marine Invasion Research Laboratory, Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
| | | | | | - Gregory M. Ruiz
- Marine Invasion Research Laboratory, Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
| | - Susan L. Williams
- Bodega Marine Laboratory and Department of Evolution and Ecology, University of California at Davis, Bodega Bay, California, United States of America
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Marine Research Institute, Klaipeda University, Klaipeda, Lithuania
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25
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PCR-based assay for Mya arenaria detection from marine environmental samples and tracking its invasion in coastal ecosystems. J Nat Conserv 2018. [DOI: 10.1016/j.jnc.2018.02.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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26
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Bourne SD, Hudson J, Holman LE, Rius M. Marine Invasion Genomics: Revealing Ecological and Evolutionary Consequences of Biological Invasions. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/13836_2018_21] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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27
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Darling JA, Frederick RM. Nucleic acids-based tools for ballast water surveillance, monitoring, and research. JOURNAL OF SEA RESEARCH 2018; 133:43-52. [PMID: 30147432 PMCID: PMC6104837 DOI: 10.1016/j.seares.2017.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Understanding the risks of biological invasion posed by ballast water-whether in the context of compliance testing, routine monitoring, or basic research-is fundamentally an exercise in biodiversity assessment, and as such should take advantage of the best tools available for tackling that problem. The past several decades have seen growing application of genetic methods for the study of biodiversity, driven in large part by dramatic technological advances in nucleic acids analysis. Monitoring approaches based on such methods have the potential to increase dramatically sampling throughput for biodiversity assessments, and to improve on the sensitivity, specificity, and taxonomic accuracy of traditional approaches. The application of targeted detection tools (largely focused on PCR but increasingly incorporating novel probe-based methodologies) has led to a paradigm shift in rare species monitoring, and such tools have already been applied for early detection in the context of ballast water surveillance. Rapid improvements in community profiling approaches based on high throughput sequencing (HTS) could similarly impact broader efforts to catalogue biodiversity present in ballast tanks, and could provide novel opportunities to better understand the risks of biotic exchange posed by ballast water transport-and the effectiveness of attempts to mitigate those risks. These various approaches still face considerable challenges to effective implementation, depending on particular management or research needs. Compliance testing, for instance, remains dependent on accurate quantification of viable target organisms; while tools based on RNA detection show promise in this context, the demands of such testing require considerable additional investment in methods development. In general surveillance and research contexts, both targeted and community-based approaches are still limited by various factors: quantification remains a challenge (especially for taxa in larger size classes), gaps in nucleic acids reference databases are still considerable, uncertainties in taxonomic assignment methods persist, and many applications have not yet matured sufficiently to offer standardized methods capable of meeting rigorous quality assurance standards. Nevertheless, the potential value of these tools, their growing utilization in biodiversity monitoring, and the rapid methodological advances over the past decade all suggest that they should be seriously considered for inclusion in the ballast water surveillance toolkit.
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Affiliation(s)
- John A. Darling
- National Exposure Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Raymond M. Frederick
- National Risk Management Research Laboratory, U.S. Environmental Protection Agency, Edison, NJ, USA
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28
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BluePharmTrain: Biology and Biotechnology of Marine Sponges. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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29
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Leray M, Knowlton N. Censusing marine eukaryotic diversity in the twenty-first century. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0331. [PMID: 27481783 PMCID: PMC4971183 DOI: 10.1098/rstb.2015.0331] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2016] [Indexed: 11/12/2022] Open
Abstract
The ocean constitutes one of the vastest and richest biomes on our planet. Most recent estimations, all based on indirect approaches, suggest that there are millions of marine eukaryotic species. Moreover, a large majority of these are small (less than 1 mm), cryptic and still unknown to science. However, this knowledge gap, caused by the lack of diagnostic morphological features in small organisms and the limited sampling of the global ocean, is currently being filled, thanks to new DNA-based approaches. The molecular technique of PCR amplification of homologous gene regions combined with high-throughput sequencing, routinely used to census unculturable prokaryotes, is now also being used to characterize whole communities of marine eukaryotes. Here, we review how this methodological advancement has helped to better quantify the magnitude and patterns of marine eukaryotic diversity, with an emphasis on taxonomic groups previously largely overlooked. We then discuss obstacles remaining to achieve a global understanding of marine eukaryotic diversity. In particular, we argue that 18S variable regions do not provide sufficient taxonomic resolution to census marine life, and suggest combining broad eukaryotic surveys targeting the 18S rRNA region with more taxon-focused analyses of hypervariable regions to improve our understanding of the diversity of species, the functional units of marine ecosystems. This article is part of the themed issue ‘From DNA barcodes to biomes’.
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Affiliation(s)
- Matthieu Leray
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Nancy Knowlton
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
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30
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Pochon X, Zaiko A, Fletcher LM, Laroche O, Wood SA. Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications. PLoS One 2017; 12:e0187636. [PMID: 29095959 PMCID: PMC5667844 DOI: 10.1371/journal.pone.0187636] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/23/2017] [Indexed: 11/19/2022] Open
Abstract
High-throughput sequencing metabarcoding studies in marine biosecurity have largely focused on targeting environmental DNA (eDNA). DNA can persist extracellularly in the environment, making discrimination of living organisms difficult. In this study, bilge water samples (i.e., water accumulating on-board a vessel during transit) were collected from 15 small recreational and commercial vessels. eDNA and eRNA molecules were co-extracted and the V4 region of the 18S ribosomal RNA gene targeted for metabarcoding. In total, 62.7% of the Operational Taxonomic Units (OTUs) were identified at least once in the corresponding eDNA and eRNA reads, with 19.5% unique to eDNA and 17.7% to eRNA. There were substantial differences in diversity between molecular compartments; 57% of sequences from eDNA-only OTUs belonged to fungi, likely originating from legacy DNA. In contrast, there was a higher percentage of metazoan (50.2%) and ciliate (31.7%) sequences in the eRNA-only OTUs. Our data suggest that the presence of eRNA-only OTUs could be due to increased cellular activities of some rare taxa that were not identified in the eDNA datasets, unusually high numbers of rRNA transcripts in ciliates, and/or artefacts produced during the reverse transcriptase, PCR and sequencing steps. The proportions of eDNA/eRNA shared and unshared OTUs were highly heterogeneous within individual bilge water samples. Multiple factors including boat type and the activities performed on-board, such as washing of scientific equipment, may play a major role in contributing to this variability. For some marine biosecurity applications analysis, eDNA-only data may be sufficient, however there are an increasing number of instances where distinguishing the living portion of a community is essential. For these circumstances, we suggest only including OTUs that are present in both eDNA and eRNA data. OTUs found only in the eRNA data need to be interpreted with caution until further research provides conclusive evidence for their origin.
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Affiliation(s)
- Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
- * E-mail:
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
- Marine Science and Technology Centre, Klaipeda University, Klaipeda, Lithuania
| | | | - Olivier Laroche
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Susanna A. Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Environmental Research Institute, University of Waikato, Hamilton, New Zealand
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31
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Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière-Roussel A, Altermatt F, Creer S, Bista I, Lodge DM, de Vere N, Pfrender ME, Bernatchez L. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Mol Ecol 2017; 26:5872-5895. [PMID: 28921802 DOI: 10.1111/mec.14350] [Citation(s) in RCA: 589] [Impact Index Per Article: 84.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/31/2017] [Accepted: 09/05/2017] [Indexed: 12/14/2022]
Abstract
The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing ("HTS") platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed "environmental DNA" or "eDNA"). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called "eDNA metabarcoding" and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.
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Affiliation(s)
- Kristy Deiner
- Atkinson Center for a Sustainable Future, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Holly M Bik
- Department of Nematology, University of California, Riverside, CA, USA
| | - Elvira Mächler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Mathew Seymour
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales Building, Bangor University, Bangor, Gwynedd, UK
| | | | - Florian Altermatt
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales Building, Bangor University, Bangor, Gwynedd, UK
| | - Iliana Bista
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales Building, Bangor University, Bangor, Gwynedd, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - David M Lodge
- Atkinson Center for a Sustainable Future, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Natasha de Vere
- Conservation and Research Department, National Botanic Garden of Wales, Llanarthne, Carmarthenshire, UK.,Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Michael E Pfrender
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, Notre Dame, IN, USA
| | - Louis Bernatchez
- IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, QC, Canada
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32
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Wood SA, Zaiko A, Richter I, Inglis GJ, Pochon X. Development of a real-time polymerase chain reaction assay for the detection of the invasive Mediterranean fanworm, Sabella spallanzanii, in environmental samples. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:17373-17382. [PMID: 28589279 DOI: 10.1007/s11356-017-9357-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
The Mediterranean fanworm, Sabella spallanzanii Gmelin 1791, was first detected in the Southern Hemisphere in the 1990s and is now abundant in many parts of southern Australia and in several locations around northern New Zealand. Once established, it can proliferate rapidly, reaching high densities with potential ecological and economic impacts. Early detection of new S. spallanzanii incursions is important to prevent its spread, guide eradication or control efforts and to increase knowledge on the species' dispersal pathways. In this study, we developed a TaqMan probe real-time polymerase chain reaction assay targeting a region of the mitochondrial cytochrome oxidase I gene. The assay was validated in silico and in vitro using DNA from New Zealand and Australian Sabellidae with no cross-reactivity detected. The assay has a linear range of detection over seven orders of magnitude with a limit of detection reached at 12.4 × 10-4 ng/μL of DNA. We analysed 145 environmental (water, sediment and biofouling) samples and obtained positive detections only from spiked samples and those collected at a port where S. spallanzanii is known to be established. This assay has the potential to enhance current morphological and molecular-based methods, through its ability to rapidly and accurately identify S. spallanzanii in environmental samples.
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Affiliation(s)
- Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.
- Environmental Research Institute, University of Waikato, Hamilton, New Zealand.
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Marine Science and Technology Centre, Klaipeda University, Klaipeda, Lithuania
| | - Ingrid Richter
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Graeme J Inglis
- National Institute of Water and Atmospheric Research Ltd, Christchurch, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
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33
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Pagenkopp Lohan KM, Fleischer RC, Carney KJ, Holzer KK, Ruiz GM. Molecular characterisation of protistan species and communities in ships’ ballast water across three U.S. coasts. DIVERS DISTRIB 2017. [DOI: 10.1111/ddi.12550] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Katrina M. Pagenkopp Lohan
- Marine Invasions Laboratory Smithsonian Environmental Research Center Edgewater MD USA
- Center for Conservation Genomics Smithsonian Conservation Biology Institute National Zoological Park Washington DC USA
| | - Robert C. Fleischer
- Center for Conservation Genomics Smithsonian Conservation Biology Institute National Zoological Park Washington DC USA
| | - Katharine J. Carney
- Marine Invasions Laboratory Smithsonian Environmental Research Center Edgewater MD USA
| | - Kimberly K. Holzer
- Marine Invasions Laboratory Smithsonian Environmental Research Center Edgewater MD USA
| | - Gregory M. Ruiz
- Marine Invasions Laboratory Smithsonian Environmental Research Center Edgewater MD USA
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34
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Leray M, Knowlton N. Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding. PeerJ 2017; 5:e3006. [PMID: 28348924 PMCID: PMC5364921 DOI: 10.7717/peerj.3006] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/20/2017] [Indexed: 12/15/2022] Open
Abstract
DNA metabarcoding, the PCR-based profiling of natural communities, is becoming the method of choice for biodiversity monitoring because it circumvents some of the limitations inherent to traditional ecological surveys. However, potential sources of bias that can affect the reproducibility of this method remain to be quantified. The interpretation of differences in patterns of sequence abundance and the ecological relevance of rare sequences remain particularly uncertain. Here we used one artificial mock community to explore the significance of abundance patterns and disentangle the effects of two potential biases on data reproducibility: indexed PCR primers and random sampling during Illumina MiSeq sequencing. We amplified a short fragment of the mitochondrial Cytochrome c Oxidase Subunit I (COI) for a single mock sample containing equimolar amounts of total genomic DNA from 34 marine invertebrates belonging to six phyla. We used seven indexed broad-range primers and sequenced the resulting library on two consecutive Illumina MiSeq runs. The total number of Operational Taxonomic Units (OTUs) was ∼4 times higher than expected based on the composition of the mock sample. Moreover, the total number of reads for the 34 components of the mock sample differed by up to three orders of magnitude. However, 79 out of 86 of the unexpected OTUs were represented by <10 sequences that did not appear consistently across replicates. Our data suggest that random sampling of rare OTUs (e.g., small associated fauna such as parasites) accounted for most of variation in OTU presence–absence, whereas biases associated with indexed PCRs accounted for a larger amount of variation in relative abundance patterns. These results suggest that random sampling during sequencing leads to the low reproducibility of rare OTUs. We suggest that the strategy for handling rare OTUs should depend on the objectives of the study. Systematic removal of rare OTUs may avoid inflating diversity based on common β descriptors but will exclude positive records of taxa that are functionally important. Our results further reinforce the need for technical replicates (parallel PCR and sequencing from the same sample) in metabarcoding experimental designs. Data reproducibility should be determined empirically as it will depend upon the sequencing depth, the type of sample, the sequence analysis pipeline, and the number of replicates. Moreover, estimating relative biomasses or abundances based on read counts remains elusive at the OTU level.
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Affiliation(s)
- Matthieu Leray
- National Museum of Natural History, Smithsonian Institution, Washington, D.C., USA; Smithsonian Tropical Research Institute, Smithsonian Institution, Panama City, Balboa, Ancon, Republic of Panama
| | - Nancy Knowlton
- National Museum of Natural History, Smithsonian Institution , Washington , D.C. , USA
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35
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Casabianca S, Cornetti L, Capellacci S, Vernesi C, Penna A. Genome complexity of harmful microalgae. HARMFUL ALGAE 2017; 63:7-12. [PMID: 28366402 DOI: 10.1016/j.hal.2017.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 01/09/2017] [Accepted: 01/09/2017] [Indexed: 06/07/2023]
Abstract
During the past decade, next generation sequencing (NGS) technologies have provided new insights into the diversity, dynamics, and metabolic pathways of natural microbial communities. But, these new techniques face challenges related to the genome size and level of genome complexity of the species under investigation. Moreover, the coverage depth and the short-read length achieved by NGS based approaches also represent a major challenge for assembly. These factors could limit the use of these high-throughput sequencing methods for species lacking a reference genome and characterized by a high level of complexity. In the present work, the evolutionary history, mainly consisting of gene transfer events from bacteria and unicellular eukaryotes to microalgae, including harmful species, is discussed and reviewed as it relates to NGS application in microbial communities, with a particular focus on harmful algal bloom species and dinoflagellates. In the context of genetic population studies, genotyping-by-sequencing (GBS), an NGS based approach, could be used for the discovery and analysis of single nucleotide polymorphisms (SNPs). The NGS technologies are still relatively new and require further improvement. Specifically, there is a need to develop and standardize tools and approaches to handle large data sets, which have to be used for the majority of HAB species characterized by evolutionary highly dynamic genomes.
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Affiliation(s)
- Silvia Casabianca
- Department of Biomolecular Sciences, University of Urbino, Viale Trieste 296, 61121 Pesaro, Italy; CoNISMa, Italian Interuniversity Consortium on Marine Sciences, Piazzale Flaminio 9, 00196, Rome, Italy
| | - Luca Cornetti
- Institute for Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland
| | - Samuela Capellacci
- Department of Biomolecular Sciences, University of Urbino, Viale Trieste 296, 61121 Pesaro, Italy; CoNISMa, Italian Interuniversity Consortium on Marine Sciences, Piazzale Flaminio 9, 00196, Rome, Italy
| | - Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all'Adige, 38010 Trento, Italy
| | - Antonella Penna
- Department of Biomolecular Sciences, University of Urbino, Viale Trieste 296, 61121 Pesaro, Italy; CoNISMa, Italian Interuniversity Consortium on Marine Sciences, Piazzale Flaminio 9, 00196, Rome, Italy.
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36
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Muñoz-Colmenero M, Martínez JL, Roca A, Garcia-Vazquez E. NGS tools for traceability in candies as high processed food products: Ion Torrent PGM versus conventional PCR-cloning. Food Chem 2017; 214:631-636. [DOI: 10.1016/j.foodchem.2016.07.121] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 07/12/2016] [Accepted: 07/20/2016] [Indexed: 11/28/2022]
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37
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Kamenova S, Bartley T, Bohan D, Boutain J, Colautti R, Domaizon I, Fontaine C, Lemainque A, Le Viol I, Mollot G, Perga ME, Ravigné V, Massol F. Invasions Toolkit. ADV ECOL RES 2017. [DOI: 10.1016/bs.aecr.2016.10.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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38
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Viard F, David P, Darling JA. Marine invasions enter the genomic era: three lessons from the past, and the way forward. Curr Zool 2016; 62:629-642. [PMID: 29491950 PMCID: PMC5804250 DOI: 10.1093/cz/zow053] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/15/2016] [Indexed: 01/22/2023] Open
Abstract
The expanding scale and increasing rate of marine biological invasions have been documented since the early 20th century. Besides their global ecological and economic impacts, non-indigenous species (NIS) also have attracted much attention as opportunities to explore important eco-evolutionary processes such as rapid adaptation, long-distance dispersal and range expansion, and secondary contacts between divergent evolutionary lineages. In this context, genetic tools have been extensively used in the past 20 years. Three important issues appear to have emerged from such studies. First, the study of NIS has revealed unexpected cryptic diversity in what had previously been assumed homogeneous entities. Second, there has been surprisingly little evidence of strong founder events accompanying marine introductions, a pattern possibly driven by large propagule loads. Third, the evolutionary processes leading to successful invasion have been difficult to ascertain due to faint genetic signals. Here we explore the potential of novel tools associated with high-throughput sequencing (HTS) to address these still pressing issues. Dramatic increase in the number of loci accessible via HTS has the potential to radically increase the power of analyses aimed at species delineation, exploring the population genomic consequences of range expansions, and examining evolutionary processes such as admixture, introgression, and adaptation. Nevertheless, the value of this new wealth of genomic data will ultimately depend on the ability to couple it with expanded "traditional" efforts, including exhaustive sampling of marine populations over large geographic scales, integrated taxonomic analyses, and population level exploration of quantitative trait differentiation through common-garden and other laboratory experiments.
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Affiliation(s)
- Frédérique Viard
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7144, Lab. Adaptation Et Diversité En Milieu Marin, Team Div&Co, Station Biologique De Roscoff, Roscoff 29682, France
| | - Patrice David
- CEFE UMR 5175, CNRS-Université De Montpellier-UM III-EPHE, 1919 Route De Mende, Montpellier Cedex 34293, France
| | - John A. Darling
- National Exposure Research Laboratory, United States Environmental Protection Agency, Research Triangle Park, NC 27711, USA
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39
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Keskin E, Unal EM, Atar HH. Detection of rare and invasive freshwater fish species using eDNA pyrosequencing: Lake Iznik ichthyofauna revised. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.05.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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Al-Rshaidat MMD, Snider A, Rosebraugh S, Devine AM, Devine TD, Plaisance L, Knowlton N, Leray M. Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea. Genome 2016; 59:724-37. [PMID: 27584940 DOI: 10.1139/gen-2015-0208] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
High-throughput sequencing (HTS) of DNA barcodes (metabarcoding), particularly when combined with standardized sampling protocols, is one of the most promising approaches for censusing overlooked cryptic invertebrate communities. We present biodiversity estimates based on sequencing of the cytochrome c oxidase subunit 1 (COI) gene for coral reefs of the Gulf of Aqaba, a semi-enclosed system in the northern Red Sea. Samples were obtained from standardized sampling devices (Autonomous Reef Monitoring Structures (ARMS)) deployed for 18 months. DNA barcoding of non-sessile specimens >2 mm revealed 83 OTUs in six phyla, of which only 25% matched a reference sequence in public databases. Metabarcoding of the 2 mm - 500 μm and sessile bulk fractions revealed 1197 OTUs in 15 animal phyla, of which only 4.9% matched reference barcodes. These results highlight the scarcity of COI data for cryptobenthic organisms of the Red Sea. Compared with data obtained using similar methods, our results suggest that Gulf of Aqaba reefs are less diverse than two Pacific coral reefs but much more diverse than an Atlantic oyster reef at a similar latitude. The standardized approaches used here show promise for establishing baseline data on biodiversity, monitoring the impacts of environmental change, and quantifying patterns of diversity at regional and global scales.
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Affiliation(s)
- Mamoon M D Al-Rshaidat
- a Department of Biological Sciences, The University of Jordan, Amman 11942, Jordan.,b Laboratory for Molecular Microbial Ecology, Marine Science Station, The University of Jordan and Yarmouk University, Aqaba 77110, Jordan
| | - Allison Snider
- c National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Sydney Rosebraugh
- c National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Amanda M Devine
- c National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Thomas D Devine
- c National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Laetitia Plaisance
- c National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Nancy Knowlton
- c National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Matthieu Leray
- c National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
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Geoffroy A, Destombe C, Kim B, Mauger S, Raffo MP, Kim MS, Le Gall L. Patterns of genetic diversity of the cryptogenic red alga Polysiphonia morrowii (Ceramiales, Rhodophyta) suggest multiple origins of the Atlantic populations. Ecol Evol 2016; 6:5635-47. [PMID: 27547343 PMCID: PMC4983580 DOI: 10.1002/ece3.2135] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/22/2016] [Accepted: 03/27/2016] [Indexed: 11/16/2022] Open
Abstract
The red alga Polysiphonia morrowii, native to the North Pacific (Northeast Asia), has recently been reported worldwide. To determine the origin of the French and Argentine populations of this introduced species, we compared samples from these two areas with samples collected in Korea and at Hakodate, Japan, the type locality of the species. Combined analyses of chloroplastic (rbcL) and mitochondrial (cox1) DNA revealed that the French and Argentine populations are closely related and differ substantially from the Korean and Japanese populations. The genetic structure of P. morrowii populations from South Atlantic and North Atlantic, which showed high haplotype diversity compared with populations from the North Pacific, suggested the occurrence of multiple introduction events from areas outside of the so‐called native regions. Although similar, the French and Argentine populations are not genetically identical. Thus, the genetic structure of these two introduced areas may have been modified by cryptic and recurrent introduction events directly from Asia or from other introduced areas that act as introduction relays. In addition, the large number of private cytoplasmic types identified in the two introduced regions strongly suggests that local populations of P. morrowii existed before the recent detection of these invasions. Our results suggest that the most likely scenario is that the source population(s) of the French and Argentine populations was not located only in the North Pacific and/or that P. morrowii is a cryptogenic species.
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Affiliation(s)
- Alexandre Geoffroy
- UPMC Univ Paris 06UMI 3614 Biologie évolutive et écologie des algues Station Biologique de Roscoff Place Georges Teissier 29682 Roscoff France; CNRS UMI 3614 Biologie évolutive et écologie des algues Station Biologique de Roscoff 29682 Roscoff France
| | - Christophe Destombe
- UPMC Univ Paris 06UMI 3614 Biologie évolutive et écologie des algues Station Biologique de Roscoff Place Georges Teissier 29682 Roscoff France; CNRS UMI 3614 Biologie évolutive et écologie des algues Station Biologique de Roscoff 29682 Roscoff France
| | - Byeongseok Kim
- Department of Biology Jeju National University 66 Jejudaehakno Jeju-si, Jeju-do 690-756 Korea
| | - Stéphane Mauger
- UPMC Univ Paris 06UMI 3614 Biologie évolutive et écologie des algues Station Biologique de Roscoff Place Georges Teissier 29682 Roscoff France; CNRS UMI 3614 Biologie évolutive et écologie des algues Station Biologique de Roscoff 29682 Roscoff France
| | - María Paula Raffo
- Laboratorio de Algas Marinas Bentónicas Centro para el Estudio de Sistemas Marinos (CESIMAR) Centro Nacional Patagónico (CENPAT-CONICET) Bvd. Brown 2915 Puerto Madryn U9120ACF Chubut Argentina
| | - Myung Sook Kim
- Department of Biology Jeju National University 66 Jejudaehakno Jeju-si, Jeju-do 690-756 Korea
| | - Line Le Gall
- Muséum National d'Histoire Naturelle (MNHN) Institut de Systématique, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC EPHE 57 rue Cuvier CP 39 75231 Paris Cedex 05 France
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Brown EA, Chain FJJ, Zhan A, MacIsaac HJ, Cristescu ME. Early detection of aquatic invaders using metabarcoding reveals a high number of non-indigenous species in Canadian ports. DIVERS DISTRIB 2016. [DOI: 10.1111/ddi.12465] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Emily A. Brown
- Department of Biology; McGill University; 1205 Docteur Penfield Montreal QC H3A 1B1 Canada
- Great Lakes Institute for Environmental Research; University of Windsor; Windsor ON N9B 3P4 Canada
| | - Frédéric J. J. Chain
- Department of Biology; McGill University; 1205 Docteur Penfield Montreal QC H3A 1B1 Canada
| | - Aibin Zhan
- Research Centre for Eco-Environmental Sciences; Chinese Academy of Sciences; 18 Shuangqing Road Haidian District Beijing 100085 China
| | - Hugh J. MacIsaac
- Great Lakes Institute for Environmental Research; University of Windsor; Windsor ON N9B 3P4 Canada
| | - Melania E. Cristescu
- Department of Biology; McGill University; 1205 Docteur Penfield Montreal QC H3A 1B1 Canada
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Zaiko A, Schimanski K, Pochon X, Hopkins GA, Goldstien S, Floerl O, Wood SA. Metabarcoding improves detection of eukaryotes from early biofouling communities: implications for pest monitoring and pathway management. BIOFOULING 2016; 32:671-684. [PMID: 27212415 DOI: 10.1080/08927014.2016.1186165] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/26/2016] [Indexed: 06/05/2023]
Abstract
In this experimental study the patterns in early marine biofouling communities and possible implications for surveillance and environmental management were explored using metabarcoding, viz. 18S ribosomal RNA gene barcoding in combination with high-throughput sequencing. The community structure of eukaryotic assemblages and the patterns of initial succession were assessed from settlement plates deployed in a busy port for one, five and 15 days. The metabarcoding results were verified with traditional morphological identification of taxa from selected experimental plates. Metabarcoding analysis identified > 400 taxa at a comparatively low taxonomic level and morphological analysis resulted in the detection of 25 taxa at varying levels of resolution. Despite the differences in resolution, data from both methods were consistent at high taxonomic levels and similar patterns in community shifts were observed. A high percentage of sequences belonging to genera known to contain non-indigenous species (NIS) were detected after exposure for only one day.
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Affiliation(s)
- Anastasija Zaiko
- a Coastal and Freshwater Group , Cawthron Institute , Nelson , New Zealand
- b Marine Science and Technology Center , Klaipeda University , Klaipeda , Lithuania
| | - Kate Schimanski
- a Coastal and Freshwater Group , Cawthron Institute , Nelson , New Zealand
- c School of Biological Sciences , University of Canterbury , Christchurch , New Zealand
| | - Xavier Pochon
- a Coastal and Freshwater Group , Cawthron Institute , Nelson , New Zealand
- d Institute of Marine Science , University of Auckland , Auckland , New Zealand
| | - Grant A Hopkins
- a Coastal and Freshwater Group , Cawthron Institute , Nelson , New Zealand
| | - Sharyn Goldstien
- c School of Biological Sciences , University of Canterbury , Christchurch , New Zealand
| | - Oliver Floerl
- a Coastal and Freshwater Group , Cawthron Institute , Nelson , New Zealand
| | - Susanna A Wood
- a Coastal and Freshwater Group , Cawthron Institute , Nelson , New Zealand
- e Environmental Research Institute , Waikato University , Hamilton , New Zealand
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Devloo-Delva F, Miralles L, Ardura A, Borrell YJ, Pejovic I, Tsartsianidou V, Garcia-Vazquez E. Detection and characterisation of the biopollutant Xenostrobus securis (Lamarck 1819) Asturian population from DNA Barcoding and eBarcoding. MARINE POLLUTION BULLETIN 2016; 105:23-29. [PMID: 26971231 DOI: 10.1016/j.marpolbul.2016.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/01/2016] [Accepted: 03/04/2016] [Indexed: 06/05/2023]
Abstract
DNA efficiently contributes to detect and understand marine invasions. In 2014 the potential biological pollutant pygmy mussel (Xenostrobus securis) was observed for the first time in the Avilés estuary (Asturias, Bay of Biscay). The goal of this study was to assess the stage of invasion, based on demographic and genetic (DNA Barcoding) characteristics, and to develop a molecular tool for surveying the species in environmental DNA. A total of 130 individuals were analysed for the DNA Barcode cytochrome oxidase I gene in order to determine genetic diversity, population structure, expansion trends, and to inferring introduction hits. Reproduction was evidenced by bimodal size distributions of 1597 mussels. High population genetic variation and genetically distinct clades might suggest multiple introductions from several source populations. Finally, species-specific primers were developed within the DNA barcode for PCR amplification from water samples in order to enabling rapid detection of the species in initial expansion stages.
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Affiliation(s)
- Floriaan Devloo-Delva
- Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n, 33006 Oviedo, Spain
| | - Laura Miralles
- Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n, 33006 Oviedo, Spain
| | - Alba Ardura
- USR3278-CRIOBE-CNRS-EPHE. Laboratoire d'excellence "CORAIL". Université de Perpignan-CBETM. 58 Rue Paul Alduy. 66860-Perpignan, CEDEX. France
| | - Yaisel J Borrell
- Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n, 33006 Oviedo, Spain
| | - Ivana Pejovic
- Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n, 33006 Oviedo, Spain
| | - Valentina Tsartsianidou
- Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n, 33006 Oviedo, Spain
| | - Eva Garcia-Vazquez
- Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n, 33006 Oviedo, Spain.
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Dowle EJ, Pochon X, C. Banks J, Shearer K, Wood SA. Targeted gene enrichment and high-throughput sequencing for environmental biomonitoring: a case study using freshwater macroinvertebrates. Mol Ecol Resour 2015; 16:1240-54. [DOI: 10.1111/1755-0998.12488] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 11/12/2015] [Accepted: 11/12/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Eddy J. Dowle
- Cawthron Institute; 98 Halifax Street 7010 Nelson New Zealand
- Department of Entomology; Kansas State University; Waters Hall Manhattan KS 66502 USA
| | - Xavier Pochon
- Cawthron Institute; 98 Halifax Street 7010 Nelson New Zealand
- Institute of Marine Science; University of Auckland; PO Box 349 Warkworth 0941 New Zealand
| | | | - Karen Shearer
- Cawthron Institute; 98 Halifax Street 7010 Nelson New Zealand
| | - Susanna A. Wood
- Cawthron Institute; 98 Halifax Street 7010 Nelson New Zealand
- Environmental Research Insitute University of Waikato; Private Bag 3105 3240 Hamilton New Zealand
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Steichen JL, Quigg A. Assessing the viability of microorganisms in the ballast water of vessels transiting the North Atlantic Ocean. MARINE POLLUTION BULLETIN 2015; 101:258-266. [PMID: 26455784 DOI: 10.1016/j.marpolbul.2015.09.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/25/2015] [Accepted: 09/30/2015] [Indexed: 06/05/2023]
Abstract
Testing phytoplankton viability within ballast tanks and receiving waters of ballast water discharge remain understudied. Potentially harmful dinoflagellates and diatoms are transported via ballast water to Galveston Bay, Texas (USA), home to three major ports: Houston, Texas City and Galveston. Ballast water from vessels transiting the North Atlantic Ocean was inoculated into treatments representing low and high salinity conditions similar to the Ports of Houston and Galveston respectively. Phytoplankton in ballast water growout experiments were deemed viable and showed growth in low and mid salinities with nutrient enrichment. Molecular methods identified several genera: Dinophysis, Gymnodinium, Gyrodinium, Heterocapsa, Peridinium, Scrippsiella, Chaetoceros and Nitzschia. These phytoplankton genera were previously identified in Galveston Bay except Scrippsiella. Phytoplankton, including those capable of forming harmful algal blooms leading to fish and shellfish kills, are transported to Galveston Bay via ballast water, and are viable when introduced to similar salinity conditions found in Galveston Bay ports.
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Affiliation(s)
- Jamie L Steichen
- Department of Oceanography, Texas A&M University, 3146 TAMU, College Station, TX 77843, United States; Department of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Parkway, Galveston, TX 77553, United States.
| | - Antonietta Quigg
- Department of Oceanography, Texas A&M University, 3146 TAMU, College Station, TX 77843, United States; Department of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Parkway, Galveston, TX 77553, United States
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Zaiko A, Martinez JL, Ardura A, Clusa L, Borrell YJ, Samuiloviene A, Roca A, Garcia-Vazquez E. Detecting nuisance species using NGST: Methodology shortcomings and possible application in ballast water monitoring. MARINE ENVIRONMENTAL RESEARCH 2015; 112:64-72. [PMID: 26174116 DOI: 10.1016/j.marenvres.2015.07.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 06/20/2015] [Accepted: 07/01/2015] [Indexed: 06/04/2023]
Abstract
Detecting the presence of potential invasive species in ballast water is a priority for preventing their spread into new environments. Next generation sequencing technologies are being increasingly used for exploring and assessing biodiversity from environmental samples. Here we apply high throughput sequencing from DNA extracted from ballast water (BW) samples employing two different platforms, Ion Torrent and 454, and compare the putative species catalogues from the resulting Operational Taxonomic Units (OTU). Water samples were taken from the RV Polastern ballast tank in five different days between the second and the twentieth navigation day. Pronounced decrease of oxygen concentration and increase of temperature occurred in the BW during this time, coincident with a progressively higher proportion of unassigned OTU and short reads indicating DNA degradation. Discrepancy between platforms for species catalogues was consistent with previously published bias in AT-rich sequences for Ion Torrent platform. Some putative species detected from the two platforms increased in frequency during the Polarstern travel, which suggests they were alive and therefore tolerant to adverse conditions. OTU assigned to the highly invasive red alga Polysiphonia have been detected at low but increasing frequency from the two platforms. Although in this moment NGST could not replace current methods of sampling, sorting and individual taxonomic identification of BW biota, it has potential as an exploratory methodology especially for detecting scarce species.
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Affiliation(s)
- Anastasija Zaiko
- Marine Science and Technology Center, Klaipeda University, H. Manto 84, 92294 Klaipeda, Lithuania; Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, 7010 Nelson, New Zealand
| | - Jose L Martinez
- Sequencing Unit, Edificio Severo Ochoa, C/ Julian Claveria s/n, University of Oviedo, Oviedo 33006, Spain
| | - Alba Ardura
- Marine Science and Technology Center, Klaipeda University, H. Manto 84, 92294 Klaipeda, Lithuania; Department of Functional Biology, C/ Julian Claveria s/n, University of Oviedo, Oviedo 33006, Spain
| | - Laura Clusa
- Department of Functional Biology, C/ Julian Claveria s/n, University of Oviedo, Oviedo 33006, Spain
| | - Yaisel J Borrell
- Department of Functional Biology, C/ Julian Claveria s/n, University of Oviedo, Oviedo 33006, Spain
| | - Aurelija Samuiloviene
- Marine Science and Technology Center, Klaipeda University, H. Manto 84, 92294 Klaipeda, Lithuania; Department of Ecology and Biology, Klaipeda University, H. Manto 84, 92294 Klaipeda, Lithuania
| | - Agustín Roca
- Department of Functional Biology, C/ Julian Claveria s/n, University of Oviedo, Oviedo 33006, Spain
| | - Eva Garcia-Vazquez
- Department of Functional Biology, C/ Julian Claveria s/n, University of Oviedo, Oviedo 33006, Spain.
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48
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Zaiko A, Samuiloviene A, Ardura A, Garcia-Vazquez E. Metabarcoding approach for nonindigenous species surveillance in marine coastal waters. MARINE POLLUTION BULLETIN 2015; 100:53-59. [PMID: 26422121 DOI: 10.1016/j.marpolbul.2015.09.030] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/24/2015] [Accepted: 09/17/2015] [Indexed: 06/05/2023]
Abstract
In this study, high-throughput sequencing (HTS) metabarcoding was applied for the surveillance of plankton communities within the southeastern (SE) Baltic Sea coastal zone. These results were compared with those from routine monitoring survey and morphological analyses. Four of five nonindigenous species found in the samples were identified exclusively by metabarcoding. All of them are considered as invasive in the Baltic Sea with reported impact on the ecosystem and biodiversity. This study indicates that, despite some current limitations, HTS metabarcoding can provide information on the presence of exotic species and advantageously complement conventional approaches, only requiring the same monitoring effort as before. Even in the currently immature status of HTS, this combination of HTS metabarcoding and observational records is recommended in the early detection of marine pests and delivery of the environmental status metrics of nonindigenous species.
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Affiliation(s)
- Anastasija Zaiko
- Marine Science and Technology Centre, Klaipeda University, H. Manto 84, LT 92294 Klaipeda, Lithuania; Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, 7010 Nelson, New Zealand.
| | - Aurelija Samuiloviene
- Marine Science and Technology Centre, Klaipeda University, H. Manto 84, LT 92294 Klaipeda, Lithuania
| | - Alba Ardura
- Marine Science and Technology Centre, Klaipeda University, H. Manto 84, LT 92294 Klaipeda, Lithuania; Department of Functional Biology, University of Oviedo, C/ Julian Claveria s/n., 33006 Oviedo, Spain
| | - Eva Garcia-Vazquez
- Department of Functional Biology, University of Oviedo, C/ Julian Claveria s/n., 33006 Oviedo, Spain
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