scholarly journals Considerations for metabarcoding-based port biological baseline surveys aimed at marine non-indigenous species monitoring and risk-assessments

2019 ◽  
Author(s):  
Anaïs Rey ◽  
Oihane C. Basurko ◽  
Naiara Rodriguez-Ezpeleta
Keyword(s):  
Environmental Dna ◽  
Cost Effective ◽  
Taxonomic Composition ◽  
Risk Assessments ◽  
List Type ◽  
Indigenous Species ◽  
Promising Alternative ◽  
International Convention ◽  
Outer Estuary ◽  
Non Indigenous Species

AbstractMonitoring introduction and spread of non-indigenous species via maritime transport and performing risk assessments require port biological baseline surveys. Yet, the comprehensiveness of these surveys is often compromised by the large number of habitats present in a port, the seasonal variability and the time-consuming morphological approach used for taxonomic identification. Metabarcoding represents a promising alternative for rapid comprehensive port biological baseline surveys, but its application in this context requires further assessments.We applied metabarcoding (based on barcodes of the Cytochrome c oxidase subunit I and of the 18S ribosomal RNA gene) to 192 port samples collected i) from diverse habitats (water column – including environmental DNA and zooplankton, sediment and fouling structures), ii) at different sites (from inner to outer estuary), and iii) during the four seasons of the year.By comparing the biodiversity metrics derived from each sample group, we show that each sampling method resulted in a distinct community profile and that environmental DNA alone cannot substitute for organismal sampling, and that, although sampling at different seasons and locations resulted in higher observed biodiversity, operational results can be obtained by sampling selected locations and seasons.By assessing the taxonomic composition of the samples, we show that metabarcoding data allowed the detection of previously recorded non-indigenous species as well as to reveal presence of new ones, even if in low abundance.Synthesis and application. Our comprehensive assessment of metabarcoding for port biological baseline surveys sets the basics for cost-effective, standardized and comprehensive monitoring of non-indigenous species and for performing risk assessments in ports. This development will contribute to the implementation of the recently entered into force International Convention for the Control and Management of Ships’ Ballast Water and Sediments.

scholarly journals The current state of DNA barcoding of macroalgae in the Mediterranean Sea: presently lacking but urgently required

2020 ◽  
Vol 63 (3) ◽  
pp. 253-272 ◽  
Author(s):  
Angela G. Bartolo ◽  
Gabrielle Zammit ◽  
Akira F. Peters ◽  
Frithjof C. Küpper
Keyword(s):  
Mediterranean Sea ◽  
Dna Barcoding ◽  
Environmental Dna ◽  
Cost Effective ◽  
Indigenous Species ◽  
Biodiversity Monitoring ◽  
Current State ◽  
Dna Libraries ◽  
The Mediterranean ◽  
Non Indigenous Species

AbstractThis review article explores the state of DNA barcoding of macroalgae in the Mediterranean Sea. Data from the Barcode of Life Data System (BOLD) were utilised in conjunction with a thorough bibliographic review. Our findings indicate that from around 1124 records of algae in the Mediterranean Sea, only 114 species have been barcoded. We thus conclude that there are insufficient macroalgal genetic data from the Mediterranean and that this area would greatly benefit from studies involving DNA barcoding. Such research would contribute to resolving numerous questions about macroalgal systematics in the area and address queries related to biogeography, especially those concerned with non-indigenous species. It could also possibly result in the development and application of better, cost-effective biodiversity monitoring programmes emanating from UN conventions and EU Directives. One possible way of achieving this is to construct DNA libraries via sequencing and barcoding, subsequently enabling better cost-effective biodiversity monitoring through environmental DNA metabarcoding.

scholarly journals Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA

NeoBiota ◽  
2021 ◽  
Vol 70 ◽  
pp. 151-165
Author(s):  
Francesco Zangaro ◽  
Benedetta Saccomanno ◽  
Eftychia Tzafesta ◽  
Fabio Bozzeda ◽  
Valeria Specchia ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Special Focus ◽  
Indigenous Species ◽  
Dna Barcodes ◽  
Identification Of Species ◽  
The Mediterranean ◽  
Taxonomic Groups ◽  
Non Indigenous Species

The biodiversity of the Mediterranean Sea is currently threatened by the introduction of Non-Indigenous Species (NIS). Therefore, monitoring the distribution of NIS is of utmost importance to preserve the ecosystems. A promising approach for the identification of species and the assessment of biodiversity is the use of DNA barcoding, as well as DNA and eDNA metabarcoding. Currently, the main limitation in the use of genomic data for species identification is the incompleteness of the DNA barcode databases. In this research, we assessed the availability of DNA barcodes in the main reference libraries for the most updated inventory of 665 confirmed NIS in the Mediterranean Sea, with a special focus on the cytochrome oxidase I (COI) barcode and primers. The results of this study show that there are no barcodes for 33.18% of the species in question, and that 45.30% of the 382 species with COI barcode, have no primers publicly available. This highlights the importance of directing scientific efforts to fill the barcode gap of specific taxonomic groups in order to help in the effective application of the eDNA technique for investigating the occurrence and the distribution of NIS in the Mediterranean Sea.

scholarly journals Evaluating the potential of ecological niche modelling as a component in marine non-indigenous species risk assessments

2015 ◽  
Vol 97 (1-2) ◽  
pp. 470-487 ◽  
Author(s):  
Sonja Leidenberger ◽  
Matthias Obst ◽  
Robert Kulawik ◽  
Kerstin Stelzer ◽  
Karin Heyer ◽  
...  
Keyword(s):  
Ecological Niche ◽  
Ecological Niche Modelling ◽  
Risk Assessments ◽  
Indigenous Species ◽  
Niche Modelling ◽  
Non Indigenous Species

Environmental DNA sampling protocols for the surveillance of marine non-indigenous species v3

2021 ◽  
Author(s):  
Luca Mirimin ◽  
Dulaney Miller ◽  
Sara Fernandez
Keyword(s):  
Invasive Species ◽  
Environmental Samples ◽  
Environmental Dna ◽  
Indigenous Species ◽  
Sampling Protocols ◽  
Dna Sampling ◽  
Marine Invasive Species ◽  
Monitoring And Surveillance ◽  
Non Indigenous Species

This document describes a series of protocols for the collection of environmental samples intended for the monitoring and surveillance of marine invasive species by means of eDNA metabarcoding analysis, as described in the associated publication (Fernandez et al. 2021: https://doi.org/10.1016/j.marpolbul.2021.112893).

Environmental DNA sampling protocols for the surveillance of marine non-indigenous species in Irish coastal waters

2021 ◽  
Vol 172 ◽  
pp. 112893
Author(s):  
Sara Fernandez ◽  
Dulaney L. Miller ◽  
Luke E. Holman ◽  
Arjan Gittenberger ◽  
Alba Ardura ◽  
...  
Keyword(s):  
Coastal Waters ◽  
Environmental Dna ◽  
Indigenous Species ◽  
Sampling Protocols ◽  
Dna Sampling ◽  
Non Indigenous Species

scholarly journals Higher-order patterns of aquatic species spread through the global shipping network

2019 ◽  
Author(s):  
Mandana Saebi ◽  
Jian Xu ◽  
Erin K. Grey ◽  
David M. Lodge ◽  
Nitesh Chawla
Keyword(s):  
Ballast Water ◽  
Cost Effective ◽  
The United States ◽  
Higher Order ◽  
Accurate Estimation ◽  
Targeted Prevention ◽  
Indigenous Species ◽  
First Order ◽  
Non Indigenous Species ◽  
Higher Order Networks

AbstractThe introduction and establishment of non-indigenous species (NIS) through global ship movements is a significant threat to marine ecosystems and economies. While ballast-vectored invasions have been partly addressed by some national policies and an international agreement regulating the concentrations of organisms in ballast water, biofouling-vectored invasions remain a large risk. Development of additional realistic and cost-effective ship-borne NIS policies requires an accurate estimation of NIS spread risk from both ballast water and biofouling. In this paper, we demonstrate that first-order Markov assumptions limit accurate modeling of NIS spread risks through the global shipping network. In contrast, we show that higher-order patterns overcome this limitation by revealing indirect pathways of NIS transfer. We accomplish this by developing Species Flow Higher-Order Networks (SF-HON), which we developed independently for ballast and biofouling, for comparison with first-order Markovian models of ballast and biofouling. We evaluated SF-HON predictions using the largest available datasets of invasive species for Europe and the United States. We show that not only does SF-HON yield more accurate NIS spread risk predictions than first-order models and existing higher-order models, but also that there are important differences in NIS spread via the ballast and biofouling vectors. Our work provides information that policymakers can use to develop more efficient and targeted prevention strategies for ship-borne NIS spread management, especially as management of biofouling is of increasing concern.

scholarly journals Biodiversity assessments in the 21st century: the potential of insect traps to complement environmental samples for estimating eukaryotic and prokaryotic diversity using high-throughput DNA metabarcoding

Genome ◽  
2019 ◽  
Vol 62 (3) ◽  
pp. 147-159 ◽  
Author(s):  
Camila D. Ritter ◽  
Sibylle Häggqvist ◽  
Dave Karlsson ◽  
Ilari E. Sääksjärvi ◽  
A. Muthama Muasya ◽  
...  
Keyword(s):  
Species Identification ◽  
Environmental Dna ◽  
Cost Effective ◽  
Taxonomic Composition ◽  
Soil Samples ◽  
Morphological Studies ◽  
Prokaryotic Diversity ◽  
Dna Metabarcoding ◽  
Morphological Species ◽  
Ecosystem Interactions

The rapid loss of biodiversity, coupled with difficulties in species identification, call for innovative approaches to assess biodiversity. Insects make up a substantial proportion of extant diversity and play fundamental roles in any given ecosystem. To complement morphological species identification, new techniques such as metabarcoding make it possible to quantify insect diversity and insect–ecosystem interactions through DNA sequencing. Here we examine the potential of bulk insect samples (i.e., containing many non-sorted specimens) to assess prokaryote and eukaryote biodiversity and to complement the taxonomic coverage of soil samples. We sampled 25 sites on three continents and in various ecosystems, collecting insects with SLAM traps (Brazil) and Malaise traps (South Africa and Sweden). We then compared our diversity estimates with the results obtained with biodiversity data from soil samples from the same localities. We found a largely different taxonomic composition between the soil and insect samples, testifying to the potential of bulk insect samples to complement soil samples. Finally, we found that non-destructive DNA extraction protocols, which preserve insect specimens for morphological studies, constitute a promising choice for cost-effective biodiversity assessments. We propose that the sampling and sequencing of insect samples should become a standard complement for biodiversity studies based on environmental DNA.

scholarly journals Advantages and Limitations of Environmental DNA/RNA Tools for Marine Biosecurity: Management and Surveillance of Non-indigenous Species

2018 ◽  
Vol 5 ◽  
Author(s):  
Anastasija Zaiko ◽  
Xavier Pochon ◽  
Eva Garcia-Vazquez ◽  
Sergej Olenin ◽  
Susanna A. Wood
Keyword(s):  
Environmental Dna ◽  
Indigenous Species ◽  
Non Indigenous Species

scholarly journals Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water

2018 ◽  
Author(s):  
Luke E. Holman ◽  
Mark de Bruyn ◽  
Simon Creer ◽  
Gary Carvalho ◽  
Julie Robidart ◽  
...  
Keyword(s):  
Early Detection ◽  
Community Composition ◽  
Environmental Sample ◽  
Environmental Dna ◽  
Community Change ◽  
Small Subunit ◽  
Careful Consideration ◽  
Indigenous Species ◽  
Sample Type ◽  
Non Indigenous Species

AbstractEnvironmental DNA (eDNA) surveys are increasingly being used for biodiversity monitoring, principally because they are sensitive and can provide high resolution community composition data. Despite considerable progress in recent years, eDNA studies examining how different environmental sample types can affect species detectability remain rare. Comparisons of environmental samples are especially important for providing best practice guidance on early detection and subsequent mitigation of non-indigenous species. Here we used eDNA metabarcoding of COI (cytochrome c oxidase subunit I) and 18S (nuclear small subunit ribosomal DNA) genes to compare community composition between sediment and water samples in artificial coastal sites across the United Kingdom. We first detected markedly different communities and a consistently greater number of distinct operational taxonomic units in sediment compared to water. We then compared our eDNA datasets with previously published rapid assessment biodiversity surveys and found excellent concordance among the different survey techniques. Finally, our eDNA surveys detected many non-indigenous species, including several newly introduced species, highlighting the utility of eDNA metabarcoding for both early detection and temporal / spatial monitoring of non-indigenous species. We conclude that careful consideration on environmental sample type is needed when conducting eDNA surveys, especially for studies assessing community change.

scholarly journals How many Non-Indigenous Species occurring in the Mediterranean Sea can actually be identified through environmental DNA? A gap analysis of NIS DNA barcodes in the reference libraries

2021 ◽  
Vol 4 ◽  
Author(s):  
Maurizio Pinna ◽  
Francesco Zangaro ◽  
Eftychia Tzafesta ◽  
Valeria Specchia
Keyword(s):  
Alien Species ◽  
Mediterranean Sea ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Indigenous Species ◽  
Dna Barcodes ◽  
Molecular Tools ◽  
Amplification Process ◽  
The Mediterranean ◽  
Non Indigenous Species

The Mediterranean Sea is known for hosting a high diversity of species, with more than 17,000 reported marine species, one fifth which are endemic. Moreover, the number of non-indigenous species (NIS) in the Mediterranean Sea is recently reported to be increasing. The monitoring and the distribution of NIS is a key requirement for the conservation and management of the ecosystems, as also foreseen by the regulation (EU) No 1143/2014 of the European Parliament and of the Council of 22 October 2014 on the prevention and management of the introduction and spread of invasive alien species. A promising innovative approach for the identification of species and biodiversity is the use of molecular tools (DNA barcoding and metabarcoding). Combined with environmental DNA (eDNA) extracted from environmental samples like water or sediment, traces of species can be identified. Currently, the main limitation in the use of molecular tools (DNA barcoding and metabarcoding, eDNA) for species identification is the incompleteness of the DNA barcode reference databases. We assessed the extent of gaps in DNA barcode reference libraries, using the most updated inventory of 666 confirmed alien species occurring in the Mediterranean Sea. Also, the availability of primers for the amplification process was investigated. 32.58% of these species lack DNA barcodes in the reference libraries. Also, 70% of the retrieved NIS in the DNA barcode libraries lack the public availability of the primers used for the amplification process. The results of this study allow us to direct scientific efforts towards specific taxonomic groups in order to complete the NIS DNA barcode reference libraries and enable effective application of eDNA in investigations of the occurrence and the distribution of NIS in the Mediterranean Sea, and in the first sighting of still unknown NIS.

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