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 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 Scientific collaboration for early detection of invaders results in a significant update on estimated range: lessons from Stenothoe georgiana Bynum & Fox 1977

2020 ◽  
Author(s):  
GEMMA MARTÍNEZ-LAIZ ◽  
MACARENA ROS ◽  
JOSÉ MANUEL GUERRA-GARCÍA ◽  
AGNESE MARCHINI ◽  
VICTORIA FERNÁNDEZ-GONZÁLEZ ◽  
...  
Keyword(s):  
Early Detection ◽  
First Record ◽  
Western Mediterranean ◽  
Mediterranean Coast ◽  
Amphipod Species ◽  
Indigenous Species ◽  
Scientific Cooperation ◽  
Vectors Of Introduction ◽  
Non Indigenous Species ◽  
Effective Spread

Detection of new non-indigenous species is often delayed when taxonomically challenging taxa are involved, such as small-sized marine organisms. The present study highlights the relevance of scientific cooperation in the early detection of the invader amphipod Stenothoe georgiana. Originally described from North Carolina (USA), the species was recently found in Chile and the Western Mediterranean. Here, we provide the first record of the species in Macaronesia, Atlantic coasts of continental Europe, North Africa and Australia, and extend its known distribution along the Mediterranean coast. Just like other small crustaceans, shipping (including recreational boating) and aquaculture are probably the main vectors of introduction and secondary spread for this amphipod species. This case of S. georgiana sheds light on the importance of promoting taxonomical knowledge, and building multidisciplinary expertise networks that ensure an effective spread of alien species information. We also encourage the implementation of standardized monitoring methodologies to facilitate early detection of small mobile invaders. 

Non-indigenous marine macroalgae in native communities: a case study in the British Isles

2008 ◽  
Vol 88 (4) ◽  
pp. 693-698 ◽  
Author(s):  
Frederic Mineur ◽  
Mark P. Johnson ◽  
Christine A. Maggs
Keyword(s):  
Species Richness ◽  
Northern Ireland ◽  
Community Composition ◽  
Native Species ◽  
Positive Relationship ◽  
Marine Macroalgae ◽  
Indigenous Species ◽  
Species Introduction ◽  
Southern England ◽  
Non Indigenous Species

It has traditionally been considered that areas with high natural species richness are likely to be more resistant to non-indigenous species than those with lower numbers of species. However, this theory has been the subject of a debate over the last decade, since some studies have shown the opposite trend. In the present study, a macroalgal survey was carried out at 24 localities in Northern Ireland and southern England, using a quadrat approach in the lower littoral. The two opposing hypotheses were tested (negative versus positive relationship between native and non-indigenous species richness) in this marine environment. The effect of the presence of ‘impacts’, potential sources of disturbance and species introduction (e.g. marina, harbour or aquaculture), was also tested. A positive relationship was found between the number of non-indigenous species and the native species richness at the three different scales tested (quadrats, sites and localities). At no scale did a richer native assemblage appear to restrict the establishment of introduced species. The analyses revealed greater species richness and different community composition, as well as more non-indigenous species, in southern England relative to Northern Ireland. The presence of the considered impacts had an effect on the community composition and species richness in southern England but not in Northern Ireland. Such impacts had no effect on the non-indigenous species richness in either area.

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.

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 Early detection of aquatic invaders using metabarcoding reveals a high number of non-indigenous species in Canadian ports

2016 ◽  
Vol 22 (10) ◽  
pp. 1045-1059 ◽  
Author(s):  
Emily A. Brown ◽  
Frédéric J. J. Chain ◽  
Aibin Zhan ◽  
Hugh J. MacIsaac ◽  
Melania E. Cristescu
Keyword(s):  
Early Detection ◽  
Indigenous Species ◽  
Non Indigenous Species
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