scholarly journals Phytoplankton assessment and Non-Indigenous species monitoring through eDNA metabarcoding in marine ecosystems

2021 ◽  
Vol 4 ◽  
Author(s):  
Sara Fernandez ◽  
Dulaney Miller ◽  
Luca Mirimin
Keyword(s):  
Environmental Dna ◽  
Biodiversity Loss ◽  
High Volume ◽  
Indigenous Species ◽  
Molecular Tools ◽  
Bisphosphate Carboxylase ◽  
Dna Metabarcoding ◽  
Group A ◽  
Study Sites ◽  
Non Indigenous Species

Invasive Alien Species (IAS) are one of the most contributing constituents of biodiversity loss with the distribution range of an increasing number of IAS being artificially re-shaped by human activities. Rapid and effective tools are therefore needed in order to monitor changes in biodiversity and the dispersal of IAS. Molecular tools such as environmental DNA metabarcoding are being progressively included in the tool kit for IAS monitoring, however, the literature is largely focused on metazoans markers targeting regions such as COI and 18S and scarce studies include a marker for plants or algae. Here, we have tested a marker in ribulose-1,5-bisphosphate carboxylase-oxygenase chloroplast region to assess phytoplankton through environmental DNA metabarcoding. Several sample types (low and high-volume water filtration, sediment grabs, net tows) were deployed at twelve study sites along the Irish coast to determine which technique would perform better for the targeted group. A total of eleven NIS were detected during the study. Low-volume surface water filtering exceeded in NIS detection and recovered the highest diversity with 123 species detected. High volume samplers were the ones recovering the lowest number of OTUs (N= 53). Western sites (Galway Bay) had greater diversity and the highest number of total NIS compared to eastern sites in Carlingford, Dublin and Waterford. These results have shown the need for a specific IAS surveillance and has served as a basis to implement the use of eDNA metabarcoding and algae markers in future monitoring programs.

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.

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.

A revision of the French Telothelepodidae and Thelepodidae (Annelida, Terebelliformia), with descriptions of three species and first European record of a non-indigenous species

Zootaxa ◽  
2020 ◽  
Vol 4810 (2) ◽  
pp. 305-327
Author(s):  
NICOLAS LAVESQUE ◽  
MARIO H. LONDOÑO-MESA ◽  
GUILLEMINE DAFFE ◽  
PAT HUTCHINGS
Keyword(s):  
New Species ◽  
Identification Key ◽  
Indigenous Species ◽  
Molecular Tools ◽  
European Species ◽  
Arcachon Bay ◽  
Asiatic Species ◽  
Three New Species ◽  
Non Indigenous Species

Telothelepodidae and Thelepodidae from French waters are revised based on material available in French marine stations and newly collected specimens. This work is the second part of the Spaghetti Project aiming to revise French species of “Spaghetti” worms. It describes three new species using both morphological and molecular tools: Streblosoma cabiochi n. sp., Streblosoma lindsayae n. sp. and Thelepus corsicanus n. sp. This study also permitted us to detect the presence of an Asiatic species, Thelepus japonicus, in Arcachon Bay and Normandy, introduced via oysters transfers. An identification key for European species of both families is also provided. 

scholarly journals On linking mechanism to invasive species impact

2021 ◽  
Author(s):  
Marc Cadotte
Keyword(s):  
Invasive Species ◽  
Biodiversity Loss ◽  
Indigenous Species ◽  
Native Plant ◽  
Minimal Impact ◽  
Vincetoxicum Rossicum ◽  
Biodiversity Change ◽  
Non Indigenous Species ◽  
Native Plant Diversity ◽  
Invasive Species Impact

Species invasion represents one of the major drivers of biodiversity change globally, yet there is widespread confusion about the nature of non-indigenous species (NIS) impact. This stems from differing notions of what constitutes invasive species ‘impact’ and the scales at which it should be assessed. At local scales, the mechanisms of impact on competitors can be classified into four scenarios: 1) minimal impact from NIS inhabiting unique niche space; 2) neutral impact spread across the community and proportional to NIS abundance; 3) targeted impact on a small number of competitors with overlapping niches; and 4) pervasive impact that is disproportionate to NIS abundance and caused by modifications that filter out other species. I developed a statistical test to distinguish these four mechanisms based on community rank-abundance curves and then created a scale-independent standardized impact score. Using an example long-term dataset, that has high native plant diversity and an abundance gradient of the invasive vine, Vincetoxicum rossicum, I show that impact resulted in either targeted extirpations or widespread biodiversity loss. Regardless of whether NIS impact is neutral, targeted or pervasive, the net outcome will be the homogenization of ecosystems and reduced biodiversity at larger scales, perhaps reducing ecosystem resilience.

scholarly journals Assessment of species gaps in DNA barcode libraries of non-indigenous species (NIS) occurring in European coastal regions

2020 ◽  
Vol 4 ◽  
Author(s):  
Sofia Duarte ◽  
Pedro E. Vieira ◽  
Filipe O. Costa
Keyword(s):  
Sequence Data ◽  
Dna Barcode ◽  
Indigenous Species ◽  
Coastal Environments ◽  
Taxonomic Assignment ◽  
Dna Sequence Data ◽  
Marker Data ◽  
Dna Metabarcoding ◽  
Assessment Techniques ◽  
Non Indigenous Species

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.

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 On linking mechanism to invasive species impact

2021 ◽  
Author(s):  
Marc Cadotte
Keyword(s):  
Invasive Species ◽  
Scale Up ◽  
Biodiversity Loss ◽  
Indigenous Species ◽  
Native Plant ◽  
Minimal Impact ◽  
Vincetoxicum Rossicum ◽  
Non Indigenous Species ◽  
Native Plant Diversity ◽  
Invasive Species Impact

Species invasion represents one of the major drivers of biodiversity change globally, yet there is widespread scientific and popular confusion and controversy about the nature of non-indigenous species (NIS) impact. This confusion stems from differing notions and understanding of what constitutes invasive species ‘impact’ and the scales at which it should be assessed. I argue that the proximate mechanisms determining invasive species impact happen at smaller scales where species interact, and by understanding these mechanisms, we can scale up to a broader understanding of how invasive species impact biodiversity. The mechanisms of NIS impact on potential competitors can be classified into four scenarios: 1) minimal impact from NIS inhabiting unique niche space; 2) neutral impact spread across the community and proportional to NIS abundance; 3) targeted impact on a small number of competitors with overlapping niches; and 4) pervasive impact that is disproportionate to NIS abundance and ostensibly caused by ecosystem modification that filters out other species. I develop a statistical test to distinguish these four mechanisms based on community rank-abundance curves. Using an example dataset from plant communities invaded by the dominant invasive vine, Vincetoxicum rossicum, I show that in long-term plots that had high native plant diversity and where V. rossicum increased, impact resulted in either targeted extirpations (scenario 3) or widespread biodiversity loss (scenario 4). Regardless of whether NIS impact is neutral, targeted or pervasive, the net outcome will be the homogenization of ecosystems and reduced biodiversity at larger scales, perhaps reducing ecosystem resilience.

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 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
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