scholarly journals Saint Peter and Saint Paul Archipelago barcoded: fish diversity in the remoteness and DNA barcodes reference library for metabarcoding monitoring

2021 ◽  
Author(s):  
Marcelo Merten Cruz ◽  
Lilian Sander Hoffmann ◽  
Thales R. O. de Freitas
Keyword(s):  
Standard Procedure ◽  
Saint Paul ◽  
Molecular Techniques ◽  
Fish Diversity ◽  
Its Sequencing ◽  
Dna Barcodes ◽  
Reference Library ◽  
Anthropogenic Pressures ◽  
Dna Metabarcoding ◽  
Saint Peter

Abstract Anthropogenic pressures have been depleting the global biodiversity. In order to monitor the changes in ecosystems, molecular techniques can be used to characterize species composition. Among molecular markers capable of identifying species, the COI is the most used, and its sequencing is the standard procedure of how taxonomic information can be surveyed. Despite this, new possibilities of biodiversity profiling have become possible through the assessment of highly fragmented DNA molecules in environmental samples. Now, medium- and short-length markers are used in metabarcoding studies. Here, a survey of marine fish from the Saint Peter and Saint Paul Archipelago was barcoded, in which the COI barcode procedure identified 21 species of 11 families of fish. Then, the first extensive COI library of these islands located in isolation was constructed; from these sequences, the most appropriate primer pair for future metabarcoding studies was identified. The new Saint Peter and Saint Paul sequence database has 9,183 sequences from 165 species and 62 families of fish. The overall mean distance among all sequences was 0.4. This distance reveals that the archipelago is a reservoir of biodiversity as this attribute is higher than other islands around the world. Due to this, the protection of the archipelago should be enhanced and well monitored with science-based approaches such as DNA metabarcoding. In this case, the primer pair specifically designed from this library should be considered.

scholarly journals Correction to: A vagrant black-headed Gull (Chroicocephalus ridibundus) documented from Saint Peter and Saint Paul archipelago: Brazil’s first record

2021 ◽  
Author(s):  
Antônio Coimbra de Brum ◽  
Renata Brentano ◽  
Rosalinda Carmela Montone ◽  
Maria Virginia Petry
Keyword(s):  
Saint Paul ◽  
First Record ◽  
Saint Peter

scholarly journals The use of eDNA and DNA metabarcoding in monitoring the ecological condition of Norwegian lakes

2021 ◽  
Vol 4 ◽  
Author(s):  
Sara Atienza Casas ◽  
Markus Majaneva ◽  
Thomas Jensen ◽  
Marie Davey ◽  
Frode Fossøy ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Ecological Status ◽  
Ecological Condition ◽  
Molecular Techniques ◽  
Taxonomic Resolution ◽  
Potential Cost ◽  
Running Water ◽  
National Monitoring ◽  
Monitoring Programs ◽  
Dna Metabarcoding

Biodiversity assessments using molecular identification of organisms through high-throughput sequencing techniques have been a game changer in ecosystem monitoring, providing increased taxonomic resolution, more objective identifications, potential cost reductions, and reduced processing times. The use of DNA metabarcoding of bulk samples and environmental DNA (eDNA) is now widespread but is not yet universally implemented in national monitoring programs. While bulk sample metabarcoding involves extraction of DNA from organisms in a sample, eDNA analysis involves obtaining DNA directly from environmental samples, which can include microorganisms, meiofauna-size taxa and macrofauna traces such as larval stages, skin and hair cells, gametes, faeces and free DNA bound to particles. In Norway, freshwater biomonitoring in compliance with the EU Water Framework Directive (WFD) is conducted on several administrative levels, including national monitoring programs for running water, small and large lakes. These programs typically focus on a fraction of the actual biodiversity present in the monitored habitats (Weigand 2019). DNA metabarcoding of both bulk samples and eDNA samples are relevant tools for future freshwater biomonitoring in Norway. The aim of this PhD project is to develop assessment protocols based on DNA-metabarcoding and eDNA of benthic invertebrates, microcrustaceans and fish that can be used as standard biomonitoring tools to assess the ecological condition of lakes. The main topics addressed will be: - Development of protocols throughout the eDNA-metabarcoding workflow (i.e. sampling, filtration, preservation, extraction, amplification and sequencing) suitable to execute biodiversity assessments and determine the ecological status of lakes. - Comparison of the results obtained using molecular tools and traditional morphology-based approaches in order to assess the feasibility of such techniques to be incorporated as standard biomonitoring tools, such as the ones implemented under the provisions of the WFD. - Evaluate the effect of improved taxonomic resolution from molecular techniques on determining the ecological status of lakes, both by broadening the number of taxa analyzed and by identifying more taxa to species level. - Assess the feasibility of using eDNA extracted from water samples, taken at different depths and fish densities, to measure fish abundance/biomass as a proxy to calculate the ecological quality indices regulated in the WFD. - Analyze the coverage and resolution provided by reference libraries for certain taxa, such as crustacea, in order to assess the reliability and precision of taxonomic assignments.

scholarly journals A pilot for implementing environmental DNA (eDNA) based methods into environmental and biomonitoring

2021 ◽  
Vol 4 ◽  
Author(s):  
Tiina Laamanen ◽  
Veera Norros ◽  
Sanna Suikkanen ◽  
Mikko Tolkkinen ◽  
Kristiina Vuorio ◽  
...  
Keyword(s):  
Best Practices ◽  
Information Exchange ◽  
State Of The Art ◽  
Environmental Dna ◽  
Bulk Sample ◽  
The State ◽  
Molecular Techniques ◽  
Future Research ◽  
Dna Metabarcoding

Environmental DNA (eDNA) and other molecular based approaches are revolutionizing the field of biomonitoring. These approaches undergo rapid modifications, and it is crucial to develop the best practices by sharing the newest information and knowledge. In our ongoing project we: assess the state-of-the-art of eDNA methods at Finnish Environment Institute SYKE; identify concrete next steps towards the long-term aim of implementing eDNA methods into environmental and biomonitoring; promote information exchange on eDNA methods and advance future research efforts both within SYKE and with our national and international partners. assess the state-of-the-art of eDNA methods at Finnish Environment Institute SYKE; identify concrete next steps towards the long-term aim of implementing eDNA methods into environmental and biomonitoring; promote information exchange on eDNA methods and advance future research efforts both within SYKE and with our national and international partners. Scientific background Well-functioning and intact natural ecosystems are essential for human well-being, provide a variety of ecosystem services and contain a high diversity of organisms. However, human activities such as eutrophication, pollution, land-use or invasive species, are threatening the state and functioning of ecosystems from local to global scale (e.g. Benateau et al. 2019; Reid et al. 2018; Vörösmarty et al. 2010). New molecular techniques in the field and in the laboratory have enabled sampling and identification of much of terrestrial, marine and freshwater biodiversity. These include environmental DNA (eDNA, e.g. Valentini et al. 2016) and bulk-sample DNA metabarcoding approaches (e.g. Elbrecht et al. 2017) and targeted RNA-based methods (e.g. Mäki and Tiirola 2018). The eDNA technique uses DNA that is released from organisms into their environment, from which a signal of organisms’ presence in the system can be obtained. For example, in aquatic ecosystems, eDNA is typically extracted from sediment or filtered water samples (e.g. Deiner et al. 2016), and this approach is distinguished from bulk DNA metabarcoding, where organisms are directly identified from e.g. complete biological monitoring samples (e.g. Elbrecht et al. 2017). Despite the demonstrated potential of environmental and bulk-sample DNA metabarcoding approaches in recent years, there are still significant bottlenecks to their routine use that need to be addressed (e.g. Pawlowski et al. 2020). Methods and implementati on The project is divided into three work packages: WP1 Gathering existing knowledge, identifying knowledge gaps and proposing best practices, WP2 Roadmap to implementation and WP3 eDNA monitoring pilot. Please see more details in the Fig. 1

scholarly journals Fish diversity in European lakes: geographical factors dominate over anthropogenic pressures

2013 ◽  
Vol 58 (9) ◽  
pp. 1779-1793 ◽  
Author(s):  
Sandra Brucet ◽  
Stephanie Pédron ◽  
Thomas Mehner ◽  
Torben L. Lauridsen ◽  
Christine Argillier ◽  
...  
Keyword(s):  
Fish Diversity ◽  
Anthropogenic Pressures ◽  
Geographical Factors

Trophic ecology of large pelagic fish in the Saint Peter and Saint Paul Archipelago, Brazil

2019 ◽  
Vol 70 (10) ◽  
pp. 1402 ◽  
Author(s):  
F. V. Albuquerque ◽  
A. F. Navia ◽  
T. Vaske ◽  
O. Crespo ◽  
F. H. V. Hazin
Keyword(s):  
Trophic Ecology ◽  
Feeding Habits ◽  
Saint Paul ◽  
Pelagic Fish ◽  
Trophic Niche ◽  
Trophic Relationships ◽  
Main Prey ◽  
Important Prey ◽  
Saint Peter ◽  
Prey Items

Trophic relationships of large pelagic predators can determine the structure and dynamics of oceanic food webs. The feeding habits and trophic ecology of five large pelagic fish (Acanthocybium solandri, Coryphaena hippurus, Elagatis bipinnulata, Thunnus albacares and Thunnus atlanticus) in the Saint Peter and Saint Paul Archipelago were evaluated to determine whether there is a trophic-niche overlap or resource partitioning among them. Eighty prey items found in 1528 stomachs were identified and grouped into Cephalopoda, Cnidaria, Crustacea, Gastropoda, Teleostei and Tunicata. Exocoetidae and Scombridae were the main prey in the diet of Acanthocybium solandri. In C. hippurus, Cheilopogon cyanopterus and Exocoetus volitans were the most important prey items, whereas C. cyanopterus was the main prey for T. albacares. Thunnus atlanticus consumed a great proportion of invertebrate species, with shrimps of Sergestidae family being particularly important. The gastropod Cavolinia sp. was the most important prey for E. bipinnulata. The five species had a high trophic specialisation and a high trophic level (>4.4), whereas most dietary overlaps were consistently low. The most important factor for diet dissimilarity was the consumption of Exocoetidade. All species were classified as top predators with varied diets, indicating their structural and functional importance in the food web of the Archipelago.

scholarly journals FISH DIVERSITY DETECTION AT PORT AND URBAN CANAL AREA USING ENVIRONMENTAL DNA METABARCODING

2018 ◽  
Vol 74 (2) ◽  
pp. I_474-I_479 ◽  
Author(s):  
Satomi KAMIMURA ◽  
Yasunori KOZUKI ◽  
Sosuke OTANI ◽  
Rin HIRAKAWA ◽  
Kazuki IWAMI ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Fish Diversity ◽  
Canal Area ◽  
Dna Metabarcoding

scholarly journals Demersal Fish Diversity and Molecular Taxonomy in the Bering Sea and Chukchi Sea

2021 ◽  
Author(s):  
xuehua wang ◽  
Yuan Li ◽  
Nan Zhang ◽  
Puqing Song ◽  
Ran Zhang ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Bering Sea ◽  
Chukchi Sea ◽  
Molecular Taxonomy ◽  
Demersal Fish ◽  
Fish Diversity ◽  
Dna Barcodes ◽  
The Family ◽  
Arctic Fish ◽  
The Bering Sea

Abstract DNA barcoding by sequencing a standard region of cytochrome c oxidase subunit I (COⅠ) provides an accurate, rapid method for identifying different species. In this study, we provide a molecular taxonomic assessment of demersal fishes in the Bering Sea and Chukchi Sea based on DNA barcoding, and a total of 123 mitochondrial COⅠ partial fragments with a length of 652 bp were obtained. The consensus among all sequences was determined by alignment via a BLAST search in GenBank. Phylogenetic relationships were reconstructed on the basis of neighbor-joining (NJ) trees and barcoding gaps. The 39 species investigated in this analysis were distributed among 10 families. Five families within Scorpaeniformes including 19 species accounted for almost half of the species. The next largest group was Perciformes, with 9 species, followed by Pleuronectiformes and Gadiformes, with 5 species each, and the smallest number of species belonged to Rajiformes. At the family level, Cottidae was the largest family, followed by Zoarcidae, accounting for 8 species. The other eight families—Gadidae, Pleuronectidae, Psychrolutidae, Agonidae, Liparidae, Ammodytidae, Hexagrammidae, and Rajidae—accounted for a smaller proportion of species. In brief, our study shows that DNA barcodes are an effective tool for studying fish diversity and phylogeny in the Bering Sea and Chukchi Sea. The contribution of DNA barcoding to identifying Arctic fish species may benefit further Arctic fish studies on biodiversity, biogeography and conservation in the future.

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