Final Report Summary - LUSOAQUABARCODE (Implementing DNA barcoding into aquatic biodiversity research in Portugal and priming new macrobenthos monitoring tools)
The ERG LusoAquaBarcode (LAB) aimed at implementing DNA barcoding into aquatic biodiversity research in Portugal, and Europe, and priming the development of new macrobenthos monitoring tools.
LAB and the hosting research unit (Centre of Environmental and Molecular Biology – CBMA) worked as a hub to implement and develop the national network “Barcoding Aquatic Life (BAL@pt)”. This network comprised a diverse group of aquatic biodiversity experts and institutions to accomplish the project’s goals, involving actively research groups from mainly 6 Portuguese universities, the fisheries research agency (currently IPMA), the Portuguese Malacology Institute (IPM) and the National Museum of Natural History, Lisbon, along with several international collaborations.
Working in parallel with another grant obtained from national funds (FCT-funded Lusitanian Marine Barcode of Life), LAB contributed to the creation and development of a reference library of DNA barcodes for over 300 species of marine invertebrates of Portugal, with emphasis on three main groups: annelids, crustaceans and molluscs. This reference library is lodged and web-available in the Barcode of Life Datasystems (BOLD) in order to enable public access upon publication. The library records integrate specimen data, including collection metadata, GPS coordinates, taxonomy and images of the specimens, together with molecular data, comprising DNA barcode sequences, trace files and information on primers used. An identical reference library of has been created for fish species from Portugal, which currently comprises DNA barcodes for over 150 species, including the majority of the exploited species.
These references libraries, while standing on their own has a unique and valuable resource for the European community, contributed additionally to greatly improve our taxonomic knowledge at the species level in all major taxa examined, with multiple examples of clarified uncertainties and detection of potential (or confirmed) undescribed species, among which stand some species of great economic impact.
Efforts devoted to the technical improvement of the DNA barcoding pipeline, resulted in the design of novel PCR primers for DNA barcode amplification in a broad range of marine metazoans, therefore facilitating the accelerated growth of the reference libraries for marine life while enlarging their taxonomic breadth.
Focusing on end-users needs, a final taxonomic congruency check was proposed for implementation at the terminal end of the DNA barcoding pipeline. It consists on a ranking system in which species DNA barcodes are attributed a taxonomic reliability grades (A to E), this way providing an empirical metric for the reliability of species identifications when using reference DNA barcodes.
The reference libraries initiated (and continuously expanding) in the scope of this and other parallel projects, have a multitude of applications and uses. They provide an alternative identification system for marine species whenever morphology-based identifications are not possible or difficult, allowing quick and reliable identifications from body parts of any organism included in the library and at any developmental stage. Specific expertise in a given taxonomic group is not required to perform reliable DNA barcode-based identifications. Among other applications, these reference libraries can be used for identification of fish and shellfish in markets and fisheries landings, or for identification of their larvae in zooplanktonic surveys.
Environmental monitoring under the EU Water Framework directive is another salient application of this species identification resource, namely in this case, of utmost relevance for monitoring estuarine macrobenthic communities. The DNA barcode reference libraries for marine invertebrates can be used in conjunction with next generation DNA sequencing technologies (NGS) to improve the scale, and increase the frequency and amount of samples in monitoring campaigns of estuarine macrobenthic communities. LAB provided significant leverage for the design and implementation of a research grant, which is currently addressing the development of a NGS-based metabarcoding approach for application in the scope of estuarine macrobenthic communities.
LAB and the hosting research unit (Centre of Environmental and Molecular Biology – CBMA) worked as a hub to implement and develop the national network “Barcoding Aquatic Life (BAL@pt)”. This network comprised a diverse group of aquatic biodiversity experts and institutions to accomplish the project’s goals, involving actively research groups from mainly 6 Portuguese universities, the fisheries research agency (currently IPMA), the Portuguese Malacology Institute (IPM) and the National Museum of Natural History, Lisbon, along with several international collaborations.
Working in parallel with another grant obtained from national funds (FCT-funded Lusitanian Marine Barcode of Life), LAB contributed to the creation and development of a reference library of DNA barcodes for over 300 species of marine invertebrates of Portugal, with emphasis on three main groups: annelids, crustaceans and molluscs. This reference library is lodged and web-available in the Barcode of Life Datasystems (BOLD) in order to enable public access upon publication. The library records integrate specimen data, including collection metadata, GPS coordinates, taxonomy and images of the specimens, together with molecular data, comprising DNA barcode sequences, trace files and information on primers used. An identical reference library of has been created for fish species from Portugal, which currently comprises DNA barcodes for over 150 species, including the majority of the exploited species.
These references libraries, while standing on their own has a unique and valuable resource for the European community, contributed additionally to greatly improve our taxonomic knowledge at the species level in all major taxa examined, with multiple examples of clarified uncertainties and detection of potential (or confirmed) undescribed species, among which stand some species of great economic impact.
Efforts devoted to the technical improvement of the DNA barcoding pipeline, resulted in the design of novel PCR primers for DNA barcode amplification in a broad range of marine metazoans, therefore facilitating the accelerated growth of the reference libraries for marine life while enlarging their taxonomic breadth.
Focusing on end-users needs, a final taxonomic congruency check was proposed for implementation at the terminal end of the DNA barcoding pipeline. It consists on a ranking system in which species DNA barcodes are attributed a taxonomic reliability grades (A to E), this way providing an empirical metric for the reliability of species identifications when using reference DNA barcodes.
The reference libraries initiated (and continuously expanding) in the scope of this and other parallel projects, have a multitude of applications and uses. They provide an alternative identification system for marine species whenever morphology-based identifications are not possible or difficult, allowing quick and reliable identifications from body parts of any organism included in the library and at any developmental stage. Specific expertise in a given taxonomic group is not required to perform reliable DNA barcode-based identifications. Among other applications, these reference libraries can be used for identification of fish and shellfish in markets and fisheries landings, or for identification of their larvae in zooplanktonic surveys.
Environmental monitoring under the EU Water Framework directive is another salient application of this species identification resource, namely in this case, of utmost relevance for monitoring estuarine macrobenthic communities. The DNA barcode reference libraries for marine invertebrates can be used in conjunction with next generation DNA sequencing technologies (NGS) to improve the scale, and increase the frequency and amount of samples in monitoring campaigns of estuarine macrobenthic communities. LAB provided significant leverage for the design and implementation of a research grant, which is currently addressing the development of a NGS-based metabarcoding approach for application in the scope of estuarine macrobenthic communities.