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Assessing the seasonal and spatial dynamics of zooplankton through DNA metabarc...
Moutinho, Jorge; Flores, Diego Carreira; Gomes, Pedro T.; Costa, Filipe O.; Duarte, Sofia Alexandra FerreiraZooplankton are key components of estuarine trophic networks. However, routine monitoring is hindered by the difficulty of morphology-based identification. DNA-based methods allow us to circumvent some of these hurdles, providing precise species identifications regardless of the taxonomic expertise of the investigator or the developmental stage of the specimens. However, the process is dependent on the complete...
Current status and topical issues on the use of eDNA-based targeted detection o...
Duarte, Sofia Alexandra Ferreira; Simões, Luara Aparecida; Costa, Filipe O.Animal detection through DNA present in environmental samples (eDNA) is a valuable tool for detecting rare species, that are difficult to observe and monitor. eDNA-based tools are underpinned by molecular evolutionary principles, key to devising tools to efficiently single out a targeted species from an environmental sample. Here, we present a comprehensive review of the use of eDNA-based methods for the detect...
Catch me if you can: current status and topical issues on the use of eDNA-based...
Duarte, Sofia Alexandra Ferreira; Simões, Luara Aparecida; Costa, Filipe O.Animal detection through DNA present in environmental samples (eDNA) is a valuable tool for detecting rare species, that are difficult to observe and monitor. eDNA-based tools are underpinned by molecular evolutionary principles, which are key to devising tools to efficiently single out a targeted species from an environmental sample, using carefully chosen marker regions and customized primers. Here, we presen...
Compilation, revision, and annotation of DNA barcodes of marine invertebrate No...
Lavrador, Ana Sofia Castro; Fontes, João T.; Vieira, Pedro Emanuel Ferreira Reis; Costa, Filipe O.; Duarte, Sofia Alexandra FerreiraThe introduction of non-indigenous species (NIS) is one of the major threats to the integrity of European coastal ecosystems. DNA-based assessments have been increasingly adopted for monitoring NIS. However, the accuracy of DNA-based taxonomic assignments is largely dependent on the completion and reliability of DNA barcode reference libraries. As such, we aimed to compile and audit a DNA barcode reference libr...
Macrozoobenthos monitoring in Portuguese transitional waters in the scope of th...
Duarte, Sofia Alexandra Ferreira; Vieira, Pedro Emanuel Ferreira Reis; Leite, Barbara R.; Teixeira, Marcos André Machado Lima; Neto, João MiguelDespite the growing use and potential of DNA metabarcoding to improve and expedite macrozoobenthos monitoring, its employment in Water Framework Directive (WFD) monitoring of transitional ecosystems still remains largely unexplored. In the current study, we addressed this research gap by building upon the biomonitoring network program of the Portuguese Environmental Agency (APA). The ecological condition of 20 ...
Artificial seaweed substrates complement ARMS in DNA metabarcoding-based monito...
Leite, Barbara R.; Duarte, Sofia Alexandra Ferreira; Troncoso, Jesús S.; Costa, Filipe O.We used DNA metabarcoding to compare macrozoobenthic species colonization between autonomous reef monitoring structures (ARMS) and artificial seaweed monitoring systems (ASMS). We deployed both substrates in two different locations (Ría de Vigo and Ría de Ferrol, NW Iberian coast) and collected them after 6, 9, and 12 months to assess species composition of the colonizing communities through high-throughput seq...
Hurdles and opportunities in implementing marine biosecurity systems in data-po...
Carvalho, Susana; Shchepanik, Hailey; Aylagas, Eva; Berumen, Michael L.; Costa, Filipe O.; Costello, Mark John; Duarte, Sofia Alexandra FerreiraManaging marine nonindigenous species (mNIS) is challenging, because marine environments are highly connected, allowing the dispersal of species across large spatial scales, including geopolitical borders. Cross-border inconsistencies in biosecurity management can promote the spread of mNIS across geopolitical borders, and incursions often go unnoticed or unreported. Collaborative surveillance programs can enha...
Environmental DNA metabarcoding for benthic monitoring: A review of sediment sa...
Pawlowski, J.; Bruce, K.; Panksep, K.; Aguirre, F. I.; Amalfitano, S.; Apothéloz-Perret-Gentil, L.; Baussant, T.; Bouchez, A.; Carugati, L.Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft s...
Status and prospects of marine NIS detection and monitoring through (e)DNA meta...
Duarte, Sofia Alexandra Ferreira; Vieira, Pedro Emanuel Ferreira Reis; Lavrador, Ana Sofia Castro; Costa, Filipe O.In coastal ecosystems, non-indigenous species (NIS) are recognized as a major threat to biodiversity, ecosystem functioning and socio-economic activities. Here we present a systematic review on the use of metabarcoding for NIS surveillance in marine and coastal ecosystems, through the analysis of 42 publications. Metabarcoding has been mainly applied to environmental DNA (eDNA) from water samples, but also to D...
Surveillance of non-indigenous invertebrate species through DNA metabarcoding i...
Lavrador, Ana Sofia Castro; Amaral, Fábio G.; Vieira, Pedro Emanuel Ferreira Reis; Costa, Filipe O.; Duarte, Sofia Alexandra FerreiraDNA metabarcoding has been widely used in biodiversity assessments as a complement to traditional morphology-based techniques. This technique is useful for the early detection and surveillance of non-indigenous species (NIS) in aquatic ecosystems. When introduced to new locations, NIS can establish, and become invasive, which may cause severe alterations to native ecosystems and biodiversity. As most introducti...