Establishing the foundations for a sustainable use of deep‐sea resources relies on increasing knowledge this inaccessible ecosystem, which is challenging with traditional methods. The analysis environmental DNA (eDNA) emerges as an alternative, but it has been scarcely applied to fish. Here, we have analyzed fish eDNA contained in oceanic vertical profile samples (up 2000 m depth) collected throughout continental slope Bay Biscay. We detected 52 different species, 25 were classified found...

Abstract To successfully implement environmental DNA‐based (eDNA) diversity monitoring, the completeness and accuracy of reference databases used for taxonomic assignment eDNA sequences are among challenges to be tackled. Here, we have developed a workflow that evaluates current status GenBank marine fishes. For given combination species barcodes, gap analysis is performed potentially erroneous identified. Our based on four most genes (cytochrome c oxidase subunit 1, 12S rRNA, 16S cytochrome...

Abstract Multispecies and ecosystem models, which are key for the implementation of ecosystem‐based approaches to fisheries management, require extensive data on trophic interactions between marine organisms, including changes over time. DNA metabarcoding, by allowing simultaneous taxonomic identification community present in hundreds samples, could be used speeding up large‐scale stomach content collection. Yet, metabarcoding routinely implemented, technical challenges should addressed,...

Cetacean conservation requires ecosystem-scale management with special focus on food webs. Rorquals and sperm whales are top predators of complex open ocean webs and, although mesopelagic fish cephalopods predated by these cetaceans, their contribution to diets is not fully understood. Here, we aimed better describe the consumption identifying preferred species consumed rorquals at mid-latitudes. To do so, combined cephalopod community composition inferred from whale faecal marine...

In the face of increasing anthropogenic pressures on estuarine ecosystems, methods to efficiently and reliably assess their ecological status are essential. This study explores integration environmental DNA analysis into AZTI's Fish Index (AFI) ecosystems. Surface water eDNA sampling bottom trawl surveys were performed across multiple estuaries in Basque Country, Spain, resulting species data used calculate AFI scores. metabarcoding consistently detected higher fish richness than trawling,...

Ciliates are globally distributed eukaryotic organisms inhabiting virtually all environments on Earth. Although ciliates range from 10 µm to a few millimetres in cell size, they repeatedly reported the pico-sized fraction (<2-3 µm) of molecular surveys. Here, we used existing data sets (BioMarKs and Tara Oceans) with different size fractions demonstrate that ciliate signal, probably derived breakage during filtration, is informative reliable study marine biodiversity biogeography. We then...

Abstract Mesozooplankton is a key component of the ocean, regulating global processes such as carbon pump, and ensuring energy transfer from lower to higher trophic levels. Yet, knowledge on mesozooplankton diversity, distribution connectivity at scale still fragmented. To fill this gap, we applied DNA metabarcoding samples collected during Malaspina‐2010 circumnavigation expedition across Atlantic, Indian Pacific oceans surface bathypelagic depths. We highlight scarce diversity identify...

To evaluate the effect of temperature on two amoeba strains genera Acanthamoeba and Hartmannella separately treated depending their life stage, trophozoite or cyst, when cells are directly exposed under controlled conditions.For thermal treatments, three temperatures were selected 50, 60 70°C, a microcosm was designed using dialysis bags. The inactivation each strain determined method based most probable number quantification agar plates. results showed that for all strains, treatment more...

The bioindicator potential of the microeukaryotic community in a full-scale A2O wastewater treatment process was assessed after deactivating internal recirculation one two parallel lines plant. deactivation (NIR-line), led to strong decrease nitrogen removal efficiency (53 % ammonia-uptake NIR-line versus 97 unaltered line or IR-line), as well lower organic matter (95 BOD5 IR-line). microeukaryote structure changed greatly confirming trends observed experimental studies and showed abundance...

A new peritrich species highly tolerant to ammonium and nitrite, Epistylis camprubii n. sp., was found adhered the biofilm of two advanced wastewater treatment plants treating high ammonium-loaded in Rubi, Spain. Its morphology, oral infraciliature phylogenetic position clade were studied. The is a vase-shaped peritrich, constricted below peristomial lip, with an vivo average length 58.7 ± 10.1 µm, width 32.0 5.4 longitudinally striated, compact stalk that occasionally exhibits uneven...

Abstract Expectations are high regarding the potential of eDNA metabarcoding for diversity monitoring. To make this approach suitable purpose, completeness and accuracy reference databases used taxonomic assignment sequences among challenges to be tackled. Yet, despite ongoing efforts increase coverage databases, key species lacking, incorrect records in widely repositories such as GenBank have been reported. This compromises studies, especially diverse groups marine fishes. Here, we...

<ns3:p>Background Siphonophores are diverse, globally distributed hydrozoans that play a central role in marine trophic webs worldwide. However, they still constitute an understudied fraction of the open ocean gelatinous taxa, mainly due to challenges related siphonophore sampling and identification, which have led general knowledge gap about their diversity, distribution abundance. Methods Here, we provide global overview oceanic vertical siphonophores using DNA metabarcoding data from 77...

Mesozooplankton is a key component of the ocean, regulating global processes such as carbon pump, and ensuring energy transfer from lower to higher trophic levels. Yet, despite importance understanding mesozooplankton diversity, distribution connectivity at scale predict impact climate change in marine ecosystems, there still fragmented knowledge. To fill this gap, we applied DNA metabarcoding samples collected during Malaspina-2010 circumnavigation expedition across temperate tropical...

Abstract The deep-sea remains among the most unknown ecosystems on Earth despite its relevant role in carbon sequestration and increasing threat due to interest by fishing mining industries. This, together with recent discovery that upper layer of this ecosystem (mesopelagic zone) harbors about 90% fish biomass Earth, claims for a deeper understanding so foundations sustainable use resources can be established. analysis environmental DNA (eDNA) collected from water column emerges as an...

Environmental DNA (eDNA) metabarcoding, the process of sequencing collected from environment for producing biodiversity inventories, is increasingly being applied to assess fish diversity and distribution in marine environments. Yet, successful application this technique deeply relies on accurate complete reference databases used taxonomic assignment. The most markers eDNA metabarcoding studies are cytochrome C oxidase subunit 1 (COI), 16S ribosomal RNA (16S), 12S (12S) b (cyt b) genes,...

Abstract Multispecies and ecosystem models, which are key for the implementation of ecosystem-based approaches to fisheries management, require extensive data on trophic interactions between marine organisms, including changes over time. DNA metabarcoding (the simultaneous identification all taxa in a sample by sequencing short region) could be used speeding up large-scaled stomach content collection. Yet, routinely implemented, technical challenges should addressed, such as potentially...