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AtlantECO Final Scientific Conference - One Ocean, One Heath: Microbiomes of the Atlantic Seascape

AtlantECO, Consortium

Abstract

The AtlantECO Final Conference The research and innovation project AtlantECO, funded by the European Union, is in its final year. It brought together experts from Europe, South America and Africa, conducting research on the Atlantic Ocean Microbiomes, Microplastics and Seascape connectivity. The objective of the project is to provide knowledge-based resources for a better understanding and management of the Atlantic Ocean and its ecosystem services. AtlantECO also engaged with citizens and actors from the industry and policy sectors in order to stimulate responsible behaviour and Blue Growth. The AtlantECO Final Scientific Conference was an opportunity for AtlantECO partners and other European and international research projects (e.g. Mission Atlantic, iAtlantic, SUMMER, NECCTON, eDNAbyss, BioGeoScapes, EXPORTS, APERO, ACE, GO-SHIP) to present & discuss their latest findings and approaches. One Ocean, One Health The scientific community is increasingly asked to integrate fundamental research and socio-economic evaluations in order to address societal needs, inform policy makers, support the economy, and advance international cooperation. Under the UN Decade of Ocean Science, this endeavour is embodied in the concept of One Ocean, One Health. While the focus of the AtlantECO Final Scientific Conference is to present & discuss scientific results, participants are asked to highlight how their science is relevant to that concept. To that end, the AtlantECO Final Scientific Conference was organised around a handful of Themes that correspond to key ecosystem services provided by Microbiomes of the Atlantic Seascape, i.e. climate regulation, food provision, health provision and regulation, deep sea ecosystems support, and biodiversity. Microbiomes of the Atlantic Seascape The Atlantic seascape is made of 3D physical processes such as large river plumes, upwelling and downwelling associated with coastal winds and mesoscale eddies, boundary currents and gyres. This highly dynamic system shapes the diversity of marine microbiomes and the ecosystem services that they provide. While the human microbiome is composed principally of bacteria, marine microbiomes consist of a much broader ensemble of microscopic organisms that inhabit river plumes, coastal waters, the open ocean, the atmosphere and plastic particles, i.e. the plastisphere. Microbiomes of the Atlantic Seascape can be used to develop diagnostic tools and metrics that assess the health status of the Atlantic Ocean. The AtlantECO Final Scientific Conference was an opportunity to present & discuss innovative methods, new digital knowledge, multi-omics approaches, data analysis & modelling, and assessments & forecasts that help us better understand Microbiomes of the Atlantic Seascape.

Full text

Session: Health Provision & Regulation Final Scientific Conference, 15-19 September 2025 New technologies for high-resolution detection of toxigenic algae Julie Robidart, Nathan Hubot, Ahmed Alrefaey, Raffaella Casotti Insert title HABs economic impact >$100M / year Geographic ranges are expanding for some species Frequency and duration of blooms are expanding Impacts of harmful algae https://cdn.coastalscience.noaa.gov/page-attachments/news/NHABON_Framewk_WkshpReport_12-18-20_Final.pdf Pseudonitzschia spp. Responsible for amnesic shellfish poisoning Accumulation in the foodweb: toxic to humans and can lead to mass mortality in marine mammals and birds Toxin: domoic acid Biomarker: dab operon Insert title A biomarker for toxigenic Pseudonitzschia Species Isolate Accession LAMP Amplification Pseudo-nitzschia multistriata SZN-B954 + Pseudo-nitzschia multistriata SZN-B955 + Pseudo-nitzschia pungens CCAP 1061/44 + Pseudo-nitzschia multiseries NWFSC 713 + Pseudo-nitzschia multiseries NWFSC 714 + Pseudo-nitzschia multiseries NWFSC 715 + Pseudo-nitzschia multiseries ML-54 + Pseudo-nitzschia multiseries ML-55 + Pseudo-nitzschia multiseries ML-56 + Pseudo-nitzschia multiseries ML-59 + Karenia brevis CCMP2228 - Karenia mikimotoi CCAP 1127/2 - Alexandrium tamarense CCAP 1119/25 - Synechococcus sp CCAP 1479/9 - Prorcentrum lima CCAP 1136/12 - Alexandrium minutum CCAP 1119/15 - Lingulodinium polyedra CCAP 1121/7 - Prorcentrum cordatum CCAP 1136/16 - Ahmed Alrefaey Insert title Genetic sensing workflow RoCSI eDNA / omics autosampler AmpliTRON Lab-on-a-chip eDNA / cell concentration Cell lysis & DNA purification Target gene detection + + Microfluidic DNA extraction Insert title Genetic sensing workflow RoCSI eDNA / omics autosampler AmpliTRON Lab-on-a-chip eDNA / cell concentration Cell lysis & DNA purification Target gene detection ++ Microfluidic DNA extraction Insert title Genetic sensing workflow Lab-on-a-chip Target gene detection eDNA / cell concentration Cell lysis & DNA purification ++ Microfluidic DNA extraction Insert title Dimethyl adipimidate (DMA)+functionalized silica bead extraction Alrefaey et al., in review Lab-on-a-chip redesign for genetic sensing Insert title Genetic sensing workflow Lab-on-a-chip Target gene detection LoC microfluidics with updated: Fluorescence excitation and detection Temperature control eDNA / cell concentration Cell lysis & DNA purification + + Insert title Lab-on-a-chip technology: traditional chemical assays; Automated in situ sensing comparable to bench analyses Lab-on-a-chip microfluidics Insert title Gulf of Naples Screening for dabD in Naples Mare Chiara Sarno River Nathan Hubot RoCSI eDNA / omics autosampler •Take autosamples across the bay over 2 days •Amplify Pseudonitzschia dabD with AmpliTRON If positive: •Confirm sequence identification •Quantify gene abundances per L 6 June 13 June Insert title Gulf of Naples Screening for dabD in Naples Mare Chiara Sarno River Nathan Hubot 6 June 13 June 10^3 cells 10^4 cells 10^5 cells Sarno River sample Insert title Alrefaey et al., in review Conclusions •RoCSI eDNA autosampler effective for collecting Pseudonitzschia •AmpliTRON is effective for genetic detection of Pseudonitzschia (≥ 102 LoD) at field stations •Collection-extraction-detection using the RoCSI and AmpliTRON is about 90 minutes •103 – 104 cells quantified at the Sarno River site in the Gulf of Naples •Lab-on-a-chip with bespoke optics (fluorescence) and temperature control is suitable for genetic sensing •Taking the automated DMA-extraction into the workflow, the limit of detection for Pseudonitzschia is 15 x below the statutory limit for testing in the UK Insert title Alrefaey et al., in review Next steps •Finish screening the Naples samples for dabD, publication of demonstration of workflow Sensor design •Finalise design of miniaturised lab-on-a-chip genetic sensor: cell pre-concentration pressure-balanced with submersible optics and temperature control •Fabricate the final design and trial in situ Thank you @EU_AtlantECO @eu.atlanteco @eu.atlanteco @atlantecoproject This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 862923. This output reflects only the author’s view and the European Union cannot be held responsible for any use that may be made of the information contained therein. 21