High-Throughput Sequencing of Environmental DNA as a Tool for Monitoring Eukaryotic Communities and Potential Pathogens in a Coastal Upwelling Ecosystem

18 pages, 5 tables, 7 figures.-- This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY)The marine environment includes diverse microeukaryotic organisms that play important functional roles in the ecosystem. With molecular approaches, eukaryotic taxonomy has been improved, complementing classical analysis. In this study, DNA metabarcoding was performed to describe putative pathogenic eukaryotic microorganisms in sediment and marine water fractions collected in Galicia (NW Spain) from 2016 to 2018. The composition of eukaryotic communities was distinct between sediment and water fractions. Protists were the most diverse group, with the clade TSAR (Stramenopiles, Alveolata, Rhizaria, and Telonemida) as the primary representative organisms in the environment. Harmful algae and invasive species were frequently detected. Potential pathogens, invasive pathogenic organisms as well as the causative agents of harmful phytoplanktonic blooms were identified in this marine ecosystem. Most of the identified pathogens have a crucial impact on the aquacultural sector or affect to relevant species in the marine ecosystem, such as diatoms. Moreover, pathogens with medical and veterinary importance worldwide were also found, as well as pathogens that affect diatoms. The evaluation of the health of a marine ecosystem that directly affects the aquacultural sector with a zoonotic concern was performed with the metabarcoding assayThis work was conducted with the support of the projects AGL2015-65705-R (Ministerio de Economía y Competitividad, Spain), IN607B 2019/01 (Consellería de Economía, Emprego e Industria–GAIN, Xunta de Galicia), 0474_BLUEBIOLAB Fondo Europeo de Desarrollo Regional FEDER en el marco del programa Interreg V A España – Portugal (POCTEP) 2014-2020, and VIVALDI (678589) (EU H2O20). RR-C wishes to thank the Axencia Galega de Innovación (GAIN, Xunta de Galicia) for her predoctoral contract IN606A-2018/020Peer reviewe