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

Abstract

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 assay.

Co-occurrence and diversity patterns of benthonic and planktonic communities in a shallow marine ecosystem

“…Although the OTU tables were different, our results agree with those reported by Rıós-Castro et al (2021), with an overall of 70%-95% of eukaryotic OTUs taxonomically classified (Figure 5). The eukaryote community greatly varied among all compartments and among the different samplings from each environmental compartment (Figure 5).…”

“…The raw eukaryote OTU table obtained after the sequencing of the V9 region of the 18S rRNA gene, performed by Rıós-Castro et al (2021), was considered to construct co-occurrence networks of prokaryotes and eukaryotes. OTUs with a combined abundance ≤ 5 reads were considered in the present study to increase the number of nonrepresentative taxa and to be able to identify biotic and abiotic correlations of eukaryote and prokaryote communities, including not such representative taxa.…”

“…After the subsampling procedure performed in this study, 6,731 prokaryote OTUs were obtained and therefore considered in the following analyses (Table 1). The eukaryote sequencing results were detailed in Rıós-Castro et al (2021). After the eukaryote OTU table subsampling procedure performed in the present study, 6,819 eukaryote OTUs were obtained and considered in the following analyses.…”

“…The composition of the main eukaryote groups (Archaeplastida, Fungi, Metazoa, and Protist) present in sediment and the water column was previously described in Rıós-Castro et al (2021), although no temporal variations were considered in each ecological fraction. In the present study, eukaryotic community composition was more deeply described.…”

“…Previous studies on microbial planktonic diversity in Rıá de Vigo have mostly focused on the seasonal dynamics of a prokaryote or small (<20 mm cell size) eukaryote community in surface shelf waters (>30-m depth) (Hernando-Morales et al, 2018;Hernańdez-Ruiz et al, 2018) and on the description of cooccurrence networks of eukaryotic and prokaryotic associations in the epipelagic zone (Joglar et al, 2021). However, the eukaryotic and prokaryotic diversity in shallow environments (<5-m depth) within Rıá de Vigo, including sediment and water samples, has not been explored thus far except for a eukaryote study by Rıós-Castro et al (2021).…”