Dinoflagellates constitute an abundant and diversified component of marine plankton, mostly associated with stratified conditions typical of late spring through autumn in temperate regions. Yet, difficulties with the identification of many species limit the knowledge of their composition and seasonal succession. Here we use a 3‐year V4‐18S rDNA metabarcoding dataset (4,366,007 reads, 4650 Amplicon Sequence Variants, ASVs) coll...

Long‐term ecological research has revealed the impact of climate on marine ecosystems at multiple time scales. Changes in the pelagic system have been detected at the LTER‐MC site in the Gulf of Naples (Tyrrhenian Sea, western Mediterranean) since 1984. Here we analyzed the time series to determine whether zooplankton had significantly changed over the three decades 1984–2015. In addition to the seasonal cycle as the main mode...

The presence of phytoplankton parasites along the water column was explored at the Long‐Term Ecological Station MareChiara (LTER‐MC) in the Gulf of Naples (Mediterranean Sea) in October 2019. Microscopy analyses showed diatoms dominating the phytoplankton community in the upper layers (0–20 m). Metabarcoding data from the water column showed the presence of Chytridiomycota predominantly in the upper layers coinciding with the...

Coastal phytoplankton present remarkable variability because of complex patterns and relationships of hydrological parameters at the land–sea interface. We analysed a time series of 917 phytoplankton samples collected in the period 1984–2010 at the coastal station LTER‐MC (Gulf of Naples, Mediterranean Sea) with the aims of determining: (i) whether recurrent species associations are recognizable in this variable coastal enviro...

Pseudo-nitzschia is a widespread genus of marine pennate diatoms comprising 58 species of which 28 can produce the neurotoxin domoic acid, causative of Amnesic Shellfish Poisoning (ASP). Species of the genus are found in both oceanic and coastal waters where they can form large blooms. The timing and magnitude of blooms is generally described based on water samples collected at the surface, while limited information is availab...

Our study focuses on bacterial communities associated with two benthic, epiphytic dinoflagellates, Gambierdiscus australes and Ostreopsis cf. ovata , isolated from coastal waters of Las Palmas, Gran Canaria, and grown in clonal cultures. The goal was to characterize the stable bacterial consortia found within the phycosphere of each dinoflagellate species and establish into which functional group they fell. High‐throughput seq...

Blooms of the toxic dinoflagellates Ostreopsis have become common along rocky shores of the Mediterranean Sea. In addition to health problems for beach-goers, Ostreopsis toxins may accumulate in benthic marine animals used for human consumption, which however at times have shown signals of stress and even mortality. In order to elucidate the actual relationships between Ostreopsis and benthic invertebrates, we exposed mussels...

Aim Plankton diversity is a pivotal element of marine ecosystem stability and functioning. A major obstacle in the assessment of diversity is the lack of consistency between patterns assessed by molecular and morphological data. This work aims to reconcile the two in a single richness measure, to investigate the environmental drivers affecting this measure, and finally to predict its spatio‐temporal patterns. Location and time...

Summary High‐throughput sequencing (HTS) metabarcoding is commonly applied to assess phytoplankton diversity. Usually, haplotypes are grouped into operational taxonomic units (OTUs) through clustering, whereby the resulting number of OTUs depends on chosen similarity thresholds. We applied, instead, a phylogenetic approach to infer taxa among 18S rDNA V4‐metabarcode haplotypes gathered from 48 time‐series samples using the mar...

Coastal areas host valuable but vulnerable marine ecosystems subjected to increasing anthropogenic pressure and climate change consequences. To assess the impact of these pressures, monitoring programs have proliferated in coastal areas, but most of them follow locally established procedures for quality control (QC). The well-established QC procedure of open ocean data cannot simply be extended to the highly variable coastal a...

Summary We compared the composition of eukaryotic communities using two genetic markers (18S rRNA V4 and V9 regions) at 27 sites sampled during Ocean Sampling Day 2014, with a focus on photosynthetic groups and, more specifically green algae (Chlorophyta). Globally, the V4 and V9 regions of the 18S rRNA gene provided similar images of alpha diversity and ecological patterns. However, V9 provided 20% more OTUs built at 97% iden...

The internal organization of plankton communities plays a key role in biogeochemical cycles and in the functioning of aquatic ecosystems. In this study, the structure of a marine plankton community (including both unicellular and multicellular organisms) was inferred by applying an ecological network approach to species abundances observed weekly at the long‐term ecological research station M are C hiara ( LTER ‐ MC ) in the G...

Summary Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant E uropean coastal sites. Environmental deoxyribonucleic acid ( DNA ) and ribonucleic acid ( RNA ) from three size fractions (pico‐, nano‐ and micro/mesoplankton), as well as from dissolved DNA and surface sedi...