The oligotrophy of the southern Adriatic Sea is characterized by seasonal stratification which enables nutrient supply to the euphotic layer. A set of interdisciplinary methods was used to elucidate the diversity and co-dependency of bacterio- and phytoplankton of the water column during the stratification period of July 2021. A total of 95 taxa were determined by microscopy: 58 diatoms, 27 dinoflagellates, 6 coccolithophores, and 4 other autotrophs, which included Chlorophyceae, Chrysophyceae, and Cryptophytes. Nanophytoplankton abundances were higher in comparison to microphytoplankton. The prokaryotic plankton community as revealed by HTS was dominated by Proteobacteria (41–73%), Bacteroidota (9.5–27%), and cyanobacteria (1–10%), while the eukaryotic plankton community was composed of parasitic Syndiniales (45–80%), Ochrophyta (2–18%), Ciliophora (2–21%), Chlorophytes (2–4%), Haptophytes (1–4%), Bacillariophyta (1–13%), Pelagophyta (0.5–12%) and Chrysophyta (0.5–3%). Flow cytometry analysis has recorded Prochlorococcus and photosynthetic picoeukaryotes as more abundant in deep chlorophyll maximum (DCM), and Synechococcus and heterotrophic bacteria as most abundant in surface and thermocline layers. Surface, thermocline, and DCM layers were distinct considering community diversity, temperature, and nutrient correlations, while extreme nutrient values at the beginning of the investigating period indicated a possible nutrient flux. Nutrient and temperature were recognized as the main environmental drivers of phytoplankton and bacterioplankton community abundance.

The European Marine Omics Biodiversity Observation Network (EMO BON) is a long-term genomic observatory run by the European Research Infrastructure European Marine Biological Resource Centre (EMBRC). It was established in 2021 to support the challenges of biodiversity observation and unsystematic management of biodiversity data in the European seas. EMO BON introduced and coordinated the systematic and harmonised observation of biodiversity amongst more than fourteen marine stations in the European coastline. Here, we report the next release (Release 2) of shotgun metagenomic data from seawater and sediment microbial communities.

The phycosphere, the organic‐rich microenvironment surrounding phytoplankton cells, mediates interactions between algae and other microorganisms, mainly prokaryotes. We investigated associations between Chaetoceros spp., one of the most abundant diatom genera in coastal waters, and particle‐attached prokaryotic communities. Monthly samples were collected from October 2017 to September 2018 at a fixed station in the Gulf of Naples (Italy). Light microscopy counts of Chaetoceros were integrated with 16S rRNA gene metabarcoding data, and bipartite network analyses were applied to infer putative species‐specific associations. Most inferred associations involved taxa previously reported in diatom‐associated assemblages, such as Alphaproteobacteria and Bacteroidetes and Archaeal taxa including Thermoplasmata and Marine Group II. The networks included both single and (2–3) grouped Chaetoceros species. Interestingly, most of the species involved were chain‐forming, although the functional role of this trait in shaping prokaryotic associations remains unclear. Overall, our results broaden the range of prokaryotic taxa potentially associated with Chaetoceros and highlight new possible interkingdom interactions in coastal marine ecosystems.