The advent of metabarcoding (metaB) in aquatic ecology has provided a huge amount of information on plankton biodiversity worldwide. However, the large datasets obtained with that approach are still partially explored, especially for what concerns the study of trophic interactions and food webs. In this study, we analysed a metaB time series from the Long‐Term Ecological Research station MareChiara (LTER‐MC) in the Gulf of Naples, Mediterranean Sea, Italy, to describe the link between plankton diversity and food‐web structure. We derived co‐occurrence networks from metaB time series, identified putative trophic interactions among co‐occurrences based on biological information (body size and trophic habit) available for planktonic organisms detected by metaB, and converted co‐occurrence networks into conceptual models of food webs. The latter showed structural properties resembling ecological processes, because network modularity (the presence of semi‐independent sub‐networks) paralleled trophic hierarchy (the dimensional difference between predator and prey). We also analysed the role of planktonic organisms in maintaining network modularity. The largest predators occupied distinct modules, suggesting niche partitioning, whereas the smallest preys worked as fundamental connectors between larger predators (and different modules). Overall, the presence of trophic hierarchy and modularity shown herein supports the view of the high ecological resilience of plankton, pursued via food‐web rewiring, to environmental shifts.

Environmental DNA metabarcoding (eDNA metaB) is fundamental for monitoring marine biodiversity and its spread in coastal ecosystems. We applied eDNA metaB to seawater samples to investigate the spatiotemporal variability of plankton and small pelagic fish, comparing sites with different environmental conditions across a coast-to-offshore gradient at river mouths along the Campania coast (Italy) over 2 years (2020–2021). We found a marked seasonality in the planktonic community at the regional scale, likely owing to the hydrodynamic connection among sampling sites, which was derived from numerical simulations. Nonetheless, spatial variability among plankton communities was detected during summer. Overall, slight changes in plankton and fish composition resulted in the potential reorganization of the pelagic food web at the local scale. This work supports the utility of eDNA metaB in combination with hydrodynamic modelling to study marine biodiversity in the water column of coastal systems. This article is part of the theme issue ‘Connected interactions: enriching food web research by spatial and social interactions’.

Transitional waters (TWs), such as coastal lagoons, are bodies of surface water at the transition between saline and freshwater domains. These environments play a vital role in guaranteeing ecosystem services, including provision of food, protection against meteorological events, as anthropogenic carbon sinks, and in filtering of pollutants. Due to the escalating overpopulation characterising coastlines worldwide, transitional systems are over-exploited, degraded, and reduced in their macroscopic features. However, information on the impact of anthropogenic pressures on planktonic organisms in these systems is still scanty and fragmented. Herein, we summarise the literature, with a special focus on coastal lagoons undergoing anthropogenic pressure. Specifically, we report on the implications of human impacts on the ecological state of plankton, i.e., a fundamental ecological component of aquatic ecosystems. Literature information indicates that human forces may alter ecosystem structures and functions in coastal lagoons, as in other TWs such as estuaries, hampering the phytoplankton–zooplankton link, i.e., the main trophic process occurring in those communities, and which sustains aquatic productivity. Changes in the dominance and lifestyle of key planktonic players, plus the invasion of ‘alien’ species, and consequent regime shifts, are among the most common outcomes of human disturbance.

The NEREA (Naples Ecological REsearch for Augmented observatories) initiative aims to establish an augmented observatory in the Gulf of Naples (GoN), designed to advance the understanding of marine ecosystems through a holistic approach. Inspired by the Tara Oceans expedition and building on the scientific legacy of the MareChiara Long-Term Ecological Research (LTER-MC) site, NEREA integrates traditional physical, chemical, and biological measurements with state-of-the-art methodologies such as metabarcoding and metagenomics. Here we present the first 10 months of NEREA data, collected from April 2019 to January 2020, encompassing physico-chemical parameters, plankton biodiversity (e.g., microscopy and flow cytometry), prokaryotic and eukaryotic metabarcoding, a prokaryotic gene catalogue, and a collection of 3818 prokaryotic Metagenome-Assembled Genomes (MAGs). NEREA’s efforts produce a significant volume of multifaceted data, which enhances our understanding of marine ecosystems and promotes the development of scientific hypotheses and ideas.

Copepods dominate marine zooplankton in abundance and play key roles in pelagic food webs. These small crustaceans show high taxonomic and functional diversity. Although there has been considerable research on their taxonomy, only a few studies have focused on their functional traits. In this study, we analyzed the functional traits of 95 copepod species, considering their body size, trophic regime, feeding behavior, and spawning strategy. Based on samples collected during two surveys (autumn 2020 and summer 2021) located in the coastal waters of three gulfs (Gaeta, Naples, and Salerno) in the highly populated Campania region (the central Tyrrhenian Sea, NW Mediterranean), we identified nine functional groups of copepods with different characteristics. The group that comprised herbivorous copepods with feeding currents and a broadcast strategy was the most abundant in both seasons and all gulfs. This group was dominated by Acartia clausi, Centropages typicus, Temora stylifera, and the Paracalanus parvus complex. The other functional groups showed differences in their temporal and spatial distribution. Our study reports the functional diversity of copepods along the Campania coast, thus contributing to advancing our knowledge of the planktonic trophic structure in a region of considerable importance due to its marine resources and services.