Disentangling physical and biological drivers of phytoplankton dynamics in a coastal system

The NEREA Augmented Observatory: an integrative approach to marine coastal ecology

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.

Population bottlenecks and sexual recombination shape diatom microevolution

Diatoms are single-celled organisms that contribute approximately 20% of the global primary production and play a crucial role in biogeochemical cycles and trophic chains. Despite their ecological importance, our knowledge of microevolution is limited. We developed a model using the SLiM evolutionary framework to address this knowledge gap. As a reference, we used the diatom Pseudo-nitzschia multistriata, which has been extensively studied in the Gulf of Naples. Our model recapitulates what we observe in natural populations, with microevolutionary processes that occur annually during a three-stage bloom phase. Interestingly, we found that non-bloom phases allow the population to maintain sex-generated diversity produced during blooms. This finding suggests that non-bloom phases are critical to counteract bloom-related pressures and mitigate genetic divergence at the species level. Moreover, our model showed that despite the consistent genetic differentiation during bloom phases, the population tends to return to pre-bloom states. While our model is limited to neutral dynamics, our study provides valuable insights into diatoms' microevolution, paving the way to explore the ecological implications of the life history dynamics of these organisms.

Gulf of Naples Advanced Model (GNAM): A Multiannual Comparison with Coastal HF Radar Data and Hydrological Measurements in a Coastal Tyrrhenian Basin

High-resolution modelling systems have increasingly become an essential requirement to investigate ocean dynamics over a wide range of spatial and temporal scales, and to integrate the punctual ocean observations. When applied in coastal areas, they also have the potential to provide a detailed representation of transport and exchange processes at the sub-basin scale. This paper presents a validation exercise between the surface fields generated by the regional ocean modeling system (ROMS), developed for the Tyrrhenian Sea and downscaled for the Gulf of Naples (GNAM Gulf of Naples advanced model), and a 4 year-long (2009–2012) record of high-frequency radar (HFR) data. The comparison between hourly and seasonal model results and HFR surface fields is focused on the Gulf of Naples (GoN), where an observational network of three HFR sites has been operational since 2004, and on a specific subdomain characterized by the presence of the Sarno river, a long-term ecological research station (LTER-MC) and one important canyon area. An evaluation on a transect delimiting inshore–offshore zones in the GoN is also presented. The GNAM model was also compared with in situ hydrological parameters of temperatures and salinities retrieved at the LTER-MC fixed monitoring station. According to the skill metrics, basic circulation features are accurately reproduced by the circulation model, despite some model drawbacks in terms of increment of energy content in the surface current field occurring during specific seasonal events. The results allow us to identify potential model errors and to suggest useful improvements, the outcome also confirms the unique capability of HF radar systems to provide fine-scale measurements for the validation of numerical models and to counterbalance the lack of high-resolution measurements in coastal areas.

Photoperiod-driven rhythms reveal multi-decadal stability of phytoplankton communities in a highly fluctuating coastal environment

Phytoplankton play a pivotal role in global biogeochemical and trophic processes and provide essential ecosystem services. However, there is still no broad consensus on how and to what extent their community composition responds to environmental variability. Here, high-frequency oceanographic and biological data collected over more than 25 years in a coastal Mediterranean site are used to shed light on the temporal patterns of phytoplankton species and assemblages in their environmental context. Because of the proximity to the coast and due to large-scale variations, environmental conditions showed variability on the short and long-term scales. Nonetheless, an impressive regularity characterised the annual occurrence of phytoplankton species and their assemblages, which translated into their remarkable stability over decades. Photoperiod was the dominant factor related to community turnover and replacement, which points at a possible endogenous regulation of biological processes associated with species-specific phenological patterns, in analogy with terrestrial plants. These results highlight the considerable stability and resistance of phytoplankton communities in response to different environmental pressures, which contrast the view of these organisms as passively undergoing changes that occur at different temporal scales in their habitat, and show how, under certain conditions, biological processes may prevail over environmental forcing.

Enhanced Chlorophyll-a in the Coastal Waters near the Eastern Guangdong during the Downwelling Favorable Wind Period

Phytoplankton dynamics, which are highly sensitive to the ecosystem condition and change, are different in coastal waters and open ocean. Previous researches mainly focused on the open ocean dynamic in the South China Sea (SCS), but few research on the Eastern Guangdong (EGD), especially during a period of downwelling-favorable winds. In fact, the influence of topographic irregularities, downwelling, continental outflows, and cold, nutrient-rich currents from Fujian-Zhejiang coastal waters (ZFC) of the East China Sea (ECS) on the spatial distribution of Chlorophyll a (Chl a) in EGD coastal waters could be significant. This study utilized ocean color time series and meteorological and hydrographic data jointly from July 2002 to June 2020 to investigate the heterogeneous regional specific distribution pattern of Chl a in EGD and the environmental determinants in different regions subdivided by water depth. Then the temporal and spatial distribution pattern of Chl a in EGD in winter were discussed in detail by applying an Empirical Orthogonal Function (EOF) analysis, GaoFeng-1 (GF-1) satellite data and in situ measured dataset. The sea surface temperature (SST) in February was negatively related with Chl a in shallow coastal waters less than 60 m deep due to the nutrient-rich, cold waters from ZFC. The monthly mean photosynthetically active radiation (PAR) and precipitation showed significant effects on the phytoplankton growth over regions with a depth less than 10 m. An area with higher Chl a concentration in the downwelling zone were detected in winter. By an examining the temporal variability in meridional distribution of the mean Chl a at 22.41°N and 22.21°N, a symmetrical peak was observed. The coastal fronts extended southwestward from the southeastern coast of Guangdong Province to Dangan Island in the SCS. In addition, a cross-shelf filament was detected near the coast of Shanwei, Guangdong, China on 8 January 2020.

Wind Direction Data from a Coastal HF Radar System in the Gulf of Naples (Central Mediterranean Sea)

Results on the accuracy of SeaSonde High Frequency (HF) radar wind direction measurements in the Gulf of Naples (Southern Tyrrhenian Sea, Central Mediterranean Sea) are here presented. The investigation was carried out for a winter period (2 February–6 March) and for one summer month (August) of the reference year 2009. HF radar measurements were compared with in situ recordings from a weather station and with model data, with the aim of resolving both small scale and large scale dynamics. The analysis of the overall performance of the HF radar system in the Gulf of Naples shows that the data are reliable when the wind speed exceeds a 5 m/s threshold. Despite such a limitation, this study confirms the potentialities of these systems as monitoring platforms in coastal areas and suggests further efforts towards their improvement.

Do plankton reflect the environmental quality status? The case of a post-industrial Mediterranean Bay

While the effects of industrial contamination in coastal areas may persist for years in benthos communities, plankton should not show permanent impairments because of their high spatial dynamics, fast turnover times and pronounced seasonality. To test this hypothesis, in 2019 we conducted five surveys in the Bay of Pozzuoli (Gulf of Naples, Mediterranean Sea), in front of a dismissed steel factory and in the adjacent inshore coastal waters. High seasonal variability was observed for bacteria, phytoplankton and mesozooplankton, whereas plankton spatial gradients were relatively smooth during each survey. Plankton biomass and diversity did not reveal any effects of past industrial activities not even at the innermost stations of the Bay, which however showed some signals of present anthropogenic pressure. Hydrodynamic and morphological features likely play a prominent role in maintaining a relatively good status of the plankton of the Bay, which hints at the relevance of coastal circulation and meteorological dynamics to revitalize areas impacted by human activities.

An Integrated Reconstruction of the Multiannual Wave Pattern in the Gulf of Naples (South-Eastern Tyrrhenian Sea, Western Mediterranean Sea)

Surface gravity waves retrieved by a network of HF (High Frequency) radars and measured in situ by an ADCP (Acoustic Doppler Current Profiler) current meter connected to an elastic beacon were used to carry out a multiple-year characterization of the wave field of the Gulf of Naples (south-eastern Tyrrhenian Sea, western Mediterranean). The aim of the work was to create a climatology of the study area and to demonstrate the potential of an integrated platform for coastal studies. The patterns recorded by the different instruments were in agreement with the wave climatology of the southern Tyrrhenian Sea as well as with previous scores for the same area. The results presented in this work also highlight seasonal and interannual consistency in the wave patterns for each site. In a wider context, this study demonstrates the potential of HF radars as long-term monitoring tools of the wave field in coastal basins, and supports the development of integrated observatories to address large-scale scientific challenges such as coastal ocean dynamics and the impact of global change on the local dynamics.

Experiments and Agent Based Models of Zooplankton Movement within Complex Flow Environments

The movement of plankton is often dictated by local flow patterns, particularly during storms and in environments with strong flows. Reefs, macrophyte beds, and other immersed structures can provide shelter against washout and drastically alter the distributions of plankton as these structures redirect and slow the flows through them. Advection-diffusion and agent-based models are often used to describe the movement of plankton within marine and fresh water environments and across multiple scales. Experimental validation of such models of plankton movement within complex flow environments is challenging because of the difference in both time and spatial scales. Organisms on the scale of 1 mm or less swim by beating their appendages on the order of 1 Hz and are advected meters to kilometers over days, weeks, and months. One approach to study this challenging multiscale problem is to insert actively moving agents within a background flow field. Open source tools to implement this sort of approach are, however, limited. In this paper, we combine experiments and computational fluid dynamics with a newly developed agent-based modeling platform to quantify plankton movement at the scale of tens of centimeters. We use Artemia spp., or brine shrimp, as a model organism given their availability and ease of culturing. The distribution of brine shrimp over time was recorded in a flow tank with simplified physical models of macrophytes. These simplified macrophyte models were 3D-printed arrays of cylinders of varying heights and densities. Artemia nauplii were injected within these arrays, and their distributions over time were recorded with video. The detailed three-dimensional flow fields were quantified using computational fluid dynamics and validated experimentally with particle image velocimetry. To better quantify plankton distributions, we developed an agent-based modeling framework, Planktos, to simulate the movement of plankton immersed within such flow fields. The spatially and temporally varying Artemia distributions were compared across models of varying heights and densities for both the experiments and the agent-based models. The results show that increasing the density of the macrophyte bed drastically increases the average time it takes the plankton to be swept downstream. The height of the macrophyte bed had less of an effect. These effects were easily observed in both experimental studies and in the agent-based simulations.

Eddy Detection in HF Radar-Derived Surface Currents in the Gulf of Naples

Submesoscale eddies play an important role in the energy transfer from the mesoscale down to the dissipative range, as well as in tracer transport. They carry inorganic matter, nutrients and biomass; in addition, they may act as pollutant conveyors. However, synoptic observations of these features need high resolution sampling, in both time and space, making their identification challenging. Therefore, HF coastal radar were and are successfully used to accurately identify, track and describe them. In this paper we tested two already existing algorithms for the automated detection of submesoscale eddies. We applied these algorithms to HF radar velocity fields measured by a network of three radar systems operating in the Gulf of Naples. Both methods showed shortcomings, due to the high non-geostrophy of the observed currents. For this reason we developed a third, novel algorithm that proved to be able to detect highly asymmetrical eddies, often not properly identified by the previous ones. We used the results of the application of this algorithm to estimate the eddy boundary profiles and the eddy spatial distribution.

Rewiring and indirect effects underpin modularity reshuffling in a marine food web under environmental shifts

Species are characterized by physiological and behavioral plasticity, which is part of their response to environmental shifts. Nonetheless, the collective response of ecological communities to environmental shifts cannot be predicted from the simple sum of individual species responses, since co-existing species are deeply entangled in interaction networks, such as food webs. For these reasons, the relation between environmental forcing and the structure of food webs is an open problem in ecology. To this respect, one of the main problems in community ecology is defining the role each species plays in shaping community structure, such as by promoting the subdivision of food webs in modules-that is, aggregates composed of species that more frequently interact-which are reported as community stabilizers. In this study, we investigated the relationship between species roles and network modularity under environmental shifts in a highly resolved food web, that is, a "weighted" ecological network reproducing carbon flows among marine planktonic species. Measuring network properties and estimating weighted modularity, we show that species have distinct roles, which differentially affect modularity and mediate structural modifications, such as modules reconfiguration, induced by environmental shifts. Specifically, short-term environmental changes impact the abundance of planktonic primary producers; this affects their consumers' behavior and cascades into the overall rearrangement of trophic links. Food web re-adjustments are both direct, through the rewiring of trophic-interaction networks, and indirect, with the reconfiguration of trophic cascades. Through such "systemic behavior," that is, the way the food web acts as a whole, defined by the interactions among its parts, the planktonic food web undergoes a substantial rewiring while keeping almost the same global flow to upper trophic levels, and energetic hierarchy is maintained despite environmental shifts. This behavior suggests the potentially high resilience of plankton networks, such as food webs, to dramatic environmental changes, such as those provoked by global change.

Combining Marine Ecology and Economy to Roadmap the Integrated Coastal Management: A Systematic Literature Review

Integrated coastal management (ICM) relies on the inclusion of economic issues within marine ecology. To assess the progress of this integration, we applied topic modelling and network analysis to explore the pertinent literature (583 Isi-WoS, and 5459 Scopus papers). We classified the topics of interest (i.e., concepts, approaches, and sectors) that combined ecological and economic issues within marine science, we aggregated these topics in fields pertinent to ICM, and tracked the knowledge-exchange between these fields by using an information-flow network. Main findings were: (i) the high trans-disciplinary fashion of studies about marine protection and of those about commercial fisheries, (ii) the weak interaction between studies focusing on potential biohazards and those about environmental management, (iii) the isolation, in the overall information-flow, of studies about ecotourism and aquaculture. We included in a roadmap all the integration routes we detected within ICM, based on the combination of ecological and economic issues. We conclude that, to improve integration, ICM should: (i) Exploit marine protection as a bridge between ecological and economic concepts and approaches, and between maritime economy sectors, (ii) employ systems ecology to pursue trans-disciplinary investigations, (iii) complement systems ecology with citizen science by means of inclusive economic initiatives, such as ecotourism.

Time series and beyond: multifaceted plankton research at a marine Mediterranean LTER site

Plankton are a pivotal component of the diversity and functioning of coastal marine ecosystems. A long time-series of observations is the best tool to trace their patterns and variability over multiple scales, ultimately providing a sound foundation for assessing, modelling and predicting the effects of anthropogenic and natural environmental changes on pelagic communities. At the same time, a long time-series constitutes a formidable asset for different kinds of research on specific questions that emerge from the observations, whereby the results of these complementary studies provide precious interpretative tools that augment the informative value of the data collected. In this paper, we review more than 140 studies that have been developed around a Mediterranean plankton time series gathered in the Gulf of Naples at the station LTER-MC since 1984. These studies have addressed different topics concerning marine plankton, which have included: i) seasonal patterns and trends; ii) taxonomic diversity, with a focus on key or harmful algal species and the discovery of many new taxa; iii) molecular diversity of selected species, groups of species or the whole planktonic community; iv) life cycles of several phyto- and zooplankton species; and v) interactions among species through trophic relationships, parasites and viruses. Overall, the products of this research demonstrate the great value of time series besides the record of fluctuations and trends, and highlight their primary role in the development of the scientific knowledge of plankton much beyond the local scale.

Plankton dynamics across the freshwater, transitional and marine research sites of the LTER-Italy Network. Patterns, fluctuations, drivers

A first synoptic and trans-domain overview of plankton dynamics was conducted across the aquatic sites belonging to the Italian Long-Term Ecological Research Network (LTER-Italy). Based on published studies, checked and complemented with unpublished information, we investigated phytoplankton and zooplankton annual dynamics and long-term changes across domains: from the large subalpine lakes to mountain lakes and artificial lakes, from lagoons to marine coastal ecosystems. This study permitted identifying common and unique environmental drivers and ecological functional processes controlling seasonal and long-term temporal course. The most relevant patterns of plankton seasonal succession were revealed, showing that the driving factors were nutrient availability, stratification regime, and freshwater inflow. Phytoplankton and mesozooplankton displayed a wide interannual variability at most sites. Unidirectional or linear long-term trends were rarely detected but all sites were impacted across the years by at least one, but in many case several major stressor(s): nutrient inputs, meteo-climatic variability at the local and regional scale, and direct human activities at specific sites. Different climatic and anthropic forcings frequently co-occurred, whereby the responses of plankton communities were the result of this environmental complexity. Overall, the LTER investigations are providing an unparalleled framework of knowledge to evaluate changes in the aquatic pelagic systems and management options.