Encapsulated in sediments: eDNA deciphers the ecosystem history of one of the most polluted European marine sites.

The Anthropocene is characterized by dramatic ecosystem changes driven by human activities. The impact of these activities can be assessed by different geochemical and paleontological proxies. However, each of these proxies provides only a fragmentary insight into the effects of anthropogenic impacts. It is highly challenging to reconstruct, with a holistic view, the state of the ecosystems from the preindustrial period to the present day, covering all biological components, from prokaryotes to multicellular eukaryotes. Here, we used sedimentary ancient DNA (sedaDNA) archives encompassing all trophic levels of biodiversity to reconstruct the two century-natural history in Bagnoli-Coroglio (Gulf of Pozzuoli, Tyrrhenian Sea), one of the most polluted marine-coastal sites in Europe. The site was characterized by seagrass meadows and high eukaryotic diversity until the beginning of the 20th century. Then, the ecosystem completely changed, with seagrasses and associated fauna as well as diverse groups of planktonic and benthic protists being replaced by low diversity biota dominated by dinophyceans and infaunal metazoan species. The sedaDNA analysis revealed a five-phase evolution of the area, where changes appear as the result of a multi-level cascade effect of impacts associated with industrial activities, urbanization, water circulation and land-use changes. The sedaDNA allowed to infer reference conditions that must be considered when restoration actions are to be implemented.

Homeostatic swimming of zooplankton upon crowding: the case of the copepod Centropages typicus.

Crowding has a major impact on the dynamics of many material and biological systems, inducing effects as diverse as glassy dynamics and swarming. While this issue has been deeply investigated for a variety of living organisms, more research remains to be done on the effect of crowding on the behaviour of copepods, the most abundant metazoans on Earth. To this aim, we experimentally investigate the swimming behaviour, used as a dynamic proxy of animal adaptations, of males and females of the calanoid copepod Centropages typicus at different densities of individuals (10, 50 and 100 ind. l-1) by performing three-dimensional single-organism tracking. We find that the C. typicus motion is surprisingly unaffected by crowding over the investigated density range. Indeed, the mean square displacements as a function of time always show a crossover from ballistic to Fickian regime, with poor variations of the diffusion constant on increasing the density. Close to the crossover, the displacement distributions display exponential tails with a nearly density-independent decay length. The trajectory fractal dimension, D3D ≅ 1.5, and the recently proposed 'ecological temperature' also remain stable on increasing the individual density. This suggests that, at least over the range of animal densities used, crowding does not impact on the characteristics of C. typicus swimming motion, and that a homeostatic mechanism preserves the stability of its swimming performance.

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.

Into the bloom: Molecular response of pelagic tunicates to fluctuating food availability.

The planktonic tunicates appendicularians and thaliaceans are highly efficient filter feeders on a wide range of prey size including bacteria and have shorter generation times than any other marine grazers. These traits allow some tunicate species to reach high population densities and ensure their success in a favourable environment. However, there are still few studies focusing on which genes and gene pathways are associated with responses of pelagic tunicates to environmental variability. Herein, we present the effect of food availability increase on tunicate community and gene expression at the Marquesas Islands (South-East Pacific Ocean). By using data from the Tara Oceans expedition, we show that changes in phytoplankton density and composition trigger the success of a dominant larvacean species (an undescribed appendicularian). Transcriptional signature to the autotroph bloom suggests key functions in specific physiological processes, i.e., energy metabolism, muscle contraction, membrane trafficking, and proteostasis. The relative abundance of reverse transcription-related Pfams was lower at bloom conditions, suggesting a link with adaptive genetic diversity in tunicates in natural ecosystems. Downstream of the bloom, pelagic tunicates were outcompeted by copepods. Our work represents the first metaomics study of the biological effects of phytoplankton bloom on a key zooplankton taxon.

Distinctive diffusive properties of swimming planktonic copepods in different environmental conditions.

Suspensions of small planktonic copepods represent a special category in the realm of active matter, as their size falls within the range of colloids, while their motion is so complex that it cannot be rationalized according to basic models of self-propelled particles. Indeed, the wide range of individual variability and swimming patterns resemble the behaviour of much larger animals. By analysing hundreds of three-dimensional trajectories of the planktonic copepod Clausocalanus furcatus, we investigate the possibility of detecting how the motion of this species is affected by different external conditions, such as the presence of food and the effect of gravity. While this goal is hardly achievable by direct inspection of single organism trajectories, we show that this is possible by focussing on simple average metrics commonly used to characterize colloidal suspensions, such as the mean square displacement and the dynamic correlation functions. We find that the presence of food leads to the onset of a clear localization that separates a short-time ballistic from a long-time diffusive regime. Such a benchmark reflects the tendency of C. furcatus to remain temporally feeding in a limited space and disappears when food is absent. Localization is clearly evident in the horizontal plane, but is negligible in the vertical direction, due to the effect of gravity. Our results suggest that simple average descriptors may provide concise and useful information on the swimming properties of planktonic copepods, even though single organism behaviour is strongly heterogeneous.

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.

Insights on the drivers of genetic divergence in the European anchovy.

Anchovies represent the largest world's marine fish catches and the current threats on their populations impose a sustainable exploitment based on sound scientific information. In the European anchovy (Engraulis encrasicolus), the existence of several populations has been proposed but a global view is missing. Using a multidisciplinary approach, here we assessed the divergence among different ecotypes and its possible causes. SNPs have revealed two functionally distinct ecotypes overlapping in the Central Mediterranean, with one ecotype confined near the river estuaries. The same SNPs outliers also segregated two distinct populations in the near Atlantic, despite their large spatial distance. In addition, while most studies suggested that adaptation to low salinity is key to divergence, here we show that the offshore ecotype has higher environmental tolerance and an opportunistic feeding behaviour, as assessed by the study of environmental conditions, anchovy diet and trophic levels, and passive egg dispersal. These results provide insights into the anchovy evolutionary history, stressing the importance of behaviour in shaping ecotypes.

Molecular phylogeny of Oncaeidae (Copepoda) using nuclear ribosomal internal transcribed spacer (ITS rDNA).

Copepods belonging to the Oncaeidae family are commonly and abundantly found in marine zooplankton. In the Mediterranean Sea, forty-seven oncaeid species occur, of which eleven in the Gulf of Naples. In this Gulf, several Oncaea species were morphologically analysed and described at the end of the XIX century by W. Giesbrecht. In the same area, oncaeids are being investigated over seasonal and inter-annual scales at the long-term coastal station LTER-MC. In the present work, we identified six oncaeid species using the nuclear ribosomal internal transcribed spacers (ITS rDNA) and the mitochondrial cytochrome c oxidase subunit I (mtCOI). Phylogenetic analyses based on these two genomic regions validated the sisterhood of the genera Triconia and the Oncaea sensu stricto. ITS1 and ITS2 phylogenies produced incongruent results about the position of Oncaea curta, calling for further investigations on this species. We also characterised the ITS2 region by secondary structure predictions and found that all the sequences analysed presented the distinct eukaryotic hallmarks. A Compensatory Base Change search corroborated the close relationship between O. venusta and O. curta and between O. media and O. venusta already identified by ITS phylogenies. The present results, which stem from the integration of molecular and morphological taxonomy, represent an encouraging step towards an improved knowledge of copepod biodiversity: The two complementary approaches, when applied to long-term copepod monitoring, will also help to better understanding their genetic variations and ecological niches of co-occurring species.

Analysis of self-overlap reveals trade-offs in plankton swimming trajectories.

Movement is a fundamental behaviour of organisms that not only brings about beneficial encounters with resources and mates, but also at the same time exposes the organism to dangerous encounters with predators. The movement patterns adopted by organisms should reflect a balance between these contrasting processes. This trade-off can be hypothesized as being evident in the behaviour of plankton, which inhabit a dilute three-dimensional environment with few refuges or orienting landmarks. We present an analysis of the swimming path geometries based on a volumetric Monte Carlo sampling approach, which is particularly adept at revealing such trade-offs by measuring the self-overlap of the trajectories. Application of this method to experimentally measured trajectories reveals that swimming patterns in copepods are shaped to efficiently explore volumes at small scales, while achieving a large overlap at larger scales. Regularities in the observed trajectories make the transition between these two regimes always sharper than in randomized trajectories or as predicted by random walk theory. Thus, real trajectories present a stronger separation between exploration for food and exposure to predators. The specific scale and features of this transition depend on species, gender and local environmental conditions, pointing at adaptation to state and stage-dependent evolutionary trade-offs.

Unexpected Regularity in Swimming Behavior of Clausocalanus furcatus Revealed by a Telecentric 3D Computer Vision System.

Planktonic copepods display a large repertoire of motion behaviors in a three-dimensional environment. Two-dimensional video observations demonstrated that the small copepod Clausocalanus furcatus, one the most widely distributed calanoids at low to medium latitudes, presented a unique swimming behavior that was continuous and fast and followed notably convoluted trajectories. Furthermore, previous observations indicated that the motion of C. furcatus resembled a random process. We characterized the swimming behavior of this species in three-dimensional space using a video system equipped with telecentric lenses, which allow tracking of zooplankton without the distortion errors inherent in common lenses. Our observations revealed unexpected regularities in the behavior of C. furcatus that appear primarily in the horizontal plane and could not have been identified in previous observations based on lateral views. Our results indicate that the swimming behavior of C. furcatus is based on a limited repertoire of basic kinematic modules but exhibits greater plasticity than previously thought.