De Novo Assembly of the Genome of the Sea Urchin Paracentrotus lividus (Lamarck 1816).

The Mediterranean purple sea urchin Paracentrotus lividus (Lamarck 1816) is a remarkable model system for molecular, evolutionary and cell biology studies, particularly in the field of developmental biology. We sequenced the genome, performed a de novo assembly, and analysed the assembly content. The genome of P. lividus was sequenced using Illumina NextSeq 500 System (Illumina) in a 2 × 150 paired-end format. More than 30,000 open reading frames (ORFs), (more than 8000 are unique), were identified and analysed to provide molecular tools accessible for the scientific community. In particular, several genes involved in complex innate immune responses, oxidative metabolism, signal transduction, and kinome, as well as genes regulating the membrane receptors, were identified in the P. lividus genome. In this way, the employment of the Mediterranean sea urchin for investigations and comparative analyses was empowered, leading to the explanation of cis-regulatory networks and their evolution in a key developmental model occupying an important evolutionary position with respect to vertebrates and humans.

Immune and Reproductive Biomarkers in Female Sea Urchins Paracentrotus lividus under Heat Stress.

The functioning of the immune and reproductive systems is crucial for the fitness and survival of species and is strongly influenced by the environment. To evaluate the effects of short-term heat stress (HS) on these systems, confirming and deepening previous studies, female sea urchin Paracentrotus lividus were exposed for 7 days to 17 °C, 23 and 28 °C. Several biomarkers were detected such as the ferric reducing power (FRAP), ABTS-based total antioxidant capacity (TAC-ABTS), nitric oxide metabolites (NOx), total thiol levels (TTL), myeloperoxidase (MPO) and protease (PA) activities in the coelomic fluid (CF) and mitochondrial membrane potential (MMP), H2O2 content and intracellular pH (pHi) in eggs and coelomocytes, in which TAC-ABTS and reactive nitrogen species (RNS) were also analyzed. In the sea urchins exposed to HS, CF analysis showed a decrease in FRAP levels and an increase in TAC-ABTS, TTL, MPO and PA levels; in coelomocytes, RNS, MMP and H2O2 content increased, whereas pHi decreased; in eggs, increases in MMP, H2O2 content and pHi were found. In conclusion, short-term HS leads to changes in five out of the six CF biomarkers analyzed and functional alterations in the cells involved in either reproductive or immune activities.

Effects of biodegradable-based microplastics in Paracentrotus lividus Lmk embryos: Morphological and gene expression analysis.

Plastic pollution is a remarkable environmental issue. In fact, plastic is widespread in the lifetime and serious environmental problems are caused by the improper management of plastic end of life, being plastic litter detected in any environment. Efforts are put to implement the development of sustainable and circular materials. In this scenario, biodegradable polymers, BPs, are promising materials if correctly applied and managed at the end of life to minimize environmental problems. However, a lack of data on BPs fate and toxicity on marine organisms, limits their applicability. In this research, the impact of microplastics obtained from BPs, BMPs, were analyzed on Paracentrotus lividus. Microplastics were produced from five biodegradable polyesters at laboratory scale by milling the pristine polymers, under cryogenic conditions. Morphological analysis of P. lividus embryos exposed to polycaprolactone (PCL), polyhydroxy butyrate (PHB) and polylactic acid (PLA) showed their delay and malformations, which at molecular level are due to variation in expression levels of eighty-seven genes involved in various cellular processes, such as skeletogenesis, differentiation and development, stress, and detoxification response. Exposure to poly(butylene succinate) (PBS) and poly(butylene succinate-co-adipate) (PBSA) microplastics showed no detectable effects on P. lividus embryos. These findings contribute with important data on the effect of BPs on the physiology of marine invertebrates.

The "Bald Disease" of the Sea Urchin Paracentrotus lividus: Pathogenicity, Molecular Identification of the Causative Agent and Therapeutic Approach.

In recent decades, various species of Mediterranean sea urchins, including Paracentrotus lividus, have been subject to widespread seasonal episodes of mass mortality whose causative agents are still unclear. In particular, P. lividus is subject to late winter events of mortality, due to a disease manifested by a massive loss of spines and the presence of greenish amorphous material on the tests (i.e., the sea urchin skeleton consisting of spongeous calcite). Documented mortality events show a seasonal epidemic diffusion and might produce economic losses also in aquaculture facilities, besides the environmental constraints to its diffusion. We collected individuals showing conspicuous lesions on the body surface and reared them in recirculated aquaria. Samples of external mucous were collected along with coelomic liquids and cultured to isolate bacterial and fungal strains, further submitted to molecular identification through the amplification of prokaryotic 16S rDNA. In addition, pools of infected sea urchins were reared in recirculated tanks after short baths in a formulated therapeutic compound and their survival rates were compared to non-treated individuals for variable periods. Here, we aimed at a redescription of the etiopathogenetic nature of the parasites and tested the efficacy of a possible treatment, to be proposed for aquaculture purposes.

PAHs and PCBs Affect Functionally Intercorrelated Genes in the Sea Urchin Paracentrotus lividus Embryos.

Polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) represent the most common pollutants in the marine sediments. Previous investigations demonstrated short-term sublethal effects of sediments polluted with both contaminants on the sea urchin Paracentrotus lividus after 2 months of exposure in mesocosms. In particular, morphological malformations observed in P. lividus embryos deriving from adults exposed to PAHs and PCBs were explained at molecular levels by de novo transcriptome assembly and real-time qPCR, leading to the identification of several differentially expressed genes involved in key physiological processes. Here, we extensively explored the genes involved in the response of the sea urchin P. lividus to PAHs and PCBs. Firstly, 25 new genes were identified and interactomic analysis revealed that they were functionally connected among them and to several genes previously defined as molecular targets of response to the two pollutants under analysis. The expression levels of these 25 genes were followed by Real Time qPCR, showing that almost all genes analyzed were affected by PAHs and PCBs. These findings represent an important further step in defining the impacts of slight concentrations of such contaminants on sea urchins and, more in general, on marine biota, increasing our knowledge of molecular targets involved in responses to environmental stressors.

Sub-Chronic Effects of Slight PAH- and PCB-Contaminated Mesocosms in Paracentrotus lividus Lmk: A Multi-Endpoint Approach and De Novo Transcriptomic.

Sediment pollution is a major issue in coastal areas, potentially endangering human health and the marine environments. We investigated the short-term sublethal effects of sediments contaminated with polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) on the sea urchin Paracentrotus lividus for two months. Spiking occurred at concentrations below threshold limit values permitted by the law (TLVPAHs = 900 µg/L, TLVPCBs = 8 µg/L, Legislative Italian Decree 173/2016). A multi-endpoint approach was adopted, considering both adults (mortality, bioaccumulation and gonadal index) and embryos (embryotoxicity, genotoxicity and de novo transcriptome assembly). The slight concentrations of PAHs and PCBs added to the mesocosms were observed to readily compartmentalize in adults, resulting below the detection limits just one week after their addition. Reconstructed sediment and seawater, as negative controls, did not affect sea urchins. PAH- and PCB-spiked mesocosms were observed to impair P. lividus at various endpoints, including bioaccumulation and embryo development (mainly PAHs) and genotoxicity (PAHs and PCBs). In particular, genotoxicity tests revealed that PAHs and PCBs affected the development of P. lividus embryos deriving from exposed adults. Negative effects were also detected by generating a de novo transcriptome assembly and its annotation, as well as by real-time qPCR performed to identify genes differentially expressed in adults exposed to the two contaminants. The effects on sea urchins (both adults and embryos) at background concentrations of PAHs and PCBs below TLV suggest a need for further investigations on the impact of slight concentrations of such contaminants on marine biota.

Two Benthic Diatoms, Nanofrustulum shiloi and Striatella unipunctata, Encapsulated in Alginate Beads, Influence the Reproductive Efficiency of Paracentrotus lividus by Modulating the Gene Expression.

Physiological effects of algal metabolites is a key step for the isolation of interesting bioactive compounds. Invertebrate grazers may be fed on live diatoms or dried, pelletized, and added to compound feeds. Any method may reveal some shortcomings, due to the leaking of wound-activated compounds in the water prior to ingestion. For this reason, encapsulation may represent an important step of bioassay-guided fractionation, because it may assure timely preservation of the active compounds. Here we test the effects of the inclusion in alginate (biocompatible and non-toxic delivery system) matrices to produce beads containing two benthic diatoms for sea urchin Paracentrotus lividus feeding. In particular, we compared the effects of a diatom whose influence on P. lividus was known (Nanofrustulum shiloi) and those of a diatom suspected to be harmful to marine invertebrates, because it is often present in blooms (Striatella unipunctata). Dried N. shiloi and S. unipunctata were offered for one month after encapsulation in alginate hydrogel beads and the larvae produced by sea urchins were checked for viability and malformations. The results indicated that N. shiloi, already known for its toxigenic effects on sea urchin larvae, fully conserved its activity after inclusion in alginate beads. On the whole, benthic diatoms affected the embryogenesis of P. lividus, altering the expression of several genes involved in stress response, development, skeletogenesis and detoxification processes. Interactomic analysis suggested that both diatoms activated a similar stress response pathway, through the up-regulation of hsp60, hsp70, NF-κB, 14-3-3 ε and MDR1 genes. This research also demonstrates that the inclusion in alginate beads may represent a feasible technique to isolate diatom-derived bioactive compounds.

Sea urchin chronicles. The effect of oxygen super-saturation and marine polluted sediments from Bagnoli-Coroglio Bay on different life stages of the sea urchin Paracentrotus lividus.

In marinas and harbours, the accumulation of pollutants in sediments, combined with poor exchange of water with the open sea, poses a major environmental threat. The presence of photosynthetic organisms and the related oxygen production, however, may alleviate the negative effects of environmental contamination on heterotrophic organisms, enhancing their physiological defences. Furthermore, possible transgenerational buffer effects may increase the ability of natural populations to face environmental stress. Here we tested the occurrence of transgenerational effects on larvae of the sea urchin Paracentrotus lividus, whose parents were exposed, during the gametogenesis, to contaminated sediments subject to two temporal patterns of water re-suspension events and normal- (90%) vs. super-saturated (200%) levels of O2. The study site was Bagnoli-Coroglio (Gulf of Naples, southern Tyrrhenian Sea), a historically polluted brownfield and Site of National Interest for which environmental restoration options are currently under exploration. Larvae from different adult populations were significantly, although not linearly, affected by the interaction of all factors to which parents were exposed, at both 24h and 48h post fertilization. Specifically, the exposure of larvae to elutriates from contaminated sediments determined a developmental delay, a reduction in size and an increased percentage of abnormalities in all larval populations independently of their parental exposure. On the contrary, larvae from parents exposed to contaminated sediments, when reared in clean filtered sea water, succeeded in developing until the echinopluteus stage after 48h, with size and abundance comparable to those of larvae from control parents. Pre-exposure of parents to contaminated sediments did not successfully buffer the negative effects of elutriates on their offspring, and no positive effects of 'super-saturated' levels of O2 in response to contaminants were observed, suggesting that the Bagnoli-Coroglio area is currently not suitable for the re-stocking or re-introduction of this species.

How sea urchins face microplastics: Uptake, tissue distribution and immune system response.

Plastic pollution represents one of the major threats to the marine environment. A wide range of marine organisms has been shown to ingest microplastics due to their small dimensions (less than 1 mm). This negatively affects some biological processes, such as feeding, energy reserves and reproduction. Very few studies have been performed on the effect of microplastics on sea urchin development and virtually none on adults. The aim of this work was to evaluate the uptake and distribution of fluorescent labelled polystyrene microbeads (micro-PS) in the Mediterranean sea urchin Paracentrotus lividus and the potential impact on circulating immune cells. Differential uptake was observed in the digestive and water vascular systems as well as in the gonads based on microbeads size (10 and 45 µm in diameter). Treatment of sea urchins with particles of both sizes induced an increase of the total number of immune cells already after 24 h. No significant differences were observed among immune cell types. However, the ratio between red and white amoebocytes, indicative of sea urchin healthy status, increased with both particles. This effect was detectable already at 24 h upon exposure to smaller micro-PS (10 µm). An increase of intracellular levels of reactive oxygen and nitrogen species was observed at 24 h upon both micro-PS exposure, whereas at later time these levels became comparable to those of controls. A significant increase of total antioxidant capacity was observed after treatment with 10 µm micro-PS. Overall data provide the first evidence on polystyrene microbeads uptake and tissue distribution in sea urchins, indicating a stress-related impact on circulating immune cells.

Oxygen supersaturation mitigates the impact of the regime of contaminated sediment reworking on sea urchin fertilization process.

Dismissed industrial plants with chronic environmental contamination globally affect all levels of biological organization in concert with other natural and anthropogenic perturbations. Assessing the impact of such perturbations and finding effective ways to mitigate them have clear ecological and societal implications. Through indoor manipulative experiments, we assessed here the effects of the temporal regime of reworking of contaminated sediment from the Bagnoli-Coroglio brownfield (Tyrrhenian Sea, Italy) on the fertilization process in Paracentrotus lividus. Adult sea urchins were kept for one month in tanks containing contaminated sediment that was re-suspended according to two temporal patterns of water turbulence differing in the time intervals between consecutive events of agitation (mimicking the storms naturally occurring in the study area) in seawater with natural vs. supersaturated oxygenation levels. At the end of the treatment, gametes were collected and used to test the hypothesis that the regime of contaminated sediment reworking negatively, but reversibly, affects morphological and physiological traits of the fertilized eggs. We found that aggregated events of sediment re-suspension had profound negative effects on gamete interactions and Ca2+ signaling at fertilization. The same experimental condition also inflicted marked ultrastructural changes in eggs. Importantly, however, such detrimental effects were inhibited by increased oxygenation. By contrast, the regime of sediment re-working with a longer interval between consecutive turbulent events had only marginal effects. Thus, the current and predicted changes of climate-related disturbance appear to modulate the biological effects of chronic contamination in post-industrial areas, suggesting that environmental rehabilitation via restoration of habitat-forming primary producers such as seagrasses or algal canopies could alleviate the pollutants' effects on resident biota.

Morphological and molecular responses of the sea urchin Paracentrotus lividus to highly contaminated marine sediments: The case study of Bagnoli-Coroglio brownfield (Mediterranean Sea).

Marine sediments store complex mixtures of compounds, including heavy metals, organotins and a large array of other contaminants. Sediment quality monitoring, characterization and management are priorities, due to potential impacts of the above compounds on coastal waters and their biota, especially in cases of pollutants released during dredging activities. Harbours and marinas, as well as estuaries and bays, where limited exchanges of water occurr, the accumulation of toxic compounds poses major concerns for human and environmental health. Here we report the effects of highly contaminated sediments from the site of national interest Bagnoli-Coroglio (Tyrrhenian Sea, Western Mediterranean) on the sea urchin Paracentrotus lividus, considered a good model for ecotoxicological studies. Adult sea urchins were reared one month in aquaria in the presence of contaminated sediment that was experimentally subject to different patterns of re-suspension events (mimicking the effect of natural storms occurring in the field), crossed with O2 enrichment versus natural gas exchanges in the water. The development of embryos deriving from adult urchins exposed to such experimental conditions was followed until the pluteus stage, checking the power of contaminated sediment to induce morphological malformations and its eventual buffering by high oxygenation. Real-Time qPCR analysis revealed that the expression of several genes (among the fifty analyzed, involved in different functional processes) was targeted by contaminated sediments more than those exposed in oxygen-enriched condition. Our findings have biological and ecological relevance in terms of assessing the actual impact on local organisms of chronic environmental contamination by heavy metals and polycyclic aromatic hydrocarbons affecting the Bagnoli-Coroglio area, and of exploring enhanced sediment and water oxygenation as a promising tool to mitigate the effects of contamination in future environmental restoration actions.

Noxious effects of the benthic diatoms Cocconeis scutellum and Diploneis sp. on sea urchin development: Morphological and de novo transcriptomic analysis.

Diatoms are often the dominating group of benthic microalgae living on different types of bottom substrates. Their effects on invertebrate consumers is not well-documented. We here investigate the effects of feeding on another two benthic diatoms, Cocconeis scutellum and Diploneis sp., isolated from leaves of the seagrass Posidonia oceanica, on the sea urchin Paracentrotus lividus. Our results indicate a noxious effect on sea urchin embryos spawned from adults fed on Diploneis sp., with an increasing number of malformed embryos with respect to those spawned from adults fed on Ulva rigida (used as a feeding control). In contrast C. scutellum did not induce any morphological effect on embryos, similar to control non-diatom diets. Moreover, de novo obtained transcriptome indicated that oxidation-reduction process, translation, proton and electron transmembrane transport, ATP/RNA/GTP/heme/calcium and metal ion binding, NADH dehydrogenase activity, cytochrome c oxidase were affected by feeding of sea urchins on Diploneis sp. Our findings have considerable ecological significance considering that diatom biomass ingested by the sea urchin in these experiments is within the range of cell densities characterizing P. oceanica leaves where sea urchins live and spawn.

Toxigenic effects of two benthic diatoms upon grazing activity of the sea urchin: morphological, metabolomic and de novo transcriptomic analysis.

Diatoms are unicellular algae playing a key role as photosynthetic organisms in the world's ocean food webs. The chemical ecology of planktonic diatoms is well documented, but few studies have reported on the effects of benthic diatoms on their consumers, also due to difficulties in the collection, quantification and massive culturing of benthic species. Here for the first time we investigate the effects of feeding on two abundantly occurring benthic diatoms, Nanofrustulum shiloi and Cylindrotheca closterium, isolated from the leaves of the seagrass Posidonia oceanica, on the sea urchin Paracentrotus lividus. Adult P. lividus were fed for one month on diets of either one of the two diatoms and on the green alga Ulva rigida, used as a feeding control. By combining morphological, metabolomic and de novo transcriptomic approaches, we demonstrate toxigenic effect on embryos generated by females fed with these benthic diatoms. Furthermore, chemical analysis reveal the presence of polyunsaturated aldehydes only for N. shiloi, and a high production of other oxylipins (cytotoxic compounds on their grazers and on cancer cell lines) for both diatoms, including some additional peaks not correlated to the canonic oxylipins commonly observed in planktonic diatoms. These findings open new perspectives in the study of diatom secondary metabolites influencing their grazers.