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Interspecific comparison of DNA damage can provide information on the relative vulnerability of marine organisms to toxicants that induce oxidative genotoxicity. Hydrogen peroxide (H2O2) is an oxidative toxicant that causes DNA strand breaks and nucleotide oxidation and is used in multiple industries including Atlantic salmon aquaculture to treat infestations of ectoparasitic sea lice. H2O2 (up to 100 mM) can be released into the water after sea lice treatment, with potential consequences of exposure in nontarget marine organisms. The objective of the current study was to measure and compare differences in levels of H2O2-induced oxidative DNA damage in coelomocytes from Scottish sea urchins Echinus esculentus , Paracentrotus lividus , and Psammechinus miliaris. Coelomocytes were exposed to H2O2 (0–50 mM) for 10 min, cell concentration and viability were quantified, and DNA damage was measured by the fast micromethod, an alkaline unwinding DNA method, and the modified fast micromethod with nucleotide-specific enzymes. Cell viability was >92% in all exposures and did not differ from controls. Psammechinus miliaris coelomocytes had the highest oxidative DNA damage with 0.07 ± 0.01, 0.08 ± 0.01, and 0.07 ± 0.01 strand scission factors (mean ± SD) after incubation with phosphate-buffered saline, formamidopyrimidine-DNA glycosylase, and endonuclease-III, respectively, at 50 mM H2O2. Exposures to 0.5 mM H2O2 (100-fold dilution from recommended lice treatment concentration) induced oxidative DNA damage in all three species of sea urchins, suggesting interspecific differences in vulnerabilities to DNA damage and/or DNA repair mechanisms. Understanding impacts of environmental genotoxicants requires understanding species-specific susceptibilities to DNA damage, which can impact long-term stability in sea urchin populations in proximity to aquaculture farms. [ABSTRACT FROM AUTHOR]

Echinobase (https://echinobase.org) is a central online platform that generates, manages and hosts genomic data relevant to echinoderm research. While the resource primarily serves the echinoderm research community, the recent release of an excellent quality genome for the frequently studied purple sea urchin (Strongylocentrotus purpuratus genome, v5.0) has provided an opportunity to adapt to the needs of a broader research community across other model systems. To this end, establishing pipelines to identify orthologous genes between echinoderms and other species has become a priority in many contexts including nomenclature, linking to data in other model organisms, and in internal functionality where data gathered in one hosted species can be associated with genes in other hosted echinoderms. This paper describes the orthology pipelines currently employed by Echinobase and how orthology data are processed to yield 1:1 ortholog mappings between a variety of echinoderms and other model taxa. We also describe functions of interest that have recently been included on the resource, including an updated developmental time course for S. purpuratus , and additional tracks for genome browsing. These data enhancements will increase the accessibility of the resource to non-echinoderm researchers and simultaneously expand the data quality and quantity available to core Echinobase users. Database URL : https://echinobase.org [ABSTRACT FROM AUTHOR]

Environmental variation experienced by a species across space and time can promote the maintenance of genetic diversity that may be adaptive in future global change conditions. Selection experiments have shown that purple sea urchin, Strongylocentrotus purpuratus , populations have adaptive genetic variation for surviving pH conditions at the "edge" (pH 7.5) of conditions experienced in nature. However, little is known about whether populations have genetic variation for surviving low-pH events beyond those currently experienced in nature or how variation in pH conditions affects organismal and genetic responses. Here, we quantified survival, growth, and allele frequency shifts in experimentally selected developing purple sea urchin larvae in static and variable conditions at three pH levels: pH 8.1 (control), pH 7.5 (edge-of-range), and pH 7.0 (extreme). Variable treatments recovered body size relative to static treatments, but resulted in higher mortality, suggesting a potential tradeoff between survival and growth under pH stress. However, within each pH level, allele frequency changes were overlapping between static and variable conditions, suggesting a shared genetic basis underlying survival to mean pH regardless of variability. In contrast, genetic responses to pH 7.5 (edge) versus pH 7.0 (extreme) conditions were distinct, indicating a unique genetic basis of survival. In addition, loci under selection were more likely to be in exonic regions than regulatory, indicating that selection targeted protein-coding variation. Loci under selection in variable pH 7.5 conditions, more similar to conditions periodically experienced in nature, performed functions related to lipid biosynthesis and metabolism, while loci under selection in static pH 7.0 conditions performed functions related to transmembrane and mitochondrial processes. While these results are promising in that purple sea urchin populations possess genetic variation for surviving extreme pH conditions not currently experienced in nature, they caution that increased acidification does not result in a linear response but elicits unique physiological stresses and survival mechanisms. [ABSTRACT FROM AUTHOR]

Apoptosis and autophagy are fundamental mechanisms of programed cell death activated during protostome and deuterostome embryonic development, contributing to the creation and remodeling of different anatomical structures. Programed cell death has been investigated at morphological and biochemical levels, but there is a lack of information concerning gene expression of death factors during deuterostome embryonic development. In this study, we analyze the expression patterns of 13 genes involved in autophagy, extrinsic and intrinsic apoptosis during blastula, gastrula, and pluteus stages of the sea urchin Paracentrotus lividus embryonic development. Results suggested the occurrence of all death mechanisms investigated, highlighting the simultaneous involvement of apoptosis and autophagy during embryonic development. In particular, gastrula was the developmental stage where the majority of death genes were highly expressed. During gastrulation apoptotic processes are fundamental for tissue remodeling, such as cavity formation and removal of inner ectodermal cells. This is the first report that identifies a panel of cell death genes in the P. lividus genome and analyzes their expression variations during ontogenesis. [ABSTRACT FROM AUTHOR]

The distribution and function of many marine species is largely determined by the effect of abiotic drivers on their reproduction and early development, including those drivers associated with elevated CO2 and global climate change. A number of studies have therefore investigated the effects of elevated pCO2 on a range of reproductive parameters, including sperm motility and fertilisation success. To date, most of these studies have not examined the possible synergistic effects of other abiotic drivers, such as the increased frequency of hypoxic events that are also associated with climate change. The present study is therefore novel in assessing the impact that an hypoxic event could have on reproduction in a future high CO2 ocean. Specifically, this study assesses sperm motility and fertilisation success in the sea urchin Paracentrotus lividus exposed to elevated pCO2 for 6 months. Gametes extracted from these pre-acclimated individuals were subjected to hypoxic conditions simulating an hypoxic event in a future high CO2 ocean. Sperm swimming speed increased under elevated pCO2 and decreased under hypoxic conditions resulting in the elevated pCO2 and hypoxic treatment being approximately equivalent to the control. There was also a combined negative effect of increased pCO2 and hypoxia on the percentage of motile sperm. There was a significant negative effect of elevated pCO2 on fertilisation success, and when combined with a simulated hypoxic event there was an even greater effect. This could affect cohort recruitment and in turn reduce the density of this ecologically and economically important ecosystem engineer therefore potentially effecting biodiversity and ecosystem services. [ABSTRACT FROM AUTHOR]

Increased atmospheric CO2 concentration is leading to changes in the carbonate chemistry and the temperature of the ocean. The impact of these processes on marine organisms will depend on their ability to cope with those changes, particularly the maintenance of calcium carbonate structures. Both a laboratory experiment (long-term exposure to decreased pH and increased temperature) and collections of individuals from natural environments characterized by low pH levels (individuals from intertidal pools and around a CO2 seep) were here coupled to comprehensively study the impact of near-future conditions of pH and temperature on the mechanical properties of the skeleton of the euechinoid sea urchin Paracentrotus lividus. To assess skeletal mechanical properties, we characterized the fracture force, Young's modulus, second moment of area, material nanohardness, and specific Young's modulus of sea urchin test plates. None of these parameters were significantly affected by low pH and/or increased temperature in the laboratory experiment and by low pH only in the individuals chronically exposed to lowered pH from the CO2 seeps. In tidal pools, the fracture force was higher and the Young's modulus lower in ambital plates of individuals from the rock pool characterized by the largest pH variations but also a dominance of calcifying algae, which might explain some of the variation. Thus, decreases of pH to levels expected for 2100 did not directly alter the mechanical properties of the test of P. lividus. Since the maintenance of test integrity is a question of survival for sea urchins and since weakened tests would increase the sea urchins' risk of predation, our findings indicate that the decreasing seawater pH and increasing seawater temperature expected for the end of the century should not represent an immediate threat to sea urchins vulnerability. [ABSTRACT FROM AUTHOR]

We studied the spatial variation in recruitment and the population dynamics of the sea urchin Paracentrotus lividus, analysing the effect of depth and presence of sea urchin aggregations on population structure. Over 90% of the observed recruits (individuals under 1 year of age) were concentrated in aggregations found in shallow waters. In these areas, a positive linear relationship was found between adult and recruit density, possibly due to higher survival rates of juveniles taking refuge among the spines of adults. The scarcity of recruits and the presence of adult sea urchins at depths of 8 and 12 m suggest the migration of part of the population towards deep areas when individuals reach a size of ∼40 mm. In light of these results, the implementation of harvest refugia for sea urchins in shallow areas could constitute an effective fishery management tool for this species. High population densities could enhance recruitment, given the inverse density dependence of this process, while their migratory pattern would guarantee biomass exportation towards deeper fishing grounds. [ABSTRACT FROM PUBLISHER]

Across heterogeneous landscapes, populations may have adaptive differences in gene regulation that adjust their physiologies to match local environments. Such differences could have origins in acclimation or in genetically fixed variation between habitats. Here we use common-garden experiments to evaluate differences in gene expression between populations of the purple sea urchin, Strongylocentrotus purpuratus, spanning 1700 km and average temperature differences of 5°C to 8°C. Across expression profiles from 18,883 genes after 3 years of common conditions, we find highly correlated expression patterns (Pearson's r = 0.992) among most genes. However, 66 genes were differentially expressed, including many ribosomal protein and biomineralization genes, which had higher expression in urchins originally from the southern population. Gene function analyses revealed slight but pervasive expression differences in genes related to ribosomal function, metabolism, transport, 'bone' development, and response to stimuli. In accord with gene expression patterns, a post-hoc spine regrowth experiment revealed that urchins of southern origin regrew spines at a faster rate than northern urchins. These results suggest that there may be genetically controlled, potentially adaptive differences in gene regulation across habitats and that gene expression differences may be under strong enough selection to overcome high, dispersal-mediated gene flow in this marine species. [ABSTRACT FROM AUTHOR]

Fernández-Boán, M., Freire, J., Parma, A. M., Fernández, L., and Orensanz, J. M. 2013. Monitoring the fishing process in the sea urchin diving fishery of Galicia – ICES Journal of Marine Science, 70: 604–617.The assessment and management of small-scale benthic fisheries requires attention to the spatial structure of stocks and patterns of effort allocation. Spatial information helps in the interpretation of fisheries data, and is required for designing spatially explicit management strategies, often prescribed in the case of benthic fisheries. Monitoring of boats with GPS, combined with port interviews, was evaluated as an approach to investigate the spatial pattern of fishing intensity and catch per unit of effort (CPUE) in the sea urchin (Paracentrotus lividus) diving fishery from Galicia, Spain. Fishing opportunities (FOs), relatively small regions of high fishing intensity, were identified and mapped at a fine scale. New FOs were first visited at an approximately constant rate. Concentration analysis shows that effort intensity was not uniformly distributed within FOs. CPUE did not exhibit a significant trend throughout the season, either at the scale of the aggregated fishery or within individual FOs. Catch per area and area covered per unit of diving time were inversely related, indicating that fishers stay longer in high-density patches. While abundance is the primary driver of effort allocation, other factors contributing to suitability were identified. Based on these results, we discuss realistic options for the monitoring of this and comparable fisheries. [ABSTRACT FROM PUBLISHER]

Soualili, D., Dubois, P., Gosselin, P., Pernet, P., and Guillou, M. 2008 Assessment of seawater pollution by heavy metals in the neighbourhood of Algiers: use of the sea urchin, Paracentrotus lividus, as a bioindicator. – ICES Journal of Marine Science, 65: 132–139.The objective of the study was to assess the levels of contamination by heavy metals near the Algiers metropolis, using a combination of chemical and toxicological data gained from analyses of sediments and biological parameters characteristic of the sea urchin, Paracentrotus lividus. Zinc, lead, cadmium, copper, and iron concentrations were determined in sediments and in sea urchin gonads. Sediment toxicity was assessed by bioassay based on the larval development of sea urchins. The most numerous larval abnormalities were found in a site near Algiers identified as highly polluted by lead. The levels of the other metals across the study area fell within the background concentrations reported in the literature for the Mediterranean Sea, with the exception of zinc, which showed high values in female gonads. [ABSTRACT FROM PUBLISHER]

Background Sea-urchin granuloma is a chronic granulomatous reaction arising after injury with sea-urchin spines. Classified as an allergic foreign-body type of granuloma, it is believed to be a delayed-type reaction to an as yet unidentified antigen. In a clinicopathological study, 50 biopsy specimens from 35 patients diagnosed as having sea-urchin granuloma caused by Paracentrotus lividus, we found different inflammatory patterns that in some cases suggested a mycobacterial infection. Objectives To investigate and identify mycobacterial DNA in formalin-fixed and paraffin-embedded skin biopsy specimens diagnosed as sea-urchin granulomas. Methods A search combining polymerase chain reaction amplification using Mycobacterium genus-specific primers, and subsequent restriction enzyme analysis enabling identification to the species level, was performed in 41 samples. Results Amplification of a 924-bp DNA fragment encoding mycobacterial 16S rRNA gene was positive in eight biopsy specimens from seven patients (21%). M. marinum-specific restriction patterns were identified in three samples. Conclusions Although further controlled studies are necessary, from these data it would appear that myobacteria may play a pathogenic role in some cases of sea-urchin granuloma. [ABSTRACT FROM AUTHOR]