EchinoDB: An update to the web-based application for genomic and transcriptomic data on Echinoderms.

Here we release a new version of EchinoDB (https://echinodb.uncc.edu). EchinoDB is a database of genomic and transcriptomic data on echinoderms. The initial database consisted of groups of 749,397 orthologous and paralogous transcripts arranged in orthoclusters by sequence similarity. The new version of EchinoDB includes RNA-seq data of the brittle star Ophioderma brevispinum and high-quality genomic assembly data of the green sea urchin Lytechinus variegatus. In addition, we enabled keyword searches for annotated data and installed an updated version of Sequenceserver to allow BLAST searches. The data are downloadable in FASTA format. The first version of EchinoDB appeared in 2016 and was implemented in GO on a local server. The new version has been updated using R Shiny to include new features and improvements in the application. Furthermore, EchinoDB now runs entirely in the cloud for increased reliability and scaling. EchinoDB enjoys a user base drawn from the fields of phylogenetics, developmental biology, genomics, physiology, neurobiology, and regeneration. As use cases, we illustrate how EchinoDB is used in discovering pathways and gene regulatory networks involved in the tissue regeneration process.

Evidence for Association of Vibrio Echinoideorum with Tissue Necrosis on Body Shell of the Green Sea Urchin Strongylocentrotus Droebachiensis

“Sea urchin lesion syndrome” is known as sea urchins disease with the progressive development of necrotic epidermal tissue and loss of external organs, including appendages on the outer body surface. Recently, a novel strain, Vibrio echinoideorum has been isolated from the lesions of green sea urchin (Strongylocentrotus droebachiensis), an economically important mariculture species in Norway. V. echinoideorum has not been reported elsewhere in association of with green sea urchin lesion syndrome. Therefore, in this study, an immersion based bacterial challenge experiment was performed to expose sea urchins (wounded and non-wounded) to V. echinoideorum, thereby mimicking a nearly natural host-pathogen interaction under controlled conditions. This infection experiment demonstrated that only the injured sea urchins developed the lesion to a significant degree when exposed to V. echinoideorum. Pure cultures of the employed bacterial strain was recovered from the infected animals and its identity was confirmed by the MALDI-TOF MS spectra profiling. Additionally, the hemolytic phenotype of V. echinoideorum substantiated its virulence potential towards the host, and this was also supported by the cytolytic effect on red spherule cells of sea urchins. Furthermore, the genome sequence of V. echinoideorum was assumed to encode potential virulence genes and were subjected for in silico comparison with the established virulence factors of Vibrio vulnificus and Vibrio tasmaniensis. This comparative virulence profile provided novel insights about virulence genes and their putative functions related to chemotaxis, adherence, invasion, evasion of the host immune system, and damage of host tissue and cells. Thus, it supports the pathogenicity of V. echinoideorum. In conclusion, the interaction of V. echinoideorum with injured sea urchins appears to be essential for the development of lesion syndrome and therefore, revealing its potentiality as an opportunistic pathogen.

New Echinoderm-Crab Epibiotic Associations from the Coastal Barents Sea

During diving surveys for a Russian research project that monitored introduced species, red king crabs (Paralithodes camtschaticus) were collected at a coastal site of the Barents Sea to study the structure and dynamics of this species. Sampling of the organisms colonizing the crabs was part of this research project. For the first time, the presence of relatively large specimens of the common starfish Asterias rubens as epibionts of P. camtschaticus was observed in July 2010, 2018, and 2019. In 2010 and 2019, we also found three other echinoderm species (the Atlantic sea cucumber Cucumaria frondosa, the green sea urchin Strongylocentrotus droebachiensis, and the brittle star Ophiura sarsii). These findings add to the current list of associated species on king crabs not only in the Barents Sea but also in native areas of this host. Red king crabs have been documented as predators for these echinoderm species, and our records show additional possible interactions between king crabs and echinoderms in this region. More likely, the epibiotic lifestyle allows these echinoderms to avoid predation from red king crabs. There are no potential disadvantages derived by red king crabs through their relationships with the echinoderm epibionts due to low occurrences of these associations. We suggest no negative effects for the local red king crab population and populations of other commercial species in the Barents Sea.

Observations from the Hydrolysis of the Green Sea Urchin (Strongylocentrotus Droebachiensis)

There is a large amount of co-product generated by the sea urchin fisheries around the world, as well as a growing interest in removing large quantities of undersize and low value sea urchins from barren areas in the northern Atlantic and Pacific coasts. The authors believe there is scope to develop a hydrolysate product from this and this study gives preliminary observations on the characteristics of hydrolysate from the sea urchin Strongylocentrotus droebachiensis. The biochemical composition for S. droebachiensis were; water 64.1%, protein 3.4%, oil 0.9% and ash 29.8%. Amino acid composition, molecular weight distribution, lipid-class and fatty acid composition are also presented. The authors suggest a sensory-panel mapping be undertaken on future sea urchin hydrolysates. Possible uses for the hydrolysate are unclear at this stage but the combination of amino acids and the relatively high levels of Glycine, Aspartic acid, and Glutamic acid should be further investigated.

A seascape approach for guiding effective habitat enhancement

Kelp habitats are threatened across the globe, and because of their ecological importance, active conservation and restoration solutions are needed. The use of man-made structures as artificial reefs is one way to enhance kelp habitat by providing suitable substrata, but in the past the ecology of artificial structures has been investigated mainly in contrast to natural coastal habitats, not as elements integrated into the seascape. Indeed, it is now emerging that structuring processes, including ecological interactions (e.g., herbivory), can depend on properties of the surrounding seascape. In Eastern Canada, grazing by the green sea urchin can jeopardize the success of artificial reefs for kelp enhancement. Urchin activity is, however, likely to be influenced by the bottom composition, and thus a seascape approach is needed to integrate urchin behavior and habitat heterogeneity. Adopting a spatially explicit framework, we investigated whether the seascape creates areas of differential grazing risk for kelp by affecting urchin habitat use. Specifically, we transplanted kelp onto modules of artificial substrata distributed on a heterogeneous area that we mapped for bottom type and algal cover. After following kelp survival and urchin distribution over time, we modeled kelp survival as function of urchin metrics and coupled it to urchin use of the habitat models to map grazing risk in the area. Kelp survival was a function of the frequency of the urchins presence. Urchins avoided sandy patches, while bottom composition and algal cover modulated the within-patch urchin use of the habitat, creating heterogeneity in grazing risk. Discrete seascape features (boulders) also increased the grazing risk locally. The heterogeneity of coastal seafloor can thus play a major role in determining the ecological outcomes on artificial structures. Incorporating this information when planning artificial reefs could minimize the detrimental grazing risk, thereby increasing the success of artificial reefs for kelp habitat enhancement.