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A fundamental question in ecology is how organisms survive food deprivation. In the ocean, climate change is impacting the phenology of food availability for early life‐history stages of animals. In this study, we undertook an integrative analysis of larvae of the sea urchin Strongylocentrotus purpuratus—an important keystone species in marine ecology and a molecular biological model organism in developmental biology. Specifically, to identify the mechanisms of resilience that maintain physiological state and the ability of organisms to recover from food deprivation, a suite of molecular biological, biochemical, physiological and whole organism measurements was completed. Previous studies focused on the importance of energy reserves to sustain larvae during periods of food deprivation. We show, however, that utilization of endogenous energy reserves only supplied 15% of the metabolic requirements of long‐term survival (up to 22 days) in the absence of particulate food. This large energy gap was not supplied by larvae feeding on bacteria. Estimates of larval ability to transport dissolved organic matter directly from seawater showed that such substrates could fully supply metabolic needs. Integrative approaches allowed for filtering of gene expression signatures, linked with gene network analyses and measured biochemical and physiological traits, to identify biomarkers of resilience. We identified 14 biomarkers related to nutrition‐responsive gene expression, of which a specific putative amino acid transporter gene was quantified in a single larva experiencing continuous nutritional stress. Advances in applications of gene expression technologies offer novel approaches to determine the physiological state of marine larval forms in ecological settings undergoing environmental change. see also the Perspective by George N. Somero [ABSTRACT FROM AUTHOR]

Species range shifts due to changing ocean conditions are occurring around the world. As species move, they build new interaction networks as they shift from or into new ecological communities. Typically, species ranges are modeled individually, but biotic interactions have been shown to be important to creating more realistic modeling outputs for species. To understand the importance of consumer interactions in Eastern Pacific kelp forest species distributions, we used a Maxent framework to model a key foundation species, giant kelp (Macrocystis pyrifera), and a dominant herbivore, purple sea urchins (Strongylocentrotus purpuratus). With neither species having previously been modeled in the Eastern Pacific, we found evidence for M. pyrifera expansion in the northern section of its range, with no projected contraction at the southern range edge. Despite its known co-occurrence with M. pyrifera, models of S. purpuratus showed a non-concurrent southern range contraction and a co-occurring northern range expansion. While the co-occurring shifts may lead to increased spatial competition for suitable substrate, this non-concurrent contraction could result in community wide impacts such as herbivore release, tropicalization, or ecosystem restructuring. [ABSTRACT FROM AUTHOR]

Without general adaptative immunity, invertebrates evolved a vast number of heterogeneous non-self recognition strategies. One of those well-known adaptations is the expansion of the immune receptor gene superfamily coding for scavenger receptor cysteine-rich domain containing proteins (SRCR) in a few invertebrates. Here, we investigated the evolutionary history of the SRCR gene superfamily (SRCR-SF) across 29 metazoan species with an emphasis on invertebrates. We analyzed their domain architectures, genome locations and phylogenetic distribution. Our analysis shows extensive genome-wide duplications of the SRCR-SFs in Amphimedon queenslandica and Strongylocentrotus purpuratus. Further molecular evolution study reveals various patterns of conserved cysteines in the sponge and sea urchin SRCR-SFs, indicating independent and convergent evolution of SRCR-SF expansion during invertebrate evolution. In the case of the sponge SRCR-SFs, a novel motif with seven conserved cysteines was identified. Exon–intron structure analysis suggests the rapid evolution of SRCR-SFs during gene duplications in both the sponge and the sea urchin. Our findings across nine representative metazoans also underscore a heightened expression of SRCR-SFs in immune-related tissues, notably the digestive glands. This observation indicates the potential role of SRCR-SFs in reinforcing distinct immune functions in these invertebrates. Collectively, our results reveal that gene duplication, motif structure variation, and exon–intron divergence might lead to the convergent evolution of SRCR-SF expansions in the genomes of the sponge and sea urchin. Our study also suggests that the utilization of SRCR-SF receptor duplication may be a general and basal strategy to increase immune diversity and tissue specificity for the invertebrates. [ABSTRACT FROM AUTHOR]

The SpTransformer (SpTrf) gene family in the purple sea urchin, Strongylocentrotus purpuratus, encodes immune response proteins. The genes are clustered, surrounded by short tandem repeats, and some are present in genomic segmental duplications. The genes share regions of sequence and include repeats in the coding exon. This complex structure is consistent with putative local genomic instability. Instability of the SpTrf gene cluster was tested by 10 days of growth of Escherichia coli harboring bacterial artificial chromosome (BAC) clones of sea urchin genomic DNA with inserts containing SpTrf genes. After the growth period, the BAC DNA inserts were analyzed for size and SpTrf gene content. Clones with multiple SpTrf genes showed a variety of deletions, including loss of one, most, or all genes from the cluster. Alternatively, a BAC insert with a single SpTrf gene was stable. BAC insert instability is consistent with variations in the gene family composition among sea urchins, the types of SpTrf genes in the family, and a reduction in the gene copy number in single coelomocytes. Based on the sequence variability among SpTrf genes within and among sea urchins, local genomic instability of the family may be important for driving sequence diversity in this gene family that would be of benefit to sea urchins in their arms race with marine microbes. [ABSTRACT FROM AUTHOR]

An important goal of many studies in molecular ecology is to utilize molecular tools to elucidate how critical traits like metabolism and growth are affected by environmental stressors and how organisms offset these stresses by adaptive molecular‐level responses. Stress from food deprivation may be critical for early developmental stages that require a continued supply of substrates for energy metabolism and growth if development is to be completed. In a 'From the Cover' article in this issue of Molecular Ecology, Li et al. (2023) examined the effects of withholding food (unicellular algae) on 10 traits of larvae of the purple sea urchin (Strongylocentrotus purpuratus), ranging from the molecular level (gene expression) to morphology. Overall, this study sheds new light on the plasticity of larval development and the tight linkages that exist among traits as they respond to changes in food availability. Importantly, shifts in the sources of food utilized under different dietary treatments show the plasticity of these larvae to alter reliance on endogenous energy stores and dissolved organic matter (DOM) as algae deprivation continues. The effects of global change on the amounts and phenology of productivity in the seas make this type of integrated, multi‐level analysis an important tool for predicting the future states of marine ecosystems. [ABSTRACT FROM AUTHOR]

Background: Spotting disease infects a variety of sea urchin species across many different marine locations. The disease is characterized by discrete lesions on the body surface composed of discolored necrotic tissue that cause the loss of all surface appendages within the lesioned area. A similar, but separate disease of sea urchins called bald sea urchin disease (BSUD) has overlapping symptoms with spotting disease, resulting in confusions in distinguishing the two diseases. Previous studies have focus on identifying the underlying causative agent of spotting disease, which has resulted in the identification of a wide array of pathogenic bacteria that vary based on location and sea urchin species. Our aim was to investigate the spotting disease infection by characterizing the microbiomes of the animal surface and various tissues. Results: We collected samples of the global body surface, the lesion surface, lesioned and non-lesioned body wall, and coelomic fluid, in addition to samples from healthy sea urchins. 16S rRNA gene was amplified and sequenced from the genomic DNA. Results show that the lesions are composed mainly of Cyclobacteriaceae, Cryomorphaceae, and a few other taxa, and that the microbial composition of lesions is the same for all infected sea urchins. Spotting disease also alters the microbial composition of the non-lesioned body wall and coelomic fluid of infected sea urchins. In our closed aquarium systems, sea urchins contracted spotting disease and BSUD separately and therefore direct comparisons could be made between the microbiomes from diseased and healthy sea urchins. Conclusion: Results show that spotting disease and BSUD are separate diseases with distinct symptoms and distinct microbial compositions. [ABSTRACT FROM AUTHOR]

Background: Spotting disease infects a variety of sea urchin species across many different marine locations. The disease is characterized by discrete lesions on the body surface composed of discolored necrotic tissue that cause the loss of all surface appendages within the lesioned area. A similar, but separate disease of sea urchins called bald sea urchin disease (BSUD) has overlapping symptoms with spotting disease, resulting in confusions in distinguishing the two diseases. Previous studies have focus on identifying the underlying causative agent of spotting disease, which has resulted in the identification of a wide array of pathogenic bacteria that vary based on location and sea urchin species. Our aim was to investigate the spotting disease infection by characterizing the microbiomes of the animal surface and various tissues. Results: We collected samples of the global body surface, the lesion surface, lesioned and non-lesioned body wall, and coelomic fluid, in addition to samples from healthy sea urchins. 16S rRNA gene was amplified and sequenced from the genomic DNA. Results show that the lesions are composed mainly of Cyclobacteriaceae, Cryomorphaceae, and a few other taxa, and that the microbial composition of lesions is the same for all infected sea urchins. Spotting disease also alters the microbial composition of the non-lesioned body wall and coelomic fluid of infected sea urchins. In our closed aquarium systems, sea urchins contracted spotting disease and BSUD separately and therefore direct comparisons could be made between the microbiomes from diseased and healthy sea urchins. Conclusion: Results show that spotting disease and BSUD are separate diseases with distinct symptoms and distinct microbial compositions. [ABSTRACT FROM AUTHOR]

Within the developing embryo is a microcosm of cell type diversity. Single cell RNA-sequencing (scRNA-seq) is used to reveal cell types, typically by grouping cells according to their gene regulatory states. However, both across and within these regulatory states are additional layers of cellular diversity represented by the differential expression of genes that govern cell function. Here, we analyzed scRNA-seq data representing the late gastrula stage of Strongylocentrotus purpuratus (purple sea urchin) to understand the patterning of transporters belonging to the ABC and SLC families. These transporters handle diverse substrates from amino acids to signaling molecules, nutrients and xenobiotics. Using transporter-based clustering, we identified unique transporter patterns that are both shared across cell lineages, as well as those that were unique to known cell types. We further explored three patterns of transporter expression in mesodermal cells including secondary mesenchyme cells (pigment cells and blastocoelar cells) and skeletogenic cells (primary mesenchyme cells). The results revealed the enrichment of SMTs potentially involved in nutrient absorption (SLC5A9, SLC7A11, SLC35F3 , and SLC52A3) and skeletogenesis (SLC9A3 , SLC13A2/3/5 , and SLC39A13) in pigment cells and blastocoelar cells respectively. The results indicated that the strategy of clustering by cellular activity can be useful for discovering cellular populations that would otherwise remain obscured. [Display omitted] • We examined small molecule transporters (SMTs) in sea urchin scRNAseq data. • SMTs were related to neurotransmitters, nutrients and biomineralization. • We clustered cells on the basis of SMT expression i.e. "activity patterns" (APs). • Distinctive SMT APs were found in sub-populations of mesenchymal cells. • The APs revealed cryptic skeletogenic secondary mesenchymal cells. [ABSTRACT FROM AUTHOR]

Organisms experience environments that vary across both space and time. Such environmental heterogeneity shapes standing genetic variation and may influence species' capacity to adapt to rapid environmental change. However, we know little about the kind of genetic variation that is involved in local adaptation to environmental variability. To address this gap, we sequenced the whole genomes of 140 purple sea urchins (Strongylocentrotus purpuratus) from seven populations that vary in their degree of pH variability. Despite no evidence of global population structure, we found a suite of single-nucleotide polymorphisms (SNPs) tightly correlated with local pH variability (outlier SNPs), which were overrepresented in regions putatively involved in gene regulation (long noncoding RNA and enhancers), supporting the idea that variation in regulatory regions is important for local adaptation to variability. In addition, outliers in genes were found to be (i) enriched for biomineralization and ion homeostasis functions related to low pH response, (ii) less central to the protein-protein interaction network, and (iii) underrepresented among genes highly expressed during early development. Taken together, these results suggest that loci that underlie local adaptation to pH variability in purple sea urchins fall in regions with potentially low pleiotropic effects (based on analyses involving regulatory regions, network centrality, and expression time) involved in low pH response (based on functional enrichment). [ABSTRACT FROM AUTHOR]

The ability to perceive and respond to light stimuli is fundamental not only for spatial vision but also to many other light-mediated interactions with the environment. In animals, light perception is performed by specific cells known as photoreceptors and, at molecular level, by a group of GPCRs known as opsins. Sea urchin larvae possess a group of photoreceptor cells (PRCs) deploying a Go-Opsin (Opsin3.2) which have been shown to share transcription factors and morphology with PRCs of the ciliary type, raising new questions related to how this sea urchin larva PRC is specified and whether it shares a common ancestor with ciliary PRCs or it if evolved independently through convergent evolution. To answer these questions, we combined immunohistochemistry and fluorescent in situ hybridization to investigate how the Opsin3.2 PRCs develop in the sea urchin Strongylocentrotus purpuratus larva. Subsequently, we applied single-cell transcriptomics to investigate the molecular signature of the Sp-Opsin3.2-expressing cells and show that they deploy an ancient regulatory program responsible for photoreceptors specification. Finally, we also discuss the possible functions of the Opsin3.2-positive cells based on their molecular fingerprint, and we suggest that they are involved in a variety of signaling pathways, including those entailing the thyrotropin-releasing hormone. [ABSTRACT FROM AUTHOR]

How strongly predators and prey interact is both notoriously context dependent and difficult to measure. Yet across taxa, interaction strength is strongly related to predator size, prey size and prey density, suggesting that general cross‐taxonomic relationships could be used to predict how strongly individual species interact.Here, we ask how accurately do general size‐scaling relationships predict variation in interaction strength between specific species that vary in size and density across space and time?To address this question, we quantified the size and density dependence of the functional response of the California spiny lobster Panulirus interruptus, foraging on a key ecosystem engineer, the purple sea urchin Strongylocentrotus purpuratus, in experimental mesocosms. Based on these results, we then estimated variation in lobster–urchin interaction strength across five sites and 9 years of observational data. Finally, we compared our experimental estimates to predictions based on general size‐scaling relationships from the literature.Our results reveal that predator and prey body size has the greatest effect on interaction strength when prey abundance is high. Due to consistently high urchin densities in the field, our simulations suggest that body size—relative to density—accounted for up to 87% of the spatio‐temporal variation in interaction strength. However, general size‐scaling relationships failed to predict the magnitude of interactions between lobster and urchin; even the best prediction from the literature was, on average, an order of magnitude (+18.7×) different than our experimental predictions.Harvest and climate change are driving reductions in the average body size of many marine species. Anticipating how reductions in body size will alter species interactions is critical to managing marine systems in an ecosystem context. Our results highlight the extent to which differences in size‐frequency distributions can drive dramatic variation in the strength of interactions across narrow spatial and temporal scales. Furthermore, our work suggests that species‐specific estimates for the scaling of interaction strength with body size, rather than general size‐scaling relationships, are necessary to quantitatively predict how reductions in body size will alter interaction strengths. [ABSTRACT FROM AUTHOR]

Along the Palos Verdes Peninsula in southern California, high densities of Strongylocentrotus purpuratus (purple sea urchin) have consumed almost all macroalgae on large expanses (61 ha) of rocky reef habitat, creating "urchin barrens." Mesocentrotus franciscanus (red sea urchin) harvesting comprises an important fishery in the region, as their gonads are sold as a high-value sushi product called "uni." However, with a lack of macroalgal food resources, urchins in barrens are smaller and exist in a starved state, meaning little, if any, gonad product is available to the fishery. To restore local kelp forests and increase gonad biomass available to the M. franciscanus fishery, beginning in October 2013, S. purpuratus were culled in barrens to a target density of 2 per m2 across 5.2 ha of rocky reef on the Palos Verdes Peninsula. Mesocentrotus franciscanus were collected from urchin barren, restoration, and kelp reference sites from April to November 2014 to compare differences in gonad production among the three site types. Culling S. purpuratus resulted in the recovery of normal seasonal M. franciscanus gonad production throughout the 8-month study. Mesocentrotus franciscanus gonad weights at a given test diameter length in restoration sites were equivalent to, and sometimes exceeded, the gonad production of those from the kelp reference sites. The urchin test length distributions of collected M. franciscanus were consistently smaller at urchin barren sites than at kelp reference sites, while those in restoration sites generally fell in between. [ABSTRACT FROM AUTHOR]

Septate junctions (SJs) evolved as cell-cell junctions that regulate the paracellular barrier and integrity of epithelia in invertebrates. Multiple morphological variants of SJs exist specific to different epithelia and/or phyla but the biological significance of varied SJ morphology is unclear because the knowledge of the SJ associated proteins and their functions in non-insect invertebrates remains largely unknown. Here we report cell-specific expression of nine candidate SJ genes in the early life stages of the sea urchin Strongylocentrotus purpuratus. By use of in situ RNA hybridization and single cell RNA-seq we found that the expression of selected genes encoding putatively SJ associated transmembrane and cytoplasmic scaffold molecules was dynamically regulated during epithelial development in the embryos and larvae with different epithelia expressing different cohorts of SJ genes. We focused a functional analysis on SpMesh, a homolog of the Drosophila smooth SJ component Mesh, which was highly enriched in the endodermal epithelium of the mid- and hindgut. Functional perturbation of SpMesh by both CRISPR/Cas9 mutagenesis and vivo morpholino-mediated knockdown shows that loss of SpMesh does not disrupt the formation of the gut epithelium during gastrulation. However, loss of SpMesh resulted in a severely reduced gut-paracellular barrier as quantitated by increased permeability to 3–5 ​kDa FITC-dextran. Together, these studies provide a first look at the molecular SJ physiology during the development of a marine organism and suggest a shared role for Mesh-homologous proteins in forming an intestinal barrier in invertebrates. Results have implications for consideration of the traits underlying species-specific sensitivity of marine larvae to climate driven ocean change. [Display omitted] • We identify nine candidate septate junction genes during sea urchin development. • Putative SJ gene mRNAs are enriched in the ectoderm and endoderm. • Integral protein SpMesh is a mid- and hindgut-specific SJ component. • SpMesh is necessary for paracellular gut barrier formation. [ABSTRACT FROM AUTHOR]

The recent collapse of predatory sunflower sea stars (Pycnopodia helianthoides) owing to sea star wasting disease (SSWD) is hypothesized to have contributed to proliferation of sea urchin barrens and losses of kelp forests on the North American west coast. We used experiments and a model to test whether restored Pycnopodia populations may help recover kelp forests through their consumption of nutritionally poor purple sea urchins (Strongylocentrotus purpuratus) typical of barrens. Pycnopodia consumed 0.68 S. purpuratus d−1, and our model and sensitivity analysis shows that the magnitude of recent Pycnopodia declines is consistent with urchin proliferation after modest sea urchin recruitment, and even small Pycnopodia recoveries could generally lead to lower densities of sea urchins that are consistent with kelp-urchin coexistence. Pycnopodia seem unable to chemically distinguish starved from fed urchins and indeed have higher predation rates on starved urchins owing to shorter handling times. These results highlight the importance of Pycnopodia in regulating purple sea urchin populations and maintaining healthy kelp forests through top-down control. The recovery of this important predator to densities commonly found prior to SSWD, whether through natural means or human-assisted reintroductions, may therefore be a key step in kelp forest restoration at ecologically significant scales. [ABSTRACT FROM AUTHOR]

Thyroid Hormones (THs) are a class of signaling molecules produced by coupling iodine with tyrosine residues. In vertebrates, extensive data support their important role in a variety of processes such as metabolism, development and metamorphosis. On the other hand, in invertebrates, the synthesis and role of the THs have been, so far, poorly investigated, thus limiting our understanding of the function and evolution of this important animal signaling pathway. In sea urchins, for example, while several studies focused on the availability and function of external sources of iodotyrosines, preliminary evidence suggests that an endogenous TH pathway might be in place. Here, integrating available literature with an in silico analysis, various homologous genes of the vertebrate TH molecular toolkit have been identified in the sea urchin Strongylocentrotus purpuratus. They include genes involved in the synthesis (Sp-Pxdn), metabolism (Sp-Dios), transport (Sp-Ttrl, Sp-Mct7/8/10) and response (Sp-Thr, Sp-Rxr and Sp-Integrin αP) to thyroid hormones. To understand the cell type(s) involved in TH synthesis and/or response, we studied the spatial expression of the TH toolkit during urchin development. Exploiting single-cell transcriptomics data in conjunction with in situ hybridization and immunohistochemistry, we identified cell types that are potentially producing or responding to THs in the sea urchin. Finally, growing sea urchin embryos until the larva stage with and without a source of inorganic iodine, we provided evidence that iodine organification is important for larval skeleton growth. [ABSTRACT FROM AUTHOR]

A new multispecies benthic invertebrate monitoring program is being developed to quantitatively monitor stock abundance over time on the British Columbia (BC) coast. This dive survey is designed to monitor abundance of Green (Strongylocentrotus droebachiensis), Red (Mesocentrotus franciscanus) and Purple (Strongylocentrotus purpuratus) Sea Urchin, Giant Red Sea Cucumber (Apostichopus californicus), Northern Abalone (Haliotis kamtschatkana), Sunflower Star (Pycnopodia helianthoides) and Pacific Geoduck (Panopea generosa) populations, and also to collect detailed habitat information on substrate and algae. The survey protocol was developed in 2016 and is described in detail. Pilot surveys were conducted in different areas of the coast from 2016 to 2021. Data from these pilot surveys, along with data from single-species surveys (1978 to 2021), were analysed to make recommendations on optimal survey design for the new monitoring program. The methods included reviewing singlespecies analyses that informed sampling intensity on transects, looking at historic maximum transect lengths, investigating stratification variables, and using an acceptance sampling method to determine the minimum required number of transects, given predefined risks and probabilities associated with being above or below reference points. In addition, densities of the Giant Red Sea Cucumber and size and habitat subsets of Red Sea Urchin populations were estimated as an example of how these data could be used to assess stock status in the future. The recommendations on survey design are to: 1) Use the dive survey protocol described in Appendix A of the Research Document; 2) Exclude sections of shoreline with fetch values lower than 20,000 m or higher than 2.52 million m; 3) Ensure surveys occur at the same time of year to avoid introducing seasonal variation to the data; 4) Use the common (across species) coast wide standard deviation-to-mean ratio of density (animals per m2) equal to 1.27 in calculations to determine the target number of transects to be sampled; 5) Conduct at least 240 transects coast wide to estimate stock status; 6) Implement a two-stage, random sampling design that minimizes the time required to cover the entire BC coast and optimizes the efficient use of available resources; and 7) Continue to explore pre- or post-stratification variables to improve survey precision, as data become available. [ABSTRACT FROM AUTHOR]

Fibrinogen-related proteins (FREPs) have been identified in several animals. They are involved in the body's defense, acting as mediators of phagocytosis. Ficolins and intelectins are some of the most studied Fibrinogen-related Domain (FReD)-containing lectins. In this work, we have isolated a singular FReD-containing lectin, which cannot be classified as ficolin or intelectin. ELL (Echinometra lucunter lectin) was isolated from coelomic plasma by affinity chromatography on xanthan gum. Primary structure was determined by tandem mass spectrometry. Moreover, antimicrobial activity of ELL was evaluated against planktonic cells and biofilm of Escherichia coli , Staphylococcus aureus and S. epidermidis. ELL showed hemagglutinating activity in Ca2+ presence, which was inhibited by glycoprotein mucin and thyroglobulin. Complete amino acid sequence consisted of 229 residues, including a FReD in the N-terminal. Searches for similarity found that ELL was very close to putative proteins from Strongylocentrotus purpuratus. ELL showed moderate similarity with uncharacterized sea stars proteins and protochordate intelectins. ELL was able to inhibit the planktonic growth of the Gram-positive bacteria and significantly reduce the biofilm formation of all bacteria tested. In conclusion, we identified a new type of FReP-containing lectin with some structural and functional conservation towards intelectins. • A Fibrinogen-related protein (FREP) was isolated from sea urchin Echinometra lcuunter. • ELL she is the first member of a new family of FREPs found in echinoderms. • ELL seems to be involved in the defense of the E. lucunter. • ELL was able to inhibit the planktonic growth of the Gram-positive bacteria. [ABSTRACT FROM AUTHOR]

Phenotypic plasticity and adaptive evolution enable population persistence in response to global change. However, there are few experiments that test how these processes interact within and across generations, especially in marine species with broad distributions experiencing spatially and temporally variable temperature and pCO2. We employed a quantitative genetics experiment with the purple sea urchin, Strongylocentrotus purpuratus, to decompose family-level variation in transgenerational and developmental plastic responses to ecologically relevant temperature and pCO2. Adults were conditioned to controlled non-upwelling (high temperature, low pCO2) or upwelling (low temperature, high pCO2) conditions. Embryos were reared in either the same conditions as their parents or the crossed environment, and morphological aspects of larval body size were quantified. We find evidence of family-level phenotypic plasticity in response to different developmental environments. Among developmental environments, there was substantial additive genetic variance for one body size metric when larvae developed under upwelling conditions, although this differed based on parental environment. Furthermore, cross-environment correlations indicate significant variance for genotype-by-environment interactive effects. Therefore, genetic variation for plasticity is evident in early stages of S. purpuratus, emphasizing the importance of adaptive evolution and phenotypic plasticity in organismal responses to global change. [ABSTRACT FROM AUTHOR]

Prey state and prey density mediate antipredator responses that can shift community structure and alter ecosystem processes. For example, well-nourished prey at low densities (i.e., prey with higher per capita predation risk) should respond strongly to predators. Although prey state and density often co-vary across habitats, it is unclear if prey responses to predator cues are habitat-specific. We used mesocosms to compare the habitat-specific responses of purple sea urchins (Strongylocentrotus purpuratus) to waterborne cues from predatory lobsters (Panulirus interruptus). We predicted that urchins from kelp forests (i.e., in well-nourished condition) tested at low densities typically observed in this habitat would respond more strongly to predation risk than barren urchins (i.e., in less nourished condition) tested at high densities typically observed in this habitat. Indeed, when tested at densities associated with respective habitats, urchins from forests, but not barrens, reduced kelp grazing by 69% when exposed to lobster risk cues. Barren urchins that were unresponsive to predator cues at natural, high densities suddenly responded strongly to lobster cues when conspecific densities were reduced. Strong responses of low densities of barren urchins persisted across feeding history (i.e. 0–64 days of starvation). This suggests that barren urchins can respond to predators but typically do not because of high conspecific densities. Because high densities of urchins in barrens should weaken the non-consumptive effects of lobsters, urchins in these habitats may continue to graze in the presence of predators thereby providing a feedback that maintains urchin barrens. [ABSTRACT FROM AUTHOR]

Understanding the role of animal behaviour in linking individuals to ecosystems is central to advancing knowledge surrounding community structure, stability and transition dynamics. Using 22 years of long‐term subtidal monitoring, we show that an abrupt outbreak of purple sea urchins (Strongylocentrotus purpuratus), which occurred in 2014 in southern Monterey Bay, California, USA, was primarily driven by a behavioural shift, not by a demographic response (i.e. survival or recruitment). We then tracked the foraging behaviour of sea urchins for 3 years following the 2014 outbreak and found that behaviour is strongly associated with patch state (forest or barren) transition dynamics. Finally, in 2019, we observed a remarkable recovery of kelp forests at a deep rocky reef. We show that this recovery was associated with sea urchin movement from the deep reef to shallow water. These results demonstrate how changes in grazer behaviour can facilitate patch dynamics and dramatically restructure communities and ecosystems. [ABSTRACT FROM AUTHOR]

Over the last decade, an overabundance of purple urchins (Strongylocentrotus purpuratus) that exert destructive grazing pressure on essential kelp forest habitat has caused a rapid expansion of barren grounds along the southwest coast of North America. Although the harvesting of several urchin species has led to high-value fisheries worldwide, purple urchins presently have little to no commercial value, especially in a malnourished, barren condition. Harvesting purple urchins from barrens and enhancing their roe through aquaculture has the potential to transform these destructive grazers into high-quality seafood that also benefits the ecological restoration of kelp forests. We collected purple urchins from barrens and fed them whole kelp (Macrocystis pyrifera) or two different formulations of prepared feed in a Recirculating Aquaculture System (RAS). The gonad index (GI) of urchins fed the two prepared diets doubled in 6 weeks, increased from an initial barren condition (mean GI ± SE = 6.8 ± 0.7%) to a marketable yield (GI > 15%) in 9 weeks, and was significantly greater than the GI of urchins fed kelp (11.7 ± 1.2%). Analyses of proximate constituents and amino acid composition of gonad tissue also revealed differences among the roe of urchins fed the three diets for 9 weeks. In particular, one of the two prepared feeds resulted in a significantly greater amount of bitter-tasting amino acids in enhanced gonads compared to urchins fed whole kelp, suggesting that the other prepared formulation we tested produces a more natural flavor profile. Our results highlight an untapped potential to quickly produce a highly valued seafood product from seemingly low-value purple urchins. Echinoculture could thereby serve as a tool to stimulate urchin industries that could also facilitate the restoration of kelp forests from urchin barrens. [ABSTRACT FROM AUTHOR]

Sea urchins, one of the few echinoids harvested for human consumption, are found in archaeological sites from coastal settings around the world spanning at least the past ∼15,000 years. Sea urchin tests and spines are commonly found in archaeological shell middens on California's Channel Islands, sometimes forming dense "urchin lenses." Though ubiquitous, the fragile nature of their test (outer shell) results in a high degree of fragmentation, complicating identification and quantification in archaeological assemblages. I discuss issues regarding archaeological sea urchin remains off the coast of western North America and present a method for estimating the sizes of harvested purple (Strongylocentrotus purpuratus) and red (Mesocentrotus franciscanus) sea urchins through allometry, allowing archaeologists to configure size/age estimates for harvested populations in the past. These methods are applied to two archaeological assemblages from San Nicolas and San Miguel islands, revealing evidence of a potential urchin proliferation event in the California Bight during the late Middle Holocene, and relative consistency in the primary types and sizes of harvested specimens through time. As a keystone species dominating ecological interactions in kelp forest ecosystems, sea urchin remains can provide deep historical perspective on the relative state of intertidal ecosystems. [ABSTRACT FROM AUTHOR]

The gene regulatory network (GRN) that underlies echinoderm skeletogenesis is a prominent model of GRN architecture and evolution. KirrelL is an essential downstream effector gene in this network and encodes an Ig-superfamily protein required for the fusion of skeletogenic cells and the formation of the skeleton. In this study, we dissected the transcriptional control region of the kirrelL gene of the purple sea urchin, Strongylocentrotus purpuratus. Using plasmid-and bacterial artificial chromosome-based transgenic reporter assays, we identified key cis-regulatory elements (CREs) and transcription factor inputs that regulate Sp-kirrelL, including direct, positive inputs from two key transcription factors in the skeletogenic GRN, Alx1 and Ets1. We next identified kirrelL cis-regulatory regions from seven other echinoderm species that together represent all classes within the phylum. By introducing these heterologous regulatory regions into developing sea urchin embryos we provide evidence of their remarkable conservation across ~500 million years of evolution. We dissected in detail the kirrelL regulatory region of the sea star, Patiria miniata, and demonstrated that it also receives direct inputs from Alx1 and Ets1. Our findings identify kirrelL as a component of the ancestral echinoderm skeletogenic GRN. They support the view that GRN subcircuits, including specific transcription factor–CRE interactions, can remain stable over vast periods of evolutionary history. Lastly, our analysis of kirrelL establishes direct linkages between a developmental GRN and an effector gene that controls a key morphogenetic cell behavior, cell–cell fusion, providing a paradigm for extending the explanatory power of GRNs. [ABSTRACT FROM AUTHOR]

Brachyury is a T-box family transcription factor and plays pivotal roles in morphogenesis. In sea urchin embryos, Brachyury is expressed in the invaginating endoderm, and in the oral ectoderm of the invaginating mouth opening. The oral ectoderm is hypothesized to serve as a signaling center for oral (ventral)-aboral (dorsal) axis formation and to function as a ventral organizer. Our previous results of a single-cell RNA-seq (scRNA-seq) atlas of early Strongylocentrotus purpuratus embryos categorized the constituent cells into 22 clusters, in which the endoderm consists of three clusters and the oral ectoderm four clusters (Foster et al., 2020). Here we examined which clusters of cells expressed Brachyury in relation to the morphogenesis and the identity of the ventral organizer. Our results showed that cells of all three endoderm clusters expressed Brachyury in blastulae. Based on expression profiles of genes involved in the gene regulatory networks (GRNs) of sea urchin embryos, the three clusters are distinguishable, two likely derived from the Veg2 tier and one from the Veg1 tier. On the other hand, of the four oral-ectoderm clusters, cells of two clusters expressed Brachyury at the gastrula stage and genes that are responsible for the ventral organizer at the late blastula stage, but the other two clusters did not. At a single-cell level, most cells of the two oral-ectoderm clusters expressed organizer-related genes, nearly a half of which coincidently expressed Brachyury. This suggests that the ventral organizer contains Brachyury -positive cells which invaginate to form the stomodeum. This scRNA-seq study therefore highlights significant roles of Brachyury- expressing cells in body-plan formation of early sea urchin embryos, though cellular and molecular mechanisms for how Brachyury functions in these processes remain to be elucidated in future studies. [Display omitted] • Brachyury, a T-box family transcription factor, is expressed in the invaginating endoderm, and oral ectoderm of the sea urchin • The oral ectoderm is hypothesized to serve as a ventral organizer. • By a single-cell RNA-seq (scRNA-seq) analysis early Strongylocentrotus purpuratus embryos are categorized into 22 constituent cell ​clusters. • The Brachyury -positive oral-ectodermal cell cluster showed high levels of expression of genes responsible for the oral signaling center. • Results support the model that the ventral organizer is a property of Brachyury -positive oral ectodermal cells. [ABSTRACT FROM AUTHOR]

Identifying the molecular fingerprint of organismal cell types is key for understanding their function and evolution. Here, we use single- cell RNA sequencing (scRNA- seq) to survey the cell types of the sea urchin early pluteus larva, representing an important developmental transition from non- feeding to feeding larva. We identify 21 distinct cell clusters, representing cells of the digestive, skeletal, immune, and nervous systems. Further subclustering of these reveal a highly detailed portrait of cell diversity across the larva, including the identification of neuronal cell types. We then validate important gene regulatory networks driving sea urchin development and reveal new domains of activity within the larval body. Focusing on neurons that co- express Pdx- 1 and Brn1/2/4, we identify an unprecedented number of genes shared by this population of neurons in sea urchin and vertebrate endocrine pancreatic cells. Using differential expression results from Pdx- 1 knockdown experiments, we show that Pdx1 is necessary for the acquisition of the neuronal identity of these cells. We hypothesize that a network similar to the one orchestrated by Pdx1 in the sea urchin neurons was active in an ancestral cell type and then inherited by neuronal and pancreatic developmental lineages in sea urchins and vertebrates. [ABSTRACT FROM AUTHOR]

Background: The evolutionary history of cell types provides insights into how morphological and functional complexity arose during animal evolution. Photoreceptor cell types are particularly broadly distributed throughout Bilateria; however, their evolutionary relationship is so far unresolved. Previous studies indicate that ciliary photoreceptors are homologous at least within chordates, and here, we present evidence that a related form of this cell type is also present in echinoderm larvae. Results: Larvae of the purple sea urchin Strongylocentrotus purpuratus have photoreceptors that are positioned bilaterally in the oral/anterior apical neurogenic ectoderm. Here, we show that these photoreceptors express the transcription factor Rx, which is commonly expressed in ciliary photoreceptors, together with an atypical opsin of the GO family, opsin3.2, which localizes in particular to the cilia on the cell surface of photoreceptors. We show that these ciliary photoreceptors express the neuronal marker synaptotagmin and are located in proximity to pigment cells. Furthermore, we systematically identified additional transcription factors expressed in these larval photoreceptors and found that a majority are orthologous to transcription factors expressed in vertebrate ciliary photoreceptors, including Otx, Six3, Tbx2/3, and Rx. Based on the developmental expression of rx, these photoreceptors derive from the anterior apical neurogenic ectoderm. However, genes typically involved in eye development in bilateria, including pax6, six1/2, eya, and dac, are not expressed in sea urchin larval photoreceptors but are instead co-expressed in the hydropore canal. Conclusions: Based on transcription factor expression, location, and developmental origin, we conclude that the sea urchin larval photoreceptors constitute a cell type that is likely homologous to the ciliary photoreceptors present in chordates. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are a class of small, endogenous, non‐coding RNAs that regulate gene expression through transcriptional repression of messenger RNA. They play significant roles in many physiological and biochemical processes in eukaryotes. Ocean acidification can impact the development, survival, growth and physiology of many marine organisms. Here, we performed miRNA transcriptome analysis of the sea urchin Strongylocentrotus purpuratus larvae exposed to CO2‐driven seawater acidification. We generated 10.6 and 10.8 million clean reads from the malformed S. purpuratus larva after CO2 treatment and the larvae with the normal bone development respectively. A total of 682 conserved and 17 novel miRNAs were identified. Target genes of the differential expression miRNAs were also predicted, which contained growth‐related genes (collagenase, collagen and HSP70‐binding protein 1), spicule formation‐related gene (carbonic anhydrase transcript variant X1) and skeletogenesis‐related genes (breast carcinoma amplified sequence 2). Target genes of the differentially expressed miRNAs were used to perform KEGG pathway analysis and were found to be involved in the proteasome and oxidative phosphorylation. These results provide a relatively large number of miRNAs transcriptome resource and provide a foundation for further analyses on the functional and molecular mechanisms of S. purpuratus larvae impacted by ocean acidification. [ABSTRACT FROM AUTHOR]

Marine heatwaves (MHWs) are projected to increase in intensity and frequency over the coming decades, and it is imperative to assess the adaptive capacity of marine organisms to these extreme temperature events. Given the nature of MHWs to last days to weeks in a region, these events may have overarching impacts on phenological events like reproduction and development. Here, the role of adult thermal history and transgenerational plasticity may be an important pathway by which MHWs are transduced to impact community structure. In this study, we sought to explore the effects of paternal thermal history in the purple urchin, Strongylocentrotus purpuratus, on a crucial aspect of reproduction, fertilization. Using ecologically relevant temperatures representative of both MHW events that occurred in 2014–2020 and non-MHW temperatures in our region of the California Large Marine Ecosystem, we conditioned male S. purpuratus for 28 days to either a high, MHW or a low, non-MHW temperature. Following the temperature acclimation of adults, sperm performance was tested for individual males by conducting fertilization success trials at varying temperatures and sperm concentrations. While sperm appeared robust to elevated temperature during fertilization, sperm produced by high-temperature-acclimated males had overall diminished performance as compared to those acclimated to non-MHW temperatures. These results suggest MHW events will have a negative impact on fertilization in situ for S. purpuratus populations. Furthermore, these results highlight the importance of considering both male and female environmental history in projections of reproduction under climate change scenarios. [ABSTRACT FROM AUTHOR]

Sea urchins are key grazers in coastal seas, where they can survive a variety of conditions and diets, enhancing their ecological impact on kelp forests and other ecosystems. Using 16S rRNA gene sequencing, we characterized bacterial communities associated with guts of the two dominant sea urchin species in southern California, the red urchin Mesocentrotus franciscanus, and the purple urchin Strongylocentrotus purpuratus. Our results show that the two urchin species have distinct gut microbiomes that vary with habitat. The taxonomic composition of their microbiomes suggests that they may facilitate digestion of food and be a source of nutrition themselves. These results highlight the role of microbiomes within macroorganisms as an extended ecological trait, and suggest that microbes may be crucial to resource use and partitioning in co‐occurring species. [ABSTRACT FROM AUTHOR]

Globally, kelp forests are threatened by multiple stressors, including increasing grazing by sea urchins. With coastal upwelling predicted to increase in intensity and duration in the future, understanding whether kelp forest and urchin barren urchins are differentially affected by upwelling-related stressors will give insight into how future conditions may affect the transition between kelp forests and barrens. We assessed how current and future-predicted changes in the duration and magnitude of upwelling-associated stressors (low pH, dissolved oxygen, and temperature) affected the performance of purple sea urchins (Strongylocentrotus purpuratus) sourced from rapidly-declining bull kelp (Nereocystis leutkeana) forests and nearby barrens and maintained on habitat-specific diets. Kelp forest urchins were of superior condition to barrens urchins, with ~ 6–9 times more gonad per body mass. Grazing and condition in kelp forest urchins were more negatively affected by distant-future and extreme upwelling conditions, whereas grazing and survival in urchins from barrens were sensitive to both current-day and all future-predicted upwelling, and to increases in acidity, hypoxia, and temperature regardless of upwelling. We conclude that urchin barren urchins are more susceptible to increases in the magnitude and duration of upwelling-related stressors than kelp forest urchins. These findings have important implications for urchin population dynamics and their interaction with kelp. [ABSTRACT FROM AUTHOR]

In the LT experiment, 72 H. crassispina and M. nudus were reared following the same method as in the HT experiment, exceptthattheseawatertemperaturewasdecreasedfrom14°C for H. crassispina and 15°C for M. nudus at the cooling rate of 2.5°C-week 1 .The lowest seawater temperature of the recirculatedrearingsystemsislimitedto1.5°C. Carbon(C)andnitrogen(N)contentsofthegonadsandgut Thegonadsandgutof H. crassispinaand M. nudusintheHTand LT experiments were dried at 80°C in a hot-air convection oven for 1 week and then powdered with a beads cell disrupter (Micro Smash MS-100, TOMY, Tokyo, Japan).The tissue powder was analysed by an Auto NCS analysis instrument (FLASH 2000, Thermo Fisher Scientific, Massachusetts, USA; liner regression as calibrationmethod)forCandNcontents. TheKruskal-WallistestandtheSteel- Dwass multiple comparison test were performed for the significantdifferencesin(i)the RRandLR of H. crassispina and M. nudus among temperatures in the HT experiment, (ii)theLRof H. crassispina and the RR of M. nudus among temperatures in the LT experiment,and(iii)theFRandtheCcontentsof M. nudusgutsandthe Ccontentof H.crassispinagonadsamongtemperaturesintheHT experiment. [Extracted from the article]

We seek to manipulate gene function here through CRISPR-Cas9 editing of cis-regulatory sequences, rather than the more typical mutation of coding regions. This approach would minimize secondary effects of cellular responses to nonsense mediated decay pathways or to mutant protein products by premature stops. This strategy also allows for reducing gene activity in cases where a complete gene knockout would result in lethality, and it can be applied to the rapid identification of key regulatory sites essential for gene expression. We tested this strategy here with genes of known function as a proof of concept, and then applied it to examine the upstream genomic region of the germline gene Nanos2 in the sea urchin, Strongylocentrotus purpuratus. We first used CRISPR-Cas9 to target established genomic cis-regulatory regions of the skeletogenic cell transcription factor, Alx1, and the TGF-β signaling ligand, Nodal , which produce obvious developmental defects when altered in sea urchin embryos. Importantly, mutation of cis-activator sites (Alx1) and cis-repressor sites (Nodal) result in the predicted decreased and increased transcriptional output, respectively. Upon identification of efficient gRNAs by genomic mutations, we then used the same validated gRNAs to target a deadCas9-VP64 transcriptional activator to increase Nodal transcription directly. Finally, we paired these new methodologies with a more traditional, GFP reporter construct approach to further our understanding of the transcriptional regulation of Nanos2 , a key gene required for germ cell identity in S. purpuratus. With a series of reporter assays, upstream Cas9-promoter targeted mutagenesis, coupled with qPCR and in situ RNA hybridization, we concluded that the promoter of Nanos2 drives strong mRNA expression in the sea urchin embryo, indicating that its primordial germ cell (PGC)-specific restriction may rely instead on post-transcriptional regulation. Overall, we present a proof-of-principle tool-kit of Cas9-mediated manipulations of promoter regions that should be applicable in most cells and embryos for which CRISPR-Cas9 is employed. • We seek to test gene function by CRISPR-Cas9 editing of cis-regulatory sequences. • Targeting cis-regulatory sites enables unique control over endogenous transcriptional levels. • We optimize this approach using the well annotated test genes, Alx1 and Nodal. • Specific accumulation of Nanos2 in the germ line appears largely post-transcriptional. [ABSTRACT FROM AUTHOR]

Consumer and predator foraging behavior can impart profound trait-mediated constraints on community regulation that scale up to influence the structure and stability of ecosystems. Here, we demonstrate how the behavioral response of an apex predator to changes in prey behavior and condition can dramatically alter the role and relative contribution of top-down forcing, depending on the spatial organization of ecosystem states. In 2014, a rapid and dramatic decline in the abundance of a mesopredator (Pycnopodia helianthoides) and primary producer (Macrocystis pyrifera) coincided with a fundamental change in purple sea urchin (Strongylocentrotus purpuratus) foraging behavior and condition, resulting in a spatial mosaic of kelp forests interspersed with patches of sea urchin barrens. We show that this mosaic of adjacent alternative ecosystem states led to an increase in the number of sea otters (Enhydra lutris nereis) specializing on urchin prey, a population-level increase in urchin consumption, and an increase in sea otter survivorship. We further show that the spatial distribution of sea otter foraging efforts for urchin prey was not directly linked to high prey density but rather was predicted by the distribution of energetically profitable prey. Therefore, we infer that spatially explicit sea otter foraging enhances the resistance of remnant forests to overgrazing but does not directly contribute to the resilience (recovery) of forests. These results highlight the role of consumer and predator trait-mediated responses to resource mosaics that are common throughout natural ecosystems and enhance understanding of reciprocal feedbacks between top-down and bottom-up forcing on the regional stability of ecosystems. [ABSTRACT FROM AUTHOR]

In marine ecosystems, fishing often targets predators, which can drive direct and indirect effects on entire food webs. Marine reserves can induce trophic cascades by increasing predator density and body size, thereby increasing predation pressure on populations of herbivores, such as sea urchins. In California's northern Channel Islands, two species of sea urchins are abundant: the red urchin Mesocentrotus franciscanus, which is targeted by an economically valuable fishery, and the virtually unfished purple urchin Strongylocentrotus purpuratus. We hypothesized that urchin populations inside marine reserves would be depressed by higher predation, but that red urchins would be less affected due to fishing outside reserves. Instead, our analyses revealed that purple urchin populations were unaffected by reserves, and red urchin biomass significantly increased in response to protection. Therefore, urchin biomass overall has increased inside reserves, and we found no evidence that giant kelp is positively affected by reserves. Our results reveal the overwhelming direct effect of protecting fished species in marine reserves over indirect effects that are often predicted but seldom clearly documented. Indirect effects due to marine reserves may eventually occur in some cases, but very effective predators, large reserves or extended time periods may be needed to induce them. [ABSTRACT FROM AUTHOR]

Widespread decline in underwater forests, formed by kelps and other macroalgae, is occurring in all oceans. Loss of the vulnerable surface canopy typically leads to alternate rocky reef states dominated by substrate-near, understory vegetation, or reefs without any large fleshy macroalgae such as sea urchin barrens. Such alternate reef states represent a major shift in food availability and quality, and may impact kelp-preferring grazers forced to rely on less nutritious foods. Here we investigate the physiological responses of grazers to changes in food quality and quantity. We quantify the mass-independent oxygen consumption (ṀO 2), as a proxy of whole-organism physiology, of four grazing invertebrate species (two sea urchins: Mesocentrotus franciscanus and Strongylocentrotus purpuratus ; and two gastropods: Pomaulax gibberosus and Tegula pulligo) provisioned with one of three diet treatments over seven weeks: 1) higher quality, canopy kelp, 2) lower quality, substrate-near kelp, or 3) restricted: no kelp. We further test for differences in the heat resistance of four grazers using an acute, near-lethal heat exposure after completion of the provisioning period. Food restrictions had the strongest influence on oxygen consumption in the two urchins (mass-independent ṀO 2 was reduced by 26–78%). By contrast, the two gastropod grazers did not display metabolic depression under food restrictions. Although kelp restrictions had clear physiological consequences in sea urchins, overall, the type of kelp provisioned (Macrocystis and Saccharina) did not relate to oxygen consumption after seven weeks. While heat resistance was also similar across food treatments, unfed individuals showed a slight tendency for lower heat tolerance compared to fed individuals. These results suggest a weak coupling between heat resistance and food quality and quantity, at least for these species and at short time spans. Our work highlights the importance of diet diversity and metabolic depression as strategies to cope with the energetic costs of warming. • Kelp availability influences grazers metabolic strategy and heat stress tolerance. • Sea urchins depressed metabolism when kelp was unavailable. • Strategies such as metabolic depression may allow urchins to persist in barrens. • Heat resistance was decoupled from metabolic performance and kelp food source. • Lack of food may reduce heat tolerance in subtidal grazers. [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]

Sea urchins are voracious herbivores that influence the ecological structure and function of nearshore ecosystems throughout the world. Like many species that produce planktonic larvae, their recruitment is thought to be particularly sensitive to climatic fluctuations that directly or indirectly affect adult reproduction and larval transport and survival. Yet how climate alters sea urchin populations in space and time by modifying larval recruitment and year‐class strength on the time‐scales that regulate populations remains understudied. Using a, spatially replicated weekly‐biweekly data set spanning 27 yr and 1100 km of coastline, we characterized seasonal, interannual, and spatial patterns of larval settlement of the purple sea urchin (Strongylocentrotus purpuratus). We show that large spatial differences in temporal patterns of larval settlement were associated with different responses to fluctuations in ocean temperature and climate. Importantly, we found a strong correlation between larval settlement and regional year class strength suggesting that such temporal and spatial variation in settlement plays an important role in controlling population dynamics. These results provide strong evidence over extensive temporal and spatial domains that climatic fluctuations shape broad‐scale patterns of larval settlement and subsequent population structure of an important marine herbivore known to control the productivity, community state, and provisioning services of marine ecosystems. [ABSTRACT FROM AUTHOR]

Identifying cell states during development from their mRNA profiles provides insight into their gene regulatory network. Here, we leverage the sea urchin embryo for its well-established gene regulatory network to interrogate the embryo using single cell RNA sequencing.We tested eight developmental stages in Strongylocentrotus purpuratus, from the eight-cell stage to late in gastrulation.We used these datasets to parse out 22major cell states of the embryo, focusing on key transition stages for cell type specification of each germ layer. Subclustering of these major embryonic domains revealed over 50 cell states with distinct transcript profiles. Furthermore, we identified the transcript profile of two cell states expressing germ cell factors, one we conclude represents the primordial germ cells and the other state is transiently present during gastrulation. We hypothesize that these cells of the Veg2 tier of the early embryo represent a lineage that converts to the germ line when the primordial germ cells are deleted. This broad resource will hopefully enable the community to identify other cell states and genes of interest to expose the underpinning of developmental mechanisms. [ABSTRACT FROM AUTHOR]

Cells bearing pigment have diverse roles and are often under strict evolutionary selection. Here, we explore the regulation of pigmented cells in the purple sea urchin Strongylocentrotus purpuratus, an emerging model for diverse pigment function. We took advantage of single cell RNA-seq (scRNAseq) technology and discovered that pigment cells in the embryo segregated into two distinct populations, a mitotic cluster and a post-mitotic cluster. Gcm is essential for expression of several genes important for pigment function, but is only transiently expressed in these cells. We discovered unique genes expressed by pigment cells and test their expression with double fluorescence in situ hybridization. These genes include new members of the fmo family that are expressed selectively in pigment cells of the embryonic and in the coelomic cells of the adult - both cell-types having immune functions. Overall, this study identifies nodes of molecular intersection ripe for change by selective evolutionary pressures. [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]

The effects of increasing soya bean lecithin (SL) levels (0%, 2% and 4% of diet dry matter, DM) at two fish oil (FO) levels (0% and 3% DM) on gonad index, colour and biochemical composition of Strongylocentrotus purpuratus were evaluated using a 3 × 2 factorial design with six iso‐nitrogenous formulated diets. All diets generated an increase in gonad index of more than 9%. Dietary FO had a positive effect on diet digestibility and accumulation of proteins in the gonad. Soy lecithin did not affect gonad composition, but improved its coloration, decreased gonad feed conversion ratio and increased gonad protein efficiency. There was a clear effect of diets on sea urchins gonad protein, ash and fatty acid content, in particular, decreasing the n‐3/n‐6 ratio associated with a decrease in 20:5n‐3 when SL levels increased. Nevertheless, 22:6n‐3 levels increased by week 12 in all treatments, and diets with SL increased the content of 20:4n‐6 in gonads. A decrease in bitter‐tasting amino acids such as histidine, cysteine, valine and methionine was observed in all treatments with a concomitant increase in isoleucine levels. We recommend using a diet containing 3% of FO and 2% of SL to increase food consumption, diet digestibility, improving marketable gonad colour and an increasing gonad n‐6 fatty acids and C22:6n‐3. In addition, the present study paves the way for future research in the use of FO and SL as an additive in diets for S. purpuratus towards the goal of increasing gonad size and nutritional quality. [ABSTRACT FROM AUTHOR]

Embryonic development is arguably the most complex process an organism undergoes during its lifetime, and understanding this complexity is best approached with a systems-level perspective. The sea urchin has become a highly valuable model organism for understanding developmental specification, morphogenesis, and evolution. As a non-chordate deuterostome, the sea urchin occupies an important evolutionary niche between protostomes and vertebrates. Lytechinus variegatus (Lv) is an Atlantic species that has been well studied, and which has provided important insights into signal transduction, patterning, and morphogenetic changes during embryonic and larval development. The Pacific species, Strongylocentrotus purpuratus (Sp), is another well-studied sea urchin, particularly for gene regulatory networks (GRNs) and cis -regulatory analyses. A well-annotated genome and transcriptome for Sp are available, but similar resources have not been developed for Lv. Here, we provide an analysis of the Lv transcriptome at 11 timepoints during embryonic and larval development. Temporal analysis suggests that the gene regulatory networks that underlie specification are well-conserved among sea urchin species. We show that the major transitions in variation of embryonic transcription divide the developmental time series into four distinct, temporally sequential phases. Our work shows that sea urchin development occurs via sequential intervals of relatively stable gene expression states that are punctuated by abrupt transitions. • L. variegatus transcriptome was sequenced at 11 timepoints • Gene expression changes are temporally punctuated rather than smooth. • Punctuated ​gene expression changes occur at key developmental transitions including hatching and gastrulation [ABSTRACT FROM AUTHOR]

Determination of the median effective concentration (EC50) of Cu on Mytilus galloprovincialis larvae by diffusive gradient in thin films (DGT) has been shown to effectively reduce the need to consider dissolved organic carbon (DOC) concentration and quality. A standard toxicity test protocol was used to validate previously modeled protective effects, afforded to highly sensitive marine larvae by ligand competition, in 5 diverse site waters. The results demonstrate significant narrowing of M. galloprovincialis toxicological endpoints, where EC50s ranged from 3.74 to 6.67 μg/L as CDGT Cu versus 8.76 to 26.8 μg/L as dissolved Cu (CuDISS) over a DOC range of 0.74 to 3.11 mg/L; Strongylocentrotus purpuratus EC50s were 10.5 to 19.3 μg/L as CDGT Cu versus 22.7 to 67.1 μg/L as CuDISS over the same DOC range. The quality of DOC was characterized by fluorescence excitation and emission matrices. The results indicate that the heterogeneity of competing Cu binding ligands, in common marine waters, minimizes the need for class determinations toward explaining the degree of protection. Using conservative assumptions, an M. galloprovincialis CDGT Cu EC50 of 3.7 µg/L and corresponding criterion maximum concentration CDGT Cu of 1.8 µg/L, for universal application by regulatory compliance‐monitoring programs, are proposed as a superior approach toward both integration of dynamic water quality over effective exposure periods and quantification of biologically relevant trace Cu speciation. Environ Toxicol Chem 2020;39:873–881. © 2020 SETAC [ABSTRACT FROM AUTHOR]

Fasting has been shown to increase longevity and alter immune function in a variety of animals, but little is understood about how reduced caloric intake may impact regeneration and infections in animals that must regularly repair and regenerate tissue in marine environments that contain high levels of bacteria. We examined the possibility that fasting could enhance spine regeneration and reduce bacteremia in the purple sea urchin Strongylocentrotus purpuratus. A small number of spines were removed from urchins and rates of spine regrowth and levels of culturable bacteria from the coelomic fluid were measured for 21 days in fed and fasted urchins. Fasted urchins had higher rates of spine regrowth and lower levels of colony-forming units (CFU) per milliliter of coeolomic fluid. The predominant bacteria in the coelomic fluid was isolated and identified by DNA sequence-based methods as Vibrio cyclitrophicus. After 21 days, fasted and fed urchins were injected with V. cyclitrophicus. Two hours after injection, fed urchins had about 25% more culturable bacteria remaining in their coelomic fluid compared to fasted urchins. We found no evidence that fasting altered coelomic fluid cell number or righting response, indicators of physiologic and behavioral stress in urchins. Our results demonstrate that V. cyclitrophicus is present in purple urchin coelomic fluid, that fasting can increase spine regeneration and that fasted urchins have much lower levels of culturable bacteria in their coelomic fluid than fed urchins. Overall, our data suggests that fasting may ultimately reduce bacteremia and infection in injured or damaged urchins. [ABSTRACT FROM AUTHOR]

Temporally consistent individual differences in behavior impact many ecological processes. We simultaneously examined the effects of individual variation in prey activity level, covering behavior, and body size on prey survival with predators using an urchin–lobster system. Specifically, we tested the hypothesis that slow‐moving purple sea urchins (Strongylocentrotus purpuratus) and urchins who deploy extensive substrate (pebbles and stones) covering behavior will out‐survive active urchins that deploy little to no covering behavior when pitted against a predator, the California spiny lobster (Panulirus interruptus). We evaluated this hypothesis by first confirming whether individual urchins exhibit temporally consistent differences in activity level and covering behavior, which they did. Next, we placed groups of four urchins in mesocosms with single lobster and monitored urchin survival for 108 hr. High activity level was negatively associated with survival, whereas urchin size and covering behavior independently did not influence survival. The negative effect of urchin activity level on urchin survival was strong for smaller urchins and weaker for large urchins. Taken together, these results suggest that purple urchin activity level and size jointly determine their susceptibility to predation by lobsters. This is potentially of great interest, because predation by recovering lobster populations could alter the stability of kelp forests by culling specific phenotypes, like foraging phenotypes, from urchin populations. [ABSTRACT FROM AUTHOR]

Transgenerational plasticity occurs when the conditions experienced by the parental generation influence the phenotype of their progeny. This may in turn affect progeny performance and physiological tolerance, providing a means by which organisms cope with rapid environmental change. We conditioned adult purple sea urchins, Strongylocentrotus purpuratus , to combined p CO 2 and temperature conditions reflective of in situ conditions of their natural habitat, the benthos in kelp forests of nearshore California, and then assessed the performance of their progeny raised under different p CO 2 levels. Adults were conditioned during gametogenesis to treatments that reflected static non-upwelling (~650 μatm p CO 2 , ~17 °C) and upwelling (~1300 μatm p CO 2 , ~13 °C) conditions. Following approximately 4 months of conditioning, the adults were spawned and embryos were raised under low p CO 2 (~450 μatm p CO 2) or high p CO 2 (~1050 μatm p CO 2) treatments to determine if differential maternal conditioning impacted the progeny response to a single abiotic stressor: p CO 2. We examined the size, protein content, and lipid content of eggs from both sets of conditioned female urchins. Offspring were sampled at four stages of early development: hatched blastula, gastrula, prism, and echinopluteus. This resulted in four sets of offspring: (1) progeny from non-upwelling-conditioned mothers raised under low p CO 2 , (2) progeny from non-upwelling-conditioned mothers raised under high p CO 2 , (3) progeny from upwelling-conditioned mothers raised under low p CO 2 , and (4) progeny from upwelling-conditioned mothers raised under high p CO 2. We then assessed the effects of maternal conditioning along with the effects of developmental p CO 2 levels on body size of the progeny. Our results showed that differential maternal conditioning had no impact on average egg size, although non-upwelling females produced eggs that were more variable in size. Maternal conditioning did not affect protein content but did have a modest impact on egg lipid content. Developing embryos whose mothers were conditioned to simulated upwelling conditions (~1300 μatm p CO 2 , ~13 °C) were greater in body size, although this effect was no longer evident at the echinopluteus larval stage. Although maternal conditioning affected offspring body size, the p CO 2 levels under which the embryos were raised did not. Overall, this laboratory study provides insight into how transgenerational effects may function in nature. The impacts of parental environmental history on progeny phenotype during early development have important implications regarding recruitment success and population-level effects. • Differential maternal conditioning did not affect egg size or protein content. • Simulated upwelling conditions increased maternal provisioning of lipids to eggs. • Maternal conditioning to simulated upwelling increased embryo body size. [ABSTRACT FROM AUTHOR]

Phenotypic plasticity, within and across generations, is a strategy by which organisms can respond rapidly to environmental change. Epigenetic modifications, such as DNA methylation, have been proposed to be involved in phenotypic plasticity. We examined the potential for the environment to mediate both transgenerational and intragenerational plasticity in DNA methylation and phenotypes in early stages of the purple sea urchin, Strongylocentrotus purpuratus , an ecologically important herbivore in kelp forest ecosystems. This approach involved a controlled laboratory experiment where adult urchins were acclimated during gametogenesis to upwelling (~1300 μatm p CO 2 & 13 °C) or non-upwelling (~650 μatm p CO 2 & 17 °C) conditions that are representative of their kelp forest habitat. Progeny from these adults were raised in either high (~1050 μatm) or low (~450 μatm) p CO 2 treatments and sampled at three developmental stages. Differences in condition experienced by mothers were associated with differentially methylated genes in the offspring. However, differences in developmental conditions corresponded to little observable effects on gene methylation in the progeny. Variation in gene body methylation across treatments was correlated with body size of the embryos and larvae, illustrating a potential link between transgenerational phenotypic plasticity and DNA methylation. Overall, our results suggest that epigenetic factors such as DNA methylation have the potential to contribute to phenotypic plasticity in a transgenerational framework, and further, that epigenetic processes may act as a mechanism of rapid response to environmental change. • Maternal environment impacts DNA methylation of early stage offspring. • Developmental environment has a minimal impact on DNA methylation. • DNA methylation differences across developmental stages are minimal. • Differences in DNA methylation is associated with body size of embryos. [ABSTRACT FROM AUTHOR]

Sea urchin larvae reduce developmental rates accompanied by changes in their energy budget when exposed to acidified conditions. The necessity to maintain highly alkaline conditions in their digestive systems led to the hypothesis that gastric pH homeostasis is a key trait affecting larval energy budgets leading to distinct tipping points for growth and survival. To test this hypothesis, sea urchin (Strongylocentrotus purpuratus) larvae were reared for 10 days in different pH conditions ranging from pH 7.0 to pH 8.2. Survival, development and growth rates were determined demonstrating severe impacts < pH 7.2. To test the effects of pH on midgut alkalization we measured midgut pH and monitored the expression of acid-base transporters. While larvae were able to maintain their midgut pH at 8.9-9.1 up to an acidification level of pH 7.2, midgut pH was decreased in the lower pH treatments. The maintenance of midgut pH under low pH conditions was accompanied by dynamic changes in the expression level of midgut acid-base transporters. Metabolic rates of the larvae increased with decreasing pH and reached a threshold between pH 7.0 and pH 7.3 where metabolic rates decreased again. Methylation analyses on promoter CpG islands were performed for midgut acid-base transporter genes to test for possible epigenetic modifications after 10-day exposure to different pH conditions. This analysis demonstrated no correlation between methylation level and pH treatments suggesting low potential for epigenetic modification of acid-base transporters upon short-term exposure. Since a clear tipping point was identified at pH 7.2, which is much lower than near-future ocean acidification (OA) scenarios, this study suggests that the early development of the purple sea urchin larva has a comparatively high tolerance to seawater acidification with substantial acclimation capacity and plasticity in a key physiological trait under near-future OA conditions. • We determined the sensitivity thresholds for survival development and growth in sea urchin larvae exposed to acidified conditions. • Determination of midgut pH, metabolic rates and expression of acid-base transporters demonstrates a physiological tipping point at pH 7.2. • This work demonstrates substantial resilience of an important environmental engineer to the ongoing phenomenon of ocean acidification. [ABSTRACT FROM AUTHOR]

Detritus can fundamentally shape and sustain food webs, and shredders can facilitate its availability. Most of the biomass of the highly productive giant kelp, Macrocystis pyrifera, becomes detritus that is exported or falls to the seafloor as litter. We hypothesized that sea urchins process kelp litter through shredding, sloppy feeding and egestion, making kelp litter more available to benthic consumers. To test this, we conducted a mesocosm experiment in which an array of kelp forest benthic consumers were exposed to 13C- and 15N-labelled Macrocystis with or without the presence of sea urchins, Strongylocentrotus purpuratus. Our results showed that several detritivore species consumed significant amounts of kelp, but only when urchins were present. Although they are typically portrayed as antagonistic grazers in kelp forests, sea urchins can have a positive trophic role, capturing kelp litter before it is exported and making it available to a suite of benthic detritivores. [ABSTRACT FROM AUTHOR]