Archaeocytes in sponges: simple cells of complicated fate

Archaeocytes are considered a key cell type in sponges (Porifera). They are believed to be multifunctional cells performing various functions, from nutrient digestion to acting as adult stem cells (ASCs). Thus, archaeocytes are mentioned in discussions on various aspects of sponge biology. As presumed ASCs of an early-diverged animal taxon, archaeocytes are of great fundamental interest for further progress in understanding tissue functioning in metazoans. However, the term 'archaeocyte' is rather ambiguous in its usage and understanding, and debates surrounding archaeocytes have persisted for over a century, reflecting the ongoing complexity of understanding their nature. This article presents a comprehensive revision of the archaeocyte concept, including both its historical development and biological features (i.e. taxonomic distribution, characteristics, and functions). The term 'archaeocyte' and its central aspects were introduced as early as the end of the 19th century based on data mainly from demosponges. Remarkably, despite the general lack of comparative and non-histological data, these early studies already regarded archaeocytes as the ASCs of sponges. These early views were readily inherited by subsequent studies, often without proper verification, shaping views on many aspects of sponge biology for more than a century. Taking into account all available data, we propose considering the archaeocytes as a cell type specific to the class Demospongiae. Clear homologues of archaeocytes are absent in other sponge classes. In demosponges, the term 'archaeocytes' refers to mesohyl cells that have an amoeboid shape, nucleolated nuclei, and non-specific inclusions in the cytoplasm. The absence of specific traits makes the archaeocytes a loosely defined and probably heterogeneous cell population, rendering the exhaustive characterisation of the 'true' archaeocyte population impossible. At the same time, the molecular characterisation of archaeocytes is only beginning to develop. Stemness and almost unlimited potency have always been at the core of the traditional archaeocyte concept. However, currently, the most consistent data on archaeocyte stem cell function come only from developing gemmules of freshwater sponges. For tissues of adult demosponges, the data favour a two-component stem cell system, in which archaeocytes may cooperate with another stem cell population, choanocytes. Simultaneously, cells with archaeocyte morphology function as macrophages in demosponges, participating in the food digestion cycle and immune defence. Such cells should be denoted with the more neutral term 'nucleolar amoebocytes', as the term 'archaeocyte' not only describes the morphology of a cell but also introduces the proposition of its stem nature. Thus, the future usage of the term 'archaeocyte' should be limited to cases where a cell is shown or at least presumed to be a stem cell.

The Octocoral Trait Database: a global database of trait information for octocoral species

Trait-based approaches are revolutionizing our understanding of high-diversity ecosystems by providing insights into the principles underlying key ecological processes, such as community assembly, species distribution, resilience, and the relationship between biodiversity and ecosystem functioning. In 2016, the Coral Trait Database advanced coral reef science by centralizing trait information for stony corals (i.e., Subphylum Anthozoa, Class Hexacorallia, Order Scleractinia). However, the absence of trait data for soft corals, gorgonians, and sea pens (i.e., Class Octocorallia) limits our understanding of ecosystems where these organisms are significant members and play pivotal roles. To address this gap, we introduce the Octocoral Trait Database, a global, open-source database of curated trait data for octocorals. This database houses species- and individual-level data, complemented by contextual information that provides a relevant framework for analyses. The inaugural dataset, OctocoralTraits v2.2, contains over 97,500 global trait observations across 98 traits and over 3,500 species. The database aims to evolve into a steadily growing, community-led resource that advances future marine science, with a particular emphasis on coral reef research.

The molecular basis of octocoral calcification revealed by genome and skeletal proteome analyses

The ability of octocorals and stony corals to deposit calcium carbonate (CaCO3) has contributed to their ecological success. Whereas stony corals possess a homogeneous aragonite skeleton, octocorals have developed distinct skeletal structures composed of different CaCO3 polymorphs and a skeletal organic matrix. Nevertheless, the molecular basis of skeletal structure formation in octocorals remains inadequately understood. Here, we sequenced the genomes and skeletal proteomes of two calcite-forming octocorals, namely Paragorgia papillata and Chrysogorgia sp. The assembled genomes sizes were 618.13 Mb and 781.04 Mb for P. papillata and Chrysogorgia sp., respectively, with contig N50s of 2.67 Mb and 2.61 Mb. Comparative genomic analyses identified 162 and 285 significantly expanded gene families in the genomes of P. papillata and Chrysogorgia sp., respectively, which are primarily associated with biomineralization and immune response. Furthermore, comparative analyses of skeletal proteomes demonstrated that corals with different CaCO3 polymorphs share a fundamental toolkit comprising cadherin, von Willebrand factor type A, and carbonic anhydrase domains for calcified skeleton deposition. In contrast, collagen is abundant in the calcite-forming octocoral skeletons but occurs rarely in aragonitic stony corals. Additionally, certain collagens have developed domains related to matrix adhesion and immunity, which may confer novel genetic functions in octocoral calcification. These findings enhance our understanding of the diverse forms of coral biomineralization processes and offer preliminary insights into the formation and evolution of the octocoral skeleton.

An Improved RNA Extraction Method for Octocorals and Its Application in Transcriptome Analysis of Dark-Induced Bleaching Octocoral

Octocorals, vital components of reef ecosystems, inhabit various marine environments across diverse climate zones, spanning from tropical shallows to frigid deep-sea regions. Certain octocoral species, notably Lobophytum and Sinularia, are particularly intriguing due to their production of diverse metabolites, warranting continuous investigation. Although octocorals played the roles in coral ecosystems, the studies are rare in comparison to scleractinian corals, especially in transcriptomic and genomic data. However, RNA extraction was massively interfered by the polysaccharides and secondary metabolites produced from octocoral holobiont. For this purpose, five lysis buffer systems and two extraction processes were examined for the RNA extraction efficiency in octocorals. We found CTAB/10%SDS as a new method for RNA extraction from six different octocoral genera. Furthermore, our new method is enable to extract RNA with good quality for downstream application such as quantitative PCR and RNA sequencing. Finally, comparative transcriptomic analysis between healthy octocorals and those dark-induced bleaching corals in Lobophytum hsiehi revealed extracellular matrix and immunity-related genes may play the important roles in coral-symbiodinium symbiosis. We believe that this study's findings and the developed RNA extraction method will serve as valuable references for future research, particularly in octocorals.

Exploring the trends of adaptation and evolution of sclerites with regards to habitat depth in sea pens

Octocorals possess sclerites, small elements comprised of calcium carbonate (CaCO₃) that are important diagnostic characters in octocoral taxonomy. Among octocorals, sea pens comprise a unique order (Pennatulacea) that live in a wide range of depths. Habitat depth is considered to be important in the diversification of octocoral species, but a lack of information on sea pens has limited studies on their adaptation and evolution across depth. Here, we aimed to reveal trends of adaptation and evolution of sclerite shapes in sea pens with regards to habitat depth via phylogenetic analyses and ancestral reconstruction analyses. Colony form of sea pens is suggested to have undergone convergent evolution and the loss of axis has occurred independently across the evolution of sea pens. Divergences of sea pen taxa and of sclerite forms are suggested to depend on habitat depths. In addition, their sclerite forms may be related to evolutionary history of the sclerite and the surrounding chemical environment as well as water temperature. Three-flanged sclerites may possess the tolerance towards the environment of the deep sea, while plate sclerites are suggested to be adapted towards shallower waters, and have evolved independently multiple times. The common ancestor form of sea pens was predicted to be deep-sea and similar to family Pseudumbellulidae in form, possessing sclerites intermediate in form to those of alcyonaceans and modern sea pens such as spindles, rods with spines, and three-flanged sclerites with serrated edges sclerites, as well as having an axis and bilateral traits.

Crystallographic control of the fabrication of an extremely sophisticated shell surface microornament in the glass scallop Catillopecten

The external surface microornament of the glass scallops Catillopecten natalyae and malyutinae is made by calcitic spiny projections consisting of a stem that later divides into three equally spaced and inclined branches (here called aerials). C. natalyae contains larger and smaller aerials, whereas C. malyutinae only secreted aerials of the second type. A remarkable feature is that aerials within each type are fairly similar in size and shape and highly co-oriented, thus constituting a most sophisticated microornament. We demonstrate that aerials are single crystals whose morphology is strongly controlled by the crystallography, with the stem being parallel to the c-axis of calcite, and the branches extending along the edges of the {104} calcite rhombohedron. They grow epitaxially onto the foliated prisms of the outer shell layer. The co-orientation of the prisms explains that of the aerials. We have developed a model in which every aerial grows within a periostracal pouch. When this pouch reaches the growth margin, the mantle initiates the production of the aerial. Nevertheless, later growth of the aerial is remote, i.e. far from the contact with the mantle. We show how such an extremely sophisticated microornament has a morphology and co-orientation which are determined by crystal growth.

Predicting habitat suitability and range shifts under projected climate change for two octocorals in the north-east Atlantic

Species distribution models have become a valuable tool to predict the distribution of species across geographic space and time. In this study, maximum entropy models were constructed for two temperate shallow-water octocoral species, the pink sea fan (Eunicella verrucosa) and dead man's fingers (Alcyonium digitatum), to investigate and compare habitat suitability. The study area covered the north-east Atlantic from the Bay of Biscay to the British Isles and southern Norway; this area includes both the northern range of E. verrucosa and the middle-northern range of A. digitatum. The optimal models for each species showed that, overall, slope, temperature at the seafloor and wave orbital velocity were important predictors of distribution in both species. Predictions of habitat suitability showed areas of present-day (1951-2000) suitable habitat where colonies have not yet been observed, particularly for E. verrucosa, where areas beyond its known northern range limit were identified. Moreover, analysis with future layers (2081-2100) of temperature and oxygen concentration predicted a sizable increase in habitat suitability for E. verrucosa beyond these current range limits under the Representative Concentration Pathway 8.5 scenario. This suggests that projected climate change may induce a potential range expansion northward for E. verrucosa, although successful colonisation would also be conditional on other factors such as dispersal and interspecific competition. For A. digitatum, this scenario of projected climate change may result in more suitable habitat in higher latitudes, but, as with E. verrucosa, there is a degree of uncertainty in the model predictions. Importantly, the results from this study highlight present-day areas of high habitat suitability which, if combined with knowledge on population density, could be used to identify priority areas to enhance protection and ensure the long-term survival of these octocoral species in the region.