Sponges are key ecosystem engineers that shape, structure and enhance the biodiversity of marine benthic communities globally. Sponge aggregations and reefs are recognized as vulnerable marine ecosystems (or VMEs) due to their susceptibility to damage from bottom-contact fishing gears. Ensuring their long-term sustainability, preservation, and ecosystem functions requires the implementation of sound scientific conservation tools. Here, the genetic diversity, structure, and connectivity of the deep-sea glass sponge, Vazella pourtalesii (Schmidt, 1870), was investigated using 1,102 neutral SNPs obtained in RADseq. This species is distributed across the northwest Atlantic from Florida, USA to Nova Scotia, Canada and we sequenced samples covering this full distribution and provided evidence of strong genetic structure with two distinct clusters: Florida together with the Carolina Shelves and the Scotian Shelf. We estimated moderate levels of diversity with low migration across large distances (> 1000 kms) and high connectivity at smaller scales (< 300 kms). Further, fishing pressure on genetic diversity was evaluated, within two Sponge Conservation Areas (SCAs) on the Scotian Shelf. Those areas have different disturbance histories, and cumulative fishing pressure. Slightly lower levels of genetic diversity were found inside the SCAs, and yet they encompassed a high proportion of the diversity observed within the Scotian Shelf. We provide baseline data for future monitoring of the SCAs, discussing our findings in the light of existing area-based management tools.

We present a genome assembly from a specimen of Xestospongia muta (Caribbean barrel sponge; Porifera; Demospongiae; Haplosclerida; Petrosiidae). The genome sequence has a total length of 158.52 megabases. Most of the assembly (99.56%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.99 kilobases in length. Several symbiotic bacterial genomes were assembled as MAGs, including Candidatus Poribacteria species, Candidatus Latescibacteria, Acidobacteriota, Actinomycetota Gemmatimonadota, multiple Chloroflexota and the archaeon Nitrosopumilus. Gene annotation of this assembly on Ensembl identified 20,220 protein-coding genes.

After more than four decades, the field of sponge biotechnology has finally overcome its most formidable obstacle: establishing a sponge cell line. Cells from the deep water marine sponge Geodia barretti divide rapidly and continuously in optimized nutrient media, clearing the path for new lines of research--whether to uncover how multicellular life evolved from unicellular organisms, study the origins of animal-microbe symbiosis, or develop production strains to industrialize new sponge-derived drugs and exploit the untapped biotechnological potential of the Porifera. Now is an exciting time in sponge biotechnology, so what's next?

We present a genome assembly from a specimen of Xestospongia muta (Caribbean barrel sponge; Porifera; Demospongiae; Haplosclerida; Petrosiidae). The genome sequence has a total length of 158.52 megabases. Most of the assembly (99.56%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.99 kilobases in length. Several symbiotic bacterial genomes were assembled as MAGs, including Candidatus Poribacteria species, Candidatus Latescibacteria, Acidobacteriota, Actinomycetota Gemmatimonadota, multiple Chloroflexota and the archaeon Nitrosopumilus. Gene annotation of this assembly on Ensembl identified 20,220 protein-coding genes.

Although cell cultures from marine invertebrates have great potential as valuable tools in various scientific fields, nearly all attempts to culture these cells in vitro have consistently failed, and the reasons for this remain unclear. The ongoing failure to develop stable, long-term cell cultures from marine invertebrates, despite varied species and methods employed, highlights significant knowledge gaps in understanding their in vitro requirements. These gaps impede progress, underscoring the complexity of marine invertebrate cells and the need for innovative approaches to overcome challenges in the field. When reviewing recent literature on the key data deficiencies and challenges behind the failure to develop marine invertebrate cell cultures, we identified and discussed four major knowledge gaps: (1) optimizing culture media, (2) strategies to extend stemness of isolated cells, (3) using "omics" to enhance cell culture, and (4) selecting suitable cell types for in vitro cultures. Bridging these gaps is crucial for advancing marine invertebrate cell culture systems. Yet, given the current state-of-the-art, addressing these gaps and advancing the discipline necessitate comprehensive, integrated, and species- or cell-specific strategies, along with close collaboration among laboratories working on diverse species.

Coral reefs are threatened by recurrent mortality incidents in their native habitats brought on by natural and anthropogenic stressors. Elevated temperature has been indicated as a major causing factor. Although ongoing research is focused on corals, sponges are an important benthic organism on coral reefs and are often overlooked. An accurate and standardized method is needed to determine the environmental limits and thresholds of sponges commonly found on coral reefs. We established an in vitro sponge cell model and evaluated the effect of elevated temperatures on primary cell cultures of five common Florida reef sponges-Agelas clathrodes, Aplysina fulva, Cliona varians, Geodia neptuni, and Xestospongia muta. Analysis of the results revealed that the impact of increased temperatures had no significant effect at the cellular level, but there are changes at the molecular level. Shifts in the sponges' transcriptomic profiles induced by increased temperatures, trigger processes related to signal transduction, apoptosis, and cell repair pathways. Further elevation of temperature corresponding to local extremes activated the immune response and programmed cell death. The results of the present study are based on both cellular and molecular data obtained from the in vitro cell model which highlight the minimal response of all five species to thermal stress, providing an insight into the mechanisms involved in the adaptive process. Furthermore, they suggest a resilience of these sponges to the current thermal extremes, but a combination of factors could still lead to a loss of sponges on reefs. This study forms the basis for use of in vitro sponge cell models to evaluate other environmental parameters and stressors on additional sponge species.

Sponges (Porifera) contain many peptide-specialized metabolites with potent biological activities and significant roles in shaping marine ecology. It is well established that symbiotic bacteria produce bioactive "sponge" peptides, both on the ribosome (RiPPs) and nonribosomally. Here, we demonstrate that sponges themselves also produce many bioactive macrocyclic peptides, such as phakellistatins and related proline-rich macrocyclic peptides (PRMPs). Using the Stylissa carteri sponge transcriptome, methods were developed to find sequences encoding 46 distinct RiPP-type core peptides, of which ten encoded previously identified PRMP sequences. With this basis set, the genome and transcriptome of the sponge Axinella corrugata was interrogated to find 35 PRMP precursor peptides encoding 31 unique core peptide sequences. At least 11 of these produced cyclic peptides that were present in the sponge and could be characterized by mass spectrometry, including stylissamides A-D and seven previously undescribed compounds. Precursor peptides were encoded in the A. corrugata genome, confirming their animal origin. The peptides contained signal peptide sequences and highly repetitive recognition sequence-core peptide elements with up to 25 PRMP copies in a single precursor. In comparison to sponges without PRMPs, PRMP sponges are incredibly enriched in potentially secreted polypeptides, with >23,000 individual signal peptide encoding genes found in a single transcriptome. The similarities between PRMP biosynthetic genes and neuropeptides in terms of their biosynthetic logic suggest a fundamental biology linked to circular peptides, possibly indicating a widespread and underappreciated diversity of signaling peptide post-translational modifications across the animal kingdom.

Background Deucravacitinib is a first-in-class, oral, selective, allosteric TYK2 inhibitor approved in multiple countries for treatment of adults with plaque psoriasis. In PAISLEY, a 48-week, phase 2, randomized controlled trial (NCT03252587) that assessed deucravacitinib in patients with active systemic lupus erythematosus (SLE), a greater proportion of patients receiving deucravacitinib achieved SLE Responder Index-4 responses at Weeks 32 and 48 vs placebo. Patient-reported outcomes (PROs) were collected as exploratory endpoints at 48 weeks. Methods Patients with SLE (N=363) were randomized 1:1:1:1 to placebo (n=90) or deucravacitinib 3 mg twice daily (BID; n=91), 6 mg BID (n=93), or 12 mg once daily (QD; n=89). Patients assessed pain levels on a numeric rating scale (NRS) and completed the Patient-Reported Outcome Measurement Information System (PROMIS) Fatigue 7a Short Form and 36-Item Short Form (SF-36). Missing data were imputed using control-based pattern imputation. Results are descriptive. Results Baseline characteristics were comparable across groups (table 1). At Week 48, greater mean changes from baseline in pain and fatigue were reported with deucravacitinib 3 mg BID, 6 mg BID, and 12 QD vs placebo (figure 1). Mean improvements in pain and fatigue were greater than minimum clinically important differences (MCIDs) of −1.0 and −4.0, respectively, with all doses of deucravacitinib vs only pain with placebo. Mean scores [SD] at Week 48 numerically improved with deucravacitinib 3 mg BID, 6 mg BID, and 12 mg QD vs placebo, respectively; pain NRS: 3.6 [2.7], 3.7 [2.6], 3.6 [2.8], 4.7 [2.7]; PROMIS Fatigue: 52.4 [10.2], 52.6 [10.0], 51.9 [10.6], 54.4 [10.9]; SF-36 physical component: 44.7 [10.0], 44.6 [9.3], 45.1 [11.0], 41.5 [10.5]; and SF-36 mental component scores: 46.7 [12.6], 46.3 [13.1], 47.3 [12.6], 45.2 [12.9]. Additional subgroup analyses are ongoing. Conclusions Patients with SLE receiving deucravacitinib reported improvements over placebo in NRS pain, fatigue, and health-related quality of life at Week 48.

Sponges are recognized as a diverse and abundant component of mesophotic and deep-sea ecosystems worldwide. In Flower Garden Banks National Marine Sanctuary region within the northwestern Gulf of Mexico, sponges thrive among diverse biological and geological habitats between 16–200+ m deep (i.e., coral reefs and communities, algal nodules, and coralline algae reefs, mesophotic reefs, patch reefs, scarps, ridges, soft substrate, and rocky outcrops). A synoptic guide is presented, developed by studying common sponge species in the region, through direct sampling and in-situ photographic records. A total of 64 species is included: 60 are Demospongiae (14 orders), two are Hexactinellida (one order), and two are Homoscleromorpha (one order). Thirty-four taxa are identified to species and 13 were identified to have affinity with, but were not identical to, a known species. Fifteen taxa could only be identified to genus level, and the species remain as uncertain (incerta sedis), with the potential to represent new species or variants of known species. One specimen received only a family assignation. This study extends geographic or mesophotic occurrence data for eleven known species and includes several potentially new species. This work improves our knowledge of Gulf of Mexico sponge biodiversity and highlights the importance of the region for scientists and resource managers.

Class Demospongiae is the largest in the phylum Porifera (Sponges) and encompasses nearly 8,000 accepted species in three subclasses: Keratosa, Verongimorpha, and Heteroscleromorpha. Subclass Heteroscleromorpha contains ∼90% of demosponge species and is subdivided into 17 orders. The higher level classification of demosponges underwent major revision as the result of nearly three decades of molecular studies. However, because most of the previous molecular work only utilized partial data from a small number of nuclear and mitochondrial (mt) genes, this classification scheme needs to be tested by larger datasets. Here we compiled a mt dataset for 136 demosponge species-including 64 complete or nearly complete and six partial mt-genome sequences determined or assembled for this study-and used it to test phylogenetic relationships among Demospongiae in general and Heteroscleromorpha in particular. We also investigated the phylogenetic position of Myceliospongia araneosa, a highly unusual demosponge without spicules and spongin fibers, currently classified as Demospongiae incertae sedis, for which molecular data were not available. Our results support the previously inferred sister-group relationship between Heteroscleromorpha and Keratosa + Verongimorpha and suggest five main clades within Heteroscleromorpha: Clade C0 composed of order Haplosclerida; Clade C1 composed of Scopalinida, Sphaerocladina, and Spongillida; Clade C2 composed of Axinellida, Biemnida, Bubarida; Clade C3 composed of Tetractinellida; and Clade C4 composed of Agelasida, Clionaida, Desmacellida, Merliida, Suberitida, Poecilosclerida, Polymastiida, and Tethyida. The inferred relationships among these clades were (C0(C1(C2(C3+C4)))). Analysis of molecular data from M. araneosa placed it in the C3 clade as a sister taxon to the highly skeletonized tetractinellids Microscleroderma sp. and Leiodermatium sp. Molecular clock analysis dated divergences among the major clades in Heteroscleromorpha from the Cambrian to the Early Silurian, the origins of most heteroscleromorph orders in the middle Paleozoic, and the most basal splits within these orders around the Paleozoic to Mesozoic transition. Overall, the results of this study are mostly congruent with the accepted classification of Heteroscleromorpha, but add temporal perspective and new resolution to phylogenetic relationships within this subclass.

The potential of sponge-derived chemicals for pharmaceutical applications remains largely unexploited due to limited available biomass. Although many have attempted to culture marine sponge cells in vitro to create a scalable production platform for such biopharmaceuticals, these efforts have been mostly unsuccessful. We recently showed that Geodia barretti sponge cells could divide rapidly in M1 medium. In this study we established the first continuous marine sponge cell line, originating from G. barretti. G. barretti cells cultured in OpM1 medium, a modification of M1, grew more rapidly and to a higher density than in M1. Cells in OpM1 reached 1.74 population doublings after 30 min, more than twofold higher than the already rapid growth rate of 0.74 population doublings in 30 min in M1. The maximum number of population doublings increased from 5 doublings in M1 to at least 98 doublings in OpM1. Subcultured cells could be cryopreserved and used to inoculate new cultures. With these results, we have overcome a major obstacle that has blocked the path to producing biopharmaceuticals with sponge cells at industrial scale for decades.

This chapter reviews the current knowledge regarding Cuba’s mesophotic coral ecosystems (MCEs). The first studies of MCEs in Cuba were conducted by Kühlmann in 1964 and Zlatarski and Martínez Estalella in the 1970s. In 2017, a joint Cuba-USA expedition was conducted to characterize the MCEs along the entire coastline of Cuba using remotely operated vehicle surveys. A total of 477 taxa of benthic macrobiota and 151 species of fish were identified, and 343 specimens of benthic invertebrates and algae were collected to verify taxonomy and assess population genetic structure. The primary geomorphological features are the deep island slope (125– >150 m), deep fore-reef escarpment (the “wall,” 50–125 m), and deep fore-reef slope (30–50 m). Most vertical surfaces of the wall have dense cover of sponges, algae, octocorals, and black corals. Cuban mesophotic corals appeared quite healthy as compared to many shallow Caribbean reef sites; only 0.53% (mainly Agaricia spp.) showed signs of bleaching, and just 0.09% displayed signs of disease/morbidity. Percent cover of the bottom was dominated by algae (23.45%) and sponges (20.41%). Sites outside of marine protected areas generally had lower fish abundances, a possible indicator of historical overfishing. Lionfish were observed at most sites, but abundances were low compared to other Caribbean regions. Cuba’s MCEs encompass the entire Cuban archipelago, representing a vast and ecologically important resource that may play an important role in regional coral reef connectivity and persistence across the Gulf of Mexico and wider Caribbean.

EDITORIAL article Front. Mar. Sci., 20 January 2023Sec. Deep-Sea Environments and Ecology Volume 10 - 2023 | https://doi.org/10.3389/fmars.2023.1132451

Cryptosporidium sp. are apicomplexan parasites that cause significant morbidity and possible mortality in humans and valuable livestock. There are no drugs on the market that are effective in the population most severely affected by this parasite. This study is the first high-throughput screen for potent anti-Cryptosporidium natural products sourced from a unique marine compound library. The Harbor Branch Oceanographic Institute at Florida Atlantic University has a collection of diverse marine organisms some of which have been subjected to medium pressure liquid chromatography to create an enriched fraction library. Numerous active compounds have been discovered from this library, but it has not been tested against Cryptosporidium parvum. A high-throughput in vitro growth inhibition assay was used to test 3764 fractions in the library, leading to the identification of 23 fractions that potently inhibited the growth of Cryptosporidium parvum. Bioassay guided fractionation of active fractions from a deep-sea sponge, Leiodermatium sp., resulted in the purification of leiodolide A, the major active compound in the organism. Leiodolide A displayed specific anti-Cryptosporidium activity at a half maximal effective concentration of 103.5 nM with selectivity indexes (SI) of 45.1, 11.9, 19.6 and 14.3 for human ileocecal colorectal adenocarcinoma cells (HCT-8), human hepatocellular carcinoma cells (Hep G2), human neuroblastoma cells (SH-SY5Y) and green monkey kidney cells (Vero), respectively. The unique structure of leiodolide A provides a valuable drug scaffold on which to develop new anti-Cryptosporidium compounds and supports the importance of screening natural product libraries for new chemical scaffolds.

Las esponjas son organismos cruciales en los arrecifes de coral mesofóticos (30-150 m de profundidad) por su diversidad, abundancia y múltiples funciones ecológicas. El presente estudio tiene como objetivo caracterizar la variación espacial de la diversidad de esponjas en seis arrecifes mesofóticos protegidos del suroccidente de Cuba. Se analizaron 1402 imágenes obtenidas con un Vehículo Operado a Distancia (Mohawk ROV), durante la expedición científica conjunta Cuba-Estados Unidos a bordo del buque de investigaciones Walton Smith en 2017. La investigación se enmarca en la zona mesofótica inferior y en dos intervalos de profundidad: 50-80 m y 80-125 m. Se identificaron 170 especies de esponjas, 41 comunes a las registradas en arrecifes someros de la región suroccidental. En la lista taxonómica se distinguen 15 especies y nueve géneros recientemente identificados para Cuba, y las nuevas especies Callyspongia alcoladoi y C. pedroi descritas para la ciencia en 2018, además de nuevos registros para las localidades analizadas. Sólo nueve especies fueron encontradas en ambos intervalos de profundidad en todos los sitios. La península de Guanahacabibes presentó el mayor número de especies con respecto al archipiélago de los Canarreos. Las variaciones de la cantidad de especies entre sitios pueden estar relacionadas fundamentalmente a las diferencias geomorfológicas encontradas entre los arrecifes analizados. El total de especies disminuyó con la profundidad en cinco de los seis sitios estudiados, siendo un factor deter- minante en la distribución de las especies. Se registraron 30 especies con nuevos valores de profundidad máxima para la región del Atlántico Tropical Occidental. Recibido: 26-08-2021 Aceptado: 21-10-2021 Publicado: 10-01-2022 Editor: Maickel Armenteros

Production of sponge-derived bioactive compounds in vitro has been proposed as an alternative to wild harvest, aquaculture, and chemical synthesis to meet the demands of clinical drug development and manufacture. Until recently, this was not possible because there were no marine invertebrate cell lines. Recent breakthroughs in the development of sponge cell lines and rapid cell division in improved nutrient media now make this approach a viable option. We hypothesized that three-dimensional (3-D) cell cultures would better represent how sponges function in nature, including the production of bioactive compounds. We successfully cultured sponge cells in 3-D matrices using FibraCel® disks, thin hydrogel layers, and gel microdroplets (GMDs). For in vitro production of bioactive compounds, the use of GMDs is recommended. Nutrients and sponge products rapidly diffuse into and out of the 3-D matrix, the GMDs may be scaled up in spinner flasks, and cells and/or secreted products can be easily recovered. Research on scale-up and production is in progress in our laboratory.