Clones or clans: the genetic structure of a deep-sea sponge,Aphrocallistes vastus,in unique sponge reefs of British Columbia, Canada

The genome of the reef-building glass sponge Aphrocallistes vastus provides insights into silica biomineralization

Well-annotated and contiguous genomes are an indispensable resource for understanding the evolution, development, and metabolic capacities of organisms. Sponges, an ecologically important non-bilaterian group of primarily filter-feeding sessile aquatic organisms, are underrepresented with respect to available genomic resources. Here we provide a high-quality and well-annotated genome of Aphrocallistes vastus, a glass sponge (Porifera: Hexactinellida) that forms large reef structures off the coast of British Columbia (Canada). We show that its genome is approximately 80 Mb, small compared to most other metazoans, and contains nearly 2500 nested genes, more than other genomes. Hexactinellida is characterized by a unique skeletal architecture made of amorphous silicon dioxide (SiO₂), and we identified 419 differentially expressed genes between the osculum, i.e. the vertical growth zone of the sponge, and the main body. Among the upregulated ones, mineralization-related genes such as glassin, as well as collagens and actins, dominate the expression profile during growth. Silicateins, suggested being involved in silica mineralization, especially in demosponges, were not found at all in the A. vastus genome and suggests that the underlying mechanisms of SiO₂ deposition in the Silicea sensu stricto (Hexactinellida + Demospongiae) may not be homologous.

Sponge diversification in marine lakes: Implications for phylogeography and population genomic studies on sponges

The relative influence of geography, currents, and environment on gene flow within sessile marine species remains an open question. Detecting subtle genetic differentiation at small scales is challenging in benthic populations due to large effective population sizes, general lack of resolution in genetic markers, and because barriers to dispersal often remain elusive. Marine lakes can circumvent confounding factors by providing discrete and replicated ecosystems. Using high-resolution double digest restriction-site-associated DNA sequencing (4826 Single Nucleotide Polymorphisms, SNPs), we genotyped populations of the sponge Suberites diversicolor (n = 125) to test the relative importance of spatial scales (1-1400 km), local environmental conditions, and permeability of seascape barriers in shaping population genomic structure. With the SNP dataset, we show strong intralineage population structure, even at scales <10 km (average F ST = 0.63), which was not detected previously using single markers. Most variation was explained by differentiation between populations (AMOVA: 48.8%) with signatures of population size declines and bottlenecks per lake. Although the populations were strongly structured, we did not detect significant effects of geographic distance, local environments, or degree of connection to the sea on population structure, suggesting mechanisms such as founder events with subsequent priority effects may be at play. We show that the inclusion of morphologically cryptic lineages that can be detected with the COI marker can reduce the obtained SNP set by around 90%. Future work on sponge genomics should confirm that only one lineage is included. Our results call for a reassessment of poorly dispersing benthic organisms that were previously assumed to be highly connected based on low-resolution markers.

Implications of population connectivity studies for the design of marine protected areas in the deep sea: An example of a demosponge from the Clarion-Clipperton Zone

The abyssal demosponge Plenaster craigi inhabits the Clarion-Clipperton Zone (CCZ) in the northeast Pacific, a region with abundant seafloor polymetallic nodules with potential mining interest. Since P. craigi is a very abundant encrusting sponge on nodules, understanding its genetic diversity and connectivity could provide important insights into extinction risks and design of marine protected areas. Our main aim was to assess the effectiveness of the Area of Particular Environmental Interest 6 (APEI-6) as a potential genetic reservoir for three adjacent mining exploration contract areas (UK-1A, UK-1B and OMS-1A). As in many other sponges, COI showed extremely low variability even for samples ~900 km apart. Conversely, the 168 individuals of P. craigi, genotyped for 11 microsatellite markers, provided strong genetic structure at large geographical scales not explained by isolation by distance (IBD). Interestingly, we detected molecular affinities between samples from APEI-6 and UK-1A, despite being separated ~800 km. Although our migration analysis inferred very little progeny dispersal of individuals between areas, the major differentiation of OMS-1A from the other areas might be explained by the occurrence of predominantly northeasterly transport predicted by the HYCOM hydrodynamic model. Our study suggests that although APEI-6 does serve a conservation role, with species connectivity to the exploration areas, it is on its own inadequate as a propagule source for P. craigi for the entire eastern portion of the CCZ. Our new data suggest that an APEI located to the east and/or the south of the UK-1, OMS-1, BGR, TOML and NORI areas would be highly valuable.

Assessing condition and ecological role of deep-water biogenic habitats: Glass sponge reefs in the Salish Sea

Biogenic habitats play important roles in shallow-water ecosystems, but their roles in deeper waters are less well-studied. We quantitatively assessed 19 glass sponge reefs in the Salish Sea for live reef-building sponge cover and biodiversity, explored potential drivers behind variation observed among reefs, and quantified individual and collective roles the reefs play in filtration and carbon removal. The reefs support diverse and abundant communities of invertebrates and fish, with 115 unique taxonomic groups observed. Sponge cover varied widely between reefs: percent live reef-building sponge cover ranged from 0.2 to 17.5% and proportion of live reef habitat category ranged from 0.2 to 92%. These differences were predominantly driven by the seabed terrain characteristics such as seafloor rugosity, curvature, and depth; human pressure measures explored in this study - density of anthropogenic objects and fishing footprint over the past 17 years - did not mask the natural influence of seabed terrain. The difference in sponge cover between the reefs led to wide variation in ecosystem function with individual reefs processing between 465 and 47,300 L/m² per day. Collectively, each day the 19 reefs filter 1.04 × 10¹¹ L of water which corresponds to 1% of the total water volume in Strait of Georgia and Howe Sound combined. The reefs remove up to 1 g of carbon per m² per day, comparable to carbon sequestration rates reported for terrestrial old growth forests and to "blue carbon" sequestration rates by marine vegetation. Implications for sponge reef conservation and monitoring are discussed.