We explore the distribution of sponges along dissolved silica (dSi) concentration gradients to test whether sponge assemblages are related to dSi and to assess the validity of fossil sponges as a palaeoecological tool for inferring dSi concentrations of the past oceans. We extracted sponge records from the publically available Global Biodiversity Information Facility (GBIF) database and linked these records with ocean physiochemical data to evaluate if there is any correspondence between dSi concentrations of the waters sponges inhabit and their distribution. Over 320,000 records of Porifera were available, of which 62,360 met strict quality control criteria. Our analyses was limited to the taxonomic levels of family, order and class. Because dSi concentration is correlated with depth in the modern ocean, we also explored sponge taxa distributions as a function of depth. We observe that while some sponge taxa appear to have dSi preferences (e.g., class Hexactinellida occurs mostly at high dSi), the overall distribution of sponge orders and families along dSi gradients is not sufficiently differentiated to unambiguously relate dSi concentrations to sponge taxa assemblages. We also observe that sponge taxa tend to be similarly distributed along a depth gradient. In other words, both dSi and/or another variable that depth is a surrogate for, may play a role in controlling sponge spatial distribution and the challenge is to distinguish between the two. We conclude that inferences about palaeo-dSi concentrations drawn from the abundance of sponges in the stratigraphic records must be treated cautiously as these animals are adapted to a great range of dSi conditions and likely other underlying variables that are related to depth. Our analysis provides a quantification of the dSi ranges of common sponge taxa, expands on previous knowledge related to their bathymetry preferences and suggest that sponge taxa assemblages are not related to particular dSi conditions. 

Biosilicification has driven variation in the global Si cycle over geologic time. The evolution of different eukaryotic lineages that convert dissolved Si (DSi) into mineralized structures (higher plants, siliceous sponges, radiolarians and diatoms) has driven a secular decrease in DSi in the global ocean leading to the low DSi concentrations seen today. Recent studies, however, have questioned the timing previously proposed for the DSi decreases and the concentration changes through deep time, which would have major implications for the cycling of carbon and other key nutrients in the ocean. Here, we combine relevant genomic data with geological data and present new hypotheses regarding the impact of the evolution of biosilicifying organisms on the DSi inventory of the oceans throughout deep time. Although there is no fossil evidence for true silica biomineralization until the late Precambrian, the timing of the evolution of silica transporter genes suggests that bacterial silicon-related metabolism has been present in the oceans since the Archean with eukaryotic silicon metabolism already occurring in the Neoproterozoic. We hypothesize that biological processes have influenced oceanic DSi concentrations since the beginning of oxygenic photosynthesis.

Invertebrates living at methane seeps such as mussels and clams gain nutrition through symbiosis with chemosynthetic, chiefly methanotrophic and thiotrophic bacteria. Lipid biomarkers, including their compound-specific carbon stable isotope compositions, extracted from the host tissues are predestined for deciphering the various sources of diets and the associations among varying environments, endosymbionts, and hosts. Here, we investigated lipid inventories of soft tissues of two bathymodiolin mussel species hosting aerobic methanotrophic bacteria (Gigantidas platifrons from Site F and Gigantidas haimaensis from Haima seeps), one bathymodiolin mussel with thiotrophic bacteria (Bathymodiolus aduloides from Haima seeps), and one vesicomyid clam (Archivesica marissinica from Haima seeps) from the South China Sea. The gills of mussels hosting methanotrophic symbionts were found to contain high amounts of lipids of aerobic methanotrophic bacteria, such as the 4,4-dimethyl lanosterol, and other 4-methyl sterols, and the type I methanotroph-specific monounsaturated fatty acids (MUFAs) C16:1ω9 and C16:1ω8. Production of methyl-sterols is favored over fatty acids at low oxygen concentrations, as demonstrated in culture experiments with Methylococcus capsulatus. Since lesser fatty acids and abundant sterols are found in G. haimaensis compared to G. platifrons, G. haimaensis apparently lived at very low oxygen levels. Extremely high levels of MUFAs C16:1ω7 and C18:1ω7 were found in gill tissue of both B. aduloides and the vesicomyid clam A. marissinica. Given the absence of ω8 fatty acids, both B. aduloides and the vesicomyid clam contain thiotrophic bacteria only. The occurrence of 13C-enriched 24-methylenecholesterol in B. aduloides indicates that the animal complemented its diet by filter-feeding (ca. 3% of the total sterol inventory) on photosynthetically derived carbon, whereas the majority of sterols are pointing to a diet relying on endosymbionts. Different types of 4-methyl sterols were observed between the thiotroph-containing mussel and methanotroph-containing mussels, suggesting different biosynthetic steps are present from lanosterol to cholesterol between animal hosts and aerobic methanotrophs. Among the four bivalve species, specific lipid biomarker patterns diagnostic for either the symbionts or the hosts yielded similar δ13C values in each species, indicating that the host obtained its nutrition either directly from the symbionts or derived at least most of its carbon in this way. The information derived from lipid biomarkers of bivalves and their corresponding symbionts in modern environments is vital to interpret data from the rock record, where most other methods to study microbial community composition are not applicable.

The dissolution of the biogenic silica that constitutes the skeletons of silicifying organisms is an important mechanism for regenerating dissolved silicon in the ocean. The silica skeletons deposited to the seafloor after the organisms die keep dissolving until becoming definitively buried. The low dissolution rate of sponge skeletons compared to that of diatom skeletons favors their burial and makes sponges (Phylum Porifera) to function as important silicon sinks in the oceans. However, it remains poorly understood whether the large variety of siliceous skeletons existing in the Porifera involves similar variability in their dissolution rates, which would affect the general conceptualization of these organisms as silicon sinks. Herein we investigated kinetics of silica dissolution for major types of skeletons in the three siliceous lineages of Porifera, following standardized digestion conditions in 1% sodium carbonate with orbital agitation at 85°C. The results are compared with those of a previous study conducted under identical conditions, which considered diatom silica, sponge silica, and lithogenic silica. Unexpectedly, the silica of homoscleromorph sponges dissolved only a bit slower than that of freshly cultured diatoms and as fast as diatom earth. However, the rest of sponge skeletons were far more resistant, although with some differences: the isolated spicules of hexactinellid sponges dissolved slightly faster than when forming frameworks of fused spicules, being hexactinellid frameworks as resistant to dissolution as the silica of demosponges, irrespective of occurring in the form of isolated spicules or frameworks. The experiments also indicated that the complexation of sponge silica with aluminum and with chitin does not increase its resistance to dissolution. Because the rapidly-dissolving homoscleromorph sponges represent less than 1% of extant sponges, the sponge skeletons are still conceptualized as important silicon sinks due to their comparative resistance to dissolution. Yet, the turnover of silica into dissolved silicon will always be faster in environments dominated by hexactinellids with isolated spicules than in environments dominated by other hexactinellids and/or demosponges. We discuss whether the time required for a given silica type to completely dissolve in 1% sodium carbonate could be a predictor of its preservation ratio in marine sediments.

The natural dynamics of fluid flow at methane seeps and increasingly human activities influence the biogeochemistry of the microenvironment and further determine the activity of the chemosynthetic communities within these ecosystems. However, ways to reconstruct short-term fluid flow dynamics and to decipher the influence of scientific exploration at seeps are limited. In this study, we present high-resolution trace elements/Ca ratios (Li/Ca, Mg/Ca, Ti/Ca, Mn/Ca, Co/Ca, Cu/Ca, Zn/Ca, Sr/Ca, Zr/Ca, Mo/Ca, Ba/Ca, Th/Ca and U/Ca ratios) from the shells of two species of chemosymbiotic bivalves (the thiotrophic vesicomyid clam Archivesica marissinica and the methanotrophic mussel Gigantidas haimaensis) from the Haima cold seeps of the South China Sea. We found that the complex distribution patterns of some trace elements (Mg/Ca, Sr/Ca, Mo/Ca and U/Ca ratios) in G. haimaensis are largely controlled by mineral composition or age. The observation of Co/Ca and Ba/Ca ratios in both species indicate strong physiological and environmental control on the incorporation of trace elements during the biomineralization process. Besides, the distribution patterns of other trace elements provide information that can be used to discuss open issues such as the loss of trace elements after death of the bivalves, and the possible influence of human activities such as sediment disturbance. Overall, this study emphasizes the potential for using high-resolution element geochemistry of seep bivalve shells to reveal the physiological and environmental factors that control the growth of bivalves, and to elucidate the potential history of fluid discharge at cold seeps.