21 pages, 4 figures, 3 tables.-- This work is distributed under the Creative Commons Attribution 4.0 License, The element silicon (Si) is required for the growth of silicified organisms in marine environments, such as diatoms. These organisms consume vast amounts of Si together with N, P, and C, connecting the biogeochemical cycles of these elements. Thus, understanding the Si cycle in the ocean is critical for understanding wider issues such as carbon sequestration by the ocean’s biological pump. In this
review, we show that recent advances in process studies indicate that total Si inputs and outputs, to and from the world ocean, are 57% and 37% higher, respectively, than previous estimates. We also update the total ocean silicic acid inventory value, which is about 24% higher than previously estimated. These changes are significant, modifying factors such as the geochemical residence time of Si, which is now
about 8000 years, 2 times faster than previously assumed. In addition, we present an updated value of the global annual pelagic biogenic silica production (255 Tmol Si yr-1) based on new data from 49 field studies and 18 model outputs, and we provide a first estimate of the global annual benthic biogenic silica production due to sponges (6 Tmol Si yr-1). Given these important modifications, we hypothesize that the modern ocean Si cycle is at approximately steady state with inputs D 14:8(+-2:6) Tmol Si yr-1
and outputs D 15:6(+-2:4) Tmol Si yr-1. Potential impacts of global change on the marine Si cycle are discussed, This work was supported by the French National Research Agency (18-CEO1-0011-01) and by the Spanish Ministry of Science, Innovation and Universities (PID2019-108627RB-I00), Peer reviewed

Supplementary material.-- 1 file, This Excel file is the Supplementary Table 1 of the book chapter entitled "Nitrogen And Phosphorus Cycling Through Marine Sponges: Physiology, cytology, genomics, and ecological implications". It includes the 33 studies published before early 2021 in which ammonium, nitrite, nitrate, and/or phosphate net fluxes have been measured in marine sponges, which have been used in the overall calculations made in the chapter, This study has been partially supported by grant MICIU-PID2019-108627RB-I00 to Manuel Maldonado, No

11 pages, 9 figures, 1 table.-- Data Availability Statement: The raw data supporting the conclusion of this article will be made available by the authors, without undue reservation., Marine sponges (phylum Porifera) form symbioses with diverse microbial communities that can be transmitted
between generations through their developmental stages. Here, we integrate embryology and microbiology to
review how symbiotic microorganisms are transmitted in this early-diverging lineage. We describe that vertical transmission
is widespread but not universal, that microbes are vertically transmitted during a select developmental window,
and that properties of the developmental microbiome depends on whether a species is a high or low microbial
abundance sponge. Reproduction, development, and symbiosis are thus deeply rooted, but why these partnerships
form remains the central and elusive tenet of these developmental symbioses., Open Access funding enabled and organized by Projekt DEAL. T.J.C. was
supported by a post-doctoral fellowship from the Alexander von Humboldt
Foundation; M.M. was supported by the Ministerio de Ciencia e Innovación
(PID2019-108627RB-I00); L.S. was supported by the Max Planck Institute for
Evolutionary Biology; L.P. was supported by the GEOMAR Helmholtz Centre
for Ocean Research; T.C.G.B. was supported by the Deutsche Forschungsgemeinschaft,
the CRC 1182 (“Origin and Function of Metaorganisms”), and the
Canadian Institute for Advanced Research; and U.H. was supported by the
Deutsche Forschungsgemeinschaft, the CRC 1182 (“Origin and Function of
Metaorganisms”), and the Gordon and Betty Moore Foundation (GBMF9352)., With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)., Peer reviewed

The dataset includes 7 spreadsheets with the following contents:
- READ ME
- Standing STOCK living sponges
- Sponge Si consumption FLUX
- Si RESERVOIR in sediments
- Sponge Si FLUXES in sediments
- DIATOM Si fluxes&stocks (Fig.5)
- Calculations for discussion, This Excel file includes the data and tracked calculations of the manuscript entitled "Sponge contribution to the silicon cycle of a diatom-rich shallow bay", This research was supported by:
- the Spanish Ministry grants CTM2015-67221-R and MICIU: #PID2019-108627RB-I00 to Manuel Maldonado
- the grant 12735 – AO2020 of the French National research program EC2CO to Jacques Grall
- the ISblue project, Interdisciplinary graduate school for the blue planet (ANR-17-EURE-0015), co-funded by a grant from the French government under the program "Investissements d'Avenir", and the “Xunta de Galicia” postdoctoral grant IN606B-2019/002 to María López-Acosta., No

These datasets are supplementary data files for a study that investigates the relationship between the silicon isotopic composition of sponge skeletal silica and seawater characteristics in sponge habitats, specifically the concentration of dissolved silicic acid and its Si isotopic signature. The study revisits the historical dataset, including a detailed examination of each datapoint to identify biases related to environmental, biological and taxonomic factors. We also contribute new isotopic data obtained, specifically targeting underrepresented low-silicic-acid, shallow- water environments., Ministry of Economy, Industry and Competitiveness
MINECO-CTM2015-67221-R
Ministerio de Ciencia, Innovación y Universidades
MICIU-PID2019-108627RB-I00
Ministerio de Ciencia, Innovación y Universidades
MICIU-PID2023-151426NB-100, Peer reviewed

15 pages, 7 figures, 4 tables.-- Data availability: European Nucleotide Archive: Crambe crambe. Accession number PRJEB65618; https://identifiers.org/ena.embl/PRJEB65618. The genome sequence is released openly for reuse. The Crambe crambe genome sequencing initiative is part of the Aquatic Symbiosis Genomics (ASG) project (https://www.ebi.ac.uk/ena/browser/view/PRJEB43743). All raw sequence data and the assembly have been deposited in INSDC databases. The genome will be annotated using available RNA-Seq data and presented through the Ensembl pipeline at the European Bioinformatics Institute. Raw data and assembly accession identifiers are reported in Table 1 and Table 2, We present a genome assembly from an individual Crambe crambe (Porifera; Demospongiae; Poecilosclerida; Crambeidae). The host genome sequence is 143.20 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.53 kilobases in length. Several symbiotic prokaryotic genomes were assembled as MAGs, including two relevant sponge symbionts, the Candidatus Beroebacter blanensis/AqS2 clade (Tethybacterales, Gammaproteobacteria) of LMA sponges, and the widely distributed archaeal Nitrosopumilus sp. clade, This work was funded by the Gordon and Betty Moore Foundation through a grant (GBMF8897) to the Wellcome Sanger Institute to support the Aquatic Symbiosis Genomics Project, and by Wellcome through core funding to the Wellcome Sanger Institute (220540). Collection and preservation were funded by a grant of the Spanish Government (PID2019-108627RB-I00) to MM, This work contributes to the Institut de Ciències del Mar "Severo Ochoa Centre of Excellence" accreditation CEX2024-001494-S funded by AEI 10.13039/501100011033 of the Spanish Ministry of Science and Innovation, Peer reviewed

This study investigates the relationship between the silicon (Si) isotopic composition of sponge skeletal silica (δ³⁰Si<inf>bSi</inf>) and seawater characteristics in sponge habitats, specifically the concentration of dissolved silicic acid and its Si isotopic signature (δ³⁰Si<inf>dSi</inf>). Initially, these correlations were considered a promising calibration proxies for paleoceanographic reconstructions, but the incorporation of subsequent data points into the dataset over the past decade has highlighted complexities in how sponges fractionate silicon isotopes during silicification processes. We revisit the historical dataset, including a detailed examination of each datapoint to identify biases related to environmental, biological, and taxonomic factors. We also contribute new isotopic data obtained by multi-collector inductively coupled plasma mass spectrometer analysis, specifically targeting underrepresented low-silicic-acid environments. This revised dataset highlights that anomalies in the calibration, in particular species with fused skeletal frameworks, remain incongruous. We found that part of the problem is that the relationship between silicic acid concentration and δ³⁰Si<inf>bSi</inf> in the revised dataset of only Demospongiae follows a distinct, statistically robust, non-linear trend different from the weak, linear fit in Hexactinellida. Consequently, isotopic data from these two sponge classes should not be combined for calibration analysis, if possible. Yet, while the robust non-linear regression for only Demospongiae revitalizes the proxy, the relationship becomes asymptotic at silicic acid values above 200 μM, limiting its applicability to Cenozoic and Mesozoic conditions and excluding early Paleozoic scenarios with high concentrations of silicic acid. Practical recommendations for using and improving the proxy are discussed., The authors thank C. Sitjà for help with silica cleaning, and G. de Souza, M. López-Acosta, L. Cassarino, C. Maden, L. Leria, and M. Brzezinski for valuable comments on early draft versions of the manuscript. This research was funded by grants MINECO-CTM2015-67221-R, MICIU-PID2019-108627RB-I00, and MICIU-PID2023-151426NB-100 to Manuel Maldonado. In addition, this research also benefited from partial funding support by Biodiversa+, the European Biodiversity Partnership under the 2021–2022 BiodivProtect joint call for research proposals, co-funded by the European Commission (GA N°101052342) and with the funding organizations CSIC and Fundación Biodiversidad., Peer reviewed

18 pages, 7 figures, We present a genome assembly from an individual Petrosia ficiformis (stone sponge; Porifera; Demospongiae; Haplosclerida; Petrosiidae). The genome sequence is 191.3 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.89 kilobases in length. Gene annotation of the host organism assembly identified 18,339 protein coding genes. The metagenome of the specimen was also assembled, and 112 binned bacterial genomes were identified, including 57 high-quality MAGs. Besides MAGs characteristic of HMA sponge symbionts (i.e., Chloroflexota, Acidobacteriota), the P. ficiformis specific symbiont Candidatus Synechococcus feldmanni (formerly Aphanocapsa feldmanni (Cyanobacteriota) was recovered, as well as notably MAGs of several candidate phyla (Candidatus Latescibacteria, Poribacteria, Tectomicrobia, Dadabacteria, Kapabacteria and Binatia), This work was funded by the Gordon and Betty Moore Foundation through a grant (GBMF8897) to the Wellcome Sanger Institute to support the Aquatic Symbiosis Genomics Project, and by Wellcome through core funding to the Wellcome Sanger Institute (220540). Collection and preservation were funded by a grant of the Spanish Government (PID2019-108627RB-I00) to MM, Peer reviewed

We present a genome assembly from a specimen of Corticium candelabrum (sponge; Porifera; Homoscleromorpha; Homosclerophorida; Plakinidae). The genome sequence has a total length of 185.49 megabases. Most of the assembly (99.4%) is scaffolded into 22 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.19 kilobases in length. Gene annotation of this assembly on Ensembl identified 26,198 protein-coding genes. The metagenome of the specimen was also assembled, and 53 binned bacterial genomes were identified, including 44 high-quality MAGs that were typical of high microbial abundance sponge and included, besides the phyla Chloroflexota (class Dehalococcoidia), Acidobacteriota (order Acidomicrobiales), Alpha- and Gammaproteobacteria, also representatives of several candidatus phyla (Candidatus Latescibacterota, Binatota, Poribacteria)., This work was funded by the Gordon and Betty Moore Foundation through a grant (GBMF8897) to the Wellcome Sanger Institute to support the Aquatic Symbiosis Genomics Project, and by Wellcome through core funding to the Wellcome Sanger Institute (220540). Collection and preservation were funded by a grant of the Spanish Government (PID2019-108627RB-I00) to MM.
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., Peer reviewed

Sponges are the only metazoans capable of making silica skeletons through incorporation of silicic acid (dSi) from seawater, which is polymerized using silicifying proteins. Uptake involves functional cooperation between aquaglyceroporin channels (gAQP) and arsenite efflux pumps (ArsB), a dSi transport system that, surprisingly, also functions in plants. Compared to plants, the silicon selectivity filter of sponge gAQPs is shown here to have replaced hydrophilic residues with hydrophobic ones, reducing water permeation during silicon transport. Phylogenetic analyses of 201 gAQP and 161 ArsB sequences reveal that these transporters, having prokaryotic origins, were already present in ancestral sponges, preceding the emergence of silicifying proteins and fossilized silica skeletons. Through Hexactinellida diversification, the functional interdependence of gAQP and ArsB transporters shaped a remarkable coevolution via synchronized gene duplications. This coevolution was disrupted in Demospongiae, because Heteroscleromorpha demosponges acquired, via horizontal gene transfer, a microbial gAQP that partially displaced ancestral gAQPs. This acquisition and that of an autapomorphic silicifying protein (silicatein) coincided with an exceptional diversification in Heteroscleromorpha. In contrast, sponge lineages that never developed silicifying proteins (Keratosa, Verongimorpha, Calcarea) or acquired them post-Cambrian (Homoscleromorpha, Chondrilla) lost gAQP genes while retaining ArsB homologs, implying selection against a passive dSi influx for sponges lacking dSi polymerization machinery. Thus, the ability to precipitate dSi-ie forming skeleton-likely arose as an adaptive response in early askeletal sponges to the damaging, high dSi concentrations of Precambrian oceans. The evolutionary history of dSi transporters and the fossil record support that such adaptation evolved independently four times within Porifera., This work has primarily been funded by two research grants of the Spanish Ministry of Science, Innovation and Universities (MICIU) to M.M. (DARK-Si, PID2019-108627RB-I00; PRO-Si, PID2023-151426NB-I00). In addition, this research also benefited from partial funding support by Biodiversa+, the European Biodiversity Partnership under the 2021-2022 BiodivProtect joint call for research proposals, co-funded by the European Commission (GA N°101052342) and with the funding organizations CSIC and Fundación Biodiversidad. This study benefited from access to sponge genome data generated by the Wellcome Sanger Institute for the Aquatic Symbiosis Genomics Project (https://www.sanger.ac.uk/collaboration/aquatic-symbiosis-genomics-project/), funded by the Gordon and Betty Moore Foundation and the Wellcome Trust., Peer reviewed