The present dataset is based on a nine site study of fine seabed topography in intertidal zones. Four coral sites (Maupiti A, B and C and Niau islands) and five rocky sites (Ars en Ré, Socoa, Parlementia A and B and Banneg island) have been explored. The data has been gathered using on-foot GNSS RTK for all sites (Trimble R8/R8S and Leica sytems) except Banneg island, where aerial Lidar data from Litto3D program has been used. The horizontal resolution varies between 3.8 and 12cm allowing to describe a wide range of spatial scales (generally over 3 spectral decades). The data has been processed to explore the statistical and spectral metrics which can be used to characterize the architectural complexity of seabeds.

The present database is composed of a polygon shape file (.shp) dedicated to GIS applications. This seafloor surface represents the area within which (sub-)outcropping methane derived authigenic carbonates were identified based on ship-borne multibeam bathymetry and seafloor backscatter data; as displayed in Figs. 4 and S1a of Dupré et al. 2020 (Dupré S, Loubrieu B, Pierre C, Scalabrin C, Guérin C, Ehrhold A, Ogor A, Gautier E, Ruffine L, Biville R, Saout J, Breton C, Floodpage J, Lescanne M (2020) The Aquitaine Shelf Edge (Bay of Biscay): A Primary Outlet for Microbial Methane Release. Geophysical Research Letters 47 (7):e2019GL084561. doi:10.1029/2019gl084561). The presence of (sub-)outcropping methane-derived authigenic carbonates at the seafloor was confirmed by remotely-operated-vehicle dives during the GAZCOGNE2 marine expedition. The acoustic data were acquired in 2013 on board the R/V Le Suroît during the GAZCOGNE1 expedition with two ship-borne multibeam echosounders, the Kongsberg EM302 and EM2040, with transmission frequency of 30 and 200 kHz, respectively. Details on multibeam data acquisition, processing and interpretation of sub-outcropping methane-derived authigenic carbonate structures are presented in Dupré et al 2020 (including a Supporting Information section). Cited from Dupré et al 2020: “The carbonates are exclusively located along the shelf edge with the majority (98%) between 140 and 220 m water depths. The (sub-)outcropping carbonates are spread over a 375 km2 area that extends over a distance of 80 km between the Cap Ferret and Capbreton canyons. The western spatial limit of the methane-derived authigenic carbonates coincides with the shelf break.”

The Eiffel Tower active hydrothermal chimney is a major edifice investigated in deep-sea vent ecology at the Lucky Strike hydrothermal field (~ -1700 m), along the northern Mid-Atlantic Ridge (37.3°N, 32.3°W). This edifice, raising ~20 m over the surrounding seafloor, is associated with black smoker fluids flowing at >300°C as well as diffusion areas colonized by large Bathymodiolus azoricus mussel assemblages and microbial mats. This vent edifice was surveyed with vertical overlapping transects by ROV Victor6000 using an HD camera during the MoMARSAT2020 cruise. This dataset is part of a larger temporal series performed with other 3D reconstructions at the Eiffel Tower hydrothermal edifice that was used to investigate temporal dynamics of the edifice topography and the vent assemblages (Van Audenhaege et al. in prep.; see section "Note").

Sea fans (order : Alcyonacea) are the most remarkable and easily identifiable species of the subtidal hard substrate communities (Gili and Ros, 1985). From an ecological point of view, sea fans play an essential role (Gili and Coma, 1998) by increasing the biomass and the diversity of hard substrates (Mitchell et al, 1992; Ballesteros, 2006) via an umbrella species role providing habitat for small epifauna and a refuge for many fish (Ross and Quatrini, 2007). When their density is high enough, they form animal forests (sensu Rossi et al 2017) and become engineering species by modifying the level of turbulence and therefore of sedimentation of propagules in the benthic boundary layer (Chamberlain and Graus, 1975). In the shallow rocky habitats of the Mediterranean, five species of sea fans dominate: the white gorgonian Eunicella singularis (Esper, 1791), the orange gorgonian Leptogorgia sarmentosa (Esper, 1789), the yellow gorgonian Eunicella cavolinii (Koch, 1887), the red gorgonian Paramuricea clavata (Risso, 1826), and the red coral Corallium rubrum (Linnaeus, 1758). Some of these species, characterized by long life span, have been included in the management plans of the Gulf of Lion Marine Protected Areas, with surveys for the monitoring of the demographic structure of E. Singularis (Réserve Naturelle Marine de Cerbère-Banyuls, Aire Marine Protégée Agathoise) and C. rubrum (Réserve Naturelle Marine de Cerbère-Banyuls, Parc Marin de la Côte Bleue). In parallel with these management-related surveys, some scientific studies on the demographic structure and ecology of P. clavata, E. singularis and C. rubrum, with the aim of documenting mass mortality events (Cerrano et al. al., 2000, Garrabou et al., 2001) have been undertaken in the Parc Marin de la Côte Bleue, in the Parc National de Port-Cros, along the Côte Vermeille and Cap de Creus coast and in the Cinque Terre National Park (Garrabou and Harmelin, 2002, Torrents et al., 2005 ; Linares et al. 2008 Linares et al., 2010 ; Santangelo et al., 2011; Gori et al., 2011a ; Gori et al. 2011b; Rossi et al., 2008). The present database gathers two extensive inventory of sea fans populations performed between 2013 and 2015 in the Gulf of Lion and between 2018 and 2019 in the Ligurian Sea. The same protocol was applied to estimate the population density of the five species in 585 stations. The 585 stations were defined a priori on a regular mesh mapping the main hard-bottom substrate units of the Gulf of Lion (Côte Bleue, Plateau des Aresquiers, Plateau du Cap d'Agde, Cap Leucate, Côte Vermeille), and surrounding the ports of Toulon, La Spezia and Bastia (Figure 1). The spacing between stations was varied from 100m to 800 m according to bathymetry steepness. Each station was geo-referenced from the surface and located on the sea bed with a mooring. Counts of individuals of the five species were made by scuba divers trained to species identification in four quadrats (1m x 1m), positionned at 5 m from the mooring along the sea bed, in the four cardinal directions. In total, the sampling required 1500 dives. References Ballesteros E. 2006. Mediterranean coralligenous assemblages: a synthesis of present knowledge Oceanography and Marine Biology: An Annual Review 44, 123-195 Carpine C, Grasshoff M. 1975. Les gorgonaires de la Mediterranee. Bull Inst Oceanogr Monaco 71:1–140 Cerrano, C., Bavestrello G., Bianchi C.N., Cattaneo R. Vietti, S. Bava, C. Morganti, C. Morri, P. Picco, G. Sara S. Schiaparelli S. Siccardi A. & Sponga, F. 2000. A catastrophic mass-mortality episode of gorgonians and other organisms in the Ligurian Sea (Northwestern Mediterranean), summer 1999. Ecology Letters 3: 284–293. Chamberlain J.J. A., Graus, R.R. 1975. Water Flow and Hydromechanical Adaptations of Branched Reef Corals. : Bulletin of Marine Science 25 (1): 112-125 Garrabou J., Perez T., Sartoretto S., Harmelin J.G., 2001. Mass mortality event in red coral Corallium rubrum populations in the Provence region (France, NW Mediterranean). Mar Ecol Prog Ser 217:263–272 Garrabou J., Harmelin G. 2002. A 20-year study on life-history traits of a harvested long-lived temperate coral in the NW Mediterranean: insights into conservation and management needs. J Anim Ecol 71:966–978 Gili, J.M., & Ros, J. 1985. Study and cartography of the benthic communities of the Medes Islands (NE Spain). Marine Ecology 6, 219–238. Gili J.M. and Coma R. 1998. Benthic suspension feeders: their paramount role in littoral marine substrates. TREE 13 (8): 316-321 Gori, A., Rossi, S., Linares, C., Berganzo, E., Orejas, C., Dale, M. & Gili, J.M. 2011a. Size and spatial structure in deep versus shallow populations of the Mediterranean gorgonian Eunicella singularis (Cap de Creus, Northwestern Mediterranean Sea)” Marine Biology, DOI: 10.1007/s00227-011-1686-7 Gori A., Rossi S., Berganzo E., Pretus J.L., Dale M.R.T., Gili J.M. 2011b. Spatial distribution patterns of the gorgonians Eunicella singularis, Paramuricea clavata and Leptogorgia sarmentosa (Cape of Creus, Northwestern Mediterranean Sea). Mar Biol 158:143-158 Linares C, Coma R, Garrabou J, Diaz D, Zabala M. 2008. Size distribution, density and disturbance in two Mediterranean gorgonians: Paramuricea clavata and Eunicella singularis. J Appl Ecol 45:688–699 Linares C., Bianchimani O., Torrents O., Marschal C., Drap P., Garrabou J., 2010. Marine Protected Areas and the conservation of long-lived marine invertebrates : the Mediterranean red coral. Marine Ecology Progress Series 402: 69-79. Mitchell, N. D., Dardeau, M. R., Schroeder,W. W., Benke, A. C. 1992. Secondary production of gorgonian corals in the northern Gulf of Mexico. Mar Ecol. Prog. Ser. 87: 275-281 Ross S., Quattrini A. 2007. The fish fauna associated with deep coral banks off the southeastern United States. Deep Sea Research I (54): 975-1007. Rossi S, Bramanti L, Gori A, Orejas C. 2017. An Overview of the Animal Forests of the World. In book: Marine Animal Forests, pp.1-26. SPRINGER.[DOI: 10.1007/978-3-319-17001-5_1-1] Santangelo G., Bramanti L., Rossi S., Tsounis G., Vielmini I., Lott C., Gili J.M. 2011. Spatial patterns of variation in recruitment and post-recruitment processes of the Mediterranean precious gorgonian coral Corallium rubrum. Journal of Experimental Marine Biology and Ecology. DOI: 10.1016/j.jembe.2011.10.030 Torrents O., Garrabou J., Marshal C., Harmelin J.G., 2005. Age and size at first reproduction in the commercially exploited red coral Corallium rubrum (L.) in the Marseilles area (France, NW Mediterranean). Biol Conserv 121: 391–397 Rossi S., Tsounis G., Orejas C., Padrón T., Gili J.M., Bramanti L., Teixidó N. and Gutt J. 2008. Survey of deep-dwelling red coral (Corallium rubrum ) populations at Cap de Creus (NW Mediterranean). Marine Biology 154 (3): 533-545.

These bathymetric data were produced using the interferometric side-scan sonar onboard the Haliotis Research Vessel, Operated by Genavir, for the French Oceanographic Fleet, in October 2022, during the oceanographic campaign HISOPE (l'Haliotis pour l’Imagerie Sismique d’Orbetello et Pyrgi Etrusques). The investigated area is located in front of the tombolo di Feniglia, in the Gulf of Porto Ercole. The goal of the campaign was to image the sedimentary architecture of the Tombolo di Feniglia Acquisition took place from October 1st to October 6th 2022. Data were acquired by eng. Quentin Layahe, Genavir, onboard the Haliotis, piloted by Serge Garcia, and post-processed using the software Globe, developed by the IFREMER, by Dr.Gilles Brocard (Archéorient, University of Lyon 2, France) and Alessandro Conforti, research engineer at the CNR (Italian national center for research) at Orosi, Sardinia.

Bathymetry grid, with a pixel resolution of 10 m, from bathymetry data acquired during the 2010 Bathysaintes cruise (https://doi.org/10.17600/10030020). Data were controlled and processed with the Ifremer Caraibes software.

Data of parameters presented as figures in the manuscript: Biogenic silica (BSi: µmol.L-1), Lithogenic silicon (LSi: µmol.L-1), Total Chlorophyll a (TChla: mg.m-3) and Fucoxanthin (Fuco: mg.m-3). Note that: - Total fraction for BSi and LSi is available from Niskin bottles (> 0.8 µm) and in situ pumps (> 0.45 µm); - Size-fractions for BSi and LSi is available from in situ pumps only (5-53 µm; > 53 µm); - Total fraction for TChla and Fuco is available from Niskin bottles (> 0.7 µm). - Integrated data (0-200 m) is available from Niskin Bottles. Acronym explanations: - Sampling type: ISP = In Situ Pump; ISP-SF = In Situ Pump with Size-Fraction; NSK = Niskin. - Method used for BSi and LSi computation: NOC = No Correction applied; RAG = Correction using the method used from the protocol established by Ragueneau et al. (2005); ACR = Average Crustal Ratio method used when one of the criterion from the protocol established by Ragueneau et al. (2005) is not respected. - bdl = Below Detection Limit For further explanations in the method, should you please refer to the Material and Methods section in the manuscript (revised version submitted in Marine Chemistry).

The mooring was deployed on 15 September 2017 from Norwegian Research Vessel Lance at 80.6°N and 7.26°E (depth of 730 m) in the Yermak Pass over the Yermak Plateau north of Svalbard. It comprised 3 instruments: an upward-looking RDI 75kHz, a Long Ranger Acoustic Doppler Current Profiler (ADCP) at 340 m with 16 m vertical resolution (25 bins of 16 m each) and a 2-hour sampling time; a Seabird SBE37 measuring temperature, salinity and pressure at 348 m with 10-minute sampling time; and an Aquadopp current meter at 645 m with a 2-hour sampling time. The mooring was retrieved on the 19 July 2020 by Norwegian Icebreaker K.V. Svalbard. The present dataset features: (i) the ADCP 50-hour smoothed daily velocities, conservative temperature and pressure time series interpolated every 10 meters within the 20-330m layer, (ii) the Aquadopp 50-hour smoothed daily velocities and pressure time series at 645 m; and (iii) the SBE37 50-hour smoothed daily conservative temperature, absolute salinity and pressure time series at 348 m.

This seismic data set was recorded in September 2015 on board the R/V Pourquoi Pas? during the GHASS cruise (IFREMER) on the western Black Sea, offshore Romania. The available profiles (part of the collected data) within this deposit are located on the continental slope, bathymetry between 500 to 1200 meters. The pre-processing of the seismic data included common midpoint binning @6.25 meters, trace and shot edition, source delay correction, and a 35-375 Hz band pass filtering. Detailed Root Mean Square Velocity analyses were performed on semblance panels computed using super gathers every 150 m. Normal Move Out time correction was then applied on the Common Mid Point (CMP) using these velocities prior to stack. Interval velocities were computed using the Dix equation. The velocity model was then interpolated every CMP location, converted to depth and smoothed to perform post-stack depth migration. The depth migrated sections and the depth velocity models have been output to standard SEG-Y rev1 format (https://library.seg.org/pb-assets/technical-standards/seg_y_rev1-1686080991247.pdf) with values written using “big-endian” byte ordering and IEEE floating-point. For a given profile, both SEGY files have the same number of traces and the same bin locations. Velocity unit is in meter.second-1. The depth sampling is set to 0.5 meter for both files. The recording delay is zero for the depth migration SEGY files. The delay is coded in meters and constant for a given depth velocity SEGY file, stored within the Trace Header (bytes 109-110). Trace coordinates are also stored within the Trace Header using WGS84 +DDDMMSS.ss format with a scale factor of -100 (bytes 81-88, which means that the value has to divided by 100) . For more convenient access to the location of the profiles, these coordinates are also stored into ASCII files using decimal degrees.

IAOOS14, IAOOS15 and IAOOS25 were deployed from the Korean Icebreaker R/V Araon during cruises in the northern Chukchi Sea. IAOOS14 and IAOOS15 were deployed 300 m apart on the same floe on 12 August 2015 in the Makarov Basin (80.8°N;173°E) and they drifted together remaining always less than 6 km apart. IAOOS25 was deployed on 15 August 2017 south-west Mendeleev Ridge (77.7°N;180°E) and drifted westward to the continental slope of the East Siberian Sea. IAOOS14 and IAOOS25 stopped transmitting on 9 October 2015 and 19 November 2017 respectively, likely due to the loss of their profilers while crossing relatively shallow bathymetry. IAOOS15 dataset ends in 15 October 2015. Ocean profilers were PROVOR SPI (from French manufacturer NKE) equipped with a Seabird SBE41 CTD (Conductivity, Temperature, Depth) and a dissolved oxygen (DO) Aandera 4330 optode. The profilers were set to perform two upward profiles a day from 800 m (IAOOS 14), 300 m (IAOOS 15) and 420 m (IAOOS 25), upward starting at approximately 6 am and 6 pm. The present dataset is composed of CTD-DO data from IAOOS 14 and 15, and CTD data from IAOOS 25 in the Makarov Basin, corrected from salinity errors and interpolated vertically every 0.5 m.