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Files needed for Quality Control checks of the SISALworkbook_v12 (Comas-Bru and Harrison, 2019). This includes a Python script (wb_check_v12_compatible.py) for automatic checks and an R script (plot_agemodels_hiatus_v12) for manual checks. Instructions on how to run these scripts are provided in a README_instructions.txt file. See supplementary material of Comas-Bru et al (2020, https://doi.org/10.5194/essd-2020-39) for further information on the checks.

Future deep-sea mining for polymetallic nodules in abyssal plains will negatively impact the benthic ecosystem, but it is largely unclear whether this ecosystem will be able to recover from mining disturbance and if so, to what extent and at what timescale. During the “DISturbance and reCOLonization” (DISCOL) experiment, a total of 22 % of the seafloor within a 10.8 km2 circular area of the nodule-rich seafloor in the Peru Basin (SE Pacific) was ploughed in 1989 to bury nodules and mix the surface sediment. This area was revisited 0.1, 0.5, 3, 7, and 26 years after the disturbance to assess macrofauna, invertebrate megafauna and fish density and diversity. We used this unique abyssal faunal time series to develop carbon-based food web models for each point in the time series using the linear inverse modeling approach for sediments subjected to two disturbance levels: (1) outside the plough tracks; not directly disturbed by plough, but probably suffered from additional sedimentation; and (2) inside the plough tracks. Total faunal carbon stock was always higher outside plough tracks compared with inside plough tracks. After 26 years, the carbon stock inside the plough tracks was 54 % of the carbon stock outside plough tracks. Deposit feeders were least affected by the disturbance, with modeled respiration, external predation, and excretion rates being reduced by only 2.6 % inside plough tracks compared with outside plough tracks after 26 years. In contrast, the respiration rate of filter and suspension feeders was 79.5 % lower in the plough tracks after 26 years. The “total system throughput” (T..), i.e., the total sum of modeled carbon flows in the food web, was higher throughout the time series outside plough tracks compared with the corresponding inside plough tracks area and was lowest inside plough tracks directly after the disturbance (8.63 × 10−3 ± 1.58 × 10−5 mmol C m−2 d−1). Even 26 years after the DISCOL disturbance, the discrepancy of T.. between outside and inside plough tracks was still 56 %. Hence, C cycling within the faunal compartments of an abyssal plain ecosystem remains reduced 26 years after physical disturbance, and a longer period is required for the system to recover from such a small-scale sediment disturbance experiment.

This paper presents an analysis of the distributions of nonlinear crests, troughs and heights of deep water waves from mixed following sea states generated mechanically in an offshore basin and compares with previous results for mixed crossing seas from the same experiment. The random signals at the wavemaker in both types of mixed seas are characterized by bimodal spectra following the model of Guedes Soares (1984). In agreement with the Benjamin–Feir mechanism, the high-frequency spectrum shows a decrease in the peak magnitude and downshift of the peak with the distance, as well as reduction of the tail. The observed statistics and probabilistic distributions exhibit, in general, increasing effects of third-order nonlinearity with the distance from the wavemaker. However, this effect is less pronounced in the wave systems with two following wave trains than in the crossing seas, given that they have identical initial characteristics of the bimodal spectra. The relevance of third-order effects due to free modes only is demonstrated and assessed by excluding the vertically asymmetric distortions induced by bound wave effects of second and third order. The fact that for records characterized by relatively large coefficient of kurtosis, the empirical distributions for the non-skewed profiles continue deviating from the linear predictions, corroborate the relevance of free wave interactions and thus the need of using higher-order models for the description of wave data.

This work aims at characterising the seamount physiography and biology in the OSPAR Convention limits (north-east Atlantic Ocean) and Mediterranean Sea. We first inferred potential abundance, location and morphological characteristics of seamounts, and secondly, summarized the existing biological, geological and oceanographic in situ research, identifying examples of well-studied seamounts. Our study showed that the seamount population in the OSPAR area (north-east Atlantic) and in the Mediterranean Sea is large with around 557 and 101 seamount-like features, respectively. Similarly, seamounts occupy large areas of about 616 000 km2 in the OSPAR region and of about 89 500 km2 in the Mediterranean Sea. The presence of seamounts in the north-east Atlantic has been known since the late 19th century, but overall knowledge regarding seamount ecology and geology is still relatively poor. Only 37 seamounts in the OSPAR area (3.5% of all seamounts in the region), 22 in the Mediterranean Sea (9.2% of all seamounts in the region) and 25 in the north-east Atlantic south of the OSPAR area have in situ information. Seamounts mapped in both areas are in general very heterogeneous, showing diverse geophysical characteristics. These differences will likely affect the biological diversity and production of resident and associated organisms.

Biological communities populating the Mediterranean Sea, which is situated at the northern boundary of the subtropics, are often claimed to be particularly affected by global warming. This is indicated, for instance, by the introduction of (sub)tropical species of fish or invertebrates that can displace local species. This raises the question of whether microbial communities are similarly affected, especially in the Levantine basin where sea surface temperatures have significantly risen over the last 25 years (0.50 ± 0.11 °C in average per decade, P Prochlorococcus and Synechococcus, was examined during two cruises through both eastern and western Mediterranean Sea basins held in September 1999 (PROSOPE cruise) and in June–July 2008 (BOUM cruise). Diversity was studied using dot blot hybridization with clade-specific 16S rRNA oligonucleotide probes and/or clone libraries of the 16S-23S ribosomal DNA Internal Transcribed Spacer (ITS) region, with a focus on the abundance of clades that may constitute bioindicators of warm waters. During both cruises, the dominant Prochlorococcus clade in the upper mixed layer at all stations was HLI, a clade typical of temperate waters, whereas the HLII clade, the dominant group in (sub)tropical waters, was only present at very low concentrations. The Synechococcus community was dominated by clades I, III and IV in the northwestern waters of the Gulf of Lions and by clade III and groups genetically related to clades WPC1 and VI in the rest of the Mediterranean Sea. In contrast, only a few sequences of clade II, a group typical of warm waters, were observed. These data indicate that local cyanobacterial populations have not yet been displaced by their (sub)tropical counterparts.

The deep-sea hydrothermal vent mussel Bathymodiolus azoricus is a symbiont bearing bivalve that is found in great abundance at the Menez Gwen and Lucky Strike vent sites and in close vicinity off the Azores region near the Mid-Atlantic Ridge (MAR). The distinct relationships that vent mussels have developed with their physical and chemical environments are likely reflected in global gene expression profiles providing thus a means to distinguish geographically distinct vent mussels on the basis of gene expression studies, fluorescence in situ hybridization (FISH) experiments and 16S rRNA amplicon sequencing, to assess the natural expression of bacterial genes and vent mussel immune genes and the constitutive distribution and relative abundance of endosymbiotic bacteria within gill tissues. Our results confirmed the presence of methanotroph-related endosymbionts in Menez Gwen vent mussels whereas Lucky Strike specimens seem to harbor a different bacterial morphotype when a methane monooxygenase gene specific probe was used. No qualitative differences could be visualized between Menez Gwen and Lucky Strike individuals when tested with sulfur-oxidizing-related nucleic-acid probe. Quantitative PCR (qPCR) studies revealed varied gene expression profiles in both Menez Gwen and Lucky Strike mussel gill tissues for the immune genes selected. Genes encoding transcription factors presented noticeably low levels of fold expression whether in MG or LS animals whereas the genes encoding effector molecules appeared to have higher levels expression in MG gill tissues. The peptidoglycan recognition molecule, encoding gene, PGRP presented the highest level of transcriptional activity among the genes analyzed in MG gill tissues, seconded by carcinolectin and thus denoting the relevance of immune recognition molecules in early stage of the immune responses onset. Genes regarded as encoding molecules involved in signaling pathways were consistently expressed in both MG and LS gill tissues. Remarkably, the immunity-related GTPase encoding gene demonstrated in LS samples, the highest level of expression among the signaling molecule encoding genes tested when expressions levels were compared between MG and LG animals. A differential expression analysis of bacterial genes between MG and LS indicated a clear expression signature in LS gill tissues. The bacterial community structure ensued from the 16S rRNA sequencing analyses pointed at a unpredicted conservation of endosymbiont bacterial loads between MG and LS samples. Taken together, our results support the premise that Bathymodiolus azoricus exhibits different transcriptional statuses depending on which hydrothermal vent site it is collected from and within the same collection site while exhibiting differential levels of expression of genes corresponding to different immune functional categories. The present study represents a first attempt to characterize gene expression signatures in hydrothermal vent animals issued from distinct deep-sea environmental sites based on immune and bacterial genes expressions.

In this study, Algal Pigment Index 2 (API2) is investigated in Sagres, an area located in the Atlantic off the southwestern Iberian Peninsula. Standard results provided by the MEdium Resolution Image Spectrometer (MERIS) ocean colour sensor were compared with alternative data products, determined through a regional inversion scheme, using both MERIS and in situ remote sensing reflectances (Rrs) as input data. The reference quantity for performance assessment is in situ total chlorophyll a (TChl a) concentration estimated through a phytoplankton absorption coefficient (i.e. equivalent to API2). Additional comparison of data products has also been addressed for TChl a concentration determined by high-performance liquid chromatography. The MERIS matchup analysis revealed a systematic underestimation of TChl a, which was confirmed with an independent comparison of product map analysis. The study demonstrates the importance of regional algorithms for the study area that could complement upcoming standard results of the current Sentinel-3/OLCI space mission.

The seismic stratigraphy of the Tagus estuary ebb-tidal delta of Lisbon (Portugal) is investigated with the purpose of searching for evidences of possible sedimentary or erosive features associated with landslides or mass wasting deposits (MTD) events. A special attention was given to events that could have been triggered by large earthquakes that are known to have struck the West of Portugal and Spain in historical and pre-historical times. These earthquakes destroyed Lisbon at least twice in the last 500 years, being the 1755 Lisbon earthquake of estimated magnitude >8.5. To investigate these geological features the seismic reflection dataset used in this work consists of Chirp (Lisboa98 dataset), Sparker single channel (PACEMAKER 2011 dataset) and multichannel seismic (MCS) data (TAGUSDELTA 2013 dataset). Cross-lines of MCS data were acquired crossing the core sampling sites done in previous works. Calibration of the seismic lines width the core data led to infer that the Tagus ebb delta started its formation around 17ky BP and it consists of two main stratigraphic units, the younger of which initiated its formation at approximately 13ky BP. The lower deltaic unit contains several MTDs and/or landslides that could not be mapped with the present dataset. In the upper unit we report the existence of a landslide with 10km of length, 4.5km of width and 20m of maximum thickness that accounted for the collapse of half of the Tagus river delta front. The internal structure of the landslide varies laterally. The main different aspects are, as follows, i) the landslide can be dismembered along slope due to stretching parallel associated to differential movement along slope, ii) it can show internal discontinuities that represent mechanical detachments that separate imbricate wedges and iii) distal deposited bodies completely detached from the main landslide body. The age of the landslide is discussed; an estimated age of >8ky BP is proposed by stratigraphic correlation with existent cores in the Tagus pro-delta. The trigger mechanisms are discussed; there appears to be a correlation between large earthquakes and tsunami and onshore/offshore high energy deposits. The non-collapsed half of the delta front contains extensive shallow gas of still unknown origin and nature that was found thanks to the seismic surveys carried out in this study. Further geochemical and isotope studies are needed to investigate the origin of the gas as well as geotechnical studies are needed to investigate the rheology and stability of the delta. The stratigraphic model produced for the study area indicates subsidence of tens of meters from Pliocene times as the post-LGM deposits and possible coastal paleo-scarps fit well with the sea level curve for this interval whilst the Pliocene-Lower Quaternary appear to be tens of meters below the same curve. The estimation of the amount of subsidence needs a good chronostratigraphic control of the external continental shelf bodies.