A 25-years dataset of ageostrophic, Ekman and Stokes surface currents in the Mediterranean Sea (AGESC-Med).

A 25-years surface velocity data-set for the Mediterranean Sea is presented in this paper. The velocity data is obtained using a modified Ekman model which allows us to obtain an analytical solution for the surface currents using satellite altimetry and available wind and waves data from synoptic observations. The new database consists of 6-hourly ocean surface velocities (integrated over one-meter depth) including the geostrophic component and the Ekman and Stokes velocity components driven by the wind and waves, between 1993 to 2018, and covering the whole Mediterranean Sea with a spatial resolution of 1/8∘. The resulting Ageostrophic, Ekman and Stokes Currents in the Mediterranean basin (AGESC-Med) was validated validated with real drifters collected by the Italian National Institute of Oceanography and Experimental Geophysics (OGS). The AGECS-Med product improves the currently available sea surfave velocity fields obtained from altimetry, as well as analyze the meoscale ageostrophic dynamics induced by wind and waves.

Optimal wave reflection as a mechanism for seagrass self-organization.

Ecosystems threatened by climate change can boost their resilience by developing spatial patterns. Spatially regular patterns in wave-exposed seagrass meadows are attributed to self-organization, yet underlying mechanisms are not well understood. Here, we show that these patterns could emerge from feedbacks between wave reflection and seagrass-induced bedform growth. We derive a theoretical model for surface waves propagating over a growing seagrass bed. Wave-induced bed shear stress shapes bedforms which, in turn, trigger wave reflection. Numerical simulations show seagrass pattern development once wave forcing exceeds a critical amplitude. In line with Mediterranean Sea field observations, these patterns have half the wavelength of the forcing waves. Our results raise the hypothesis that pattern formation optimizes the potential of seagrass meadows to reflect wave energy, and a clear direction for future field campaigns. If wave-reflecting pattern formation increases ecosystem resilience under globally intensifying wave climates, these ecosystems may inspire nature-based coastal protection measures.

Shoreline response to sea-level rise according to equilibrium beach profiles.

Shoreline position is a key parameter of a beach state, often used as a descriptor of the response of the system to changes in external forcing, such as sea-level rise. Changes in shoreline position are the result of coupled hydrodynamic and morphodynamic processes happening in the nearshore and acting at different temporal scales. Due to this complexity, methodologies aimed at reproducing shoreline evolution at decadal time scale require many simplifications. Simpler methods usually consider an equilibrium beach profile whose shape depends only on beach morphology, and whose location varies depending on incoming forcing. Here, we derive a general equation for shoreline evolution using equilibrium beach profiles. We particularize it based on several common assumptions, and evaluate changes on shoreline position caused by sea-level rise, combined with simultaneous wave and high-frequency sea-level forcing. We compare our model against other analytical equilibrium beach profile-based models and with a dynamic model explicitly computing sediment transport. Results indicate that: (i) it is necessary to consider the area of the emerged beach subject to marine forcing rather than focusing only on the submerged part, (ii) the rates of shoreline recession may change for narrow beaches, defined as those for which marine forcings act onto all of their aerial surface, and (iii) Bruun's Rule can describe beach shoreline evolution, but the uncertainty in selecting the landward boundary of the active profile entails a huge uncertainty in the magnitude of shoreline evolution. This problematic uncertainty can be drastically reduced if instantaneous forcing conditions are used instead of the arbitrary emerged/submerged active profile boundaries typically defined by only one statistic parameter of extreme conditions.

Ten years of morphodynamic data at a micro-tidal urban beach: Cala Millor (Western Mediterranean Sea).

Systematic and sustained high quality measurements of nearshore waves and beach morphology are crucial to understand morphodynamic processes that determine beach evolution, to unravel the effects of global warming on sandy coasts and thus improve forecasting models. In 2011 a comprehensive beach monitoring program, the first in the Mediterranean Sea, started at Cala Millor Beach on the island of Mallorca (Spain). The aim was to provide long-term datasets of near-shore morphodynamics in a carbonate sandy micro-tidal and semi-embayed beach fronted by a Posidonia oceanica seagrass meadow. We present our morphological and hydrodynamical dataset of Cala Millor covering more than a decade. The dataset includes topobathymetries, shoreline positions obtained from video cameras, meteorological parameters from a weather station, currents, as well as waves and sea level from ADCP measurements and sediment size. This free and unrestricted archived dataset can be used to support the modelling of erosion-deposition patterns, calibrate beach evolution models, and as a result to propose adaptation and mitigation actions under different global change scenarios.

A 60 year wave hindcast dataset in the Caribbean Sea.

This article presents a 60 years wave hindcast from 1958 to 2017, covering the Colombian Caribbean basin. Each output consists on 6-hour field of significant wave height H s , mean wave period T m - 01 , T mm - 10 and mean direction θ m with a resolution of 11.8 km × 11.4 km. The simulation was performed using SWAN model forced with JRA-55 wind fields. Model data is validated against NOAA buoy 42058 located in the central Caribbean. The resolution and time spam of this database allows to perform either coastal engineering projects as well as to perform research in seasonal and interannual wave climate variability including large return periods to evaluate coastal vulnerability.

Corrigendum to 'A 60 year wave hindcast dataset in the Caribbean Sea' Data in Brief, 37 (2021)/ 107153.

[This corrects the article DOI: 10.1016/j.dib.2021.107153.].

Effect of small scale transport processes on phytoplankton distribution in coastal seas.

Coastal ocean ecosystems are major contributors to the global biogeochemical cycles and biological productivity. Physical factors induced by the turbulent flow play a crucial role in regulating marine ecosystems. However, while large-scale open-ocean dynamics is well described by geostrophy, the role of multiscale transport processes in coastal regions is still poorly understood due to the lack of continuous high-resolution observations. Here, the influence of small-scale dynamics (O(3.5-25) km, i.e. spanning upper submesoscale and mesoscale processes) on surface phytoplankton derived from satellite chlorophyll-a (Chl-a) is studied using Lagrangian metrics computed from High-Frequency Radar currents. The combination of complementary Lagrangian diagnostics, including the Lagrangian divergence along fluid trajectories, provides an improved description of the 3D flow geometry which facilitates the interpretation of two non-exclusive physical mechanisms affecting phytoplankton dynamics and patchiness. Attracting small-scale fronts, unveiled by backwards Lagrangian Coherent Structures, are associated to negative divergence where particles and Chl-a standing stocks cluster. Filaments of positive divergence, representing large accumulated upward vertical velocities and suggesting accrued injection of subsurface nutrients, match areas with large Chl-a concentrations. Our findings demonstrate that an accurate characterization of small-scale transport processes is necessary to comprehend bio-physical interactions in coastal seas.

Endophytic microbial diversity of the halophyte Arthrocnemum macrostachyum across plant compartments.

In this study, the microbial community structures of the endosphere of the halophyte Arthrocnemum macrostachyum were evaluated from two locations in Mallorca, Spain, focusing on three plant compartments (roots, green and red stems) compared to the rhizospheric soil where the plants grew. The physicochemical parameters of the rhizospheric soils differed between locations, and the soils were characterized by different microbial community structures. Accordingly, the endophytic community composition, mainly composed of putatively halophilic organisms, was highly influenced by the rhizospheric soil microbiota, as revealed by the co-occurrence of the major endophytic taxa in the endosphere and the rizospheric soils. Moreover, the reduction of diversity from the endorhizosphere towards the red leaves may support the fact that part of colonization of the plant by bacteria could have an origin in the rhizospheric soils through the roots and subsequent migration to the aerial parts of the plant. Finally, there were certain relevant ubiquitous taxa, such as Chromohalobacter canadensis, Rudaea cellulosilytica (never reported before as endophytic), Psychrobacter sp., Bradyrhizobium sp. and Halomonas sp., that, due their moderate halophilic nature, seemed to find an optimal environment inside the plants. Some of these relevant endophytes were not always detectable in their respective soils, and were probably part of the soils' rare biosphere, which would gain preponderance in a favorable endophytic environment.

Crohn associated microbial communities associated to colonic mucosal biopsies in patients of the western Mediterranean.

Next generation sequencing approaches allow the retrieval of several orders of magnitude larger numbers of amplified single sequences in 16S rRNA diversity surveys than classical methods. However, the sequences are only partial and thus lack sufficient resolution for a reliable identification. The OPU approach used here, based on a tandem combination of high quality 454 sequences (mean >500 nuc) applying strict OTU thresholds, and phylogenetic inference based on parsimony additions to preexisting trees, seemed to improve the identification yields at the species and genus levels. A total of thirteen biopsies of Crohn-diagnosed patients (CD) and seven healthy controls (HC) were studied. In most of the cases (73%), sequences were affiliated to known species or genera and distinct microbial patterns could be distinguished among the CD subjects, with a common depletion of Clostridia and either an increased presence of Bacteroidetes (CD1) or an anomalous overrepresentation of Proteobacteria (CD2). Faecalibacterium prausnitzii presence was undetectable in CD, whereas Bacteroides vulgatus-B. dorei characterized HC and some CD groups. Altogether, the results showed that a microbial composition with predominance of Clostridia followed by Bacteroidetes, with F. prausnitzii and B. vulgatus-B. dorei as major key bacteria, characterized what could be considered a balanced structure in HC. The depletion of Clostridia seemed to be a common trait in CD.

Moderate halophilic bacteria colonizing the phylloplane of halophytes of the subfamily Salicornioideae (Amaranthaceae).

Halophytes accumulate large amounts of salt in their tissues, and thus are susceptible to colonization by halotolerant and halophilic microorganisms that might be relevant for the growth and development of the plant. Here, the study of 814 cultured strains and 14,189 sequences obtained by 454 pyrosequencing were combined in order to evaluate the presence, abundance and diversity of halophilic, endophytic and epiphytic microorganisms in the phytosphere of leaves of members of the subfamily Salicornioideae from five locations in Spain and Chile. Cultures were screened by the tandem approach of MALDI-TOF/MS and 16S rRNA gene sequencing. In addition, differential centrifugation was used to enrich endophytes for further DNA isolation, 16S rRNA gene amplification and 454 pyrosequencing. Culturable and non-culturable data showed strong agreement with a predominance of Proteobacteria, Firmicutes and Actinobacteria. The most abundant isolates corresponded to close relatives of the species Chromohalobacter canadensis and Salinicola halophilus that comprised nearly 60% of all isolates and were present in all plants. Up to 66% of the diversity retrieved by pyrosequencing could be brought into pure cultures and the community structures were highly dependent on the compartment where the microorganisms thrived (plant surface or internal tissues).

Response of sulfate-reducing bacteria to an artificial oil-spill in a coastal marine sediment.

In situ mesocosm experiments using a calcareous sand flat from a coastal area of the island of Mallorca in the Mediterranean Sea were performed in order to study the response of sulfate-reducing bacteria (SRB) to controlled crude oil contamination, or heavy contamination with naphthalene. Changes in the microbial community caused by the contamination were monitored by a combination of comparative sequence analysis of 16S rRNA genes, fluorescence in situ hybridization, cultivation approaches and metabolic activity rates. Our results showed that crude oil and naphthalene negatively influenced the total microbial community as the natural increase in cell numbers due to the seasonal dynamics was attenuated. However, both contaminants enhanced the sulfate reduction rates, as well as the culturability of SRB. Our results suggested the presence of autochthonous deltaproteobacterial SRBs that were able to degrade crude oil or polycyclic aromatic hydrocarbons such as naphthalene in anaerobic sediment layers.