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Jordi A.,CSIC - Mediterranean Institute for Advanced Studies | Wang D.-P.,State University of New York at Stony Brook
Environmental Modelling and Software | Year: 2012

This paper presents the Stony Brook Parallel Ocean Model (sbPOM) for execution on workstations, Linux clusters and massively parallel supercomputers. The sbPOM is derived from the Princenton Ocean Model (POM), a widely used community ocean circulation model. Two-dimensional data decomposition of the horizontal domain is used with a halo of ghost cells to minimize communication between processors. Communication consists of the exchange of information between neighbor processors based on the Message Passing Interface (MPI) standard interface. The Parallel-NetCDF library is also implemented to achieve a high efficient input and output (I/O). Parallel performance is tested on an IBM Blue Gene/L massively parallel supercomputer, and efficiency using up to 2048 processors remains very good. © 2012 Elsevier Ltd.

Duarte C.M.,University of Western Australia | Duarte C.M.,CSIC - Mediterranean Institute for Advanced Studies
Trends in Ecology and Evolution | Year: 2014

The 200-kiloannus (ka) use of red ochre and shells by humans is interpreted as a simple clue of symbolic thinking. Integration of multiple lines of evidence supports the opinion that the use of red ochre and shells might have had direct significance for human evolution. Use of seafood and red ochre supplies docosahexaenoic acid (DHA), possibly iron, and other essential nutrients for brain development and reproductive health, improving human fitness and triggering brain growth. The fitness advantages to humans of using shells, and possibly red ochre, might have selected for artistic and symbolic expression, and, thereby, lead to social cohesion. Current global health syndromes show that an adequate supply of seafood and iron continues to play a fundamental role in human health. © 2014 Elsevier Ltd.

Javaloyes J.,University of the Balearic Islands | Balle S.,CSIC - Mediterranean Institute for Advanced Studies
Optics Express | Year: 2012

Multimode dynamics in bidirectional laser cavities can be accurately described by folding space into time delay. This results in a set of delayed algebraic equations that preserve the dynamics of all cavity modes while drastically reducing number of degrees of freedom. This reduction allows for both linear stability analysis and bifurcation diagram reconstruction, as well as integration times reduced by orders of magnitude. © 2012 Optical Society of America.

Acosta-Gonzalez A.,CSIC - Experimental Station of El Zaidín | Rossello-Mora R.,CSIC - Mediterranean Institute for Advanced Studies | Marques S.,CSIC - Experimental Station of El Zaidín
Environmental Microbiology | Year: 2013

The influence of massive crude oil contamination on the microbial population of coastal sediments was investigated in the Cíes Islands 18 and 53 months after the tanker Prestige sank off the NW coast of Spain. Communities were studied by means of culturable and non-culturable methods at three horizons in the sediment (2-5cm, 12-15cm and 25-30cm) in an area heavily affected by the spill. Most probable number of aerobic hydrocarbon degraders was highest in the upper zone and decreased dramatically with depth. Aromatic oxidizing nitrate-reducing bacteria counts were slightly higher than aerobes in the oxidized layer, and also decreased considerably with depth. Iron-reducing bacteria were barely detectable. The highest counts were obtained for sulfate-reducing bacteria, which represented the most relevant fraction of aromatic oxidizers, being maximal at 12-15cm depth. The community response to high pollution levels was characterized by an increase in culturable populations active towards crude oil components despite the strong decay in the total cell counts. Analysis of whole 16S rRNA gene libraries obtained from the two sampling times and different depths (1460 sequences in all) showed a predominance of Gamma- and Deltaproteobacteria, which was confirmed by fluorescent in situ hybridization. Desulfobacteraceae was the most abundant group among Deltaproteobacteria, followed by sequences affiliated with the order Myxococcales. All retrieved sequences of this order affiliated with a marine myxobacterial clade. Interestingly, sequences affiliated to the order Desulfarculales constituted half of the Deltaproteobacteria sequences retrieved from the heaviest contaminated sample. Principal coordinates analysis of 16S rRNA gene libraries suggested fluctuation in the community distribution with time. Changes in the abundance of certain groups such as Bacteroidetes contributed to these observed differences. Although predominance of certain metabolic types in each horizon could be delimited, a considerable overlap in the use of electron acceptors was observed, confirming that each selected zone could be influenced by more than one respiratory metabolism. Altogether, our results evidence the presence in these sediments of a microbial community with potential to respond against hydrocarbon contamination, consistent with the long pollution history of the site. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Santamaria L.,CSIC - Mediterranean Institute for Advanced Studies | Mendez P.F.,CSIC - Mediterranean Institute for Advanced Studies
Evolutionary Applications | Year: 2012

The intensity and speed of human alterations to the planet's ecosystems are yielding our static, ahistorical view of biodiversity obsolete. Human actions frequently trigger fast evolutionary responses, affect extant genetic variation and result in the establishment of new communities and co-evolutionary networks for which we lack past analogues. Contemporary evolution interplays with ecological changes to determine the response of organisms and ecosystems to anthropogenic pressures. Examples on wild species include responses to harvest (e.g. fisheries, hunting, angling), habitat loss and fragmentation (e.g. genetic effects of isolation), biotic exchange (e.g. evolutionary responses to control measures), climate change (e.g. local adaptation and its interplay with dispersal processes) and the responses of endangered species to conservation measures. A review of international and EU biodiversity policies showed numerous opportunities for the integration of evolutionary knowledge, with the realistic prospect of improving their efficacy. Such opportunities should be extended to other sectoral policies of direct relevance for biodiversity - notably nature conservation, fisheries, agriculture, water resources, spatial planning and climate change. These avenues for improvement are, however, challenged by the low level of enforcement of biodiversity policies, linked to the nonbinding nature of most biodiversity-policy documents, and the decreasing representation of biodiversity in EU's research policy. © 2012 Blackwell Publishing Ltd.

Goldstein R.E.,University of Cambridge | Polin M.,University of Cambridge | Tuval I.,CSIC - Mediterranean Institute for Advanced Studies
Physical Review Letters | Year: 2011

A fundamental issue in the biology of eukaryotic flagella is the origin of synchronized beating observed in tissues and organisms containing multiple flagella. Recent studies of the biflagellate unicellular alga Chlamydomonas reinhardtii provided the first evidence that the interflagellar coupling responsible for synchronization is of hydrodynamic origin. To investigate this mechanism in detail, we study here synchronization in Chlamydomonas as its flagella slowly regrow after mechanically induced self-scission. The duration of synchronized intervals is found to be strongly dependent on flagellar length. Analysis within a stochastic model of coupled phase oscillators is used to extract the length dependence of the interflagellar coupling and the intrinsic beat frequencies of the two flagella. Physical and biological considerations that may explain these results are proposed. © 2011 American Physical Society.

Rossello-Mora R.,CSIC - Mediterranean Institute for Advanced Studies
Environmental Microbiology | Year: 2012

Taxonomy in the second decade of the 21st century is benefiting from technological advances in molecular microbiology, especially those related to genomics. Gene and genome databases are significantly increasing due to intense research activities in the field of molecular ecology and genomics. Taxa, and especially species, are tailored by means of the recognition of a phylogenetic, genomic and phenotypic coherence that reveal their uniqueness in the classification schema. Phylogenetic coherence is mainly revealed by means of 16S rRNA gene analyses for which curated databases such as EzTaxon and LTP provide a valuable tool for tree reconstruction to taxonomy users. On the other hand, in silico full or partial genomic sequence comparisons are called on to substitute cumbersome techniques such as DNA-DNA hybridization (DDH) to genomically circumscribe species. DDH similarity values around 70% would be equivalent to ANI values of 96%. Finally, finding an exclusive phenotypic property for the taxa to be classified is of paramount relevance to producing an operative and predictive classification system. The current methods used for taxonomic classification require significant laboratory experimentation, and generally will not produce interactive databases. The new high-throughput metabolomic technologies, such as ICR-FT and MALDI-TOF mass spectrometry methods, open the door to the construction of metabolic databases for taxonomic purposes. It is to be foreseen that, in the future, taxonomists will benefit significantly from public databases speeding up the classification process. However, serious effort will be needed to harmonize them and to prevent inaccurate material. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Marba N.,CSIC - Mediterranean Institute for Advanced Studies | Duarte C.M.,CSIC - Mediterranean Institute for Advanced Studies
Global Change Biology | Year: 2010

Rapid warming of the Mediterranean Sea threatens marine biodiversity, particularly key ecosystems already stressed by other impacts such as Posidonia oceanica meadows. A 6-year monitoring of seawater temperature and annual P. oceanica shoot demography at Cabrera Archipelago National Park (Balearic Islands, Western Mediterranean) allowed us to determine if warming influenced shoot mortality and recruitment rates of seagrasses growing in relative pristine environments. The average annual maximum temperature for 2002-2006 was 1 °C above temperatures recorded in 1988-1999 (26.6 °C), two heat waves impacted the region (with seawater warming up to 28.83 °C in 2003 and to 28.54 °C in 2006) and the cumulative temperature anomaly, above the 1988-1999 mean annual maximum temperature, during the growing season (i.e. degree-days) ranged between 0 °C in 2002 and 70 °C in 2003. Median annual P. oceanica shoot mortality rates varied from 0.067 year-1 in 2002 to 0.123 year-1 in 2003, and exceeded recruitment rates in all stations and years except in shallow stations for year 2004. Interannual fluctuations in shoot recruitment were independent of seawater warming (P>0.05). P. oceanica meadows experienced a decline throughout the study period at an average rate of -0.050±0.020 year-1. Interannual variability in P. oceanica shoot mortality was coupled (R2>0.40) to seawater warming variability and increasing water depth: shoot mortality rates increased by 0.022 year-1 (i.e. an additional 2% year-1) for each additional degree of annual maximum temperature and by 0.001 year-1 (i.e. 0.1% year-1) for each accumulated degree water temperature remained above 26.6 °C during the growing season. These results demonstrate that P. oceanica meadows are highly vulnerable to warming, which can induce steep declines in shoot abundance as well indicating that climate change poses a significant threat to this important habitat. © 2010 Blackwell Publishing Ltd.

Vaquer-Sunyer R.,CSIC - Mediterranean Institute for Advanced Studies | Duarte C.M.,CSIC - Mediterranean Institute for Advanced Studies
Global Change Biology | Year: 2011

The effect of warming on the oxygen requirements and the survival of benthic organisms under hypoxia was tested using a meta-analysis of published results of experiments evaluating the effects of temperature on the median lethal time and median lethal concentration of benthic macrofauna under hypoxia. The meta-analysis confirmed that survival times under hypoxia were reduced by on average 74% and that median lethal concentration increased by on average 16% when marine benthic organisms were exposed to warmer temperatures. Warming reduced survival times of marine benthic macrofauna under hypoxia by a median of 3.95±1.67h°C-1 and increased the oxygen thresholds for hypoxia-driven mortality by a median of 1.02±0.15% saturation°C-1 or 0.07±0.01mgO2L-1°C-1. The corresponding Q10 values averaged 3.01±0.29 for the median survival time and 2.09±0.20 for the median lethal oxygen concentration. Use of these Q10 values predicts that the 4°C warming expected during the 21st century will lead to survival times 35.6% lower under hypoxia and that the threshold oxygen concentrations for high mortality to occur will increase by, on average, 25.5% if bottom water temperature increased by 4°C. Hence, ocean warming is expected to increase the vulnerability of benthic macrofauna to reduced oxygen concentrations and expand the area of coastal ecosystems affected by hypoxia. © 2010 Blackwell Publishing Ltd.

Marcos M.,CSIC - Mediterranean Institute for Advanced Studies
Global and Planetary Change | Year: 2015

The spatial and temporal scales of variability of ocean bottom pressure (Pb) in the Mediterranean Sea are characterized and their relationship with sea level was assessed using a high resolution eddy-permitting regional ocean model spanning the period 1999-2011. It was found that rapid (periods of a few days) bottom pressure fluctuations are coherent with sea level and are decoupled between the eastern and western basins as a result of topographic constraints. In the longer periods, steric processes gained relevance away from the coast and partially broke the coherence between sea level and Pb, especially on the western basin. Results confirm that sea level changes are predominantly barotropic over most of the basin and at all time scales, except for the annual cycle. Along the coasts sea level fluctuations reflected local steric processes taking place in their vicinity. This effect was stronger on the western basin, whereas the coasts of the Eastern Mediterranean arise as the most suitable proxies for basin wide long term (>60days) mean sea level (or ocean bottom pressure) changes at non-seasonal periods. © 2014 Elsevier B.V.

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