The structure of Mediterranean rocky reef ecosystems across environmental and human gradients, and conservation implications

Historical exploitation of the Mediterranean Sea and the absence of rigorous baselines makes it difficult to evaluate the current health of the marine ecosystems and the efficacy of conservation actions at the ecosystem level. Here we establish the first current baseline and gradient of ecosystem structure of nearshore rocky reefs at the Mediterranean scale. We conducted underwater surveys in 14 marine protected areas and 18 open access sites across the Mediterranean, and across a 31-fold range of fish biomass (from 3.8 to 118 g m22). Our data showed remarkable variation in the structure of rocky reef ecosystems. Multivariate analysis showed three alternative community states: (1) large fish biomass and reefs dominated by non-canopy algae, (2) lower fish biomass but abundant native algal canopies and suspension feeders, and (3) low fish biomass and extensive barrens, with areas covered by turf algae. Our results suggest that the healthiest shallow rocky reef ecosystems in the Mediterranean have both large fish and algal biomass. Protection level and primary production were the only variables significantly correlated to community biomass structure. Fish biomass was significantly larger in well-enforced no-take marine reserves, but there were no significant differences between multi-use marine protected areas (which allow some fishing) and open access areas at the regional scale. The gradients reported here represent a trajectory of degradation that can be used to assess the health of any similar habitat in the Mediterranean, and to evaluate the efficacy of marine protected areas.

Crustacean and aquatic insect assemblages in the Mediterranean coastal ecosystems of Empord`a wetlands (NE Iberian peninsula)

Coastal wetlands are characterized by high biodiversity, which is one of the main criteria considered when establishing protection policies or when proposing adequate management actions. In this study, the crustacean and aquatic insect composition of the Empord`a wetlands is described. These two faunal groups contribute highly to the total biodiversity in these wetlands but are seldom considered when managing natural areas. A selection (84 sampling points) of all water body types present in the Empord`a wetlands were sampled monthly (surber and dip net with a 250 μm mesh). Sampling was carried out during 3 surveys (1991-92, 1996-97 and 1999-2000). A rich fauna of 125 crustacean and 295 aquatic insect taxa was identified. We characterized each water body type using the most abundant species and the relative species richness of the taxonomic groups. A classification of the water body types, according to similarity between inventories, groups the brackish and hyperhaline systems in one cluster and the various freshwater systems in another one. Among freshwater systems, lotic waters and freshwater wetlands have a high similarity, whereas rice fields and freshwater springs have a low similarity

Identification and conservation of remnant genetic resources of brown trout in relict populations from Western Mediterranean streams

Brown trout is a cold-adapted freshwater species with restricted distribution to headwater streams in rivers of the South European peninsulas, where populations are highly vulnerable because Mediterranean regions are highly sensitive to the global climatic warming. Moreover, these populations are endangered due to the introgressive hybridization with cultured stocks. Individuals from six remnant populations in Western Mediterranean rivers were sequenced for the complete mitochondrial DNA control region and genotyped for 11 nuclear markers. Three different brown trout lineages were present in the studied region. Significant genetic divergence was observed among locations and a strong effect of genetic drift was suggested. An important stocking impact (close to 25%) was detected in the zone. Significant correlations between mitochondrial-based rates of hatchery introgression and water flow variation suggested a higher impact of stocked females in unstable habitats. In spite of hatchery introgression, all populations remained highly differentiated, suggesting that native genetic resources are still abundant. However, climatic predictions indicated that suitable habitats for the species in these rivers will be reduced and hence trout populations are highly endangered and vulnerable. Thus, management policies should take into account these predictions to design upstream refuge areas to protect remnant native trout in the region

Organic carbon and nutrient (P, N) concentrations of water and sediment in several aquatic environment types of a Mediterranean coastal wetland (Empordà Wetlands, NE Iberian Peninsula)

Total sediment and water organic carbon and nutrient (nitrogen and phosphorus) concentrations of different environment types of a Mediterranean coastal wetland (temporary and brackish, temporary and freshwater, semi-permanent and brackish, and permanent and brackish basins) were analysed during two hydroperiods. A nitrogen limitation was found for both sediment and water. The total organic carbon concentration of the water was significantly related to the water level, which varies throughout the hydroperiods. In contrast, the total organic carbon concentration of the sediment was not related to water level. However, significant differences in total organic carbon of the sediment were found between hydroperiods. On the other hand, total organic carbon of the sediment varied spatially, being higher in temporary brackish basins with lower sand content, and lower in permanent and semi-permanent brackish basins with higher sand content

Combining genetic and demographic data for the conservation of a Mediterranean habitat-forming species

The integration of ecological and evolutionary data is highly valuable for conservation planning. However, it has been rarely used in the marine realm, where the adequate design of marine protected areas (MPAs) is urgently needed. Here, we examined the interacting processes underlying the patterns of genetic structure and demographic strucuture of a highly vulnerable Mediterranean habitat-forming species (i.e. Paramuricea clavata (Risso, 1826)), with particular emphasis on the processes of contemporary dispersal, genetic drift, and colonization of a new population. Isolation by distance and genetic discontinuities were found, and three genetic clusters were detected; each submitted to variations in the relative impact of drift and gene flow. No founder effect was found in the new population. The interplay of ecology and evolution revealed that drift is strongly impacting the smallest, most isolated populations, where partial mortality of individuals was highest. Moreover, the eco-evolutionary analyses entailed important conservation implications for P. clavata. Our study supports the inclusion of habitat-forming organisms in the design of MPAs and highlights the need to account for genetic drift in the development of MPAs. Moreover, it reinforces the importance of integrating genetic and demographic data in marine conservation.

Multi-Scale Integrated Analysis of Societal and Ecosystem Metabolism (MUSIASEM): an outline of rationale and theory

This paper presents an outline of rationale and theory of the MuSIASEM scheme (Multi-Scale Integrated Analysis of Societal and Ecosystem Metabolism). First, three points of the rationale behind our MuSIASEM scheme are discussed: (i) endosomatic and exosomatic metabolism in relation to Georgescu-Roegen’s flow-fund scheme; (2) the bioeconomic analogy of hypercycle and dissipative parts in ecosystems; (3) the dramatic reallocation of human time and land use patterns in various sectors of modern economy. Next, a flow-fund representation of the MUSIASEM scheme on three levels (the whole national level, the paid work sectors level, and the agricultural sector level) is illustrated to look at the structure of the human economy in relation to two primary factors: (i) human time - a fund; and (ii) exosomatic energy - a flow. The three levels representation uses extensive and intensive variables simultaneously. Key conceptual tools of the MuSIASEM scheme - mosaic effects and impredicative loop analysis - are explained using the three level flow-fund representation. Finally, we claim that the MuSIASEM scheme can be seen as a multi-purpose grammar useful to deal with sustainability issues.

Technological innovation in creative clusters. The case of laser in conservation of artworks in Florence

The field of laser application to the restoration and cleaning of cultural assets is amongst the most thriving developments of recent times. Ablative laser technological systems are able to clean and protect inestimable works of art subject to atmospheric agents and degradation over time. This new technology, which has been developing for the last forty year, is now available to restorers and has received a significant success all over Europe. An important contribution in the process of laser innovation has been carried out in Florence by local actors belonging to a creative cluster. The objects of the analysis are the genesis of this innovation in this local Florentine context, and the relationships among the main actors who have contributed in it. The study investigates how culture can play a part in the generation of ideas and innovations, and which are the creative environments that can favour it. In this context, the issue of laser technologies for the restoration of cultural heritage has been analysed as a case study in the various paths taken by the Creative Capacity of the Culture (CCC).

Acoustic transport of charge and spins in GaAs-based heterostructures

Report for the scientific sojourn carried out at the Paul Drude Institut für Festkörperelektronik of the Stanford University, USA, from 2010 to 2012. The objective of this project is the transport and control of electronic charge and spin along GaAs-based semiconductor heterostructures. The electronic transport has been achieved by taking advantage of the piezolectric field induced by surface acoustic waves in non-centrosymmetric materials like GaAs. This piezolectric field separates photogenerated electrons and holes at different positions along the acoustic wave, where they acummulate and are transported at the same velocity as the wave. Two different kinds of structures have been studied: quantum wells grown along the (110) direction, both intrinsic and n-doped, as well as GaAs nanowires. The analysis of the charge acoustic transport was performed by micro-photoluminescence, whereas the detection of the spin transport was done either by analyzing the polarization state of the emitted photoluminescence or by Kerr reflectometry. Our results in GaAs quantum wells show that charge and spin transport is clearly observed at the non-doped structures,obtaining spin lifetimes of the order of several nanoseconds, whereas no acoutically induced spin transport was detected for the n-doped quantum wells. In the GaAs nanowires, we were able of transporting successfully both electrons and holes along the nanowire axis, but no conservation of the spin polarization has been observed until now. The photoluminescence emitted by these structures after acoustic transport, however, shows anti-bunching characteristics, making this system a very good candidate for its use as single photon emitters.

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution

Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are “genomic fossils” valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an important problem in computational genomics, and is also critical for obtaining an accurate picture of a genome’s structure and function. However, no consensus computational scheme for defining and detecting pseudogenes has been developed thus far. As part of the ENCyclopedia Of DNA Elements (ENCODE) project, we have compared several distinct pseudogene annotation strategies and found that different approaches and parameters often resulted in rather distinct sets of pseudogenes. We subsequently developed a consensus approach for annotating pseudogenes (derived from protein coding genes) in the ENCODE regions, resulting in 201 pseudogenes, two-thirds of which originated from retrotransposition. A survey of orthologs for these pseudogenes in 28 vertebrate genomes showed that a significant fraction (∼80%) of the processed pseudogenes are primate-specific sequences, highlighting the increasing retrotransposition activity in primates. Analysis of sequence conservation and variation also demonstrated that most pseudogenes evolve neutrally, and processed pseudogenes appear to have lost their coding potential immediately or soon after their emergence. In order to explore the functional implication of pseudogene prevalence, we have extensively examined the transcriptional activity of the ENCODE pseudogenes. We performed systematic series of pseudogene-specific RACE analyses. These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues.

Self-organized criticality and synchronization in a coupled map lattice model of integrate-and-fire oscillators

We introduce two coupled map lattice models with nonconservative interactions and a continuous nonlinear driving. Depending on both the degree of conservation and the convexity of the driving we find different behaviors, ranging from self-organized criticality, in the sense that the distribution of events (avalanches) obeys a power law, to a macroscopic synchronization of the population of oscillators, with avalanches of the size of the system.

The effect of pesticides and alien invesive species on soil biota and litter decomposition rates in a Mediterrean-climate ecosystem of Western Australia

Ecosystems are complex systems and changing one of their components can alter their whole functioning. Decomposition and biodiversity are two factors that play a role in this stability, and it is vital to study how these two factors are interrelated and how other factors, whether of human origin or not, can affect them. This study has tested different hypotheses regarding the effects of pesticides and invasive species on the biodiversity of the soil fauna and litter decomposition rate. Decomposition was measured using the litterbags technique. Our results indicate that pesticides had a negative effect on decomposition whereas invasive species increased decomposition rate. At the same time, the diversity of the soil biota was unaffected by either factor. These results allow us to better understand the response of important ecosystem functions to human‐induced alterations, in order to mitigate harmful effects or restore them wherever necessary.

Effects of nutrients and turbulence on the production of transparent exopolymer particles: a mesocosm study

The production of transparent exopolymer particles (TEP) in response to several environmental variables was studied in 2 mesocosm experiments. The first (Expt 1) examined a gradient of 4 nutrient levels; the second (Expt 2) examined different conditions of silicate availability and zooplankton presence. Tanks were separated in 2 series, one subjected to turbulence and the other not influenced by turbulence. In tanks with nutrient addition, TEP were rapidly formed, with net apparent production rates closely linked to chl a growth rates, suggesting that phytoplankton cells were actively exuding TEP precursors. High nutrient availability increased the absolute concentration of TEP; however, the relative quantity of TEP produced was found to be lower, as TEP concentration per unit of phytoplankton biomass was inversely related to the initial nitrate dose. In Expt 1, an increase in TEP volume (3 to 48 µm equivalent spherical diameter) with nutrient dose was observed; in Expt 2, both silicate addition and turbulence enhanced TEP production and favored aggregation to larger TEP (>48 µm). The presence of zooplankton lowered TEP concentration and changed the size distribution of TEP, presumably by grazing on TEP or phytoplankton. For lower nutrient concentrations, the ratio of particulate organic carbon (POC) to particulate organic nitrogen (PON) followed the Redfield ratio. At higher nutrient conditions, when nutrients were exhausted during the post-bloom, a decoupling of carbon and nitrogen dynamics occurred and was correlated to TEP formation, with a large flow of carbon channeled toward the TEP pool in turbulent tanks. TEP accounted for an increase in POC concentration of 50% in high-nutrient and turbulent conditions. The study of TEP dynamics is crucial to understanding the biogeochemical response of the aquatic system to forcing variables such as nutrient availability and turbulence intensity.

Photographic rectification of the graphic documentation of historical and archaeological heritage: The case of the southern facade of the Praetorium tower in Tarragona (Tarraco, Hispania Citerior)

This article details the use of photographic rectification as support for the graphic documentation of historical and archaeological heritage and specifically the southern facade of the Torre del Pretori (Praetorium Tower) in Tarragona. The Praetorium Tower is part of a larger monumental complex and one of the towers that connected different parts of the Tarraco Provincial Forum, the politic-administrative centre of the ancient capital of Hispania Citerioris. It is therefore a valuable example of the evolution of Roman urban architecture. The aim of this project is to provide accurate graphic documentation of the structure to facilitate the restoration and conservation of the tower, as well as to provide a more profound architectural and archaeological understanding of the Roman forum. The use of photographic rectification enabled us to overcome the spatial and time difficulties involved in collecting data caused by the size and location of the building. Specific software made it easier to obtain accurate two-dimensional images. For this reason, in our case, photographic rectification helped us to make a direct analysis of the monument and facilitated interpretation of the architectural stratigraphy. We currently separate the line of research into two concepts: the construction processes and the architecture of the building. The documentation collected permitted various analyses: the characterisation of the building modules, identification of the tools used to work the building materials, etc. In conclusion, the use of orthoimages is a powerful tool that permits the systematic study of a Roman building that has evolved over the centuries and is now in a modern urban context.

The efficiency of indicator groups for the conservation of amphibians in the Brazilian Atlantic Forest

The adequate selection of indicator groups of biodiversity is an important aspect of the systematic conservation planning. However, these assessments differ in the spatial scale, in the methods used and in the groups considered to accomplish this task, which generally produces contradictory results. The quantification of the spatial congruence between species richness and complementarity among different taxonomic groups is a fundamental step to identify potential indicator groups. Using a constructive approach, the main purposes of this study were to evaluate the performance and efficiency of eight potential indicator groups representing amphibian diversity in the Brazilian Atlantic Forest. Data on the geographic range of amphibian species that occur in the Brazilian Atlantic Forest was overlapped to the full geographic extent of the biome, which was divided into a regular equal-area grid. Optimization routines based on the concept of complementarily were applied to verify the performance of each indicator group selected in relation to the representativeness of the amphibians in the Brazilian Atlantic Forest as a whole, which were solved by the algorithm"simulated annealing", through the use of the software MARXAN. Some indicator groups were substantially more effective than others in regards to the representation of the taxonomic groups assessed, which was confirmed by the high significance of data (F = 312.76; p < 0.01). Leiuperidae was considered as the best indicator group among the families analyzed, as it showed a good performance, representing 71% of amphibian species in the Brazilian Atlantic Forest (i.e. 290 species), which may be associated with the diffuse geographic distribution of its species. This study promotes understanding of how the diversity standards of amphibians can be informative for systematic conservation planning on a regional scale.

Interactions of bacteria and fungi on decomposing litter: differential extracellular enzyme activities

Fungi and bacteria are key agents in plant litter decomposition in freshwater ecosystems. However, the specific roles of these two groups and their interactions during the decomposition process are unclear. We compared the growth and patterns of degradativeenzymes expressed by communities of bacteria and fungi grown separately and in coexistence on Phragmites leaves. The two groups displayed both synergistic and antagonistic interactions. Bacteria grew better together with fungi than alone. In addition, there was a negative effect of bacteria on fungi, which appeared to be caused by suppression of fungal growth and biomass accrual rather than specifically affecting enzyme activity. Fungi growing alone had a high capacity for the decomposition of plant polymers such as lignin, cellulose, and hemicellulose. In contrast, enzyme activities were in general low when bacteria grew alone, and the activity of key enzymes in the degradation of lignin and cellulose (phenol oxidase and cellobiohydrolase) was undetectable in the bacteria-only treatment. Still, biomass-specific activities of most enzymes were higher in bacteria than in fungi. The low total activity and growth of bacteria in the absence of fungi in spite of apparent high enzymatic efficiency during the degradation of many substrates suggest that fungi provide the bacteria with resources that the bacteria were not able to acquire on their own, most probably intermediate decomposition products released by fungi that could be used by bacteria