CoCoNet: towards coast to coast networks of marine protected areas (from the shore to the high and deep sea), coupled with sea-based wind energy potential

This volume contains the main results of the EC FP7 “The Ocean of Tomorrow” Project CoCoNet, divided in two sections: 1) a set of guidelines to design networks of Marine Protected Areas in the Mediterranean and the Black Seas; 2) a smart wind chart that will allow evaluating the possibility of installing Offshore Wind Farms in both seas. The concept of Cells of Ecosystem Functioning, based on connectivity, is introduced to define natural units of management and conservation. The definition of Good Environmental Status, as defined in the Marine Strategy Framework Directive, is fully embraced to set the objectives of the project, by adopting a holistic approach that integrates a full set of disciplines, ranging from physics to bio-ecology, economics, engineering and many sub-disciplines. The CoCoNet Consortium involved scientist sfrom 22 states, based in Africa, Asia, and Europe, contributing to build a coherent scientific community.peer-reviewe

The enlargement of the Suez Canal and introduction of non-indigenous species to the Mediterranean Sea

The Suez Canal is one of the most important waterways in the world – during the last year 17,148 ships passed through the Canal – reducing emissions, saving time, and operating costs to shippers. The rapid increase in ship size from the “Post-Suezmax” (> 12,000 TEU) to the latest container vessels (> 19,000 TEU) now requires enlargements of port facilities and canals. A project of this magnitude, and with potentially negative environmental outcomes, requires a transparent and scientifically sound “Environmental Impact Assessment” (EIA). An explicit obligation on Parties to the Convention on Biological Diversity (https://www.cbd.int/doc/ legal/cbd-en.pdf) was made to consider transboundary impacts on biodiversity, particularly those associated with invasive non-indigenous species

Effect of different soil treatments on production and chemical composition of essential oils extracted from Foeniculum vulgare Mill., Origanum vulgare L. and Thymus vulgaris L

The aim of the present study was to investigate how essential oil production and associated chemical composition and related biological activity could be influenced by different cultivation treatments and distillation method. Foeniculum vulgare Mill. (fennel), Origanum vulgare L. (oregano), and Thymus vulgaris L. (thyme) were cultivated in absence of any fertilizer (control) and in presence of three different fertilizers: a chemical one with augmented of mineral phosphorus and potassium, a second added with hydrolysed organic substance and mineral phosphorus and potassium (organic-mineral) and a third one treated with high content of organic nitrogen of protein origin (organic). The plants were subjected to steam distillation using two modalities: recycled and continuous to obtain 32 essential oil samples. Chemical composition analysis was performed by gas chromatography-mass spectrometry; in vitro antimicrobial activity was evaluated by broth microdilution method. In general, the recycled distillation method appeared to have a slightly higher yield than the continuous method. The "mineral" and "organic-mineral" treatments resulted in the higher yield compared to the "organic" or "control" treatments, and this was particularly evident in the recycled method. The "control" plants had a lower yield of essential oils. Anethole (13.9-59.5%) and estragole (13.4-52.2%) were the main constituents of fennel oils, p-cymene and its derivatives carvacrol and thymol were the main constituents of oregano and thyme samples. The antimicrobial activity of thyme oils on Staphylococcus aureus ranged from 0.31 to 0.16% (v/v); a lower effect of oregano samples and no activity of fennel samples were observed. The essential oils failed to inhibit the growth of Pseudomonas aeruginosa strains

Learning biophysically-motivated parameters for alpha helix prediction

<p>Abstract</p> <p>Background</p> <p>Our goal is to develop a state-of-the-art protein secondary structure predictor, with an intuitive and biophysically-motivated energy model. We treat structure prediction as an optimization problem, using parameterizable cost functions representing biological "pseudo-energies". Machine learning methods are applied to estimate the values of the parameters to correctly predict known protein structures.</p> <p>Results</p> <p>Focusing on the prediction of alpha helices in proteins, we show that a model with 302 parameters can achieve a Q_{<it>α </it>}value of 77.6% and an SOV_{<it>α </it>}value of 73.4%. Such performance numbers are among the best for techniques that do not rely on external databases (such as multiple sequence alignments). Further, it is easier to extract biological significance from a model with so few parameters.</p> <p>Conclusion</p> <p>The method presented shows promise for the prediction of protein secondary structure. Biophysically-motivated elementary free-energies can be learned using SVM techniques to construct an energy cost function whose predictive performance rivals state-of-the-art. This method is general and can be extended beyond the all-alpha case described here.</p

Spatial patterns and temporal variability of seagrass connectivity in the Mediterranean Sea

Aim The endemic seagrass Posidonia oceanica is a key component of the coastal seascapes of the Mediterranean Sea, where it provides crucial ecosystem services and promotes the assembly of diverse ecological communities. Although protection policies exist, P. oceanica meadows have been steadily declining in the recent past because of human activities and climate change. Here, we quantitatively analyse basin-wide patterns of seagrass connectivity over a 30-year-long period and identify connectivity hotspots that may serve as priority targets for conservation actions. Location Mediterranean Sea. Time period 1987-2016. Major taxa studied The seagrass P. oceanica. Methods A biophysical Lagrangian approach is used to simulate dispersal of seagrass fruits operated by marine currents. Connectivity metrics (self-retention, indegree and outdegree) are evaluated on top of Lagrangian simulations to identify the most ecologically connected areas. Time series of local connectivity scores are analysed to study temporal variability and possibly detect trends at different spatial scales. Results Spatio-temporal variability is an important component of seagrass connectivity in the Mediterranean. Connectivity hotspots are unevenly distributed in all of its four main sub-basins, and along both European and African coastlines. Although statistically significant local trends in connectivity are generally quite infrequent across the whole basin, they appear to be relatively more prevalent in connectivity hotspots. The interannual variability of average connectivity scores seems to be at least partially linked to meteorological fluctuations. Main conclusions The present study represents a step forward in the application of a quantitative, scalable and replicable methodological framework for the prioritization of seagrass conservation actions in the Mediterranean large marine ecosystem, a challenging environment characterized by complex socio-economic boundary conditions and high sensitivity to the localized effects of global climate change

Meiofauna communities, nematode diversity and C degradation rates in seagrass (Posidonia oceanica L.) and unvegetated sediments invaded by the algae Caulerpa cylindracea (Sonder)

We investigated meiofauna and sedimentary C cycling in seagrass (Posidonia oceanica) and unvegetated sediments invaded and not invaded by the non-indigenous tropical algae Caulerpa cylindracea. In both habitats, invaded sediments were characterized by higher organic matter contents. No effect was observed for prokaryotes and C degradation rates. In seagrass sediments, C turnover in invaded beds was about half that in not invaded ones. Meiofaunal communities varied significantly among invaded and not invaded grounds only in bare sediments. In both habitats, nematode species richness and assemblage composition were not affected by the algae. The effect of C. cylindracea on the turnover and nestedness components of the Jaccard dissimilarity varied between the two habitats. We show that the presence of C. cylindracea gives rise to variable consequences on meiofauna biodiversity and C cycling in different habitats. We conclude that further studies across different habitats and ecological components are needed to ultimately understand and predict the consequences of C. cylindracea invasion in shallow Mediterranean ecosystems

Design of marine protected areas in a human-dominated seascape

Conservation of the Mediterranean marine ecosystems is particularly challenging; high biodiversity is combined with high human population densities and a long history of resource exploitation. Residents and users of coastal areas often perceive marine conservation and management as limiting factors to economic development. Under these conditions, the creation of comprehensive systems of marine protected areas (MPAs) can be problematic. We selected a stretch of coast in southern Italy as a representative example of a Mediterranean coastline and nearshore marine ecosystems, featuring a complex matrix of vulnerable habitats in a landscape fragmented by multiple human activities and associated stressors. Through the use of site-selection algorithms, we investigated how human activities constrain MPA planning. Rather than assuming that patches of the same habitat found at different locations are interchangeable, we considered the scenario of a heterogeneous landscape of human impacts creating high variability in habitat quality. Despite widespread human influence, identification of portions of habitats to be protected from direct human disturbance as core no-take areas is still possible using the inclusion of 10 and 30% of low and high priority habitat, respectively, in reserves as a conservation target. Implementation of MPAs with a limited protection scheme that also include several small no-take areas could represent a feasible strategy for the conservation of Mediterranean coastal marine habitats. Moreover, MPAs could be combined with coastal zoning of activities as a means of further controlling effects over broader areas and allowing for recovery of degraded areas. Site-selection algorithms are invaluable tools for conservation planning. However, careful consideration of the potential constraints imposed by local human activities and future research aimed at filling existing gaps in understanding the ecology are crucial for making this approach useful in marine conservation planning

CoCoNet: Towards Coast to Coast Networks of marine protected areas (from the shore to the high and deep sea), coupled with sea-based wind energy potential

This volume contains the main results of the EC FP7 ``The Ocean of Tomorrow'' Project CoCoNet, divided in two sections: 1) a set of guidelines to design networks of Marine Protected Areas in the Mediterranean and the Black Seas; 2) a smart wind chart that will allow evaluating the possibility of installing Offshore Wind Farms in both seas. The concept of Cells of Ecosystem Functioning, based on connectivity, is introduced to define natural units of management and conservation. The definition of Good Environmental Status, as defined in the Marine Strategy Framework Directive, is fully embraced to set the objectives of the project, by adopting a holistic approach that integrates a full set of disciplines, ranging from physics to bio-ecology, economics, engineering and many sub-disciplines. The CoCoNet Consortium involved scientist sfrom 22 states, based in Africa, Asia, and Europe, contributing to build a coherent scientific community

The Enlargement of the Suez Canal and Introduction of Non-Indigenous Species to the Mediterranean Sea

The Suez Canal is one of the most important waterways in the world – during the last year 17,148 ships passed through the Canal – reducing emissions, saving time, and operating costs to shippers. The rapid increase in ship size from the “Post-Suezmax” (> 12,000 TEU) to the latest container vessels (> 19,000 TEU) now requires enlargements of port facilities and canals. A project of this magnitude, and with potentially negative environmental outcomes, requires a transparent and scientifically sound “Environmental Impact Assessment” (EIA). An explicit obligation on Parties to the Convention on Biological Diversity (https://www.cbd.int/doc/ legal/cbd-en.pdf) was made to consider transboundary impacts on biodiversity, particularly those associated with invasive non-indigenous species