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This study investigates the bottlenose dolphin (Tursiops truncatus, Montagu 1821) habitat use in the Portofino marine protected area (NW Italy) and adjacent waters, a core area for the dolphins and a highly touristic area in the Mediterranean Sea. A permanent automated real-time passive acoustic monitoring system, able to detect and track dolphins continuously, was tested in the area within the activities of the Life+ Nature project ARION. The habits of bottlenose dolphins was investigated considering the resident rate inside the area, which quantifies the amount of time dolphins spent in these waters, by means of random forest regression. The dependency of dolphin resident rate was analyzed in relation to four explanatory variables: sea surface temperature, season, time of day, and proximity to the coast. Dolphins spent more time in the area during spring and when sea surface temperature ranged between 15-16°C. Summer resulted the season with lower dolphin residency with significant difference between working day and weekend, in the last the lowest residency was recorded. Main findings provide important information to properly manage the area in order to protect bottlenose dolphins., Competing Interests: The commercial IT company Softeco Sismat S.r.l. is one of the three associated beneficiaries of the EU LIFE+ project named ARION (grant number: LIFE09 NAT/IT/000190 ARION). The authors Christian Melchiorre (ChM) and Gianni Viano (GV) are employed by the commercial IT company named Softeco Sismat S.r.l. that provided support in the form of salaries for these authors [ChM, GV]. The contribution of the authors employed by this commercial company (ChM, GV) mainly consists on the production of data analysis tools (automated detection alarm generation, creation of the detection database, etc.) and web platforms for data sharing (smartphone app, project web site, etc.). No restrictions are applied by this commercial company on any kind of product regarding this study. This commercial affiliation does not alter our adherence to PLOS ONE policies on sharing data and materials.

Global climate change has increased the frequency and intensity of extreme heat anomalies and consequent mass coral bleaching events. Long-term dynamics of hard coral cover, bioconstruction potential, carbonate deposition, and reef accretion was monitored over a 20-year period on Maldivian coral reefs in order to investigate the effects of high-temperature anomalies on coral reef accretion and their recovery potential. Changes experienced by shallow reefs between 1997 and 2017 were evaluated by considering five different bioconstructional guilds and the BioConstruction Potential index (BCP), a proxy for the constructional capacity of reefs. Abnormally high temperatures in 1998 and 2016 led to severe coral bleaching and consequent mortality, especially of the primary builders. Renewed carbonate deposition was not documented until 2-3 years after the bleaching, and 6-9 years passed until constratal (i.e., low relief) growth was achieved. Finally, 14-16 years were required to reach accretion rates high enough to ensure superstratal (i.e., high relief) growth. Coral mortality in the Maldives during the 2016 bleaching event was lower than in 1998, and the initial recovery was faster and occurred via a different trajectory than in 1998. Rising levels of anthropogenic carbon emissions are predicted to accelerate sea level rise and trigger severe coral bleaching events at least twice per decade, a frequency that will (a) prevent coral recovery, (b) nullify reef accretion, and consequently, (c) result in the drowning of Maldivian reefs under the worst climate projections., (© 2018 John Wiley & Sons Ltd.)

Marine caves are unique and vulnerable habitats exhibiting high biodiversity and heterogeneity, but threatened by multiple global and local disturbances. Marine caves, although widely distributed along the Mediterranean coast, suffer for the lack of quantitative data on their structure and function, which hinder their conservation status assessment. Thanks to the availability of a nearly 30-year-long series of data (1986-2013), we evaluated ecosystem change in the Bergeggi marine cave (Ligurian Sea, NW Mediterranean), a cave with a complex shape and high habitat heterogeneity. Non-taxonomic descriptors were adopted, namely growth forms (GF) and trophic guilds (TG), which are informative about ecosystem structure and functioning, respectively. The cave experienced a general trend of change during the last three decades, mainly due to the decline in the cover of sessile organisms (especially 3-dimensional forms) matched by an increase of turf and sediment, thus causing the structural and functional homogenization of the cave community. While change before 2004 had been attributed to climatic factors (especially to the summer heat waves of 1999 and 2003), the most important rate of change was observed between 2009 and 2013, coinciding with recent major beach nourishments and the extension of the neighbouring Vado Ligure harbour, thus providing evidences on the importance of local disturbances deriving from coastal interventions. Monitoring the status of cave ecosystems is urgently needed, and the use of effective indicators, such as the specific traits here adopted (morphology and feeding strategy), could provide effective tools to assist marine cave conservation., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

The availability of marine habitats maps remains limited due to difficulty and cost of working at sea. Reduced light penetration in the water hampers the use of optical imagery, and acoustic methods require extensive sea-truth activities. Predictive spatial modelling may offer an alternative to produce benthic habitat maps based on complete acoustic coverage of the seafloor together with a comparatively low number of sea truths. This approach was applied to the coralligenous reefs of the Marine Protected Area of Tavolara - Punta Coda Cavallo (NE Sardinia, Italy). Fuzzy clustering, applied to a set of observations made by scuba diving and used as sea truth, allowed recognising five coralligenous habitats, all but one existing within EUNIS (European Nature Information System) types. Variable importance plots showed that the distribution of habitats was driven by distance from coast, depth, and lithotype, and allowed mapping their distribution over the MPA. Congruence between observed and predicted distributions and accuracy of the classification was high. Results allowed calculating the occurrence of the distinct coralligenous habitats in zones with different protection level. The five habitats are unequally protected since the protection regime was established when detailed marine habitat maps were not available. A SWOT (Strengths-Weaknesses-Opportunities-Threats) analysis was performed to identify critical points and potentialities of the method. The method developed proved to be reliable and the results obtained will be useful when modulating on-going and future management actions in the studied area and in other Mediterranean MPAs to develop conservation efforts at basin scale., (Copyright © 2018. Published by Elsevier Ltd.)

Marine bioconstructions are biodiversity-rich, three-dimensional biogenic structures, regulating key ecological functions of benthic ecosystems worldwide. Tropical coral reefs are outstanding for their beauty, diversity and complexity, but analogous types of bioconstructions are also present in temperate seas. The main bioconstructions in the Mediterranean Sea are represented by coralligenous formations, vermetid reefs, deep-sea cold-water corals, Lithophyllum byssoides trottoirs, coral banks formed by the shallow-water corals Cladocora caespitosa or Astroides calycularis, and sabellariid or serpulid worm reefs. Bioconstructions change the morphological and chemicophysical features of primary substrates and create new habitats for a large variety of organisms, playing pivotal roles in ecosystem functioning. In spite of their importance, Mediterranean bioconstructions have not received the same attention that tropical coral reefs have, and the knowledge of their biology, ecology and distribution is still fragmentary. All existing data about the spatial distribution of Italian bioconstructions have been collected, together with information about their growth patterns, dynamics and connectivity. The degradation of these habitats as a consequence of anthropogenic pressures (pollution, organic enrichment, fishery, coastal development, direct physical disturbance), climate change and the spread of invasive species was also investigated. The study of bioconstructions requires a holistic approach leading to a better understanding of their ecology and the application of more insightful management and conservation measures at basin scale, within ecologically coherent units based on connectivity: the cells of ecosystem functioning., (© 2018 Elsevier Ltd. All rights reserved.)

A new method based on photographic sampling coupled with in situ observations was applied to 53 stations along the French Mediterranean coast, to assess the integrity of coralligenous reefs affected by different levels of anthropogenic pressure. The conservation state of the assemblages characterizing these habitats was then assessed by an index - the INDEX-COR - that integrates three metrics: (i) the sensitivity of the taxa to organic matter and sediment deposition, (ii) the observable taxonomic richness, and (iii) the structural complexity of the assemblages. The sensitivity of INDEX-COR was tested and showed good correlation with the Level of Pressure calculated for each station according to expert judgment and field observations., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

A conceptual model was constructed for the functioning the algae-dominated rocky reef ecosystem of the Mediterranean Sea. The Ecosystem-Based Quality Index (reef-EBQI) is based upon this model. This index meets the objectives of the EU Marine Strategy Framework Directive. It is based upon (i) the weighting of each compartment, according to its importance in the functioning of the ecosystem; (ii) biological parameters assessing the state of each compartment; (iii) the aggregation of these parameters, assessing the quality of the ecosystem functioning, for each site; (iv) and a Confidence Index measuring the reliability of the index, for each site. The reef-EBQI was used at 40 sites in the northwestern Mediterranean. It constitutes an efficient tool, because it is based upon a wide set of functional compartments, rather than upon just a few species; it is easy and inexpensive to implement, robust and not redundant with regard to already existing indices., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Marine coastal ecosystems are affected by a vast array of human-induced disturbances and stresses, which are often capable of overwhelming the effects of natural changes. Despite the conceptual and practical difficulty in differentiating between disturbance and stress, which are often used interchangeably, the two terms bear different ecological meanings. Both are external agents, but the former causes mortality or physical damage (subtraction of biomass), whereas the latter causes physiological alteration (reduction in productivity). Sensitivity of marine organisms may thus have a dual connotation, being influenced in different ways by disturbance and by stress following major environmental change. Coralligenous assemblages, which shape unique biogenic formations in the Mediterranean Sea, are considered highly sensitive to change. In this paper, we propose a method to differentiate between disturbance and stress to assess the ecological status of the coralligenous assemblages. Disturbance sensitivity level (DSL) and stress sensitivity level (SSL) of the sessile organisms thriving in the coralligenous assemblages were combined into the integrated sensitivity level of coralligenous assemblages (ISLA) index. Changes in the coralligenous status were assessed in space, along a gradient of stress (human-induced pressures) at several sites of the western Mediterranean, and in time, from a long-term series (1961-2008) at Mesco Reef (Ligurian Sea) that encompasses a mass mortality event in the 1990s. The quality of the coralligenous assemblages was lower in highly urbanised sites than that in sites in both marine protected areas and areas with low levels of urbanisation; moreover, the quality of the assemblages at Mesco Reef decreased during the last 50years. Reduction in quality was mainly due to the increase in stress-tolerant and/or opportunist species (e.g. algal turfs, hydroids and encrusting sponges), the disappearance of the most sensitive macroalgae (e.g. Udoteaceae and erect Rhodophyta) and macro-invertebrates (e.g. Savalia savaglia, Alcyonium coralloides and Smittina cervicornis), and the appearance of invasive alien algal species. Although the specific indices of SSL or DSL well illustrated the changes in the spatial or temporal datasets, respectively, their integration in the ISLA index was more effective in measuring the change experienced by the coralligenous assemblages in both space and time., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Marine caves are unique and vulnerable habitats, threatened by multiple global and local disturbances. Whilst the effects of climate change on marine caves have already been investigated, no information exists about the effects of local human impacts, such as coastal development, on these habitats. This study investigated the impact of the construction of a touristic harbour on two shallow underwater marine caves in the Ligurian Sea (NW Mediterranean). As a standard methodology for monitoring marine caves does not exist yet, changes over time on the benthic community were assessed adopting two different non-taxonomic descriptors: trophic guilds and growth forms. Harbour construction caused an increase of sediment load within the caves, with a consequent decline of filter feeder organisms. Abundance of small organisms, such as encrusting and flattened sponges, was greatly reduced in comparison to organisms with larger and erect growth forms, such as domed mounds and pedunculated sponges. Our study indicated that growth forms and trophic guilds are effective descriptors for evaluating changes over time in marine caves, and could be easily standardised and applied in monitoring plans. In addition, as the harbour construction impacted differently according to the cave topography, the use of a systematic sampling in different zones of an underwater cave is recommended., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

The dearth of long-time series hampers the measurement of the ecosystem change that followed the global marine climate shift of the 1980-90s. The sessile communities of Portofino Promontory reefs (Ligurian Sea, NW Mediterranean) have been discontinuously studied since the 1950s. Collating information from various sources, three periods of investigations have been distinguished: 1) 1950-70s; 2) 1980-90s; 3) 2000-10s. A cooler phase in time 1 was followed by a rapid warming in time 2, to stabilize at about 0.5°C higher in time 3. Human pressure grew impressively, especially after the establishment of a MPA in 1999. Multivariate analyses evidenced a major change of community composition in time 2. Some species disappeared or got rarer, many found refuge at depth, and among the newcomers there were recently introduced alien species. This study demonstrated the importance of descriptive historical data to understand magnitude and pattern of change in the long term evolution of marine ecosystems., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Within the framework of the EU Life+ project named LIFE09 NAT/IT/000190 ARION, a permanent automated real-time passive acoustic monitoring system for the improvement of the conservation status of the transient and resident population of bottlenose dolphin (Tursiops truncatus) has been implemented and installed in the Portofino Marine Protected Area (MPA), Ligurian Sea. The system is able to detect the simultaneous presence of dolphins and boats in the area and to give their position in real time. This information is used to prevent collisions by diffusing warning messages to all the categories involved (tourists, professional fishermen and so on). The system consists of two gps-synchronized acoustic units, based on a particular type of marine buoy (elastic beacon), deployed about 1 km off the Portofino headland. Each one is equipped with a four-hydrophone array and an onboard acquisition system which can record the typical social communication whistles emitted by the dolphins and the sound emitted by boat engines. Signals are pre-filtered, digitized and then broadcast to the ground station via wi-fi. The raw data are elaborated to get the direction of the acoustic target to each unit, and hence the position of dolphins and boats in real time by triangulation.

Coral reefs are degrading worldwide, but little information exists on their previous conditions for most regions of the world. Since 1989, we have been studying the Maldives, collecting data before, during and after the bleaching and mass mortality event of 1998. As early as 1999, many newly settled colonies were recorded. Recruits shifted from a dominance of massive and encrusting corals in the early stages of recolonisation towards a dominance of Acropora and Pocillopora by 2009. Coral cover, which dropped to less than 10% after the bleaching, returned to pre-bleaching values of around 50% by 2013. The 2004 tsunami had comparatively little effect. In 2014, the coral community was similar to that existing before the bleaching. According to descriptors and metrics adopted, recovery of Maldivian coral reefs took between 6 and 15years, or may even be considered unachieved, as there are species that had not come back yet., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Understanding the effects of environmental change on ecosystems requires the identification of baselines that may act as reference conditions. However, the continuous change of these references challenges our ability to define the true natural status of ecosystems. The so-called sliding baseline syndrome can be overcome through the analysis of quantitative time series, which are, however, extremely rare. Here we show how combining historical quantitative data with descriptive 'naturalistic' information arranged in a chronological chain allows highlighting long-term trends and can be used to inform present conservation schemes. We analysed the long-term change of a coralligenous reef, a marine habitat endemic to the Mediterranean Sea. The coralligenous assemblages of Mesco Reef (Ligurian Sea, NW Mediterranean) have been studied, although discontinuously, since 1937 thus making available both detailed descriptive information and scanty quantitative data: while the former was useful to understand the natural history of the ecosystem, the analysis of the latter was of paramount importance to provide a formal measure of change over time. Epibenthic assemblages remained comparatively stable until the 1990s, when species replacement, invasion by alien algae, and biotic homogenisation occurred within few years, leading to a new and completely different ecosystem state. The shift experienced by the coralligenous assemblages of Mesco Reef was probably induced by a combination of seawater warming and local human pressures, the latter mainly resulting in increased water turbidity; in turn, cumulative stress may have favoured the establishment of alien species. This study showed that the combined analysis of quantitative and descriptive historical data represent a precious knowledge to understand ecosystem trends over time and provide help to identify baselines for ecological management.

The upper portion of the meadows of the protected Mediterranean seagrass Posidonia oceanica occurs in the region of the seafloor mostly affected by surf-related effects. Evaluation of its status is part of monitoring programs, but proper conclusions are difficult to draw due to the lack of definite reference conditions. Comparing the position of the meadow upper limit with the beach morphodynamics (i.e. the distinctive type of beach produced by topography and wave climate) provided evidence that the natural landwards extension of meadows can be predicted. An innovative model was therefore developed in order to locate the region of the seafloor where the meadow upper limit should lie in natural conditions (i.e. those governed only by hydrodynamics, in absence of significant anthropogenic impact). This predictive model was validated in additional sites, which showed perfect agreement between predictions and observations. This makes the model a valuable tool for coastal management., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Making nature's value visible to humans is a key issue for the XXI century and it is crucial to identify and measure natural capital to incorporate benefits or costs of changes in ecosystem services into policy. Emergy analysis, a method able to analyze the overall functioning of a system, was applied to reckon the value of main ecosystem services provided by Posidonia oceanica, a fragile and precious Mediterranean seagrass ecosystem. Estimates, based on calculation of resources employed by nature, resulted in a value of 172 € m(-2)a(-1). Sediment retained by meadow is most relevant input, composing almost the whole P. oceanica value. Remarks about economic losses arising from meadow regression have been made through a time-comparison of meadow maps. Suggested procedure represents an operative tool to provide a synthetic monetary measure of ecosystem services to be employed when comparing natural capital to human and financial capitals in a substitutability perspective., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Conservation research aims at understanding whether present protection schemes are adequate for the maintenance of ecosystems structure and function across time. We evaluated long-term variation in rocky reef communities by comparing sites surveyed in 1993 and again in 2008. This research took place in Tigullio Gulf, an emblematic case study where various conservation measures, including a marine protected area, have been implemented to manage multiple human uses. Contrary to our prediction that protection should have favored ecosystem stability, we found that communities subjected to conservation measures (especially within the marine protected area) exhibited the greatest variation toward architectural complexity loss. Between 1993 and 2008, chronic anthropogenic pressures (especially organic load) that had already altered unprotected sites in 1993 expanded their influence into protected areas. This expansion of human pressure likely explains our observed changes in the benthic communities. Our results suggest that adaptive ecosystem-based management (EBM), that is management taking into account human interactions, informed by continuous monitoring, is needed in order to attempt reversing the current trend towards less architecturally complex communities. Protected areas are not sufficient to stop ecosystem alteration by pressures coming from outside. Monitoring, and consequent management actions, should therefore extend to cover the relevant scales of those pressures.

Using the Conservation Index, which measures the proportional amount of dead matte relative to live Posidonia oceanica, we assessed the health of 15 P. oceanica meadows at a regional scale along the coast of Liguria (NW Mediterranean). These areas were characterized by different degrees of anthropization, from highly urbanized sites to marine protected areas. Two different scenarios were identified according to depth: in shallow zones, the health of P. oceanica meadows was related to the degree of anthropization along the coastline. In contrast, in deep zones, most meadows exhibited poor health, independent of both the degree of disturbance and the legal measures protecting the area. Working synergistically with the regional impact of increased water turbidity, local impacts from the coast were recognized as the main causes of the severe regression of most Ligurian P. oceanica meadows. We conclude that marine protected areas alone are not sufficient to guarantee the protection of P. oceanica meadows. We emphasize the need for a management network involving the Sites of Community Interest (SCIs) containing P. oceanica meadows.

The key species Posidonia oceanica is the dominant endemic seagrass in the Mediterranean Sea and its meadows are considered as one of the most important and productive ecosystems in coastal waters. Covering the seabed from the surface down to about 40 m, meadows of P. oceanica are often affected by mechanical direct damages caused by boat anchoring and mooring activities. Negative effects of these activities have been shown to be recorded by P. oceanica at two different levels: the individual level (phenology of the plant) and the population level (structure of the meadow). We investigated the effect of an anchoring chain system on the P. oceanica meadow of Prelo cove (NW Mediterranean Sea) at two different depths (shallow, deep) and at three different situations of P. oceanica bottom cover (high, medium, low). Several standardized descriptors of the meadow health, working either at the individual or at the population level, were analysed in order to quantify the impact of the deployment of the chain system. A symmetrical BACI design was adopted to detect the impact, where multiple disturbed sites were contrasted with multiple controls in two distinct times, i.e. right few days after the chain settling (early) and 4 months later the disturbance (late). The anchoring chain system has been shown to strongly affect the meadow in terms of shoot density decline and rhizome baring, especially in the deep portions and where the cover of the meadow was low. All descriptors working at the population level proved effective in detecting the impact of the anchoring system. In contrast, descriptors working at the individual level did not show a consistent response to the impact. Our results pointed out the imperative necessity to proper regulate the boat anchoring and mooring activities on the P. oceanica meadows and the adoption of seagrass friendly mooring technology is thus recommended.

A system of five adjacent Posidonia oceanica meadows facing the waterfront of Genoa city (Ligurian Sea, NW Mediterranean) was investigated over different spatial scales (meters-kilometers) using three environmental indices: conservation index (CI), substitution index (SI) and phase-shift index (PSI). CI revealed differences mostly at large spatial scale, distinguishing the poor condition of the meadows closest to Genoa centre and harbour from the comparatively healthy condition of the farthest meadows. SI showed differences mostly at small spatial scale (i.e., within meadows), suggesting the influence of local factors in the re-colonisation of regressed meadows by the seagrass Cymodocea nodosa and/or the invasive alga Caulerpa racemosa. Mapping of PSI showed that the meadows closest to Genoa centre and harbour have undergone a nearly total phase shift and have no real potential for recovery: attempts to re-establish P. oceanica there might be a waste of time and money. On the contrary, the meadows farthest from Genoa centre and harbour showed a comparatively low level of phase shift and could still fully recover given specific management actions.

Eight shallow water Posidonia oceanica meadows were sampled in June 1999 along 300 km of the Ligurian coast and were compared through shoot density and lepidochronology. The growth of the seagrass was examined in the light of climate fluctuations and local stresses, colonisation by alien, invasive alga Caulerpa taxifolia, and effects of the oil spill from the tanker "Haven", and other anthropogenic impacts. Both shoot density and lepidochronology pointed to a generalised state of regression of all the meadows. The analysis of long-term growth curves of the rhizomes showed a positive trend parallel to the increase of air temperature. Two main groups of meadows were individuated on the basis of growth curve similarity. The first included four meadows, namely Ventimiglia, Imperia, Noli and Prelo, that were characterised by average values of rhizome growth of 8-9.1 mmyear(-1) and shoot density greater than 200 shootsm(-2). Although the Imperia meadow was the only one where the alien invasive alga C. taxifolia was found, it did not show differences for rhizome growth in comparison to the other meadows. The second group was formed by meadows that had suffered past anthropogenic impacts: Arenzano and Monterosso al Mare. They showed higher rhizome growth rates (9.4-10.6 mmyear(-1)) and shoot densities between 200 and 100 shootsm(-2). At Arenzano, where "Haven" oil was stranded in April 1991, no rhizome older than 8 years was found, thus confirming the shoot mortality induced by the oil spill event. The two last meadows exhibited growth curves very different from all the others: Portovenere, is a shallow meadow where P. oceanica merely survives in an extremely degraded situation with highest rhizome growth rate (12 mmyear(-1)), the other, Riva Trigoso, is the only meadow implanted on rock and had the lowest growth rates (7.1 mm year(-1)).