Mediterranean Institute for Advanced Studies

DNA-DNA hybridization (DDH) has been used for nearly 50 years as the gold standard for prokaryotic species circumscriptions at the genomic level. It has been the only taxonomic method that offered a numerical and relatively stable species boundary, and its use has had a paramount influence on how the current classification has been constructed. However, now, in the era of genomics, DDH appears to be an outdated method for classification that needs to be substituted. The average nucleotide identity (ANI) between two genomes seems the most promising method since it mirrors DDH closely. Here we examine the work package JSpecies as a user-friendly, biologist-oriented interface to calculate ANI and the correlation of the tetranucleotide signatures between pairwise genomic comparisons. The results agreed with the use of ANI to substitute DDH, with a narrowed boundary that could be set at approximately 95-96%. In addition, the JSpecies package implemented the tetranucleotide signature correlation index, an alignment-free parameter that generally correlates with ANI and that can be of help in deciding when a given pair of organisms should be classified in the same species. Moreover, for taxonomic purposes, the analyses can be produced by simply randomly sequencing at least 20% of the genome of the query strains rather than obtaining their full sequence.

Coastal ecosystems and the services they provide are adversely affected by a wide variety of human activities. In particular, seagrass meadows are negatively affected by impacts accruing from the billion or more people who live within 50 km of them. Seagrass meadows provide important ecosystem services, including an estimated $1.9 trillion per year in the form of nutrient cycling; an order of magnitude enhancement of coral reef fish productivity; a habitat for thousands of fish, bird, and invertebrate species; and a major food source for endangered dugong, manatee, and green turtle. Although individual impacts from coastal development, degraded water quality, and climate change have been documented, there has been no quantitative global assessment of seagrass loss until now. Our comprehensive global assessment of 215 studies found that seagrasses have been disappearing at a rate of 110 km(2) yr(-1) since 1980 and that 29% of the known areal extent has disappeared since seagrass areas were initially recorded in 1879. Furthermore, rates of decline have accelerated from a median of 0.9% yr(-1) before 1940 to 7% yr(-1) since 1990. Seagrass loss rates are comparable to those reported for mangroves, coral reefs, and tropical rainforests and place seagrass meadows among the most threatened ecosystems on earth.

Recent research has highlighted the valuable role that coastal and marine ecosystems play in sequestering carbon dioxide (CO 2 ). The carbon (C) sequestered in vegetated coastal ecosystems, specifically mangrove forests, seagrass beds, and salt marshes, has been termed “blue carbon”. Although their global area is one to two orders of magnitude smaller than that of terrestrial forests, the contribution of vegetated coastal habitats per unit area to long‐term C sequestration is much greater, in part because of their efficiency in trapping suspended matter and associated organic C during tidal inundation. Despite the value of mangrove forests, seagrass beds, and salt marshes in sequestering C, and the other goods and services they provide, these systems are being lost at critical rates and action is urgently needed to prevent further degradation and loss. Recognition of the C sequestration value of vegetated coastal ecosystems provides a strong argument for their protection and restoration; however, it is necessary to improve scientific understanding of the underlying mechanisms that control C sequestration in these ecosystems. Here, we identify key areas of uncertainty and specific actions needed to address them.

There is a rising concern regarding the accumulation of floating plastic debris in the open ocean. However, the magnitude and the fate of this pollution are still open questions. Using data from the Malaspina 2010 circumnavigation, regional surveys, and previously published reports, we show a worldwide distribution of plastic on the surface of the open ocean, mostly accumulating in the convergence zones of each of the five subtropical gyres with comparable density. However, the global load of plastic on the open ocean surface was estimated to be on the order of tens of thousands of tons, far less than expected. Our observations of the size distribution of floating plastic debris point at important size-selective sinks removing millimeter-sized fragments of floating plastic on a large scale. This sink may involve a combination of fast nano-fragmentation of the microplastic into particles of microns or smaller, their transference to the ocean interior by food webs and ballasting processes, and processes yet to be discovered. Resolving the fate of the missing plastic debris is of fundamental importance to determine the nature and significance of the impacts of plastic pollution in the ocean.

UNLABELLED: JSpecies Web Server (JSpeciesWS) is a user-friendly online service for in silico calculating the extent of identity between two genomes, a parameter routinely used in the process of polyphasic microbial species circumscription. The service measures the average nucleotide identity (ANI) based on BLAST+ (ANIb) and MUMmer (ANIm), as well as correlation indexes of tetra-nucleotide signatures (Tetra). In addition, it provides a Tetra Correlation Search function, which allows to rapidly compare selected genomes against a continuously updated reference database with currently about 32 000 published whole and draft genome sequences. For comparison, own genomes can be uploaded and references can be selected from the JSpeciesWS reference database. The service indicates whether two genomes share genomic identities above or below the species embracing thresholds, and serves as a fast way to allocate unknown genomes in the frame of the hitherto sequenced species. AVAILABILITY AND IMPLEMENTATION: JSpeciesWS is available at http://jspecies.ribohost.com/jspeciesws SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: mrichter@ribocon.com.

Ocean acidification represents a threat to marine species worldwide, and forecasting the ecological impacts of acidification is a high priority for science, management, and policy. As research on the topic expands at an exponential rate, a comprehensive understanding of the variability in organisms' responses and corresponding levels of certainty is necessary to forecast the ecological effects. Here, we perform the most comprehensive meta-analysis to date by synthesizing the results of 228 studies examining biological responses to ocean acidification. The results reveal decreased survival, calcification, growth, development and abundance in response to acidification when the broad range of marine organisms is pooled together. However, the magnitude of these responses varies among taxonomic groups, suggesting there is some predictable trait-based variation in sensitivity, despite the investigation of approximately 100 new species in recent research. The results also reveal an enhanced sensitivity of mollusk larvae, but suggest that an enhanced sensitivity of early life history stages is not universal across all taxonomic groups. In addition, the variability in species' responses is enhanced when they are exposed to acidification in multi-species assemblages, suggesting that it is important to consider indirect effects and exercise caution when forecasting abundance patterns from single-species laboratory experiments. Furthermore, the results suggest that other factors, such as nutritional status or source population, could cause substantial variation in organisms' responses. Last, the results highlight a trend towards enhanced sensitivity to acidification when taxa are concurrently exposed to elevated seawater temperature.

Research that combines all available studies of biological responses to regional and global climate change shows that 81–83% of all observations were consistent with the expected impacts of climate change. These findings were replicated across taxa and oceanic basins. Past meta-analyses of the response of marine organisms to climate change have examined a limited range of locations1,2, taxonomic groups2,3,4 and/or biological responses5,6. This has precluded a robust overview of the effect of climate change in the global ocean. Here, we synthesized all available studies of the consistency of marine ecological observations with expectations under climate change. This yielded a meta-database of 1,735 marine biological responses for which either regional or global climate change was considered as a driver. Included were instances of marine taxa responding as expected, in a manner inconsistent with expectations, and taxa demonstrating no response. From this database, 81–83% of all observations for distribution, phenology, community composition, abundance, demography and calcification across taxa and ocean basins were consistent with the expected impacts of climate change. Of the species responding to climate change, rates of distribution shifts were, on average, consistent with those required to track ocean surface temperature changes. Conversely, we did not find a relationship between regional shifts in spring phenology and the seasonality of temperature. Rates of observed shifts in species’ distributions and phenology are comparable to, or greater, than those for terrestrial systems.

The Mediterranean Sea is a marine biodiversity hot spot. Here we combined an extensive literature analysis with expert opinions to update publicly available estimates of major taxa in this marine ecosystem and to revise and update several species lists. We also assessed overall spatial and temporal patterns of species diversity and identified major changes and threats. Our results listed approximately 17,000 marine species occurring in the Mediterranean Sea. However, our estimates of marine diversity are still incomplete as yet-undescribed species will be added in the future. Diversity for microbes is substantially underestimated, and the deep-sea areas and portions of the southern and eastern region are still poorly known. In addition, the invasion of alien species is a crucial factor that will continue to change the biodiversity of the Mediterranean, mainly in its eastern basin that can spread rapidly northwards and westwards due to the warming of the Mediterranean Sea. Spatial patterns showed a general decrease in biodiversity from northwestern to southeastern regions following a gradient of production, with some exceptions and caution due to gaps in our knowledge of the biota along the southern and eastern rims. Biodiversity was also generally higher in coastal areas and continental shelves, and decreases with depth. Temporal trends indicated that overexploitation and habitat loss have been the main human drivers of historical changes in biodiversity. At present, habitat loss and degradation, followed by fishing impacts, pollution, climate change, eutrophication, and the establishment of alien species are the most important threats and affect the greatest number of taxonomic groups. All these impacts are expected to grow in importance in the future, especially climate change and habitat degradation. The spatial identification of hot spots highlighted the ecological importance of most of the western Mediterranean shelves (and in particular, the Strait of Gibraltar and the adjacent Alboran Sea), western African coast, the Adriatic, and the Aegean Sea, which show high concentrations of endangered, threatened, or vulnerable species. The Levantine Basin, severely impacted by the invasion of species, is endangered as well. This abstract has been translated to other languages (File S1).

Hypoxia is a mounting problem affecting the world's coastal waters, with severe consequences for marine life, including death and catastrophic changes. Hypoxia is forecast to increase owing to the combined effects of the continued spread of coastal eutrophication and global warming. A broad comparative analysis across a range of contrasting marine benthic organisms showed that hypoxia thresholds vary greatly across marine benthic organisms and that the conventional definition of 2 mg O(2)/liter to designate waters as hypoxic is below the empirical sublethal and lethal O(2) thresholds for half of the species tested. These results imply that the number and area of coastal ecosystems affected by hypoxia and the future extent of hypoxia impacts on marine life have been generally underestimated.

One of the major impediments to the integration of lentic ecosystems into global environmental analyses has been fragmentary data on the extent and size distribution of lakes, ponds, and impoundments. We use new data sources, enhanced spatial resolution, and new analytical approaches to provide new estimates of the global abundance of surface-water bodies. A global model based on the Pareto distribution shows that the global extent of natural lakes is twice as large as previously known (304 million lakes; 4.2 million km2 in area) and is dominated in area by millions of water bodies smaller than 1 km2. Similar analyses of impoundments based on inventories of large, engineered dams show that impounded waters cover approximately 0.26 million km2. However, construction of low-tech farm impoundments is estimated to be between 0.1% and 6% of farm area worldwide, dependent upon precipitation, and represents ≫77,000 km2 globally, at present. Overall, about 4.6 million km2 of the earth's continental “land” surface (≫3%) is covered by water. These analyses underscore the importance of explicitly considering lakes, ponds, and impoundments, especially small ones, in global analyses of rates and processes.

Abstract. The carbon burial in vegetated sediments, ignored in past assessments of carbon burial in the ocean, was evaluated using a bottom-up approach derived from upscaling a compilation of published individual estimates of carbon burial in vegetated habitats (seagrass meadows, salt marshes and mangrove forests) to the global level and a top-down approach derived from considerations of global sediment balance and a compilation of the organic carbon content of vegeatated sediments. Up-scaling of individual burial estimates values yielded a total carbon burial in vegetated habitats of 111 Tmol C y-1. The total burial in unvegetated sediments was estimated to be 126 Tg C y-1, resulting in a bottom-up estimate of total burial in the ocean of about 244 Tg C y-1, two-fold higher than estimates of oceanic carbon burial that presently enter global carbon budgets. The organic carbon concentrations in vegetated marine sediments exceeds by 2 to 10-fold those in shelf/deltaic sediments. Top-down recalculation of ocean sediment budgets to account for these, previously neglected, organic-rich sediments, yields a top-down carbon burial estimate of 216 Tg C y-1, with vegetated coastal habitats contributing about 50%. Even though vegetated carbon burial contributes about half of the total carbon burial in the ocean, burial represents a small fraction of the net production of these ecosystems, estimated at about 3388 Tg C y-1, suggesting that bulk of the benthic net ecosystem production must support excess respiration in other compartments, such as unvegetated sediments and the coastal pelagic compartment. The total excess organic carbon available to be exported to the ocean is estimated at between 1126 to 3534 Tg C y-1, the bulk of which must be respired in the open ocean. Widespread loss of vegetated coastal habitats must have reduced carbon burial in the ocean by about 30 Tg C y-1, identifying the destruction of these ecosystems as an important loss of CO2 sink capacity in the biosphere.

Recent attention has focused on the high rates of annual carbon sequestration in vegetated coastal ecosystems--marshes, mangroves, and seagrasses--that may be lost with habitat destruction ('conversion'). Relatively unappreciated, however, is that conversion of these coastal ecosystems also impacts very large pools of previously-sequestered carbon. Residing mostly in sediments, this 'blue carbon' can be released to the atmosphere when these ecosystems are converted or degraded. Here we provide the first global estimates of this impact and evaluate its economic implications. Combining the best available data on global area, land-use conversion rates, and near-surface carbon stocks in each of the three ecosystems, using an uncertainty-propagation approach, we estimate that 0.15-1.02 Pg (billion tons) of carbon dioxide are being released annually, several times higher than previous estimates that account only for lost sequestration. These emissions are equivalent to 3-19% of those from deforestation globally, and result in economic damages of $US 6-42 billion annually. The largest sources of uncertainty in these estimates stems from limited certitude in global area and rates of land-use conversion, but research is also needed on the fates of ecosystem carbon upon conversion. Currently, carbon emissions from the conversion of vegetated coastal ecosystems are not included in emissions accounting or carbon market protocols, but this analysis suggests they may be disproportionally important to both. Although the relevant science supporting these initial estimates will need to be refined in coming years, it is clear that policies encouraging the sustainable management of coastal ecosystems could significantly reduce carbon emissions from the land-use sector, in addition to sustaining the well-recognized ecosystem services of coastal habitats.

There is a long-standing controversy as to whether drought limits photosynthetic CO2 assimilation through stomatal closure or by metabolic impairment in C3 plants. Comparing results from different studies is difficult due to interspecific differences in the response of photosynthesis to leaf water potential and/or relative water content (RWC), the most commonly used parameters to assess the severity of drought. Therefore, we have used stomatal conductance (g) as a basis for comparison of metabolic processes in different studies. The logic is that, as there is a strong link between g and photosynthesis (perhaps co-regulation between them), so different relationships between RWC or water potential and photosynthetic rate and changes in metabolism in different species and studies may be 'normalized' by relating them to g. Re-analysing data from the literature using light-saturated g as a parameter indicative of water deficits in plants shows that there is good correspondence between the onset of drought-induced inhibition of different photosynthetic sub-processes and g. Contents of ribulose bisphosphate (RuBP) and adenosine triphosphate (ATP) decrease early in drought development, at still relatively high g (higher than 150 mmol H20 m(-2) s(-1)). This suggests that RuBP regeneration and ATP synthesis are impaired. Decreased photochemistry and Rubisco activity typically occur at lower g (<100 mmol H20 m(-2) s(-1)), whereas permanent photoinhibition is only occasional, occurring at very low g (<50 mmol H20 m(-2) s(-1)). Sub-stomatal CO2 concentration decreases as g becomes smaller, but increases again at small g. The analysis suggests that stomatal closure is the earliest response to drought and the dominant limitation to photosynthesis at mild to moderate drought. However, in parallel, progressive down-regulation or inhibition of metabolic processes leads to decreased RuBP content, which becomes the dominant limitation at severe drought, and thereby inhibits photosynthetic CO2 assimilation.

Functional magnetic resonance imaging is used to extract functional networks connecting correlated human brain sites. Analysis of the resulting networks in different tasks shows that (a) the distribution of functional connections, and the probability of finding a link versus distance are both scale-free, (b) the characteristic path length is small and comparable with those of equivalent random networks, and (c) the clustering coefficient is orders of magnitude larger than those of equivalent random networks. All these properties, typical of scale-free small-world networks, reflect important functional information about brain states.

Taxonomy relies on three key elements: characterization, classification and nomenclature. All three elements are dynamic fields, but each step depends on the one which precedes it. Thus, the nomenclature of a group of organisms depends on the way they are classified, and the classification (among other elements) depends on the information gathered as a result of characterization. While nomenclature is governed by the Bacteriological Code, the classification and characterization of prokaryotes is an area that is not formally regulated and one in which numerous changes have taken place in the last 50 years. The purpose of the present article is to outline the key elements in the way that prokaryotes are characterized, with a view to providing an overview of some of the pitfalls commonly encountered in taxonomic papers.

Ecosystem reconfigurations arising from climate-driven changes in species distributions are expected to have profound ecological, social, and economic implications. Here we reveal a rapid climate-driven regime shift of Australian temperate reef communities, which lost their defining kelp forests and became dominated by persistent seaweed turfs. After decades of ocean warming, extreme marine heat waves forced a 100-kilometer range contraction of extensive kelp forests and saw temperate species replaced by seaweeds, invertebrates, corals, and fishes characteristic of subtropical and tropical waters. This community-wide tropicalization fundamentally altered key ecological processes, suppressing the recovery of kelp forests.

Climate change challenges organisms to adapt or move to track changes in environments in space and time. We used two measures of thermal shifts from analyses of global temperatures over the past 50 years to describe the pace of climate change that species should track: the velocity of climate change (geographic shifts of isotherms over time) and the shift in seasonal timing of temperatures. Both measures are higher in the ocean than on land at some latitudes, despite slower ocean warming. These indices give a complex mosaic of predicted range shifts and phenology changes that deviate from simple poleward migration and earlier springs or later falls. They also emphasize potential conservation concerns, because areas of high marine biodiversity often have greater velocities of climate change and seasonal shifts.

Seagrasses cover about 0.1–0.2% of the global ocean, and develop highly productive ecosystems which fulfil a key role in the coastal ecosystem. Widespread seagrass loss results from direct human impacts, including mechanical damage (by dredging, fishing, and anchoring), eutrophication, aquaculture, siltation, effects of coastal constructions, and food web alterations; and indirect human impacts, including negative effects of climate change (erosion by rising sea level, increased storms, increased ultraviolet irradiance), as well as from natural causes, such as cyclones and floods. The present review summarizes such threats and trends and considers likely changes to the 2025 time horizon. Present losses are expected to accelerate, particularly in South-east Asia and the Caribbean, as human pressure on the coastal zone grows. Positive human effects include increased legislation to protect seagrass, increased protection of coastal ecosystems, and enhanced efforts to monitor and restore the marine ecosystem. However, these positive effects are unlikely to balance the negative impacts, which are expected to be particularly prominent in developing tropical regions, where the capacity to implement conservation policies is limited. Uncertainties as to the present loss rate, derived from the paucity of coherent monitoring programmes, and the present inability to formulate reliable predictions as to the future rate of loss, represent a major barrier to the formulation of global conservation policies. Three key actions are needed to ensure the effective conservation of seagrass ecosystems: (1) the development of a coherent worldwide monitoring network, (2) the development of quantitative models predicting the responses of seagrasses to disturbance, and (3) the education of the public on the functions of seagrass meadows and the impacts of human activity.

Abstract Policies aiming to preserve vegetated coastal ecosystems (VCE; tidal marshes, mangroves and seagrasses) to mitigate greenhouse gas emissions require national assessments of blue carbon resources. Here, we present organic carbon (C) storage in VCE across Australian climate regions and estimate potential annual CO 2 emission benefits of VCE conservation and restoration. Australia contributes 5–11% of the C stored in VCE globally (70–185 Tg C in aboveground biomass, and 1,055–1,540 Tg C in the upper 1 m of soils). Potential CO 2 emissions from current VCE losses are estimated at 2.1–3.1 Tg CO 2 -e yr -1 , increasing annual CO 2 emissions from land use change in Australia by 12–21%. This assessment, the most comprehensive for any nation to-date, demonstrates the potential of conservation and restoration of VCE to underpin national policy development for reducing greenhouse gas emissions.

We review the photosynthetic responses to drought in field-grown grapevines and other species. As in other plant species, the relationship between photosynthesis and leaf water potential and/or relative water content in field-grown grapevines depends on conditions during plant growth and measurements. However, when light-saturated stomatal conductance was used as the reference parameter to reflect drought intensity, a common response pattern was observed that was much less dependent on the species and conditions. Many photosynthetic parameters (e.g. electron transport rate, carboxylation efficiency, intrinsic water-use efficiency, respiration rate in the light, etc.) were also more strongly correlated with stomatal conductance than with water status itself. Moreover, steady-state chlorophyll fluorescence also showed a high dependency on stomatal conductance. This is discussed in terms of an integrated down-regulation of the whole photosynthetic process by CO2 availability in the mesophyll. A study with six Mediterranean shrubs revealed that, in spite of some marked interspecific differences, all followed the same pattern of dependence of photosynthetic processes on stomatal conductance, and this pattern was quite similar to that of grapevines. Further analysis of the available literature suggests that the above-mentioned pattern is general for C3 plants. Even though the patterns described do not necessarily imply a cause and effect relationship, they can help our understanding of the apparent contradictions concerning stomatal vs. non-stomatal limitations to photosynthesis under drought. The significance of these findings for the improvement of water-use efficiency of crops is discussed.