ALBERT

Description: To the Editor: Mass spectrometry–based proteomics has become an important component of biological research. Numerous proteomics methods have been developed to identify and quantify the proteins in biological and clinical samples1, identify pathways affected by endogenous and exogenous perturbations2 and characterize protein complexes3. Despite successes, the interpretation of vast proteomics data…

Description: Greenland's bed topography is a primary control on ice flow, grounding line migration, calving dynamics, and subglacial drainage. Moreover, fjord bathymetry regulates the penetration of warm Atlantic water (AW) that rapidly melts and undercuts Greenland's marine-terminating glaciers. Here we present a new compilation of Greenland bed topography that assimilates seafloor bathymetry and ice thickness data through a mass conservation approach. A new 150 m horizontal resolution bed topography/bathymetric map of Greenland is constructed with seamless transitions at the ice/ocean interface, yielding major improvements over previous data sets, particularly in the marine-terminating sectors of northwest and southeast Greenland. Our map reveals that the total sea level potential of the Greenland ice sheet is 7.42 ± 0.05 m, which is 7 cm greater than previous estimates. Furthermore, it explains recent calving front response of numerous outlet glaciers and reveals new pathways by which AW can access glaciers with marine-based basins, thereby highlighting sectors of Greenland that are most vulnerable to future oceanic forcing.

Description: Monthly zonal mean climatologies of atmospheric measurements from satellite instruments can have biases due to the non-uniform sampling of the atmosphere by the instruments. We characterize potential sampling biases in stratospheric trace gas climatologies of the Stratospheric Processes and their Role in Climate (SPARC) Data Initiative using chemical fields from a chemistry climate model simulation and sampling patterns from 16 satellite-borne instruments. The exercise is performed for the long-lived stratospheric trace gases O3 and H2O. Monthly sample biases for O3 exceed 10% for many instruments in the high latitude stratosphere and in the upper troposphere/lower stratosphere, while annual mean sampling biases reach values of up to 20% in the same regions for some instruments. Sampling biases for H2O are generally smaller than for O3, although still notable in the upper troposphere/lower stratosphere and Southern Hemisphere high latitudes. The most important mechanism leading to monthly sampling bias is the non-uniform temporal sampling of many instruments, i.e., the fact that for many instruments, monthly means are produced from measurements which span less than the full month in question. Similarly, annual mean sampling biases are well explained by non-uniformity in the month-to-month sampling by different instruments. Non-uniform sampling in latitude and longitude are shown to also lead to non-negligible sampling biases, which are most relevant for climatologies which are otherwise free of sampling biases due to non-uniform temporal sampling.

Description: The Calabrian Arc (CA) subduction system is part of the Africa-Eurasia plate boundary, is one of the most seismically active regions in the Mediterranean Sea, and has been struck repeatedly by destructive historical earthquakes. In this study we investigate the effects of historical earthquakes on abyssal marine sedimentation through the analysis of the turbidite record. We collected gravity cores in tectonically controlled basins where the eastern Mediterranean pelagic sequence is interbedded with re-sedimented units. Textural, micropaleontological, geochemical and mineralogical signatures reveal three turbidite events in the last Millennium. We dated the turbidite sequences from two different cores using different radiometric methods, while the average time interval between successive turbidite beds was estimated from pelagic sediment thickness and sedimentation rates; chronologies were refined through age modelling that provided age ranges (2σ) of each turbidite bed. The results suggest that turbidite emplacement was triggered by three historical earthquakes recorded in the area (i.e. the 1908, 1693 and 1169 events); their magnitude, epicentral location and associated tsunamis support causative faults located in the Ionian Sea. The source for all the turbidites, as inferred from their mineralogy, is the metamorphic basement outcropping in southern Calabria and/or North-Eastern Sicily. Turbidite composition and cable breaks for the 1908 event have been used to infer likely travelling paths and seismogenic faults in the subduction system. Our findings suggest that Ionian Sea turbidites represent more than 80% of sedimentation and may be seabed archives of paleo-earthquakes capable of reconstructing seismicity back in time, during several earthquake cycles. Key Points We examine interplay between historical seismicity, mass failures and turbidites We reconstruct chronology of earthquake triggered turbidites in the Ionian Sea Turbidite composition has been used to reconstruct sediment source

Description: Coccolithophores have influenced the global climate for over 200 million years. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO 2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO 2 production or uptake, sequestration and export to the deep ocean. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions. © 2013 Macmillan Publishers Limited. All rights reserved.

Description: Aim: Human activities have introduced numerous non-native species (NNS) worldwide. Understanding and predicting large-scale NNS establishment patterns remain fundamental scientific challenges. Here, we evaluate if NNS composition represents a proportional subset of the total species pool available to invade (i.e. total global biodiversity), or, conversely, certain taxa are disproportionately pre-disposed to establish in non-native areas. Location: Global. Time period: Present day. Major taxa studied: Global diversity. Methods: We compiled one of the most comprehensive global databases of NNS (36,822 established species) to determine if NNS diversity is a representative proportional subset of global biodiversity. Results: Our study revealed that, while NNS diversity mirrors global biodiversity to a certain extent, due to significant deviance from the null model it is not always a representative proportional subset of global biodiversity. The strength of global biodiversity as a predictor depended on the taxonomic scale, with successive lower taxonomic levels less predictive than the one above it. Consequently, on average, 58%, 42% and 28% of variability in NNS numbers were explained by global biodiversity for phylum, class and family respectively. Moreover, global biodiversity was a similarly strong explanatory variable for NNS diversity among regions, but not habitats (i.e. terrestrial, freshwater and marine), where it better predicted NNS diversity for terrestrial than for freshwater and marine habitats. Freshwater and marine habitats were also greatly understudied relative to invasions in the terrestrial habitats. Over-represented NNS relative to global biodiversity tended to be those intentionally introduced and/or ‘hitchhikers’ associated with deliberate introductions. Finally, randomness is likely an important factor in the establishment success of NNS. Main conclusions: Besides global biodiversity, other important explanatory variables for large-scale patterns of NNS diversity likely include propagule and colonization pressures, environmental similarity between native and non-native regions, biased selection of intentionally introduced species and disparate research efforts of habitats and taxa.

Description: THE Sierra Leone Rise, located in the east equatorial Atlantic, forms a discontinuous chain of seamounts as shallow as 2 km extending with a general NE–SW trend from near the Sierra Leone coast of Africa, to the St Paul fracture zone near the Mid-Atlantic Ridge (Fig. 1). The origin of this feature has remained a topic of discussion. Sheridan et al.1 have hypothesised that the Sierra Leone Rise is a volcanic structure formed at the beginning of the opening of the Atlantic in the early Cretaceous period. The twin features of the Sierra Leone and the Ceara Rises are probably of oceanic origin and were created 80 Myr ago or later in their present-day position with respect to Africa and South America2. The Atlantic ocean exhibits several similar aseismic structures which appear symmetrically oriented with respect to the mid-oceanic ridge, such as the Walvis–Rio Grande Rise and the Iceland Faeroes–Iceland Greenland Ridges. These structures are volcanic edifices having a composition similar to that found in their associated islands3–7. Deep sea drilling of the Ceara Rise8,9 penetrated a basaltic basement of the upper Cretaceous period (Maestrichtian) (Leg 39, Site 354). Similarly, a DSDP hole (Leg 41, Site 366) on the Sierra Leone Rise, penetrated sediments of the same period, without reaching basement10. We report here the discovery of alkali-rich volcanics in an area of the Sierra Leone Rise. The sediment overlying the rock fragments is aged ∼45 Myr.

Description: Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth1, 2. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology3, 4, 5. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (approx40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.

Description: Microbial activity is a fundamental component of oceanic nutrient cycles. Photosynthetic microbes, collectively termed phytoplankton, are responsible for the vast majority of primary production in marine waters. The availability of nutrients in the upper ocean frequently limits the activity and abundance of these organisms. Experimental data have revealed two broad regimes of phytoplankton nutrient limitation in the modern upper ocean. Nitrogen availability tends to limit productivity throughout much of the surface low-latitude ocean, where the supply of nutrients from the subsurface is relatively slow. In contrast, iron often limits productivity where subsurface nutrient supply is enhanced, including within the main oceanic upwelling regions of the Southern Ocean and the eastern equatorial Pacific. Phosphorus, vitamins and micronutrients other than iron may also (co-)limit marine phytoplankton. The spatial patterns and importance of co-limitation, however, remain unclear. Variability in the stoichiometries of nutrient supply and biological demand are key determinants of oceanic nutrient limitation. Deciphering the mechanisms that underpin this variability, and the consequences for marine microbes, will be a challenge. But such knowledge will be crucial for accurately predicting the consequences of ongoing anthropogenic perturbations to oceanic nutrient biogeochemistry.