ALBERT

Description: Marine phytoplankton blooms are annual spring events that sustain active and diverse bloom-associated bacterial populations. Blooms vary considerably in terms of eukaryotic species composition and environmental conditions, but a limited number of heterotrophic bacterial lineages — primarily members of the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria — dominate these communities. In this Review, we discuss the central role that these bacteria have in transforming phytoplankton-derived organic matter and thus in biogeochemical nutrient cycling. On the basis of selected field and laboratory-based studies of flavobacteria and roseobacters, distinct metabolic strategies are emerging for these archetypal phytoplankton-associated taxa, which provide insights into the underlying mechanisms that dictate their behaviours during blooms.

Description: Owing to the turbulent nature of the ocean, mesoscale eddies are omnipresent. The impact of these transitory and approximately circular sea surface temperature fronts on the overlying atmosphere is not well known. Stationary fronts such as the Gulf Stream have been reported to lead to pronounced atmospheric changes1, 2. However, the impact of transient ocean eddies on the atmosphere has not been determined systematically, except on winds and to some extent clouds3, 4, 5, 6. Here, we examine the atmospheric conditions associated with over 600,000 individual eddies in the Southern Ocean, using satellite data. We show that ocean eddies locally affect near-surface wind, cloud properties and rainfall. The observed pattern of atmospheric change is consistent with a mechanism in which sea surface temperature anomalies associated with the oceanic eddies modify turbulence in the atmospheric boundary layer. In the case of cyclonic eddies, this modification triggers a slackening of near-surface winds, a decline in cloud fraction and water content, and a reduction in rainfall. We conclude that transient mesoscale ocean structures can significantly affect much larger atmospheric low-pressure systems that swiftly pass by at the latitudes investigated.

Description: An influence of solar irradiance variations on Earth’s surface climate has been repeatedly suggested, based on correlations between solar variability and meteorological variables1. Specifically, weaker westerly winds have been observed in winters with a less active sun, for example at the minimum phase of the 11-year sunspot cycle2, 3, 4. With some possible exceptions5, 6, it has proved difficult for climate models to consistently reproduce this signal7, 8. Spectral Irradiance Monitor satellite measurements indicate that variations in solar ultraviolet irradiance may be larger than previously thought9. Here we drive an ocean–atmosphere climate model with ultraviolet irradiance variations based on these observations. We find that the model responds to the solar minimum with patterns in surface pressure and temperature that resemble the negative phase of the North Atlantic or Arctic Oscillation, of similar magnitude to observations. In our model, the anomalies descend through the depth of the extratropical winter atmosphere. If the updated measurements of solar ultraviolet irradiance are correct, low solar activity, as observed during recent years, drives cold winters in northern Europe and the United States, and mild winters over southern Europe and Canada, with little direct change in globally averaged temperature. Given the quasiregularity of the 11-year solar cycle, our findings may help improve decadal climate predictions for highly populated extratropical regions

Description: Microbial mats collected at cold methane seeps in the Black Sea carry out anaerobic oxidation of methane (AOM) to carbon dioxide using sulfate as the electron acceptor. These mats, which predominantly consist of sulfate-reducing bacteria and archaea of the ANME-1 and ANME-2 type, contain large amounts of proteins very similar to methyl-coenzyme M reductase from methanogenic archaea. Mass spectrometry of mat samples revealed the presence of two nickel-containing cofactors in comparable amounts, one with the same mass as coenzyme F430 from methanogens (m/z = 905) and one with a mass that is 46 Da higher (m/z = 951). The two cofactors were isolated and purified, and their constitution and absolute configuration were determined. The cofactor with m/z = 905 was proven to be identical to coenzyme F430 from methanogens. For the m/z = 951 species, high resolution ICP-MS pointed to F430 + CH2S as the molecular formula, and LA-ICP-SF MS finally confirmed the presence of one sulfur atom per nickel. Esterification gave two stereoisomeric pentamethyl esters with m/z = 1021, which could be purified by reverse phase HPLC and were subjected to comprehensive NMR analysis, allowing determination of their constitution and configuration as (172S)−172-methylthio-F430 pentamethyl ester and (172R)−172-methylthio-F430 pentamethyl ester. The corresponding diastereoisomeric pentaacids could also be separated by HPLC and were correlated to the esters via mild hydrolysis of the latter. Equilibration of the pentaacids under acid catalysis showed that the (172S) isomer is the naturally occurring albeit thermodynamically less stable one. The more stable (172R) isomer (80% at equilibrium) is an isolation artifact generated under the acidic conditions necessary for the isolation of the cofactors from the calcium carbonate-encrusted mats.

Description: The anaerobic oxidation of methane (AOM) with sulphate, an area currently generating great interest in microbiology, is accomplished by consortia of methanotrophic archaea (ANME) and sulphate-reducing bacteria1, 2. The enzyme activating methane in methanotrophic archaea has tentatively been identified as a homologue of methyl-coenzyme M reductase (MCR) that catalyses the methane-forming step in methanogenic archaea3, 4. Here we report an X-ray structure of the 280 kDa heterohexameric ANME-1 MCR complex. It was crystallized uniquely from a protein ensemble purified from consortia of microorganisms collected with a submersible from a Black Sea mat catalysing AOM with sulphate4. Crystals grown from the heterogeneous sample diffract to 2.1 Å resolution and consist of a single ANME-1 MCR population, demonstrating the strong selective power of crystallization. The structure revealed ANME-1 MCR in complex with coenzyme M and coenzyme B, indicating the same substrates for MCR from methanotrophic and methanogenic archaea. Differences between the highly similar structures of ANME-1 MCR and methanogenic MCR include a F430 modification, a cysteine-rich patch and an altered post-translational amino acid modification pattern, which may tune the enzymes for their functions in different biological contexts.

Description: Iron limits phytoplankton growth and hence the biological carbon pump in the Southern Ocean1. Models assessing the impacts of iron on the global carbon cycle generally rely on dust input and sediment resuspension as the predominant sources2, 3. Although it was previously thought that most iron from deep-ocean hydrothermal activity was inaccessible to phytoplankton because of the formation of particulates4, it has been suggested that iron from hydrothermal activity5, 6, 7 may be an important source of oceanic dissolved iron8, 9, 10, 11, 12, 13. Here we use a global ocean model to assess the impacts of an annual dissolved iron flux of approximately 9×108 mol, as estimated from regional observations of hydrothermal activity11, 12, on the dissolved iron inventory of the world’s oceans. We find the response to the input of hydrothermal dissolved iron is greatest in the Southern Hemisphere oceans. In particular, observations of the distribution of dissolved iron in the Southern Ocean3 (Chever et al., manuscript in preparation; Bowie et al., manuscript in preparation) can be replicated in our simulations only when our estimated iron flux from hydrothermal sources is included. As the hydrothermal flux of iron is relatively constant over millennial timescales14, we propose that hydrothermal activity can buffer the oceanic dissolved iron inventory against shorter-term fluctuations in dust deposition.

Description: Biological N2 fixation is an important part of the marine nitrogen cycle as it provides a source of new nitrogen that can support biological carbon export and sequestration. Research in the past decade has focused on determining the patterns of distribution and abundance of diazotrophs, defining the environmental features leading to these patterns and characterizing the factors that constrain marine N2 fixation overall. In this Review, we describe how variations in the deposition of iron from dust to different ocean basins affects the limiting nutrient for N2 fixation and the distribution of different diazotrophic species. However, many questions remain about marine N2 fixation, including the role of temperature, fixed nitrogen species, CO2 and physical forcing in controlling N2 fixation, as well as the potential for heterotrophic N2 fixation.

Description: New light is shed on Worthington's concept of the North Atlantic circulation, postulating the existence of two anticyclonic gyres. This concept, which seems to have been laid to rest in the last decade, has now been reinforced by the results of a simple linear Sverdrup circulation model yielding a band of westward transport all across the North Atlantic at about the Azores latitude. This narrow band is called the Azores Countercurrent (AzCC) and matches the position of westward flow required by Worthington's “northern gyre.” An anomaly in the meridional change of the wind-stress curl in the eastern North Atlantic has been identified as the driving mechanism. A comparison with observations shows that the AzCC is verified in many analyses of historical datasets and synoptic surveys. A lack of the AzCC in other analyses is probably due to missing meridional sections, strong smoothing, and the superimposed Ekman flow close to the sea surface directed to the southeast. The AzCC has not been verified in low-resolution general circulation models applying simplified wind-stress fields and large friction coefficients, but there is evidence for its existence in recent high-resolution models driven by realistic wind stresses. Based on these findings, a new pattern for the wind-driven upper ocean circulation of the midlatitude North Atlantic is presented.

Description: Although rising global sea levels will affect the shape of coastlines over the coming decades1, 2, the most severe and catastrophic shoreline changes occur as a consequence of local and regional-scale processes. Changes in sediment supply3 and deltaic subsidence4, 5, both natural or anthropogenic, and the occurrences of tropical cyclones4, 5 and tsunamis6 have been shown to be the leading controls on coastal erosion. Here, we use satellite images of South American mangrove-colonized mud banks collected over the past twenty years to reconstruct changes in the extent of the shoreline between the Amazon and Orinoco rivers. The observed timing of the redistribution of sediment and migration of the mud banks along the 1,500 km muddy coast suggests the dominant control of ocean forcing by the 18.6 year nodal tidal cycle7. Other factors affecting sea level such as global warming or El Niño and La Niña events show only secondary influences on the recorded changes. In the coming decade, the 18.6 year cycle will result in an increase of mean high water levels of 6 cm along the coast of French Guiana, which will lead to a 90 m shoreline retreat.

Description: The Pacific sector of Antarctica, including both the Antarctic Peninsula and continental West Antarctica, has experienced substantial warming in the past 30 years. An increase in the circumpolar westerlies, owing in part to the decline in stratospheric ozone concentrations since the late 1970s, may account for warming trends in the peninsula region in austral summer and autumn. The more widespread warming in continental West Antarctica (Ellsworth Land and Marie Byrd Land) occurs primarily in austral winter and spring, and remains unexplained. Here we use observations of Antarctic surface temperature and global sea surface temperature, and atmospheric circulation data to show that recent warming in continental West Antarctica is linked to sea surface temperature changes in the tropical Pacific. Over the past 30 years, anomalous sea surface temperatures in the central tropical Pacific have generated an atmospheric Rossby wave response that influences atmospheric circulation over the Amundsen Sea, causing increased advection of warm air to the Antarctic continent. General circulation model experiments show that the central tropical Pacific is a critical region for producing the observed high latitude response. We conclude that, by affecting the atmospheric circulation at high southern latitudes, increasing tropical sea surface temperatures may account for West Antarctic warming through most of the twentieth century.

Description: Microscopy, confocal Raman spectroscopy and powder X-ray diffraction (PXRD) were used for in situ investigations of the CO2-hydrocarbon exchange process in gas hydrates and its driving forces. The study comprises the exposure of simple structure I CH4 hydrate and mixed structure II CH4–C2H6 and CH4–C3H8 hydrates to gaseous CO2 as well as the reverse reaction, i.e., the conversion of CO2-rich structure I hydrate into structure II mixed hydrate. In the case of CH4–C3H8 hydrates, a conversion in the presence of gaseous CO2 from a supposedly more stable structure II hydrate to a less stable structure I CO2-rich hydrate was observed. PXRD data show that the reverse process requires longer initiation times, and structural changes seem to be less complete. Generally, the exchange process can be described as a decomposition and reformation process, in terms of a rearrangement of molecules, and is primarily induced by the chemical potential gradient between hydrate phase and the provided gas phase. The results show furthermore the dependency of the conversion rate on the surface area of the hydrate phase, the thermodynamic stability of the original and resulting hydrate phase, as well as the mobility of guest molecules and formation kinetics of the resulting hydrate phase.

Description: Zircon is a common mineral in continental crustal rocks. As it is not easily altered in processes such as erosion or transport, this mineral is often used in the reconstruction of geological processes such as the formation and evolution of the continents. Zircon can also survive under conditions of the Earth’s mantle, and rare cases of zircons crystallizing in the mantle significantly before their entrainment into magma and eruption to the surface have been reported1,2,3. Here we analyse the isotopic and trace element compositions of large zircons of gem quality from the Eger rift, Bohemian massif, and find that they are derived from the mantle. (U–Th)/He analyses suggest that the zircons as well as their host basalts erupted between 29 and 24 million years ago, but fragments from the same xenocrysts reveal U–Pb ages between 51 and 83 million years. We note a lack of older volcanism and of fragments from the lower crust, which suggests that crustal residence time before eruption is negligible and that most rock fragments found in similar basalts from adjacent volcanic fields equilibrated under mantle conditions. We conclude that a specific chemical environment in this part of the Earth’s upper mantle allowed the zircons to remain intact for about 20–60 million years.

Description: The synthetic production of monodisperse single magnetic domain nanoparticles at ambient temperature is challenging. In nature, magnetosomes--membrane-bound magnetic nanocrystals with unprecedented magnetic properties--can be biomineralized by magnetotactic bacteria. However, these microbes are difficult to handle. Expression of the underlying biosynthetic pathway from these fastidious microorganisms within other organisms could therefore greatly expand their nanotechnological and biomedical applications. So far, this has been hindered by the structural and genetic complexity of the magnetosome organelle and insufficient knowledge of the biosynthetic functions involved. Here, we show that the ability to biomineralize highly ordered magnetic nanostructures can be transferred to a foreign recipient. Expression of a minimal set of genes from the magnetotactic bacterium Magnetospirillum gryphiswaldense resulted in magnetosome biosynthesis within the photosynthetic model organism Rhodospirillum rubrum. Our findings will enable the sustainable production of tailored magnetic nanostructures in biotechnologically relevant hosts and represent a step towards the endogenous magnetization of various organisms by synthetic biology.

Description: Marine phytoplankton blooms are annual spring events that sustain active and diverse bloom-associated bacterial populations. Blooms vary considerably in terms of eukaryotic species composition and environmental conditions, but a limited number of heterotrophic bacterial lineages — primarily members of the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria — dominate these communities. In this Review, we discuss the central role that these bacteria have in transforming phytoplankton-derived organic matter and thus in biogeochemical nutrient cycling. On the basis of selected field and laboratory-based studies of flavobacteria and roseobacters, distinct metabolic strategies are emerging for these archetypal phytoplankton-associated taxa, which provide insights into the underlying mechanisms that dictate their behaviours during blooms.

Description: A sigma-coordinate, primitive equation ocean circulation model is used to explore the problem of the remnant generation of trapped waves about a tall, circular, isolated seamount by an incident oscillatory barotropic current. The numerical solutions are used to extend prior studies into the fully nonlinear regime, and in particular to quantify and interpret the occurrence of residual circulation. Specific attention is also devoted to the dependence of the resonance and rectification mechanisms on stratification, forcing frequency, and choice of subgrid-scale viscous closure. Resonantly generated trapped waves of significant amplitude are found to occur broadly in parameter space; a precise match between the frequency of the imposed incident current and the frequency of the trapped free wave is not necessary to produce substantial excitation of the trapped wave. The maximum amplification factors produced in these numerical solutions, O(100) times the strength of the incident current, are consistent with previous studies. In the presence of nonlinear advection, strong residual currents are produced. The time-mean circulation about the seamount is dominated by a strong bottom-intensified, anticyclonic circulation closely trapped to the seamount. Maximum local time-mean current amplitudes are found to be as large as 37% of the magnitude of the propagating waves. In addition to the strong anticyclonic residual flow, there is a weaker secondary circulation in the vertical-radial plane characterized by downwelling over the top of the seamount at all depths. Maximum vertical downwelling rates of several tens of meters per day occur at the summit of the seamount. The vertical mass flux implied by this systematic downwelling is balanced by a slow radial flux of mass directed outward along the flanks of the seamount. Time-mean budgets for the radial and azimuthal components of momentum show that horizontal eddy fluxes of momentum are responsible for transporting net radial and azimuthal momentum from the far field to the upper flanks of the seamount. There, Coriolis and pressure gradient forces provide the dominant balances in the radial direction. However, the Coriolis force and viscous effects provide the primary balance for the azimuthal component.

Description: North Atlantic air-sea heat and freshwater flux data from several sources are used to estimate the conversion rate of water from one density to another throughout the range of sea surface density. This cross-isopycnal mass flux varies greatly over the ocean, with a maximum of 32.2 × 106 m3 s−1 at σ = 26.1 kg m−3 (toward greater densities) and a minimum of −7.6 × 106 m3 s−1 (toward lesser densities) at σ = 23.0 kg m−3. The air-sea fluxes force water to accumulate in three density bands: one at the lowest sea surface densities generated by heating; one centered near the density of subtropical mode water; and one spanning subpolar mode water densities. The transfer of water to the highest and lowest densities is balanced by mixing, which returns water to the middle density range, and also by boundary sources or sinks. Integrating the cross-isopycnal flux over all densities gives an annual average sinking of about 9 × 1O6 m3 s−1, which presumably escapes across the equator and must be balanced by a similar inflow. Comparison with estimates from tracer studies suggests that the renewal of tracer characteristics at a given density may occur without the existence of an annual average mass source at that density, because along- and cross-isopycnal mixing can renew a tracer without supplying mass.

Description: Vertebrates have evolved a sophisticated adaptive immune system that relies on an almost infinite diversity of antigen receptors that are clonally expressed by specialized immune cells that roam the circulatory system. These immune cells provide vertebrates with extraordinary antigen-specific immune capacity and memory, while minimizing self-reactivity. Plants, however, lack specialized mobile immune cells. Instead, every plant cell is thought to be capable of launching an effective immune response. So how do plants achieve specific, self-tolerant immunity and establish immune memory? Recent developments point towards a multilayered plant innate immune system comprised of self-surveillance, systemic signalling and chromosomal changes that together establish effective immunity.

Description: To survey hepatitis B virus (HBV) integration in liver cancer genomes, we conducted massively parallel sequencing of 81 HBV-positive and 7 HBV-negative hepatocellular carcinomas (HCCs) and adjacent normal tissues. We found that HBV integration is observed more frequently in the tumors (86.4%) than in adjacent liver tissues (30.7%). Copy-number variations (CNVs) were significantly increased at HBV breakpoint locations where chromosomal instability was likely induced. Approximately 40% of HBV breakpoints within the HBV genome were located within a 1,800-bp region where the viral enhancer, X gene and core gene are located. We also identified recurrent HBV integration events (in ≥4 HCCs) that were validated by RNA sequencing (RNA-seq) and Sanger sequencing at the known and putative cancer-related TERT, MLL4 and CCNE1 genes, which showed upregulated gene expression in tumor versus normal tissue. We also report evidence that suggests that the number of HBV integrations is associated with patient survival.

Description: WHILE ammonites and all other ectocochleate cephalopods became extinct, nautiloids survived relatively unchanged from the Ordovician, suggesting that they are unusually well adapted to their niche. Here we obtain high-resolution tracks of Nautilus positions and depths, combined with telemetered jet pressures, which clarify both its lifestyle and economics. Nautilus is more active in nature than in captivity1, but its energy costs are lower than projected2,3. Viewing Nautilus as 'vertic', rather than benthic, resolves this contradiction. Records show that the cost of transport is the same in any direction within a vertical plane. Living on a reef face swept by a lateral current means that vertical movements4,5 sample large areas for chemical trails. A detected trail can be followed upcurrent in the slow-moving boundary layer, but no effort is wasted on horizontal movement without good prospects for food; long-range movements are downcurrent and made by drifting. Once fed, a Nautilus can reduce its energy costs by moving to deeper, cooler waters, where a single meal can last for months.

Description: Climate warming at the end of the last glaciation caused ice caps on Icelandic volcanoes to retreat. Removal of surface ice load is thought to have decreased pressures in the underlying mantle, triggering decompression melting, enhanced magma generation and increased volcanic activity1–3. Present-day climate change could have the same effect, although there may be a time lag of hundreds of years between magma generation and eruption4,5. However, in addition to increased magma generation, pressure changes associated with ice retreat should also alter the capacity for storing magma within the crust. Here we use a numerical model to evaluate the effect of the current decrease in ice load on magma storage in the crust at the Kverkfjöll volcanic system, located partially beneath Iceland’s largest ice cap. We compare the model results with radar and global positioning system measurements of surface displacement and changes in crustal stress between 2007 and 2008, during the intrusion of a deep dyke at Upptyppingar. We find that although the main component of stress recorded during dyke intrusion relates to plate extension, another component of stress is consistent with the stress field caused by the retreating ice cap. We conclude that the retreating ice cap led to enhanced capture of magma within the crust. We suggest that ice-cap retreat can promote magma storage, rather than eruption, at least in the short term.

Description: The elemental stoichiometry of sea water and particulate organic matter is remarkably similar. This observation led Redfield to hypothesize that the oceanic ratio of nitrate to phosphate is controlled by the remineralization of phytoplankton biomass1. The Redfield ratio is used universally to quantitatively link the marine nitrogen and phosphorus cycles in numerous biogeochemical applications2,3,4. Yet, empirical and theoretical studies show that the ratio of nitrogen to phosphorus in phytoplankton varies greatly with taxa5,6 and growth conditions7,8,9. Here we present a dynamic five-box ecosystem model showing that non-Redfield utilization of dissolved nitrogen and phosphorus by non-nitrogen-fixing phytoplankton controls the magnitude and distribution of nitrogen fixation. In our simulations, systems dominated by rapidly growing phytoplankton with low nitrogen to phosphorus uptake ratios reduce the phosphorus available for nitrogen fixation. In contrast, in systems dominated by slow-growing phytoplankton with high nitrogen to phosphorus uptake ratios nitrogen deficits are enhanced, and nitrogen fixation is promoted. We show that estimates of nitrogen fixation are up to fourfold too high when non-Redfield uptake stoichiometries are ignored. We suggest that the relative abundance of fast- and slow-growing phytoplankton controls the amount of new nitrogen added to the ocean.

Description: Numerical tools are essential for the prediction and evaluation of conventional hydrocarbon reservoir performance. Gas hydrates represent a vast natural resource with a significant energy potential. The numerical codes/tools describing processes involved during the dissociation (induced by several methods) for gas production from hydrates are powerful, but they need validation by comparison to empirical data to instill con fidence in their predictions. In this study, we successfully reproduce experimental data of hydrate dissociation using the TOUGH+HYDRATE (T+H) code. Methane(CH4)hydrate growth and dissociation in partially water- and gas-saturated Bentheim sandstone were spatially resolved using Magnetic Resonance Imaging (MRI), which allows the in situ monitoring of saturation and phase transitions. All the CH4 that had been initially converted to gas hydrate was recovered during depressurization. The physical system was reproduced numerically, usingboth a simplified 2D model and a 3D grid involving complex Voronoi elements. We modeled dissociation using both the equilibrium and the kinetic reaction options in T+H, and we used a range of kinetic parameters for sensitivity analysis and curve fitting. We successfully reproduced the experimental results, which confirmed the empirical data that demonstrated that heattransport was the limiting factor during dissociation. Dissociation was more sensitive to kinetic parameters than anticipated, which indicates that kinetic limitations may be important in short-term core studies and a necessity in such simulations. This is the first time T+H has been used to predict empirical nonmonotonic dissociation behavior, where hydrate dissociation and reformation occurred as parallel events.

Description: Methane hydrate, a potential future energy resource, is known to occur naturally in vast quantities beneath the ocean floor and in permafrost regions. It is important to evaluate how much methane is recoverable from these hydrate reserves. This article introduces the theoretical background of HydrateResSim, the National Energy Technology Laboratory (NETL) methane production simulator for hydrate-containing reservoirs, originally developed for NETL by Lawrence Berkeley National Laboratory (LBNL). It describes the mathematical model that governs the dissociation of methane hydrate by depressurization or thermal stimulation of the system, including the transport of multiple temperature-dependent components in multiple phases through a porous medium. The model equations are obtained by incorporating the multiphase Darcy’s law for gas and liquid into both the mass component balances and the energy conservation equations. Two submodels in HydrateResSim for hydrate dissociation are also considered: a kinetic model and a pure thermodynamic model. Contrary to more traditional reservoir simulations, the set of model unknowns or primary variables in HydrateResSim changes throughout the simulation as a result of the formation or dissociation of ice and hydrate phases during the simulation. The primary variable switch method (PVSM) is used to effectively track these phase changes. The equations are solved by utilizing the implicit time finite-difference method on the grid system, which can properly describe phase appearance or disappearance as well as the boundary conditions. The Newton-Raphson method is used to solve the linear equations after discretization and setup of the Jacobian matrix. We report here the application of HydrateResSim to a three-component, four-phase flow system in order to predict the methane produced from a laboratory-scale reservoir. The first results of HydrateResSim code in a peer-reviewed publication are presented in this article. The numerical solution was verified against the state-of-the art simulator TOUGH+Hydrate. The model was then used to compare twodissociation theories: kinetic and pure equilibrium. Generally, the kinetic model revealed a lower dissociation rate than the equilibrium model. The hydrate dissociation patterns differed significantly when the thermal boundary condition was shifted from adiabatic to constant-temperature. The surface area factor was found to have an important effect on the rate of hydrate dissociation for the kinetic model. The deviation between the kinetic and equilibrium models was found to increase with decreasing surface area factor.

Description: Scattered groups of these ancient fish may all stem from a single remote population. Coelacanths were discovered in the Comoros archipelago to the northwest of Madagascar in 1952. Since then, these rare, ancient fish have been found to the south off Mozambique, Madagascar and South Africa, and to the north off Kenya and Tanzania — but it was unclear whether these are separate populations or even subspecies. Here we show that the genetic variation between individuals from these different locations is unexpectedly low. Combined with earlier results from submersible and oceanographic observations1, 2, our findings indicate that a separate African metapopulation is unlikely to have existed and that locations distant from the Comoros were probably inhabited relatively recently by either dead-end drifters or founders that originated in the Comoros.

Description: Two new cyclic peroxides, 2 and 3, were isolated from a sample of the Norwegian sponge Plakortis simplex. Their structures including relative stereochemistry were elucidated by interpretation of MS and NMR data. Compound 3 exhibited moderate in vitro activity against six solid human tumor cell lines with IC50 values in the range 7−15 μg/mL.

Description: The exponentially increasing number of sequenced genomes necessitates fast, accurate, universally applicable and automated approaches for the delineation of prokaryotic species. We developed specI (species identification tool; http://www.bork.embl.de/software/specI/), a method to group organisms into species clusters based on 40 universal, single-copy phylogenetic marker genes. Applied to 3,496 prokaryotic genomes, specI identified 1,753 species clusters. Of 314 discrepancies with a widely used taxonomic classification, 〉62% were resolved by literature support.

Description: There have been decades, such as 2000–2009, when the observed globally averaged surface-temperature time series shows little increase or even a slightly negative trend1 (a hiatus period). However, the observed energy imbalance at the top-of-atmosphere for this recent decade indicates that a net energy flux into the climate system of about 1 W m−2 (refs 2, 3) should be producing warming somewhere in the system4,5. Here we analyse twenty-first-century climate-model simulations that maintain a consistent radiative imbalance at the top-of-atmosphere of about 1 W m−2 as observed for the past decade. Eight decades with a slightly negative global mean surface-temperature trend show that the ocean above 300 m takes up significantly less heat whereas the ocean below 300 m takes up significantly more, compared with non-hiatus decades. The model provides a plausible depiction of processes in the climate system causing the hiatus periods, and indicates that a hiatus period is a relatively common climate phenomenon and may be linked to La Niña-like conditions.

Description: Antarctic Bottom Water flows into the western North Atlantic across the equator, shifting from the western side to the eastern side of the trough between the American continents and the Mid-Atlantic Ridge as it continues north. This is puzzling because such large-scale motion is thought to be controlled by dynamics that disallows an eastern boundary current. Previous explanations for the transposition involve a (necessarily small-scale) density current that changes sides because of the change in sign of rotation across the equator, or a topographic effect that changes the sign of the effective mean vorticity gradient and thus requires an eastern boundary current. Here an alternative explanation for the overall structure of bottom flow is given. A source of mass to a thin bottom layer is assumed to upwell uniformly across its interface into a less dense layer at rest. A simple formula for the magnitude of the upwelling and thickness of the layer is derived that depends on the source strength to the bottom layer. For a strong enough source, the bottom layer thickness is zero along a grounding curve that separates the bottom water from the western boundary and confines it to the east. A band of recirculating interior flow occurs, supplied by an isolated northern and western boundary current. Similar structures appear to exist in the Antarctic Bottom Water of the western North Atlantic.

Description: Results of a three-dimensional primitive equation model are presented simulating turbulent mesoscale motions in the seasonal thermocline on an f plane. The model is based on a hybrid vertical coordinate scheme and conserves isopycnic potential vorticity. Mesoscale turbulence is modeled in terms of an unstable potential vorticity front. The model integration starts from a purely zonal, 60-km-wide geostrophically balanced jet, on which is superimposed a small initial perturbation. The most unstable mode exhibits a wavelength of 85 km and is driven by a mixed type of instability. Characteristic dynamical ingredients of the wave are enhanced cyclonic and anticyclonic relative vorticity in the troughs and the ridges, respectively, due to the curvature of the flow. Vertical motion of up to 10 m d−1 occurring downstream of the ridges (downwelling) and downstream of the troughs (upwelling) is driven by geostrophic advection of relative vorticity. The contrast of static stability across the front is changing during amplification of the instability: in troughs the stability is decreasing whereas in ridges it is increasing. The density field exhibits local anomalies of the isopycnals' depths (bumps) due to the ageostrophic cross-jet advection of potential vorticity streamers wound up in cyclones and anticyclones. Locally, the potential vorticity gradients are enhanced, creating a multiple front structure. The model results support observations and findings of earlier atmospheric and oceanic models. It is emphasized that mesoscale turbulent structures may have a profound influence on primary productivity, mixed-layer, and internal wave dynamics.

Description: As the complex interplay of forces in the ocean responds to climate change, the dynamics of global ocean circulation are shifting.

Description: The circulation of the northeastern Atlantic Ocean at intermediate depths is characterized by watermass transformation processes that involve Iceland–Scotland Overflow Water (ISOW) from the northeast, Labrador Sea Water (LSW) from the west, and Mediterranean Water from the south. Field observations were carried out with 89 eddy-resolving floats (RAFOS and MARVOR types). The data coverage achieved is remarkably high and enables a comprehensive study of the eastern basins between Iceland and the Azores. The trajectories show typical pathways of the water masses involved and the role that the complex bottom topography plays in defining them. The ISOW paths tend to lean against the slopes of the Reykjanes Ridge and Rockall Plateau. Westward escapes through multiple gaps in the ridge are possible, superimposed on a sustained southward flow in the eastern basin along the Mid-Atlantic Ridge. LSW pathways leading to the eastern basins are subject to high variability in flow direction and eddy activity. In addition to a selection of characteristic trajectories, maps of the horizontal distributions of Lagrangian eddy kinetic energy and integral time scales are presented. These reveal distinct areas of intensified mixing in the Iceland Basin, as well as the sharp contrast between the subpolar and subtropical dynamics. A self-contained eddy detection scheme is applied to obtain statistics on individual eddy properties and their abundance. It is suggested that much of the intensified mixing can be related to cyclonic activity, particularly in the subpolar region.

Description: The Vasco—Cirene field experiment, in January—February 2007, targeted the Seychelles—Chagos thermocline ridge (SCTR) region, with the main purpose of investigating Madden—Julian Oscillation (MJO)-related SST events. The Validation of the Aeroclipper System under Convective Occurrences (Vasco) experiment (Duvel et al. 2009) and Cirene cruise were designed to provide complementary views of air—sea interaction in the SCTR region. While meteorological balloons were deployed from the Seychelles as a part of Vasco, the Research Vessel (R/V) Suroît was cruising the SCTR region as a part of Cirene. more: The Vasco—Cirene program explores how strong air—sea interactions promoted by the shallow thermocline and high sea surface temperature in the Seychelles—Chagos thermocline ridge results in marked variability at synoptic, intraseasonal, and interannual time scales. The Cirene oceanographic cruise collected oceanic, atmospheric, and air—sea flux observations in this region in January—February 2007. The contemporaneous Vasco field experiment complemented these measurements with balloon deployments from the Seychelles. Cirene also contributed to the development of the Indian Ocean observing system via deployment of a mooring and 12 Argo profilers. Unusual conditions prevailed in the Indian Ocean during January and February 2007, following the Indian Ocean dipole climate anomaly of late 2006. Cirene measurements show that the Seychelles—Chagos thermocline ridge had higher-than-usual heat content with subsurface anomalies up to 7°C. The ocean surface was warmer and fresher than average, and unusual eastward currents prevailed down to 800 m. These anomalous conditions had a major impact on tuna fishing in early 2007. Our dataset also sampled the genesis and maturation of Tropical Cyclone Dora, including high surface temperatures and a strong diurnal cycle before the cyclone, followed by a 1.5°C cooling over 10 days. Balloonborne instruments sampled the surface and boundary layer dynamics of Dora. We observed small-scale structures like dry-air layers in the atmosphere and diurnal warm layers in the near-surface ocean. The Cirene data will quantify the impact of these finescale features on the upper-ocean heat budget and atmospheric deep convection.

Description: The mechanisms involved in setting the annual cycle of the Florida Current transport are revisited using an adjoint model approach. Adjoint sensitivities of the Florida Current transport to wind stress reproduce a realistic seasonal cycle with an amplitude of ~1.2 Sv (1 Sv ≡ 106 m3 s−1). The annual cycle is predominantly determined by wind stress forcing and related coastal upwelling (downwelling) north of the Florida Strait along the shelf off the North American coast. Fast barotropic waves propagate these anomalies southward and reach the Florida Strait within a month, causing an amplitude of ~1 Sv. Long baroclinic planetary Rossby waves originating from the interior are responsible for an amplitude of ~0.8 Sv but have a different phase. The sensitivities corresponding to the first baroclinic mode propagate westward and are highly influenced by topography. Considerable sensitivities are only found west of the Mid-Atlantic Ridge, with maximum values at the western shelf edge. The second baroclinic mode also has an impact on the Florida Current variability, but only when a mean flow is present. A second-mode wave train propagates southwestward from the ocean bottom on the western side of the Mid-Atlantic Ridge between ~36° and 46°N and at Flemish Cap, where the mean flow interacts with topography, to the surface. Other processes such as baroclinic waves along the shelf and local forcing within the Florida Strait are of minor importance.

Description: The residual effect of surface gravity waves on mean flows in the upper ocean is investigated using thickness weighted mean (TWM) theory applied in a vertically Lagrangian and horizontally Eulerian coordinate system. Depth-dependent equations for the conservation of volume, momentum, and energy are derived. These equations allow for (i) finite amplitude fluid motions, (ii) the horizontal divergence of currents and (iii) a concise treatment of both the kinematic and viscous boundary conditions at the sea surface. Under the assumptions of steady and monochromatic waves and a uniform turbulent viscosity, the TWM momentum equations are used to illustrate the pressure- and viscosity-induced momentum fluxes through the surface that are implicit in previous studies of the wave-induced modification of the classical Ekman spiral problem. The TWM approach clarifies, in particular, the surface momentum flux associated with the so-called virtual wave stress of Longuet-Higgins. Overall the TWM framework can be regarded as an alternative to the three-dimensional Lagrangian mean framework of Pierson. Moreover the TWM framework can be used to include the residual effect of surface waves in large-scale circulation models. In specific models that carry the TWM velocity appropriate for advecting tracers as their velocity variable, the turbulent viscosity term should be modified so that the viscosity acts only on the Eulerian mean velocity.

Description: The fields of immunology, microbiology, nutrition and metabolism are rapidly converging. Here we expand on a diet-microbiota model as the basis for the greater incidence of asthma and autoimmunity in developed countries.

Description: The mammalian gastrointestinal tract, the site of digestion and nutrient absorption, harbors trillions of beneficial commensal microbes from all three domains of life. Commensal bacteria, in particular, are key participants in the digestion of food, and are responsible for the extraction and synthesis of nutrients and other metabolites that are essential for the maintenance of mammalian health. Many of these nutrients and metabolites derived from commensal bacteria have been implicated in the development, homeostasis and function of the immune system, suggesting that commensal bacteria may influence host immunity via nutrient- and metabolite-dependent mechanisms. Here we review the current knowledge of how commensal bacteria regulate the production and bioavailability of immunomodulatory, diet-dependent nutrients and metabolites and discuss how these commensal bacteria–derived products may regulate the development and function of the mammalian immune system.

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: In bacteria, foreign nucleic acids are silenced by clustered, regularly interspaced, short palindromic repeats (CRISPR)--CRISPR-associated (Cas) systems. Bacterial type II CRISPR systems have been adapted to create guide RNAs that direct site-specific DNA cleavage by the Cas9 endonuclease in cultured cells. Here we show that the CRISPR-Cas system functions in vivo to induce targeted genetic modifications in zebrafish embryos with efficiencies similar to those obtained using zinc finger nucleases and transcription activator-like effector nucleases.

Description: In this paper we use the historical hydrographic data base for the South Atlantic Ocean to investigate (i) the hydrographic boundary between the subtropical gyre and the Antarctic Circumpolar Current (ACC), the Sub-tropical Front (STF), and (ii) the southern current band of the gyre, which is called the South Atlantic Current (SAC). The STF begins in the west in the Brazil-Falkland (Malvinas) confluence zone, but at locations at and west of 45°W this front is often coincident with the Brazil Current front. East of 45°W the STF appears to be a distinct feature to at least the region south of Africa, whereupon it continues into the Indian Ocean. The associated current band of increased zonal speed is the SAC, which, except for one instance, is found at or north of the surface STF until Indian Ocean water from the Agulhas retroflection is reached. A reversal of baroclinicity in the STF is observed south of a highly saline Agulhas ring, causing the SAC to separate from the STF and turn north into the Benguela Current. Zonal flow south of the STF is generally weak and serves to separate the South Atlantic and circumpolar currents. In the Argentine Basin, the SAC has a typical volume transport of 30 Sv (1 Sv = 106m3s−1) in the upper 1000 m relative to a deep potential density surface (σ4 = 45.87 kg m−3), and can be as high as 37 Sv. It is thus comparable to, or stronger than, the Brazil Current. In the Cape Basin, the transport of the SAC is reduced to about 15 SY before it turns north to feed the Benguela Current. In late 1983 this flow was joined by about 8 Sv of water from the Agulhas Current.

Description: In this study a scenario is developed of two adjacent Mediterranean Water eddies (meddies) as they were observed merging and drifting through the Iberian Basin. Observations are based on four RAFOS floats (at 850–1050 dbar), two hydrographic surveys (centered roughly at 38°N, 24°W), and trajectories of surface drifters (drogued at 100 m). In April 1991, the meddy A was identified and labeled by surface drifters. During the revisit one month later two meddies were encountered, B1 and B2, in the vicinity of the former meddy A. The coalescence of B1 (subsequently identified as A, one month older) and B2 is inferred from a simple kinematic model describing the observed movement of the RAFOS floats for up to three months after the second CTD survey. The deduced vorticity front, radius ∼15 km, within B1 was of insufficient strength to keep the core waters of B1 isolated and prevent the absorption of B1 by B2. The resulting meddy (B1 + B2) showed a clear near-surface dynamical signal. Its deep root (1800 m) could explain the expulsion from the meddy of the remaining RAFOS float and surface drifter at the time of the meddy's collision with the Josephine Seamount. For the first time, a set of Lagrangian and hydrographic observations give direct evidence that neighboring meddies can merge as predicted by theoretical considerations.

Description: The total transport of Antarctic Bottom Water across the Rio Grande Rise, including the western boundary, the Vema Channel, and the Hunter Channel is estimated from hydrographic measurements across these pathways. The contribution of the Vema Channel is greatest at 3.9 × 106 m3 s−1, which is very close to earlier estimates. The western boundary current contribution is 2.0 × 106 m3 s−1 and that of the Hunter Channel 0.7 × 106 m3 s−1. The lower values outside the Vema Channel are offset by the important source of mass they form to the lower density classes of bottom water. About 40% of the flow is concentrated in the highest density class representing the source of Weddell Sea Deep Water to the Brazil Basin. The flow structure is characterized by horizontal and vertical recirculation.

Description: There has been concern about recent temperature trends and the future effects of CO2 concentrations in the atmosphere1,2; but instrumental records only cover a few decades to a few centuries and it is essential that proxy data sources, such as pollen spectra from peats and lake sediments, be carefully interpreted as climate records. Several workers have shown statistically significant associations between the modern pollen rain and climatic parameters, an approach that by-passes the recognition of pollen/vegetation units. Statistically defined equations that associate abiotic and biotic elements are called transfer functions. We report here on the application of transfer function equations to nine middle and late Holocene peat and lake sediment sequences from northern Canada (Fig. 1).

Description: In this paper, the historical hydrographic database for the south Indian Ocean is used to investigate (i) the hydrographic boundary between the subtropical gyre and the Antarctic Circumpolar Current (ACC), the subtropical front (STF), and especially (ii) the southern current band of the gyre. A current band of increased zonal speeds in the upper 1000 m is found just north of the STF in the west near South Africa and at the surface STF in the open Indian Ocean until the waters off the coast of Australia are reached. As neither any other investigation of this current nor a name for it are known, the flow has been called the South Indian Ocean Current (SIOC). This name is anologous to the same current band in the South Atlantic Ocean, the South Atlantic Current. The STF is located in the entire south Indian Ocean near 40-degrees-S. The associated current band of increased zonal speeds is the SIOC, which is found at or north of the STF. East of 100-degrees-E the SIOC separates from the STF and continues to the northeast. The zonal flow south of the STF is normally weak and serves to separate the South Indian Ocean and Circumpolar currents. Near Africa the SIOC has a typical volume transport of 60 Sv (1 Sv = 10(6) m3 s-1) in the upper 1000 m relative to deep potential density surfaces of sigma(4) = 45.87 kg m-3 (2800-3500 m) or sigma(2) = 36.94 kg m-3 (1500-2500 m). Near western Australia the SIOC is reduced to about 10 Sv as it turns to the northeast.

Description: Hydrothermal vents emit sulphur and metals to the ocean1. Particular attention has been paid to hydrothermal fluxes of iron2–4, a limiting micronutrient of marine primary production5. Vent-derived ironwas previously thought to rapidly oxidize and precipitate around vents6. However, organic matter can bind to and stabilize dissolved and particulate iron in hydrothermal plumes7–9, facilitating its dispersion into the open ocean10. Here, we report measurements of the chemical speciation of sulphide and iron in high-temperature fluids emanating from vents in the East Pacific Rise and the Eastern Lau Spreading Center. We show that pyrite nanoparticles—composed of iron and sulphur—account for up to 10% of the filterable iron (less than 200nm in size) in these fluids. We suggest that these particles form before the discharge of the vent fluid. We estimate that pyrite nanoparticles sink more slowly than larger plume particles, and are more resistant to oxidation than dissolved Fe(II) and FeS.We suggest that the discharge of iron in the form of pyrite nanoparticles increases the probability that vent-derived iron will be transported over long distances in the deep ocean.

Description: The microenvironmental dynamics of the microbial mat of black band disease (BBD) and its less virulent precursor, cyanobacterial patch (CP), were extensively profiled using microsensors under different light intensities with respect to O(2), pH and H(2)S. BBD mats exhibited vertical stratification into an upper phototrophic and lower anoxic and sulphidic zone. At the progression front of BBD lesions, high sulphide levels up to 4977 μM were measured in darkness along with lower than ambient levels of pH (7.43±0.20). At the base of the coral-BBD microbial mat, conditions were hypoxic or anoxic depending on light intensity exposure. In contrast, CP mats did not exhibit strong microchemical stratification with mostly supersaturated oxygen conditions throughout the mats at all light intensities and with levels of pH generally higher than in BBD. Two of three replicate CP mats were devoid of sulphide, while the third replicate showed only low levels of sulphide (up to 42 μM) present in darkness and at intermediate light levels. The level of oxygenation and sulphide correlated well with lesion migration rates, that is virulence of the mats, which were greater in BBD than in CP. The results suggest that biogeochemical microgradients of BBD shaped by the complex microbial community, rather than a defined pathogen, are the major trigger for high virulence and the associated derived coral mortality of this disease.

Description: Many aspects of barnacle body form are known to be developmentally plastic. Perhaps the most striking examples of such plasticity occur in their feeding legs and unusually long penises, the sizes and shapes of which can change dramatically and adaptively with changes in conspecific density and local water flow conditions. However, whether variation in overall appendage form is mirrored by structural responses in cuticle and muscle is not known. In order to determine how structural variation underlies phenotypic plasticity in barnacle appendages, we examined barnacles occurring at low and high population densities from one wave-protected and one wave-exposed site. We used histological sectioning and fluorescence microscopy of feeding legs and penises to compare cuticle thickness, muscle thickness, and muscle organization, and artificial penis inflation to compare penis extensibility. We observed striking differences in cuticle thickness, muscle thickness, and muscle organization between sites that differed in water velocity, but we found no clear differences associated with variation in conspecific density. Penis extensibility also did not differ consistently between sites. These results are consistent with an adaptive explanation for much of the remarkable and complex variation in barnacle feeding leg and penis morphology among sites that differ in water velocity.

Description: Organic detritus passing from the sea surface through the water column to the sea floor controls nutrient regeneration, fuels benthic life and affects burial of organic carbon in the sediment record. Particle trap systems have enabled the first quantification of this important process. The results suggest that the dominant mechanism of vertical transport is by rapid settling of rare large particles, most likely of faecal pellets or marine snow of the order of 〉200 μm in diameter, whereas the more frequent small particles have an insignificant role in vertical mass flux4–6. The ultimate source of organic detritus is biological production in surface waters of the oceans. I determine here an empirical relationship that predicts organic carbon flux at any depth in the oceans below the base of the euphotic zone as a function of the mean net primary production rate at the surface and depth-dependent consumption. Such a relationship aids in estimating rates of decay of organic matter in the water column, benthic and water column respiration of oxygen in the deep sea and burial of organic carbon in the sediment record.

Description: The suggestion is advanced that the remarkably low static stability of Antarctic surface waters may arise from a feedback loop involving global deep-water temperatures. If deep-water temperatures are too warm, this promotes Antarctic convection, thereby strengthening the inflow of Antarctic Bottom Water into the ocean interior and cooling the deep ocean. If deep waters are too cold, this promotes Antarctic stratification allowing the deep ocean to warm because of the input of North Atlantic Deep Water. A steady-state deep-water temperature is achieved such that the Antarctic surface can barely undergo convection. A two-box model is used to illustrate this feedback loop in its simplest expression and to develop basic concepts, such as the bounds on the operation of this loop. The model illustrates the possible dominating influence of Antarctic upwelling rate and Antarctic freshwater balance on global deep-water temperatures.

Description: An empirical model for the temperature of subsurface water entrained into the ocean mixed layer (Te) is presented and evaluated to improve sea surface temperature anomaly (SSTA) simulations in an intermediate ocean model (IOM) of the tropical Pacific. An inverse modeling approach is adopted to estimate Te from an SSTA equation using observed SST and simulated upper-ocean currents. A relationship between Te and sea surface height (SSH) anomalies is then obtained by utilizing a singular value decomposition (SVD) of their covariance. This empirical scheme is able to better parameterize Te anomalies than other local schemes and quite realistically depicts interannual variability of Te, including a nonlocal phase lag relation of Te variations relative to SSH anomalies over the central equatorial Pacific. An improved Te parameterization naturally leads to better depiction of the subsurface effect on SST variability by the mean upwelling of subsurface temperature anomalies. As a result, SSTA simulations are significantly improved in the equatorial Pacific; a comparison with other schemes indicates that systematic errors of the simulated SSTAs are significantly small—apparently due to the optimized empirical Teparameterization. Cross validation and comparisons with other model simulations are made to illustrate the robustness and effectiveness of the scheme. In particular it is demonstrated that the empirical Te model constructed from one historical period can be successfully used to improve SSTA simulations in another.

Description: The western Pacific subtropical high (WPSH) is closely related to Asian climate. Previous examination of changes in the WPSH found a westward extension since the late 1970s, which has contributed to the inter-decadal transition of East Asian climate. The reason for the westward extension is unknown, however. The present study suggests that this significant change of WPSH is partly due to the atmosphere's response to the observed Indian Ocean-western Pacific (IWP) warming. Coordinated by a European Union's Sixth Framework Programme, Understanding the Dynamics of the Coupled Climate System (DYNAMITE), five AGCMs were forced by identical idealized sea surface temperature patterns representative of the IWP warming and cooling. The results of these numerical experiments suggest that the negative heating in the central and eastern tropical Pacific and increased convective heating in the equatorial Indian Ocean/ Maritime Continent associated with IWP warming are in favor of the westward extension of WPSH. The SST changes in IWP influences the Walker circulation, with a subsequent reduction of convections in the tropical central and eastern Pacific, which then forces an ENSO/Gill-type response that modulates the WPSH. The monsoon diabatic heating mechanism proposed by Rodwell and Hoskins plays a secondary reinforcing role in the westward extension of WPSH. The low-level equatorial flank of WPSH is interpreted as a Kelvin response to monsoon condensational heating, while the intensified poleward flow along the western flank of WPSH is in accord with Sverdrup vorticity balance. The IWP warming has led to an expansion of the South Asian high in the upper troposphere, as seen in the reanalysis.

Description: The new aromatic polyketides genoketide A1, genoketide A2 and prechrysophanol glucuronide are biosynthetic intermediates of the octaketide chrysophanol. They were isolated from the alkaliphilic strain Streptomyces sp. AK 671 together with the new metabolite chrysophanol glucuronide. The structures of the compounds were elucidated by mass spectrometry and NMR methods. Genoketide A2 exhibited a slight and prechrysophanol glucuronide a more pronounced inhibition of the proliferation of L5178y lymphoma cells.

Description: Predicting the evolution of climate over decadal timescales requires a quantitative understanding of the dynamics that govern the meridional overturning circulation (MOC)1. Comprehensive ocean measurement programmes aiming to monitor MOC variations have been established in the subtropical North Atlantic2, 3 (RAPID, at latitude 26.5° N, and MOVE, at latitude 16° N) and show strong variability on intraseasonal to interannual timescales. Observational evidence of longer-term changes in MOC transport remains scarce, owing to infrequent sampling of transoceanic sections over past decades4, 5. Inferences based on long-term sea surface temperature records, however, supported by model simulations, suggest a variability with an amplitude of plusminus1.5–3 Sv (1 Sv = 106 m3 s-1) on decadal timescales in the subtropics6. Such variability has been attributed to variations of deep water formation in the sub-arctic Atlantic, particularly the renewal rate of Labrador Sea Water7. Here we present results from a model simulation that suggest an additional influence on decadal MOC variability having a Southern Hemisphere origin: dynamic signals originating in the Agulhas leakage region at the southern tip of Africa. These contribute a MOC signal in the tropical and subtropical North Atlantic that is of the same order of magnitude as the northern source. A complete rationalization of observed MOC changes therefore also requires consideration of signals arriving from the south.

Description: The eddy correlation technique is rapidly becoming an established method for resolving dissolved oxygen fluxes in natural aquatic systems. This direct and noninvasive determination of oxygen fluxes close to the sediment by simultaneously measuring the velocity and the dissolved oxygen fluctuations has considerable advantages compared to traditional methods. This paper describes the measurement principle and analyzes the spatial and temporal scales of those fluctuations as a function of turbulence levels. The magnitudes and spectral structure of the expected fluctuations provide the required sensor specifications and define practical boundary conditions for the eddy correlation instrumentation and its deployment. In addition, data analysis and spectral corrections are proposed for the usual nonideal conditions, such as the time shift between the sensor pair and the limited frequency response of the oxygen sensor. The consistency of the eddy correlation measurements in a riverine reservoir has been confirmed—observing a night–day transition from oxygen respiration to net oxygen production, ranging from −20 to +5 mmol m−2 day−1—by comparing two physically independent, eddy correlation instruments deployed side by side. The natural variability of the fluctuations calls for at least ∼1 h of flux data record to achieve a relative accuracy of better than ∼20%. Although various aspects still need improvement, eddy correlation is seen as a promising and soon-to-be widely applied method in natural waters.

Description: Some studies of ocean climate model experiments suggest that regional changes in dynamic sea level could provide a valuable indicator of trends in the strength of the Atlantic meridional overturning circulation (MOC). This paper describes the use of a sequence of global ocean–ice model experiments to show that the diagnosed patterns of sea surface height (SSH) anomalies associated with changes in the MOC in the North Atlantic (NA) depend critically on the time scales of interest. Model hindcast simulations for 1958–2004 reproduce the observed pattern of SSH variability with extrema occurring along the Gulf Stream (GS) and in the subpolar gyre (SPG), but they also show that the pattern is primarily related to the wind-driven variability of MOC and gyre circulation on interannual time scales; it is reflected also in the leading EOF of SSH variability over the NA Ocean, as described in previous studies. The pattern, however, is not useful as a “fingerprint” of longer-term changes in the MOC: as shown with a companion experiment, a multidecadal, gradual decline in the MOC [of 5 Sv (1 Sv ≡ 106 m3 s−1) over 5 decades] induces a much broader, basin-scale SSH rise over the mid-to-high-latitude NA, with amplitudes of 20 cm. The detectability of such a trend is low along the GS since low-frequency SSH changes are effectively masked here by strong variability on shorter time scales. More favorable signal-to-noise ratios are found in the SPG and the eastern NA, where a MOC trend of 0.1 Sv yr−1 would leave a significant imprint in SSH already after about 20 years.

Description: The relationship between carbon dioxide and climate over millions of years has been a source of controversy. Fossilized liverwort leaves can help illuminate both temperature and atmospheric carbon dioxide levels from 200 to 60 million years ago.

Description: Despite similar physical properties, the Northern and Southern Atlantic subtropical gyres have different biogeochemical regimes. The Northern subtropical gyre, which is subject to iron deposition from Saharan dust1, is depleted in the nutrient phosphate, possibly as a result of iron-enhanced nitrogen fixation2. Although phosphate depleted, rates of carbon fixation in the euphotic zone of the North Atlantic subtropical gyre are comparable to those of the South Atlantic subtropical gyre3, which is not phosphate limited. Here we use the activity of the phosphorus-specific enzyme alkaline phosphatase to show potentially enhanced utilization of dissolved organic phosphorus occurring over much of the North Atlantic subtropical gyre. We find that during the boreal spring up to 30% of primary production in the North Atlantic gyre is supported by dissolved organic phosphorus. Our diagnostics and composite map of the surface distribution of dissolved organic phosphorus in the subtropical Atlantic Ocean reveal shorter residence times in the North Atlantic gyre than the South Atlantic gyre. We interpret the asymmetry of dissolved organic phosphorus cycling in the two gyres as a consequence of enhanced nitrogen fixation in the North Atlantic Ocean4, which forces the system towards phosphorus limitation. We suggest that dissolved organic phosphorus utilization may contribute to primary production in other phosphorus-limited ocean settings as well.

Description: Changes in the ventilation of the oxygen minimum zone (OMZ) of the tropical North Atlantic are studied using oceanographic data from 18 research cruises carried out between 28.5° and 23°W during 1999–2008 as well as historical data referring to the period 1972–85. In the core of the OMZ at about 400-m depth, a highly significant oxygen decrease of about 15 μmol kg−1 is found between the two periods. During the same time interval, the salinity at the oxygen minimum increased by about 0.1. Above the core of the OMZ, within the central water layer, oxygen decreased too, but salinity changed only slightly or even decreased. The scatter in the local oxygen–salinity relations decreased from the earlier to the later period suggesting a reduced filamentation due to mesoscale eddies and/or zonal jets acting on the background gradients. Here it is suggested that latitudinally alternating zonal jets with observed amplitudes of a few centimeters per second in the depth range of the OMZ contribute to the ventilation of the OMZ. A conceptual model of the ventilation of the OMZ is used to corroborate the hypothesis that changes in the strength of zonal jets affect mean oxygen levels in the OMZ. According to the model, a weakening of zonal jets, which is in general agreement with observed hydrographic evidences, is associated with a reduction of the mean oxygen levels that could significantly contribute to the observed deoxygenation of the North Atlantic OMZ.

Description: Seasonal reconstructions of the Southern Hemisphere annular mode (SAM) index are derived to extend the record before the reanalysis period, using station sea level pressure (SLP) data as predictors. Two reconstructions using different predictands are obtained: one [Jones and Widmann (JW)] based on the first principal component (PC) of extratropical SLP and the other (Fogt) on the index of Marshall. A regional-based SAM index (Visbeck) is also considered.These predictands agree well post-1979; correlations decline in all seasons except austral summer for the full series starting in 1958. Predictand agreement is strongest in spring and summer; hence agreement between the reconstructions is highest in these seasons. The less zonally symmetric SAM structure in winter and spring influences the strength of the SAM signal over land areas, hence the number of stations included in the reconstructions. Reconstructions from 1865 were, therefore, derived in summer and autumn and from 1905 in winter and spring. This paper examines the skill of each reconstruction by comparison with observations and reanalysis data. Some of the individual peaks in the reconstructions, such as the most recent in austral summer, represent a full hemispheric SAM pattern, while others are caused by regional SLP anomalies over the locations of the predictors. The JW and Fogt reconstructions are of similar quality in summer and autumn, while in winter and spring the Marshall index is better reconstructed by Fogt than the PC index is by JW. In spring and autumn the SAM shows considerable variability prior to recent decades.

Description: Piceamycin, a new macrolactam polyketide antibiotic, was detected by HPLC-diode array screening in extracts of Streptomyces sp. GB 4-2, which was isolated from the mycorrhizosphere of Norway spruce. The structure of piceamycin was determined by mass spectrometry and NMR experiments. It showed inhibitory activity against Gram-positive bacteria, selected human tumor cell lines and protein tyrosine phosphatase 1B. The Journal of Antibiotics (2009) 62, 513-518; doi:10.1038/ja.2009.64; published online 17 July 2009

Description: Climate models used to produce global warming scenarios exhibit widely diverging responses of the thermohaline circulation (THC). To investigate the mechanisms responsible for this variability, a regional Atlantic Ocean model driven with forcing diagnosed from two coupled greenhouse gas simulations has been employed. One of the coupled models (MPI) shows an almost constant THC, the other (GFDL) shows a declining THC in the twenty-first century. The THC evolution in the regional model corresponds rather closely to that of the respective coupled simulation, that is, it remains constant when driven with the forcing from the MPI model, and declines when driven with the GFDL forcing. These findings indicate that a detailed representation of ocean processes in the region covered by the Atlantic model may not be critical for the simulation of the overall THC changes in a global warming scenario, and specifically that the coupled model’s rather coarse representation of water mass formation processes in the subpolar North Atlantic is unlikely to be the primary cause for the large differences in the THC evolution. Sensitivity experiments have confirmed that a main parameter governing the THC response to global warming is the density of the intermediate waters in the Greenland–Iceland–Norwegian Seas, which in turn influences the density of the North Atlantic Deep Water, whereas changes in the air–sea heat and freshwater fluxes over the subpolar North Atlantic are only of moderate importance, and mainly influence the interannual–decadal variability of THC. Finally, as a consequence of changing surface fluxes, the Labrador Sea convection ceases by about 2030 under both forcings (i.e., even in a situation where the overall THC is stable) indicating that the eventual breakdown of the convection is likely but need not coincide with substantial THC changes.

Description: Shortly after the advent of the first imaging passive microwave sensor on board a research satellite an anomalous climate feature was observed within the Weddell Sea. During the years 1974–1976, a 250 × 103 km2 area within the seasonal sea ice cover was virtually free of winter sea ice. This feature, the Weddell Polynya, was created as sea ice formation was inhibited by ocean convection that injected relatively warm deep water into the surface layer. Though smaller, less persistent polynyas associated with topographically induced upwelling at Maud Rise frequently form in the area, there has not been a reoccurrence of the Weddell Polynya since 1976. Archived observations of the surface layer salinity within the Weddell gyre suggest that the Weddell Polynya may have been induced by a prolonged period of negative Southern Annular Mode (SAM). During negative SAM the Weddell Sea experiences colder and drier atmospheric conditions, making for a saltier surface layer with reduced pycnocline stability. This condition enables Maud Rise upwelling to trigger sustained deep-reaching convection associated with the polynya. Since the late 1970s SAM has been close to neutral or in a positive state, resulting in warmer, wetter conditions over the Weddell Sea, forestalling repeat of the Weddell Polynya. A contributing factor to the Weddell Polynya initiation may have been a La Niña condition, which is associated with increased winter sea ice formation in the polynya area. If the surface layer is made sufficiently salty due to a prolonged negative SAM period, perhaps aided by La Niña, then Maud Rise upwelling meets with positive feedback, triggering convection, and a winter persistent Weddell Polynya.

Description: This study explores the influence of phytoplankton on the tropical Pacific heat budget. A hybrid coupled model for the tropical Pacific that is based on a primitive equation reduced-gravity multilayer ocean model, a dynamic ocean mixed layer, an atmospheric mixed layer, and a statistical atmosphere is used. The statistical atmosphere relates deviations of the sea surface temperature from its mean to wind stress anomalies and allows for the rectification of the annual cycle and the El Niño–Southern Oscillation (ENSO) phenomenon through the positive Bjerknes feedback. Furthermore, a nine-component ecosystem model is coupled to the physical variables of the ocean. The simulated chlorophyll concentrations can feed back onto the ocean heat budget by their optical properties, which modify solar light absorption in the surface layers. It is shown that both the surface layer concentration as well as the vertical profile of chlorophyll have a significant effect on the simulated mean state, the tropical annual cycle, and ENSO. This study supports a previously suggested hypothesis (Timmermann and Jin) that predicts an influence of phytoplankton concentration of the tropical Pacific climate mean state and its variability. The bioclimate feedback diagnosed here works as follows: Maxima in the subsurface chlorophyll concentrations lead to an enhanced subsurface warming due to the absorption of photosynthetically available shortwave radiation. This warming triggers a deepening of the mixed layer in the eastern equatorial Pacific and eventually a reduction of the surface ocean currents (Murtugudde et al.). The weakened south-equatorial current generates an eastern Pacific surface warming, which is strongly enhanced by the Bjerknes feedback. Because of the deepening of the mixed layer, the strength of the simulated annual cycle is also diminished. This in turn leads to an increase in ENSO variability.

Description: The authors present the first quantitative comparison between new velocity datasets and high-resolution models in the North Atlantic subpolar gyre [1/10° Parallel Ocean Program model (POPNA10), Miami Isopycnic Coordinate Ocean Model (MICOM), ° Atlantic model (ATL6), and Family of Linked Atlantic Ocean Model Experiments (FLAME)]. At the surface, the model velocities agree generally well with World Ocean Circulation Experiment (WOCE) drifter data. Two noticeable exceptions are the weakness of the East Greenland coastal current in models and the presence in the surface layers of a strong southwestward East Reykjanes Ridge Current. At depths, the most prominent feature of the circulation is the boundary current following the continental slope. In this narrow flow, it is found that gridded float datasets cannot be used for a quantitative comparison with models. The models have very different patterns of deep convection, and it is suggested that this could be related to the differences in their barotropic transport at Cape Farewell. Models show a large drift in watermass properties with a salinization of the Labrador Sea Water. The authors believe that the main cause is related to horizontal transports of salt because models with different forcing and vertical mixing share the same salinization problem. A remarkable feature of the model solutions is the large westward transport over Reykjanes Ridge [10 Sv (Sv ≡ 106 m3 s−1) or more]

Description: Recent observations show dramatic changes of the Arctic atmosphere–ice–ocean system. Here the authors demonstrate, through the analysis of a vast collection of previously unsynthesized observational data, that over the twentieth century the central Arctic Ocean became increasingly saltier with a rate of freshwater loss of 239 ± 270 km3 decade−1. In contrast, long-term (1920–2003) freshwater content (FWC) trends over the Siberian shelf show a general freshening tendency with a rate of 29 ± 50 km3 decade−1. These FWC trends are modulated by strong multidecadal variability with sustained and widespread patterns. Associated with this variability, the FWC record shows two periods in the 1920s–30s and in recent decades when the central Arctic Ocean was saltier, and two periods in the earlier century and in the 1940s–70s when it was fresher. The current analysis of potential causes for the recent central Arctic Ocean salinification suggests that the FWC anomalies generated on Arctic shelves (including anomalies resulting from river discharge inputs) and those caused by net atmospheric precipitation were too small to trigger long-term FWC variations in the central Arctic Ocean; to the contrary, they tend to moderate the observed long-term central-basin FWC changes. Variability of the intermediate Atlantic Water did not have apparent impact on changes of the upper–Arctic Ocean water masses. The authors’ estimates suggest that ice production and sustained draining of freshwater from the Arctic Ocean in response to winds are the key contributors to the salinification of the upper Arctic Ocean over recent decades. Strength of the export of Arctic ice and water controls the supply of Arctic freshwater to subpolar basins while the intensity of the Arctic Ocean FWC anomalies is of less importance. Observational data demonstrate striking coherent long-term variations of the key Arctic climate parameters and strong coupling of long-term changes in the Arctic–North Atlantic climate system. Finally, since the high-latitude freshwater plays a crucial role in establishing and regulating global thermohaline circulation, the long-term variations of the freshwater content discussed here should be considered when assessing climate change and variability.

Description: In this study, the authors discuss two different parameterizations for the effect of mixed layer eddies, one based on ageostrophic linear stability analysis (ALS) and the other one based on a scaling of the potential energy release by eddies (PER). Both parameterizations contradict each other in two aspects. First, they predict different functional relationships between the magnitude of the eddy fluxes and the Richardson number (Ri) related to the background state. Second, they also predict different vertical structure functions for the horizontal eddy fluxes. Numerical simulations for two different configurations and for a large range of different background conditions are used to evaluate the parameterizations. It turns out that PER is better suited to capture the Ri dependency of the magnitude of the eddy fluxes. On the other hand, the vertical structure of the meridional eddy fluxes predicted by ALS is more accurate than that of PER, while the vertical structure of the vertical eddy fluxes is well predicted by both parameterizations. Therefore, this study suggests the use of the magnitude of PER and the vertical structure functions of ALS for an improved parameterization of mixed layer eddy fluxes.

Description: Concerns about the slow pace of climate mitigation have led to renewed dialogue about solar-radiation management, which could be achieved by adding reflecting aerosols to the stratosphere1, 2, 3, 4, 5, 6. Modelling studies suggest that solar-radiation management could produce stabilized global temperatures and reduced global precipitation4, 5, 6. Here we present an analysis of regional differences in a climate modified by solar-radiation management, using a large-ensemble modelling experiment that examines the impacts of 54 scenarios for global temperature stabilization. Our results confirm that solar-radiation management would generally lead to less extreme temperature and precipitation anomalies, compared with unmitigated greenhouse gas emissions. However, they also illustrate that it is physically not feasible to stabilize global precipitation and temperature simultaneously as long as atmospheric greenhouse gas concentrations continue to rise. Over time, simulated temperature and precipitation in large regions such as China and India vary significantly with different trajectories for solar-radiation management, and they diverge from historical baselines in different directions. Hence, it may not be possible to stabilize the climate in all regions simultaneously using solar-radiation management. Regional diversity in the response to different levels of solar-radiation management could make consensus about the optimal level of geoengineering difficult, if not impossible, to achieve.

Description: Marine sponges are well known for their associations with highly diverse, yet very specific and often highly similar microbiota. The aim of this study was to identify potential bacterial sub-populations in relation to sponge phylogeny and sampling sites and to define the core bacterial community. 16S ribosomal RNA gene amplicon pyrosequencing was applied to 32 sponge species from eight locations around the world's oceans, thereby generating 2567 operational taxonomic units (OTUs at the 97% sequence similarity level) in total and up to 364 different OTUs per sponge species. The taxonomic richness detected in this study comprised 25 bacterial phyla with Proteobacteria, Chloroflexi and Poribacteria being most diverse in sponges. Among these phyla were nine candidate phyla, six of them found for the first time in sponges. Similarity comparison of bacterial communities revealed no correlation with host phylogeny but a tropical sub-population in that tropical sponges have more similar bacterial communities to each other than to subtropical sponges. A minimal core bacterial community consisting of very few OTUs (97%, 95% and 90%) was found. These microbes have a global distribution and are probably acquired via environmental transmission. In contrast, a large species-specific bacterial community was detected, which is represented by OTUs present in only a single sponge species. The species-specific bacterial community is probably mainly vertically transmitted. It is proposed that different sponges contain different bacterial species, however, these bacteria are still closely related to each other explaining the observed similarity of bacterial communities in sponges in this and previous studies. This global analysis represents the most comprehensive study of bacterial symbionts in sponges to date and provides novel insights into the complex structure of these unique associations.

Description: In this study, we present a single-cell genomics approach for the functional characterization of the candidate phylum Poribacteria, members of which are nearly exclusively found in marine sponges. The microbial consortia of the Mediterranean sponge Aplysina aerophoba were singularized by fluorescence-activated cell sorting, and individual microbial cells were subjected to phi29 polymerase-mediated 'whole-genome amplification'. Pyrosequencing of a single amplified genome (SAG) derived from a member of the Poribacteria resulted in nearly 1.6 Mb of genomic information distributed among 554 contigs analyzed in this study. Approximately two-third of the poribacterial genome was sequenced. Our findings shed light on the functional properties and lifestyle of a possibly ancient bacterial symbiont of marine sponges. The Poribacteria are mixotrophic bacteria with autotrophic CO(2)-fixation capacities through the Wood-Ljungdahl pathway. The cell wall is of Gram-negative origin. The Poribacteria produce at least two polyketide synthases (PKSs), one of which is the sponge-specific Sup-type PKS. Several putative symbiosis factors such as adhesins (bacterial Ig-like domains, lamininin G domain proteins), adhesin-related proteins (ankyrin, fibronectin type III) and tetratrico peptide repeat domain-encoding proteins were identified, which might be involved in mediating sponge-microbe interactions. The discovery of genes coding for 24-isopropyl steroids implies that certain fossil biomarkers used to date the origins of metazoan life on earth may possibly be of poribacterial origin. Single-cell genomic approaches, such as those shown herein, contribute to a better understanding of beneficial microbial consortia, of which most members are, because of the lack of cultivation, inaccessible by conventional techniques.

Description: THE vestimentiferan tubeworm Riftia pachyptila is found around hydrothermal vent areas in the deep sea. Intracellular bacterial chemoautotrophic symbionts use the oxidation of sulphide from the effluent of the vents as an energy source for CO2 fixation. They apparently provide most or all of the nutritional requirements for their gutless hosts1–5. This kind of symbiosis has since been found in many other species from various other phyla from other habitats6–9. Here we present results that the bacteria of R. pachyptila may cover a significant fraction of their respiratory needs by the use of nitrate in addition to oxygen. Nitrate is reduced to nitrite, which may be the end product (nitrate respiration)10 or it may be further reduced to nitrogen gas (denitrification)11. This metabolic trait may have an important role in the colonization of hypoxic habitats in general by animals with this kind of symbiosis.

Description: Abyssal temperature and velocity observations performed within the framework of the Neutrino Mediterranean Observatory, a project devoted to constructing a km3-scale underwater telescope for the detection of high-energy cosmic neutrinos, demonstrate cross-fertilization between subnuclear physics and experimental oceanography. Here we use data collected south of Sicily in the Ionian abyssal plain of the Eastern Mediterranean (EM) basin to show for the first time that abyssal vortices exist in the EM, at depths exceeding 2,500 m. The eddies consist of chains of near-inertially pulsating mesoscale cyclones/anticyclones. They are embedded in an abyssal current flowing towards North-Northwest. The paucity of existing data does not allow for an unambiguous determination of the vortex origin. A local generation mechanism seems probable, but a remote genesis cannot be excluded a priori. The presence of such eddies adds further complexity to the discussion of structure and evolution of water masses in the EM.

Description: Salinity is a major factor controlling the distribution of biota in aquatic systems, and most aquatic multicellular organisms are either adapted to life in saltwater or freshwater conditions. Consequently, the saltwater–freshwater mixing zones in coastal or estuarine areas are characterized by limited faunal and floral diversity. Although changes in diversity and decline in species richness in brackish waters is well documented in aquatic ecology, it is unknown to what extent this applies to bacterial communities. Here, we report a first detailed bacterial inventory from vertical profiles of 60 sampling stations distributed along the salinity gradient of the Baltic Sea, one of world's largest brackish water environments, generated using 454 pyrosequencing of partial (400 bp) 16S rRNA genes. Within the salinity gradient, bacterial community composition altered at broad and finer-scale phylogenetic levels. Analogous to faunal communities within brackish conditions, we identified a bacterial brackish water community comprising a diverse combination of freshwater and marine groups, along with populations unique to this environment. As water residence times in the Baltic Sea exceed 3 years, the observed bacterial community cannot be the result of mixing of fresh water and saltwater, but our study represents the first detailed description of an autochthonous brackish microbiome. In contrast to the decline in the diversity of multicellular organisms, reduced bacterial diversity at brackish conditions could not be established. It is possible that the rapid adaptation rate of bacteria has enabled a variety of lineages to fill what for higher organisms remains a challenging and relatively unoccupied ecological niche.

Description: The Denmark Strait overflow water is the largest dense water plume from the Nordic seas to feed the lower limb of the Atlantic Meridional Overturning Circulation. Its primary source is commonly thought to be the East Greenland Current. However, the recent discovery of the North Icelandic Jet—a deep-reaching current that flows along the continental slope of Iceland—has called this view into question. Here we present high-resolution measurements of hydrography and velocity north of Iceland, taken during two shipboard surveys in October 2008 and August 2009. We find that the North Icelandic Jet advects overflow water into the Denmark Strait and constitutes a pathway that is distinct from the East Greenland Current. We estimate that the jet supplies about half of the total overflow transport, and infer that it is the primary source of the densest overflow water. Simulations with an ocean general circulation model suggest that the import of warm, salty water from the North Icelandic Irminger Current and water-mass transformation in the interior Iceland Sea are critical to the formation of the jet. We surmise that the timescale for the renewal of the deepest water in the meridional overturning cell, and its sensitivity to changes in climate, could be different than presently envisaged.

Description: The Messina Strait, that separates peninsular Italy from Sicily, is one of the most seismically active areas of the Mediterranean. The structure and seismotectonic setting of the region are poorly understood, although the area is highly populated and important infrastructures are planned there. New seismic reflection data have identified a number of faults, as well as a crustal scale NE-trending anticline few km north of the strait. These features are interpreted as due to active right-lateral transpression along the north-eastern Sicilian offshore, coexisting with extensional and right-lateral transtensional tectonics in the southern Messina Strait. This complex tectonic network appears to be controlled by independent and overlapping tectonic settings, due to the presence of a diffuse transfer zone between the SE-ward retreating Calabria subduction zone relative to slab advance in the western Sicilian side.

Description: Calculations of the size and density of atmospheric aerosols are complicated by the fact that they can exist at concentrations highly supersaturated with respect to dissolved salts and supercooled with respect to ice. Densities and apparent molar volumes of solutes in aqueous solutions containing the solutes H2SO4, HNO3, HCl, Na2SO4, NaNO3, NaCl, (NH4)2SO4, NH4NO3, and NH4Cl have been critically evaluated and represented using fitted equations from 0 to 50 °C or greater and from infinite dilution to concentrations saturated or supersaturated with respect to the dissolved salts. Using extrapolated densities of high-temperature solutions and melts, the relationship between density and concentration is extended to the hypothetical pure liquid solutes. Above a given reference concentration of a few mol kg−1, it is observed that density increases almost linearly with decreasing temperature, and comparisons with available data below 0 °C suggest that the fitted equations for density can be extrapolated to very low temperatures. As concentration is decreased below the reference concentration, the variation of density with temperature tends to that of water (which decreases as temperature is reduced below 3.98 °C). In this region below the reference concentration, and below 0 °C, densities are calculated using extrapolated apparent molar volumes which are constrained to agree at the reference concentrations with an equation for the directly fitted density. Calculated volume properties agree well with available data at low temperatures, for both concentrated and dilute solutions. Comparisons are made with literature data for temperatures of maximum density. Apparent molar volumes at infinite dilution are consistent, on a single ion basis, to better than ±0.1 cm3 mol−1 from 0 to 50 °C. Volume properties of aqueous NaHSO4, NaOH, and NH3 have also been evaluated, at 25 °C only. In part 2 of this work (ref 1) an ion interaction (Pitzer) model has been used to calculate apparent molar volumes of H2SO4 in 0−3 mol kg−1 aqueous solutions of the pure acid and to represent directly the effect of the HSO4− ↔ H+ + SO42− reaction. The results are incorporated into the treatment of aqueous H2SO4 density described here. Densities and apparent molar volumes from −20 to 50 °C, and from 0 to 100 wt % of solute, are tabulated for the electrolytes listed in the title and have also been incorporated into the extended aerosol inorganics model (E-AIM, http://www.aim.env.uea.ac.uk/aim/aim.php) together with densities of the solid salts and hydrates.

Description: Population genomics — in which genetic variation across the genome is studied in many individuals — has so far been limited to species for which reference genomes are available. A recent study shows how transcriptomics can be used to extend population genomics research across a far greater range of organisms. This advance promises important new insights int…

Description: The growth of oceanic plates at mid-ocean ridges, crustal accretion, occurs by a combination of magmatic and tectonic processes. Magmatic processes along ridges spreading at fast, intermediate and slowrates, continually add volcanic material to a centrally located spreading axis. This creates a narrowband of young volcanic rocks. However, at ridges spreading at ultraslow rates, diminished volcanism allows entire blocks of mantle to spread on the sea floor by tectonic processes. Remote imaging has advanced our observational understanding of crustal accretion, but temporal constraints are required to quantitatively understand ultraslow-spreading ridge construction. Here, we use U-series eruption ages of volcanic rocks collected from the ultraslow-spreading Southwest Indian Ridge. Unexpectedly, we find young volcanic eruption ages that are broadly dispersed throughout the rift valley, indicating that crustal accretion of young volcanic rocks is not confined to a narrow central spreading axis. As areas of young volcanism are observed close to distinct fault surfaces, we propose that the widely dispersed volcanism may result frommagma rising along faults. Our results indicate that axial-centric spreading models may not accurately describe crustal accretion at ultraslow-spreading ridges, prompting the re-evaluation of these models.

Description: Northern Hemisphere stratospheric variability is investigated with respect to chaotic behavior using time series from three different variables extracted from four different reanalysis products and two numerical model runs with different forcing. The time series show red spectra at all frequencies and the probability distribution functions show persistent deviations from a Gaussian distribution. An exception is given by the numerical model forced with perpetual winter conditions—a case that shows more variability and follows a Gaussian distribution, suggesting that the deviation from Gaussianity found in the observations is due to the transition between summer and winter variability. To search for the presence of a chaotic attractor the correlation dimension and entropy, the Lyapunov spectrum, and the associated Kaplan–Yorke dimension are estimated. A finite value of the dimensions can be computed for each variable and data product, with the correlation dimension ranging between 3.0 and 4.0 and the Kaplan–Yorke dimension between 3.3 and 5.5. The correlation entropy varies between 0.6 and 1.1. The model runs show similar values for the correlation and Lyapunov dimensions for both the seasonally forced run and the perpetual-winter run, suggesting that the structure of a possible chaotic attractor is not determined by the seasonality in the forcing, but must be given by other mechanisms.

Description: Seafloor vents spewing mineral-rich plumes of hydrothermal fluid — termed black smokers — can persist at mid-ocean ridges for decades or longer. Earthquake data indicate that ongoing magma injection may determine their locations.

Description: Southern Hemisphere (SH) stratospheric variability is investigated with respect to chaotic behavior using time series from three different variables extracted from four different reanalysis products. The results are compared with the same analysis applied to the Northern Hemisphere (NH). The probability density functions (PDFs) for the SH show persistent deviations from a Gaussian distribution. The variability is given by white spectra for low frequencies, a slope of −1 for intermediate frequencies, and −3 slopes for high frequencies. Considering the time series for winter and summer separately, PDFs show a Gaussian distribution and the variability spectra change their slopes, indicating the role of the transition between winter and summer variability in shaping the time series. The correlation (D2) and the Kaplan–Yorke (DKY) dimensions are estimated. A finite value of the dimensions can be computed for each variable and data product, except for the NCEP zonal-mean zonal wind and temperature data, which violate the requirement D2 ≤ DKY, possibly owing to the presence of spurious trends and inconsistencies in the data. The value of D2 ranges between 2.6 and 3.9, while DKY ranges between 3.0 and 4.5. The results show that both D2 and DKY display large variability in their values both for different datasets and for different variables within the same dataset. The variability of the values of D2 and DKY thus leaves open the question about the existence of a low-dimensional attractor or if the finite dimensions of the system are the result of the projection of a larger attractor in a low-dimensional embedding space.

Description: Marine-derived fungi have been shown in recent years to produce a plethora of new bioactive secondary metabolites, some of them featuring new carbon frameworks hitherto unprecedented in nature. These compounds are of interest as new lead structures for medicine as well as for plant protection. The aim of this protocol is to give a detailed description of methods useful for the isolation and cultivation of fungi associated with various marine organisms (sponges, algae and mangrove plants) for the extraction, characterization and structure elucidation of biologically active secondary metabolites produced by these marine-derived endophytic fungi, and for the preliminary evaluation of their pharmacological properties based on rapid 'in house' screening systems. Some results exemplifying the positive outcomes of the protocol are given at the end. From sampling in marine environment to completion of the structure elucidation and bioactivity screening, a period of at least 3 months has to be scheduled.

Description: The Denmark Strait Overflow (DSO) supplies about one-third of the North Atlantic Deep Water and is critical to global thermohaline circulation. Knowledge of the pathways of DSO through the Irminger Basin and its transformation there is still incomplete, however. The authors deploy over 10 000 Lagrangian particles at the Denmark Strait in a high-resolution ocean model to study these issues. First, the particle trajectories show that the mean position and potential density of dense waters cascading over the Denmark Strait sill evolve consistently with hydrographic observations. These sill particles transit the Irminger Basin to the Spill Jet section (65.25°N) in 5–7 days and to the Angmagssalik section (63.5°N) in 2–3 weeks. Second, the dense water pathways on the continental shelf are consistent with observations and particles released on the shelf in the strait constitute a significant fraction of the dense water particles recorded at the Angmagssalik section within 60 days (~25%). Some particles circulate on the shelf for several weeks before they spill off the shelf break and join the overflow from the sill. Third, there are two places where the water density following particle trajectories decreases rapidly due to intense mixing: to the southwest of the sill and southwest of the Kangerdlugssuaq Trough on the continental slope. After transformation in these places, the overflow particles exhibit a wide range of densities.

Description: The sensitivities of the Brewer–Dobson circulation (BDC) to different distributions of tropical SST heating are investigated in an idealized aquaplanet model. It is found that an increase in tropical SSTs generally leads to an acceleration of tropical upwelling and an associated reduction in the age of air (AOA) in the polar stratosphere and that the AOA near the subtropical tropopause is correlated with local isentropic mixing of tropospheric air with stratospheric air. The zonal distribution of SST perturbations has a major impact on the vertical and meridional structure of the BDC as compared with other SST characteristics. Zonally localized SST heatings tend to generate a shallow acceleration of the stratospheric residual circulation, enhanced isentropic mixing associated with a weakened stratospheric jet, and a reduction in AOA mostly within the polar vortex. In contrast, SST heatings with a zonally symmetric structure tend to produce a deep strengthening of the stratospheric residual circulation, suppressed isentropic mixing associated with a stronger stratospheric jet, and a decrease of AOA in the entire stratosphere. The shallow versus deep strengthening of the stratospheric residual circulation change has been linked to wave propagation and dissipation in the subtropical lower stratosphere rather than wave generation in the troposphere, and the former can be strongly affected by the vertical position of the subtropical jet. These results suggest that, while the longitudinally localized SST trends under climate change may contribute to the change in the shallow branch of the BDC, the upward shift of the subtropical jet associated with the zonal SST heating can impact the deep branch of the BDC.

Description: The authors test the hypothesis that recent observed trends in surface westerlies in the Southern Hemisphere are directly consequent on observed trends in the timing of stratospheric final warming events. The analysis begins by verifying that final warming events have an impact on tropospheric circulation in a simplified GCM driven by specified equilibrium temperature distributions. Seasonal variations are imposed in the stratosphere only. The model produces qualitatively realistic final warming events whose influence extends down to the surface, much like what has been reported in observational analyses. The authors then go on to study observed trends in surface westerlies composited with respect to the date of final warming events. If the considered hypothesis were correct, these trends would appear to be much weaker when composited with respect to the date of the final warming events. The authors find that this is not the case, and accordingly they conclude that the observed surface changes cannot be attributed simply to this shift toward later final warming events.

Description: Many marine sponges are hosts to dense and phylogenetically diverse microbial communities that are located in the extracellular matrix of the animal. The candidate phylum Poribacteria is a predominant member of the sponge microbiome and its representatives are nearly exclusively found in sponges. Here we used single-cell genomics to obtain comprehensive insights into the metabolic potential of individual poribacterial cells representing three distinct phylogenetic groups within Poribacteria. Genome sizes were up to 5.4 Mbp and genome coverage was as high as 98.5%. Common features of the poribacterial genomes indicated that heterotrophy is likely to be of importance for this bacterial candidate phylum. Carbohydrate-active enzyme database screening and further detailed analysis of carbohydrate metabolism suggested the ability to degrade diverse carbohydrate sources likely originating from seawater and from the host itself. The presence of uronic acid degradation pathways as well as several specific sulfatases provides strong support that Poribacteria degrade glycosaminoglycan chains of proteoglycans, which are important components of the sponge host matrix. Dominant glycoside hydrolase families further suggest degradation of other glycoproteins in the host matrix. We therefore propose that Poribacteria are well adapted to an existence in the sponge extracellular matrix. Poribacteria may be viewed as efficient scavengers and recyclers of a particular suite of carbon compounds that are unique to sponges as microbial ecosystems.

Description: Marine sponges (phylum Porifera) often contain dense and diverse microbial communities, which can constitute up to 35% of the sponge biomass. The genome of one sponge, Amphimedon queenslandica, was recently sequenced, and this has provided new insights into the origins of animal evolution. Complementary efforts to sequence the genomes of uncultivated sponge symbionts have yielded the first glimpse of how these intimate partnerships are formed. The remarkable microbial and chemical diversity of the sponge–microorganism association, coupled with its postulated antiquity, makes sponges important model systems for the study of metazoan host–microorganism interactions, and their evolution, as well as for enabling access to biotechnologically important symbiont-derived natural products. In this Review, we discuss our current understanding of the interactions between marine sponges and their microbial symbiotic consortia, and highlight recent insights into these relationships from genomic studies.

Description: Collectively, marine sediments comprise the largest reservoir of methane on Earth. The flux of methane from the sea bed to the overlying water column is mitigated by the sulphate-dependent anaerobic oxidation of methane by marine microbes within a discrete sedimentary horizon termed the sulphate–methane transition zone. According to conventional isotope systematics, the biological consumption of methane leaves a residue of methane enriched in 13C (refs 1, 2, 3). However, in many instances the methane within sulphate–methane transition zones is depleted in 13C, consistent with the production of methane, and interpreted as evidence for the intertwined anaerobic oxidation and production of methane4, 5, 6. Here, we report results from experiments in which we incubated cultures of microbial methane consumers with methane and low levels of sulphate, and monitored the stable isotope composition of the methane and dissolved inorganic carbon pools over time. Residual methane became progressively enriched in 13C at sulphate concentrations above 0.5 mM, and progressively depleted in 13C below this threshold. We attribute the shift to 13C depletion during the anaerobic oxidation of methane at low sulphate concentrations to the microbially mediated carbon isotope equilibration between methane and carbon dioxide. We suggest that this isotopic effect could help to explain the 13C-depletion of methane in subseafloor sulphate–methane transition zones.

Description: Whether the characteristics of tropical cyclones have changed or will change in a warming climate — and if so, how — has been the subject of considerable investigation, often with conflicting results. Large amplitude fluctuations in the frequency and intensity of tropical cyclones greatly complicate both the detection of long-term trends and their attribution to rising levels of atmospheric greenhouse gases. Trend detection is further impeded by substantial limitations in the availability and quality of global historical records of tropical cyclones. Therefore, it remains uncertain whether past changes in tropical cyclone activity have exceeded the variability expected from natural causes. However, future projections based on theory and high-resolution dynamical models consistently indicate that greenhouse warming will cause the globally averaged intensity of tropical cyclones to shift towards stronger storms, with intensity increases of 2–11% by 2100. Existing modelling studies also consistently project decreases in the globally averaged frequency of tropical cyclones, by 6–34%. Balanced against this, higher resolution modelling studies typically project substantial increases in the frequency of the most intense cyclones, and increases of the order of 20% in the precipitation rate within 100 km of the storm centre. For all cyclone parameters, projected changes for individual basins show large variations between different modelling studies.

Description: Marine sponges (phylum Porifera) are among the oldest multicellular animals (metazoans), the sea's most prolific producers of bioactive metabolites, and of considerable ecological importance due to their abundance and ability to filter enormous volumes of seawater. In addition to these important attributes, sponge microbiology is now a rapidly expanding field.

Description: Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with 〉3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.