ALBERT

Description: Micro-Raman spectroscopy has been used on adult bivalve shells to investigate organic and inorganic shell components but has not yet been applied to bivalve larvae. It is known that the organic matrix of larval shells contains pigments, but less is known about the presence or source of these molecules in larvae. We investigated Raman spectra of seven species of bivalve larvae to assess the types of pigments present in shells of each species and how the ratio of inorganic : organic material changes in a dorso-ventral direction. In laboratory experiments, we reared larvae of three clam species in waters containing different organic signatures to determine if larvae incorporated compounds from source waters into their shells. We found differences in spectra and pigments between most species but found less intraspecific differences. A neural network classifier for Raman spectra classified five out of seven species with greater than 85% accuracy. There were slight differences between the amount and type of pigment present along the shell, with the prodissoconch I and shell margin areas being the most variable. Raman spectra of 1-day-old larvae were found to be differentiable when larvae were reared in waters with different organic signatures. With micro-Raman spectroscopy, it may be possible to identify some unknown species in the wild and trace their natal origins, which could enhance identification accuracy of bivalve larvae and ultimately aid management and restoration efforts.

Description: Tephra provides regional chronostratigraphical marker horizons that can link different climate archives with highly needed accuracy and precision. The results presented in this work exemplify, however, that the intermittent storage of tephra in ice sheets and during its subsequent iceberg transport, especially during glacial stages, constitutes a potential source of serious error for the application of tephrochronology to Nordic Seas and North Atlantic sediment archives. The peak shard concentration of the rhyolitic component of the North Atlantic Ash Zone II (NAAZ-II) tephra complex, often used to correlate marine and ice core records in Marine Isotope Stage (MIS) 3, is shown to lag the eruption event by ca. 100–400 years in some North Atlantic and Norwegian Sea cores. While still allowing for a correlation of archives on millennial timescales, this time delay in deposition is a major obstacle when addressing the lead–lag relationship on short timescales (years to centuries). A precise and accurate determination of lead–lag relationships between archives recording different parts of the climate system is crucial in order to test hypotheses about the processes leading to abrupt climate change and to evaluate results from climate models. Copyright # 2011 John Wiley & Sons, Ltd.

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: 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: Many of the difficulties of staining plastic embedded tissues for light and electron microscopy derive from physical exclusion of hydrophilic staining reagents by hydrophobic embedding media. Structures which stain most intensely with hydrophilic reagents usually contain less hydrophobic plastic than do non-staining structures. Such incomplete infiltration is apparently caused by exclusion of viscous, hydrophobic monomers by physically dense and/or well hydrated tissue elements. In keeping with this, generalized staining of tissues embedded in hydrophobic media does occur when hydrophobic reagents are used. Staining of plastic-free structures with single hydrophilic reagents or with sequences of such reagents, is, however, largely rate-controlled. The surprising similarity of hydrophilic and hydrophobic plastic embedding media is discussed. Limits of this simple model are explored, with a consideration of the roles of fixative and of monomer-tissue reactions

Description: INTRODUCTION: Lichens are self-sustaining partnerships comprising fungi as shape-forming partners for their enclosed symbiotic algae. They produce a tremendous diversity of metabolites (1050 metabolites described so far). OBJECTIVES: A comparison of metabolic profiles in nine lichen species belonging to three genera (Lichina, Collema and Roccella) by using an optimised extraction protocol, determination of the fragmentation pathway and the in situ localisation for major compounds in Roccella species. METHODS: Chemical analysis was performed using a complementary study combining a Taguchi experimental design with qualitative analysis by high-performance liquid chromatography coupled with mass spectrometry techniques. RESULTS: Optimal conditions to obtain the best total extraction yield were determined as follows: mortar grinding to a fine powder, two successive extractions, solid:liquid ratio (2:60) and 700 rpm stirring. Qualitative analysis of the metabolite profiling of these nine species extracted with the optimised method was corroborated using MS and MS/MS approaches. Nine main compounds were identified: 1 β-orcinol, 2 orsellinic acid, 3 putative choline sulphate, 4 roccellic acid, 5 montagnetol, 6 lecanoric acid, 7 erythrin, 8 lepraric acid and 9 acetylportentol, and several other compounds were reported. Identification was performed using the m/z ratio, fragmentation pathway and/or after isolation by NMR analysis. The variation of the metabolite profile in differently organised parts of two Roccella species suggests a specific role of major compounds in developmental stages of this symbiotic association. CONCLUSION: Metabolic profiles represent specific chemical species and depend on the extraction conditions, the kind of the photobiont partner and the in situ localisation of major compounds.

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: Uncertainty over the identity and age of Toba tephras across peninsular India persists, with radiometric age dates contradicting earlier compositional data, which have been used to identify this important Stratigraphie marker as the Youngest Toba Tuff (YTT). To address this issue, new single glass shard analyses have been performed for samples from Morgaon and Bori (north-western India), which have recently been dated at c. 800 ka. These, and indeed all Toba tephra samples thus far analysed from India, show the presence of four populations of glass shards (defined by their Ba/Y ratio), which uniquely identifies them as products of the c. 75-ka Youngest Toba eruption. Confirmation that the YTT fingerprint is characteristic comes from new analyses of Oldest Toba Tuff (OTT) glass shards from five sites in the Indian Ocean. These are compositionally identical to Layer D from the ODP site 758 Sediment core (c. 800 ka), and belong to a single, low-Ba population, clearly different from YTT. These analyses show that there is essentially no reworked OTT material in the YTT eruption, and indicate unequivocally that all known Toba tephra occurrences in India belong to the c. 75-ka Youngest Toba eruption.

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: Fucoidan, a sulfated polysaccharide in brown seaweed, has various biological activities including anti-tumor activity. We investigated the effects of fucoidan on the apoptosis of human promyeloid leukemic cells and fucoidan-mediated signaling pathways. Fucoidan induced apoptosis of HL-60, NB4, and THP-1 cells, but not K562 cells. Fucoidan treatment of HL-60 cells induced activation of caspases-8, -9, and -3, the cleavage of Bid, and changed mitochondrial membrane permeability. Fucoidan-induced apoptosis, cleavage of procaspases, and changes in the mitochondrial membrane permeability were efficiently blocked by depletion of mitogen-activated protein kinase (MAPK) kinase kinase 1 (MEKK1), and inhibitors of MAPK kinase 1 (MEK1) and c Jun NH2-terminal kinase (JNK). The phosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2) and JNK was increased in fucoidan-treated HL-60, NB4, and THP-1 cells, but not K562 cells. ERK1/2 activation occurred at earlier times than JNK activation and JNK activation was blocked by MEK1 inhibitor. In addition, fucoidan-induced apoptosis was inhibited by addition of glutathione and/or L-NAME, and fucoidan decreased intracellular glutathione concentrations and stimulated nitric oxide (NO) production. Buthionine-[R,S]-sulfoximine rendered HL-60 cells more sensitive to fucoidan. Depletion of MEKK1 and inhibition of MEK1 restored the intracellular glutathione content and abrogated NO production, whereas inhibition of JNK activation by SP600125 restored intracellular glutathione content but failed to inhibit NO production in fucoidan-treated HL-60 cells. These results suggest that activation of MEKK1, MEK1, ERK1/2, and JNK, depletion of glutathione, and production of NO are important mediators in fucoidan-induced apoptosis of human leukemic cells

Description: Axial volcanic ridges (AVRs) are found on most slow-spreading mid-ocean ridges and are thought to be the main locus of volcanism there. In this study we present high-resolution mapping of a typical, well-defined AVR on the Mid-Atlantic Ridge at 45°N. The AVR is characterized by “hummocky terrain,” composed typically of hummocks with pillowed or elongate pillowed flanks with pillowed or lobate lava flow summits, often with small haystacks sitting on their highest points. The AVR is surrounded by several areas of “flat seafloor,” composed of lobate and sheet lava flows. The spatial and morphological differences between these areas indicate different eruption processes operating on and off the AVR. Volcanic fissures are found all around and on the AVR, although those with the greatest horizontal displacement are found on the ridge crest and flat seafloor. Clusters of fissures may represent volcanic vents. Extremely detailed comparisons of sediment coverage and examination of contact relations around the AVR suggest that many of the areas of flat seafloor are of a similar age or younger than the hummocky terrain of the AVR. Additionally, all the lavas surveyed have similar degrees of sediment cover, suggesting that the AVR was either built or resurfaced in the same 50 ka time frame as the flat seafloor.

Description: Forazoline A, a novel antifungal polyketide with in vivo efficacy against Candida albicans, was discovered using LCMS-based metabolomics to investigate marine-invertebrate-associated bacteria. Forazoline A had a highly unusual and unprecedented skeleton. Acquisition of 13C–13C gCOSY and 13C–15N HMQC NMR data provided the direct carbon–carbon and carbon–nitrogen connectivity, respectively. This approach represents the first example of determining direct 13C–15N connectivity for a natural product. Using yeast chemical genomics, we propose that forazoline A operated through a new mechanism of action with a phenotypic outcome of disrupting membrane integrity.

Description: Direct estimations of turbulent fluxes and atmospheric stability were performed from a sonic anemometer at 50 m height on a meteorological mast at the Horns Rev wind farm in the North Sea. The stability and flux estimations from the sonic measurements are compared with bulk results from a cup anemometer at 15 m height and potential temperature differences between the water and the air above. Surface flux estimations from the advanced weather research and forecast (WRF) model are also validated against the sonic and bulk data. The correlation between the sonic and bulk estimates of friction velocity is high and the highest among all velocity comparisons. From the sonic–bulk–WRF inter-comparison, it is found that the atmospheric stability measures at the sonic height tend to be closer to the neutral value than the WRF and bulk estimates, which are performed within an air layer closer to the surface, not only from a systematic bulk and WRF under-prediction of the friction velocity when compared with the sonic value but also because of the lower magnitude of the sonic heat flux compared with that from the WRF simulations. Although they are not measured but parameterized or estimated, the bulk–WRF comparisons of friction velocity and 10 m wind speed show good agreement. It is also shown that on a long-term basis, the WRF and bulk estimates of stability are nearly equal and that a correction towards a slightly stable atmospheric condition has to be applied to the long-term wind profile at Horns Rev and at other locations over the North Sea, the correction being larger for points close to the coast.

Description: Mutations or environmental factors that result in reversal of conspicuous left–right asymmetries provide an opportunity to study developmental mechanisms. They may also provide insight into evolutionary changes in asymmetry states within and between species. King crabs (family Lithodidae) have a larger right claw and females typically exhibit a dextrally offset abdomen. Nevertheless, I observed a high incidence of left handedness in laboratory reared box crabs (Lopholithodes foraminatus) and captured the first known egg-bearing female lithodid to exhibit reversed asymmetry. This provided a unique opportunity to characterize the reversed phenotype and to compare the incidence of reversed asymmetry in the offspring of normal and reversed females. Asymmetry of the chelae became apparent in the first postzoeal stage (glaucothoe) and handedness was maintained through subsequent instars. Females with larger left claws developed reversed abdominal asymmetry by the fourth crab stage. No reversed asymmetry was observed in the mandibles of zoea larvae or juveniles of either handedness. The incidence of reversed asymmetry in glaucothoe reared from one reversed and three normal females was high (between 20% and 30%), and independent of maternity (P=0.67). Removal of the right cheliped of fourth stage zoeae, and the major cheliped of glaucothoe, did not reverse the direction of asymmetry. Elevated larval rearing temperature also did not affect the frequency of reversed individuals. This lack of evidence for either heritability or induction of handedness is enigmatic. Further investigation of reversed asymmetry in lithodid crabs may provide valuable insights into the development and evolution of bilateral asymmetries.

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: Eutrophication, coupled with loss of herbivory due to habitat degradation and overharvesting, has increased the frequency and severity of macroalgal blooms worldwide. Macroalgal blooms interfere with human activities in coastal areas, and sometimes necessitate costly algal removal programmes. They also have many detrimental effects on marine and estuarine ecosystems, including induction of hypoxia, release of toxic hydrogen sulphide into the sediments and atmosphere, and the loss of ecologically and economically important species. However, macroalgal blooms can also increase habitat complexity, provide organisms with food and shelter, and reduce other problems associated with eutrophication. These contrasting effects make their overall ecological impacts unclear. We conducted a systematic review and meta-analysis to estimate the overall effects of macroalgal blooms on several key measures of ecosystem structure and functioning in marine ecosystems. We also evaluated some of the ecological and methodological factors that might explain the highly variable effects observed in different studies. Averaged across all studies, macroalgal blooms had negative effects on the abundance and species richness of marine organisms, but blooms by different algal taxa had different consequences, ranging from strong negative to strong positive effects. Blooms' effects on species richness also depended on the habitat where they occurred, with the strongest negative effects seen in sandy or muddy subtidal habitats and in the rocky intertidal. Invertebrate communities also appeared to be particularly sensitive to blooms, suffering reductions in their abundance, species richness, and diversity. The total net primary productivity, gross primary productivity, and respiration of benthic ecosystems were higher during macroalgal blooms, but blooms had negative effects on the productivity and respiration of other organisms. These results suggest that, in addition to their direct social and economic costs, macroalgal blooms have ecological effects that may alter their capacity to deliver important ecosystem services.

Description: Transfer of the small gaseous molecules CO2 and NH3 across biological membranes, long thought to occur solely by simple diffusion, is now known to be facilitated by members of two multigene families: aquaporins (AQP) and rhesus (Rh) proteins. Although it is accepted that AQP1 and Rh proteins are involved in CO2 and NH3 transfer, respectively, the idea that a single channel can exhibit selectivity for both gases is controversial. Indeed, studies using the same in vitro model (human red blood cells) have provided evidence both for and against a role for Rh proteins as CO2 channels. Thus, this study was initiated to provide in vivo evidence for a dual function of Rh proteins as ammonia and CO2 channels. Here, we show that in zebrafish (Danio rerio), direct ammonia–CO2 competition experiments in adults or translational knockdowns of Rh proteins in larvae affects both ammonia and CO2 excretion. These results suggest that Rh proteins in zebrafish may be common pathways for transport of ammonia and CO2.

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: Metagenomic techniques are used to analyse bacterial communities allowing both culturable and unculturable species to be represented. However, the screening of oral metagenomic samples can be hindered by high animal host DNA content. This study evaluated methods for the reduction of human DNA concentrations within oral metagenomic samples. Plaque samples were collected from 27 patients presenting with periodontal disease and treated to remove human DNA using either selective lysis of eukaryotic cells at several buffer concentrations or differential centrifugation after treatment with trypsin and/or detergents. Human and bacterial DNA levels were determined by quantitative polymerase chain reaction (qPCR). The human DNA content of plaque extracts was significantly reduced by all treatments compared with an untreated control (P 〈 0.05). However, differential centrifugation simultaneously reduced the bacterial DNA content unless samples were pretreated with a detergent. Observations of Gram stained samples that were processed using differential centrifugation without detergent suggest that many bacteria remain adhered to human cells. An approach that uses differential centrifugation in parallel with selective lysis is recommended to fully represent the oral microbiota in metagenomic samples, including those tightly adhered to human cells and more delicate bacteria such as Mycoplasma.

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: The evolution of internal structure plays a pivotal role in the macroscopic response of granular materials to applied loads. A case in point is the so‐called ‘stress–dilatancy relation’, a cornerstone of Soil Mechanics. Numerous attempts have been made to unravel the connection between stress–dilatancy and the evolution of fabric and contact forces in a deforming granular medium. We re‐examine this connection in light of the recent findings on force chain evolution, in particular, that of collective force chain failure by buckling. This study is focussed on two‐dimensional deformation of dense granular assemblies. Analysis of individual and collective force chain bucklings is undertaken using data from a discrete element simulation. It is shown that the kinematics of force chain buckling lead to significant levels of local dilatation being developed in the buckling force chain particles and their confining first‐ring neighbors. Findings from the simulation are used to guide the development of a lattice model of collective, localized force chain buckling. Consideration of the statics and kinematics of this process yields a new stress–dilatancy relation. The physics of buckling, even at its simplest form, introduces a richness into the stress–dilatancy formulation in a way that preserves the essential aspects of fabric evolution, specifically the buckling mode.

Description: Marine myxobacteria (Enhygromyxa, Plesiocystis, Pseudoenhygromyxa, Haliangium) are phylogenetically distant from their terrestrial counterparts. Salimabromide is the first natural product from the Plesiocystis/Enhygromyxa clade of obligatory marine myxobacteria. Salimabromide has a new tetracyclic carbon skeleton, comprising a brominated benzene ring, a furano lactone residue, and a cyclohexane ring, bridged by a seven-membered cyclic moiety. The absolute configuration was deduced from experimental and calculated CD data. Salimabromide revealed antibiotic activity towards Arthrobacter cristallopoietes.

Description: Stable isotopic values on planktonic foraminifera in a suite of cores from basins across the SE Baffin Shelf are used to extract a record of meltwater events during Termination I deglaciation. Resolution and Hatton basins lie on the SE Baffin Shelf at water depths 〉 500 m, seaward of major conduits for ice drainage from the eastern sector of the Laurentide Ice Sheet (LIS). Accelerator mass spectrometry 14C dates are used to constrain our chronology of events in ten cores. In Resolution Basin, three cores have 14C AMS dates on foraminifera of 〉 20 ka at their bases; whereas Hatton Basin cores terminate in sediments 〈 13 kyr. Sedimentation rates varied between 0.1 to 4.5 m/ka. Stable oxygen and carbon isotopic ratios were obtained on 146 samples of the planktonic foraminifera Neogloboquadrina pachyderma (Ehrenberg) sinistral, from seven of the ten cores. No evidence was found to indicate that test morphology or size affected ∂18O. Between 7 and 13.5 ka the surface water on the shelf was on average 1 ‰ lower than the open ocean signal. Significant temporal variations were found in both ∂18O and ∂13C. Evidence for significant low ∂18O events occurred between 13 and 8 ka. The ∂13C record from the planktonic foraminifera suggests a threefold division of events between 13 and 7 ka, with positive values between 10.8 and 13.0 ka, negative values between 9 and 10.8 ka, and positive values from 7 to 9 ka. The ∂18O data suggest the presence of meltwater on the shelf some 3,000 years prior to the first late glacial dates on terrestrial deglaciation (at circa 10.4 ka). “Hudson Strait must be the real key to the importance of the calving process during deglaciation, because it is potentially the largest marine outlet for the Laurentide Ice Sheet and because it leads into the very center of the ice sheet.....the rates of calving through Hudson Strait during the period of initial ∂18O rise unfortunately are unknown.”

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: 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: Cormorants, Phalacocorax spp., have great potential to affect recreational fisheries and have increased substantially in abundance over the last decades in UK inland waters. Fabricated refuges provide a potential means of reducing fish losses, yet the benefits of such structures may be marginal if natural shelters are abundant and favoured, or if strong density-dependence limits refuge use. This study examined the efficacy of artificial shelters in mesocosm enclosures that allowed standardised and replicated observations of roach, Rutilus rutilus (L.), distribution. When given a choice between occupying open water, simulated reedbeds and artificial brushwood shelters, roach used brushwood shelters extensively across a range of fish densities. When fish had a choice of occupying open water or reedbeds offering no overhead cover, they actively avoided reedbeds and used open water almost exclusively. Occupation of reedbeds was positively related to the amount of overhead cover they provided. When artificial brushwood shelters and reedbeds offered complete overhead cover, brushwood shelters were occupied twice as much as reedbeds. Artificial shelters may therefore have wide application in stillwaters with abundant reedbeds unless the reedbeds are coupled with extensive overhead cover.

Description: Methane is a potent greenhouse gas and large-scale rapid release of methane from hydrate may have contributed to past abrupt climate change inferred from the geological record. The discovery in 2008 of over 250 plumes of methane gas escaping from the seabed of the West Svalbard continental margin at ~400 m water depth (mwd) suggests that hydrate is dissociating in the present-day Arctic. Here we model the dynamic response of hydrate-bearing sediments over a period of 2300 years and investigate ocean warming as a possible cause for present-day and likely future dissociation of hydrate, within 350–800 mwd, west of Svalbard. Future temperatures are given by two climate models, HadGEM2 and CCSM4, and scenarios, Representative Concentration Pathways (RCPs) 8.5 and 2.6. Our results suggest that over the next three centuries 5.3–29 Gg yr−1 of methane may be released to the Arctic Ocean on the West Svalbard margin.

Description: This article compares the quality of Raman images obtained using metallurgical and oil immersion objectives to map complex structures in two and three dimensions. While the performance of these objectives for depth profiling planar structures has been discussed at length in the literature, the same comparison has not yet been made for 3D mapping of complex objects, where additional complications are introduced by non-planar geometries. Studying samples with increasing complexity shows that the oil immersion objective is strongly preferred because it yields brighter images with better contrast, and eliminates some new and confusing artefacts that do not arise with simple planar objects.

Description: Although it has been more than 30 years since the discovery of deep-sea hydrothermal vents, comprehending the interconnections between hydrothermal venting and microbial life remains a challenge. Here we investigate abiotic-biotic linkages in low-temperature hydrothermal biotopes at Desperate and Lilliput on the southern Mid-Atlantic Ridge. Both sites are basalt-hosted and fluids exhibit the expected chemical signatures. However, contrasting crustal permeabilities have been proposed, supporting pervasive mixing at Desperate but restricting circulation at Lilliput. In Desperate fluids, sulfide and O2 were readily available but H2 hardly detectable. Under incubation conditions (oxic unamended, sulfide-spiked, oxic and anoxic H2 -spiked at 18°C), only sulfide oxidation by Thiomicrospira fuelled biomass synthesis. Microbial phylogenies from Desperate incubation experiments resembled those of the natural samples suggesting that the incubation conditions mimicked the environment. In Lilliput fluids, O2 was limited, whereas sulfide and H2 were enriched. Autotrophy appeared to be stimulated by residual sulfide and by amended H2 . Yet, based on bacterial phylogenies only conditions in anoxic H2 -spiked Lilliput incubations appeared similar to parts of the Lilliput habitat. In anoxic H2 -spiked Lilliput enrichments Campylobacteraceae likely supported biomass production through H2 oxidation. We argue that the diverging circulation patterns arising from different subseafloor permeabilities act as major driving forces shaping these biotope structures.

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: 1. The hypothesis that cyanobacteria have higher optimum growth temperatures and higher growth rates at the optimum as compared to chlorophytes was tested by running a controlled experiment with eight cyanobacteria species and eight chlorophyte species at six different temperatures (20–35 °C) and by performing a literature survey. 2. In the experiment, all organisms except the chlorophyte Monoraphidium minutum grew well up to 35 °C. The chlorophyte Chlamydomonas reinhardtii was the fastest-growing organism over the entire temperature range (20–35 °C). 3. Mean optimum growth temperatures were similar for cyanobacteria (29.2 °C) and chlorophytes (29.2 °C). These results are concordant with published data, yielding slightly higher mean optimum growth temperatures for cyanobacteria (27.2 °C) than for chlorophytes (26.3 °C). 4. Mean growth rates of cyanobacteria at 20 °C (0.42 day−1) were significantly lower than those of chlorophytes at 20 °C (0.62 day−1). However, at all other temperatures, there were no differences between mean growth rates of cyanobacteria and chlorophytes. 5. Mean growth rates at the optimum temperature were similar for cyanobacteria (0.92 day−1) and chlorophytes (0.96 day−1). However, analysis of published data revealed that growth rates of cyanobacteria (0.65 day−1) were significantly lower than those of chlorophytes (0.93 day−1) at their optimum temperatures. 6. Although climate warming will probably lead to an intensification of cyanobacterial blooms, our results indicate that this might not be as a result of higher growth rates of cyanobacteria compared with their chlorophyte competitors. The competitive advantage of cyanobacteria can more likely be attributed to their ability to migrate vertically and prevent sedimentation in warmer and more strongly stratified waters and to their resistance to grazing, especially when warming reduces zooplankton body size.

Description: The Swedish UNESCO World Cultural Heritage site of the Birka and Hovgården Iron Age settlements is well suited for the testing of high-resolution archaeological prospection methods. In May 2006 ground-penetrating radar (GPR) and magnetometer test measurements were conducted at Birka, resulting in data of outstanding quality and new archaeological discoveries, but also demonstrating the need for increased spatial sampling regarding GPR prospection at complex Scandinavian sites. Therefore Birka was selected as a testing ground for a pilot study investigating the suitability of the novel multichannel GPR array system MIRA (MALÅ Imaging Radar Array) for efficient, large-scale GPR surveys with very dense spatial sampling. The study was conducted in May 2008 by MALÅ Geoscience AB in collaboration with the archaeological prospection unit of the Swedish National Heritage Board. The very high-resolution three-dimensional GPR pilot survey demonstrated that it is possible to survey 1 ha and more per day with 8 cm cross-line spacing, mapping archaeological structures in unprecedented resolution, such as postholes of only 25 cm diameter. This paper describes the tested technology and methodology as well as the fieldwork and the results of the study.

Description: In many geotechnical systems, it is not uncommon to observe failure in zones of high localized strain called shear bands. The existing models predict the existence and the extent of these localizations, but provide little insight into the micromechanics within the shear bands. This research captures and compares the variation in microstructure both inside and outside of shear bands that formed in physical laboratory plane strain and companion numerical two-dimensional discrete element method (DEM) biaxial compression experiments. Unsheared and sheared laboratory specimens of Ottawa 20–30 sand of varying dilatancy were solidified using a two-stage resin impregnation procedure. The solidified specimens were sectioned and the resulting surfaces were prepared for microstructure observation using optical bright-field microscopy and stereological analysis. Statistical properties of microstructural parameters for sub-regions in a grid pattern and along predefined inclined zones were determined. Similar measurements were performed on 2D DEM simulation specimens at varying strain levels to characterize the evolution of microstructure with increasing strain. The results showed how differences evolved in the mean, standard deviation, and entropy of void distributions with increasing global strain levels. The results indicate how disorder increases and that the material within the shear band does not adhere to the classical concept of critical state, but reaches a terminal void ratio that is largely a function of initial void ratio. Furthermore, there appears to be a transition zone between the far field and the fully formed shear block, as opposed to an abrupt delineation as is traditionally inferred.

Description: Based on quantitative X-ray diffraction mineralogical analysis of cores HU2008029-0006/0008 (857-m water depth) located south of the Davis Strait sill, we seek answers to two questions: (i) the temporal correlation of NW Labrador Shelf Sea Heinrich (H-) and Baffin Bay detrital carbonate (BBDC) events, and (ii) the provenance of the sediments? A sediment-unmixing model (SedUnMix) is used to determine provenance variations. Although 12 radiocarbon dates were obtained there were many age reversals and we favour a depth/age model for HU2008029-0008PC based on correlations to well-dated neighbouring cores north and south of Davis Strait. We find no correlation between H- and BBDC events except for H-0, which appears to be a broadly synchronous event along the NE Canadian margin and is correlative with an episode of major moraine building along this flank of the Laurentide Ice Sheet. Unmixing of the sediment composition based on six potential glacial source regions indicates that the bulk of the sediment in 0008PC is derived from glacial erosion of West Greenland, but is punctuated by intervals when dolomite-rich sediments, derived from outcrops north of Baffin Bay, dominate the composition. Estimated dates on these BBDC events are -13, 25 and 30–38 cal ka BP.

Description: Core HU97048-007PC was recovered from the continental Labrador Sea slope at a water depth of 945 m, 250km seaward from the mouth of Cumberland Sound, and 400km north of Hudson Strait. Cumberland Sound is a structural trough partly floored by Cretaceous mudstones and Paleozoic carbonates. The record extends from 10 to 58 ka. On-board logging revealed a complex series of lithofacies, including buff-colored detrital carbonate-rich sediments [Heinrich (H)-events] frequently bracketed by black facies. We investigate the provenance of these facies using quantitative X-ray diffraction on drill-core samples from Paleozoic and Cretaceous bedrock from the SE Baffin Island Shelf, and on the〈2-mm sediment fraction in a transect of five cores from Cumberland Sound to the NW Labrador Sea. A sediment unmixing program was used to discriminate between sediment sources, which included dolomite-rich sediments from Baffin Bay, calcite-rich sediments from Hudson Strait and discrete sources from Cumberland Sound. Results indicated that the bulk of the sediment was derived from Cumberland Sound, but Baffin Bay contributed to sediments coeval with H-0 (Younger Dryas), whereas Hudson Strait was the source during H-events 1–4. Contributions from the Cretaceous outcrops within Cumberland Sound bracket H-events, thus both leading and lagging Hudson Strait-sourced H-events.

Description: In the North Atlantic we define H-0 as a Heinrich-like event which occurred during the Younger Dryas chron. On the SE Baffin shelf prior to 11 ka, surface water productivity was reasonably high, as measured by the numbers of diatom and planktic foraminifera per gram, but an abrupt increase in detrital carbonate (DC-0 event) (from approximately 15% up to 50% carbonate by weight) occurred at 11 ± 14C ka and continued to circa 10 ka. These deposits, 2–6 m thick, are dominated by detrital calcite and silt- and clay-sized sediments. During this event (DC-0/H-0), ice extended onto the inner shelf but did not reach the shelf break and probably originated from a center over Labrador-Ungava. As a consequence, the pattern of ice-rafted debris and sediment provenance shown by H-O in the North Atlantic is different from that during H-1 (14.5 ka) or H-2 (20 ka) when the ice sheet extended along the axis of Hudson Strait and may have reached the shelf break; for example, there is no concrete evidence for DC-O is cores on the floor of the Labrador Sea due east of Hudson Strait (HU75-55,-56), but H-O has been noted in cores off Newfoundland and west of Ireland. A coeval carbonate event to DC-0, but this one dominated by dolomite, occurs in HU82-SU5 on the west side of Davis Strait with a source either from northern Baffin Bay or Cumberland Sound. Although other sources for North Atlantic detrital carbonate cannot be totally excluded, our evidence suggests that H-0 represents the expression of glaciological instability of the Laurentide Ice Sheet within the general region of Hudson Strait and probably to the north (Cumberland Sound and northernmost Baffin Bay). There is one younger DC event, dated circa 8.4 ka, present in sediments along the Labrador margin and in Hudson Strait, which represents the final collapse of the ice sheet within Hudson Strait and Hudson Bay.

Description: In virtually every assessment of responses to large-scale crises and disasters, coordination is identified as a critical failure factor. After the crisis, official committees and political opponents often characterize the early phases of the response as a ‘failure to coordinate.’ Not surprisingly, improved coordination quickly emerges as the prescribed solution. Coordination, then, is apparently both the problem and the solution. But the proposed solutions rarely solve the problem: coordination continues to mar most crises and disasters. In the absence of a shared body of knowledge on coordination, it is hard to formulate a normative framework that allows for systematic assessment of coordination in times of crisis. As coordination is widely perceived as an important function of crisis and disaster management, this absence undermines a fair and balanced assessment of crisis management performance. This paper seeks to address that void. We aim to develop a framework that explains both the failure and success of crisis coordination. We do this by exploring the relevant literature, reformulating what coordination is and distilling from research the factors that cause failure and success.

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: The purine alkaloid caffeine is a major component of many beverages such as coffee and tea. Caffeine and its metabolites theobromine and xanthine have been shown to have antioxidant properties. Caffeine can also act as adenosine-receptor antagonist. Although it has been shown that adenosine and antioxidants promote wound healing, the effect of caffeine on wound healing is currently unknown. To investigate the effects of caffeine on processes involved in epithelialisation, we used primary human keratinocytes, HaCaT cell line and ex vivo model of human skin. First, we tested the effects of caffeine on cell proliferation, differentiation, adhesion and migration, processes essential for normal wound epithelialisation and closure. We used 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) proliferation assay to test the effects of seven different caffeine doses ranging from 0·1 to 5 mM. We found that caffeine restricted cell proliferation of keratinocytes in a dose-dependent manner. Furthermore, scratch wound assays performed on keratinocyte monolayers indicated dose-dependent delays in cell migration. Interestingly, adhesion and differentiation remained unaffected in monolayer cultures treated with various doses of caffeine. Using a human ex vivo wound healing model, we tested topical application of caffeine and found that it impedes epithelialisation, confirming in vitro data. We conclude that caffeine, which is known to have antioxidant properties, impedes keratinocyte proliferation and migration, suggesting that it may have an inhibitory effect on wound healing and epithelialisation. Therefore, our findings are more in support of a role for caffeine as adenosine-receptor antagonist that would negate the effect of adenosine in promoting wound healing.

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: Geoengineering, especially its potentially fast and high-leverage versions, is often justified as a necessary response to possible future climate emergencies. In this article, we take the notion of ‘necessity’ in international law as a starting point in assessing how rapid, high-leverage geoengineering might be justified legally. The need to specify reliably ‘grave and imminent peril’ makes such a justification difficult because our scientific ability to predict abrupt climate change, for example, as tipping elements, is limited. The time it takes to establish scientific consensus as well as policy acceptance restricts the scope for effective forewarning and so pre-emptive justifications for geoengineering become more tempting. While recognizing that dangerous, large-scale impacts of climate change is becoming increasingly difficult to avoid, the pre-emptive, emergency frame is problematic. We suggest that arguments from emergency operate on a high level of uncertainty and tend toward hubristic attempts to shape the future, as well as tending to close down rather than open up space for deliberation. We conclude that the emergency frame is not likely to go away, that ignoring or repressing it is a dangerous response, and that more effort is required to defuse and disarm emergency rhetoric.

Description: In May 2006 high-resolution measurements using ground-penetrating radar (GPR) and magnetic gradiometer systems conducted over selected areas at the site of the Viking Age settlement and trading place Birka in central Sweden demonstrated the suitability of these methods for archaeological prospection of Scandinavian proto-urban settlements. The non-invasive geophysical surveys revealed numerous structural details of the settlement: houses, property boundaries, track-ways, buried remains of the town ramparts dating from different building periods, including a gate, were mapped with a manually operated single-channel GPR system and a four-channel magnetometer array. The combination of these two prospection methods, state-of-the-art data processing and visualization and archaeological interpretation within a geographical information system resulted in valuable new information about the UNESCOWorld Cultural Heritage Site Birka-Hovgården.We present methodology and results of this first archaeological prospection case study conducted in 2006.

Description: The eastern Mediterranean transient (EMT) was caused by a combination of high‐salinity waters intruding into the Aegean Sea and the two particularly strong winters of 1991–1992 and 1992–1993. The approach in this chapter is to search for specific signatures in the historic hydrographic observations, which date back to 1910. To deal with the problem that up into the 1950s the data not only are of limited precision but also have gaps of about 20 years, it is advantageous to consider the fact that the evolution of the actual EMT is rather well documented over a similar time span. The chapter begins by outlining the characteristics of the current EMT. Thereafter, a selection of suitable hydrographic observations among the available historic data is provided to compare these with signatures expected from the evolution of the actual EMT.

Description: This article presents a fundamental study on the role of particle breakage on the shear behavior of granular soils using the three-dimensional (3-D) discrete element method. The effects of particle breakage on the stress ratio, volumetric strain, plastic deformation, and shear failure behavior of dense crushable specimens undergoing plane strain shearing conditions are thoroughly investigated through a variety of micromechanical analyses and mechanism demonstrations. The simulation of a granular specimen is based on the effective modeling of realistic fracture behavior of single soil particles, which is demonstrated by the qualitative agreement between the results from platen compression simulations and those from physical laboratory tests. The simulation results show that the major effects of particle breakage include the reduction of volumetric dilation and peak stress ratio and more importantly the plastic deformation mechanisms and the shear failure modes vary as a function of soil crushability. Consistent macro- and micromechanical evidence demonstrates that shear banding and massive volumetric contraction depict the two end failure modes of a dense specimen, which is dominated by particle rearrangement–induced dilation and particle crushing–induced compression, respectively, with a more general case being the combination and competition of the two failure modes in the medium range of soil crushability and confining stress. However, it is further shown that a highly crushable specimen will eventually develop a shear band at a large strain because of the continuous decay of particle breakage.

Description: Zonal wind anomalies in the western equatorial Atlantic during late boreal winter to early summer precondition boreal summer cold/warm events in the eastern equatorial Atlantic (EEA) that manifest in a strong interannual Atlantic cold tongue (ACT) variability. Local intraseasonal wind fluctuations, linked to the St. Helena anticyclone, contribute to the variability of cold tongue onset and strength, particularly during years with preconditioned shallow thermoclines. The impact of cold tongue sea surface temperature (SST) anomalies on the wind field in the Gulf of Guinea is assessed. It contributes to the northward migration of humidity and convection and possibly the West African monsoon (WAM) jump. Copyright @ 2010 Royal Meteorological Society

Description: Understanding the pre-anthropogenic Pb cycle of central North Pacific deep water has attracted a lot of attention in recent years, partly because of its unique geographical location in that it is a remote gyre system characterized by high dust fluxes and sluggish overturning circulation. However, the factors controlling Pb isotope evolution in this area over the Cenozoic are still controversial and various mechanisms have been proposed in previous studies. Here we report new Pb and Nd isotope time series of four ferromanganese crusts (two from the western Pacific near the Mariana arc and the other two from the central Pacific). Together with previously published records, we discuss for the first time the significance of a persistent and systematic Pb isotopic provinciality recorded by central North Pacific crusts over the Cenozoic. We propose that globally well mixed stratosphere volcanic aerosols could contribute Pb but have not been the major factors controlling the Pb isotope distribution in the central North Pacific over time. Island arc input (and probably enhanced hydrothermal input between about 45 and 20 Ma) likely controlled the Pb isotope provinciality and evolution prior to ~20 Ma, when coeval Pb isotope records in different crusts showed large differences and atmospheric silicate dust flux was extremely low. After the Eocene, in particular after 20 Ma, Asian dust input has become an isotopically resolvable source, while island arc-derived Pb has remained important to balance the dust input and to produce the observed Pb isotope distribution in the central North Pacific during this period.

Description: A realistic primitive-equation model of the Southern Ocean at eddying spatial resolution is used to examine the effect of ocean-surface-velocity dependence of the wind stress on the strength of near-inertial oscillations. Accounting for the ocean-surface-velocity dependence of the wind stress leads to a large reduction of wind-induced near-inertial energy of approximately 40 percent and of wind power input into the near-inertial frequency band of approximately 20 percent. A large part of this reduction can be explained by the leading-order modification to the wind stress if the ocean-surface velocity is included. The strength of the reduction is shown to be modulated by the inverse of the ocean-surface-mixed-layer depth. We conclude that the effect of surface-velocity dependence of the wind stress should be taken into account when estimating the wind-power input into the near-inertial frequency band and when estimating near-inertial energy levels in the ocean due to wind forcing.

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: The history of climate modeling begins with conceptual models, followed in the 19th century by mathematical models of energy balance and radiative transfer, as well as simple analog models. Since the 1950s, the principal tools of climate science have been computer simulation models of the global general circulation. From the 1990s to the present, a trend toward increasingly comprehensive coupled models of the entire climate system has dominated the field. Climate model evaluation and intercomparison is changing modeling into a more standardized, modular process, presenting the potential for unifying research and operational aspects of climate science

Description: This study presents a new estimate of the oceanic anthropogenic CO2(Cant) sink over the industrial era (1780 to present), from assimilation of potential temperature, salinity, radiocarbon, and CFC-11 observations in a global steady state ocean circulation inverse model (OCIM). This study differs from previous data-based estimates of the oceanic Cant sink in that dynamical constraints on ocean circulation are accounted for, and the ocean circulation is explicitly modeled, allowing the calculation of oceanic Cant storage, air-sea fluxes, and transports in a consistent manner. The resulting uncertainty of the OCIM-estimated Cant uptake, transport, and storage is significantly smaller than the comparable uncertainty from purely data-based or model-based estimates. The OCIM-estimated oceanic Cant storage is 160–166 PgC in 2012, and the oceanic Cant uptake rate averaged over the period 2000–2010 is 2.6 PgC yr−1 or about 30% of current anthropogenic CO2 emissions. This result implies a residual (primarily terrestrial) Cant sink of about 1.6 PgC yr−1 for the same period. The Southern Ocean is the primary conduit for Cant entering the ocean, taking up about 1.1 PgC yr−1 in 2012, which represents about 40% of the contemporary oceanic Cant uptake. It is suggested that the most significant source of remaining uncertainty in the oceanic Cant sink is due to potential variability in the ocean circulation over the industrial era.

Description: Contemporary genetic diversity is the product of both historical and contemporary forces, such as climatic and geological processes affecting range distribution and continuously moulded by evolutionary forces selection, gene flow and genetic drift. Predatory freshwater fishes, such as Northern Pike Esox lucius, commonly exhibit small population sizes, and several local populations are considered endangered. Pike inhabit diverse habitat types, including lakes, rivers and brackish marine waters, thus spanning from small isolated patches to large open marine systems. However, pike population structure from local to regional scales is relatively poorly described, in spite of its significance to developing conservation measures. We analysed microsatellite variation in a total of 1185 North European pike from 46 samples collected across both local and regional scales, as well as over time, to address two overarching questions: Is pike population structure associated with local and/or regional connectivity patterns, and which factors likely have the main influence on the contemporary distribution of genetic diversity? To answer this, we combined estimators of population diversity and structure to assess evidence of whether populations within (i) habitats, (ii) drainage systems and (iii) geographical regions are closer related than among these ranges, and whether patterns are temporally stable. Contrasting previous predictions that genetic drift obscures signals of postglacial colonisation history, we identified clear regional differences in population genetic signatures, suggesting a major effect of drainage divides on colonisation history and connectivity. However, several populations deviated from the general pattern, showing that local processes may be complex and need to be examined case-by-case.

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: Gas hydrate-related bottom-simulating reflectors mark the phase boundary between hydrate and free gas in the subsurface, and therefore may be used to estimate geothermal gradients and hence heat flow. The depth and temperature of the phase boundary depend on the composition of the hydrateforming gas and of the pore fluid. In the absence of direct sampling, these compositions remain unknown. We develop an alternative approach that is less sensitive to compositional uncertainties and can be applied when the bottom-simulating reflector is densely sampled in a region with significant seabed relief. We apply this approach to a three-dimensional seismic dataset from the eastern Black Sea.

Description: Stratospheric ozone depletion and emission of greenhouse gases lead to a trend of the southern annular mode (SAM) toward its high-index polarity. The positive phase of the SAM is characterized by stronger than usual westerly winds that induce changes in the physical carbon transport. Changes in the natural carbon budget of the upper 100 m of the Southern Ocean in response to a positive SAM phase are explored with a coupled ecosystem-general circulation model and regression analysis. Previously overlooked processes that are important for the upper ocean carbon budget during a positive SAM period are identified, namely, export production and downward transport of carbon north of the polar front (PF) as large as the upwelling in the south. The limiting micronutrient iron is brought into the surface layer by upwelling and stimulates phytoplankton growth and export production but only in summer. This leads to a drawdown of carbon and less summertime outgassing (or more uptake) of natural CO2. In winter, biological mechanisms are inactive, and the surface ocean equilibrates with the atmosphere by releasing CO2. In the annual mean, the upper ocean region south of the PF loses more carbon by additional export production than by the release of CO2 into the atmosphere, highlighting the role of the biological carbon pump in response to a positive SAM event.

Description: We combined data sets of measured sedimentary calcium carbonate (CaCO3) and satellite-derived pelagic primary production to parameterize the relation between CaCO3 content on the Antarctic shelves and primary production in the overlying water column. CaCO3 content predicted in this way was in good agreement with the measured data. The parameterization was then used to chart CaCO3 content on the Antarctic shelves all around the Antarctic, using the satellite-derived primary production. The total inventory of CaCO3 in the bioturbated layer of Antarctic shelf sediments was estimated to be 0.5 Pg C. This quantity is comparable to the total CO2 uptake by the Southern Ocean in only one to a few years (dependent on the uptake estimate and area considered), indicating that the dissolution of these carbonates will neither delay ocean acidification in this area nor augment the Southern Ocean CO2 uptake capacity.

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: Before making a critical evaluation of the crude oil and natural gas prospects for the years to the end of the century, it is necessary to review the geology and structure of the three German hydrocarbon-producing provinces. Furthermore, past exploration, production and reserves should be discussed. The three hydrocarbon-producing provinces are: the NW German Basin, the Upper Rhine Graben and the Molasse Basin, which together make up about 41% of West German territory (Fig. 1). The NW German Basin contains a sedimentary sequence over 8,000 m thick ranging in age from Permian to Quaternary. Gas and oil, the two natural hydrocarbons, are generally confined to separate lower and higher stratigraphic levels respectively (Fig. 2). The NW German Basin is the most important prospective area in West Germany. It extends into the North Sea. The tectonic rift feature of the Upper Rhine Graben originated in the Eocene. The Tertiary fill is over 4,000 m thick. Oil is found mainly in Mesozoic, Eocene and Oligocene rocks; the Miocene and Pliocene reservoir rocks contain natural gas almost exclusively (Fig. 3). The Molasse Basin is part of the foredeep north of the Alpine and Carpathian mountain ranges. The basin is filled with Upper Eocene to Pliocene and Quaternary sediments which, near the Alpine nappes, reach a thickness of over 5,000m (Fig. 4). During this century there were peaks in annual oil-production in 1910, 1940 and 1968 (see Fig. 5). The 1910 peak was the result of drilling activity in the Wietze oilfield. During the period 1934–1945, government financial aid was made available for drilling exploration wells. The success of this collaboration is demonstrated by the oil output in 1940 of 1 × 106 t. After World War II, many different types of oil-bearing structure were found, particularly by reflection seismic techniques in conjunction with detailed stratigraphical and palaeogeographical investigations. The success achieved can be seen by the peak of 8 × 106 t oil production for 1968 (Fig. 5) and in the growth of oil reserves (Fig. 7). Intensive exploration also enabled many new gasfields to be developed, especially in the deeper horizons of the NW German Basin. In 1971, estimated gas reserves reached 360 × 109 m3 (Fig. 11), and annual gas production in 1979 was 20.7 × 109 m3 (731 Bcf) (Fig. 9). There is, no doubt, still scope for the discovery and exploitation of oil and gas in Germany, especially in the NW German Basin where the best prospects for the future lie. This is borne out by two recent offshore oil discoveries and also by the successful application of enhanced recovery methods in the oilfields. The chances of finding more gas at the lower stratigraphic levels are promising now that gas has been discovered in the deeper parts of the Permian basin. The results of massive-hydraulic-fracturing tests in low-permeability pay-horizons are also encouraging. The deeper parts of oil- and gas-producing basins contain interesting prospects and have yet to be tested by ultra-deep wells. Provided that the economic climate remains favourable, there should be no difficulty in finding and supplying German oil and gas in the future. Geologically and technically possible reserves should be converted into proven and/or probable reserves. German crude oil will be available for several years beyond the year 2000, and German natural gas for a far longer time. A production rate of 19 to 20 × 109 m3 of gas per annum is feasible over the next twenty years, and oil production will probably not sink below 3 × 106 t/a in this period.

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: 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: Correlations between particulate organic carbon (POC) and mineral fluxes in the deep ocean have inspired the inclusion of “ballast effect” parameterizations in carbon cycle models. A recent study demonstrated regional variability in the effect of ballast minerals on the flux of POC in the deep ocean. We have undertaken a similar analysis of shallow export data from the Arctic, Atlantic, and Southern Oceans. Mineral ballasting is of greatest importance in the high-latitude North Atlantic, where 60% of the POC flux is associated with ballast minerals. This fraction drops to around 40% in the Southern Ocean. The remainder of the export flux is not associated with minerals, and this unballasted fraction thus often dominates the export flux. The proportion of mineral-associated POC flux often scales with regional variation in export efficiency (the proportion of primary production that is exported). However, local discrepancies suggest that regional differences in ecology also impact the magnitude of surface export. We propose that POC export will not respond equally across all high-latitude regions to possible future changes in ballast availability.

Description: Because the vast majority of species are well diverged, relatively little is known about the genomic architecture of speciation during the early stages of divergence. Species within recent evolutionary radiations are often minimally diverged from a genomic perspective, and therefore provide rare opportunities to address this question. Here, we leverage the hamlet radiation (Hypoplectrus spp., brightly coloured reef fishes from the tropical western Atlantic) to characterize genomic divergence during the early stages of speciation. Transect surveys and spawning observations in Belize, Honduras and Panama confirm that sympatric barred (H. puella), black (H. nigricans) and butter (H. unicolor) hamlets are phenotypically distinct and reproductively isolated, although hybrid spawnings and individuals with intermediate phenotypes are seen on rare occasions. A survey of approximately 100 000 restriction site-associated SNPs in 126 samples from the three species across the three replicate populations reveals extremely slight genomewide divergence among species (FST = 0.0038), indicating that ecomorphological differences and functional reproductive isolation are maintained in sympatry in a backdrop of extraordinary genomic similarity. Nonetheless, a very small proportion of SNPs (0.05% on average) are identified as FST outliers among sympatric species. Remarkably, a single SNP is identified as an outlier in repeated populations for the same species pair. A minicontig assembled de novo around this SNP falls into the genomic region containing the HoxCa10 and HoxCa11 genes in 10 teleost species, suggesting an important role for Hox gene evolution in this radiation. This finding, if confirmed, would provide a better understanding of the links between micro- and macroevolutionary processes.

Description: In the vast Low Nutrient Low-Chlorophyll (LNLC) Ocean, the vertical nutrient supply from the subsurface to the sunlit surface waters is low, and atmospheric contribution of nutrients may be one order of magnitude greater over short timescales. The short turnover time of atmospheric Fe and N supply (〈1 month for nitrate) further supports deposition being an important source of nutrients in LNLC regions. Yet, the extent to which atmospheric inputs are impacting biological activity and modifying the carbon balance in oligotrophic environments has not been constrained. Here, we quantify and compare the biogeochemical impacts of atmospheric deposition in LNLC regions using both a compilation of experimental data and model outputs. A metadata-analysis of recently conducted field and laboratory bioassay experiments reveals complex responses, and the overall impact is not a simple “fertilization effect of increasing phytoplankton biomass” as observed in HNLC regions. Although phytoplankton growth may be enhanced, increases in bacterial activity and respiration result in weakening of biological carbon sequestration. The application of models using climatological or time-averaged non-synoptic deposition rates produced responses that were generally much lower than observed in the bioassay experiments. We demonstrate that experimental data and model outputs show better agreement on short timescale (days to weeks) when strong synoptic pulse of aerosols deposition, similar in magnitude to those observed in the field and introduced in bioassay experiments, is superimposed over the mean atmospheric deposition fields. These results suggest that atmospheric impacts in LNLC regions have been underestimated by models, at least at daily to weekly timescales, as they typically overlook large synoptic variations in atmospheric deposition and associated nutrient and particle inputs. Inclusion of the large synoptic variability of atmospheric input, and improved representation and parameterization of key processes that respond to atmospheric deposition, is required to better constrain impacts in ocean biogeochemical models. This is critical for understanding and prediction of current and future functioning of LNLC regions and their contribution to the global carbon cycle.

Description: Summary 1. Parasitized females in mammals, fish and birds can enhance the immune defence of their offspring by transferring specific antibodies for the embryo. Likewise, social insect mothers transfer immunity despite the fact that invertebrates lack antibodies. 2.  Female trans-generational immune priming is consistent with parental investment theory, because mothers invest more into rearing their offspring than fathers. However, when immune priming is not directly linked to parental care, as is often the case in insects that abandon their eggs after oviposition, both sexes might benefit from protecting their offspring. 3. Using the red flour beetle, Tribolium castaneum, we show that after parental exposure to heat-killed bacteria, trans-generational immune priming occurs through fathers as well as mothers. 4. This novel finding challenges the traditional view that males provide only genes to their offspring in species without paternal care, and raises the possibility of a division of tasks with respect to immune protection between parents.

Description: Marine macroalgae are constantly exposed to epibacterial colonizers. The epiphytic bacterial patterns and their temporal and spatial variability on host algae are poorly understood. To investigate the interaction between marine macroalgae and epiphytic bacteria, this study tested if the composition of epibacterial communities on different macroalgae was specific and persisted under varying biotic and abiotic environmental conditions over a 2-year observation time frame. Epibacterial communities on the co-occurring macroalgae Fucus vesiculosus, Gracilaria vermiculophylla and Ulva intestinalis were repeatedly sampled in summer and winter of 2007 and 2008. The epibacterial community composition was analysed by denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene libraries. Epibacterial community profiles did not only differ significantly at each sampling interval among algal species, but also showed consistent seasonal differences on each algal species at a bacterial phylum level. These compositional patterns re-occurred at the same season of two consecutive years. Within replicates of the same algal species, the composition of bacterial phyla was subject to shifts at the bacterial species level, both within the same season but at different years and between different seasons. However, 7–16% of sequences were identified as species specific to the host alga. These findings demonstrate that marine macroalgae harbour species-specific and temporally adapted epiphytic bacterial biofilms on their surfaces. Since several algal host-specific bacteria were highly similar to other bacteria known to either avoid subsequent colonization by eukaryotic larvae or to exhibit potent antibacterial activities, algal host-specific bacterial associations are expected to play an important role for marine macroalgae.

Description: A wind-driven meso-scale pattern of temperature, salinity and oxygen was found along a transect in the northern Bornholm Basin (southern Baltic Sea). Strong winds caused currents along this transect, which shifted cold intermediate water (minimum: 3.6C) towards the south. The transect was surveyed with a towed CTD-system and hydroacoustics in parallel to investigate the distribution of sprat, Sprattus sprattus balticus (Schn.) in relation to the observed meso-scale pattern. In those parts of the transect where the cold intermediate water was observed, sprat were restricted to water layers below the halocline. In other parts of the transect, sprat moved into higher water layers and occupied a wider depth range. The important factor was temperature, which set an upper limit to the vertical sprat distribution. The development of hydrography, as measured in the field, was evaluated with a hydrodynamic model.

Description: During the last decade, global surface temperatures did not increase as rapidly as in the preceding decades. Although relatively small compared to the observed centennial scale global warming, it has renewed interest in understanding and even predicting climate on time scales of decades, and sparked a community initiative on near‐term prediction that will feature in the fifth intergovernmental panel on climate change assessment report. Decadal prediction, however, is in its infancy, with only a few publications existing. This article has three aims. The first is to make the case for decadal prediction. Decadal fluctuations in global climate similar to that of recent decades were observed during the past century. Associated with large regional changes in precipitation and climate extremes, they are of socioeconomic importance. Climate models, which capture some aspects of observed decadal variability, indicate that such variations might be partly predictable. The second aim is to describe the major challenges to skilful decadal climate prediction. One is poor understanding of mechanisms of decadal climate variability, with climate models showing little agreement. Sparse observations in the past, particularly in the ocean, are also a limiting factor to developing and testing of initialization and prediction systems. The third aim is to stress that despite promising initial results, decadal prediction is in a highly experimental stage, and care is needed in interpreting results and utilizing data from such experiments. In the long‐term, decadal prediction has the potential to improve models, reduce uncertainties in climate change projections, and be of socioeconomic benefit. Copyright © 2010 John Wiley & Sons, Ltd.

Description: Environmental perturbation, climate change and international commerce are important drivers for biological invasions. Climate anomalies can further increase levels of habitat disturbance and act synergistically to elevate invasion risk. Herein, we use a historical data set from the upper San Francisco Estuary to provide the first empirical evidence for facilitation of invasions by climate extremes. Invasive zooplankton species did not become established in this estuary until the 1970s when increasing propagule pressure from Asia coincided with extended drought periods. Hydrological management exacerbated the effects of post-1960 droughts and reduced freshwater inflow even further, increasing drought severity and allowing unusually extreme salinity intrusions. Native zooplankton experienced unprecedented conditions of high salinity and intensified benthic grazing, and life history attributes of invasive zooplankton were advantageous enough during droughts to outcompete native species and colonise the system. Extreme climatic events can therefore act synergistically with environmental perturbation to facilitate the establishment of invasive species.

Description: Recent seismic evidence suggested that most oceanic plate hydration is associated with trench-outer rise faulting prior to subduction. Hydration at trenches may have a significant impact on the subduction zone water cycle. Previous seismic experiments conducted to the northwest of Nicoya Peninsula, Northern Costa Rica, have shown that the subducting Cocos lithosphere is pervasively altered, which was interpreted to be due to both hydration (serpentinization) and fracturing of the crustal and upper-mantle rocks. New seismic wide-angle reflection and refraction data were collected along two profiles, running parallel to the Middle American trench axis offshore of central Nicaragua, revealing lateral changes of the seismic properties of the subducting lithosphere. Seismic structure along both profiles is characterized by low velocities both in the crust and upper mantle. Velocities in the uppermost mantle are found to be in the range 7.3–7.5 km s−1; thus are 8–10 per cent lower than velocities typical for unaltered peridotites and hence confirm the assumption that serpentinization is a common process at the trench-outer rise area offshore of Nicaragua. In addition, a prominent velocity anomaly occurred within the crust beneath two seamounts. Here, velocity reduction may indicate increased porosity and perhaps permeability, supporting the idea that seamounts serve as sites for water percolation and circulation.

Description: Wide-angle seismic data have been used to determine the velocity and density structure of the crust and uppermost mantle beneath the Cape Verdes mid-plate swell. Seismic modelling reveals a ‘standard’ oceanic crust, ∼8 km in thickness, with no direct evidence for low-density bodies at the base of the crust. Gravity anomaly modelling within the constraints and resolution provided by the seismic model, does not preclude, however, a layer of crustal underplate up to 3 km thick beneath the swell crest. The modelling shows that while the seismically constrained crustal structure accounts for the short-wavelength free-air gravity anomaly, it fails to fully explain the long-wavelength anomaly. The main discrepancy is over the swell crest where the gravity anomaly, after correcting for crustal structure, is higher by about 30 mGal than it is over its flanks. The higher gravity can be explained if the top 100 km of the mantle beneath the swell crest is less dense than its surroundings by 30 kg m−3. The lack of evidence for low densities and velocities in the uppermost mantle, and high densities and velocities in the lower crust, suggests that neither a depleted swell root or crustal underplate are the origin of the observed shallower-than-predicted bathymetry and that, instead, the swell is most likely supported by dynamic uplift associated with an anomalously low density asthenospheric mantle.

Description: Indoor mesocosms were used to study the combined effect of warming and of different densities of overwintering mesozooplankton (mainly copepods) on the spring development of phytoplankton in shallow, coastal waters. Similar to previous studies, warming accelerated the spring phytoplankton peak by ca. 1 day 1C1 whereas zooplankton did not significantly influence timing. Phytoplankton biomass during the experimental period decreased with warming and with higher densities of overwintering zooplankton. Similarly, average cell size and average effective particle size (here: colony size) decreased both with zooplankton density and warming. A decrease in phytoplankton particle size is generally considered at typical footprint of copepod grazing. We conclude that warming induced changes in the magnitude and structure of the phytoplankton spring bloom cannot be understood without considering grazing by overwintering zooplankton.

Description: Aim: We investigate the relationship between local and regional richness in marine fouling assemblages using an expanded and globally replicated approach by incorporating two dimensions of diversity (taxonomic and functional) and different successional stages. Location: Global. Methods: In eight different biogeographic regions (Australia, Brazil, Chile, England, Italy, Japan, Portugal and Sweden) 68 polyvinylchloride (PVC) panels (15 × 15 × 0.3 cm) were deployed for colonization. Communities colonizing panels were analysed by measuring percentage cover at each of four different successional ages: 2, 4, 6 and 8 months. Local richness was assessed as the average number of species and functional groups (FGs) per panel and regional richness was evaluated as the estimated (Jack2) asymptote of the sample-accumulation curves for species and FG on experimental panels. Results: We found that the shape of the relationship between local and regional richness depended on successional stage and the type of richness considered, i.e. taxonomic or functional richness. Hardly any relationship was detectable between local taxonomic richness and regional taxonomic richness at any successional stage. In contrast, the relation between local functional and regional functional richness shows a unimodal pattern of change during succession, passing through the stages ‘independent’, ‘unsaturated rising’, ‘saturated rising’ and once again ‘independent’. Main conclusions: The relationship between local and regional richness, whether taxonomic or functional, frequently displays independence of the two scales, particularly in early and late phases of the successional process.

Description: Novel high-pressure biotechnical systems that were developed and applied for the study of anaerobic oxidation of methane (AOM) are described. The systems, referred to as high-pressure continuous incubation system (HP-CI system) and high-pressure manifold-incubation system (HP-MI system), allow for batch, fed-batch, and continuous gas-phase free incubation at high concentrations of dissolved methane and were designed to meet specific demands for studying environmental regulation and kinetics as well as for enriching microbial biomass in long-term incubation. Anoxic medium is saturated with methane in the first technical stage, and the saturated medium is supplied for biomass incubation in the second stage. Methane can be provided in continuous operation up to 20 MPa and the incubation systems can be operated during constant supply of gas-enriched medium at a hydrostatic pressure up to 45 MPa. To validate the suitability of the high-pressure systems, we present data from continuous and fed-batch incubation of highly active samples prepared from microbial mats from the Black Sea collected at a water depth of 213 m. In continuous operation in the HP-CI system initial methane-dependent sulfide production was enhanced 10- to 15-fold after increasing the methane partial pressure from near ambient pressure of 0.2 to 10.0 MPa at a hydrostatic pressure of 16.0 MPa in the incubation stage. With a hydraulic retention time of 14 h a stable effluent sulfide concentration was reached within less than 3 days and a continuing increase of the volumetric AOM rate from 1.2 to 1.7 mmol L−1 day−1 was observed over 14 days. In fed-batch incubation the AOM rate increased from 1.5 to 2.7 and 3.6 mmol L−1 day−1 when the concentration of aqueous methane was stepwise increased from 5 to 15 mmol L−1 and 45 mmol L−1. A methane partial pressure of 6 MPa and a hydrostatic pressure of 12 MPa in manifold fed-batch incubation in the HP-MI system yielded a sixfold increase in the volumetric AOM rate. Over subsequent incubation periods AOM rates increased from 0.6 to 1.2 mmol L−1 day−1 within 26 days of incubation. No inhibition of biomass activity was observed in all continuous and fed-batch incubation experiments. The organisms were able to tolerate high sulfide concentrations and extended starvation periods.

Description: Epsilonproteobacteria have been found globally distributed in marine anoxic/sulfidic areas mediating relevant transformations within the sulfur and nitrogen cycles. In the Baltic Sea redox zones, chemoautotrophic epsilonproteobacteria mainly belong to the Sulfurimonas gotlandica GD17 cluster for which recently a representative strain, S. gotlandica GD1T, could be established as a model organism. In this study, the potential effects of changes in dissolved inorganic carbon (DIC) and pH on S. gotlandica GD1T were examined. Bacterial cell abundance within a broad range of DIC concentrations and pH values were monitored and substrate utilization was determined. The results showed that the DIC saturation concentration for achieving maximal cell numbers was already reached at 800 μmol L−1, which is well below in situ DIC levels. The pH optimum was between 6.6 and 8.0. Within a pH range of 6.6–7.1 there was no significant difference in substrate utilization; however, at lower pH values maximum cell abundance decreased sharply and cell-specific substrate consumption increased.

Description: Harmful, bloom-forming cyanobacteria (CyanoHABs) are occurring with increasing regularity in freshwater and marine ecosystems. The most commonly occurring cyanobacterial toxins are the hepatotoxic microcystin and nodularin. These cyclic hepta- and pentapeptides are synthesised nonribosomally by the gene products of the toxin gene clusters mcy and nda, respectively. Understanding of the regulation of hepatotoxin production is incomplete, although there is strong evidence supporting the roles of iron, light, higher nitrate availability and inorganic carbon in modulating microcystin levels. The majority of these studies have focused on the unicellular freshwater, microcystin-producing strain of Microcystis aeruginosa, with little attention being paid to terrestrial or marine toxin producers. This review intends to investigate the regulation of microcystin and nodularin production in unicellular and filamentous diazotrophic cyanobacteria against the background of changing climate conditions. Special focus is given to diazotrophic filamentous cyanobacteria, for example Nodularia spumigena, capable of regulating their nitrogen levels by actively fixing dinitrogen. By combining data from significant studies, an overall scheme of the regulation of toxin production is presented, focussing specifically on nodularin production in diazotrophs against the background of increasing carbon dioxide concentrations and temperatures envisaged under current climate change models. Furthermore, the risk of sustaining and spreading CyanoHABs in the future ocean is evaluated.

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 two stocks of cod (Gadus morhua L.) in the Baltic Sea are separated by two main spawning areas and main spawning periods. Migrations of juveniles and adults result in the mixing of both stocks. At present, the two stocks have been discriminated using inter alia meristics and morphometry, genetics and tagging experiments. However, using these techniques it is not possible to assign single, non-spawning individuals to a certain stock. Since otolith shape analysis has become a common method for stock discrimination and has been applied successfully to several Atlantic cod stocks, it was applied here for the Baltic cod stocks. To obtain baseline samples, spawning cod were sampled between 2005 and 2009 in the main spawning areas during the spawning periods. The otolith contours were digitized and elliptical Fourier descriptors were analyzed. Both stocks differed significantly in their otolith shapes, and individuals could be allocated with 〉90% accuracy to one of the stocks. Both Baltic cod stocks and cod from West Greenland were discriminated with 93% correct classification. These results highlight otolith shape analysis as a useful tool to discriminate adults of Baltic cod stocks.

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: Climate and weather extremes are sporadically recurring events that may have major local or regional impacts on the society and the environment. These events are typically related to unusually high or low temperature, prolonged dry or wet conditions, heavy precipitation, or extreme winds. Extreme events are part of the overall climate and weather alongside average conditions and variability, and thus are not unexpected as such. Climate change is expected to affect not only means but also variability and extremes. Some inferences can be based on past and present observations, but analyses of especially rare events are hampered by the availability of long time series. Over time, depending on how far the on-going global warming takes us from the present and the past climate conditions, the weather and climate statistics may well come to shift in ways that are well outside observational data. This may lead to shifts in frequency, intensity and geographical distribution of different extremes. Indeed, projected changes in some extremes over the 21st century are quite robust, such as generally increasing warm and decreasing cold extremes. Possible changes in some other aspects, for example storms, remain much more uncertain. Science-based information both on robust findings and on relevant uncertainties on changing extremes can provide useful information for sectorial planning, disaster risk prevention and overall reduction of societal vulnerability related to climate and weather

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: In this overview, we consider the rationale and practice of invertebrate introductions into Lithuanian waters, the current distribution of introduced species, test the theoretical expectations of introduction of peracaridan species into lakes, and summarize the large-scale consequences of these translocations. After some early attempts to transfer locally available species within the country, peracaridan species from the Ponto-Caspian region were introduced into Lithuanian waters during the 1960s (Pontogammarus robustoides, Obesogammarus crassus, Chaetogammarus warpachowskyi, Paramysis lacustris, Limnomysis benedeni and Hemimysis anomala). After their establishment at the site of first introduction in a newly constructed water reservoir on the Nemunas River, further deliberate introductions into Lithuanian lakes and water reservoirs, as well as into more distant areas, were undertaken. These introduced species soon contributed to fish diet and a subsequent increase in the production of commercially important fish was envisaged. However, our collation of available data does not support the enhancement of fish production in Lithuanian lakes. Although perch (selected as a model fish species) assimilated the introduced species into diet and sometimes in large quantities, there was no subsequent influence on somatic growth rates when compared with perch from lakes devoid of alien peracaridans. Comparisons of littoral fish communities of different lakes, and commercial catches in the lake with the most numerous populations of introduced species also indicate no significant effect on fish production. Negative consequences of introduction are more than obvious in contrast. To date, most of the introduced Ponto-Caspian amphipod and mysid species occur in different sites of the Baltic Sea basin outside Lithuania, and their further dispersal may be expected. These species, especially amphipods, have proved to be highly ecologically aggressive, inducing change in resident macroinvertebrate communities and causing increase of biological contamination (i.e. detract from naturalness). Thus, the introduction of alien fodder species was ill advised from an economic, and even adverse from an environmental perspective.

Description: 1. Macroecology has prospered in recent years due in part to the wide array of climatic data, such as those provided by theWorldClim and CliMond data sets, which has become available for research. However, important environmental variables have still been missing, including spatial data sets on UV-B radiation, an increasingly recognized driver of ecological processes. 2. We developed a set of globalUV-B surfaces (glUV) suitable to match common spatial scales in macroecology. Our data set is based on remotely sensed records fromNASA’sOzone Monitoring Instrument (Aura-OMI). Following a similar approach as for theWorldClim and CliMond data sets, we processed daily UV-B measurements acquired over a period of eight years into monthly mean UV-B data and six ecologically meaningful UV-B variables with a 15-arc minute resolution. These bioclimatic variables represent Annual Mean UV-B, UV-B Seasonality, Mean UV-B of Highest Month, Mean UV-B of Lowest Month, Sum of Monthly Mean UV-B during Highest Quarter and Sum of Monthly Mean UV-B during Lowest Quarter. We correlated our data sets with selected variables of existing bioclimatic surfaces for land and with Terra–MODIS Sea Surface Temperature for ocean regions to test for relations to known gradients and patterns. 3. UV-B surfaces showed a distinct seasonal variance at a global scale, while the intensity of UV-B radiation decreased towards higher latitudes and was modified by topographic and climatic heterogeneity. UV-B surfaces were correlated with global mean temperature and annual mean radiation data, but exhibited variable spatial associations across the globe.UV-B surfaces were otherwise widely independent of existing bioclimatic surfaces. 4. Our data set provides new climatological information relevant for macroecological analyses. As UV-B is a known driver of numerous biological patterns and processes, our data set offers the potential to generate a better understanding of these dynamics inmacroecology, biogeography, global change research and beyond. The glUV data set containing monthly mean UV-B data and six derived UV-B surfaces is freely available for download at: http://www.ufz.de/gluv.