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  • 1
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    Nature Publishing Group
    Publication Date: 2024-06-06
    Type: Article , PeerReviewed
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  • 2
    Publication Date: 2024-04-12
    Description: Bacteria use quorum sensing to orchestrate gene expression programmes that underlie collective behaviours. Quorum sensing relies on the production, release, detection and group-level response to extracellular signalling molecules, which are called autoinducers. Recent work has discovered new autoinducers in Gram-negative bacteria, shown how these molecules are recognized by cognate receptors, revealed new regulatory components that are embedded in canonical signalling circuits and identified novel regulatory network designs. In this Review we examine how, together, these features of quorum sensing signal–response systems combine to control collective behaviours in Gram-negative bacteria and we discuss the implications for host–microbial associations and antibacterial therapy.
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  • 3
    Publication Date: 2023-12-21
    Description: Remarkable technological advances have revealed ever more properties and behaviours of individual microorganisms, but the novel data generated by these techniques have not yet been fully exploited. In this Opinion article, we explain how individual-based models (IBMs) can be constructed based on the findings of such techniques and how they help to explore competitive and cooperative microbial interactions. Furthermore, we describe how IBMs have provided insights into self-organized spatial patterns from biofilms to the oceans of the world, phage–CRISPR dynamics and other emergent phenomena. Finally, we discuss how combining individual-based observations with IBMs can advance our understanding at both the individual and population levels, leading to the new approach of microbial individual-based ecology (μIBE).
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  • 4
    Publication Date: 2023-11-29
    Description: Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) is a key enzyme of the Calvin cycle, which is responsible for most of Earth's primary production. Although research on RubisCO genes and enzymes in plants, cyanobacteria and bacteria has been ongoing for years, still little is understood about its regulation and activation in bacteria. Even more so, hardly any information exists about the function of metagenomic RubisCOs and the role of the enzymes encoded on the flanking DNA owing to the lack of available function-based screens for seeking active RubisCOs from the environment. Here we present the first solely activity-based approach for identifying RubisCO active fosmid clones from a metagenomic library. We constructed a metagenomic library from hydrothermal vent fluids and screened 1056 fosmid clones. Twelve clones exhibited RubisCO activity and the metagenomic fragments resembled genes from Thiomicrospira crunogena. One of these clones was further analyzed. It contained a 35.2 kb metagenomic insert carrying the RubisCO gene cluster and flanking DNA regions. Knockouts of twelve genes and two intergenic regions on this metagenomic fragment demonstrated that the RubisCO activity was significantly impaired and was attributed to deletions in genes encoding putative transcriptional regulators and those believed to be vital for RubisCO activation. Our new technique revealed a novel link between a poorly characterized gene and RubisCO activity. This screen opens the door to directly investigating RubisCO genes and respective enzymes from environmental samples.
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  • 5
    Publication Date: 2023-11-08
    Description: Ocean acidification, the drop in seawater pH associated with the ongoing enrichment of marine waters with carbon dioxide from fossil fuel burning, may seriously impair marine calcifying organisms. Our present understanding of the sensitivity of marine life to ocean acidification is based primarily on short-term experiments, in which organisms are exposed to increased concentrations of CO2. However, phytoplankton species with short generation times, in particular, may be able to respond to environmental alterations through adaptive evolution. Here, we examine the ability of the world’s single most important calcifying organism, the coccolithophore Emiliania huxleyi, to evolve in response to ocean acidification in two 500-generation selection experiments. Specifically, we exposed E. huxleyi populations founded by single or multiple clones to increased concentrations of CO2. Around 500 asexual generations later we assessed their fitness. Compared with populations kept at ambient CO2 partial pressure, those selected at increased partial pressure exhibited higher growth rates, in both the single- and multiclone experiment, when tested under ocean acidification conditions. Calcification was partly restored: rates were lower under increased CO2 conditions in all cultures, but were up to 50% higher in adapted compared with non-adapted cultures. We suggest that contemporary evolution could help to maintain the functionality of microbial processes at the base of marine food webs in the face of global change.
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  • 6
    Publication Date: 2023-11-08
    Description: Climate variability in the tropical Atlantic Ocean is determined by large-scale ocean–atmosphere interactions, which particularly affect deep atmospheric convection over the ocean and surrounding continents1. Apart from influences from the Pacific El Niño/Southern Oscillation2 and the North Atlantic Oscillation3, the tropical Atlantic variability is thought to be dominated by two distinct ocean–atmosphere coupled modes of variability that are characterized by meridional4, 5 and zonal6, 7 sea-surface-temperature gradients and are mainly active on decadal and interannual timescales, respectively8, 9. Here we report evidence that the intrinsic ocean dynamics of the deep equatorial Atlantic can also affect sea surface temperature, wind and rainfall in the tropical Atlantic region and constitutes a 4.5-yr climate cycle. Specifically, vertically alternating deep zonal jets of short vertical wavelength with a period of about 4.5 yr and amplitudes of more than 10 cm s−1 are observed, in the deep Atlantic, to propagate their energy upwards, towards the surface10, 11. They are linked, at the sea surface, to equatorial zonal current anomalies and eastern Atlantic temperature anomalies that have amplitudes of about 6 cm s−1 and 0.4 °C, respectively, and are associated with distinct wind and rainfall patterns. Although deep jets are also observed in the Pacific12 and Indian13 oceans, only the Atlantic deep jets seem to oscillate on interannual timescales. Our knowledge of the persistence and regularity of these jets is limited by the availability of high-quality data. Despite this caveat, the oscillatory behaviour can still be used to improve predictions of sea surface temperature in the tropical Atlantic. Deep-jet generation and upward energy transmission through the Equatorial Undercurrent warrant further theoretical study.
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  • 7
    Publication Date: 2023-09-26
    Description: The dehydration of subducting oceanic crust and upper mantle has been inferred both to promote the partial melting leading to arc magmatism and to induce intraslab intermediate-depth earthquakes, at depths of 50–300 km. Yet there is still no consensus about how slab hydration occurs or where and how much chemically bound water is stored within the crust and mantle of the incoming plate. Here we document that bending-related faulting of the incoming plate at the Middle America trench creates a pervasive tectonic fabric that cuts across the crust, penetrating deep into the mantle. Faulting is active across the entire ocean trench slope, promoting hydration of the cold crust and upper mantle surrounding these deep active faults. The along-strike length and depth of penetration of these faults are also similar to the dimensions of the rupture area of intermediate-depth earthquakes.
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  • 8
    Publication Date: 2023-09-19
    Description: Nitrous oxide is a potent greenhouse gas and a key compound in stratospheric ozone depletion. In the ocean, nitrous oxide is produced at intermediate depths through nitrification and denitrification, in particular at low oxygen concentrations. Although a third of natural emissions of nitrous oxide to the atmosphere originate from the ocean, considerable uncertainties in the distribution and magnitude of the emissions still exist. Here we present high-resolution surface measurements and vertical profiles of nitrous oxide that include the highest reported nitrous oxide concentrations in marine surface waters, suggesting that there is a hotspot of nitrous oxide emissions in high-productivity upwelling ecosystems along the Peruvian coast. We estimate that off Peru, the extremely high nitrous oxide supersaturations we observed drive a massive efflux of 0.2–0.9 Tg of nitrogen emitted as nitrous oxide per year, equivalent to 5–22% of previous estimates of global marine nitrous oxide emissions. Nutrient and gene abundance data suggest that coupled nitrification–denitrification in the upper oxygen minimum zone and transport of resulting nitrous oxide to the surface by upwelling lead to the high nitrous oxide concentrations. Our estimate of nitrous oxide emissions from the Peruvian coast surpasses values from similar, highly productive areas.
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  • 9
    Publication Date: 2023-02-14
    Description: Cultivated bacteria such as actinomycetes are a highly useful source of biomedically important natural products. However, such ‘talented’ producers represent only a minute fraction of the entire, mostly uncultivated, prokaryotic diversity. The uncultured majority is generally perceived as a large, untapped resource of new drug candidates, but so far it is unknown whether taxa containing talented bacteria indeed exist. Here we report the single-cell- and metagenomics-based discovery of such producers. Two phylotypes of the candidate genus ‘Entotheonella’ with genomes of greater than 9 megabases and multiple, distinct biosynthetic gene clusters co-inhabit the chemically and microbially rich marine sponge Theonella swinhoei. Almost all bioactive polyketides and peptides known from this animal were attributed to a single phylotype. ‘Entotheonella’ spp. are widely distributed in sponges and belong to an environmental taxon proposed here as candidate phylum ‘Tectomicrobia’. The pronounced bioactivities and chemical uniqueness of ‘Entotheonella’ compounds provide significant opportunities for ecological studies and drug discovery.
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  • 10
    Publication Date: 2023-01-31
    Description: During the past decades climate and freshwater dynamics in the northwestern North Atlantic have undergone major changes. Large-scale freshening episodes, related to polar freshwater pulses, have had a strong influence on ocean variability in this climatically important region. However, little is known about variability before 1950, mainly due to the lack of long-term high-resolution marine proxy archives. Here we present the first multidecadal-length records of annually resolved Ba/Ca variations from Northwest Atlantic coralline algae. We observe positive relationships between algal Ba/Ca ratios from two Newfoundland sites and salinity observations back to 1950. Both records capture episodical multi-year freshening events during the 20th century. Variability in algal Ba/Ca is sensitive to freshwater-induced changes in upper ocean stratification, which affect the transport of cold, Ba-enriched deep waters onto the shelf (highly stratified equals less Ba/Ca). Algal Ba/Ca ratios therefore may serve as a new resource for reconstructing past surface ocean freshwater changes.
    Type: Article , PeerReviewed
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  • 11
    Publication Date: 2023-01-31
    Description: Palaeoclimate records and numerical model simulations indicate that changes in tropical and subtropical sea surface temperatures and in the annual average position of the intertropical convergence zone are linked to high-latitude climate changes on millennial to glacial–interglacial timescales. It has recently been suggested that cooling in the high latitudes associated with abrupt climate-change events is evident primarily during the northern hemisphere winter, implying increased seasonality at these times8. However, it is unclear whether such a seasonal bias also exists for the low latitudes. Here we analyse the Mg/Ca ratios of surface-dwelling foraminifera to reconstruct sea surface temperatures in the northeastern Gulf of Mexico for the past 300,000 years. We suggest that sea surface temperatures are controlled by the migration of the northern boundary of the Atlantic Warm Pool, and hence the position of the intertropical convergence zone during boreal summer, and are relatively insensitive to winter conditions. Our results suggest that summer Atlantic Warm Pool expansion is primarily affected by glacial–interglacial variability and low-latitude summer insolation. Because a clear signature of rapid climate-change events, such as the Younger Dryas cold event, is lacking in our record, we conclude that high-latitude events seem to influence only the winter Caribbean climate conditions, consistent with the hypothesis of extreme northern-hemisphere seasonality during abrupt cooling events.
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  • 12
    Publication Date: 2023-01-04
    Description: Despite the well-known limitations of linear stability theory in describing nonlinear and turbulent flows, it has been found to accurately capture the transitions between certain nonlinear flow behavior. Specifically, the transition in heat flux scaling in rotating convective flows can be well predicted by applying a linear stability analysis to simple profiles of a convective boundary layer. This fact motivates the present study of the linear mechanisms involved in the stability properties of simple convective setups subject to rotation. We look at an idealized two-layer setup and gradually add complexity by including rotation, a bounded domain, and viscosity. The two-layer setup has the advantage of allowing for the use of wave interaction theory, traditionally applied to understand stratified and homogeneous shear flow instabilities, in order to quantify the various physical mechanisms leading to the growth of convective instabilities. We quantitatively show that the physical mechanisms involved in the stabilization of convection by rotation take two different forms acting within the stratified interfacial region, and in the homogeneous mixed layers. The latter of these we associate with the tendency of a rotating flow to develop Taylor columns (TCs). This TC mechanism can lead to both a stabilization or destabilization of the instability and varies depending on the parameters of the problem. A simple criterion is found for classifying the influence of these physical mechanisms.
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  • 13
    Publication Date: 2022-12-22
    Description: Infections arising from multidrug-resistant pathogenic bacteria are spreading rapidly throughout the world and threaten to become untreatable. The origins of resistance are numerous and complex, but one underlying factor is the capacity of bacteria to rapidly export drugs through the intrinsic activity of efflux pumps. In this Review, we describe recent advances that have increased our understanding of the structures and molecular mechanisms of multidrug efflux pumps in bacteria. Clinical and laboratory data indicate that efflux pumps function not only in the drug extrusion process but also in virulence and the adaptive responses that contribute to antimicrobial resistance during infection. The emerging picture of the structure, function and regulation of efflux pumps suggests opportunities for countering their activities.
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  • 14
    Publication Date: 2022-09-21
    Description: Plant species diversity regulates the productivity1–3 and stability2,4 of natural ecosystems, along with their resilience to disturbance5,6. The influence of species diversity on the productivity of agronomic systems is less clear7–10. Plant genetic diversity is also suspected to influence ecosystem function3,11–14, although empirical evidence is scarce. Given the large range of genotypes that can be generated per species through artificial selection, genetic diversity is a potentially important leverage of productivity in cultivated systems. Here we assess the effect of species and genetic diversity on the production and sustainable supply of livestock fodder in sown grasslands, comprising single and multispecies assemblages characterized by different levels of genetic diversity, exposed to drought and non-drought conditions. Multispecies assemblages proved more productive than monocultures when subject to drought, regardless of the number of genotypes per species present. Conversely, the temporal stability of production increased only with the number of genotypes present under both drought and non-drought conditions, and was unaffected by the number of species. We conclude that taxonomic and genetic diversity can play complementary roles when it comes to optimizing livestock fodder production in managed grasslands, and suggest that both levels of diversity should be considered in plant breeding programmes designed to boost the productivity and resilience of managed grasslands in the face of increasing environmental hazards.
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  • 15
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    Nature Publishing Group
    In:  The science behind the Durban talks [Interview] | NATURE News: Q&A
    Publication Date: 2022-03-21
    Type: info:eu-repo/semantics/other
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  • 16
    Publication Date: 2022-02-18
    Description: The Atlantic Ocean receives warm, saline water from the Indo-Pacific Ocean through Agulhas leakage around the southern tip of Africa. Recent findings suggest that Agulhas leakage is a crucial component of the climate system and that ongoing increases in leakage under anthropogenic warming could strengthen the Atlantic overturning circulation at a time when warming and accelerated meltwater input in the North Atlantic is predicted to weaken it. Yet in comparison with processes in the North Atlantic, the overall Agulhas system is largely overlooked as a potential climate trigger or feedback mechanism. Detailed modelling experiments—backed by palaeoceanographic and sustained modern observations—are required to establish firmly the role of the Agulhas system in a warming climate.
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  • 17
    Publication Date: 2022-01-31
    Description: The ability of state-of-the-art regional climate models (RCMs) to simulate the trends of intense cyclone activity in the Arctic is assessed based on an ensemble of 13 simulations from 11 models from the Arctic-CORDEX initiative. Some models employ large-scale spectral nudging techniques. Cyclone characteristics simulated by the ensemble in winter and summer are compared with the results from four reanalyses (ERA-Interim, NCEP-CFSR, NASA-MERRA2 and JMA-JRA55) in winter and summer for 1981-2010 period.
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  • 18
    Publication Date: 2022-01-17
    Description: Earth's climate can be understood as a dynamical system that changes due to external forcing and internal couplings. Essential climate variables, such as surface air temperature, describe this dynamics. Our current interglacial, the Holocene (11 700 yr ago to today), has been characterized by small variations in global mean temperature prior to anthropogenic warming. However, the mechanisms and spatiotemporal patterns of fluctuations around this mean, called temperature variability, are poorly understood despite their socioeconomic relevance for climate change mitigation and adaptation. Here we examine discrepancies between temperature variability from model simulations and paleoclimate reconstructions by categorizing the scaling behavior of local and global surface air temperature on the timescale of years to centuries. To this end, we contrast power spectral densities (PSD) and their power-law scaling using simulated and observation-based temperature series of the last 6000 yr. We further introduce the spectral gain to disentangle the externally forced and internally generated variability as a function of timescale. It is based on our estimate of the joint PSD of radiative forcing, which exhibits a scale break around the period of 7 yr. We find that local temperature series from paleoclimate reconstructions show a different scaling behavior than simulated ones, with a tendency towards stronger persistence (i.e., correlation between successive values within a time series) on periods of 10 to 200 yr. Conversely, the PSD and spectral gain of global mean temperature are consistent across data sets. Our results point to the limitation of climate models to fully represent local temperature statistics over decades to centuries. By highlighting the key characteristics of temperature variability, we pave a way to better constrain possible changes in temperature variability with global warming and assess future climate risks.
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  • 19
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    Nature Publishing Group
    In:  Nature, 384 (6608). p. 421.
    Publication Date: 2021-08-20
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  • 20
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    Nature Publishing Group
    In:  Nature, 438 (7070). p. 929.
    Publication Date: 2021-08-20
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  • 21
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    Nature Publishing Group
    In:  Nature, 433 (7023). p. 212.
    Publication Date: 2021-08-16
    Description: Sexual mimicry among animals is widespread, but does it impart a fertilization advantage in the widely accepted ‘sneak–guard’ model of sperm competition? Here we describe field results in which a dramatic facultative switch in sexual phenotype by sneaker-male cuttlefish leads to immediate fertilization success, even in the presence of the consort male. These results are surprising, given the high rate at which females reject copulation attempts by males, the strong mate-guarding behaviour of consort males, and the high level of sperm competition in this complex mating system
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  • 22
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    Nature Publishing Group
    In:  Nature, 406 . pp. 955-956.
    Publication Date: 2021-07-01
    Description: Birds taking time off from breeding head for their favourite long-haul destinations. What oceanic seabirds do outside their breeding periods is something of a mystery, although altogether these "sabbaticals' add up to more than half of their lifetime and are probably a key feature of their life history. Here we use geolocation systems based on light-intensity measurements to show that during these periods wandering albatrosses (Diomedea exulans) leave the foraging grounds that they frequent while breeding for specific, individual oceanic sectors and spend the rest of the year there — each bird probably returns to the same area throughout its life. This discovery of individual home-range preferences outside the breeding season has important implications for the conservation of albatrosses threatened by the development of longline fisheries.
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  • 23
    Publication Date: 2021-04-23
    Description: The symbiotic association of corals and unicellular algae of the genus Symbiodinium in the southern Persian/Arabian Gulf (PAG) display an exceptional heat tolerance, enduring summer peak temperatures of up to 36 °C. As yet, it is not clear whether this resilience is related to the presence of specific symbiont types that are exclusively found in this region. Therefore, we used molecular markers to identify the symbiotic algae of three Porites species along 〉1000 km of coastline in the PAG and the Gulf of Oman and found that a recently described species, Symbiodinium thermophilum, is integral to coral survival in the southern PAG, the world’s hottest sea. Despite the geographic isolation of the PAG, we discovered that representatives of the S. thermophilum group can also be found in the adjacent Gulf of Oman providing a potential source of thermotolerant symbionts that might facilitate the adaptation of Indian Ocean populations to the higher water temperatures expected for the future. However, corals from the PAG associated with S. thermophilum show strong local adaptation not only to high temperatures but also to the exceptionally high salinity of their habitat. We show that their superior heat tolerance can be lost when these corals are exposed to reduced salinity levels common for oceanic environments elsewhere. Consequently, the salinity prevailing in most reefs outside the PAG might represent a distribution barrier for extreme temperature-tolerant coral/Symbiodinium associations from the PAG.
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  • 24
    Publication Date: 2021-04-23
    Description: Oceanic dissolved organic carbon (DOC) is an important carbon pool, similar in magnitude to atmospheric CO2, but the fate of its oldest forms is not well understood. Hot hydrothermal circulation may facilitate the degradation of otherwise un-reactive dissolved organic matter, playing an important role in the long-term global carbon cycle. The oldest, most recalcitrant forms of DOC, which make up most of oceanic DOC, can be recovered by solid-phase extraction. Here we present measurements of solid-phase extractable DOC from samples collected between 2009 and 2013 at seven vent sites in the Atlantic, Pacific and Southern oceans, along with magnesium concentrations, a conservative tracer of water circulation through hydrothermal systems. We find that magnesium and solid-phase extractable DOC concentrations are correlated, suggesting that solid-phase extractable DOC is almost entirely lost from solution through mineralization or deposition during circulation through hydrothermal vents with fluid temperatures of 212-401°C. In laboratory experiments, where we heated samples to 380°C for four days, we found a similar removal efficiency. We conclude that thermal degradation alone can account for the loss of solid-phase extractable DOC in natural hydrothermal systems, and that its maximum lifetime is constrained by the timescale of hydrothermal cycling, at about 40 million years
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  • 25
    Publication Date: 2021-02-25
    Description: The El Niño/Southern Oscillation (ENSO) phenomenon is the strongest natural interannual climate fluctuation1. ENSO originates in the tropical Pacific Ocean and has large effects on the ecology of the region, but it also influences the entire global climate system and affects the societies and economies of manycountries2. ENSO can be understood as an irregular low-frequency oscillation between a warm (El Niño) and a cold (La Niña) state. The strong El Niños of 1982/1983 and 1997/1998, along with the more frequent occurrences of El Niños during the past few decades, raise the question of whether human-induced 'greenhouse' warming affects, or will affect, ENSO3. Several global climate models have been applied to transient greenhouse-gas-induced warming simulations to address this question4, 6, but the results have been debated owing to the inability of the models to fully simulate ENSO (because of their coarse equatorial resolution)7. Here we present results from a global climate model with sufficient resolution in the tropics to adequately represent the narrow equatorial upwelling and low-frequency waves. When the model is forced by a realistic future scenario of increasing greenhouse-gas concentrations, more frequent El-Niño-like conditions and stronger cold events in the tropical Pacific Ocean result
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  • 26
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    Nature Publishing Group
    In:  Nature, 404 (6780). p. 814.
    Publication Date: 2021-02-25
    Description: Book review of: The Change in the Weather: People, Weather, and the Science of Climate by William K. Stevens Delacorte: 2000. 432 pp. $24.95
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  • 27
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    Nature Publishing Group
    In:  Nature, 389 (6652). pp. 683-684.
    Publication Date: 2021-02-15
    Description: Recent captures of two female giant squid ( Architeuthis ) off southern Australia have provided the first record of a mated female specimen of these almost mythical deepsea creatures. We found sperm packages (spermatophores) embedded within the skin of both ventral arms of the larger of the two specimens. It seems that male giant squids may use their muscular elongate penis to ‘inject’ sperm packages under pressure directly into the arms of females.
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  • 28
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    American Institute of Physics
    In:  Review of Scientific Instruments, 90 (12). p. 124504.
    Publication Date: 2021-01-08
    Description: Understanding mechanical interactions between hydrate and hosting sediments is critical for evaluating formation stability and associated environmental impacts of hydrate-bearing sediments during gas production. While core-scale studies of hydrate-bearing sediments are readily available and some explanations of observed results rely on pore-scale behavior of hydrate, actual pore-scale observations supporting the larger-scale phenomena are rarely available for hydrate-bearing sediments, especially with methane as guest molecules. The primary reasons for the scarcity include the challenge of developing tools for small-scale testing apparatus and pore-scale visualization capability. We present a testing assembly that combines pore-scale visualization and triaxial test capability of methane hydrate-bearing sediments. This testing assembly allows temperature regulation and independent control of four pressures: influent and effluent pore pressure, confining pressure, and axial pressure. Axial and lateral effective stresses can be applied independently to a 9.5 mm diameter and 19 mm long specimen while the pore pressure and temperature are controlled to maintain the stability of methane hydrate. The testing assembly also includes an X-ray transparent beryllium core holder so that 3D computed tomography scanning can be conducted during the triaxial loading. This testing assembly permits pore-scale exploration of hydrate-sediment interaction in addition to the traditional stress-strain relationship. Exemplary outcomes are presented to demonstrate applications of the testing assembly on geomechanical property estimations of methane-hydrate bearing sediments.
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  • 29
    Publication Date: 2020-11-23
    Description: Large amounts of the greenhouse gas methane are released from the seabed to the water column1, where it may be consumed by aerobic methanotrophic bacteria2. The size and activity of methanotrophic communities, which determine the amount of methane consumed in the water column, are thought to be mainly controlled by nutrient and redox dynamics3–7. Here, we report repeated measurements of methanotrophic activity and community size at methane seeps west of Svalbard, and relate them to physical water mass properties and modelled ocean currents. We show that cold bottom water, which contained a large number of aerobic methanotrophs, was displaced by warmer water with a considerably smaller methanotrophic community within days. Ocean current simulations using a global ocean/sea-ice model suggest that this water mass exchange is consistent with short-term variations in the meandering West Spitsbergen Current. We conclude that the shift from an offshore to a nearshore position of the current can rapidly and severely reduce methanotrophic activity in the water column. Strong fluctuating currents are common at many methane seep systems globally, and we suggest that they affect methane oxidation in the water column at other sites, too.
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  • 30
    Publication Date: 2020-11-09
    Description: Coexisting bacteria form various microbial communities in human body parts. In these ecosystems they interact in various ways and the properties of the interaction network can be related to the stability and functional diversity of the local bacterial community. In this study, we analyze the interaction network among bacterial OTUs in 11 locations of the human body. These belong to two major groups. One is the digestive system and the other is the female genital tract. In each local ecosystem we determine the key species, both the ones being in key positions in the interaction network and the ones that dominate by frequency. Beyond identifying the key players and discussing their biological relevance, we also quantify and compare the properties of the 11 networks. The interaction networks of the female genital system and the digestive system show totally different architecture. Both the topological properties and the identity of the key groups differ. Key groups represent four phyla of prokaryotes. Some groups appear in key positions in several locations, while others are assigned only to a single body part. The key groups of the digestive and the genital tracts are totally different.
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  • 31
    Publication Date: 2020-10-26
    Description: Resolving flow geometry in the mantle wedge is central to understanding the thermal and chemical structure of subduction zones, subducting plate dehydration, and melting that leads to arc volcanism, which can threaten large populations and alter climate through gas and particle emission. Here we show that isotope geochemistry and seismic velocity anisotropy provide strong evidence for trench-parallel flow in the mantle wedge beneath Costa Rica and Nicaragua. This finding contradicts classical models, which predict trench-normal flow owing to the overlying wedge mantle being dragged downwards by the subducting plate. The isotopic signature of central Costa Rican volcanic rocks is not consistent with its derivation from the mantle wedge1, 2, 3 or eroded fore-arc complexes4 but instead from seamounts of the Galapagos hotspot track on the subducting Cocos plate. This isotopic signature decreases continuously from central Costa Rica to northwestern Nicaragua. As the age of the isotopic signature beneath Costa Rica can be constrained and its transport distance is known, minimum northwestward flow rates can be estimated (63–190 mm yr-1) and are comparable to the magnitude of subducting Cocos plate motion (approx85 mm yr-1). Trench-parallel flow needs to be taken into account in models evaluating thermal and chemical structure and melt generation in subduction zones.
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  • 32
    Publication Date: 2020-10-26
    Description: The origin of the Christmas Island Seamount Province in the northeast Indian Ocean is enigmatic. The seamounts do not form the narrow, linear and continuous trail of volcanoes that would be expected if they had formed above a mantle plume1, 2. Volcanism above a fracture in the lithosphere3 is also unlikely, because the fractures trend orthogonally with respect to the east–west trend of the Christmas Island chain. Here we combine 40Ar/39Ar age, Sr, Nd, Hf and high-precision Pb isotope analyses of volcanic rocks from the province with plate tectonic reconstructions. We find that the seamounts are 47–136 million years old, decrease in age from east to west and are consistently 0–25 million years younger than the underlying oceanic crust, consistent with formation near a mid-ocean ridge. The seamounts also exhibit an enriched geochemical signal, indicating that recycled continental lithosphere was present in their source. Plate tectonic reconstructions show that the seamount province formed at the position where West Burma began separating from Australia and India, forming a new mid-ocean ridge. We propose that the seamounts formed through shallow recycling of delaminated continental lithosphere entrained in mantle that was passively upwelling beneath the mid-ocean ridge. We conclude that shallow recycling of continental lithosphere at mid-ocean ridges could be an important mechanism for the formation of seamount provinces in young ocean basins.
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  • 33
    Publication Date: 2020-10-16
    Description: Experiments have shown that ocean acidification due to rising atmospheric carbon dioxide concentrations has deleterious effects on the performance of many marine organisms(1-4). However, few empirical or modelling studies have addressed the long-term consequences of ocean acidification for marine ecosystems(5-7). Here we show that as pH declines from 8.1 to 7.8 (the change expected if atmospheric carbon dioxide concentrations increase from 390 to 750 ppm, consistent with some scenarios for the end of this century) some organisms benefit, but many more lose out. We investigated coral reefs, seagrasses and sediments that are acclimatized to low pH at three cool and shallow volcanic carbon dioxide seeps in Papua New Guinea. At reduced pH, we observed reductions in coral diversity, recruitment and abundances of structurally complex framework builders, and shifts in competitive interactions between taxa. However, coral cover remained constant between pH 8.1 and similar to 7.8, because massive Porites corals established dominance over structural corals, despite low rates of calcification. Reef development ceased below pH 7.7. Our empirical data from this unique field setting confirm model predictions that ocean acidification, together with temperature stress, will probably lead to severely reduced diversity, structural complexity and resilience Of Indo-Pacific coral reefs within this century
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  • 34
    Publication Date: 2020-10-16
    Description: Three new 22-membered macrolactone antibiotics, atacamycins A-C, were produced by Streptomyces sp. C38, a strain isolated from a hyper-arid soil collected from the Atacama Desert in the north of Chile. The metabolites were discovered in our HPLC-diode array screening and isolated from the mycelium by extraction and chromatographic purification steps. The structures were determined by mass spectrometry and NMR experiments. Atacamycins A, B and C exhibited moderate inhibitory activities against the enzyme phosphodiesterase (PDE-4B2), whereas atacamycin A showed a moderate antiproliferative activity against adeno carcinoma and breast carcinoma cells
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  • 35
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    Nature Publishing Group
    In:  Nature, 196 (4852). pp. 351-352.
    Publication Date: 2020-09-09
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  • 36
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    Nature Publishing Group
    In:  Scientific Reports, 4 (Article number: 6972).
    Publication Date: 2020-09-07
    Description: Rhodoliths are coralline red algal assemblages that commonly occur in marine habitats from the tropics to polar latitudes. They form rigid structures of high-magnesium calcite and have a good fossil record. Here I show that rhodoliths are ecosystem engineers in a high Arctic environment that increase local biodiversity by providing habitat. Gouged by boring mussels, originally solid rhodoliths become hollow ecospheres intensely colonised by benthic organisms. In the examined shelf areas, biodiversity in rhodolith-bearing habitats is significantly greater than in habitats without rhodoliths and hollow rhodoliths yield a greater biodiversity than solid ones. This biodiversity, however, is threatened because hollow rhodoliths take a long time to form and are susceptible to global change and anthropogenic impacts such as trawl net fisheries that can destroy hollow rhodoliths. Rhodoliths and other forms of coralline red algae play a key role in a plurality of environments and need improved management and protection plans.
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  • 37
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    American Institute of Physics
    In:  [Paper] In: 8. International Conference of Numerical Analysis and Applied Mathematics (ICNAAM 2010), 19.-25.09.2010, Rhodes, Greece ; pp. 612-616 .
    Publication Date: 2020-08-03
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  • 38
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    Institute of Physics
    In:  Journal of Physics - Condensed Matter, 18 (38). S2919-S2934.
    Publication Date: 2020-07-20
    Description: Loss processes in magnetic nanoparticles are discussed with respect to optimization of the specific loss power (SLP) for application in tumour hyperthermia. Several types of magnetic iron oxide nanoparticles representative for different preparation methods (wet chemical precipitation, grinding, bacterial synthesis, magnetic size fractionation) are the subject of a comparative study of structural and magnetic properties. Since the specific loss power useful for hyperthermia is restricted by serious limitations of the alternating field amplitude and frequency, the effects of the latter are investigated experimentally in detail. The dependence of the SLP on the mean particle size is studied over a broad size range from superparamagnetic up to multidomain particles, and guidelines for achieving large SLP under the constraints valid for the field parameters are derived. Particles with the mean size of 18 nm having a narrow size distribution proved particularly useful. In particular, very high heating power may be delivered by bacterial magnetosomes, the best sample of which showed nearly 1 kW g−1 at 410 kHz and 10 kA m−1. This value may even be exceeded by metallic magnetic particles, as indicated by measurements on cobalt particles.
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  • 39
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    American Institute of Physics
    In:  Journal of the Acoustical Society of America, 90 (4, Pt. 2). pp. 2255-2256.
    Publication Date: 2020-07-16
    Description: Seafloor topography is neither spatially homogeneous, nor does it obey Gaussian statistics; deviations from both of these assumptions are important from a geological and acoustic point of view. It has been found that the distribution of topographic slopes can be used as a primary tool for understanding the sources and extent of spatial heterogeneities and patterns on the seafloor. The covariance function has been widely used to characterize seafloor topography, but requires the assumption of Gaussian joint probability statistics to be valid. For heterogeneous topography characterized by large transient signals such as steep scarps and volcanoes, the covariance becomes dominated by the transients; in contrast the family slope distributions can still be used to derive stable descriptors for regions with large transient signals, as well as regions containing asymmetric features, and regions with only limited sampling. Knowledge of slopes is useful because a direct relation exists between the covariance and the slope distributions at different spatial scales. Studies of the slope distribution provide a means of identifying the presence of the non‐Gaussian elements in the topography, and flagging their spatial locations. The methods used here are demonstrated by applying them to three small patches of topography located within 20 km of each other in the Eastern Pacific. It is found that dominant azimuthal directions and dip angles differ widely between the patches. In addition, asymmetries in the cross‐sectional shapes of faulted abyssal hills are documented. [Work supported by ONR.]
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  • 40
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    American Institute of Physics
    In:  Journal of the Acoustical Society of America, 78 (4). pp. 1348-1355.
    Publication Date: 2020-07-16
    Description: Additional data from sonobuoys and the Deep Sea Drilling Project (DSDP) justify separating sound‐velocity‐depth functions and velocity gradients (in the first layer of soft marine sediments) into some geographic areas and sediment types. Based on sonobuoy and core measurements (where V is sound velocity in km/s, and h is depth in sediments in km), the following data are obtained: continental shelf basins off Sumatra and Java—V=1.484+0.710h−0.085h2; U. S. Atlantic continental rise—V=1.513+0.828h−0.138h2; deep‐sea terrigenous sediments—V=1.519+1.227h−0.473h2; and siliceous sediments of the Bering Sea— V=1.509+0.869h−0.267h2. Selected DSDP data (through leg 74) in similar areas yield: continental terrace silt–clays—V=1.505+0.712h; deep‐sea terrigenous sediments—V=1.510+1.019h; and deep‐sea siliceous sediments—V=1.533+0.761h. Computed velocity gradients from sonobuoy measurements are generally supported by the DSDP gradients. Only DSDP data give the following: hemipelagic sediments—V=1.501+1.151h; deep‐sea calcareous sediments—V=1.541+0.928h; and deep‐sea pelagic clay—V=1.526+1.046h. Where fast sediment accumulation occurs, there has not been enough time to reduce sediment pore spaces under overburden pressure; areas of slow accumulation may have relatively high sediment structural strength. Both cases have lower velocity gradients because higher porosities and consequent lower velocities persist to deeper depths.
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  • 41
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    American Institute of Physics
    In:  Journal of the Acoustical Society of America, 92 (2). pp. 962-977.
    Publication Date: 2020-07-16
    Description: High‐frequency bottom acoustic and geoacoustic data from three well‐characterized sites of different bottom composition are compared with scattering models in order to clarify the roles played by interface roughness and sediment volume inhomogeneities. Model fits to backscattering data from two silty sites lead to the conclusion that scattering from volume inhomogeneities was primarily responsible for the observed backscattering. In contrast, measured bottom roughness was sufficient to explain the backscattering seen at a sandy site. Although the sandy site had directional ripples, the model and data agree in their lack of anisotropy.
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  • 42
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    American Institute of Physics
    In:  Journal of the Acoustical Society of America, 66 (4). pp. 1093-1101.
    Publication Date: 2020-07-16
    Description: The ratio of compressional wavevelocityV p to shear wavevelocityV s , and Poisson’s ratio in marine sediments and rocks are important in modeling the sea floor for underwater acoustics,geophysics, and foundation engineering. V p and V s versus depth information was linked at common depths in terrigenous sediments (to 1000 m) and in sands (to 20 m) to yield data on V p vs V s , and V p /V s and Poisson’s ratios versus depth. Soft, terrigenous sediments usually grade with depth into mudstones and shales; V p /V s ratios vary from about 13 or more at the sea floor to about 2.6 at 1000 m. Poisson’s ratios vary from above 0.49 at the sea floor to about 0.41 at 1000 m. In sands, V p , V s , and V p /V s have very high gradients in the first few meters; below about 5 m, V p /V s ratios decrease from about 9 to about 6 at 20 m; Poisson’s ratios vary from above 0.49 at the surface to above 0.48 at 20 m. The mean value of V p /V s in 30 laboratory samples of chalk and limestone is 1.90 (standard error: 0.03); mean Poisson’s ratio is 0.31. Literature data on basalts from the sea floor are reviewed. Equations relating V p to V s are given for terrigenous sediments, sands, and basalts.
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  • 43
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    American Institute of Physics
    In:  Journal of the Acoustical Society of America, 56 (4). p. 1084.
    Publication Date: 2020-07-16
    Description: A new equation for the speed of sound in sea water has been developed with validity not only for realistic combinations of the parameters salinity, temperature, and pressure, but with extension to pure water as well. This new equation, referred to as NRL II, has a standard deviation of 0.05 m/sec. Tables are presented comparing calculations using this new model to each of eight earlier equations. Graphs are also included indicating approximate corrections that could be applied to existing sound speed profiles, but it is recommended that such profiles be recalculated and new ones obtained according to NRL II.
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  • 44
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    American Institute of Physics
    In:  Journal of the Acoustical Society of America, 32 (6). pp. 641-644.
    Publication Date: 2020-07-16
    Description: Tables for the speed of sound in sea water are presented. These tables have been prepared from an empirical formula which was derived to fit measured sound‐speed data obtained over the temperature range −3°C to 30°C, the pressure range 1.033 kg/cm2 to 1000 kg/cm2, and the salinity range 33‰ to 37‰. The discrepancy of −3.0 m/sec found by Del Grosso at 1 atm., as compared to the tables of Kuwahara, is substantiated. In addition, the pressure coefficient of sound speed observed in the present work differs from that predicted by Kuwahara.
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  • 45
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    American Institute of Physics
    In:  Journal of the Acoustical Society of America, 124 (5). pp. 2774-2782.
    Publication Date: 2020-07-16
    Description: A new equation is proposed for the calculation of sound speed in seawater as a function of temperature, salinity, depth, and latitude in all oceans and open seas, including the Baltic and the Black Sea. The proposed equation agrees to better than ±0.2m∕s with two reference complex equations, each fitting the best available data corresponding to existing waters of different salinities. The only exceptions are isolated hot brine spots that may be found at the bottom of some seas. The equation is of polynomial form, with 14 terms and coefficients of between one and three significant figures. This is a substantial reduction in complexity compared to the more complex equations using pressure that need to be calculated according to depth and location. The equation uses the 1990 universal temperature scale (an elementary transformation is given for data based on the 1968 temperature scale). It is hoped that the equation will be useful to those who need to calculate sound speed in applications of marine acoustics.
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  • 46
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    American Institute of Physics
    In:  Journal of the Acoustical Society of America, 63 (2). pp. 366-377.
    Publication Date: 2020-07-16
    Description: In studies in underwater acoustics,geophysics, and geology, the relations between soundvelocity and density allow assignment of approximate values of density to sediment and rock layers of the earth’s crust and mantle, given a seismicmeasurement of velocity. In the past, single curves of velocity versus density represented all sediment and rock types. A large amount of recent data from the Deep Sea Drilling Project (DSDP), and reflection and refraction measurements of soundvelocity, allow construction of separate velocity–density curves for the principal marine sediment and rock types. The paper uses carefully selected data from laboratory and i n s i t umeasurements to present empirical sound velocity–density relations (in the form of regression curves and equations) in terrigenous silt clays, turbidites, and shale, in calcareous materials (sediments, chalk, and limestone), and in siliceous materials (sediments, porcelanite, and chert); a published curve for DSDP basalts is included. Speculative curves are presented for composite sections of basalt and sediments. These velocity–density relations, with seismicmeasurements of velocity, should be useful in assigning approximate densities to sea‐floor sediment and rock layers for studies in marine geophysics, and in forming geoacoustic models of the sea floor for underwater acoustic studies.
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  • 47
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    American Institute of Physics
    In:  Journal of the Acoustical Society of America, 103 (3). pp. 1346-1352.
    Publication Date: 2020-07-16
    Description: Two sets of equations, covering all world oceans and seas, are presented to calculate pressure from depth for the computation of sound speed, and depth from pressure for use in ocean engineering. They are based on the algorithm of UNESCO 1983 [N. P. Fofonoff and R. C. Millard, Jr., Unesco Tech. Papers in Mar. Sci. No. 44 (1983)], and on calculations from temperature and salinity profiles. The pressure to depth conversion is presented first. The equations can be used in those cases where the desired accuracy is reduced to ±0.8 m. The equations to convert depth to pressure provide an overall accuracy between ±8000 Pa and ±1000 Pa. This leads to errors in sound speed consistently smaller than ±0.02 m/s. The discussion, and comparisons with results and other formulas, suggest that the new equations are a substantial improvement on the previous simplified ones, which should now be abandoned.
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  • 48
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    American Institute of Physics
    In:  Journal of the Acoustical Society of America, 140 (4). pp. 2695-2702.
    Publication Date: 2020-07-16
    Description: The Green's function (GF) for the scalar wave equation is numerically constructed by an advanced geometric ray-tracing method based on the eikonal approximation related to the semiclassical propagator. The underlying theory is first briefly introduced, and then it is applied to acoustics and implemented in a ray-tracing-type numerical simulation. The so constructed numerical method is systematically used to calculate the sound field in a rectangular (cuboid) room, yielding also the acoustic modes of the room. The simulated GF is rigorously compared to its analytic approximation. Good agreement is found, which proves the devised numerical approach potentially useful also for low frequency acoustic modeling, which is in practice not covered by geometrical methods.
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  • 49
    Publication Date: 2020-06-25
    Description: Naturally produced polybrominated diphenyl ethers (PBDEs) pervade the marine environment and structurally resemble toxic man-made brominated flame retardants. PBDEs bioaccumulate in marine animals and are likely transferred to the human food chain. However, the biogenic basis for PBDE production in one of their most prolific sources, marine sponges of the order Dysideidae, remains unidentified. Here, we report the discovery of PBDE biosynthetic gene clusters within sponge-microbiome-associated cyanobacterial endosymbionts through the use of an unbiased metagenome-mining approach. Using expression of PBDE biosynthetic genes in heterologous cyanobacterial hosts, we correlate the structural diversity of naturally produced PBDEs to modifications within PBDE biosynthetic gene clusters in multiple sponge holobionts. Our results establish the genetic and molecular foundation for the production of PBDEs in one of the most abundant natural sources of these molecules, further setting the stage for a metagenomic-based inventory of other PBDE sources in the marine environment.
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  • 50
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    Nature Publishing Group
    In:  Nature Immunology, 12 (1). pp. 5-9.
    Publication Date: 2020-06-25
    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.
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  • 51
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    Nature Publishing Group
    In:  Nature Immunology, 14 (7). pp. 676-684.
    Publication Date: 2020-06-25
    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.
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  • 52
    Publication Date: 2020-06-25
    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…
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  • 53
    Publication Date: 2020-06-25
    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.
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  • 54
    Publication Date: 2020-06-25
    Description: Crossover recombination reshuffies genes and prevents errors in segregation tha't Iead to extra or missing chromosomes (aneuploidy) in human eggs, a major cause of pregnancy failure and congenital disorders. Here we generate genome-wide maps of cro~sovers and chromosome segregation patterns by recovering all three products of single female meioses. Genotyping 〉4 millioninformative SNPs from 23 complete meioses allowed us to map 2,032 maternal and 1,342 paternal crossovers and to infer the segregation patterns of 529 chromosome pairs. We uncover a new reverse chromosome segregation pattern in which both homologsseparate their sister chromatids at meiosis I; detect selection for higher recombination rates in the female germ line by the elimination of aneuploid embryos; and report chromosomal drive against non recombinant chromatids at meiosis II. Collectively, our findings show !hat recombination not only affects homolog segregation at meiosis I but also the fate of sister chromatids at meiosis II.
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  • 55
    Publication Date: 2020-06-24
    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.
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  • 56
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    Nature Publishing Group
    In:  Nature Methods, 10 (9). pp. 881-884.
    Publication Date: 2020-06-24
    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.
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  • 57
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    Nature Publishing Group
    In:  Nature Methods, 13 (2). pp. 107-108.
    Publication Date: 2020-06-24
    Description: To the Editor: We congratulate Halsey et al. for their important discussion of the random nature of P values in an earlier issue of this journal1. P values from identical experiments can differ greatly in a way that is surprising to many2, 3, 4, 5, 6. The failure to appreciate this…
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  • 58
    Publication Date: 2020-06-24
    Description: Marine-derived fungi have been shown in recent years to produce a plethora of new bioactive secondary metabolites, some of them featuring new carbon frameworks hitherto unprecedented in nature. These compounds are of interest as new lead structures for medicine as well as for plant protection. The aim of this protocol is to give a detailed description of methods useful for the isolation and cultivation of fungi associated with various marine organisms (sponges, algae and mangrove plants) for the extraction, characterization and structure elucidation of biologically active secondary metabolites produced by these marine-derived endophytic fungi, and for the preliminary evaluation of their pharmacological properties based on rapid 'in house' screening systems. Some results exemplifying the positive outcomes of the protocol are given at the end. From sampling in marine environment to completion of the structure elucidation and bioactivity screening, a period of at least 3 months has to be scheduled.
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  • 59
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    Nature Publishing Group
    In:  Nature Methods, 12 (5). pp. 377-378.
    Publication Date: 2020-06-24
    Description: Today’s predictions are tomorrow’s priors
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  • 60
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    Nature Publishing Group
    In:  Nature Methods, 10 (10). pp. 996-998.
    Publication Date: 2020-06-24
    Description: Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with 〉3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.
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  • 61
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    Nature Publishing Group
    In:  Nature Reviews Microbiology, 12 (10). pp. 686-698.
    Publication Date: 2020-06-23
    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.
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  • 62
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    Nature Publishing Group
    In:  Nature Reviews Microbiology, 9 (7). pp. 499-508.
    Publication Date: 2020-06-23
    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.
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  • 63
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    Nature Publishing Group
    In:  Nature Reviews Microbiology, 12 (10). pp. 686-698.
    Publication Date: 2020-06-23
    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.
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  • 64
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    Nature Publishing Group
    In:  Nature Reviews Immunology, 12 (2). pp. 89-100.
    Publication Date: 2020-06-23
    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.
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  • 65
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    Nature Publishing Group
    In:  Nature Reviews Microbiology, 13 (8). pp. 509-523.
    Publication Date: 2020-06-23
    Description: Microorganisms produce a wealth of structurally diverse specialized metabolites with a remarkable range of biological activities and a wide variety of applications in medicine and agriculture, such as the treatment of infectious diseases and cancer, and the prevention of crop damage. Genomics has revealed that many microorganisms have far greater potential to produce specialized metabolites than was thought from classic bioactivity screens; however, realizing this potential has been hampered by the fact that many specialized metabolite biosynthetic gene clusters (BGCs) are not expressed in laboratory cultures. In this Review, we discuss the strategies that have been developed in bacteria and fungi to identify and induce the expression of such silent BGCs, and we briefly summarize methods for the isolation and structural characterization of their metabolic products.
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  • 66
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    Nature Publishing Group
    In:  Nature Reviews Genetics, 14 (6). pp. 368-369.
    Publication Date: 2020-06-23
    Description: Population genomics — in which genetic variation across the genome is studied in many individuals — has so far been limited to species for which reference genomes are available. A recent study shows how transcriptomics can be used to extend population genomics research across a far greater range of organisms. This advance promises important new insights int…
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  • 67
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    Nature Publishing Group
    In:  Nature Reviews Microbiology, 2 (5). pp. 414-424.
    Publication Date: 2020-06-23
    Description: Horizontal gene transfer is an important mechanism for the evolution of microbial genomes. Pathogenicity islands — mobile genetic elements that contribute to rapid changes in virulence potential — are known to have contributed to genome evolution by horizontal gene transfer in many bacterial pathogens. Increasing evidence indicates that equivalent elements in non-pathogenic species — genomic islands — are important in the evolution of these bacteria, influencing traits such as antibiotic resistance, symbiosis and fitness, and adaptation in general. This review discusses the recent lessons that have been learned from pathogenicity islands in pathogenic microorganisms and how they apply to the role of genomic islands in commensal, symbiotic and environmental bacteria.
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  • 68
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    Nature Publishing Group
    In:  Nature Reviews Microbiology, 10 (9). pp. 641-654.
    Publication Date: 2020-06-23
    Description: Marine sponges (phylum Porifera) often contain dense and diverse microbial communities, which can constitute up to 35% of the sponge biomass. The genome of one sponge, Amphimedon queenslandica, was recently sequenced, and this has provided new insights into the origins of animal evolution. Complementary efforts to sequence the genomes of uncultivated sponge symbionts have yielded the first glimpse of how these intimate partnerships are formed. The remarkable microbial and chemical diversity of the sponge–microorganism association, coupled with its postulated antiquity, makes sponges important model systems for the study of metazoan host–microorganism interactions, and their evolution, as well as for enabling access to biotechnologically important symbiont-derived natural products. In this Review, we discuss our current understanding of the interactions between marine sponges and their microbial symbiotic consortia, and highlight recent insights into these relationships from genomic studies.
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  • 69
    Publication Date: 2020-06-23
    Description: High-throughput techniques based on restriction site-associated DNA sequencing (RADseq) are enabling the low-cost discovery and genotyping of thousands of genetic markers for any species, including non-model organisms, which is revolutionizing ecological, evolutionary and conservation genetics. Technical differences among these methods lead to important considerations for all steps of genomics studies, from the specific scientific questions that can be addressed, and the costs of library preparation and sequencing, to the types of bias and error inherent in the resulting data. In this Review, we provide a comprehensive discussion of RADseq methods to aid researchers in choosing among the many different approaches and avoiding erroneous scientific conclusions from RADseq data, a problem that has plagued other genetic marker types in the past.
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  • 70
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    Nature Publishing Group
    In:  Nature Reviews Drug Discovery, 14 (2). pp. 111-129.
    Publication Date: 2020-06-23
    Description: Natural products have been a rich source of compounds for drug discovery. However, their use has diminished in the past two decades, in part because of technical barriers to screening natural products in high-throughput assays against molecular targets. Here, we review strategies for natural product screening that harness the recent technical advances that have reduced these barriers. We also assess the use of genomic and metabolomic approaches to augment traditional methods of studying natural products, and highlight recent examples of natural products in antimicrobial drug discovery and as inhibitors of protein–protein interactions. The growing appreciation of functional assays and phenotypic screens may further contribute to a revival of interest in natural products for drug discovery.
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  • 71
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    Nature Publishing Group
    In:  Nature Reviews Molecular Cell Biology, 15 (10). pp. 647-664.
    Publication Date: 2020-06-23
    Description: Mammalian organs are challenging to study as they are fairly inaccessible to experimental manipulation and optical observation. Recent advances in three-dimensional (3D) culture techniques, coupled with the ability to independently manipulate genetic and microenvironmental factors, have enabled the real-time study of mammalian tissues. These systems have been used to visualize the cellular basis of epithelial morphogenesis, to test the roles of specific genes in regulating cell behaviours within epithelial tissues and to elucidate the contribution of microenvironmental factors to normal and disease processes. Collectively, these novel models can be used to answer fundamental biological questions and generate replacement human tissues, and they enable testing of novel therapeutic approaches, often using patient-derived cells.
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  • 72
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    Nature Publishing Group
    In:  Scientific Data, 1 (1). Art.Nr. 140048.
    Publication Date: 2020-05-13
    Description: Knowledge of concentrations and elemental ratios of suspended particles are important for understanding many biogeochemical processes in the ocean. These include patterns of phytoplankton nutrient limitation as well as linkages between the cycles of carbon and nitrogen or phosphorus. To further enable studies of ocean biogeochemistry, we here present a global dataset consisting of 100,605 total measurements of particulate organic carbon, nitrogen, or phosphorus analyzed as part of 70 cruises or time-series. The data are globally distributed and represent all major ocean regions as well as different depths in the water column. The global median C:P, N:P, and C:N ratios are 163, 22, and 6.6, respectively, but the data also includes extensive variation between samples from different regions. Thus, this compilation will hopefully assist in a wide range of future studies of ocean elemental ratios.
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  • 73
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    American Institute of Physics
    In:  The Journal of the Acoustical Society of America, 138 (3). pp. 1253-1267.
    Publication Date: 2020-05-11
    Description: Responses obtained in consonant perception experiments typically show a large variability across stimuli of the same phonetic identity. The present study investigated the influence of different potential sources of this response variability. It was distinguished between source-induced variability, referring to perceptual differences caused by acoustical differences in the speech tokens and/or the masking noise tokens, and receiver-related variability, referring to perceptual differences caused by within- and across-listener uncertainty. Consonant-vowel combinations consisting of 15 consonants followed by the vowel /i/ were spoken by two talkers and presented to eight normal-hearing listeners both in quiet and in white noise at six different signal-to-noise ratios. The obtained responses were analyzed with respect to the different sources of variability using a measure of the perceptual distance between responses. The speech-induced variability across and within talkers and the across-listener variability were substantial and of similar magnitude. The noise-induced variability, obtained with time-shifted realizations of the same random process, was smaller but significantly larger than the amount of within-listener variability, which represented the smallest effect. The results have implications for the design of consonant perception experiments and provide constraints for future models of consonant perception.
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  • 74
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    American Institute of Physics
    In:  The Journal of the Acoustical Society of America, 78 (6). pp. 2115-2121.
    Publication Date: 2020-05-11
    Description: The acoustic backscatter of eight well‐curated ferromanganese nodules has been measured in 1 °C seawater at frequencies from 45 to 167 kHz. The nodules have diameters from 37 to 121 mm and are thought to be representative of the Cu–Ni–Co‐rich nodules from the area around 14° 40’ N, 125° 25’ W (DOMES site C). They had been collected in box cores on the Echo 1 expedition and were kept refrigerated and water soaked in air‐tight plastic bags. Acoustic backscatter variations of over 10 dB were observed while the nodule was rotated 10° to 30° about one of its principal axes. The complicated fine structure, as well as the target strength, makes it clear that nodules cannot be modeled as simple spheres.
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  • 75
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    American Institute of Physics
    In:  The Journal of the Acoustical Society of America, 58 (6). pp. 1318-1319.
    Publication Date: 2020-05-11
    Description: A simple equation is presented for the dependence of sound speed on temperature, salinity, and depth of water. The comparison with Del Grosso’s NRL II shows discrepancies of the order of tenths of m/sec for realistic values of the parameters.
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  • 76
    Publication Date: 2020-05-11
    Description: Many marine sponges are hosts to dense and phylogenetically diverse microbial communities that are located in the extracellular matrix of the animal. The candidate phylum Poribacteria is a predominant member of the sponge microbiome and its representatives are nearly exclusively found in sponges. Here we used single-cell genomics to obtain comprehensive insights into the metabolic potential of individual poribacterial cells representing three distinct phylogenetic groups within Poribacteria. Genome sizes were up to 5.4 Mbp and genome coverage was as high as 98.5%. Common features of the poribacterial genomes indicated that heterotrophy is likely to be of importance for this bacterial candidate phylum. Carbohydrate-active enzyme database screening and further detailed analysis of carbohydrate metabolism suggested the ability to degrade diverse carbohydrate sources likely originating from seawater and from the host itself. The presence of uronic acid degradation pathways as well as several specific sulfatases provides strong support that Poribacteria degrade glycosaminoglycan chains of proteoglycans, which are important components of the sponge host matrix. Dominant glycoside hydrolase families further suggest degradation of other glycoproteins in the host matrix. We therefore propose that Poribacteria are well adapted to an existence in the sponge extracellular matrix. Poribacteria may be viewed as efficient scavengers and recyclers of a particular suite of carbon compounds that are unique to sponges as microbial ecosystems.
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  • 77
    Publication Date: 2020-05-11
    Description: Marine sponges (phylum Porifera) are among the oldest multicellular animals (metazoans), the sea's most prolific producers of bioactive metabolites, and of considerable ecological importance due to their abundance and ability to filter enormous volumes of seawater. In addition to these important attributes, sponge microbiology is now a rapidly expanding field.
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  • 78
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    American Institute of Physics
    In:  The Journal of the Acoustical Society of America, 70 (5). pp. 1336-1338.
    Publication Date: 2020-05-11
    Description: The curves of optimum frequencies versus maximum range for active sonar detection under specific sets of assumptions are presented for the more recent expressions for attenuation given by Lovett [J. Acoust. Soc. Am. 58, 620–625 (1975)] for the eastern North Pacific and Thorp [J. Acoust. Soc. Am. 42, 270 (1967)] for the western North Atlantic as corrected at low frequencies by Kibblewhite et al. [J. Acoust. Soc. Am. 60, 1040–1047 (1976)].
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  • 79
    Publication Date: 2020-02-18
    Description: The climate of the North Atlantic region exhibits fluctuations on decadal timescales that have large societal consequences. Prominent examples include hurricane activity in the Atlantic1, and surface-temperature and rainfall variations over North America2, Europe3 and northern Africa4. Although these multidecadal variations are potentially predictable if the current state of the ocean is known5, 6, 7, the lack of subsurface ocean observations8 that constrain this state has been a limiting factor for realizing the full skill potential of such predictions9. Here we apply a simple approach—that uses only sea surface temperature (SST) observations—to partly overcome this difficulty and perform retrospective decadal predictions with a climate model. Skill is improved significantly relative to predictions made with incomplete knowledge of the ocean state10, particularly in the North Atlantic and tropical Pacific oceans. Thus these results point towards the possibility of routine decadal climate predictions. Using this method, and by considering both internal natural climate variations and projected future anthropogenic forcing, we make the following forecast: over the next decade, the current Atlantic meridional overturning circulation will weaken to its long-term mean; moreover, North Atlantic SST and European and North American surface temperatures will cool slightly, whereas tropical Pacific SST will remain almost unchanged. Our results suggest that global surface temperature may not increase over the next decade, as natural climate variations in the North Atlantic and tropical Pacific temporarily offset the projected anthropogenic warming.
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  • 80
    Publication Date: 2020-01-20
    Description: A bottom-simulating reflection (BSR) is a seismic reflectivity phenomenon that is widely accepted as indicating the base of the gas-hydrate stability zone. The acoustic impedance difference between sediments invaded with gas hydrate above the BSR and sediments without gas hydrate, but commonly with free gas below, are accepted as the conditions that create this reflection. The relationship between BSRs and marine gas hydrate has become so well known since the 1970s that investigators, when asked to define the most important seismic attribute of marine gas-hydrate systems, usually reply, “a BSR event.” Research conducted over the last decade has focused on calibrating seafloor seismic reflectivity across the geology of the northern Gulf of Mexico (GoM) continental slope surface to the seafloor. This research indicates that the presence and character of seafloor bright spots (SBS) can be indicators of gas hydrates in surface and near-surface sediments (Figure 1). It has become apparent that SBSs on the continental slope generally are responses to fluid and gas expulsion processes. Gas-hydrate formation is, in turn, related to these processes. As gas-hydrate research expands around the world, it will be interesting to find if SBS behavior in other deepwater settings is as useful for identifying gas-hydrate sites as in the GoM.
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  • 81
    Publication Date: 2020-01-07
    Description: Large uncertainties remain in the current and future contribution to sea level rise from Antarctica. Climate warming may increase snowfall in the continent’s interior1,2,3, but enhance glacier discharge at the coast where warmer air and ocean temperatures erode the buttressing ice shelves4,5,6,7,8,9,10,11. Here, we use satellite interferometric synthetic-aperture radar observations from 1992 to 2006 covering 85% of Antarctica’s coastline to estimate the total mass flux into the ocean. We compare the mass fluxes from large drainage basin units with interior snow accumulation calculated from a regional atmospheric climate model for 1980 to 2004. In East Antarctica, small glacier losses in Wilkes Land and glacier gains at the mouths of the Filchner and Ross ice shelves combine to a near-zero loss of 4±61 Gt yr−1. In West Antarctica, widespread losses along the Bellingshausen and Amundsen seas increased the ice sheet loss by 59% in 10 years to reach 132±60 Gt yr−1 in 2006. In the Peninsula, losses increased by 140% to reach 60±46 Gt yr−1 in 2006. Losses are concentrated along narrow channels occupied by outlet glaciers and are caused by ongoing and past glacier acceleration. Changes in glacier flow therefore have a significant, if not dominant impact on ice sheet mass balance.
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  • 82
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    Nature Publishing Group
    In:  Nature, 435 (7044). p. 901.
    Publication Date: 2019-11-11
    Description: Scattered groups of these ancient fish may all stem from a single remote population. Coelacanths were discovered in the Comoros archipelago to the northwest of Madagascar in 1952. Since then, these rare, ancient fish have been found to the south off Mozambique, Madagascar and South Africa, and to the north off Kenya and Tanzania — but it was unclear whether these are separate populations or even subspecies. Here we show that the genetic variation between individuals from these different locations is unexpectedly low. Combined with earlier results from submersible and oceanographic observations1, 2, our findings indicate that a separate African metapopulation is unlikely to have existed and that locations distant from the Comoros were probably inhabited relatively recently by either dead-end drifters or founders that originated in the Comoros.
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  • 83
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    Nature Publishing Group
    In:  Nature, 403 (6765). p. 38.
    Publication Date: 2019-11-11
    Description: Living coelacanths (Latimeria chalumnae) are normally found only in the western Indian Ocean, where they inhabit submarine caves in the Comores Islands1. Two specimens have since been caught off the island of Manado Tua, north Sulawesi, Indonesia, some 10,000 kilometres away2. We sought to determine the ecological and geographic distribution of Indonesian coelacanth populations with a view to drawing up conservation measures for this extremely rare fish2,3. During our explorations, we discovered two living Indonesian coelacanths 360 km southwest of Manado Tua.
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  • 84
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    Nature Publishing Group
    In:  Nature Biotechnology, 20 (8). pp. 788-789.
    Publication Date: 2019-10-22
    Description: normous amounts of potential energy lie buried in marine sediments in the form of reduced carbon compounds. The most familiar form of this vast energy reserve is petroleum, which drives the lion's share of today's energy economy. The next most obvious submarine energy reserve, even more abundant than petroleum, is methane. At deep-sea conditions of low temperature and high pressure, large amounts of this natural gas are found in sub-seafloor reservoirs of frozen methane hydrates [1]. Yet there is another abundant, but less obvious, marine energy reserve: sediment-associated organic carbon, which represents about 2% of the dry weight of marine sediments along continental margins. Is it possible to tap into this vast, dispersed form of submarine energy? If so, how? The answer, in part, is that microbes already have tapped into this large energy reserve. Now, in two papers, one in this issue [2] and the other in a previous issue of Science [3], researchers harness microbially generated power by constructing a fuel cell that can exploit the naturally occurring voltage gradient created by microbial activity in marine sediments.
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  • 85
    Publication Date: 2019-10-22
    Description: In many marine environments, a voltage gradient exists across the water sediment interface resulting from sedimentary microbial activity. Here we show that a fuel cell consisting of an anode embedded in marine sediment and a cathode in overlying seawater can use this voltage gradient to generate electrical power in situ. Fuel cells of this design generated sustained power in a boat basin carved into a salt marsh near Tuckerton, New Jersey, and in the Yaquina Bay Estuary near Newport, Oregon. Retrieval and analysis of the Tuckerton fuel cell indicates that power generation results from at least two anode reactions: oxidation of sediment sulfide (a by-product of microbial oxidation of sedimentary organic carbon) and oxidation of sedimentary organic carbon catalyzed by microorganisms colonizing the anode. These results demonstrate in real marine environments a new form of power generation that uses an immense, renewable energy reservoir (sedimentary organic carbon) and has near-immediate application.
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  • 86
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    Nature Publishing Group
    In:  The ISME Journal, 3 (1). pp. 4-12.
    Publication Date: 2019-09-24
    Description: Our understanding of the composition and activities of microbial communities from diverse habitats on our planet has improved enormously during the past decade, spurred on largely by advances in molecular biology. Much of this research has focused on the bacteria, and to a lesser extent on the archaea and viruses, because of the relative ease with which these assemblages can be analyzed and studied genetically. In contrast, single-celled, eukaryotic microbes (the protists) have received much less attention, to the point where one might question if they have somehow been demoted from the position of environmentally important taxa. In this paper, we draw attention to this situation and explore several possible (some admittedly lighthearted) explanations for why these remarkable and diverse microbes have remained largely overlooked in the present era of the microbe. © 2009 International Society for Microbial Ecology All rights reserved.
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  • 87
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    Nature Publishing Group
    In:  Nature, 447 . p. 383.
    Publication Date: 2019-09-23
    Description: As the complex interplay of forces in the ocean responds to climate change, the dynamics of global ocean circulation are shifting.
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  • 88
    Publication Date: 2019-09-23
    Description: Predicting the evolution of climate over decadal timescales requires a quantitative understanding of the dynamics that govern the meridional overturning circulation (MOC)1. Comprehensive ocean measurement programmes aiming to monitor MOC variations have been established in the subtropical North Atlantic2, 3 (RAPID, at latitude 26.5° N, and MOVE, at latitude 16° N) and show strong variability on intraseasonal to interannual timescales. Observational evidence of longer-term changes in MOC transport remains scarce, owing to infrequent sampling of transoceanic sections over past decades4, 5. Inferences based on long-term sea surface temperature records, however, supported by model simulations, suggest a variability with an amplitude of plusminus1.5–3 Sv (1 Sv = 106 m3 s-1) on decadal timescales in the subtropics6. Such variability has been attributed to variations of deep water formation in the sub-arctic Atlantic, particularly the renewal rate of Labrador Sea Water7. Here we present results from a model simulation that suggest an additional influence on decadal MOC variability having a Southern Hemisphere origin: dynamic signals originating in the Agulhas leakage region at the southern tip of Africa. These contribute a MOC signal in the tropical and subtropical North Atlantic that is of the same order of magnitude as the northern source. A complete rationalization of observed MOC changes therefore also requires consideration of signals arriving from the south.
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  • 89
    Publication Date: 2019-09-23
    Description: Piceamycin, a new macrolactam polyketide antibiotic, was detected by HPLC-diode array screening in extracts of Streptomyces sp. GB 4-2, which was isolated from the mycorrhizosphere of Norway spruce. The structure of piceamycin was determined by mass spectrometry and NMR experiments. It showed inhibitory activity against Gram-positive bacteria, selected human tumor cell lines and protein tyrosine phosphatase 1B. The Journal of Antibiotics (2009) 62, 513-518; doi:10.1038/ja.2009.64; published online 17 July 2009
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  • 90
    Publication Date: 2019-09-23
    Description: Global warming was reported to cause growth reductions in tropical shallow water corals in both, cooler and warmer, regions of the coral species range. This suggests regional adaptation with less heat-tolerant populations in cooler and more thermo-tolerant populations in warmer regions. Here, we investigated seasonal changes in the in situ metabolic performance of the widely distributed hermatypic coral Pocillopora verrucosa along 12 degrees latitudes featuring a steep temperature gradient between the northern (28.5 degrees N, 21-27 degrees C) and southern (16.5 degrees N, 28-33 degrees C) reaches of the Red Sea. Surprisingly, we found little indication for regional adaptation, but strong indications for high phenotypic plasticity: Calcification rates in two seasons (winter, summer) were found to be highest at 28-29 degrees C throughout all populations independent of their geographic location. Mucus release increased with temperature and nutrient supply, both being highest in the south. Genetic characterization of the coral host revealed low inter-regional variation and differences in the Symbiodinium clade composition only at the most northern and most southern region. This suggests variable acclimatization potential to ocean warming of coral populations across the Red Sea: high acclimatization potential in northern populations, but limited ability to cope with ocean warming in southern populations already existing at the upper thermal margin for corals
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  • 91
    Publication Date: 2019-09-23
    Description: Restructure data-gathering and evaluation networks to address climate change, energy, food, health and water provision, say Yonglong Lu and colleagues.
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  • 92
    Publication Date: 2019-09-23
    Description: Increasingly, spatial geochemical zonation, present as geographically distinct, subparallel trends, is observed along hotspot tracks, such as Hawaii and the Galapagos. The origin of this zonation is currently unclear. Recently zonation was found along the last B70 Myr of the Tristan-Gough hotspot track. Here we present new Sr–Nd–Pb–Hf isotope data from the older parts of this hotspot track (Walvis Ridge and Rio Grande Rise) and re-evaluate published data from the Etendeka and Parana flood basalts erupted at the initiation of the hotspot track. We show that only the enriched Gough, but not the less-enriched Tristan, component is present in the earlier (70–132 Ma) history of the hotspot. Here we present a model that can explain the temporal evolution and origin of plume zonation for both the Tristan-Gough and Hawaiian hotspots, two end member types of zoned plumes, through processes taking place in the plume sources at the base of the lower mantle.
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  • 93
    Publication Date: 2019-09-23
    Description: Increasing atmospheric CO2 concentrations are causing ocean acidification (OA), altering carbonate chemistry with consequences for marine organisms. Here we show that OA increases by 46–212% the production of phenolic compounds in phytoplankton grown under the elevated CO2 concentrations projected for the end of this century, compared with the ambient CO2 level. At the same time, mitochondrial respiration rate is enhanced under elevated CO2 concentrations by 130–160% in a single species or mixed phytoplankton assemblage. When fed with phytoplankton cells grown under OA, zooplankton assemblages have significantly higher phenolic compound content, by about 28–48%. The functional consequences of the increased accumulation of toxic phenolic compounds in primary and secondary producers have the potential to have profound consequences for marine ecosystem and seafood quality, with the possibility that fishery industries could be influenced as a result of progressive ocean changes
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  • 94
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    Nature Publishing Group
    In:  Nature Climate Change, 5 (1). pp. 4-6.
    Publication Date: 2019-09-23
    Description: A sustainable global ocean observation system requires timely implementation of the framework for ocean observing. The recent Qingdao Global Ocean Summit highlighted the need for a more coherent institutional response to maintain an integrated ocean-observing system.
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  • 95
    Publication Date: 2019-09-23
    Description: Ocean islands, seamounts and volcanic ridges are thought to form above mantle plumes. Yet, this mechanism cannot explain many volcanic features on the Pacific Ocean floor and some might instead be caused by cracks in the oceanic crust linked to the reorganization of plate motions. A distinctive bend in the Hawaiian–Emperor volcanic chain has been linked to changes in the direction of motion of the Pacific Plate, movement of the Hawaiian plume, or a combination of both. However, these links are uncertain because there is no independent record that precisely dates tectonic events that affected the Pacific Plate. Here we analyse the geochemical characteristics of lava samples collected from the Musicians Ridges, lines of volcanic seamounts formed close to the Hawaiian–Emperor bend. We find that the geochemical signature of these lavas is unlike typical ocean island basalts and instead resembles mid-ocean ridge basalts. We infer that the seamounts are unrelated to mantle plume activity and instead formed in an extensional setting, due to deformation of the Pacific Plate. 40Ar/39Ar dating reveals that the Musicians Ridges formed during two time windows that bracket the time of formation of the Hawaiian–Emperor bend, 53–52 and 48–47 million years ago. We conclude that the Hawaiian–Emperor bend was formed by plate–mantle reorganization, potentially triggered by a series of subduction events at the Pacific Plate margins.
    Type: Article , PeerReviewed
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  • 96
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    Nature Publishing Group
    In:  Nature Geoscience, 3 (10). pp. 662-663.
    Publication Date: 2019-09-23
    Description: The Census of Marine Life has succeeded in raising awareness about marine biodiversity, and contributed much to our understanding of what lives where. But the project has fallen short of its goal to estimate species abundance.
    Type: Article , PeerReviewed
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  • 97
    Publication Date: 2019-09-23
    Description: In the context of gradual Cenozoic cooling, the timing of the onset of significant Northern Hemisphere glaciation 2.7 million years ago is consistent with Milankovitch's orbital theory, which posited that ice sheets grow when polar summertime insolation and temperature are low. However, the role of moisture supply in the initiation of large Northern Hemisphere ice sheets has remained unclear. The subarctic Pacific Ocean represents a significant source of water vapour to boreal North America, but it has been largely overlooked in efforts to explain Northern Hemisphere glaciation. Here we present alkenone unsaturation ratios and diatom oxygen isotope ratios from a sediment core in the western subarctic Pacific Ocean, indicating that 2.7 million years ago late-summer sea surface temperatures in this ocean region rose in response to an increase in stratification. At the same time, winter sea surface temperatures cooled, winter floating ice became more abundant and global climate descended into glacial conditions. We suggest that the observed summer warming extended into the autumn, providing water vapour to northern North America, where it precipitated and accumulated as snow, and thus allowed the initiation of Northern Hemisphere glaciation.
    Type: Article , PeerReviewed
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  • 98
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    Nature Publishing Group
    In:  Nature Geoscience, 2 (4). pp. 243-244.
    Publication Date: 2019-09-23
    Description: The enhanced Arctic warming over the past three decades is attracting much attention. Combining forward and inverse models with observations suggests that regional changes in aerosol concentrations have contributed significantly.
    Type: Article , PeerReviewed
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  • 99
    Publication Date: 2019-09-23
    Description: Fertilization of the ocean by adding iron compounds has induced diatom-dominated phytoplankton blooms accompanied by considerable carbon dioxide drawdown in the ocean surface layer. However, because the fate of bloom biomass could not be adequately resolved in these experiments, the timescales of carbon sequestration from the atmosphere are uncertain. Here we report the results of a five-week experiment carried out in the closed core of a vertically coherent, mesoscale eddy of the Antarctic Circumpolar Current, during which we tracked sinking particles from the surface to the deep-sea floor. A large diatom bloom peaked in the fourth week after fertilization. This was followed by mass mortality of several diatom species that formed rapidly sinking, mucilaginous aggregates of entangled cells and chains. Taken together, multiple lines of evidence—although each with important uncertainties—lead us to conclude that at least half the bloom biomass sank far below a depth of 1,000 metres and that a substantial portion is likely to have reached the sea floor. Thus, iron-fertilized diatom blooms may sequester carbon for timescales of centuries in ocean bottom water and for longer in the sediments.
    Type: Article , PeerReviewed
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  • 100
    Publication Date: 2019-09-23
    Description: Carbon dioxide and light are two major prerequisites of photosynthesis. Rising CO2 levels in oceanic surface waters in combination with ample light supply are therefore often considered stimulatory to marine primary production(1-3). Here we show that the combination of an increase in both CO2 and light exposure negatively impacts photosynthesis and growth of marine primary producers. When exposed to CO2 concentrations projected for the end of this century(4), natural phytoplankton assemblages of the South China Sea responded with decreased primary production and increased light stress at light intensities representative of the upper surface layer. The phytoplankton community shifted away from diatoms, the dominant phytoplankton group during our field campaigns. To examine the underlying mechanisms of the observed responses, we grew diatoms at different CO2 concentrations and under varying levels (5-100%) of solar radiation experienced by the phytoplankton at different depths of the euphotic zone. Above 22-36% of incident surface irradiance, growth rates in the high-CO2-grown cells were inversely related to light levels and exhibited reduced thresholds at which light becomes inhibitory. Future shoaling of upper-mixed-layer depths will expose phytoplankton to increased mean light intensities(5). In combination with rising CO2 levels, this may cause a widespread decline in marine primary production and a community shift away from diatoms, the main algal group that supports higher trophic levels and carbon export in the ocean.
    Type: Article , PeerReviewed
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