ALBERT

Description: Compositional variations of amphibole stratigraphically recovered from multiple eruptions at a given volcano have a great potential to archive long-term magmatic processes in its crustal plumbing system. Calcic amphibole is a ubiquitous yet chemically and texturally diverse mineral at Mount St. Helens (MSH), where it occurs in dacites and in co-magmatic enclaves throughout the Spirit Lake stage (last ~4000 years of eruptive history). It forms three populations with distinct geochemical trends in key major and trace elements, which are subdivided into a high-Al (11–14.5 wt% Al2O3), a medium-Al (10–12.5 wt% Al2O3), and a low-Al (7.5–10 wt% Al2O3) amphibole population. The oldest investigated tephra record (Smith Creek period, 3900–3300 years BP) yields a bimodal amphibole distribution in which lower-crustal, high-Al amphibole cores (crystallized dominantly from basaltic andesite to andesite melts) and upper-crustal, low-Al amphibole rims (crystallized from rhyolitic melt) document occasional recharge of a shallow silicic mush by a more mafic melt from a lower-crustal reservoir. The sudden appearance of medium-Al amphiboles enriched in incompatible trace elements in eruptive periods younger than 2900 years BP is associated with a change in reservoir conditions toward hotter and drier magmas, which indicates recharge of the shallow silicic reservoir by basaltic melt enriched in incompatible elements. Deep-crystallizing, high-Al amphibole, however, appears mostly unaffected by such incompatible-element-enriched basaltic recharge, suggesting that these basalts bypass the lower crustal reservoir. This could be the result of the eastward offset position of the lower crustal reservoir relative to the upper crustal storage zone underneath the MSH edifice. Amphibole has proven to be a sensitive geochemical archive for uncovering storage conditions of magmas at MSH. In agreement with geophysical observations, storage and differentiation have occurred in two main zones: an upper crustal and lower crustal reservoir (the lower one being chemically less evolved). The upper crustal silicic reservoir, offset to the west of the lower crustal reservoir, has captured compositionally unusual mafic recharge (drier, hotter, and enriched in incompatible trace elements in comparison to the typical parental magmas in the region), resulting in an increased chemical diversity of amphiboles and their carrier intermediate magmas, in the last ~3000 years of MSH’s volcanic record.

Description: Current global warming results in rising sea-water temperatures, and the loss of sea ice in arctic and subarctic oceans impacts the community composition of primary producers with cascading effects on the food web and potentially on carbon export rates. This study analyzes metagenomic shotgun and diatom rbcL amplicon-sequencing data from sedimentary ancient DNA (sedaDNA) of the subarctic western Bering Sea that records phyto- and zooplankton community changes over the last glacial–interglacial cycle, including the last interglacial period (Eemian). Our data show that interglacial and glacial plankton communities differ, with distinct Eemian and Holocene plankton communities. The generally warm Holocene period is dominated by pico-sized cyanobacteria and bacteria-feeding heterotrophic protists, while the Eemian period is dominated by eukaryotic pico-sized chlorophytes and Triparmaceae. In contrast, the glacial period is characterized by micro-sized phototrophic protists, including sea-ice associated diatoms in the family Bacillariaceae and co-occurring diatom-feeding crustaceous zooplankton. Our deep-time record of plankton community changes reveals a long-term decrease in phytoplankton cell size coeval with increasing temperatures, and resembling community changes in the currently warming Bering Sea. The phytoplankton community in the warmer-than-present Eemian period is distinct from modern communities and limits the use of the Eemian as an analog for future climate scenarios. However, under enhanced future warming, the expected shift towards the dominance of small-sized phytoplankton and heterotrophic protists might result in an increased productivity, whereas the community’s potential of carbon export will be decreased, thereby weakening the subarctic Bering Sea’s function as an effective carbon sink.

Description: Background and Aims Dysregulated mineral homeostasis is common in chronic kidney disease (CKD) and associated with bone demineralization and vascular calcification. The balance between bone formation and resorption, which reflect the bone calcium (Ca) balance (BCaB), cannot be determined without bone biopsy which is invasive and not easily repeatable. Recently, we have shown that stable (i.e. non-radioactive) Ca isotopes, 42Ca and 44Ca, can be measured in serum and their ratio (δ44/42Caserum) quantitatively determines net bone gain or loss of Ca. Thus, when bone formation exceeds bone resorption, the net BCaB is positive and δ44/42Caserum is high, and when bone resorption is the predominant process δ44/42Caserum is low compared to age-matched controls. In this study we compared δ44/42Caserum against δ44/42Cabone and arterial biopsy samples (δ44/42Caartery) and the sensitivity of δ44/42Ca in predicting changes in bone histology.

Description: Macroalgal (seaweed) genomic resources are generally lacking as compared to other eukaryotic taxa, and this is particularly true in the red algae (Rhodophyta). Understanding red algal genomes is critical to understanding eukaryotic evolution given that red algal genes are spread across eukaryotic lineages from secondary endosymbiosis and red algae diverged early in the Archaeplastids. The Gracilariales is a highly diverse and widely distributed order including species that can serve as ecosystem engineers in intertidal habitats and several notorious introduced species. The genus Gracilaria is cultivated worldwide, in part for its production of agar and other bioactive compounds with downstream pharmaceutical and industrial applications. This genus is also emerging as a model for algal evolutionary ecology. Here, we report new whole genome assemblies for two species (G. chilensis and G. gracilis), a draft genome assembly of G. caudata, and genome annotation of the previously published G. vermiculophylla genome. To facilitate accessibility and comparative analysis, we integrated these data in a newly created web-based portal dedicated to red algal genomics (https://rhodoexplorer.sb-roscoff.fr). These genomes will provide a resource for understanding algal biology and, more broadly, eukaryotic evolution.

Description: The neritic-oceanic squid Illex argentinus supports one of the largest fisheries in the Southwest Atlantic. It is characterized by extensive migrations across the Patagonian Shelf and complex population structure comprising distinct seasonal spawning groups. To address uncertainty as to the demographic independence of these groups that may compromise sustainable management, a multidisciplinary approach was applied integrating statolith ageing with genome-wide single-nucleotide polymorphism (SNP) analysis. To obtain complete coverage of the spawning groups, sampling was carried out at multiple times during the 2020 fishing season and covered a large proportion of the species' range across the Patagonian Shelf. Statolith and microstructure analysis revealed three distinct seasonal spawning groups of winter-, spring-, and summer-hatched individuals. Subgroups were identified within each seasonal group, with statolith microstructure indicating differences in environmental conditions during ontogeny. Analysis of 〉10 000 SNPs reported no evidence of neutral or non-neutral genetic structure among the various groups. These findings indicate that I. argentinus across the Patagonian Shelf belong to one genetic population and a collaborative management strategy involving international stakeholders is required. The connectivity among spawning groups may represent a "bet-hedging" mechanism important for population resilience.

Description: The development and physiology of herring larvae were monitored for individuals reared in control and combined warming-acidification crossed with different food quality treatments. The experiment revealed that warming and acidification triggers a stress response at the molecular level and decrease herring larvae size-at-stage. Global change puts coastal systems under pressure, affecting the ecology and physiology of marine organisms. In particular, fish larvae are sensitive to environmental conditions, and their fitness is an important determinant of fish stock recruitment and fluctuations. To assess the combined effects of warming, acidification and change in food quality, herring larvae were reared in a control scenario (11 & DEG;C*pH 8.0) and a scenario predicted for 2100 (14 & DEG;C*pH 7.6) crossed with two feeding treatments (enriched in phosphorus and docosahexaenoic acid or not). The experiment lasted from hatching to the beginning of the post-flexion stage (i.e. all fins present) corresponding to 47 days post-hatch (dph) at 14 & DEG;C and 60 dph at 11 & DEG;C. Length and stage development were monitored throughout the experiment and the expression of genes involved in growth, metabolic pathways and stress responses were analysed for stage 3 larvae (flexion of the notochord). Although the growth rate was unaffected by acidification and temperature changes, the development was accelerated in the 2100 scenario, where larvae reached the last developmental stage at a smaller size (-8%). We observed no mortality related to treatments and no effect of food quality on the development of herring larvae. However, gene expression analyses revealed that heat shock transcripts expression was higher in the warmer and more acidic treatment. Our findings suggest that the predicted warming and acidification environment are stressful for herring larvae, inducing a decrease in size-at-stage at a precise period of ontogeny. This could either negatively affect survival and recruitment via the extension of the predation window or positively increase the survival by reducing the larval stage duration.

Description: Young grapevines (Vitis vinifera) suffer and eventually can die from the crown gall disease caused by the plant pathogen Allorhizobium vitis (Rhizobiaceae). Virulent members of A. vitis harbor a tumor-inducing plasmid and induce formation of crown galls due to the oncogenes encoded on the transfer DNA. The expression of oncogenes in transformed host cells induces unregulated cell proliferation and metabolic and physiological changes. The crown gall produces opines uncommon to plants, which provide an important nutrient source for A. vitis harboring opine catabolism enzymes. Crown galls host a distinct bacterial community, and the mechanisms establishing a crown gall–specific bacterial community are currently unknown. Thus, we were interested in whether genes homologous to those of the tumor-inducing plasmid coexist in the genomes of the microbial species coexisting in crown galls. We isolated 8 bacterial strains from grapevine crown galls, sequenced their genomes, and tested their virulence and opine utilization ability in bioassays. In addition, the 8 genome sequences were compared with 34 published bacterial genomes, including closely related plant-associated bacteria not from crown galls. Homologous genes for virulence and opine anabolism were only present in the virulent Rhizobiaceae. In contrast, homologs of the opine catabolism genes were present in all strains including the nonvirulent members of the Rhizobiaceae and non-Rhizobiaceae. Gene neighborhood and sequence identity of the opine degradation cluster of virulent and nonvirulent strains together with the results of the opine utilization assay support the important role of opine utilization for cocolonization in crown galls, thereby shaping the crown gall community.

Description: Post-collisional volcanism contains important clues for understanding the processes that prevail in orogenic belts, including those in the mantle and the uplift and collapse of continents. Here we report new geochronological and geochemical data for a suite of post-collisional Miocene to Pleistocene volcanic rocks from northwest Iran. Four groups of volcanic rocks can be distinguished according to their geochemical and isotopic signatures, including: (1) Miocene depleted lavas with high Nd and Hf but low Pb and Sr isotopic ratios, (2) less depleted lavas with quite variable Pb isotopic composition, (3) lavas with non-radiogenic Nd and Hf isotopic values, but highly radiogenic Sr and Pb isotopic composition, and (4) Pleistocene adakitic rocks with depleted isotopic signatures. The isotopic data reveal that the Miocene rocks are derived from asthenospheric and highly heterogeneous sub-continental lithospheric mantle sources. Evidence suggests that the lithospheric mantle contains recycled upper continental material and is isotopically similar to the enriched mantle two (EMII) end-member. Analysis of Sr-Nd-Pb-Hf-O isotopes in both mineral and rock groundmass, in conjunction with energy-constrained assimilation and fractional crystallization (EC-AFC) numerical modeling, demonstrates that the incorporation of continental crust during magma fractionation via AFC had an insignificant impact on the isotopic composition of the Miocene lavas. Moreover, adakites are the youngest rocks and show a geochemical signature consistent with the partial melting of a young and mafic continental lower crust. Both seismological data and geochemical signatures on these Miocene to Pleistocene volcanic rocks indicate the initiation of asthenospheric upwelling and orogen uplift in the Arabia-Eurasia collision zone, which occurred after slab break-off, following the Neotethyan closure.

Description: Eutrophication in marine waters is traditionally assessed by checking if nutrients, algal biomass and oxygen are below/above a given threshold. However, increased biomass, nutrient concentrations and oxygen demand do not lead to undesirable environmental effects if the flow of carbon/energy from primary producers toward high trophic levels is consistently preserved. Consequently, traditional indicators might provide a misleading assessment of the eutrophication risk. To avoid this, we propose to evaluate eutrophication by using a new index based on plankton trophic fluxes instead of biogeochemical concentrations. A preliminary, model-based, assessment suggests that this approach might give a substantially different picture of the eutrophication status of our seas, with potential consequences on marine ecosystem management. Given the difficulties to measure trophic fluxes in the field, the use of numerical simulations is recommended although the uncertainty associated with biogeochemical models inevitably affects the reliability of the index. However, given the effort currently in place to develop refined numerical tools describing the marine environment (Ocean Digital Twins), a reliable, model-based, eutrophication index could be operational in the near future.

Description: The seismic receiver function (RF) technique is widely used as an economic method to image earth's deep interior in a large number of seismic experiments. P-wave receiver functions (RFs) constrain crustal thickness and average Vp/Vs in the crust by analysis of the Ps phase and multiples (reflected/converted waves) from the Moho. Regional studies often show significant differences between the Moho depth constrained by RF and by reflection/refraction methods. We compare the results from RF and controlled source seismology for the Baikal Rift Zone by calculating 1480 synthetic RFs for a seismic refraction/reflection velocity model and processing them with two common RF techniques [H–κ and Common Conversion Point (CCP) stacking]. We compare the resulting synthetic RF structure with the velocity model, a density model (derived from gravity and the velocity model), and with observed RFs. Our results demonstrate that the use of different frequency filters, the presence of complex phases from sediments and gradual changes in the properties of crustal layers can lead to erroneous interpretation of RFs and incorrect geological interpretations. We suggest that the interpretation of RFs should be combined with other geophysical methods, in particular in complex tectonic regions and that the long-wavelength Bouguer gravity anomaly signal may provide effective calibration for the determination of the correct Moho depth from RF results. We propose and validate a new automated, efficient method for this calibration.

Description: Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.

Description: Biological invasions are a global challenge that has received insufficient attention. Recently available cost syntheses have provided policy- and decision makers with reliable and up-to-date information on the economic impacts of biological invasions, aiming to motivate effective management. The resultant InvaCost database is now publicly and freely accessible and enables rapid extraction of monetary cost information. This has facilitated knowledge sharing, developed a more integrated and multidisciplinary network of researchers, and forged multidisciplinary collaborations among diverse organizations and stakeholders. Over 50 scientific publications so far have used the database and have provided detailed assessments of invasion costs across geographic, taxonomic, and spatiotemporal scales. These studies have provided important information that can guide future policy and legislative decisions on the management of biological invasions while simultaneously attracting public and media attention. We provide an overview of the improved availability, reliability, standardization, and defragmentation of monetary costs; discuss how this has enhanced invasion science as a discipline; and outline directions for future development.

Description: Primary andesitic magmas could be an important component of arc magma genesis and might have played a key role in the advent of continents. Recent studies hypothesized that primary andesitic magmas occur in the oceanic arc, where the crust is thin. The Kermadec arc has the thinnest crust among all the studied oceanic arcs (〈15 km in thickness); however, there are no studies that corroborate the formation of primary andesitic magmas in the arc. The aim of this study is to develop a better understanding of primary andesites in oceanic arcs through the petrology of the Kermadec arc. Here, we present the petrology of volcanic rocks dredged from the Kibblewhite Volcano in the Kermadec arc during the R/V SONNE SO-255 expedition in 2017. Magma types range from andesite to rhyolite at the Kibblewhite Volcano, but basalts dominate at the neighboring cones. This study focuses on magnesian andesites from the northeastern flank of this volcano. The magnesian andesites are nearly aphyric and plagioclase free but contain microphenocrysts of olivine (Fo84–86) and clinopyroxene (Mg# = 81–87). Using olivine addition models, the primary magmas were estimated to contain 55–56 wt % SiO2 and 10–12 wt % MgO, similar to the high-Mg andesites observed in other convergent plate margins, indicating the generation of primary andesitic magma beneath the Kibblewhite Volcano. The trace element and isotopic characteristics of the magnesian andesites are typical of volcanic rocks from the Kermadec arc. This indicates that the subduction of a young plate or melting of a pyroxenitic source is not necessary to produce magnesian andesites. Instead, we propose that the magnesian andesites were produced by the direct melting of the uppermost mantle of the Kermadec arc. The thin crust of the Kermadec arc should yield low-pressure conditions in the uppermost mantle, allowing the sub-arc mantle to generate primary andesitic melts. This study supports the hypothesis that primary andesitic magmas generate in the arc where the crust is thin and provides a new insight into the magma genesis of the Kermadec arc.

Description: Mitochondrial genomes (mitogenomes) of flowering plants are composed of multiple chromosomes. Recombination within and between the mitochondrial chromosomes may generate diverse DNA molecules termed isoforms. The isoform copy number and composition can be dynamic within and among individual plants due to uneven replication and homologous recombination. Nonetheless, despite their functional importance, the level of mitogenome conservation within species remains understudied. Whether the ontogenetic variation translates to evolution of mitogenome composition over generations is currently unknown. Here we show that the mitogenome composition of the seagrass Zostera marina is conserved among worldwide populations that diverged ca. 350,000 years ago. Using long-read sequencing, we characterized the Z. marina mitochondrial genome and inferred the repertoire of recombination-induced configurations. To characterize the mitochondrial genome architecture worldwide and study its evolution, we examined the mitogenome in Z. marina meristematic region sampled in 16 populations from the Pacific and Atlantic oceans. Our results reveal a striking similarity in the isoform relative copy number, indicating a high conservation of the mitogenome composition among distantly related populations and within the plant germline, despite a notable variability during individual ontogenesis. Our study supplies a link between observations of dynamic mitogenomes at the level of plant individuals and long-term mitochondrial evolution.

Description: Marine algae are central to global carbon fixation and their productivity is dictated largely by resource availability. Reduced nutrient availability is predicted for vast oceanic regions as an outcome of climate change, however there is much to learn regarding response mechanisms of the tiny picoplankton that thrive in these environments, especially eukaryotic phytoplankton. Here, we investigate responses of the picoeukaryote Micromonas commoda, a green alga found throughout subtropical and tropical oceans. Under shifting phosphate (P) availability scenarios, transcriptomic analyses revealed altered expression of transfer RNA (tRNA) modification enzymes and biased codon usage of transcripts more abundant during P-limiting versus P-replete conditions, consistent with the role of tRNA modifications in regulating codon recognition. To associate the observed shift in expression of the tRNA modification enzyme complement with the tRNAs encoded by M. commoda, we also determined the tRNA repertoire of this alga revealing potential targets of the modification enzymes. Codon usage bias was particularly pronounced in transcripts encoding proteins with direct roles in managing P-limitation and photosystem-associated proteins that have ill-characterized putative functions in “light stress”. The observed codon usage bias corresponds to a proposed stress response mechanism in which the interplay between stress-induced changes in tRNA modifications and skewed codon usage in certain essential response genes drives preferential translation of the encoded proteins. Collectively, we expose a potential underlying mechanism for achieving growth under enhanced nutrient limitation, that extends beyond the catalog of up- or down-regulated protein-encoding genes, to the cell biological controls that underpin acclimation to changing environmental conditions.

Description: The dynamics of marine systems at decadal scales are notoriously hard to predict—hence references to this timescale as the “grey zone” for ocean prediction. Nevertheless, decadal-scale prediction is a rapidly developing field with an increasing number of applications to help guide ocean stewardship and sustainable use of marine environments. Such predictions can provide industry and managers with information more suited to support planning and management over strategic timeframes, as compared to seasonal forecasts or long-term (century-scale) predictions. The most significant advances in capability for decadal-scale prediction over recent years have been for ocean physics and biogeochemistry, with some notable advances in ecological prediction skill. In this paper, we argue that the process of “lighting the grey zone” by providing improved predictions at decadal scales should also focus on including human dimensions in prediction systems to better meet the needs and priorities of end users. Our paper reviews information needs for decision-making at decadal scales and assesses current capabilities for meeting these needs. We identify key gaps in current capabilities, including the particular challenge of integrating human elements into decadal prediction systems. We then suggest approaches for overcoming these challenges and gaps, highlighting the important role of co-production of tools and scenarios, to build trust and ensure uptake with end users of decadal prediction systems. We also highlight opportunities for combining narratives and quantitative predictions to better incorporate the human dimension in future efforts to light the grey zone of decadal-scale prediction.

Description: Machine learning covers a large set of algorithms that can be trained to identify patterns in data. Thanks to the increase in the amount of data and computing power available, it has become pervasive across scientific disciplines. We first highlight why machine learning is needed in marine ecology. Then we provide a quick primer on machine learning techniques and vocabulary. We built a database of & SIM;1000 publications that implement such techniques to analyse marine ecology data. For various data types (images, optical spectra, acoustics, omics, geolocations, biogeochemical profiles, and satellite imagery), we present a historical perspective on applications that proved influential, can serve as templates for new work, or represent the diversity of approaches. Then, we illustrate how machine learning can be used to better understand ecological systems, by combining various sources of marine data. Through this coverage of the literature, we demonstrate an increase in the proportion of marine ecology studies that use machine learning, the pervasiveness of images as a data source, the dominance of machine learning for classification-type problems, and a shift towards deep learning for all data types. This overview is meant to guide researchers who wish to apply machine learning methods to their marine datasets.

Description: We analyse the consistency of the delay time data in the most recent version of the ISC-EHB bulletin published by the International Seismological Centre covering the years 1964–2018. Considering that the delays are influenced by the lateral heterogeneity in the Earth’s mantle, we construct a tomographic matrix. We use singular value decomposition of the tomographic matrix for 19 707 dense clusters of earthquakes to compute objective estimates of the standard error from data that project into the null space and should be zero if there were no errors. Using a robust initial estimate of the standard deviation of the clustered delay times, we remove a small fraction of outliers before calculating the ultimate errors. We found that the errors depend on the type of body wave, depth of the earthquake (crust or mantle) and the number of decimals with which the arrival time was reported. Using these parameters, we distinguish 45 different classes of delay times for 11 different types of body waves. The errors of each class so divided generally follow a distribution that is approximately normal with a mean that ranges from 0.32 s for PKPbc waves from mantle earthquakes, to 2.82 s for S waves from shallow earthquakes bottoming in the upper mantle. The widths of the distributions of the errors themselves are small enough to serve in formal statistical quantification of the quality of fit in tomographic experiments.

Description: Volcano seismology is an essential tool for monitoring volcanic processes in the advent and during eruptions. A variety of seismic signals can be recorded at volcanoes, of which some are thought to be related to the migration of fluids which is of primary importance for the anticipation of imminent eruptions. We investigate the volcanic crises at Villarrica volcano in 2015 and report on a newly discovered very-long-period (VLP) signal that accompanies phases of periodic long period (LP) signal burst. Despite their low amplitude emergent character, we can locate the source region of the 1 Hz LP signals to the close vicinity of the volcano using a network-based correlation method. The source of the VLP signal with a period of about 30–100 s appears to locate in the vicinity of two stations a few kilometres from the summit. Both stations record very similar VLP waveforms that are correlated with the envelope of the LP bursts. A shallow magma reservoir was inferred by Contreras from surface deformation as the source of inflation following the eruption in 2015. Cyclic volume changes of 6 m3 in this reservoir at 3 km depth can explain the observed amplitudes of the vertical VLP signal. We propose that the LP signal is generated by the migration of gas or gas-rich magma that is periodically released from the inflating reservoir through a non-linear valve structure which modulates the flux, and thereby causes bursts of flow-related LP signals and pressure changes observed as VLP deformation. Our model predicts that the correlated occurrence of LP bursts and VLP surface motion depends on the intensity of the fluid flux. A weaker flux of fluids may not exceed the opening pressure of valve structure, and higher rates might maintain pressure above the closing pressure. In both cases, the VLP signal vanishes. Our observation provides constrains for models of fluid transport inside volcanoes. At Villarrica the VLP signal, and its relation to the LP activity, reveal additional information about fluxes in the magmatic reservoir that might aide forecasting of volcanic activity.

Description: The female flowers (“cones”) of the hop plant (Humulus L.) produce compounds that contribute to the flavor and other properties of beer. Hop leaves and cones produce many of the same compounds, which also confer agronomic traits such as insect and disease resistance. Targeted and untargeted ultraperformance liquid chromatography-quadrupole time-of-flight–mass spectrometry with Waters MSE technology (UPLC-QTof-MSE) metabolomics were used to compare leaf phytochemical compositions of greenhouse-grown southwestern American wild Humulus neomexicanus (A. Nelson and Cockerell) Rydb. against a group of commercial hop cultivars consisting of both pure European Humulus lupulus L. and European–North American hybrids. Principal component analysis showed a clear distinction in chemical profiles between the two groups. H. neomexicanus leaves had a significantly higher content of total α acids (p = 4.4 × 10–9), total bitter acids (p = 2.6 × 10–6), cohumulone (p = 1.0 × 10–13), humulone + adhumulone (p = 9.1 × 10–4), and the prenylflavonoids xanthohumol (p = 0.013) and desmethylxanthohumol (p = 0.029) as well as significantly higher densities of glandular trichomes (p = 1.3 × 10–6), the biosynthetic site of those compounds. Most flavonol glycosides measured were also significantly more abundant in H. neomexicanus (p = 1.5 × 10–22 to 0.0027), whereas phenolic acids were consistently, but generally nonsignificantly (p 〉 0.05), more abundant in the cultivars. The higher bitter acid, prenylflavonoid, and flavonol glycoside content of H. neomexicanus leaves may help to confer more favorable insect and disease-resistance properties.

Description: Iron is an indispensable metabolic cofactor in both pro- and eukaryotes, which engenders a natural competition for the metal between bacterial pathogens and their human or animal hosts. Bacteria secrete siderophores that extract Fe3+ from tissues, fluids, cells, and proteins; the ligand gated porins of the Gram-negative bacterial outer membrane actively acquire the resulting ferric siderophores, as well as other iron-containing molecules like heme. Conversely, eukaryotic hosts combat bacterial iron scavenging by sequestering Fe3+ in binding proteins and ferritin. The variety of iron uptake systems in Gram-negative bacterial pathogens illustrates a range of chemical and biochemical mechanisms that facilitate microbial pathogenesis. This document attempts to summarize and understand these processes, to guide discovery of immunological or chemical interventions that may thwart infectious disease.

Description: While thousands of environmental metagenomes have been mined for the presence of novel biosynthetic gene clusters, such computational predictions do not provide evidence of their in vivo biosynthetic functionality. Using fluorescent in situ enzyme assay targeting carrier proteins common to polyketide (PKS) and nonribosomal peptide synthetases (NRPS), we applied fluorescence-activated cell sorting to tunicate microbiome to enrich for microbes with active secondary metabolic capabilities. Single-cell genomics uncovered the genetic basis for a wide biosynthetic diversity in the enzyme-active cells and revealed a member of marine Oceanospirillales harboring a novel NRPS gene cluster with high similarity to phylogenetically distant marine and terrestrial bacteria. Interestingly, this synthase belongs to a larger class of siderophore biosynthetic gene clusters commonly associated with pestilence and disease. This demonstrates activity-guided single-cell genomics as a tool to guide novel biosynthetic discovery.

Description: Full waveform inversion (FWI) is a data-fitting technique capable of generating high-resolution velocity models with a resolution down to half the seismic wavelength. FWI is applied typically to densely sampled seismic data. In this study, we applied FWI to 3D wide-angle seismic data acquired using sparsely spaced ocean bottom seismometers (OBSs) from the Deep Galicia Margin west of Iberia. Our dataset samples the S-reflector, a low-angle detachment present in this area. Here we highlight differences between 2D, 2.5D and 3D-FWI performances using a real sparsely spaced dataset. We performed 3D FWI in the time domain and compared the results with 2D and 2.5D FWI results from a profile through the 3D model. When overlaid on multichannel seismic images, the 3D FWI results constrain better the complex faulting within the pre- and syn-rift sediments and crystalline crust compared to the 2D result. Furthermore, we estimate variable serpentinisation of the upper mantle below the S-reflector along the profile using 3D FWI, reaching a maximum of 45 per cent. Differences in the data residuals of the 2D, 2.5D and 3D inversions suggest that 2D inversion can be prone to overfitting when using a sparse dataset. To validate our results, we performed tests to recover the anomalies introduced by the inversions in the final models using synthetic datasets. Based on our comparison of the velocity models, we conclude that the use of 3D data can partially mitigate the problem of receiver sparsity in FWI.

Description: Probing seismic anisotropy of the lithosphere provides valuable clues on the fabric of rocks. We present a 3-D probabilistic model of shear wave velocity and radial anisotropy of the crust and uppermost mantle of Europe, focusing on the mountain belts of the Alps and Apennines. The model is built from Love and Rayleigh dispersion curves in the period range 5–149 s. Data are extracted from seismic ambient noise recorded at 1521 broad-band stations, including the AlpArray network. The dispersion curves are first combined in a linearized least squares inversion to obtain 2-D maps of group velocity at each period. Love and Rayleigh maps are then jointly inverted at depth for shear wave velocity and radial anisotropy using a Bayesian Monte Carlo scheme that accounts for the trade-off between radial anisotropy and horizontal layering. The isotropic part of our model is consistent with previous studies. However, our anisotropy maps differ from previous large scale studies that suggested the presence of significant radial anisotropy everywhere in the European crust and shallow upper mantle. We observe instead that radial anisotropy is mostly localized beneath the Apennines while most of the remaining European crust and shallow upper mantle is isotropic. We attribute this difference to trade-offs between radial anisotropy and thin (hectometric) layering in previous studies based on least-squares inversions and long period data (〉30 s). In contrast, our approach involves a massive data set of short period measurements and a Bayesian inversion that accounts for thin layering. The positive radial anisotropy (VSH 〉 VSV) observed in the lower crust of the Apennines cannot result from thin layering. We rather attribute it to ductile horizontal flow in response to the recent and present-day extension in the region.

Description: To constrain seismic anisotropy under and around the Alps in Europe, we study SKS shear wave splitting from the region densely covered by the AlpArray seismic network. We apply a technique based on measuring the splitting intensity, constraining well both the fast orientation and the splitting delay. Four years of teleseismic earthquake data were processed, from 723 temporary and permanent broad-band stations of the AlpArray deployment including ocean-bottom seismometers, providing a spatial coverage that is unprecedented. The technique is applied automatically (without human intervention), and it thus provides a reproducible image of anisotropic structure in and around the Alpine region. As in earlier studies, we observe a coherent rotation of fast axes in the western part of the Alpine chain, and a region of homogeneous fast orientation in the Central Alps. The spatial variation of splitting delay times is particularly interesting though. On one hand, there is a clear positive correlation with Alpine topography, suggesting that part of the seismic anisotropy (deformation) is caused by the Alpine orogeny. On the other hand, anisotropic strength around the mountain chain shows a distinct contrast between the Western and Eastern Alps. This difference is best explained by the more active mantle flow around the Western Alps. The new observational constraints, especially the splitting delay, provide new information on Alpine geodynamics.

Description: Seismic full waveform inversion (FWI) is a powerful method for estimating quantitative subsurface physical parameters from seismic data. As the full waveform inversion is a non-linear problem, the linearized approach updates model iteratively from an initial model, which can get trapped in local minima. In the presence of a high velocity contrast, such as at Moho, the reflection coefficient and recorded waveforms from wide-aperture seismic acquisition are extremely non-linear around critical angles. The problem at the Moho is further complicated by the interference of lower crustal (Pg) and upper mantle (Pn) turning ray arrivals with the critically reflected Moho arrivals (PmP). In order to determine velocity structure near Moho, a non-linear method should be used. We propose to solve this strong non-linear FWI problem at Moho using a trans-dimensional Markov chain Monte Carlo (MCMC) method, where the earth model between lower crust and upper mantle is idealy parameterized with a 1-D assumption using a variable number of velocity interfaces. Different from common MCMC methods that require determining the number of unknown as a fixed prior before inversion, trans-dimensional MCMC allows the flexibility for an automatic estimation of both the model complexity (e.g. the number of velocity interfaces) and the velocity-depth structure from the data. We first test the algorithm on synthetic data using four representative Moho models and then apply to an ocean bottom seismometer (OBS) data from the Mid-Atlantic Ocean. A 2-D finite-difference solution of an acoustic wave equation is used for data simulation at each iteration of MCMC search, for taking into account the lateral heterogeneities in the upper crust, which is constrained from travel time tomography and is kept unchanged during inversion; the 1-D model parameterization near Moho enables an efficient search of the trans-dimensional model space. Inversion results indicate that, with very little prior and the wide-aperture seismograms, the trans-dimensional FWI method is able to infer the posterior distribution of both the number of velocity interfaces and the velocity-depth model for a strong nonlinear problem, making the inversion a complete data-driven process. The distribution of interface matches the velocity discontinuities. We find that the Moho in the study area is a transition zone of 0.7 km, or a sharp boundary with velocities from around 7 km/s in the lower crust to 8 km/s of the upper mantle; both provide nearly identical waveform match for the field data. The ambiguity comes from the resolution limit of the band-limited seismic data and limited offset range for PmP arrivals.

Description: In this article, the concepts and background of regional climate modeling of the future Baltic Sea are summarized and state-of-the-art projections, climate change impact studies, and challenges are discussed. The focus is on projected oceanographic changes in future climate. However, as these changes may have a significant impact on biogeochemical cycling, nutrient load scenario simulations in future climates are briefly discussed as well. The Baltic Sea is special compared to other coastal seas as it is a tideless, semi-enclosed sea with large freshwater and nutrient supply from a partly heavily populated catchment area and a long response time of about 30 years, and as it is, in the early 21st century, warming faster than any other coastal sea in the world. Hence, policymakers request the development of nutrient load abatement strategies in future climate. For this purpose, large ensembles of coupled climate–environmental scenario simulations based upon high-resolution circulation models were developed to estimate changes in water temperature, salinity, sea-ice cover, sea level, oxygen, nutrient, and phytoplankton concentrations, and water transparency, together with uncertainty ranges. Uncertainties in scenario simulations of the Baltic Sea are considerable. Sources of uncertainties are global and regional climate model biases, natural variability, and unknown greenhouse gas emission and nutrient load scenarios. Unknown early 21st-century and future bioavailable nutrient loads from land and atmosphere and the experimental setup of the dynamical downscaling technique are perhaps the largest sources of uncertainties for marine biogeochemistry projections. The high uncertainties might potentially be reducible through investments in new multi-model ensemble simulations that are built on better experimental setups, improved models, and more plausible nutrient loads. The development of community models for the Baltic Sea region with improved performance and common coordinated experiments of scenario simulations is recommended.

Description: Marine macroalgae, seaweeds, are exceptionally prolific producers of halogenated natural products. Biosynthesis of halogenated molecules in seaweeds is inextricably linked to reactive oxygen species (ROS) signaling as hydrogen peroxide serves as a substrate for haloperoxidase enzymes that participate in the construction these halogenated molecules. Here, using red macroalga Asparagopsis taxiformis, a prolific producer of the ozone depleting molecule bromoform, we provide the discovery and biochemical characterization of a ROS-producing NAD(P)H oxidase from seaweeds. This discovery was enabled by our sequencing of Asparagopsis genomes, in which we find the gene encoding the ROS-producing enzyme to be clustered with genes encoding bromoform-producing haloperoxidases. Biochemical reconstitution of haloperoxidase activities establishes that fatty acid biosynthesis can provide viable hydrocarbon substrates for bromoform production. The ROS production haloperoxidase enzymology that we describe here advances seaweed biology and biochemistry by providing the molecular basis for decades worth of physiological observations in ROS and halogenated natural product biosyntheses.

Description: Fusarium oxysporum is a destructive root-infecting plant pathogen that causes significant yield losses in many economically important crop species. Hence, a deeper understanding of pathogen infection strategies is needed. With liquid chromatography-tandem mass spectrometry and gas chromatography-time of flight mass spectrometry platforms, we analyzed the metabolic changes in a time-course experiment with Arabidopsis accessions either resistant (Col-0) or susceptible (Ler-0) to isolates of Fusarium oxysporum forma specialis matthioli infection. We showed a concurrent effect of Fusarium-derived polyols and the mycotoxin beauvericin in the suppression of the immune response of susceptible hosts. A significant increase in oxidized glutathione in the resistant host was probably associated with effective reactive oxygen species-mediated resistance responses. Through a combination of targeted and untargeted metabolomics, we demonstrated the concurrent action of several Arabidopsis defense systems as well as the concurrent action of several virulence systems in the fungal attack of susceptible Arabidopsis.

Description: Intense bottom-ice algal blooms, often dominated by diatoms, are an important source of food for grazers, organic matter for export during sea ice melt, and dissolved organic carbon. Sea-ice diatoms have a number of adaptations, including accumulation of compatible solutes, that allows them to inhabit this highly variable environment characterized by extremes in temperature, salinity, and light. In addition to protecting them from extreme conditions, these compounds present a labile, nutrient-rich source of organic matter, and include precursors to climate active compounds (e.g., dimethyl sulfide [DMS]), which are likely regulated with environmental change. Here, intracellular concentrations of 45 metabolites were quantified in three sea-ice diatom species and were compared to two temperate diatom species, with a focus on compatible solutes and free amino acid pools. There was a large diversity of metabolite concentrations between diatoms with no clear pattern identifiable for sea-ice species. Concentrations of some compatible solutes (isethionic acid, homarine) approached 1 M in the sea-ice diatoms, Fragilariopsis cylindrus and Navicula cf. perminuta, but not in the larger sea-ice diatom, Nitzschia lecointei or in the temperate diatom species. The differential use of compatible solutes in sea-ice diatoms suggests different adaptive strategies and highlights which small organic compounds may be important in polar biogeochemical cycles.

Description: Deep-towed geophysical surveys require precise knowledge of navigational parameters such as instrument position and orientation because navigational uncertainties reflect in the data and therefore in the inferred geophysical properties of the subseafloor. We address this issue for the case of electrical conductivity inferred from controlled source electromagnetic data. We show that the data error is laterally variable due to irregular motion during deep towing, but also due to lateral variations in conductivity, including those resulting from topography. To address this variability and quantify the data error prior to inversion, we propose a 2-D perturbation study. Our workflow enables stable and geologically reliable results for multicomponent and multifrequency inversions. An error estimation workflow is presented, which comprises the assessment of navigational uncertainties, perturbation of navigational parameters, and forward modelling of electric field amplitudes for a homogeneous and then a heterogeneous subseafloor conductivity model. Some navigational uncertainties are estimated from variations of direct measurements. Other navigational parameters required for inversion are derived from the measured quantities and their error is calculated by means of error propagation. Some navigational parameters show direct correlation with the measured electric fields. For example, the antenna dip correlates with the vertical electric field and the depth correlates with the horizontal electric field. For the perturbation study each standard deviation is added to the navigational parameters. Forward models are run for each perturbation. Amplitude deviations are summed in quadrature with the stacking error for a total, laterally varying, data error. The error estimation is repeated for a heterogeneous subseafloor model due to the large conductivity range (several orders of magnitude), which affects the forward model. The approach enables us to utilize data from several components (multiple electric fields, frequencies and receivers) in the inversion to constrain the final model and reduce ambiguity. The final model is geologically reasonable, in this case enabling the identification of conductive metal sulphide deposits on the seafloor.

Description: Background: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea-dwelling species will allow several pending evolutionary questions to be unlocked. Findings: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.

Description: Parasites are arguably among the strongest drivers of natural selection, constraining hosts to evolve resistance and tolerance mechanisms. Although, the genetic basis of adaptation to parasite infection has been widely studied, little is known about how epigenetic changes contribute to parasite resistance and eventually, adaptation. Here, we investigated the role of host DNA methylation modifications to respond to parasite infections. In a controlled infection experiment, we used the three-spined stickleback fish, a model species for host-parasite studies, and their nematode parasite Camallanus lacustris. We showed that the levels of DNA methylation are higher in infected fish. Results furthermore suggest correlations between DNA methylation and shifts in key fitness and immune traits between infected and control fish, including respiratory burst and functional trans-generational traits such as the concentration of motile sperm. We revealed that genes associated with metabolic, developmental and regulatory processes (cell death and apoptosis) were differentially methylated between infected and control fish. Interestingly, genes such as the neuropeptide FF receptor 2 and the integrin alpha 1 as well as molecular pathways including the Th1 and Th2 cell differentiation were hypermethylated in infected fish, suggesting parasite-mediated repression mechanisms of immune responses. Altogether, we demonstrate that parasite infection contributes to genome-wide DNA methylation modifications. Our study brings novel insights into the evolution of vertebrate immunity and suggests that epigenetic mechanisms are complementary to genetic responses against parasite-mediated selection.

Description: International Ocean Discovery Program (IODP) Expedition 351 “Izu–Bonin–Mariana (IBM) Arc Origins” drilled Site U1438, situated in the north-western region of the Philippine Sea. Here volcaniclastic sediments and the igneous basement of the proto-IBM volcanic arc were recovered. To gain a better understanding of the magmatic processes and evolution of the proto-IBM arc, we studied melt inclusions hosted in fresh igneous minerals and sampled from 30- to 40-Ma-old deposits, reflecting the maturation of arc volcanism following subduction initiation at 52 Ma. We performed a novel statistical analysis on the major element composition of 237 representative melt inclusions selected from a previously published dataset, covering the full age range between 30 and 40 Ma. In addition, we analysed volatiles (H2O, S, F and Cl) and P2O5 by Secondary Ion Mass Spectrometry (SIMS) for a subset of 47 melt inclusions selected from the dataset. Based on statistical analysis of the major element composition of melt inclusions and by considering their trace and volatile element compositions, we distinguished five main clusters of melt inclusions, which can be further separated into a total of eight subclusters. Among the eight subclusters, we identified three major magma types: (1) enriched medium-K magmas, which form a tholeiitic trend (30–38 Ma); (2) enriched medium-K magmas, which form a calc-alkaline trend (30–39 Ma); and (3) depleted low-K magmas, which form a calc-alkaline trend (35–40 Ma). We demonstrate that (1) the eruption of depleted low-K calc-alkaline magmas occurred prior to 40 Ma and ceased sharply at 35 Ma; (2) the eruption of depleted low-K calc-alkaline magmas, enriched medium-K calc-alkaline magmas and enriched medium-K tholeiitic magmas overlapped between 35 and 38 − 39 Ma; and (3) the eruption of enriched medium-K tholeiitic and enriched medium-K calc-alkaline magmas became predominant thereafter at the proto-IBM arc. Identification of three major magma types are distinct from the previous work, in which enriched medium-K calc-alkaline magmas and depleted low-K calc-alkaline magmas were not identified. This indicates the usefulness of our statistical analysis as a powerful tool to partition a mixture of multivariable geochemical datasets, such as the composition of melt inclusions in this case. Our data suggest that a depleted mantle source had been replaced by an enriched mantle source due to convection beneath the proto-IBM arc from >40 to 35 Ma. Finally, thermodynamic modelling indicates that the overall geochemical variation of melt inclusions assigned to each cluster can be broadly reproduced either by crystallisation differentiation assuming P = 50 MPa (∼2-km deep) and ∼2 wt % H2O (almost saturated H2O content at 50 MPa) or P = 300 MPa (∼15-km deep) and ∼6 wt % H2O (almost saturated H2O content at 300 MPa). Assuming oxygen fugacity (fO2) of log fO2 equal to + 1 relative to nickel-nickel oxide (NNO) buffer best reproduces the overall geochemical variation of melt inclusions, but assuming a more oxidising conditions (log fO2 = +1 to + 2 NNO) likely reproduces the geochemical variation of enriched medium-K and calc-alkaline melt inclusions (30 − 39 Ma).

Description: The present study quantified prey preferences by adult males and females of the mysid Mesopodopsis wooldridgei fed the calanoid copepods Pseudodiaptomus hessei and Paracartia longipatella at varying proportions. Both sexes of M. wooldridgei showed a lack of prey switching and a strong preference for the smaller, less active P. longipatella irrespective of density. Given a lack of low-density prey refuge, this finding may have important implications for the distribution of P. longipatella in estuaries along the eastern seaboard of South Africa. Results of the present study contribute to a growing body of literature that suggests that selective predation may play an important role in structuring plankton prey populations in shallow water ecosystems.

Description: The two toothed jaws of cichlid fishes provide textbook examples of convergent evolution. Tooth phenotypes such as enlarged molar-like teeth used to process hard-shelled molluscs have evolved numerous times independently during cichlid diversification. While the ecological benefit of molar-like teeth to crush prey is known, it is unclear whether the same molecular mechanisms underlie these convergent traits. To identify genes involved in the evolution and development of enlarged cichlid teeth, we performed RNA-seq on the serially homologous toothed oral and pharyngeal jaws as well as the fourth toothless gill arch of Astatoreochromis alluaudi. We identified 27 genes that are highly upregulated on both tooth-bearing jaws compared to the toothless gill arch. Most of these genes have never been reported to play a role in tooth formation. Two of these genes (unk, rpfA) are not found in other vertebrate genomes but are present in all cichlid genomes. They also cluster genomically with two other highly expressed tooth genes (odam, scpp5) that exhibit conserved expression during vertebrate odontogenesis. Unk and rpfA were confirmed via in situ hybridization to be expressed in developing teeth of Astatotilapia burtoni. We then examined expression of the cluster's four genes in six evolutionarily independent and phylogenetically disparate cichlid species pairs each with a large- and a small-toothed species. Odam and unk commonly and scpp5 and rpfA always showed higher expression in larger-toothed cichlid jaws. Convergent trophic adaptations across cichlid diversity are associated with the repeated developmental deployment of this genomic cluster containing conserved and novel cichlid-specific genes.

Description: Polynoidae contains ~900 species within 18 subfamilies, some of them restricted to the deep sea. Macellicephalinae is the most diverse among these deep-sea subfamilies. In the abyssal Equatorial Pacific Ocean, the biodiversity of benthic communities is at stake in the Clarion-Clipperton Fracture Zone (CCFZ) owing to increased industrial interest in polymetallic nodules. The records of polychaetes in this region are scarce. Data gathered during the JPI Oceans cruise SO239 made a significant contribution to fill this gap, with five different localities sampled between 4000 and 5000 m depth. Benthic samples collected using an epibenthic sledge or a remotely operated vehicle resulted in a large collection of polynoids. The aims of this study are as follows: (1) to describe new species of deep-sea polynoids using morphology and molecular data (COI, 16S and 18S); and (2) to evaluate the monophyly of Macellicephalinae. Based on molecular and morphological phylogenetic analyses, ten subfamilies are synonymized with Macellicephalinae in order to create a homogeneous clade determined by the absence of lateral antennae. Within this clade, the Anantennata clade was well supported, being determined by the absence of a median antenna. Furthermore, 17 new species and four new genera are described, highlighting the high diversity hidden in the deep. A taxonomic key for the 37 valid genera of the subfamily Macellicephalinae is provided.

Description: Metabolites give us a window into the chemistry of microbes and are split into two subclasses: primary and secondary. Primary metabolites are required for life whereas secondary metabolites have historically been classified as those appearing after exponential growth and are not necessarily needed for survival. Many microbial species are estimated to produce hundreds of metabolites and can be affected by differing nutrients. Using various analytical techniques, metabolites can be directly detected in order to elucidate their biological significance. Currently, a single experiment can produce anywhere from megabytes to terabytes of data. This big data has motivated scientists to develop informatics tools to help target specific metabolites or sets of metabolites. Broadly, it is imperative to identify clear biological questions before embarking on a study of metabolites (metabolomics). For instance, studying the effect of a transposon insertion on phenazine biosynthesis in Pseudomonas is a very different from asking what molecules are present in a specific banana-derived strain of Pseudomonas. This review is meant to serve as a primer for a ‘choose your own adventure’ approach for microbiologists with limited mass spectrometry expertise, with a strong focus on liquid chromatography mass spectrometry based workflows developed or optimized within the past five years.

Description: Three monoterpenoid indole alkaloids (MIAs), tabernabovines A–C (1–3), were isolated from Tabernaemontana bovina. They were elucidated by spectroscopic data and computational calculations. Unlike precursors of MIAs, strictosidine and alstrostine A, alkaloid 1 consists of tryptamine and secologanin in a 2:1 ratio. Alkaloid 2 is a cage compound, and 3 possesses a bridged ring. Tabernabovine A exhibited inhibitory activity against NO production with IC50 44.1 μM compared to l-NMMA with IC50 of 48.6 μM.

Description: Euphorkanlide A (1), a highly modified ingenane diterpenoid with a C24 appendage forming an additional hexahydroisobenzofuran-fused 19-membered macrocyclic bis-lactone ring system was isolated from the roots of Euphorbia kansuensis. Its structure was determined by extensive spectroscopic analysis and quantum-chemical calculations. Compound 1 showed significant cytotoxicities against a panel of cancer cell lines (IC50s 〈 5 μM). Mechanistic study revealed that 1 could induce the generation of ROS, leading to cell cycle arrest and cell apoptosis in drug-resistant cancer cell line HCT-15/5-FU.

Description: The vast amount of plastic waste emitted into the environment and the increasing concern of potential harm to wildlife has made microplastic and nanoplastic pollution a growing environmental concern. Plastic pollution has the potential to cause both physical and chemical harm to wildlife directly or via sorption, concentration, and transfer of other environmental contaminants to the wildlife that ingest plastic. Small particles of plastic pollution, termed microplastics (〉100 nm and 〈5 mm) or nanoplastics (〈100 nm), can form through fragmentation of larger pieces of plastic. These small particles are especially concerning because of their high specific surface area for sorption of contaminants as well as their potential to translocate in the bodies of organisms. These same small particles are challenging to separate and identify in environmental samples because their size makes handling and observation difficult. As a result, our understanding of the environmental prevalence of nanoplastics and microplastics is limited. Generally, the smaller the size of the plastic particle, the more difficult it is to separate from environmental samples. Currently employed passive density and size separation techniques to isolate plastics from environmental samples are not well suited to separate microplastics and nanoplastics. Passive flotation is hindered by the low buoyancy of small particles as well as the difficulty of handling small particles on the surface of flotation media. Here we suggest exploring alternative techniques borrowed from other fields of research to improve separation of the smallest plastic particles. These techniques include adapting active density separation (centrifugation) from cell biology and taking advantage of surface-interaction-based separations from analytical chemistry. Furthermore, plastic pollution is often challenging to quantify in complex matrices such as biological tissues and wastewater. Biological and wastewater samples are important matrices that represent key points in the fate and sources of plastic pollution, respectively. In both kinds of samples, protocols need to be optimized to increase throughput, reduce contamination potential, and avoid destruction of plastics during sample processing. To this end, we recommend adapting digestion protocols to match the expected composition of the nonplastic material as well as taking measures to reduce and account for contamination. Once separated, plastics in an environmental sample should ideally be characterized both visually and chemically. With existing techniques, microplastics and nanoplastics are difficult to characterize or even detect. Their low mass and small size provide limited signal for visual, vibrational spectroscopic, and mass spectrometric analyses. Each of these techniques involves trade-offs in throughput, spatial resolution, and sensitivity. To accurately identify and completely quantify microplastics and nanoplastics in environmental samples, multiple analytical techniques applied in tandem are likely to be required.

Description: Noninvasive diagnostic by imaging combined with a contrast agent (CA) is by now the most used technique to get insight into human bodies. X-ray and magnetic resonance imaging (MRI) are widely used technologies providing complementary results. Nowadays, it seems clear that bimodal CAs could be an emerging approach to increase the patient compliance, accessing different imaging modalities with a single CA injection. Owing to versatile designs, targeting properties, and high payload capacity, nanocarriers are considered as a viable solution to reach this goal. In this study, we investigated efficient superparamagnetic iron oxide nanoparticle (SPION)-loaded iodinated nano-emulsions (NEs) as dual modal injectable CAs for X-ray imaging and MRI. The strength of this new CA lies not only in its dual modal contrasting properties and biocompatibility, but also in the simplicity of the nanoparticulate assembling: iodinated oily core was synthesized by the triiodo-benzene group grafting on vitamin E (41.7% of iodine) via esterification, and SPIONs were produced by thermal decomposition during 2, 4, and 6 h to generate SPIONs with different morphologies and magnetic properties. SPIONs with most anisotropic shape and characterized by the highest r2/r1 ratio once encapsulated into iodinated NE were used for animal experimentation. The in vivo investigation showed an excellent contrast modification because of the presence of the selected NEs, for both imaging techniques explored, that is, MRI and X-ray imaging. This work provides the description and in vivo application of a simple and efficient nanoparticulate system capable of enhancing contrast for both preclinical imaging modalities, MRI, and computed tomography.

Description: Marine prey and predators will respond to future climate through physiological and behavioral adjustments. However, our understanding of how such direct effects may shift the outcome of predator–prey interactions is still limited. Here, we investigate the effects of ocean warming and acidification on foraging behavior and biomass of a common prey (shrimps, Palaemon spp.) tested in large mesocosms harboring natural resources and habitats. Acidification did not alter foraging behavior in prey. Under warming, however, prey showed riskier behavior by foraging more actively and for longer time periods, even in the presence of a live predator. No effects of longer-term exposure to climate stressors were detected on prey biomass. Our findings suggest that ocean warming may increase the availability of some prey to predators via a behavioral pathway (i.e., increased risk-taking by prey), likely by elevating metabolic demand of prey species.

Description: Climate change influences the Baltic Sea ecosystem via its effects on oceanography and biogeochemistry. Sea surface temperature has been projected to increase by 2 to 4 °C until 2100 due to global warming; the changes will be more significant in the northern areas and less so in the south. The warming up will also diminish the annual sea ice cover by 57% to 71%, and ice season will be one to three months shorter than in the early 21st century, depending on latitude. A significant decrease in sea surface salinity has been projected because of an increase in rainfall and decrease of saline inflows into the Baltic Sea. The increasing surface flow has, in turn, been projected to increase leaching of nutrients from the soil to the watershed and eventually into the Baltic Sea. Also, acidification of the seawater and sea-level rise have been predicted. Increasing seawater temperature speeds up metabolic processes and increases growth rates of many secondary producers. Species associated with sea ice, from salt brine microbes to seals, will suffer. Due to the specific salinity tolerances, species’ geographical ranges may shift by tens or hundreds of kilometres with decreasing salinity. A decrease in pH will slow down calcification of bivalve shells, and higher temperatures also alleviate establishment of non-indigenous species originating from more southern sea areas. Many uncertainties still remain in predicting the couplings between atmosphere, oceanography and ecosystem. Especially projections of many oceanographic parameters, such as wind speeds and directions, the mean salinity level, and density stratification, are still ambiguous. Also, the effects of simultaneous changes in multiple environmental factors on species with variable preferences to temperature, salinity, and nutrient conditions are difficult to project. There is, however, enough evidence to claim that due to increasing runoff of nutrients from land and warming up of water, primary production and sedimentation of organic matter will increase; this will probably enhance anoxia and release of phosphorus from sediments. Such changes may keep the Baltic Sea in an eutrophicated state for a long time, unless strong measures to decrease nutrient runoff from land are taken. Changes in the pelagic and benthic communities are anticipated. Benthic communities will change from marine to relatively more euryhaline communities and will suffer from hypoxic events. The projected temperature increase and salinity decline will contribute to maintain the pelagic ecosystem of the Central Baltic and the Gulf of Finland in a state dominated by cyanobacteria, flagellates, small-sized zooplankton and sprat, instead of diatoms, large marine copepods, herring, and cod. Effects vary from area to area, however. In particular the Bothnian Sea, where hypoxia is less common and rivers carry a lot of dissolved organic carbon, primary production will probably not increase as much as in the other basins. The coupled oceanography-biogeochemistry ecosystem models have greatly advanced our understanding of the effects of climate change on marine ecosystems. Also, studies on climate associated “regime shifts” and cascading effects from top predators to plankton have been fundamental for understanding of the response of the Baltic Sea ecosystem to anthropogenic and climatic stress. In the future, modeling efforts should be focusing on coupling of biogeochemical processes and lower trophic levels to the top predators. Also, fine resolution species distribution models should be developed and combined with 3-D modelling, to describe how the species and communities are responding to climate-induced changes in environmental variables.

Description: UPLC–TOF/MS profiling, followed by the recently reported differential off-line LC–NMR (DOLC–NMR) and quantitative 1H NMR spectroscopy (qHNMR), led to the differential qualitative analysis and accurate quantitation of l-tryptophan-induced metabolome alterations of Penicillium roqueforti, which is typically used in making blue-mold cheese. Among the 24 metabolites identified, two tetrapeptides, namely, d-Phe-l-Val-d-Val-l-Tyr and d-Phe-l-Val-d-Val-l-Phe, as well as cis-bis(methylthio)silvatin, are reported for the first time as metabolites of P. roqueforti. Antimicrobial activity tests showed strong effects of the catabolic l-tryptophan metabolites 3-hydroxyanthranilic acid, anthranilic acid, and 3-indolacetic acid against Saccharomyces cerevisiae, with IC50 values between 15.6 and 24.0 μg/mL, while roquefortine C and cis-bis(methylthio)silvatin inhibited the growth of Gram-negative Escherichia coli and Gram-positive Bacillus subtilis with IC50 values between 30.0 and 62.5 μg/mL.

Description: This review shows that the presence of seagrass microbial community is critical for the development of seagrasses; from seed germination, through to phytohormone production and enhanced nutrient availability, and defence against pathogens and saprophytes. The tight seagrass-bacterial relationship highlighted in this review supports the existence of a seagrass holobiont and adds to the growing evidence for the importance of marine eukaryotic microorganisms in sustaining vital ecosystems. Incorporating a micro-scale view on seagrass ecosystems substantially expands our understanding of ecosystem functioning and may have significant implications for future seagrass management and mitigation against human disturbance.

Description: Microplastics (MPs) in aquatic organisms are raising increasing concerns regarding their potential damage to ecosystems. To date, Raman and Fourier transform infrared spectroscopy techniques have been widely used for detection of MPs in aquatic organisms, which requires complex protocols of tissue digestion and MP separation and are time- and reagentconsuming. This novel approach directly separates, identifies, and characterizes MPs from the hyperspectral image (HSI) of the intestinal tract content in combination with a support vector machine classification model, instead of using the real digestion/separation protocols. The procedures of HSI acquisition ( 1 min) and data analysis (5 min) can be completed within 6 min plus the sample preparation and drying time (30 min) where necessary. This method achieved a promising efficiency (recall 〉98.80%, precision 〉96.22%) for identifying five types of MPs (particles 〉0.2 mm). Moreover, the method was also demonstrated to be effective on field fish from three marine fish species, revealing satisfying detection accuracy (particles 〉0.2 mm) comparable to Raman analysis. The present technique omits the digestion protocol (reagent free), thereby significantly reducing reagent consumption, saving time, and providing a rapid and efficient method for MP analysis.

Description: Repeated and independent emergence of trait divergence that matches habitat differences is a sign of parallel evolution by natural selection. Yet, the molecular underpinnings that are targeted by adaptive evolution often remain elusive. We investigate this question by combining genome-wide analyses of copy number variants (CNVs), single nucleotide polymorphisms (SNPs), and gene expression across four pairs of lake and river populations of the three-spined stickleback (Gasterosteus aculeatus). We tested whether CNVs that span entire genes and SNPs occurring in putative cis-regulatory regions contribute to gene expression differences between sticklebacks from lake and river origins. We found 135 gene CNVs that showed a significant positive association between gene copy number and gene expression, suggesting that CNVs result in dosage effects that can fuel phenotypic variation and serve as substrates for habitat-specific selection. Copy number differentiation between lake and river sticklebacks also contributed to expression differences of two immune-related genes in immune tissues, cathepsin A and GIMAP7. In addition, we identified SNPs in cis-regulatory regions (eSNPs) associated with the expression of 1,865 genes, including one eSNP upstream of a carboxypeptidase gene where both the SNP alleles differentiated and the gene was differentially expressed between lake and river populations. Our study highlights two types of mutations as important sources of genetic variation involved in the evolution of gene expression and in potentially facilitating repeated adaptation to novel environments.

Description: Cichlid fishes provide textbook examples of explosive phenotypic diversification and sympatric speciation, thereby making them ideal systems for studying the molecular mechanisms underlying rapid lineage divergence. Despite the fact that gene regulation provides a critical link between diversification in gene function and speciation, many genomic regulatory mechanisms such as microRNAs (miRNAs) have received little attention in these rapidly diversifying groups. Therefore, we investigated the posttranscriptional regulatory role of miRNAs in the repeated sympatric divergence of Midas cichlids (Amphilophus spp.) from Nicaraguan crater lakes. Using miRNA and mRNA sequencing of embryos from five Midas species, we first identified miRNA binding sites in mRNAs and highlighted the presences of a surprising number of novel miRNAs in these adaptively radiating species. Then, through analyses of expression levels, we identified putative miRNA/gene target pairs with negatively correlated expression level that were consistent with the role of miRNA in downregulating mRNA. Furthermore, we determined that several miRNA/gene pairs show convergent expression patterns associated with the repeated benthic/limnetic sympatric species divergence implicating these miRNAs as potential molecular mechanisms underlying replicated sympatric divergence. Finally, as these candidate miRNA/gene pairs may play a central role in phenotypic diversification in these cichlids, we characterized the expression domains of selected miRNAs and their target genes via in situ hybridization, providing further evidence that miRNA regulation likely plays a role in the Midas cichlid adaptive radiation. These results provide support for the hypothesis that extremely quickly evolving miRNA regulation can contribute to rapid evolutionary divergence even in the presence of gene flow.

Description: Microplastics are ubiquitous across ecosystems, yet the exposure risk to humans is unresolved. Focusing on the American diet, we evaluated the number of microplastic particles in commonly consumed foods in relation to their recommended daily intake. The potential for microplastic inhalation and how the source of drinking water may affect microplastic consumption were also explored. Our analysis used 402 data points from 26 studies, which represents over 3600 processed samples. Evaluating approximately 15% of Americans’ caloric intake, we estimate that annual microplastics consumption ranges from 39000 to 52000 particles depending on age and sex. These estimates increase to 74000 and 121000 when inhalation is considered. Additionally, individuals who meet their recommended water intake through only bottled sources may be ingesting an additional 90000 microplastics annually, compared to 4000 microplastics for those who consume only tap water. These estimates are subject to large amounts of variation; however, given methodological and data limitations, these values are likely underestimates.

Description: The Arctic Limnocalanus macrurus is a prominent representative of large copepods which performs several essential functions in freshwater and marine ecosystems. Being a cold stenotherm species, its distribution is primarily confined to deeper water layers. Based on the long-term observations from one of the largest spatially confined natural populations of this species in the Baltic Sea, we detected profound long-term variability of L. macrurus during 1958–2016: high abundances before the 1980s, then nearly disappearance in the 1990s and recovery in the 2000s. The main environmental parameters explaining the interannual variability of L. macrurus in spring were herring spawning stock biomass in preceding year, winter severity, and bottom water temperature in preceding summer. The effect of winter severity and water temperature was also non-linear. The sliding window correlation analysis pointed to a non-stationary relationship between the abundance of L. macrurus and the key variables. Given the observed pronounced seasonality in the population structure of L. macrurus (young stages dominated in the beginning of the year and only adults were left in the population in summer and autumn) we identified the dynamics of key environmental variables to understand this species under different ecosystem configurations and different combinations of drivers of change.

Description: The Swan Islands Transform Fault (SITF) marks the southern boundary of the Cayman Trough and the ocean–continent transition of the North American–Caribbean Plate boundary offshore Honduras. The CAYSEIS experiment acquired a 180-km-long seismic refraction and gravity profile across this transform margin, ∼70 km to the west of the Mid-Cayman Spreading Centre (MCSC). This profile shows the crustal structure across a transform fault system that juxtaposes Mesozoic-age continental crust to the south against the ∼10-Myr-old ultraslow spread oceanic crust to the north. Ocean-bottom seismographs were deployed along-profile, and inverse and forward traveltime modelling, supported by gravity analysis, reveals ∼23-km-thick continental crust that has been thinned over a distance of ∼70 km to ∼10 km-thick at the SITF, juxtaposed against ∼4-km-thick oceanic crust. This thinning is primarily accommodated within the lower crust. Since Moho reflections are not widely observed, the 7.0 km s−1 velocity contour is used to define the Moho along-profile. The apparent lack of reflections to the north of the SITF suggests that the Moho is more likely a transition zone between crust and mantle. Where the profile traverses bathymetric highs in the off-axis oceanic crust, higher P-wave velocity is observed at shallow crustal depths. S-wave arrival modelling also reveals elevated velocities at shallow depths, except for crust adjacent to the SITF that would have occupied the inside corner high of the ridge-transform intersection when on axis. We use a Vp/Vs ratio of 1.9 to mark where lithologies of the lower crust and uppermost mantle may be exhumed, and also to locate the upper-to-lower crustal transition, identify relict oceanic core complexes and regions of magmatically formed crust. An elevated Vp/Vs ratio suggests not only that serpentinized peridotite may be exposed at the seafloor in places, but also that seawater has been able to flow deep into the crust and upper mantle over 20–30-km-wide regions which may explain the lack of a distinct Moho. The SITF has higher velocities at shallower depths than observed in the oceanic crust to the north and, at the seabed, it is a relatively wide feature. However, the velocity–depth model subseabed suggests a fault zone no wider than ∼5–10 km, that is mirrored by a narrow seabed depression ∼7500 m deep. Gravity modelling shows that the SITF is also underlain, at 〉2 km subseabed, by a ∼20-km-wide region of density 〉3000 kg m−3 that may reflect a broad region of metamorphism. The residual mantle Bouguer anomaly across the survey region, when compared with the bathymetry, suggests that the transform may also have a component of left-lateral trans-tensional displacement that accounts for its apparently broad seabed appearance, and that the focus of magma supply may currently be displaced to the north of the MCSC segment centre. Our results suggest that Swan Islands margin development caused thinning of the adjacent continental crust, and that the adjacent oceanic crust formed in a cool ridge setting, either as a result of reduced mantle upwelling and/or due to fracture enhanced fluid flow.

Description: Latest knowledge on the reactivity of charged nanoparticulate complexants toward aqueous metal ions is discussed in mechanistic detail. We present a rigorous generic description of electrostatic and chemical contributions to metal ion binding by nanoparticulate complexants, and their dependence on particle size, particle type (i.e., reactive sites distributed within the particle body or confined to the surface), ionic strength of the aqueous medium, and the nature of the metal ion. For the example case of soft environmental particles such as fulvic and humic acids, practical strategies are delineated for determining intraparticulate metal ion speciation, and for evaluating intrinsic chemical binding affinities and heterogeneity. The results are compared with those obtained by popular codes for equilibrium speciation modeling (namely NICA-Donnan and WHAM). Physicochemical analysis of the discrepancies generated by these codes reveals the a priori hypotheses adopted therein and the inappropriateness of some of their key parameters. The significance of the characteristic time scales governing the formation and dissociation rates of metal−nanoparticle complexes in defining the relaxation properties and the complete equilibration of the metal− nanoparticulate complex dispersion is described. The dynamic features of nanoparticulate complexes are also discussed in the context of predictions of the labilities and bioavailabilities of the metal species.

Description: Standard seismic acquisition and processing require appropriate source-receiver offsets. P-cable technology represents the opposite, namely, very short source-receiver offsets at the price of increased spatial and lateral resolution with a high-frequency source. To use this advantage, a processing flow excluding offset information is required. This aim can be achieved with a processing tuned to diffractions because point diffractions scatter the same information in offset and midpoint direction. Usually, diffractions are small amplitude events and a careful diffraction separation is required as a first step. We suggest the strategy to use a multiparameter stacking operator, e.g, common-reflection surface, and stack along the midpoint direction. The obtained kinematic wavefront attributes are used to calculate time-migration velocities. A diffractivity map serves as filter to refine the velocities. This strategy is applied to a 3D P-cable data set to obtain a time-migrated image.

Description: We present high-resolution resistivity imaging of gas hydrate pipe-like structures, as derived from marine controlled-source electromagnetic (CSEM) inversions that combine towed and ocean-bottom electric field receiver data, acquired from the Nyegga region, offshore Norway. Two-dimensional CSEM inversions applied to the towed receiver data detected four new prominent vertical resistive features that are likely gas hydrate structures, located in proximity to a major gas hydrate pipe-like structure, known as the CNE03 pockmark. The resistivity model resulting from the CSEM data inversion resolved the CNE03 hydrate structure in high resolution, as inferred by comparison to seismically constrained inversions. Our results indicate that shallow gas hydrate vertical features can be delineated effectively by inverting both ocean-bottom and towed receiver CSEM data simultaneously. The approach applied here can be utilised to map and monitor seafloor mineralisation, freshwater reservoirs, CO2 sequestration sites and near-surface geothermal systems.

Description: Pseudovibrio is a marine bacterial genus members of which are predominantly isolated from sessile marine animals, and particularly sponges. It has been hypothesised that Pseudovibrio spp. form mutualistic relationships with their hosts. Here, we studied Pseudovibrio phylogeny and genetic adaptations that may play a role in host colonization by comparative genomics of 31 Pseudovibrio strains, including 25 sponge isolates. All genomes were highly similar in terms of encoded core metabolic pathways, albeit with substantial differences in overall gene content. Based on gene composition, Pseudovibrio spp. clustered by geographic region, indicating geographic speciation. Furthermore, the fact that isolates from the Mediterranean Sea clustered by sponge species suggested host-specific adaptation or colonization. Genome analyses suggest that Pseudovibrio hongkongensis UST20140214-015BT is only distantly related to other Pseudovibrio spp., thereby challenging its status as typical Pseudovibrio member. All Pseudovibrio genomes were found to encode numerous proteins with SEL1 and tetratricopeptide repeats, which have been suggested to play a role in host colonization. For evasion of the host immune system, Pseudovibrio spp. may depend on type III, IV and VI secretion systems that can inject effector molecules into eukaryotic cells. Furthermore, Pseudovibrio genomes carry on average seven secondary metabolite biosynthesis clusters, reinforcing the role of Pseudovibrio spp. as potential producers of novel bioactive compounds. Tropodithietic acid, bacteriocin and terpene biosynthesis clusters were highly conserved within the genus, suggesting an essential role in survival e.g. through growth inhibition of bacterial competitors. Taken together, these results support the hypothesis that Pseudovibrio spp. have mutualistic relations with sponges.

Description: Methane recovery from artificial hydrate-bearing sandstones by simulated flue gas swapping was tested using a core flooding experimental setup. Seven groups of experiments were conducted to investigate the effect of hydrate saturation as well as the initial porosity and permeability of sandstones on methane production and carbon dioxide capture. The results show that the CH4 recovery efficiency and the amount of CO2 captured increase with the increase of hydrate saturation at the same initial porosity and permeability of sandstone. The highest CH4 recovery obtained is 51.6% and 99.4% of CO2 in simulated flue gas is sequestered in the hydrate phase after swapping at 9.2 MPa and 277.15 K. Hydrate saturation was 82.5% and the initial porosity and permeability of sandstone are 25.1% and 49 mD, respectively. With the increase of initial porosity and permeability of sandstone, the CH4 recovery efficiency and the amount of CO2 captured increase when other conditions (the hydrate saturation and reaction time) are similar. For investigating the CH4-flue gas swapping mechanism, a micro-differential scanning calorimetry was used to test the heat changes in the whole reaction. No noticeable endothermic or exothermic phenomenon was detected in the CH4-flue gas swapping, which indicates that CH4 hydrate would form mixed hydrates directly instead of going through a dissociation and reformation process. Based on the observed experimental results, a CH4-flue gas swapping mechanism is proposed and the reaction process is found to be essentially controlled by mass transfer.

Description: Marine methane hydrate in sands has huge potential as an unconventional gas resource; however, no field test of their production potential had been conducted. Here, we report the world’s first offshore methane hydrate production test conducted at the eastern Nankai Trough and show key findings toward future commercial production. Geological analysis indicates that hydrate saturation reaches 80% and permeability in the presence of hydrate ranges from 0.01 to 10 mdarcies. Permeable (1–10 mdarcies) highly hydrate-saturated layers enable depressurization-induced gas production of approximately 20,000 Sm3/D with water of 200 m3/D. Numerical analysis reveals that the dissociation zone expands laterally 25 m at the front after 6 days. Gas rate is expected to increase with time, owing to the expansion of the dissociation zone. It is found that permeable highly hydrate-saturated layers increase the gas–water ratio of the production fluid. The identification of such layers is critically important to increase the energy efficiency and the technical feasibility of depressurization-induced gas production from hydrate reservoirs.

Description: In the colloidal synthesis of iron sulfides, a series of dialkyl disulfides, alkyl thiols, and dialkyl disulfides (allyl, benzyl, tert-butyl, and phenyl) were employed as sulfur sources. Their reactivity was found to tune the phase between pyrite (FeS2), greigite (Fe3S4), and pyrrhotite (Fe7S8). DFT was used to show that sulfur-rich phases were favored when the C–S bond strength was low in the organosulfurs, yet temperature dependent studies and other observations indicated the reasons for phase selectivity were more nuanced; the different precursors decomposed through different reaction mechanisms, some involving the oleylamine solvent. The formation of pyrite from diallyl disulfide was carefully studied as it was the only precursor to yield FeS2. Raman spectroscopy indicated that FeS2 forms directly without an FeS intermediate, unlike most synthetic procedures to pyrite. Diallyl disulfide releases persulfide (S–S)2– due to the lower C–S bond strength relative to the S–S bond strength, as well as facile decomposition in the presence of amines through SN2′ mechanisms at elevated temperatures.

Description: A synthesis of the 12,12′-azo-analogue of ritterazine N from hecogenin is reported. Ring contraction of two 6/5 bicyclic ring systems, one trans-fused and another spiro, to 5/5 spiro ring systems is accomplished with excellent stereochemical control. Key transformations include an abnormal Baeyer–Villiger oxidation, a Norrish type I cleavage, an intramolecular dipolar [3 + 2] cycloaddition, and an intramolecular oxymecuration. Failing to uncover the β-OH ketone from the isoxazoline ring, we end up with a synthesis of a cyclic analogue of ritterazine N.

Description: Marine plastic debris is a global environmental problem. Surveys have shown that 〈5 mm plastic particles, known as microplastics, are significantly more abundant in surface seawater and on shorelines than larger plastic particles are. Nevertheless, quantification of microplastics in the environment is hampered by a lack of adequate high-throughput methods for distinguishing and quantifying smaller size fractions (〈1 mm), and this has probably resulted in an underestimation of actual microplastic concentrations. Here we present a protocol that allows high-throughput detection and automated quantification of small microplastic particles (20–1000 μm) using the dye Nile red, fluorescence microscopy, and image analysis software. This protocol has proven to be highly effective in the quantification of small polyethylene, polypropylene, polystyrene, and nylon-6 particles, which frequently occur in the water column. Our preliminary results from sea surface tows show a power-law increase in small microplastics (i.e., 〈1 mm) with a decreasing particle size. Hence, our data help to resolve speculation about the “apparent” loss of this fraction from surface waters. We consider that this method presents a step change in the ability to detect small microplastics by substituting the subjectivity of human visual sorting with a sensitive and semiautomated procedure.

Description: The Ignik Sikumi Gas Hydrate Exchange Field Experiment was conducted by ConocoPhillips in partnership with the U.S. Department of Energy, the Japan Oil, Gas and Metals National Corporation, and the U.S. Geological Survey within the Prudhoe Bay Unit on the Alaska North Slope during 2011 and 2012. The primary goals of the program were to (1) determine the feasibility of gas injection into hydrate-bearing sand reservoirs and (2) observe reservoir response upon subsequent flowback in order to assess the potential for C02 exchange for CH4 in naturally occurring gas hydrate reservoirs. Initial modeling determined that no feasible means of injection of pure C02 was likely, given the presence of free water in the reservoir. Laboratory and numerical modeling studies indicated that the injection of a mixture of C02 and N2 offered the best potential for gas injection and exchange. The test featured the following primary operational phases: (1) injection of a gaseous phase mixture of C02, N2, and chemical tracers; (2) flowback conducted at downhole pressures above the stability threshold for native CH4 hydrate; and ( 3) an extended ( 30-days) flowback at pressures near, and then below, the stability threshold of native CH4 hydrate. The test findings indicate that the formation of a range of mixed-gas hydrates resulted in a net exchange of C02 for CH4 in the reservoir, although the complexity of the subsurface environment renders the nature, extent, and efficiency of the exchange reaction uncertain. The next steps in the evaluation of exchange technology should feature multiple well applications; however, such field test programs will require extensive preparatory experimental and numerical modeling studies and will likely be a secondary priority to further field testing of production through depressurization. Additional insights gained from the field program include the following: (1) gas hydrate destabilization is self-limiting, dispelling any notion of the potential for uncontrolled destabilization; (2) gas hydrate test wells must be carefully designed to enable rapid remediation of wellbore blockages that will occur during any cessation in operations; (3) sand production during hydrate production likely can be managed through standard engineering controls; and ( 4) reservoir heat exchange during depressurization was more favorable than expected-mitigating concerns for near-wellbore freezing and enabling consideration of more aggressive pressure reduction.

Description: Ocean acidification (OA) is increasing due to anthropogenic CO2 emissions and poses a threat to marine species and communities worldwide. To better project the effects of acidification on organisms’ health and persistence, an understanding is needed of the 1) mechanisms underlying developmental and physiological tolerance and 2) potential populations have for rapid evolutionary adaptation. This is especially challenging in nonmodel species where targeted assays of metabolism and stress physiology may not be available or economical for large-scale assessments of genetic constraints. We used mRNA sequencing and a quantitative genetics breeding design to study mechanisms underlying genetic variability and tolerance to decreased seawater pH (-0.4 pH units) in larvae of the sea urchin Strongylocentrotus droebachiensis. We used a gene ontology-based approach to integrate expression profiles into indirect measures of cellular and biochemical traits underlying variation in larval performance (i.e., growth rates). Molecular responses to OA were complex, involving changes to several functions such as growth rates, cell division, metabolism, and immune activities. Surprisingly, the magnitude of pH effects on molecular traits tended to be small relative to variation attributable to segregating functional genetic variation in this species. We discuss how the application of transcriptomics and quantitative genetics approaches across diverse species can enrich our understanding of the biological impacts of climate change.

Description: To understand how ocean acidification (OA) influences sediment microbial communities, naturally CO2-rich sites are increasingly being used as OA analogues. However, the characterization of these naturally CO2-rich sites is often limited to OA-related variables, neglecting additional environmental variables that may confound OA effects. Here, we used an extensive array of sediment and bottom water parameters to evaluate pH effects on sediment microbial communities at hydrothermal CO2seeps in Papua New Guinea. The geochemical composition of the sediment pore water showed variations in the hydrothermal signature at seep sites with comparable pH, allowing the identification of sites that may better represent future OA scenarios. At these sites, we detected a 60% shift in the microbial community composition compared with reference sites, mostly related to increases inChloroflexisequences. pH was among the factors significantly, yet not mainly, explaining changes in microbial community composition. pH variation may therefore often not be the primary cause of microbial changes when sampling is done along complex environmental gradients. Thus, we recommend an ecosystem approach when assessing OA effects on sediment microbial communities under natural conditions. This will enable a more reliable quantification of OA effects via a reduction of potential confounding effects

Description: Connectivity of pelagic, early life stages via transport by ocean currents may affect survival chances of offspring, recruitment success, and mixing of stocks across management units. Based on drift model studies, transport patterns of particles representing exogenously feeding cod larvae in the transition area between North Sea and Baltic were investigated to (i) determine long-term trends and variability in advective transport of larvae from spawning grounds to juvenile nursery areas, (ii) estimate the degree of exchange between different management areas, and (iii) compare the results with spatial distributions of juvenile cod. The transport of particles showed considerable intra- and interannual variability, but also some general patterns of retention within and dispersion to different management areas. Good spatial overlap of particle end positions, representing potential juvenile settlement areas, with observed distributions of juveniles in bottom trawl surveys suggests that the drift simulations provide reasonable estimates of early life stage connectivity between cod populations in the investigated areas. High exchange rates of particles between management areas of up to ca. 70% suggest that cod populations in the investigated areas are demographically correlated. Results are discussed in relation to their relevance for stock structure, fish stock assessment, and management.

Description: This paper proposes improved guidelines for dissolved organic matter (DOM) isolation by solid phase extraction (SPE) with a styrene-divinylbenzene copolymer (PPL) sorbent, which has become an established method for the isolation of DOM from natural waters, because of its ease of application and appreciable carbon recovery. Suwannee River water was selected to systematically study the effects of critical SPE variables such as loading mass, concentration, flow rate, and up-scaling on the extraction selectivity of the PPL sorbent. High-field Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and proton nuclear magnetic resonance (H-1 NMR) spectroscopy were performed to interpret the DOM chemical space of eluates, as well as permeates and-wash liquids with molecular resolution. Up to 89% dissolved organic carbon (DOC) recovery was obtained with a DOC/PPL mass ratio of 1:800 at a DOC concentration of 20 mg/L. With the 0 application of larger loading volumes, low proportions of highly oxygenated compounds were retained on the PPL sorbent. The effects of the flow rate on the extraction selectivity of the sorbent were marginal. Up-scaling had a limited effect on the extraction selectivity with the exception of increased self-esterification with a methanol solvent, resulting in methyl ester groups. Furthermore, the SPE/PPL extract exhibited highly authentic characteristics in comparison with original water and reverse osmosis samples. These findings will be useful for reproducibly isolating DOM with representative molecular compositions from various sources and concentrations and minimizing potential inconsistencies among interlaboratory comparative studies.

Description: While we know much about the evolutionary patterns of endosymbiotic organelle origins, we know less about how the actual process unfolded within each system. This is partly due to the massive changes endosymbiosis appears to trigger, and partly because most organelles evolved in the distant past. The dinotoms are dinoflagellates with diatom endosymbionts, and they represent a relatively recent but nevertheless obligate endosymbiotic association. We have carried out deep sequencing of both the host and endosymbiont transcriptomes from two dinotoms, Durinskia baltica and Glenodinium foliaceum, to examine how the nucleocytosolic compartments have functionally integrated. This analysis showed little or no functional reduction in either the endosymbiont or host, and no evidence for genetic integration. Rather, host and endosymbiont seem to be bound to each other via metabolites, such as photosynthate exported from the endosymbiont to the host as indicated by the presence of plastidic phosphate translocators in the host transcriptome. The host is able to synthesize starch, using plant-specific starch synthases, as a way to store imported photosynthate.

Description: The first total synthesis and structure revision of (−)-11β-hydroxycurvularin (1b), a macrolide possessing a β-hydroxyketone moiety, were accomplished. The β-hydroxyketone moiety in this natural product was introduced by cleavage of the N–O bond in an isoxazoline ring that was formed diastereoselectively in a 1,5-remote stereocontrolled fashion by employing intramolecular nitrile oxide cycloaddition

Description: The exploration and proposed mining of sulfide massive deposits in deep-sea environments and increased use deep-sea tailings placement (DSTP) in coastal zones has highlighted the need to better understand the fate and effects of mine-derived materials in marine environments. Metal sulfide ores contain high concentrations of metal(loid)s, of which a large portion exist in highly mineralized or sulfidised forms and are predicted to exhibit low bioavailability. In this study, sediments were spiked with a range of natural sulfide minerals (including chalcopyrite, chalcocite, galena, sphalerite) to assess the bioavailability and toxicity to benthic invertebrates (bivalve survival and amphipod survival and reproduction). The metal sulfide phases were considerably less bioavailable than metal contaminants introduced to sediment in dissolved forms, or in urban estuarine sediments contaminated with mixtures of metal(loid)s. Compared to total concentrations, the dilute-acid extractable metal(loid) (AEM) concentrations, which are intended to represent the more oxidized and labile forms, were more effective for predicting the toxicity of the sulfide mineral contaminated sediments. The study indicates that sediment quality guidelines based on AEM concentrations provide a useful tool for assessing and monitoring the risk posed by sediments impacted by mine-derived materials in marine environments.

Description: Ubiquitous SAR11 Alphaproteobacteria numerically dominate marine planktonic communities. Because they are excruciatingly difficult to cultivate, there is comparatively little known about their physiology and metabolic responses to long- and short-term environmental changes. As surface oceans take up anthropogenic, atmospheric CO2, the consequential process of ocean acidification could affect the global biogeochemical significance of SAR11. Shipping accidents or inadvertent release of chemicals from industrial plants can have strong short-term local effects on oceanic SAR11. This study investigated the effect of 2.5-fold acidification of seawater on the metabolism of SAR11 and other heterotrophic bacterioplankton along a natural temperature gradient crossing the North Atlantic Ocean, Norwegian and Greenland Seas. Uptake rates of the amino acid leucine by SAR11 cells as well as other bacterioplankton remained similar to controls despite an instant ∼50% increase in leucine bioavailability upon acidification. This high physiological resilience to acidification even without acclimation, suggests that open ocean dominant bacterioplankton are able to cope even with sudden and therefore more likely with long-term acidification effects.

Description: The guest-exchange method (or replacement) for methane production from gas hydrates has recently received attention because it can be used for both carbon dioxide sequestration and methane production. The structure of gas hydrates is maintained as a structure I (sI) hydrate while methane molecules are exchanged with carbon dioxide. In this study, CH4 + CO2 mixed gas hydrates were examined under terahertz light at various temperatures to simulate CH4–CO2 exchange reactions. Each gas hydrate composition examined was a representative composition at each step of the exchange reaction. The molecular composition was also accurately analyzed by gas chromatography. Refractive indices calculated by the terahertz time-domain spectroscopy (THz-TDS) of gas hydrate samples were correlated to the guest composition, and this novel method was proven to be used to quantify the extent of replacement via optical constant. Furthermore, changes in the water framework from the sI hydrate to ice using THz-TDS were investigated with an increasing temperature. Overall, this study reveals the process of guest exchange and phase transition from a gas hydrate to ice via the optical properties in the terahertz region, and it offers a powerful tool in gas hydrate production.

Description: Barnacles of the genus Galkinius occupy a large spectrum of host corals, making it one of the least host-specific genera within the Pyrgomatidae. Molecular analyses show that within the genus Galkinius there are highly supported clades, suggesting that the genus Galkinius is a complex of evolutionarily significant units (ESUs). The morphology of the opercular valves has been used as the basis for the separation of species of Galkinius. In this study, morphological variability was found both between specimens within ESUs extracted from different host species and between specimens extracted from the same colony. Identifications based on the opercular valves cannot therefore be assigned to different species despite being genetically distinguishable. It is proposed that in many cases the differences between valve morphology of different species of Galkinius are the outcome of ontogeny. Allometric growth of the valves has resulted in differences in the proportions of the parts of the valve.

Description: In this pilot study, we describe a high-pressure incubation system allowing multiple subsampling of a pressurized culture without decompression. The system was tested using one piezophilic (Photobacterium profundum), one piezotolerant (Colwellia maris) bacterial strain and a decompressed sample from the Mediterranean deep sea (3044 m) determining bacterial community composition, protein production (BPP) and cell multiplication rates (BCM) up to 27 MPa. The results showed elevation of BPP at high pressure was by a factor of 1.5 ± 1.4 and 3.9 ± 2.3 for P. profundum and C. maris, respectively, compared to ambient-pressure treatments and by a factor of 6.9 ± 3.8 fold in the field samples. In P. profundum and C. maris, BCM at high pressure was elevated (3.1 ± 1.5 and 2.9 ± 1.7 fold, respectively) compared to the ambient-pressure treatments. After 3 days of incubation at 27 MPa, the natural bacterial deep-sea community was dominated by one phylum of the genus Exiguobacterium, indicating the rapid selection of piezotolerant bacteria. In future studies, our novel incubation system could be part of an isopiestic pressure chain, allowing more accurate measurement of bacterial activity rates which is important both for modeling and for predicting the efficiency of the oceanic carbon pump.

Description: Archaea associated with marine sponges are active and influence the nitrogen metabolism of sponges. However, we know little about their occurrence, specificity, and persistence. We aimed to elucidate the relative importance of host specificity and biogeographic background in shaping the symbiotic archaeal communities. We investigated these communities in sympatric sponges from the Mediterranean (Ircinia fasciculata and Ircinia oros, sampled in summer and winter) and from the Caribbean (Ircinia strobilina and Mycale laxissima). PCR cloning and sequencing of archaeal 16S rRNA and amoA genes showed that the archaeal community composition and structure were different from that in seawater and varied among sponge species. We found that the communities were dominated by ammonia-oxidizing archaea closely related to Nitrosopumilus. The community in M. laxissima differed from that in Ircinia spp., including the sympatric sponge I. strobilina; yet, geographical clusters within Ircinia spp. were observed. Whereas archaeal phylotypes in Ircinia spp. were persistent and belong to 'sponge-enriched' clusters, archaea in M. laxissima were closely related with those from diverse habitats (i.e. seawater and sediments). For all four sponge species, the expression of the archaeal amoA gene was confirmed. Our results indicate that host-specific processes, such as host ecological strategy and evolutionary history, control the sponge-archaeal communities.

Description: The ability of microorganisms to withstand long periods with extremely low energy input has gained increasing scientific attention in recent years. Starvation experiments in the laboratory have shown that a phylogenetically wide range of microorganisms evolve fitness-enhancing genetic traits within weeks of incubation under low-energy stress. Studies on natural environments that are cut off from new energy supplies over geologic time scales, such as deeply buried sediments, suggest that similar adaptations might mediate survival under energy limitation in the environment. Yet, the extent to which laboratory-based evidence of starvation survival in pure or mixed cultures can be extrapolated to sustained microbial ecosystems in nature remains unclear. In this review, we discuss past investigations on microbial energy requirements and adaptations to energy limitation, identify gaps in our current knowledge, and outline possible future foci of research on life under extreme energy limitation.

Description: The permafrost methane emission problem is the focus of attention on different climate models. Here, we present a mathematical model for permafrost lake methane emission and its influence on the climate system. We model this process using the theory of non-linear phase transitions. Further, we find that a climate catastrophe possibility depends on a value of feedback connecting the methane concentration in the atmosphere and temperature, and on the tundra permafrost methane pool.We note that the permafrost lake model that we developed for the methane emission positive feedback loop problem is a conceptual climate model.

Description: Implantable endovascular devices such as bare metal, drug eluting, and bioresorbable stents have transformed interventional care by providing continuous structural and mechanical support to many peripheral, neural, and coronary arteries affected by blockage. Although effective in achieving immediate restoration of blood flow, the long-term re-endothelialization and inflammation induced by mechanical stents are difficult to diagnose or treat. Here we present nanomaterial designs and integration strategies for the bioresorbable electronic stent with drug-infused functionalized nanoparticles to enable flow sensing, temperature monitoring, data storage, wireless power/data transmission, inflammation suppression, localized drug delivery, and hyperthermia therapy. In vivo and ex vivo animal experiments as well as in vitro cell studies demonstrate the previously unrecognized potential for bioresorbable electronic implants coupled with bioinert therapeutic nanoparticles in the endovascular system.

Description: The shrinking-core model of the formation of gas hydrates from ice spheres with well-defined geometry gives experimental access to the gas permeation in bulk hydrates which is relevant to their use as energy storage materials, their exploitation from natural resources, as well as to their role in flow assurance. Here we report on a new approach to model CO2 clathration experiments in the temperature range from 230 to 272 K. We develop a comprehensive description of the gas permeation based on the diffusion along the network of polyhedral cages, some of them being empty. Following earlier molecular dynamics simulation results, the jump from a cage to one of its empty neighbors is assumed to proceed via a “hole-in-cage-wall” mechanism involving water vacancies in cage walls. The rate-limiting process in the investigated temperature range can be explained by the creation of water-vacancy-interstitial pairs. The gas diffusion leads to a time-dependent cage filling which decreases across the hydrate layer with the distance from the particle surface. The model allows a prediction of the time needed for a complete conversion of ice spheres into clathrate as well as the time needed for a full equilibration of the cage fillings. The findings essentially support our earlier results obtained in the framework of a purely phenomenological permeation model in terms of the overall transformation kinetics, yet it provides for the first time insight into the cage equilibration processes. The diffusion of CO2 molecules through bulk hydrate is found to be about three to four times faster in comparison with the CH4 case.

Description: Spliceosomal introns are a hallmark of eukaryotic genes that are hypothesized to play important roles in genome evolution but have poorly understood origins. Although most introns lack sequence homology to each other, new families of spliceosomal introns that are repeated hundreds of times in individual genomes have recently been discovered in a few organisms. The prevalence and conservation of these introner elements (IEs) or introner-like elements in other taxa, as well as their evolutionary relationships to regular spliceosomal introns, are still unknown. Here, we systematically investigate introns in the widespread marine green alga Micromonas and report new families of IEs, numerous intron presence-absence polymorphisms, and potential intron insertion hot-spots. The new families enabled identification of conserved IE secondary structure features and establishment of a novel general model for repetitive intron proliferation across genomes. Despite shared secondary structure, the IE families from each Micromonas lineage bear no obvious sequence similarity to those in the other lineages, suggesting that their appearance is intimately linked with the process of speciation. Two of the new IE families come from an Arctic culture (Micromonas Clade E2) isolated from a polar region where abundance of this alga is increasing due to climate induced changes. The same two families were detected in metagenomic data from Antarctica-a system where Micromonas has never before been reported. Strikingly high identity between the Arctic isolate and Antarctic coding sequences that flank the IEs suggests connectivity between populations in the two polar systems that we postulate occurs through deep-sea currents. Recovery of Clade E2 sequences in North Atlantic Deep Waters beneath the Gulf Stream supports this hypothesis. Our research illuminates the dynamic relationships between an unusual class of repetitive introns, genome evolution, speciation, and global distribution of this sentinel marine alga. © 2015 The Author.

Description: Methane is a powerful greenhouse gas and its biological conversion in marine sediments, largely controlled by anaerobic oxidation of methane (AOM), is a crucial part of the global carbon cycle. However, little is known about the role of iron oxides as an oxidant for AOM. Here we provide the first field evidence for iron-dependent AOM in brackish coastal surface sediments and show that methane produced in Bothnian Sea sediments is oxidized in distinct zones of iron- and sulfate-dependent AOM. At our study site, anthropogenic eutrophication over recent decades has led to an upward migration of the sulfate/methane transition zone in the sediment. Abundant iron oxides and high dissolved ferrous iron indicate iron reduction in the methanogenic sediments below the newly established sulfate/methane transition. Laboratory incubation studies of these sediments strongly suggest that the in situ microbial community is capable of linking methane oxidation to iron oxide reduction. Eutrophication of coastal environments may therefore create geochemical conditions favorable for iron-mediated AOM and thus increase the relevance of iron-dependent methane oxidation in the future. Besides its role in mitigating methane emissions, iron-dependent AOM strongly impacts sedimentary iron cycling and related biogeochemical processes through the reduction of large quantities of iron oxides.

Description: Viruses play important roles in microbial ecology and some infectious diseases, but relatively little is known about the concentrations, sources, transformation, and fate of viruses in the atmosphere. We have measured total airborne concentrations of virus-like and bacterium-like particles (VLPs between 0.02 and 0.5 μm in size and BLPs between 0.5 and 5 μm) in nine locations: a classroom, a daycare center, a dining facility, a health center, three houses, an office, and outdoors. Indoor concentrations of both VLPs and BLPs were ∼105 particles m–3, and the virus:bacteria ratio was 0.9 ± 0.1 (mean ± standard deviation across different locations). There were no significant differences in concentration between different indoor environments. VLP and BLP concentrations in outdoor air were 2.6 and 1.6 times higher, respectively, than in indoor air. At the single outdoor site, the virus:bacteria ratio was 1.4.

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

Description: The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary amplicon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20 273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the samples. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of individual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater.

Description: Ferredoxins are electron shuttles harbouring iron–sulfur clusters that connect multiple oxido-reductive pathways in organisms displaying different lifestyles. Some prokaryotes and algae express an isofunctional electron carrier, flavodoxin, which contains flavin mononucleotide as cofactor. Both proteins evolved in the anaerobic environment preceding the appearance of oxygenic photosynthesis. The advent of an oxygen-rich atmosphere proved detrimental to ferredoxin owing to iron limitation and oxidative damage to the iron–sulfur cluster, and many microorganisms induced flavodoxin expression to replace ferredoxin under stress conditions. Paradoxically, ferredoxin was maintained throughout the tree of life, whereas flavodoxin is absent from plants and animals. Of note is that flavodoxin expression in transgenic plants results in increased tolerance to multiple stresses and iron deficit, through mechanisms similar to those operating in microorganisms. Then, the question remains open as to why a trait that still confers plants such obvious adaptive benefits was not retained. We compare herein the properties of ferredoxin and flavodoxin, and their contrasting modes of expression in response to different environmental stimuli. Phylogenetic analyses suggest that the flavodoxin gene was already absent in the algal lineages immediately preceding land plants. Geographical distribution of phototrophs shows a bias against flavodoxin-containing organisms in iron-rich coastal/freshwater habitats. Based on these observations, we propose that plants evolved from freshwater macroalgae that already lacked flavodoxin because they thrived in an iron-rich habitat with no need to back up ferredoxin functions and therefore no selective pressure to keep the flavodoxin gene. Conversely, ferredoxin retention in the plant lineage is probably related to its higher efficiency as an electron carrier, compared with flavodoxin. Several lines of evidence supporting these contentions are presented and discussed.

Description: The current difficulty in visualizing the true extent of malignant brain tumors during surgical resection represents one of the major reasons for the poor prognosis of brain tumor patients. Here, we evaluated the ability of a hand-held Raman scanner, guided by surface-enhanced Raman scattering (SERS) nanoparticles, to identify the microscopic tumor extent in a genetically engineered RCAS/tv-a glioblastoma mouse model. In a simulated intraoperative scenario, we tested both a static Raman imaging device and a mobile, hand-held Raman scanner. We show that SERS image-guided resection is more accurate than resection using white light visualization alone. Both methods complemented each other, and correlation with histology showed that SERS nanoparticles accurately outlined the extent of the tumors. Importantly, the hand-held Raman probe not only allowed near real-time scanning, but also detected additional microscopic foci of cancer in the resection bed that were not seen on static SERS images and would otherwise have been missed. This technology has a strong potential for clinical translation because it uses inert gold-silica SERS nanoparticles and a hand-held Raman scanner that can guide brain tumor resection in the operating room.

Description: Electrolytes can thermodynamically inhibit clathrate hydrate formation by lowering the activity of water in the surrounding liquid phase, causing the hydrates to form at lower temperatures and higher pressures compared to their formation in pure water. However, it has been reported that some thermodynamic hydrate inhibitors (THIs), when doped at low concentrations, could enhance the rate of gas hydrate formation. We here report a systematic study of model natural gas (a mixture of 90% methane and 10% propane) hydrate formation in strong monovalent salt solutions in a broad range of concentrations, using a high pressure automated lag time apparatus (HP-ALTA). HP-ALTA can apply a large number (〉100) of cooling ramps to a sample and construct probability distributions of gas hydrate formation for each sample. The probabilistic interpretation of data enables us to mitigate the stochastic variation inherent in the nucleation probability distributions and facilitates meaningful comparison among different samples. The electrolytes used in this work are lithium chloride (LiCl), lithium bromide (LiBr), lithium iodide (LiI), sodium chloride (NaCl), sodium bromide (NaBr), sodium iodide (NaI), potassium chloride (KCl), potassium bromide (KBr), and potassium iodide (KI). We found that (1) some salts may act as kinetic hydrate promoters at low concentrations; (2) the width of the probability distributions (stochasticity) of natural gas hydrate formation in these salt solutions was significantly narrower than that in pure water. To gain further insight, we extended the study of the solutions of the same nine salts to the formation of ice and model tetrahydrofuran (THF) hydrate for comparison.

Description: Epibiotic biofilms have the potential to control major aspects of the biology and ecology of their hosts. Their composition and function may thus be essential for the health of the host. We tested the influence of salinity on the composition of epibacterial communities associated with the brown macroalga Fucus vesiculosus. Algal individuals were incubated at three salinities (5, 19, and 25) for 14days and nonliving reference substrata (stones) were included in the experiment. Subsequently, the composition of their surface-associated bacterial communities was analyzed by 454 pyrosequencing of 16S rRNA gene sequences. Redundancy analysis revealed that the composition of epiphytic and epilithic communities significantly differed and were both affected by salinity. We found that 5% of 2494 epiphytic operational taxonomic units at 97% sequence similarity were responsible for the observed shifts. Epibacterial -diversity was significantly lower at salinity 5 but did not differ between substrata. Our results indicate that salinity is an important factor in structuring alga-associated epibacterial communities with respect to composition and/or diversity. Whether direct or indirect mechanisms (via altered biotic interactions) may have been responsible for the observed shifts is discussed.

Description: In spite of considerable insights into the microbial diversity of marine sponges, quantitative information on microbial abundances and community composition remains scarce. Here, we established qPCR assays for the specific quantification of four bacterial phyla of representative sponge symbionts as well as the kingdoms Eubacteria and Archaea. We could show that the 16S rRNA gene numbers of Archaea, Chloroflexi, and the candidate phylum Poribacteria were 4–6 orders of magnitude higher in high microbial abundance (HMA) than in low microbial abundance (LMA) sponges and that actinobacterial 16S rRNA gene numbers were 1–2 orders higher in HMA over LMA sponges, while those for Cyanobacteria were stable between HMA and LMA sponges. Fluorescence in situ hybridization of Aplysina aerophoba tissue sections confirmed the numerical dominance of Chloroflexi, which was followed by Poribacteria. Archaeal and actinobacterial cells were detected in much lower numbers. By use of fluorescence-activated cell sorting as a primer- and probe-independent approach, the dominance of Chloroflexi, Proteobacteria, and Poribacteria in A. aerophoba was confirmed. Our study provides new quantitative insights into the microbiology of sponges and contributes to a better understanding of the HMA/LMA dichotomy.

Description: Dinoflagellates harboring diatom endosymbionts (termed “dinotoms”) have undergone a process often referred to as “tertiary endosymbiosis”—the uptake of algae containing secondary plastids and integration of those plastids into the new host. In contrast to other tertiary plastids, and most secondary plastids, the endosymbiont of dinotoms is distinctly less reduced, retaining a number of cellular features, such as their nucleus and mitochondria and others, in addition to their plastid. This has resulted in redundancy between host and endosymbiont, at least between some mitochondrial and cytosolic metabolism, where this has been investigated. The question of plastidial redundancy is particularly interesting as the fate of the host dinoflagellate plastid is unclear. The host cytosol possesses an eyespot that has been postulated to be a remnant of the ancestral peridinin plastid, but this has not been tested, nor has its possible retention of plastid functions. To investigate this possibility, we searched for plastid-associated pathways and functions in transcriptomic data sets from three dinotom species. We show that the dinoflagellate host has indeed retained genes for plastid-associated pathways and that these genes encode targeting peptides similar to those of other dinoflagellate plastid-targeted proteins. Moreover, we also identified one gene encoding an essential component of the dinoflagellate plastid protein import machinery, altogether suggesting the presence of a functioning plastid import system in the host, and by extension a relict plastid. The presence of the same plastid-associated pathways in the endosymbiont also extends the known functional redundancy in dinotoms, further confirming the unusual state of plastid integration in this group of dinoflagellates.

Description: The macroalga Fucus vesiculosus carries a specific community of surface bacteria. To identify chemical compounds that possibly mediate abundance and community composition of algae-associated bacteria, we tested the effect of surface-available algal compounds on bacterial settlement and community composition under field conditions. Compounds on algal thalli were separated from the surface by extraction with organic solvents and investigated on growth inhibition and settlement of bacterial isolates. Based on in vitro data, partially purified extract fractions were then exposed to bacterial colonizers in vivo followed by bacterial enumeration and community analysis. The polar fraction of the algal surface extract revealed a significant profouling effect for Vibrionales, whereas the nonpolar fraction containing the xanthophyll pigment fucoxanthin and other unidentified nonpolar surface compounds revealed a significant 80% reduction of surface colonizing bacteria. The analysis of bacterial surface communities by 454 pyrosequencing demonstrated that the antifouling activity of nonpolar algal surface compounds was targeting the abundance of natural bacterial colonizers rather than the relative composition of bacterial members within the community. Moreover, the bacterial community composition on F.vesiculosus was markedly different from artificial control substrates and chemically manipulated experimental treatments, suggesting that other, nonextractable surface features and/or physical properties render algal-specific epiphytic bacterial communities.

Description: Following their transmission from the human to the mosquito with the bloodmeal, malaria parasites have to persevere in the mosquito midgut for approximately 1 d. During this period the parasites are highly vulnerable to factors of the mosquito midgut, including bacteria. We here aimed at determining the microbial diversity of gut bacteria of the Asian malaria vector Anophebs stephensi (Liston) during development and under different feeding regimes, including feeds on malaria parasite-infected blood. 16S rRNA and denaturing gradient gel electrophoresis analyses demonstrated an increasing reduction in the microbial diversity during mosquito development from egg to adult and identified the gram-negative bacterium Elizabethkingia meningoseptica King as the dominant species in the midgut of lab-reared male and female mosquitoes. E. meningoseptica is transmitted between generations and its predominance in the mosquito midgut was not altered by diet, when the gut microbiota was compared between sugar-fed and blood-fed female mosquitoes. Furthermore, feeds on blood infected with malaria parasites did not impact the presence of E. meningoseptica in the gut. Extracts from cultured E. meningoseptica were active against gram-positive and negative bacteria and yeast and against the blood and gametocyte transmission stages of the malaria parasite Plasmodium falciparum Welch. The antimicrobial and antiplasmodial activities of E. meningoseptica may account for its dominance in the midgut of the malaria vector.