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This narrative contains the MAG Analysis from: Clifton P Bueno de Mesquita, Wyatt H Hartman, Marcelo Ardón, Susannah G Tringe, Disentangling the effects of sulfate and other seawater ions on microbial communities and greenhouse gas emissions in a coastal forested wetland, ISME Communications, 2024; ycae040, https://doi.org/10.1093/ismeco/ycae040 Metagenomes were uploaded to IMG/M for other analyses.
Microbial communities in the world ocean are affected strongly by oceanic circulation, creating characteristic marine biomes. The high connectivity of most of the ocean makes it difficult to disentangle selective retention of colonizing genotypes (with traits suited to biome specific conditions) from evolutionary selection, which would act on founder genotypes over time. The Arctic Ocean is exceptional with limited exchange with other oceans and ice covered since the last ice age. To test whether Arctic microalgal lineages evolved apart from algae in the global ocean, we sequenced four lineages of microalgae isolated from Arctic waters and sea ice. Here we show convergent evolution and highlight geographically limited HGT as an ecological adaptive force in the form of PFAM complements and horizontal acquisition of key adaptive genes. Notably, ice-binding proteins were acquired and horizontally transferred among Arctic strains. A comparison with Tara Oceans metagenomes and metatranscriptomes confirmed mostly Arctic distributions of these IBPs. The phylogeny of Arctic-specific genes indicated that these events were independent of bacterial-sourced HGTs in Antarctic Southern Ocean microalgae.
Resource availability is a key factor driving marine bird movements and distributions, but direct information on prey availability is difficult to obtain at relevant scales. We present novel methods for describing multi-scale trophic associations, combining movement analyses of marine birds with estimates of forage fish surface aggregations from digital aerial survey data and species occupancy from bottom trawl survey data. We analyzed satellite telemetry data from northern gannets Morus bassanus , red-throated loons Gavia stellata , and long-tailed ducks Clangula hyemalis in the US Atlantic during the non-breeding period. Using discrete-time hidden Markov models to distinguish area-restricted (i.e. putative foraging) from transit movements, we examined how environmental factors influence movement, and how forage fish species distributions and surface aggregations influence habitat use by gannets and loons that have greater dietary reliance. Our results suggest that chlorophyll a concentration significantly affected movement behavior across species, highlighting the importance of higher-productivity areas around estuaries during colder months when regional productivity is low. Though variable across species and seasons, spatial cross-correlation analysis revealed that herring species (Family Clupeidae), including Atlantic menhaden Brevoortia tyrannus , may be important resources; it also showed positive spatial correlations with forage fish aggregations. This suggests that prey patch dynamics and factors driving aggregation formation may be as important as species composition. However, spatial patterns were generally low (<0.3), suggesting a mismatch in spatiotemporal resolution, exemplifying the challenges in quantifying trophic relationships in marine systems. Disentangling predator-prey relationships is critical to understanding the mechanisms driving marine bird behavior in rapidly changing marine systems.
Offshore wind energy development (OWED), while a key strategy for reducing carbon emissions, has potential negative effects to wildlife that should be examined to inform decision making and adaptive management as the industry expands. We present a conceptual framework to guide the long-term study of potential effects to birds and bats from OWED. This framework includes a focus on exposure and vulnerability as key determinants of risk. For birds and bats that are exposed to OWED, there are three main effects of interest that may impact survival and productivity: 1) collision mortality, 2) behavioral responses, including avoidance, displacement, and attraction, and 3) habitat-mediated effects to prey populations. If these OWED effects cause changes in survival and/or breeding success (e.g., fitness), they have the potential for population-level consequences, including changes in population size and structure. Understanding the influence of ecological drivers on exposure and effect parameters can help to disentangle the potential impacts of OWED from other stressors. We use this theoretical framework to summarize existing relevant knowledge and identify current priority research questions (n=22) for the eastern United States, where largescale development of OWED is primarily in the planning and early construction phase. We also identify recommendations for study design and further prioritization of research topics.
Setting the pace of life and constraining the role of members in food webs, body size can affect the structure and dynamics of communities across multiple scales of biological organization (e.g., from the individual to the ecosystem). However, its effects on shaping microbial communities, as well as underlying assembly processes, remain poorly known. Here, we analyzed microbial diversity in the largest urban lake in China and disentangled the ecological processes governing microbial eukaryotes and prokaryotes using 16S and 18S amplicon sequencing. We found that pico/nano-eukaryotes (0.22–20 μm) and micro-eukaryotes (20–200 μm) showed significant differences in terms of both community composition and assembly processes even though they were characterized by similar phylotype diversity. We also found scale dependencies whereby micro-eukaryotes were strongly governed by environmental selection at the local scale and dispersal limitation at the regional scale. Interestingly, it was the micro-eukaryotes, rather than the pico/nano-eukaryotes, that shared similar distribution and community assembly patterns with the prokaryotes. This indicated that assembly processes of eukaryotes may be coupled or decoupled from prokaryotes’ assembly processes based on eukaryote cell size. While the results support the important influence of cell size, there may be other factors leading to different levels of assembly process coupling across size classes. Additional studies are needed to quantitatively parse the influence of cell size versus other factors as drivers of coordinated and divergent community assembly processes across microbial groups. Regardless of the governing mechanisms, our results show that there are clear patterns in how assembly processes are coupled across sub-communities defined by cell size. These size-structured patterns could be used to help predict shifts in microbial food webs in response to future disturbance.
Nuclei are used for high-precision tests of the Standard Model and for studies of physics beyond the Standard Model. Without a thorough understanding of nuclei, we will not be able to meaningfully interpret the growing body of experimental data nor will we be able to disentangle new physics signals from underlying nuclear effects. This calls for accurate calculations of nuclear structure and reactions. In this work, we focus on electroweak decays in nuclei with mass number A ≤ 10 and report on ab initio Quantum Monte Carlo calculations of reduced matrix elements entering beta decays and electron captures in nuclei with mass number A ≤ 10. The many-body wave functions are calculated using selected Norfolk two- and three-nucleon potential models and associated one- and two-body axial currents at tree-level obtained from a chiral effective field theory with pions, nucleons, and Δ. The agreement with the experimental data is satisfactory except for transitions in A = 8 nuclei. In this specific case, the theory significantly underpredicts the experimental data, which indicates the need of further improvements in the corresponding nuclear wave functions. In this study, emphasis is placed on the contributions of two-body axial currents that are carefully analyzed using two-body transition densities. This allow us to study the spatial distribution and short-range behavior of two-body dynamics. In particular, the transition densities when scaled to peak at 1.0 exhibit universal short-range behavior across the considered nuclei, while they differ in the long-range tails.
We report on the use of extreme ultraviolet (XUV, 30.3 nm) radiation from the Free-electron LASer in Hamburg (FLASH) and visible (Vis, 405 nm) photons from an optical laser to investigate the relaxation and fragmentation dynamics of fluorene ions. The ultrashort laser pulses allow to resolve the molecular processes occurring on the femtosecond timescales. Fluorene is a prototypical small polycyclic aromatic hydrocarbon (PAH). Through their infrared emission signature, PAHs have been shown to be ubiquitous in the universe, and they are assumed to play an important role in the chemistry of the interstellar medium. Our experiments track the ionization and dissociative ionization products of fluorene through time-of-flight mass spectrometry and velocity-map imaging. Multiple processes involved in the formation of each of the fragment ions are disentangled through analysis of the ion images. The relaxation lifetimes of the excited fluorene monocation and dication obtained through the fragment formation channels are reported to be in the range of a few tens of femtoseconds to a few picoseconds.
Most pulsating white dwarf stars pulsate with many periods, each of which is a probe of their interior, which has made asteroseismolgy of these stars an active field. However, disentangling the multiple periodicities requires long, uninterrupted strings of data. We briefly describe the history of multi-site observing campaigns that culminated in the development of the Whole Earth Telescope in the late 1980s that still functions today. Through examples from the May 1990 campaign on GD 358, we show how critical it is to eliminate periodic gaps in data to greatly reduce aliasing in Fourier Transforms normally used to analyze the frequency content of pulsating white dwarfs. We close with a brief description of space satellite-based data, along with the advantages and disadvantages of these data compared to ground-based data.
Carbon assimilation and wood production are influenced by environmental conditions and endogenous factors, such as species auto-ecology, age, and hierarchical position within the forest structure. Disentangling the intricate relationships between those factors is more pressing than ever due to climate change’s pressure. We employed the 3D-CMCC-FEM model to simulate undisturbed forests of different ages under four climate change (plus one no climate change) Representative Concentration Pathways (RCP) scenarios from five Earth system models. In this context, carbon stocks and increment were simulated via total carbon woody stocks and mean annual increment, which depends mainly on climate trends. We find greater differences among different age cohorts under the same scenario than among different climate scenarios under the same age class. Increasing temperature and changes in precipitation patterns led to a decline in above-ground biomass in spruce stands, especially in the older age classes. On the contrary, the results show that beech forests will maintain and even increase C-storage rates under most RCP scenarios. Scots pine forests show an intermediate behavior with a stable stock capacity over time and in different scenarios but with decreasing mean volume annual increment. These results confirm current observations worldwide that indicate a stronger climate-related decline in conifers forests than in broadleaves.
A comprehensive multi-jet physics program is anticipated for experiments at future colliders. Key physics processes necessitate detectors that can distinguish signals from W and Z bosons and the Higgs boson. Typical examples include channels with or pairs and processes involving new physics in those cases where neutral particles must be disentangled from charged ones due to the presence of W or Z bosons in their final states. Such a physics program demands calorimetric energy resolution at or beyond the limits of traditional calorimetric techniques. Multiple-readout calorimetry, which aims to reduce fluctuations in energy measurements of hadronic showers, is a promising approach. The first part of this article reviews dual- and triple-readout calorimetry within a mathematical framework describing the underlying compensating mechanism. The second part proposes a potential implementation using an integrally active and total absorption detector. This model serves as the basis for several Monte Carlo studies, illustrating how the response of a multiple-readout calorimeter depends on construction parameters. Among the layouts considered, one configuration operating in triple-readout mode shows the potential to achieve an energy resolution approaching .
The Fusarium oxysporum species complex (FOSC) includes both plant and human pathogens that cause devastating plant vascular wilt diseases and threaten public health. Each F. oxysporum genome comprises core chromosomes (CCs) for housekeeping functions and accessory chromosomes (ACs) that contribute to host-specific adaptation. This study inspects global transcription factor profiles (TFomes) and their potential roles in coordinating CC and AC functions to accomplish host-specific interactions. Remarkably, we found a clear positive correlation between the sizes of TFomes and the proteomes of an organism. With the acquisition of ACs, the FOSC TFomes were larger than the other fungal genomes included in this study. Among a total of 48 classified TF families, 14 families involved in transcription/translation regulations and cell cycle controls were highly conserved. Among the 30 FOSC expanded families, Zn2-C6 and Znf_C2H2 were most significantly expanded to 671 and 167 genes per family including well-characterized homologs of Ftf1 (Zn2-C6) and PacC (Znf_C2H2) that are involved in host-specific interactions. Manual curation of characterized TFs increased the TFome repertoires by 3% including a disordered protein Ren1. RNA-Seq revealed a steady pattern of expression for conserved TF families and specific activation for AC TFs. Functional characterization of these TFs could enhance our understanding of transcriptional regulation involved in FOSC cross-kingdom interactions, disentangle species-specific adaptation, and identify targets to combat diverse diseases caused by this group of fungal pathogens.
Tassel counts provide valuable information related to flowering and yield prediction in maize, but are expensive and time-consuming to acquire via traditional manual approaches. High-resolution RGB imagery acquired by unmanned aerial vehicles (UAVs), coupled with advanced machine learning approaches, including deep learning (DL), provides a new capability for monitoring flowering. In this article, three state-of-the-art DL techniques, CenterNet based on point annotation, task-aware spatial disentanglement (TSD), and detecting objects with recursive feature pyramids and switchable atrous convolution (DetectoRS) based on bounding box annotation, are modified to improve their performance for this application and evaluated for tassel detection relative to Tasselnetv2+. The dataset for the experiments is comprised of RGB images of maize tassels from plant breeding experiments, which vary in size, complexity, and overlap. Results show that the point annotations are more accurate and simpler to acquire than the bounding boxes, and bounding box-based approaches are more sensitive to the size of the bounding boxes and background than point-based approaches. Overall, CenterNet has high accuracy in comparison to the other techniques, but DetectoRS can better detect early-stage tassels. The results for these experiments were more robust than Tasselnetv2+, which is sensitive to the number of tassels in the image.
An innovative solution for real-time monitoring of reactions within confined spaces, optimized for Raman spectroscopy applications, is presented. This approach involves the utilization of a hollow-core waveguide configured as a compact flow cell, serving both as a conduit for Raman excitation and scattering and seamlessly integrating into the effluent stream of a cracking catalytic reactor. The analytical technique, encompassing device and optical design, ensures robustness, compactness, and cost-effectiveness for implementation into process facilities. Notably, the modularity of the approach empowers customization for diverse gas monitoring needs, as it readily adapts to the specific requirements of various sensing scenarios. As a proof of concept, the efficacy of a spectroscopic approach is shown by monitoring two catalytic processes: CO 2 methanation (CO 2 + 4H 2 → CH 4 + 2H 2 O) and ammonia cracking (2NH 3 → N 2 + 3H 2 ). Leveraging chemometric data processing techniques, spectral signatures of the individual components involved in these reactions are effectively disentangled and the results are compared to mass spectrometry data. This robust methodology underscores the versatility and reliability of this monitoring system in complex chemical environments.
Laser synthesis and processing of colloids (LSPC) in liquids has gained widespread applications in producing nanomaterials of different classes of solids. While the technical processes in different cases of ablation, fragmentation or colloidal fusion may look macroscopically different in each application, the underlying fundamental mechanisms are always the same cascade of laser interaction with matter, non-thermal or thermal energy deposition, phase transitions, and the subsequent structure formation processes. Disentangling these mechanisms represents a veritable challenge, as ultrafast and structurally sensitive experimental methods are required. This review presents a discussion of how state-of-the-art experimental protocols using ultrafast lasers and sensitive structural probes, such as electrons or X-rays are able to address this challenge. In particular, it is possible to investigate LSPC on single objects using single probe pulses and avoid accumulation effects in a heterogeneous sample. The presented results capture structure formation with femtosecond and atomic scale resolution. Ultrafast time-resolved probing approaches are key to revealing the transient states and pathways that govern material transformation in LSPC.
We present here AMUSING++: the largest compilation of nearby galaxies observed with the MUSE integral-field spectrograph so far. This collection consists of 635 galaxies from different MUSE projects covering the redshift interval 0.0002 < z < 0.1. The sample and its main properties are characterized and described here. It includes galaxies of almost all morphological types, with a good coverage in its color–magnitude diagram, within the stellar mass range between 10{sup 8} and 10{sup 12} M {sub ⊙}, and with properties resembling those of a diameter-selected sample. The AMUSING++ sample is, therefore, suitable for studying, with unprecendented detail, the properties of nearby galaxies at global and local scales, providing us with more than 50 million individual spectra. We use this compilation to investigate the presence of galactic outflows. We exploit the use of combined emission-line images to explore the shape of the different ionized components and the distribution along classical diagnostic diagrams to disentangle the different ionizing sources across the optical extension of each galaxy. We use the cross-correlation function to estimate the level of symmetry of the emission lines as an indication of the presence of shocks and/or active galactic nuclei. We uncovered a total of 54 outflows, comprising ∼8% of the sample. A large number of the discovered outflows correspond to those driven by active galactic nuclei (∼60%), suggesting some bias in the selection of our sample. No clear evidence was found that outflow host galaxies are highly star-forming, and outflows appear to be found within all galaxies around the star-formation sequence.
We present the analysis of the hot-Jupiter KELT-7 b using transmission and emission spectroscopy from the Hubble Space Telescope, both taken with the Wide Field Camera 3. Our study uncovers a rich transmission spectrum that is consistent with a cloud-free atmosphere and suggests the presence of H{sub 2}O and H{sup −}. In contrast, the extracted emission spectrum does not contain strong absorption features and, although it is not consistent with a simple blackbody, it can be explained by a varying temperature–pressure profile, collision induced absorption, and H{sup −}. KELT-7 b had also been studied with other space-based instruments and we explore the effects of introducing these additional data sets. Further observations with Hubble, or the next generation of space-based telescopes, are needed to allow for the optical opacity source in transmission to be confirmed and for molecular features to be disentangled in emission.
By controlling instrumental errors to below 10 cm s{sup −1}, the EXtreme PREcision Spectrograph (EXPRES) allows for a more insightful study of photospheric velocities that can mask weak Keplerian signals. Gaussian processes (GP) have become a standard tool for modeling correlated noise in radial velocity data sets. While GPs are constrained and motivated by physical properties of the star, in some cases they are still flexible enough to absorb unresolved Keplerian signals. We apply GP regression to EXPRES radial velocity measurements of the 3.5 Gyr old chromospherically active Sun-like star, HD 101501. We obtain tight constraints on the stellar rotation period and the evolution of spot distributions using 28 seasons of ground-based photometry, as well as recent Transiting Exoplanet Survey Satellite data. Light-curve inversion was carried out on both photometry data sets to reveal the spot distribution and spot evolution timescales on the star. We find that the >5 m s{sup −1} rms radial velocity variations in HD 101501 are well modeled with a GP stellar activity model without planets, yielding a residual rms scatter of 45 cm s{sup −1}. We carry out simulations, injecting and recovering signals with the GP framework, to demonstrate that high-cadence observations are required to use GPs most efficiently to detect low-mass planets around active stars like HD 101501. Sparse sampling prevents GPs from learning the correlated noise structure and can allow it to absorb prospective Keplerian signals. We quantify the moderate to high-cadence monitoring that provides the necessary information to disentangle photospheric features using GPs and to detect planets around active stars.
NEID is a high-resolution optical spectrograph on the WIYN 3.5 m telescope at Kitt Peak National Observatory and will soon join the new generation of extreme precision radial velocity instruments in operation around the world. We plan to use the instrument to conduct the NEID Earth Twin Survey (NETS) over the course of the next 5 years, collecting hundreds of observations of some of the nearest and brightest stars in an effort to probe the regime of Earth-mass exoplanets. Even if we take advantage of the extreme instrumental precision conferred by NEID, it will be difficult to disentangle the weak (∼10 cm s{sup −1}) signals induced by such low-mass, long-period exoplanets from stellar noise for all but the quietest host stars. In this work, we present a set of quantitative selection metrics which we use to identify an initial NETS target list consisting of stars conducive to the detection of exoplanets in the regime of interest. We also outline a set of observing strategies with which we aim to mitigate uncertainty contributions from intrinsic stellar variability and other sources of noise.