Motivation: The study of bacterial genome dynamics is vital for understanding the mechanisms underlying microbial adaptation, growth, and their impact on host phenotype. Structural variants (SVs), genomic alterations of 50 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to the absence of clear reference genomes and the presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing all metagenomic samples in a series (time or other metric) into a single co-assembly graph. The log fold change in graph coverage between successive samples is then calculated to call SVs that are thriving or declining.Results: We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, particularly as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between successive time and temperature samples, suggesting host advantage. Our approach leverages previous work in assembly graph structural and coverage patterns to provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial gene flux.Availability and implementation: rhea is open source and available at: https://github.com/treangenlab/rhea.

Microbial mats are stratified communities often dominated by unicellular and filamentous phototrophs within an exopolymer matrix. It is challenging to quantify the dynamic responses of community members in situ as they experience steep gradients and rapid fluctuations of light. To address this, we developed a binary consortium using two representative isolates from hot spring mats, the unicellular oxygenic phototrophic cyanobacterium Synechococcus OS-B' (Syn OS-B') and the filamentous anoxygenic phototroph Chloroflexus MS-CIW-1 (Chfl MS-1). We quantified the motility of individual cells and entire colonies and demonstrated that Chfl MS-1 formed bundles of filaments that moved in all directions with no directional bias to light. Syn OS-B' was slightly less motile but exhibited positive phototaxis. This binary consortium displayed cooperative behavior by moving further than either species alone and formed ordered arrays where both species aligned with the light source. No cooperative motility was observed when a non-motile pilB mutant of Syn OS-B' was used instead of Syn OS-B'. The binary consortium also produced more adherent biofilm than individual species, consistent with the close interspecies association revealed by electron microscopy. We propose that cyanobacteria and Chloroflexota cooperate in forming natural microbial mats, by colonizing new niches and building robust biofilms.

Ukraine supplies a large proportion of grain and oilseeds to the world market and faces disruptions from the Russian invasion in 2022. Here we explore the combined effects of the invasion and climate change on Ukraine's irrigation. In 2021, only 1.6% of Ukraine's cropland was irrigated. Of this portion, 73% experienced substantial declines in irrigated crop production following the invasion. We estimate that by the mid-twenty-first century, three-quarters of croplands will experience water shortages, making business-as-usual rain-fed agricultural practices inadequate in addressing the challenges posed by climate change. We explore how leveraging local surface and groundwater resources could enable sustainable irrigation expansion over 18 million hectares of croplands and form a viable climate adaptation strategy. Finally, we identify regions for implementing enhancements or expansions of irrigation systems that can foster a more resilient agricultural sector-underscoring the growing importance of irrigation in sustaining crop production in Ukraine.

Understanding the climate and carbon cycle response to negative CO2 emissions is important for developing climate mitigation strategies that aim to limit global warming to a specific threshold. In this study, using a coupled climate and carbon cycle model, a novel set of nine stylized simulations are conducted with cumulative emissions of 1,000 GtC, 2,000 GtC, and 5,000 GtC over 150, 250, and 500 years, followed by identical cumulative negative emissions so that the net cumulative emissions are zero. On millennial-timescales, the climate system returns close to the preindustrial state, independent of the emission and removal pathways. However, the thermal and biogeochemical inertia of the ocean play an important role in determining the climate and carbon cycle response during the emission and removal phases. When zero net emissions are reached, surface air temperature is larger by 0-1 degrees C than the preindustrial state, and the atmospheric CO2 concentration is less by 12-29 ppm. These changes increase with both the magnitude and duration of the emission and removal pulses. In contrast, hysteresis in the relationship between global mean surface temperature and cumulative carbon emissions increases with the magnitude but decreases with the duration of emission and removal pulses. Our study highlights the role of ocean inertia in the asymmetry in climate response to emissions and removals and indicates that an earlier emission reduction implying emission/removal pathways with smaller magnitudes and shorter durations for the positive and negative emission pulses would avoid larger climate and carbon cycle impacts on centennial-timescales.

We present an analysis of Type Ia supernovae (SNe Ia) from the Carnegie Supernova Project I and II and extend the Hubble diagram from optical to near-infrared wavelengths (uBgVriYJH). We calculate the Hubble constant, H 0, using various distance calibrators: Cepheids, the tip of the red giant branch (TRGB), and surface brightness fluctuations (SBFs). Combining all methods of calibration, we derive H 0 = 71.76 +/- 0.58 (stat) +/- 1.19 (sys) km s(-1) Mpc(-1) from the B band and H 0 = 73.22 +/- 0.68 (stat) +/- 1.28 (sys) km s(-1) Mpc(-1) from the H band. By assigning equal weight to the Cepheid, TRGB, and SBF calibrators, we derive the systematic errors required for consistency in the first rung of the distance ladder, resulting in a systematic error of 1.2 similar to 1.3 km s(-1) Mpc(-1) in H 0. As a result, relative to the statistics-only uncertainty, the tension between the late-time H 0 we derive by combining the various distance calibrators and the early-time H 0 from the cosmic microwave background is reduced. The highest precision in SN Ia luminosity is found in the Y band (0.12 +/- 0.01 mag), as defined by the intrinsic scatter (sigma int). We revisit SN Ia Hubble residual-host mass correlations and recover previous results that these correlations do not change significantly between the optical and near-infrared wavelengths. Finally, SNe Ia that explode beyond 10 kpc from their host centers exhibit smaller dispersion in their luminosity, confirming our earlier findings. A reduced effect of dust in the outskirts of hosts may be responsible for this effect.

Among Neptunian mass exoplanets (20-50 M-circle plus), puffy hot Neptunes are extremely rare, and their unique combination of low mass and extended radii implies very low density (rho < 0.3 g cm(-3)). Over the last decade, only a few puffy planets have been detected and precisely characterized with both transit and radial velocity observations, most notably including WASP-107 b, TOI-1420 b, and WASP-193 b. In this paper, we report the discovery of TOI-1173 A b, a low-density ( rho=0.195-0.017+0.018 g cm(-3)) super-Neptune with P = 7.06 days in a nearly circular orbit around the primary G-dwarf star in the wide binary system TOI-1173 A/B. Using radial velocity observations with the MAROON-X and HIRES spectrographs and transit photometry from TESS, we determine a planet mass of M p = 27.4 +/- 1.7 M circle plus and radius of R p = 9.19 +/- 0.18 R circle plus. TOI-1173 A b is the first puffy super-Neptune planet detected in a wide binary system (projected separation similar to 11,400 au). We explore several mechanisms to understand the puffy nature of TOI-1173 A b and show that tidal heating is the most promising explanation. Furthermore, we demonstrate that TOI-1173 A b likely has maintained its orbital stability over time and may have undergone von-Zeipel-Lidov-Kozai migration followed by tidal circularization, given its present-day architecture, with important implications for planet migration theory and induced engulfment into the host star. Further investigation of the atmosphere of TOI-1173 A b will shed light on the origin of close-in low-density Neptunian planets in field and binary systems, while spin-orbit analyses may elucidate the dynamical evolution of the system.

We present Augustus, a catalog of distance, extinction, and stellar parameter estimates for 170 million stars from 14 mag < r < 20 mag and with divided by b divided by > 10 degrees drawing on a combination of optical to near-infrared photometry from Pan-STARRS, 2MASS, UKIDSS, and unWISE along with parallax measurements from Gaia DR2 and 3D dust extinction maps. After applying quality cuts, we find 125 million objects have "high-quality" posteriors with statistical distance uncertainties of less than or similar to 10% for objects with well-constrained stellar types. This is a substantial improvement over the distance estimates derived from Gaia parallaxes alone and in line with the recent results from Anders et al. We find the fits are able to reproduce the dereddened Gaia color-magnitude diagram accurately, which serves as a useful consistency check of our results. We show that we are able to detect large, kinematically coherent substructures in our data clearly relative to the input priors, including the Monoceros Ring and the Sagittarius Stream, attesting to the quality of the catalog. Our results are publicly available at doi:10.7910/DVN/WYMSXV. An accompanying interactive visualization can be found at http://allsky.s3-website.us-east-2.amazonaws.com.

The high contrast and spatial resolution requirements for directly imaging exoplanets requires effective coordination of wavefront control, coronagraphy, observation techniques, and post-processing algorithms. However, even with this suite of tools, identifying and retrieving exoplanet signals embedded in resolved scattered light regions can be extremely challenging due to the increased noise from scattered light off the circumstellar disk and the potential misinterpretation of the true nature of the detected signal. This issue pertains not only to imaging terrestrial planets in habitable zones within zodiacal and exozodiacal emission but also to young planets embedded in circumstellar, transitional, and debris disks. This is particularly true for H{alpha} detection of exoplanets in transitional disks. This work delves into recent H{alpha} observations of three transitional disks systems with MagAO-X, an extreme adaptive optics system for the 6.5-meter Magellan Clay telescope. We employed angular differential imaging (ADI) and simultaneous spectral differential imaging (SSDI) in combination with KLIP, a PCA algorithm in post-processing, for optimal starlight suppression and quasi-static noise removal. We discuss the challenges in protoplanet identification with MagAO-X in environments rich with scattered and reflected light from disk structures and explore a potential solution for removing noise contributions from real astronomical objects with current observation and post-processing techniques.

High-contrast imaging data analysis depends on removing residual starlight from the host star to reveal planets and disks. Most observers do this with principal components analysis (i.e. KLIP) using modes computed from the science images themselves. These modes may not be orthogonal to planet and disk signals, leading to over-subtraction. The wavefront sensor data recorded during the observation provide an independent signal with which to predict the instrument point-spread function (PSF). MagAO-X is an extreme adaptive optics (ExAO) system for the 6.5-meter Magellan Clay telescope and a technology pathfinder for ExAO with GMagAO-X on the upcoming Giant Magellan Telescope. MagAO-X is designed to save all sensor information, including kHz-speed wavefront measurements. Our software and compressed data formats were designed to record the millions of training samples required for machine learning with high throughput. The large volume of image and sensor data lets us learn a PSF model incorporating all the information available. This will eventually allow us to probe smaller star-planet separations at greater sensitivities, which will be needed for rocky planet imaging.

We present the preliminary design of GMagAO-X, the first-light high-contrast imager planned for the Giant Magellan Telescope. GMagAO-X will realize the revolutionary increase in spatial resolution and sensitivity provided by the 25 m GMT. It will enable, for the first time, the spectroscopic characterization of nearby potentially habitable terrestrial exoplanets orbiting late-type stars. Additional science cases include: reflected light characterization of mature giant planets; measurement of young extrasolar giant planet variability; characterization of circumstellar disks at unprecedented spatial resolution; characterization of benchmark stellar atmospheres at high spectral resolution; and mapping of resolved objects such as giant stars and asteroids. These, and many more, science cases will be enabled by a 21,000 actuator extreme adaptive optics system, a coronagraphic wavefront control system, and a suite of imagers and spectrographs. We will review the science-driven performance requirements for GMagAO-X, which include achieving a Strehl ratio of 70% at 800 nm on 8th mag and brighter stars, and post-processed characterization at astrophysical flux-ratios of 1e-7 at 4 lambda/D (26 mas at 800 nm) separation. We will provide an overview of the resulting mechanical, optical, and software designs optimized to deliver this performance. We will also discuss the interfaces to the GMT itself, and the concept of operations. We will present an overview of our end-to-end performance modeling and simulations, including the control of segment phasing, as well as an overview of prototype lab demonstrations. Finally, we will review the results of Preliminary Design Review held in February, 2024.