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We report 17 metagenome-assembled genomes (MAGs) recovered from microbial consortia of forest and pasture soils, in the Brazilian Eastern Amazon. Recovered MAGs constitute novel genomes with the potential to act in important ecological processes, including the degradation of carbohydrate and sulfur and nitrogen cycling.
We report 14 metagenome-assembled genomes (MAGs) recovered from agricultural soils, composts, and enrichment cultures enriched therefrom, originating from the Netherlands, Belgium and Switzerland. Recovered MAGs constitute methane-cycling related organisms sequenced from isolated cultures or environmental DNA, elucidating their metabolic potential in important ecological processes like the oxidation or production of atmospheric trace gases as methane, hydrogen, and carbon monoxide.
In this tutorial narrative, we introduce a novel template developed to enable the creation of stoichiometric genome-scale metabolic models for iron-oxidizing bacteria. We demonstrate the development of this template by applying it to Sideroxydans lithotrophicus ES-1, and validate our model using transcriptomic data (Published in Zhou et al., 2022 AEM). Below, we further show that our template facilitates the modeling of mixotrophic iron-oxidizing bacteria and metagenome-assembled genomes (MAGs), by applying our template to the MAG of the mixotrophic iron oxidizer Leptothrix ochracea (Published in Tothero et al, 2024). This work represents the first instance of a generalized and adaptable template for modeling diverse iron-oxidizing microbial systems, expanding the accessibility and applicability of metabolic modeling in this field.
This Narrative is part of a collection used in a single publication. The paper took a metagnomic and metatranscriptomic approach to examine a bioreactor's response to the presence of sulfate, which reduces the production of methane, a valuable product, while producing hydrogen sulfide, a corrosive contaminant. This Narrative collection has been created to highlight the types of analyses done for this publication. They are as follows (in order): SJ1 Metagenomes: a metagenomic analysis of sample SJ1, the initial bioreactor. SJ1 Metatranscriptomes: QC-filtered raw RNA reads were aligned to individual MAGs and assembled into transcripts. Metagenome-discovered food webs in a long-term methanogenic bioreactor and rapid switch to sulfate reducing conditions (this Narrative): the public Narrative referenced in the paper, which contains several key MAGs.
Fermentative microbial communities have the potential to serve as biocatalysts for the conversion of low-value dairy coproducts into renewable chemicals, contributing to a more sustainable global economy. To develop predictive tools for the design and operation of industrially relevant strategies that utilize fermentative microbial communities, there is a need to determine the genomic features of community members that are characteristic to the accumulation of different products. To address this knowledge gap, we performed a 282-day bioreactor experiment with a microbial community that was fed ultra-filtered milk permeate, a low-value coproduct from the dairy industry. The bioreactor was inoculated with a microbial community from an acid-phase digester. A metagenomic analysis was used to assess microbial community dynamics, construct metagenome-assembled genomes (MAGs), and evaluate the potential for lactose utilization and fermentation product synthesis of community members represented by the assembled MAGs. This analysis led us to propose that, in this reactor, members of the Actinobacteriota phylum are important in the degradation of lactose, via the Leloir pathway and the bifid shunt, and the production of acetic, lactic, and succinic acids. In addition, members of the Firmicutes phylum contribute to the chain-elongation-mediated production of butyric, hexanoic, and octanoic acids, with different microbes using either lactose, ethanol, or lactic acid as the growth substrate. We conclude that genes encoding carbohydrate utilization pathways, and genes encoding lactic acid transport into the cell, electron confurcating lactate dehydrogenase, and its associated electron transfer flavoproteins, are genomic features whose presence in Firmicutes needs to be established to infer the growth substrate used for chain elongation.
GAL08 are bacteria belonging to an uncultivated phylogenetic cluster within the phylum Acidobacteria . We detected a natural population of the GAL08 clade in sediment from a pH-neutral hot spring located in British Columbia, Canada. To shed light on the abundance and genomic potential of this clade, we collected and analyzed hot spring sediment samples over a temperature range of 24.2–79.8°C. Illumina sequencing of 16S rRNA gene amplicons and qPCR using a primer set developed specifically to detect the GAL08 16S rRNA gene revealed that absolute and relative abundances of GAL08 peaked at 65°C along three temperature gradients. Analysis of sediment collected over multiple years and locations revealed that the GAL08 group was consistently a dominant clade, comprising up to 29.2% of the microbial community based on relative read abundance and up to 4.7 × 10 5 16S rRNA gene copy numbers per gram of sediment based on qPCR. Using a medium quality threshold, 25 single amplified genomes (SAGs) representing these bacteria were generated from samples taken at 65 and 77°C, and seven metagenome-assembled genomes (MAGs) were reconstructed from samples collected at 45–77°C. Based on average nucleotide identity (ANI), these SAGs and MAGs represented three separate species, with an estimated average genome size of 3.17 Mb and GC content of 62.8%. Phylogenetic trees constructed from 16S rRNA gene sequences and a set of 56 concatenated phylogenetic marker genes both placed the three GAL08 bacteria as a distinct subgroup of the phylum Acidobacteria , representing a candidate order ( Ca. Frugalibacteriales) within the class Blastocatellia. Metabolic reconstructions from genome data predicted a heterotrophic metabolism, with potential capability for aerobic respiration, as well as incomplete denitrification and fermentation. In laboratory cultivation efforts, GAL08 counts based on qPCR declined rapidly under atmospheric levels of oxygen but increased slightly at 1% (v/v) O 2 , suggesting a microaerophilic lifestyle.
Demand for natural gas continues to climb in the United States, having reached a record monthly high of 104.9 billion cubic feet per day (Bcf/d) in November 2023. Hydraulic fracturing, a technique used to extract natural gas and oil from deep underground reservoirs, involves injecting large volumes of fluid, proppant, and chemical additives into shale units. This is followed by a “shut-in” period, during which the fracture fluid remains pressurized in the well for several weeks. The microbial processes that occur within the reservoir during this shut-in period are not well understood; yet, these reactions may significantly impact the structural integrity and overall recovery of oil and gas from the well. To shed light on this critical phase, we conducted an analysis of both pre-shut-in material alongside production fluid collected throughout the initial production phase at the Hydraulic Fracturing Test Site 2 (HFTS 2) located in the prolific Wolfcamp formation within the Permian Delaware Basin of west Texas, USA. Specifically, we aimed to assess the microbial ecology and functional potential of the microbial community during this crucial time frame. Prior analysis of 16S rRNA sequencing data through the first 35 days of production revealed a strong selection for a Clostridia species corresponding to a significant decrease in microbial diversity. Here, we performed a metagenomic analysis of produced water sampled on Day 33 of production. This analysis yielded three high-quality metagenome-assembled genomes (MAGs), one of which was a Clostridia draft genome closely related to the recently classified Petromonas tenebris. This draft genome likely represents the dominant Clostridia species observed in our 16S rRNA profile. Annotation of the MAGs revealed the presence of genes involved in critical metabolic processes, including thiosulfate reduction, mixed acid fermentation, and biofilm formation. These findings suggest that this microbial community has the potential to contribute to well souring, biocorrosion, and biofouling within the reservoir. Our research provides unique insights into the early stages of production in one of the most prolific unconventional plays in the United States, with important implications for well management and energy recovery.
Although river ecosystems constitute a small fraction of Earth’s total area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. To address this gap, we assessed how viral and microbial communities change over a 48-hour period by sampling surface water and pore water compartments of the wastewater-impacted River Erpe in Germany. We sampled every 3 hours resulting in 32 samples for which we obtained metagenomes along with geochemical and metabolite measurements. From our metagenomes, we identified 6,500 viral and 1,033 microbial metagenome assembled genomes (MAGs) and found distinct community membership and abundance associated with each river compartment (e.g., Competibacteraceae in surfacewater and Sulfurimonadaceae in pore water). We show that 17% of our viral MAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae, which we suggest are potential contributors to river carbon and nitrogen cycling via denitrification and nitrogen fixation. Together, these findings demonstrate that members of the surface water microbiome from this urban river are stable over multiple diurnal cycles. These temporal insights raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles.
Aerobic bacteria that degrade methylphosphonates and produce methane as a byproduct have emerged as key players in marine carbon and phosphorus cycles. Here, we present two new draft genome sequences of the genus Marivita that were assembled from metagenomes from hypersaline former industrial salterns and compare them to five other Marivita reference genomes. Phylogenetic analyses suggest that both of these metagenome-assembled genomes (MAGs) represent new species in the genus. Average nucleotide identities to the closest taxon were <85%. The MAGs were assembled with SPAdes, binned with MetaBAT, and curated with scaffold extension and reassembly. Both genomes contained the phnCDEGHIJLMP suite of genes encoding the full C-P lyase pathway of methylphosphonate degradation and were significantly more abundant in two former industrial salterns than in nearby reference and restored wetlands, which have lower salinity levels and lower methane emissions than the salterns. These organisms contain a variety of compatible solute biosynthesis and transporter genes to cope with high salinity levels but harbor only slightly acidic proteomes (mean isoelectric point of 6.48).
We report the first discovery of a thick-disk planet, LHS 1815b (TOI-704b, TIC 260004324), detected in the Transiting Exoplanet Survey Satellite (TESS) survey. LHS 1815b transits a bright (V = 12.19 mag, K = 7.99 mag) and quiet M dwarf located 29.87 ± 0.02 pc away with a mass of 0.502 ± 0.015 M {sub ⊙} and a radius of 0.501 ± 0.030 R {sub ⊙}. We validate the planet by combining space- and ground-based photometry, spectroscopy, and imaging. The planet has a radius of 1.088 ± 0.064 R {sub ⊕} with a 3σ mass upper limit of 8.7 M {sub ⊕}. We analyze the galactic kinematics and orbit of the host star LHS 1815 and find that it has a large probability (P {sub thick}/P {sub thin} = 6482) to be in the thick disk with a much higher expected maximal height (Z {sub max} = 1.8 kpc) above the Galactic plane compared with other TESS planet host stars. Future studies of the interior structure and atmospheric properties of planets in such systems using, for example, the upcoming James Webb Space Telescope, can investigate the differences in formation efficiency and evolution for planetary systems between different Galactic components (thick disks, thin disks, and halo).
The Dark Energy Spectroscopic Instrument Legacy Surveys, a combination of three ground-based imaging surveys, have mapped 16,000 deg{sup 2} in three optical bands (g, r, and z) to a depth 1–2 mag deeper than the Sloan Digital Sky Survey. Our work addresses one of the major challenges of wide-field imaging surveys conducted at ground-based observatories: the varying depth that results from varying observing conditions at Earth-bound sites. To mitigate these effects, the Legacy Surveys (the Dark Energy Camera Legacy Survey, or DECaLS; the Mayall z-band Legacy Survey, or MzLS; and the Beiijing-Arizona Sky Survey, or BASS) employed a unique strategy to dynamically adjust the exposure times as rapidly as possible in response to the changing observing conditions. We present the tiling and observing strategies used by the first two of these surveys. We demonstrate that the tiling and dynamic observing strategies jointly result in a more uniform-depth survey that has higher efficiency for a given total observing time compared with the traditional approach of using fixed exposure times.
Detections of massive stars in the direction of the H ii region CS 78 in NGC 6334 and of G332.809−0.132 are here presented. The region covered by the G332.809−0.132 complex coincides with the RCW 103 stellar association. In its core (40′ in radius), approximately 110 OB candidate stars (K {sub s} < 10 mag and 0.4 < A{sub K{sub s}} < 1.6 mag) were identified using 2MASS, DENIS, and GLIMPSE data. This number of OB stars accounts for more than 50% of the observed number of Lyman continuum photons from this region. Medium-resolution K-band spectra were obtained for seven early types, including one WN 8 star and one Ofpe/WN 9 star; the latter is located near the RCW 103 remnant and its luminosity is consistent with a distance of ≈3 kpc. The area analyzed encloses 9 of the 34 OB stars previously known in RCW 103, as well as IRAS 16115−5044, which we reclassify as a candidate luminous blue variable. The line of sight is particularly interesting, crossing three spiral arms; a molecular cloud at −50 (with RCW 103 in the Scutum-Crux arm) and another at −90 km s{sup −1} (in the Norma arm) are detected, both rich in massive stars and supernova remnants. We also report the detection of a B supergiant as the main ionizing source of CS 78, 2MASS J17213513−3532415. Medium-resolution H- and K-band spectra display H i and He i lines, as well as Fe ii lines. By assuming a distance of 1.35 kpc, we estimate a bolometric magnitude of −6.16, which is typical of supergiants.
We present the serendipitous discovery of a low optical-luminosity nova occurring in a D-type symbiotic binary star system in the Milky Way. We lay out the extensive archival data alongside new follow-up observations related to the stellar object CN Cha in the constellation of Chamaeleon. The object had long period (250 days), high amplitude (3 mag) optical variability in its recent past, preceding an increase in optical brightness by 8 magnitudes and a persistence at this brightness for about 3 yr, followed by a period of 1.4 mag yr{sup −1} dimming. The object’s current optical luminosity seems to be dominated by Hα emission, which also exhibits blueshifted absorption (a P-Cygni-like profile). After consideration of a number of theories to explain these myriad observations, we determine that CN Cha is most likely a symbiotic (an evolved-star–white-dwarf binary) system that has undergone a long-duration, low optical brightness, nova, placing it squarely in the class of so-called “slow novae,” of which there are only a few known examples. The duration of the optical plateau in CN Cha would make it the shortest timescale plateau of any known slow symbiotic novae.
We report the discovery of two transiting Neptunes by the HATSouth survey. The planet HATS-37Ab has a mass of 0.099±0.042 M{sub J} (31.5 ± 13.4 M {sub ⊕}) and a radius of 0.606±0.016 R{sub J}, and is on a P=4.3315 day orbit around a V=12.266±0.030 mag, 0.843{sub −0.012}{sup +0.017} M{sub ⊙} star with a radius of 0.877{sub −0.012}{sup +0.019} R{sub ⊙}. We also present evidence that the star HATS-37A has an unresolved stellar companion HATS-37B, with a photometrically estimated mass of 0.654±0.033 M{sub ⊙}. The planet HATS-38b has a mass of 0.074±0.011 M{sub J} (23.5 ± 3.5 M {sub ⊕}) and a radius of 0.614±0.017 R{sub J}, and is on a P=4.3750 day orbit around a V=12.411±0.030 mag, 0.890{sub −0.012}{sup +0.016} M{sub ⊙} star with a radius of 1.105±0.016 R{sub ⊙}. Both systems appear to be old, with isochrone-based ages of 11.46{sub −1.45}{sup +0.79} Gyr, and 11.89±0.60 Gyr, respectively. Both HATS-37Ab and HATS-38b lie in the Neptune desert and are thus examples of a population with a low occurrence rate. They are also among the lowest-mass planets found from ground-based wide-field surveys to date.
In this paper, we analyze the light variations of KIC 10975348 using photometric data delivered from the Kepler mission. This star is exceptionally faint (K {sub p} = 18.6 mag) compared to most well-studied δ Scuti stars. The Fourier analysis of the short-cadence data (i.e., Q14, Q15, and Q16, spanning 220 days) reveals that the variations are dominated by the strongest mode with a frequency of F0 = 10.231899 day{sup −1}, which is compatible with that obtained from RATS–Kepler. The other two independent modes with F1 (=13.4988 day{sup −1}) and F2 (=19.0002 day{sup −1}) are newly detected and have amplitudes two orders of magnitude smaller than F0. We note that, for the first time, this star is identified to be a high-amplitude δ Sct (HADS) star with an amplitude of about 0.7 mag, and the lower ratio of F0/F1 = 0.758 suggests that it might be a metal-rich variable star. The frequency F2 may be a third overtone mode, suggesting that this target might be a new radial triple-mode HADS star. We perform an O − C analysis using 1018 newly determined times of maximum light and derive an ephemeris formula of T {sub max} = 2456170.241912(0)+0.097734(1) × E. The O − C diagram shows that the pulsation period of KIC 10975348 seems to show no obvious change, which is in contrast to that of the majority of HADS stars. The possible cause of that may be due to the current short time span of the observations. To verify its possible period variations, regular observation from space with a longer time span in the future is needed.
In deep near-infrared imaging of the low-metallicity ([O/H] = −0.7 dex) H ii region Sh 2-127 (S127) with Subaru/MOIRCS, we detected two young clusters with 413 members (S127A) in a slightly extended H ii region and another with 338 members (S127B) in a compact H ii region. The limiting magnitude was K = 21.3 mag (10σ), corresponding to a mass detection limit of ∼0.2 M{sub ⊙}. These clusters are an order of magnitude larger than previously studied young low-metallicity clusters and larger than the majority of solar neighborhood young clusters. Fits to the K-band luminosity functions indicate very young cluster ages of 0.5 Myr for S127A and 0.1–0.5 Myr for S127B, consistent with the large extinction (up to A {sub V} ≃ 20 mag) from thick molecular clouds and the presence of a compact H ii region and class I source candidates, and suggest that the initial mass function (IMF) of the low-metallicity clusters is indistinguishable from typical solar neighborhood IMFs. Disk fractions of 28% ± 3% for S127A and 40% ± 4% for S127B are significantly lower than those of similarly aged solar neighborhood clusters (∼50%–60%). The disk fraction for S127B is higher than those of previously studied low-metallicity clusters (<30%), probably due to S127B’s age. This suggests that a large fraction of very young stars in low-metallicity environments have disks, but the disks are lost on a very short timescale. These results are consistent with our previous studies of low-metallicity star-forming regions, suggesting that a solar neighborhood IMF and low disk fraction are typical characteristics for low-metallicity regions, regardless of cluster scales.
We present the time-dependent properties of a poorly known OH/IR star, IRAS 18278+0931 (hereafter IRAS 18+09), toward the Ophiuchus constellation. We have carried out long-term optical/near-infrared photometric and spectroscopic observations to study the object. From optical R- and I-band light curves, the period of IRAS 18+09 is estimated to be 575 ± 30 days and the variability amplitudes range from ΔR ∼ 4.0 mag to ΔI ∼ 3.5 mag. From the standard period–luminosity relations, the distance (D) to the object, 4.0 ± 1.3 kpc, is estimated. Applying this distance in the radiative transfer model, the spectral energy distribution is constructed from multiwavelength photometric and IRAS-LRS spectral data, which provide the luminosity, optical depth, and gas mass-loss rate of the object to be 9600 ± 500 L {sub ⊙}, 9.1 ± 0.6 at 0.55 μm, and 1.0 × 10{sup −6} M {sub ⊙} yr{sup −1}, respectively. The current mass of the object is inferred to be in the range 1.0−1.5 M {sub ⊙} assuming solar metallicity. Notably, the temporal variation of atomic and molecular features (e.g., TiO, Na i, Ca i, CO, H{sub 2}O) over the pulsation cycle of the OH/IR star illustrates the sensitivity of the spectral features to the dynamical atmosphere as observed in pulsating AGB stars.
We make use of individual (epoch) detection data from the Pan-STARRS “3π” survey for 2863 optical ICRF3 counterparts in the five wavelength bands g, r, i, z, and y, published as part of the Data Release 2. A dedicated method based on the Functional Principal Component Analysis is developed for these sparse and irregularly sampled data. With certain regularization and normalization constraints, it allows us to obtain uniform and compatible estimates of the variability amplitudes and average magnitudes between the passbands and objects. We find that the starting assumption of affinity of the light curves for a given object at different wavelengths is violated for several percent of the sample. The distributions of rms variability amplitudes are strongly skewed toward small values, peaking at ∼0.1 mag with tails stretching to 2 mag. Statistically, the lowest variability is found for the r band and the largest for the reddest y band. A small “brighter-redder” effect is present, with amplitudes in y greater than amplitudes in g in 57% of the sample. The variability versus redshift dependence shows a strong decline with z toward redshift 3, which we interpret as the time dilation of the dominant time frequencies. The colors of radio-loud ICRF3 quasars are correlated with redshift in a complicated, wavy pattern governed by the emergence of brightest emission lines within the five passbands.