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Rapid organic carbon spiraling in a headwater stream linked with streamflow, biogeochemistry, and canopy phenology
Headwater streams are abundant worldwide and important to global biogeochemical cycles, serving as critical processors and transporters of C. C spiraling is a useful way to understand the retention and mineralization of organic C (OC) in streams. However, analyses of seasonal and interannual variability in OC spiraling are currently limited. In this study, we aimed to understand the temporal patterns and driving mechanisms of OC spiraling, which will inform our understanding of future OC changes under climate change. We used 7 y of daily data in a small headwater stream (Walker Branch, Tennessee, USA) to assess seasonal and interannual variability in OC spiraling length (S OC ) and mineralization velocity (v fOC ), as well as their potential related variables. On average, S OC in Walker Branch was ~10× shorter than in previously studied small streams, indicating strong connections between the water column and the benthic environment where OC mineralization mostly takes place. OC spiraling was faster during the more biologically active periods of spring and autumn compared with more elongated OC spiraling in summer and winter, when OC retention was lower and downstream transport was higher. Gross primary production (GPP) was most strongly related to S OC and v fOC . Photosynthetically active radiation (PAR) and NO 3 − were also positively and negatively related to v fOC , respectively. Trends toward earlier and longer canopy cover and reduced GPP and PAR may result in longer S OC and slower v fOC , reducing localized instream processing of OC and potentially shunting more OC downstream. However, long-term observations indicate reduced NO 3 − at Walker Branch, suggesting opposing effects to those of GPP and PAR, leading to faster v fOC and greater OC retention. Time-series analyses of OC spiraling in streams can enhance our understanding of current and future responses of OC processing and downstream transport to climate change, as well as implications for downstream OC dynamics.
Linking emergent phenomena and broken symmetries through one-dimensional objects and their dot/cross products
Abstract The symmetry of the whole experimental setups, including specific sample environments and measurables, can be compared with that of specimens for observable physical phenomena. We, first, focus on one-dimensional (1D) experimental setups, independent from any spatial rotation around one direction, and show that eight kinds of 1D objects (four; vector-like, the other four; director-like), defined in terms of symmetry, and their dot and cross products are an effective way for the symmetry consideration. The dot products form a Z 2 × Z 2 × Z 2 group with Abelian additive operation, and the cross products form a Z 2 × Z 2 group with Abelian additive operation or Q 8 , a non-Abelian group of order eight, depending on their signs. Those 1D objects are associated with characteristic physical phenomena. When a 3D specimen has symmetry operational similarity (SOS) with (identical or lower, but not higher, symmetries than) an 1D object with a particular phenomenon, the 3D specimen can exhibit the phenomenon. This SOS approach can be a transformative and unconventional avenue for symmetry-guided materials designs and discoveries.
Linking repeat lidar with Landsat products for large scale quantification of fire-induced permafrost thaw settlement in interior Alaska
The permafrost–fire–climate system has been a hotspot in research for decades under a warming climate scenario. Surface vegetation plays a dominant role in protecting permafrost from summer warmth, thus, any alteration of vegetation structure, particularly following severe wildfires, can cause dramatic top–down thaw. A challenge in understanding this is to quantify fire-induced thaw settlement at large scales (>1000 km 2 ). In this study, we explored the potential of using Landsat products for a large-scale estimation of fire-induced thaw settlement across a well-studied area representative of ice-rich lowland permafrost in interior Alaska. Six large fires have affected ~1250 km 2 of the area since 2000. We first identified the linkage of fires, burn severity, and land cover response, and then developed an object-based machine learning ensemble approach to estimate fire-induced thaw settlement by relating airborne repeat lidar data to Landsat products. The model delineated thaw settlement patterns across the six fire scars and explained ~65% of the variance in lidar-detected elevation change. Our results indicate a combined application of airborne repeat lidar and Landsat products is a valuable tool for large scale quantification of fire-induced thaw settlement.
Methane emission hotspots in a boreal forest-fen mosaic potentially linked to deep taliks
Permafrost thaw is transforming boreal forests into mosaics of wetlands and drier uplands. Topographic controls on hydrological and ecological conditions impact methane (CH 4 ) fluxes, contributing to uncertainty in local and regional CH 4 budgets and underlying drivers. The objective of this study was to explore CH 4 fluxes and their drivers in a transitioning boreal forest-fen ecosystem (Goldstream Valley, Alaska, USA). This landscape is characterized by thawing discontinuous permafrost and heterogeneous mosaics of fens, collapse-scar channels, and small mounds of permafrost soils. From a survey in July 2021, observed chamber CH4 fluxes included fen areas with intermediate to very high emissions (29.8–635.3 mg CH 4 m −2 d −1 ), clustered locations with CH 4 uptake (−2.11 to −0.7 mg CH 4 m −2 d −1 ), and three anomalous emission hotspots (342.4–772.4 mg CH 4 m −2 d −1 ) that were located near samples with lower emissions. Some surface and near-surface variables partially explained the spatial variation in CH 4 flux. Log-transformed CH 4 flux had a positive linear relationship with soil moisture at 20 cm depth ( R 2 = 0.31, p -value < 1e-5) and negative linear relationships with microtopography ( R 2 = 0.13, p -value < 0.006) and slope ( R 2 = 0.28, p -value < 2e-5). Methane emissions generally occurred in flat, wet, graminoid-dominated fens, whereas CH 4 uptake occurred on permafrost mounds dominated by feather mosses and woody vegetation. However, the CH 4 hotspots occurred on drier, slightly sloped locations with low or undetectable near-surface methanogen abundance, suggesting that CH 4 was produced in deeper soils. When the hotspot samples were omitted, log-transformed CH 4 flux had a positive linear relationship with near-surface methanogen abundance ( R 2 = 0.29, p -value = 0.0023), and stronger linear relationships with soil moisture, slope, and soil macronutrient concentrations. Our findings suggest that some CH 4 emission hotspots could arise from CH 4 in deep taliks. The inference that methanogenesis occurs in deep taliks was strengthened by the identification of intrapermafrost taliks across the study area using low-frequency geophysical induction. This study assesses surface spatial heterogeneity in the context of subsurface permafrost conditions and highlights the complexity of CH 4 flux patterns in transitioning forest-wetland ecosystems. To better inform regional CH 4 budgets, further research is needed to understand the spatial distribution of terrestrial CH 4 hotspots and to resolve their surface, near-surface, and subsurface drivers.
Linking stem rehydration kinetics to hydraulic traits using a novel method and mechanistic model
Background: Despite the recognized importance of hydraulic capacitance as a mechanism used by plants to maintain hydraulic functioning during high transpiration, characterizing the dynamics of capacitance remains a challenge. Methods: For this work, we used a novel ‘two-balance method’ to investigate relationships between stem rehydration kinetics and other hydraulic traits in multiple tree species, and we developed a model to explore stem rehydration kinetics further. Key Results: We found that: (1) rehydration time constants and the amount of water uptake occurring during rehydration differed significantly across species; (2) time constants did not change with declining water potential (Ψ), while water uptake increased at lower Ψ in some species; (3) longer time constants were associated with lower wood density, higher capacitance and less negative stem pressures causing 50 % loss of hydraulic conductivity (P 50 ); (4) greater water uptake occurred in stems with lower wood density and less negative P 50 values; and (5) the model could estimate the total hydraulic resistance of the rehydration path, which cannot be measured directly. Conclusions: Overall, the two-balance method can be used to examine rehydration dynamics quickly and thoroughly in detached woody stems. This method has the potential to improve our understanding of how capacitance functions across tree species, which is an often-overlooked component of whole-plant hydraulics.
ORT: a workflow linking genome-scale metabolic models with reactive transport codes
Abstract Motivation Nutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As ‘omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed. Results We propose a workflow (‘Omics to Reactive Transport—ORT) for utilizing metagenomic and environmental data to describe the effect of microbiological processes in macroscopic reactive transport models. This workflow utilizes and couples two open-source software packages: KBase (a software platform for systems biology) and PFLOTRAN (a reactive transport modeling code). We describe the architecture of ORT and demonstrate an implementation using metagenomic and geochemical data from a river system. Our demonstration uses microbiological drivers of nitrification and denitrification to predict nitrogen cycling patterns which agree with those provided with generalized stoichiometries. While our example uses data from a single measurement, our workflow can be applied to spatiotemporal metagenomic datasets to allow for iterative coupling between KBase and PFLOTRAN. Availability and implementation Interactive models available at https://pflotranmodeling.paf.subsurfaceinsights.com/pflotran-simple-model/. Microbiological data available at NCBI via BioProject ID PRJNA576070. ORT Python code available at https://github.com/subsurfaceinsights/ort-kbase-to-pflotran. KBase narrative available at https://narrative.kbase.us/narrative/71260 or static narrative (no login required) at https://kbase.us/n/71260/258. Supplementary information Supplementary data are available at Bioinformatics online.
Identification of genetic interactions with priB links the PriA/PriB DNA replication restart pathway to double-strand DNA break repair in Escherichia coli
Collisions between DNA replication complexes (replisomes) and impediments such as damaged DNA or proteins tightly bound to the chromosome lead to premature dissociation of replisomes at least once per cell cycle in Escherichia coli. Left unrepaired, these events produce incompletely replicated chromosomes that cannot be properly partitioned into daughter cells. DNA replication restart, the process that reloads replisomes at prematurely terminated sites, is therefore essential in E. coli and other bacteria. Three replication restart pathways have been identified in E. coli: PriA/PriB, PriA/PriC, and PriC/Rep. A limited number of genetic interactions between replication restart and other genome maintenance pathways have been defined, but a systematic study placing replication restart reactions in a broader cellular context has not been performed. We have utilized transposon-insertion sequencing to identify new genetic interactions between DNA replication restart pathways and other cellular systems. Known genetic interactors with the priB replication restart gene (uniquely involved in the PriA/PriB pathway) were confirmed and several novel priB interactions were discovered. Targeted genetic and imaging-based experiments with priB and its genetic partners revealed significant double-strand DNA break accumulation in strains with mutations in dam, rep, rdgC, lexA, or polA. Modulating the activity of the RecA recombinase partially suppressed the detrimental effects of rdgC or lexA mutations in ΔpriB cells. Taken together, our results highlight roles for several genes in double-strand DNA break homeostasis and define a genetic network that facilitates DNA repair/processing upstream of PriA/PriB-mediated DNA replication restart in E. coli.
Microbial community dynamics in the soil-root continuum are linked with plant species turnover during secondary succession
Grazing exclusion and land abandonment are commonly adopted to restore degraded ecosystems in semiarid and arid regions worldwide. However, the temporal variation in the soil- versus root-associated microbiome over plant species turnover during secondary succession has rarely been quantified. Using the chronosequence restored from fenced grassland and abandoned farmlands on the Loess Plateau of China, we characterized the dynamics of the soil- and root-associated microbiome of host plant with different dominance statuses during secondary succession from 0 to 40 years. Our results revealed that the root microhabitat, the host plant and their interactions were the main contributors to the bacterial community shift (R 2 = 15.5%, 8.1%, and 22.3%, respectively), and plant interspecies replacement had a greater effect on the shift in the root-associated microbial community than intraspecies replacement did during succession. The root-associated bacterial community of pioneer plants was particularly responsive to succession, especially the endosphere community. Endosphere microbial diversity was positively correlated with host plant coverage change, and the diversity and abundance of taxon recruitment into the endosphere of pioneer plants from the surrounding environment decreased as succession progressed. The community assembly processes also indicated that the endosphere microbiota are strongly selected in younger host plants, whereas stochastic processes dominate in aged host plants. Our study provides evidence of the unique response of the root-associated microbiome to the replacement of plant species during secondary succession, and the function of endosphere microbes should be considered when studying plant–microbe feedback.
Linezolid-resistant (Tn 6246 :: fexB - poxtA ) Enterococcus faecium strains colonizing humans and bovines on different continents: similarity without epidemiological link
Abstract Objectives poxtA is the most recently described gene conferring acquired resistance to linezolid, a relevant antibiotic for treating enterococcal infections. We retrospectively screened for poxtA in diverse enterococci and aimed to characterize its genetic/genomic contexts. Methods poxtA was screened by PCR in 812 enterococci from 458 samples (hospitals/healthy humans/wastewater/animals/retail food) obtained in Portugal/Angola/Tunisia (1996–2019). Antimicrobial susceptibility testing was performed for 13 antibiotics (EUCAST/CLSI). poxtA stability (∼500 generations), transfer (filter mating), clonality (SmaI-PFGE) and location (S1-PFGE/hybridization) were tested. WGS (Illumina-HiSeq) was performed for clonal representatives. Results poxtA was detected in Enterococcus faecium from six samples (1.3%): a healthy human (rectal swab) in Porto, Portugal (ST32/2001); four farm cows (milk) in Mateur, Tunisia (ST1058/2015); and a hospitalized patient (faeces) in Matosinhos, Portugal (ST1058/2015). All expressed resistance to linezolid (MIC = 8 mg/L), chloramphenicol, tetracycline and erythromycin, with variable resistance to ciprofloxacin and streptomycin. ST1058-poxtA-carrying isolates from Tunisia and Portugal differed by two SNPs and had similar plasmid content. poxtA, located in an IS1216-flanked Tn6246-like element, co-hybridized with fexB on one or more plasmids per isolate (one to three plasmids of 30–100 kb), was stable after several generations and transferred only from ST1058. ST1058 strains carried resistance/virulence genes (Efmqnr/acm) possibly induced under selective quinolone treatment. Conclusions poxtA has been circulating in Portugal since at least 2001, corresponding to the oldest description worldwide to date. We also extend the reservoir of poxtA to bovines. The similar linezolid-resistant poxtA-carrying strains colonizing humans and livestock on different continents, and without a noticeable relationship, suggests a recent transmission event or convergent evolution of E. faecium populations in different hosts and geographic regions.
Links between autophagy and lipid droplet dynamics
Abstract Autophagy is a catabolic process in which cytoplasmic components are delivered to vacuoles or lysosomes for degradation and nutrient recycling. Autophagy-mediated degradation of membrane lipids provides a source of fatty acids for the synthesis of energy-rich, storage lipid esters such as triacylglycerol (TAG). In eukaryotes, storage lipids are packaged into dynamic subcellular organelles, lipid droplets. In times of energy scarcity, lipid droplets can be degraded via autophagy in a process termed lipophagy to release fatty acids for energy production via fatty acid β-oxidation. On the other hand, emerging evidence suggests that lipid droplets are required for the efficient execution of autophagic processes. Here, we review recent advances in our understanding of metabolic interactions between autophagy and TAG storage, and discuss mechanisms of lipophagy. Free fatty acids are cytotoxic due to their detergent-like properties and their incorporation into lipid intermediates that are toxic at high levels. Thus, we also discuss how cells manage lipotoxic stresses during autophagy-mediated mobilization of fatty acids from lipid droplets and organellar membranes for energy generation.
Stellar angular momentum distribution linked to galaxy morphology
ABSTRACT We study the spatially resolved stellar specific angular momentum j* in a high-quality sample of 24 Calar Alto Legacy Integral Field Area galaxies covering a broad range of visual morphology, accounting for stellar velocity and velocity dispersion. The shape of the spaxelwise probability density function of normalized s = j*/j*mean, PDF(s), deviates significantly from the near-universal initial distribution expected of baryons in a dark matter halo and can be explained by the expected baryonic effects in galaxy formation that remove and redistribute angular momentum. Further we find that the observed shape of the PDF(s) correlates significantly with photometric morphology, where late-type galaxies have a PDF(s) that is similar to a normal distribution, whereas early types have a strongly skewed PDF(s) resulting from an excess of low-angular momentum material. Galaxies that are known to host pseudo-bulges (bulge Sérsic index nb < 2.2) tend to have less skewed bulge PDF(s), with skewness (b1rb) ≲ 0.8. The PDF(s) encodes both kinematic and photometric information and appears to be a robust tracer of morphology. Its use is motivated by the desire to move away from traditional component-based classifications which are subject to observer bias, to classification on a galaxy’s fundamental (stellar mass and angular momentum) properties. In future, PDF(s) may also be useful as a kinematic decomposition tool.
Dark matter density profiles in dwarf galaxies: linking Jeans modelling systematics and observation
ABSTRACT The distribution of dark matter in dwarf galaxies can have important implications on our understanding of galaxy formation as well as the particle physics properties of dark matter. However, accurately characterizing the dark matter content of dwarf galaxies is challenging due to limited data and complex dynamics that are difficult to accurately model. In this paper, we apply spherical Jeans modelling to simulated stellar kinematic data of spherical, isotropic dwarf galaxies with the goal of identifying the future observational directions that can improve the accuracy of the inferred dark matter distributions in the Milky Way dwarf galaxies. We explore how the dark matter inference is affected by the location and number of observed stars as well as the line-of-sight velocity measurement errors. We use mock observation to demonstrate the difficulty in constraining the inner core/cusp of the dark matter distribution with data sets of fewer than 10 000 stars. We also demonstrate the need for additional measurements to make robust estimates of the expected dark matter annihilation signal strength. For the purpose of deriving robust indirect detection constraints, we identify Ursa Major II, Ursa Minor, and Draco as the systems that would most benefit from additional stars being observed.
Model-independent constraints on Ωm and H ( z ) from the link between geometry and growth
ABSTRACT We constrain the expansion history of the Universe and the cosmological matter density fraction in a model-independent way by exclusively making use of the relationship between background and perturbations under a minimal set of assumptions. We do so by employing a Gaussian process to model the expansion history of the Universe from present time to the recombination era. The expansion history and the cosmological matter density are then constrained using recent measurements from cosmic chronometers, Type-Ia supernovae, baryon acoustic oscillations, and redshift-space distortion data. Our results show that the evolution in the reconstructed expansion history is compatible with the Planck 2018 prediction at all redshifts. The current data considered in this study can constrain a Gaussian process on H(z) to an average $9.4 {{\ \rm per\ cent}}$ precision across redshift. We find Ωm = 0.224 ± 0.066, lower but statistically compatible with the Planck 2018 cosmology. Finally, the combination of future DESI measurements with the CMB measurement considered in this work holds the promise of $8 {{\ \rm per\ cent}}$ average constraints on a model-independent expansion history as well as a five-fold tighter Ωm constraint using the methodology developed in this work.
MaNGA DynPop – II. Global stellar population, gradients, and star-formation histories from integral-field spectroscopy of 10K galaxies: link with galaxy rotation, shape, and total-density gradients
ABSTRACT This is the second paper of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) Dynamics and stellar Population (DynPop) series, which analyses the global stellar population, radial gradients, and non-parametric star-formation history of ∼10K galaxies from the MaNGA Survey final data release 17 and relates them with dynamical properties of galaxies. We confirm the correlation between the stellar population properties and the stellar velocity dispersion σe, but also find that younger galaxies are more metal-poor at fixed σe. Stellar age, metallicity, and mass-to-light ratio (M*/L) all decrease with increasing galaxy rotation, while their radial gradients become more negative (i.e. lower value at the outskirts). The exception is the slow rotators, which also appear to have significantly negative metallicity gradients, confirming the mass–metallicity gradient correlation. Massive disc galaxies in the green valley, on the $(\sigma _{\rm e},\rm age)$ plane, show the most negative age and metallicity gradients, consistent with their old central bulges surrounded by young star-forming discs and metal-poor gas accretion. Galaxies with high σe, steep total mass-density slope, low dark matter fraction, high M*/L, and high metallicity have the highest star-formation rate at earlier times, and are currently quenched. We also discover a population of low-mass star-forming galaxies with low rotation but physically distinct from the massive slow rotators. A catalogue of these stellar population properties is provided publicly.
A resolved study of the inner regions of nearby galaxies with an excess of young massive stars: missing link in the AGN–starburst connection?
ABSTRACT We have selected galaxies with very high levels of H α emission (EQW(H α) >700 Å.) in their central regions from the final data release of the MaNGA survey. Our study focuses on 14 very well-resolved nearby galaxies with stellar masses in the range 9.5 < log M*/(M⊙) < 11.5. We investigate a variety of procedures for selecting galaxy regions that are likely to harbour excess populations of young massive stars, finding that selection in the 2D space of extinction-corrected H α EQW and [S iii]/[S ii] line ratio produces the best results. By comparing stacked spectra covering these regions with stacked spectra covering normal starburst regions with 100 Å<EQW(H α) <200 Å, we obtain the following main results: (1) Clear signatures of excess Wolf–Rayet stars are found in half of the H α excess regions, (2) galaxy regions containing excess Wolf–Rayet stars are more often associated with the presence of high-ionization emission lines characteristic of accreting black holes. Excess [Ne iii] is detected in 4 out of 8 of the WR regions and there are tentative [Fe x] detections in 2 galaxies. (3) Regions of the galaxy with excess Wolf–Rayet stars are located where the interstellar medium has larger ionized gas turbulent velocities and higher neutral gas overdensities. We make a first attempt to constrain changes in the high-mass end of the stellar initial mass function (IMF) using the HR-pyPopStar evolutionary population synthesis models that include high-wavelength-resolution theoretical atmosphere libraries for Wolf–Rayet stars.
Linking transients to their host galaxies – II. A comparison of host galaxy properties and rate dependencies across supernova types
ABSTRACT We use the latest data set of supernova (SN) host galaxies to investigate how the host properties – stellar mass, star formation rate (SFR), metallicity, absolute magnitude, and colour–differ across SN types, with redshift-driven selection effects controlled. SN Ib and Ic host galaxies, on average, are more massive, metal-rich, and redder than SN II hosts. For subtypes, SN Ibn and Ic-BL have bluer hosts than their normal SN Ib and Ic siblings; SN IIb has consistent host properties with SN Ib, while hosts of SN IIn are more metal-rich than those of SN II. Hydrogen-deficient superluminous SNe feature bluer and lower luminosity hosts than most subtypes of core-collapse supernova (CC SN). Assuming simple proportionality of CC SN rates and host SFRs does not recover the observed mean host properties; either a population of long-lived progenitors or a metallicity-dependent SN production efficiency better reproduces the observed host properties. Assuming the latter case, the rates of SN II are insensitive to host metallicity, but the rates of SN Ib and Ic are substantially enhanced in metal-rich hosts by a factor of $\sim 10$ per dex increase in metallicity. Hosts of SN Ia are diverse in their observed properties; subtypes including SN Ia-91T, Ia-02cx, and Ia-CSM prefer star-forming hosts, while subtypes like SN Ia-91bg and Ca-rich prefer quiescent hosts. The rates of SN Ia-91T, Ia-02cx, and Ia-CSM are closely dependent on, or even proportional to, their host SFRs, indicating relatively short-lived progenitors. Conversely, the rates of SN Ia-91bg and Ca-rich transients are proportional to the total stellar mass, favouring long-lived progenitors.
Phosphate Limitation Responses in Marine Green Algae Are Linked to Reprogramming of the tRNA Epitranscriptome and Codon Usage Bias
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 availability scenarios, transcriptomic analyses revealed altered expression of transfer RNA modification enzymes and biased codon usage of transcripts more abundant during phosphate-limiting versus phosphate-replete conditions, consistent with the role of transfer RNA modifications in regulating codon recognition. To associate the observed shift in the expression of the transfer RNA modification enzyme complement with the transfer RNAs encoded by M. commoda, we also determined the transfer RNA 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 phosphate 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 transfer RNA 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 downregulated protein-encoding genes to the cell biological controls that underpin acclimation to changing environmental conditions.