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At least 847 records · Page 47

Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism

Abstract Background Crassulacean acid metabolism (CAM), a specialized mode of photosynthesis, enables plant adaptation to water-limited environments and improves photosynthetic efficiency via an inorganic carbon-concentrating mechanism. Kalanchoë fedtschenkoi is an obligate CAM model featuring a relatively small genome and easy stable transformation. However, the molecular responses to light quality and intensity in CAM plants remain understudied. Results Here we present a genome-wide expression atlas of K. fedtschenkoi plants grown under 12 h/12 h photoperiod with different light quality (blue, red, far-red, white light) and intensity (0, 150, 440, and 1,000 μmol m–2 s–1) based on RNA sequencing performed for mature leaf samples collected at dawn (2 h before the light period) and dusk (2 h before the dark period). An eFP web browser was created for easy access of the gene expression data. Based on the expression atlas, we constructed a light-responsive co-expression network to reveal the potential regulatory relationships in K. fedtschenkoi. Measurements of leaf titratable acidity, soluble sugar, and starch turnover provided metabolic indicators of the magnitude of CAM under the different light treatments and were used to provide biological context for the expression dataset. Furthermore, CAM-related subnetworks were highlighted to showcase genes relevant to CAM pathway, circadian clock, and stomatal movement. In comparison with white light, monochrome blue/red/far-red light treatments repressed the expression of several CAM-related genes at dusk, along with a major reduction in acid accumulation. Increasing light intensity from an intermediate level (440 μmol m-2 s-1) of white light to a high light treatment (1,000 μmol m–2 s–1) increased expression of several genes involved in dark CO2 fixation and malate transport at dawn, along with an increase in organic acid accumulation. Conclusions This study provides a useful genomics resource for investigating the molecular mechanism underlying the light regulation of physiology and metabolism in CAM plants. Our results support the hypothesis that both light intensity and light quality can modulate the CAM pathway through regulation of CAM-related genes in K. fedtschenkoi.

59 BASIC BIOLOGICAL SCIENCES↗

Accelerating Biological Insight for Understudied Genes

Synopsis The rapid expansion of genome sequence data is increasing the discovery of protein-coding genes across all domains of life. Annotating these genes with reliable functional information is necessary to understand evolution, to define the full biochemical space accessed by nature, and to identify target genes for biotechnology improvements. The majority of proteins are annotated based on sequence conservation with no specific biological, biochemical, genetic, or cellular function identified. Recent technical advances throughout the biological sciences enable experimental research on these understudied protein-coding genes in a broader collection of species. However, scientists have incentives and biases to continue focusing on well documented genes within their preferred model organism. This perspective suggests a research model that seeks to break historic silos of research bias by enabling interdisciplinary teams to accelerate biological functional annotation. We propose an initiative to develop coordinated projects of collaborating evolutionary biologists, cell biologists, geneticists, and biochemists that will focus on subsets of target genes in multiple model organisms. Concurrent analysis in multiple organisms takes advantage of evolutionary divergence and selection, which causes individual species to be better suited as experimental models for specific genes. Most importantly, multisystem approaches would encourage transdisciplinary critical thinking and hypothesis testing that is inherently slow in current biological research.

Zoology↗

Potential for functional divergence in ectomycorrhizal fungal communities across a precipitation gradient

Abstract Functional traits influence the assembly of microbial communities, but identifying these traits in the environment has remained challenging. We studied ectomycorrhizal fungal (EMF) communities inhabiting Populus trichocarpa roots distributed across a precipitation gradient in the Pacific Northwest, USA. We profiled these communities using taxonomic (meta-barcoding) and functional (metagenomic) approaches. We hypothesized that genes involved in fungal drought-stress tolerance and fungal mediated plant water uptake would be most abundant in drier soils. We were unable to detect support for this hypothesis; instead, the abundance of genes involved in melanin synthesis, hydrophobins, aquaporins, trehalose-synthases, and other gene families exhibited no significant shifts across the gradient. Finally, we studied variation in sequence homology for certain genes, finding that fungal communities in dry soils are composed of distinct aquaporin and hydrophobin gene sequences. Altogether, our results suggest that while EMF communities exhibit significant compositional shifts across this gradient, coupled functional turnover, at least as inferred using community metagenomics is limited. Accordingly, the consequences of these distinct EMF communities on plant water uptake remain critically unknown, and future studies targeting the expression of genes involved in drought stress tolerance are required.

59 BASIC BIOLOGICAL SCIENCES↗

Declines in ice cover are accompanied by light limitation responses and community change in freshwater diatoms

The rediscovery of diatom blooms embedded within and beneath the Lake Erie ice cover (2007–2012) ignited interest in psychrophilic adaptations and winter limnology. Subsequent studies determined the vital role ice plays in winter diatom ecophysiology as diatoms partition to the underside of ice, thereby fixing their location within the photic zone. Yet, climate change has led to widespread ice decline across the Great Lakes, with Lake Erie presenting a nearly “ice-free” state in several recent winters. It has been hypothesized that the resultant turbid, isothermal water column induces light limitation amongst winter diatoms and thus serves as a competitive disadvantage. To investigate this hypothesis, we conducted a physiochemical and metatranscriptomic survey that spanned spatial, temporal, and climatic gradients of the winter Lake Erie water column (2019–2020). Our results suggest that ice-free conditions decreased planktonic diatom bloom magnitude and altered diatom community composition. Diatoms increased their expression of various photosynthetic genes and iron transporters, which suggests that the diatoms are attempting to increase their quantity of photosystems and light-harvesting components (a well-defined indicator of light limitation). We identified two gene families which serve to increase diatom fitness in the turbid ice-free water column: proton-pumping rhodopsins (a potential second means of light-driven energy acquisition) and fasciclins (a means to “raft” together to increase buoyancy and co-locate to the surface to optimize light acquisition). With large-scale climatic changes already underway, our observations provide insight into how diatoms respond to the dynamic ice conditions of today and shed light on how they will fare in a climatically altered tomorrow.

54 ENVIRONMENTAL SCIENCES↗

Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12

Abstract Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests that corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community- and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.

58 GEOSCIENCES↗

Scarcity of fixed carbon transfer in a model microbial phototroph–heterotroph interaction

Although the green alga Chlamydomonas reinhardtii has long served as a reference organism, few studies have interrogated its role as a primary producer in microbial interactions. Here, we quantitatively investigated C. reinhardtii’s capacity to support a heterotrophic microbe using the established coculture system with Mesorhizobium japonicum, a vitamin B 12 -producing α-proteobacterium. Using stable isotope probing and nanoscale secondary ion mass spectrometry (nanoSIMS), we tracked the flow of photosynthetic fixed carbon and consequent bacterial biomass synthesis under continuous and diurnal light with single-cell resolution. We found that more 13 C fixed by the alga was taken up by bacterial cells under continuous light, invalidating the hypothesis that the alga’s fermentative degradation of starch reserves during the night would boost M. japonicum heterotrophy. 15 NH 4 assimilation rates and changes in cell size revealed that M. japonicum cells reduced new biomass synthesis in coculture with the alga but continued to divide—a hallmark of nutrient limitation often referred to as reductive division. Despite this sign of starvation, the bacterium still synthesized vitamin B 12 and supported the growth of a B 12 -dependent C. reinhardtii mutant. Finally, we showed that bacterial proliferation could be supported solely by the algal lysis that occurred in coculture, highlighting the role of necromass in carbon cycling. Collectively, these results reveal the scarcity of fixed carbon in this microbial trophic relationship (particularly under environmentally relevant light regimes), demonstrate B 12 exchange even during bacterial starvation, and underscore the importance of quantitative approaches for assessing metabolic coupling in algal–bacterial interactions.

59 BASIC BIOLOGICAL SCIENCES↗

Climate warming enhances biodiversity and stability of grassland soil phosphorus-cycling microbial communities

Abstract Climate warming poses significant challenges to global phosphorus sustainability, an essential component of Earth biogeochemistry cycling and water-food-energy nexus. Despite the crucial role of polyphosphate-accumulating organism as key functional microbial agents in phosphorus cycling, the impacts of global climate warming on polyphosphate accumulating organism communities remain largely enigmatic. This study investigates the effects of climate warming on the taxonomic, network, and functional profiles of soil bacterial polyphosphate-accumulating organisms, leveraging fluorescence-activated cell sorting and single-cell Raman spectroscopy. Climate warming enhances both taxonomic and functional biodiversity of polyphosphate-accumulating organisms via biotic interactions and environmental filtering, with observed functionality-biodiversity relationships supporting the functional redundancy theory. Furthermore, polyphosphate-accumulating organism network complexity and stability rise under warming with strengthened positive relationships, supporting stress gradient hypothesis and the belief that complexity begets stability. Finally, polyphosphate-accumulating organisms are significantly correlated to key ecosystem functioning in carbon and phosphorus cycling under warming. Our study suggests that preserving polyphosphate-accumulating organism communities is crucial for maintaining soil ecosystem functioning and sustainable phosphorus management in a warming world and opens avenues for predicting the responses of other functional microbial groups to climate change, beneficially or maliciously.

Environmental Sciences & Ecology↗

Phosphorolytic degradation of leaf starch via plastidic α-glucan phosphorylase leads to optimized plant growth and water use efficiency over the diel phases of Crassulacean acid metabolism

In plants with Crassulacean acid metabolism (CAM), it has been proposed that the requirement for nocturnal provision of phosphoenolpyruvate as a substrate for CO 2 uptake has resulted in a re-routing of chloroplastic starch degradation from the amylolytic route to the phosphorolytic route. To test this hypothesis, we generated and characterized four independent RNAi lines of the obligate CAM species Kalanchoë fedtschenkoi with a >10-fold reduction in transcript abundance of plastidic α-glucan phosphorylase (PHS1). The rPHS1 lines showed diminished nocturnal starch degradation, reduced dark CO 2 uptake, a reduction in diel water use efficiency (WUE), and an overall reduction in growth. A re-routing of starch degradation via the hydrolytic/amylolytic pathway was indicated by hyperaccumulation of maltose in all rPHS1 lines. Further examination indicated that whilst operation of the core circadian clock was not compromised, plasticity in modulating net dark CO 2 uptake in response to changing photoperiods was curtailed. The data show that phosphorolytic starch degradation is critical for efficient operation of the CAM cycle and for optimizing WUE. This finding has clear relevance for ongoing efforts to engineer CAM into non-CAM species as a means of boosting crop WUE for a warmer, drier future.

59 BASIC BIOLOGICAL SCIENCES↗

Can improved canopy light transmission ameliorate loss of photosynthetic efficiency in the shade? An investigation of natural variation in Sorghum bicolor

Abstract Previous studies have found that maximum quantum yield of CO2 assimilation (Φ CO2,max,app) declines in lower canopies of maize and miscanthus, a maladaptive response to self-shading. These observations were limited to single genotypes, leaving it unclear whether the maladaptive shade response is a general property of this C4 grass tribe, the Andropogoneae. We explored the generality of this maladaptation by testing the hypothesis that erect leaf forms (erectophiles), which allow more light into the lower canopy, suffer less of a decline in photosynthetic efficiency than drooping leaf (planophile) forms. On average, Φ CO2,max,app declined 27% in lower canopy leaves across 35 accessions, but the decline was over twice as great in planophiles than in erectophiles. The loss of photosynthetic efficiency involved a decoupling between electron transport and assimilation. This was not associated with increased bundle sheath leakage, based on 13C measurements. In both planophiles and erectophiles, shaded leaves had greater leaf absorptivity and lower activities of key C4 enzymes than sun leaves. The erectophile form is considered more productive because it allows a more effective distribution of light through the canopy to support photosynthesis. We show that in sorghum, it provides a second benefit, maintenance of higher Φ CO2,max,app to support efficient use of that light resource.

54 ENVIRONMENTAL SCIENCES↗

Reducing stomatal density by expression of a synthetic epidermal patterning factor increases leaf intrinsic water use efficiency and reduces plant water use in a C4 crop

Abstract Enhancing crop water use efficiency (WUE) is a key target trait for climatic resilience and expanding cultivation on marginal lands. Engineering lower stomatal density to reduce stomatal conductance (gs) has improved WUE in multiple C3 crop species. However, reducing gs in C3 species often reduces photosynthetic carbon gain. A different response is expected in C4 plants because they possess specialized anatomy and biochemistry which concentrates CO2 at the site of fixation. This modifies the relationship of photosynthesis (AN) with intracellular CO2 concentration (ci), such that photosynthesis is CO2 saturated and reductions in gs are unlikely to limit AN. To test this hypothesis, genetic strategies were investigated to reduce stomatal density in the C4 crop sorghum. Constitutive expression of a synthetic epidermal patterning factor (EPF) transgenic allele in sorghum led to reduced stomatal densities, reduced gs, reduced plant water use, and avoidance of stress during a period of water deprivation. In addition, moderate reduction in stomatal density did not increase stomatal limitation to AN. However, these positive outcomes were associated with negative pleiotropic effects on reproductive development and photosynthetic capacity. Avoiding pleiotropy by targeting expression of the transgene to specific tissues could provide a pathway to improved agronomic outcomes.

59 BASIC BIOLOGICAL SCIENCES↗

Clusters have edges: the projected phase-space structure of SDSS redMaPPer clusters

ABSTRACT We study the distribution of line-of-sight velocities of galaxies in the vicinity of Sloan Digital Sky Survey (SDSS) red-sequence Matched-filter Probabilistic Percolation (redMaPPer) galaxy clusters. Based on their velocities, galaxies can be split into two categories: galaxies that are dynamically associated with the cluster, and random line-of-sight projections. Both the fraction of galaxies associated with the galaxy clusters, and the velocity dispersion of the same, exhibit a sharp feature as a function of radius. The feature occurs at a radial scale Redge ≈ 2.2Rλ, where Rλ is the cluster radius assigned by redMaPPer. We refer to Redge as the ‘edge radius’. These results are naturally explained by a model that further splits the galaxies dynamically associated with a galaxy cluster into a component of galaxies orbiting the halo and an infalling galaxy component. The edge radius Redge constitutes a true ‘cluster edge’, in the sense that no orbiting structures exist past this radius. A companion paper tests whether the ‘halo edge’ hypothesis holds when investigating the full three-dimensional phase-space distribution of dark matter substructures in numerical simulations, and demonstrates that this radius coincides with a suitably defined splashback radius.

79 ASTRONOMY AND ASTROPHYSICS↗

Discovery of a Candidate Binary Supermassive Black Hole in a Periodic Quasar from Circumbinary Accretion Variability

Binary supermassive black holes (BSBHs) are expected to be a generic byproduct from hierarchical galaxy formation. The final coalescence of BSBHs is thought to be the loudest gravitational wave (GW) siren, yet no confirmed BSBH is known in the GW-dominated regime. While periodic quasars have been proposed as BSBH candidates, the physical origin of the periodicity has been largely uncertain. Here we report discovery of a periodicity (P=1607±7 days) at 99.95% significance (with a global p-value of ~10 –3 accounting for the look elsewhere effect) in the optical light curves of a redshift 1.53 quasar, SDSS J025214.67–002813.7. Combining archival Sloan Digital Sky Survey data with new, sensitive imaging from the Dark Energy Survey, the total ~20-yr time baseline spans ~4.6 cycles of the observed 4.4-yr (restframe 1.7-yr) periodicity. The light curves are best fit by a bursty model predicted by hydrodynamic simulations of circumbinary accretion disks. The periodicity is likely caused by accretion rate modulation by a milli-parsec BSBH emitting GWs, dynamically coupled to the circumbinary accretion disk. A bursty hydrodynamic variability model is statistically preferred over a smooth, sinusoidal model expected from relativistic Doppler boost, a kinematic effect proposed for PG1302–102. Furthermore, the frequency dependence of the variability amplitudes disfavors Doppler boost, lending independent support to the circumbinary accretion variability hypothesis. Given our detection rate of one BSBH candidate from circumbinary accretion variability out of 625 quasars, it suggests that future large, sensitive synoptic surveys such as the Vera C. Rubin Observatory Legacy Survey of Space and Time may be able to detect hundreds to thousands of candidate BSBHs from circumbinary accretion with direct implications for Laser Interferometer Space Antenna.

79 ASTRONOMY AND ASTROPHYSICS↗

Quantifying resolution in cosmological N- body simulations using self-similarity

ABSTRACT We demonstrate that testing for self-similarity in scale-free simulations provides an excellent tool to quantify the resolution at small scales of cosmological N-body simulations. Analysing two-point correlation functions measured in simulations using abacus , we show how observed deviations from self-similarity reveal the range of time and distance scales in which convergence is obtained. While the well-converged scales show accuracy below 1 per cent, our results show that, with a small force softening length, the spatial resolution is essentially determined by the mass resolution. At later times, the lower cut-off scale on convergence evolves in comoving units as a−1/2 (a being the scale factor), consistent with a hypothesis that it is set by two-body collisionality. A corollary of our results is that N-body simulations, particularly at high red-shift, contain a significant spatial range in which clustering appears converged with respect to the time-stepping and force softening but has not actually converged to the physical continuum result. The method developed can be applied to determine the resolution of any clustering statistic and extended to infer resolution limits for non-scale-free simulations.

79 ASTRONOMY AND ASTROPHYSICS↗

Probing the hadronic nature of the gamma-ray emission associated with Westerlund 2

ABSTRACT Star-forming regions have been proposed as potential Galactic cosmic ray accelerators for decades. Cosmic ray acceleration can be probed through observations of gamma-rays produced in inelastic proton–proton collisions at GeV and TeV energies. In this paper, we analyse more than 11 yr of Fermi–LAT data from the direction of Westerlund 2, one of the most massive and best-studied star-forming regions in our Galaxy. In particular, we investigate the characteristics of the bright pulsar PSR J1023–5746 that dominates the gamma-ray emission below a few GeV at the position of Westerlund 2 and the underlying extended source FGES J1023.3–5747. The analysis results in a clear identification of FGES J1023.3–5747 as the GeV counterpart of the TeV source HESS J1023-575, through its morphological and spectral properties. This identification provides new clues about the origin of the HESS J1023-575 gamma-ray emission, favouring a hadronic origin of the emission, powered by Westerlund 2, rather than a leptonic origin related to either the pulsar wind nebula associated with PSR J1023–5746 or the cluster itself. This result indirectly supports the hypothesis that star-forming regions can contribute to the cosmic ray sea observed in our Galaxy.

Mestre, Enrique↗

Intrinsic alignments of galaxies around cosmic voids

ABSTRACT The intrinsic alignments of galaxies, i.e. the correlation between galaxy shapes and their environment, are a major source of contamination for weak gravitational lensing surveys. Most studies of intrinsic alignments have so far focused on measuring and modelling the correlations of luminous red galaxies with galaxy positions or the filaments of the cosmic web. In this work, we investigate alignments around cosmic voids. We measure the intrinsic alignments of luminous red galaxies detected by the Sloan Digital Sky Survey around a sample of voids constructed from those same tracers and with radii in the ranges: [20–30; 30–40; 40–50] h−1 Mpc and in the redshift range z = 0.4−0.8. We present fits to the measurements based on a linear model at large scales, and on a new model based on the void density profile inside the void and in its neighbourhood. We constrain the free scaling amplitude of our model at small scales, finding no significant alignment at 1σ for either sample. We observe a deviation from the null hypothesis, at large scales, of 2σ for voids with radii between 20 and 30 h−1 Mpc, and 1.5σ for voids with radii between 30 and 40 h−1 Mpc and constrain the amplitude of the model on these scales. We find no significant deviation at 1σ for larger voids. Our work is a first attempt at detecting intrinsic alignments of galaxy shapes around voids and provides a useful framework for their mitigation in future void lensing studies.

79 ASTRONOMY AND ASTROPHYSICS↗

APOGEE detection of N-rich stars in the tidal tails of Palomar 5

Recent results from chemical tagging studies using Apache Point Observatory Galactic Evolution Experiment data suggest a strong link between the chemical abundance patterns of stars found within globular clusters (GC), and chemically peculiar populations in the Galactic halo field. In this paper, we analyse the chemical compositions of stars within the cluster body and tidal streams of Palomar 5, a GC that is being tidally disrupted by interaction with the Galactic gravitational potential. Here we report the identification of nitrogen-rich (N-rich) stars both within and beyond the tidal radius of Palomar 5, with the latter being clearly aligned with the cluster tidal streams; this acts as confirmation that N-rich stars are lost to the Galactic halo from GCs, and provides support to the hypothesis that field N-rich stars identified by various groups have a GC origin.

79 ASTRONOMY AND ASTROPHYSICS↗

Detection of spatial clustering in the 1000 richest SDSS DR8 redMaPPer clusters with nearest neighbor distributions

ABSTRACT Distances to the k-nearest-neighbor (kNN) data points from volume-filling query points are a sensitive probe of spatial clustering. Here, we present the first application of kNN summary statistics to observational clustering measurement, using the 1000 richest redMaPPer clusters (0.1 ≤ z ≤ 0.3) from the SDSS DR8 catalog. A clustering signal is defined as a difference in the cumulative distribution functions (CDFs) of kNN distances from fixed query points to the observed clusters versus a set of unclustered random points. We find that the k = 1, 2-NN CDFs of redMaPPer deviate significantly from the randoms’ across scales of 35 to 155 Mpc, which is a robust signature of clustering. In addition to kNN, we also measure the two-point correlation function for the same set of redMaPPer clusters versus random points, which shows a noisier and less significant clustering signal within the same radial scales. Quantitatively, the χ2 distribution for both the kNN-CDFs and the two-point correlation function measured on the randoms peak at χ2 ∼ 50 (null hypothesis), whereas the kNN-CDFs (χ2 ∼ 300, p = 1.54 × 10−36) pick up a much more significant clustering signal than the two-point function (χ2 ∼ 100, p = 1.16 × 10−6) when measured on redMaPPer. Finally, the measured 3NN and 4NN CDFs deviate from the predicted k = 3, 4-NN CDFs assuming an ideal Gaussian field, indicating a non-Gaussian clustering signal for redMaPPer clusters, although its origin might not be cosmological due to observational systematics. Therefore, kNN serves as a more sensitive probe of clustering complementary to the two point correlation function, providing a novel approach for constraining cosmology and galaxy–halo connection.

79 ASTRONOMY AND ASTROPHYSICS↗

The merger fraction of post-starburst galaxies in UNIONS

ABSTRACT Post-starburst galaxies (PSBs) are defined as having experienced a recent burst of star formation, followed by a prompt truncation in further activity. Identifying the mechanism(s) causing a galaxy to experience a post-starburst phase therefore provides integral insight into the causes of rapid quenching. Galaxy mergers have long been proposed as a possible post-starburst trigger. Effectively testing this hypothesis requires a large spectroscopic galaxy survey to identify the rare PSBs as well as high-quality imaging and robust morphology metrics to identify mergers. We bring together these critical elements by selecting PSBs from the overlap of the Sloan Digital Sky Survey and the Canada–France Imaging Survey and applying a suite of classification methods: non-parametric morphology metrics such as asymmetry and Gini-M20, a convolutional neural network trained to identify post-merger galaxies, and visual classification. This work is therefore the largest and most comprehensive assessment of the merger fraction of PSBs to date. We find that the merger fraction of PSBs ranges from 19 per cent to 42 per cent depending on the merger identification method and details of the PSB sample selection. These merger fractions represent an excess of 3–46× relative to non-PSB control samples. Our results demonstrate that mergers play a significant role in generating PSBs, but that other mechanisms are also required. However, applying our merger identification metrics to known post-mergers in the IllustrisTNG simulation shows that 70 per cent of recent post-mergers (≲200 Myr) would not be detected. Thus, we cannot exclude the possibility that nearly all PSBs have undergone a merger in their recent past.

79 ASTRONOMY AND ASTROPHYSICS↗