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At least 199 records · Page 11

Microbial contribution to post-fire tundra ecosystem recovery over the 21st century

Abstract Tundra ecosystems have experienced an increased frequency of fire, and this trend is predicted to continue throughout the 21 st Century. Post-fire recovery is underpinned by complex interactions between microbial functional groups that drive nutrient cycling. Here we use a mechanistic model to demonstrate an acceleration of the nitrogen cycle post-fire driven by changes in niche space and microbial competitive dynamics. We show that over the first 5-years post-fire, fast-growing bacterial heterotrophs colonize regions of the soil previously occupied by slower-growing saprotrophic fungi. The bacterial heterotrophs mineralize organic matter, releasing nutrients into the soil. This pathway outweighs new sources of nitrogen and facilitates the recovery of plant productivity. We broadly show here that while consideration of distinct microbial metabolisms related to carbon and nutrient cycling remains rare in terrestrial ecosystem models, they are important when considering the rate of ecosystem recovery post-disturbance and the feedback to soil nutrient cycles on centennial timescales.

54 ENVIRONMENTAL SCIENCES↗

Binding of the substrate analog methanol in the oxygen-evolving complex of photosystem II in the D1-N87A genetic variant of cyanobacteria

The solar water-splitting protein complex, photosystem II (PSII), catalyzes one of the most energetically demanding reactions in nature by using light energy to drive a catalyst capable of oxidizing water. The water oxidation reaction is catalyzed at the Mn 4 Ca-oxo cluster in the oxygen-evolving complex (OEC), which cycles through five light-driven S-state intermediates (S 0 –S 4 ). A detailed mechanism of the reaction remains elusive as it requires knowledge of the delivery and binding of substrate water in the higher S-state intermediates. In this paper, we use two-dimensional (2D) hyperfine sublevel correlation spectroscopy, in conjunction with quantum mechanics/molecular mechanics (QM/MM) and density functional theory (DFT), to probe the binding of the substrate analog, methanol, in the S 2 state of the D1-N87A variant of PSII from Synechocystis sp. PCC 6803. The results indicate that the size and specificity of the “narrow” channel is altered in D1-N87A PSII, allowing for the binding of deprotonated 13 C-labeled methanol at the Mn4(IV) ion of the catalytic cluster in the S 2 state. This has important implications on the mechanistic models for water oxidation in PSII.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Unfolding bovine α-lactalbumin with T-jump: Characterizing disordered intermediates via time-resolved x-ray solution scattering and molecular dynamics simulations

The protein folding process often proceeds through partially folded transient states. Therefore, a structural understanding of these disordered states is crucial for developing mechanistic models of the folding process. Characterization of unfolded states remains challenging due to their disordered nature, and incorporating multiple methods is necessary. Combining the time-resolved x-ray solution scattering (TRXSS) signal with molecular dynamics (MD), we are able to characterize transient partially folded states of bovine α-lactalbumin, a model system widely used for investigation of molten globule states, during its unfolding triggered by a temperature jump. We track the unfolding process between 20 μs and 70 ms and demonstrate that it passes through three distinct kinetic states. The scattering signals associated with these transient species are then analyzed with TRXSS constrained MD simulations to produce protein structures that are compatible with the input signals. Without utilizing any experimentally extracted kinetic information, the constrained MD simulation successfully drove the protein to an intermediate molten globule state; signals for two later disordered states are refined to terminal unfolded states. From our examination of the structural characteristics of these disordered states, we discuss the implications disordered states have on the folding process, especially on the folding pathway. Finally, we discuss the potential applications and limitations of this method.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Photosynthetic reaction center variants made via genetic code expansion show Tyr at M210 tunes the initial electron transfer mechanism

Significance Reaction centers (RCs) are critical to photosynthetic energy conversion. RCs in all characterized photosynthetic organisms contain two symmetrically arranged branches of chromophores and enable light-induced electron transfer with high yield. We fine-tune the properties of a key bacterial RC symmetry-breaking tyrosine via its replacement with noncanonical tyrosine analogs and determine kinetic outcomes. Results are interpreted through energetic characterization made possible by resonance Stark spectroscopy. Analysis indicates this tyrosine modulates the mechanism of the initial light-induced electron transfer, affording an alternative functional pathway that maintains the RC’s robust electron transfer. Modern molecular biology, ultrafast spectroscopy, crystallography, and energetic characterization enable the mechanistic model we describe. Our results deepen understanding of RC function and may have implications for other photocatalysts and enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae

Advances in sequencing technology have unveiled examples of nucleus-encoded polycistrons, once considered rare. Exclusively polycistronic transcripts are prevalent in green algae, although the mechanism by which multiple polypeptides are translated from a single transcript is unknown. Here, we used bioinformatic and in vivo mutational analyses to evaluate competing mechanistic models for translation of bicistronic mRNAs in green algae. High-confidence manually curated datasets of bicistronic loci from two divergent green algae, Chlamydomonas reinhardtii and Auxenochlorella protothecoides, revealed a preference for weak Kozak-like sequences for ORF 1 and an underrepresentation of potential initiation codons before the ORF 2 start codon, which are suitable conditions for leaky ribosome scanning to allow ORF 2 translation. We used mutational analysis in A. protothecoides to test the mechanism. In vivo manipulation of the ORF 1 Kozak-like sequence and start codon altered reporter expression at ORF 2, with a weaker Kozak-like sequence enhancing expression and a stronger one diminishing it. A synthetic bicistronic dual reporter demonstrated inversely adjustable activity of green fluorescent protein expressed from ORF 1 and luciferase from ORF 2, depending on the strength of the ORF 1 Kozak-like sequence. Our findings demonstrate that translation of multiple ORFs in green algal bicistronic transcripts is consistent with episodic leaky scanning of ORF 1 to allow translation at ORF 2. This work has implications for the potential functionality of upstream open reading frames (uORFs) found across eukaryotic genomes and for transgene expression in synthetic biology applications.

59 BASIC BIOLOGICAL SCIENCES↗

Growth instabilities shape morphology and genetic diversity of microbial colonies

Abstract Cellular populations assume an incredible variety of shapes ranging from circular molds to irregular tumors. While we understand many of the mechanisms responsible for these spatial patterns, little is known about how the shape of a population influences its ecology and evolution. Here, we investigate this relationship in the context of microbial colonies grown on hard agar plates. This a well-studied system that exhibits a transition from smooth circular disks to more irregular and rugged shapes as either the nutrient concentration or cellular motility is decreased. Starting from a mechanistic model of colony growth, we identify two dimensionless quantities that determine how morphology and genetic diversity of the population depend on the model parameters. Our simulations further reveal that population dynamics cannot be accurately described by the commonly-used surface growth models. Instead, one has to explicitly account for the emergent growth instabilities and demographic fluctuations. Overall, our work links together environmental conditions, colony morphology, and evolution. This link is essential for a rational design of concrete, biophysical perturbations to steer evolution in the desired direction.

Golden, Alexander↗

Correlation and co-localization of QTL for stomatal density, canopy temperature, and productivity with and without drought stress in Setaria

Abstract Mechanistic modeling indicates that stomatal conductance could be reduced to improve water use efficiency (WUE) in C4 crops. Genetic variation in stomatal density and canopy temperature was evaluated in the model C4 genus, Setaria. Recombinant inbred lines (RILs) derived from a Setaria italica×Setaria viridis cross were grown with ample or limiting water supply under field conditions in Illinois. An optical profilometer was used to rapidly assess stomatal patterning, and canopy temperature was measured using infrared imaging. Stomatal density and canopy temperature were positively correlated but both were negatively correlated with total above-ground biomass. These trait relationships suggest a likely interaction between stomatal density and the other drivers of water use such as stomatal size and aperture. Multiple quantitative trait loci (QTL) were identified for stomatal density and canopy temperature, including co-located QTL on chromosomes 5 and 9. The direction of the additive effect of these QTL on chromosome 5 and 9 was in accordance with the positive phenotypic relationship between these two traits. This, along with prior experiments, suggests a common genetic architecture between stomatal patterning and WUE in controlled environments with canopy transpiration and productivity in the field, while highlighting the potential of Setaria as a model to understand the physiology and genetics of WUE in C4 species.

59 BASIC BIOLOGICAL SCIENCES↗

Impact of Blast Overpressure on the Pharmacokinetics of Various Antibiotics in Sprague Dawley Rats

ABSTRACT Introduction Combat injuries are complex and multimodal. Most injuries to the extremities occur because of explosive devices such as improvised explosive devices. Blast exposure dramatically increases the risk of infection in combat wounds, and there is limited available information on the best antibiotic treatments for these injuries. We previously demonstrated that mice exposed to blast displayed a delayed clearance of cefazolin from the plasma and liver; further semi-mechanistic modeling determined that cefazolin concentrations in the skin of these mice were reduced. Our objective was to investigate the effects of blast on the pharmacokinetics of antibiotics of different types used for the treatment of combat wounds in the rat model. Materials and Methods Male Sprague Dawley rats were exposed to blast overpressure followed by injection of a bolus of animal equivalent doses of an antibiotic (cefazolin, cefepime, ertapenem, or clindamycin) into the tail vein at 1-hour post-blast exposure. Blood was collected at predetermined time points via repeated sampling from the tail vein. Animals were also euthanized at predetermined time points, at which time liver, kidney, skin, and blood via cardiac puncture were collected. Antibiotic concentrations were determined by ultra-performance liquid chromatography–tandem mass spectrometry. Results Blast-exposed rats exhibited a similar rate of clearance compared to non-blasted rats in the blood, liver, kidney, and skin, which is inconsistent with the data regarding cefazolin in blast-exposed mice. Conclusions Our results in rats do not recapitulate our previous observation of delayed cefazolin clearance in mice following the blast overpressure exposure. Although using rats permitted us to collect multiple blood samples from the same animals, rats may not be a suitable model for measuring the pharmacokinetics of antibiotics following blast. The interpretation of the results may be challenging because of variation in data among rat subjects in the same sample groups.

General & Internal Medicine↗

Hypothesis on the dust-borne atmospheric transport of Coccidioides , causative fungal pathogen for coccidioidomycosis (Valley fever)

For many decades, the fungal pathogen (Coccidioides spp.) that causes coccidioidomycosis (Valley fever) has been associated with dust exposure. However, the mechanism of atmospheric transport of arthroconidia has yet to be defined. As such, it is unclear whether the association between dust exposure and Coccidioides is coincidental or not: do soil-disturbing events simultaneously cause both free-floating Coccidioides conidia and dust particles (i.e., particulate matter) to become entrained in the atmosphere, or is Coccidioides attached to dust particles and they are jointly suspended? In this short article, we propose the dust-borne atmospheric transport hypothesis: Coccidioides conidia are transported in the atmosphere attached to dust particles, which protect the fungi from harsh environmental conditions like desiccation and UV exposure, allowing them to travel far while remaining viable in comparison to free-floating aerial transport. If true, the dust-borne atmospheric transport hypothesis provides a means for mechanistically modeling the transport and exposure risk of Coccidioides via atmospheric dispersion modeling and suggests health implications from simultaneous exposure to dust and a fungal pathogen.

54 ENVIRONMENTAL SCIENCES↗

Structural basis for cloverleaf RNA-initiated viral genome replication

The genomes of positive-strand RNA viruses serve as a template for both protein translation and genome replication. In enteroviruses, a cloverleaf RNA structure at the 5' end of the genome functions as a switch to transition from viral translation to replication by interacting with host poly(C)-binding protein 2 (PCBP2) and the viral 3CD pro protein. We determined the structures of cloverleaf RNA from coxsackievirus and poliovirus. Cloverleaf RNA folds into an H-type four-way junction and is stabilized by a unique adenosine-cytidine-uridine (A•C-U) base triple involving the conserved pyrimidine mismatch region. The two PCBP2 binding sites are spatially proximal and are located on the opposite end from the 3CD pro binding site on cloverleaf. We determined that the A•C-U base triple restricts the flexibility of the cloverleaf stem–loops resulting in partial occlusion of the PCBP2 binding site, and elimination of the A•C-U base triple increases the binding affinity of PCBP2 to the cloverleaf RNA. Based on the cloverleaf structures and biophysical assays, we propose a new mechanistic model by which enteroviruses use the cloverleaf structure as a molecular switch to transition from viral protein translation to genome replication.

59 BASIC BIOLOGICAL SCIENCES↗

Latitudinal shifts of soil microbial biomass seasonality

Soil microbes ultimately drive the mineralization of soil organic carbon and thus ecosystem functions. We compiled a dataset of the seasonality of microbial biomass carbon (MBC) and developed a semi-mechanistic model to map monthly MBC across the globe. MBC exhibits an equatorially symmetric seasonality between the Northern and Southern Hemispheres. In the Northern Hemisphere, MBC peaks in autumn and is minimal in spring at low latitudes (<25°N), peaks in the spring and is minimal in autumn at mid-latitudes (25°N to 50°N), while peaks in autumn and is minimal in spring at high latitudes (>50°N). This latitudinal shift of MBC seasonality is attributed to an interaction of soil temperature, soil moisture, and substrate availability. The MBC seasonality is inconsistent with patterns of heterotrophic respiration, indicating that MBC as a proxy for microbial activity is inappropriate at this resolution. This study highlights the need to explicitly represent microbial physiology in microbial models. The interactive controls of environments and substrate on microbial seasonality provide insights for better representing microbial mechanisms in simulating ecosystem functions at the seasonal scale.

54 ENVIRONMENTAL SCIENCES↗

Fracturing in Wet Granular Media Illuminated by Photoporomechanics

Here, we study fluid-induced deformation and fracture of granular media and apply photoporomechanics to uncover the underpinning grain-scale mechanics. We fabricate spherical photoelastic particles of 2-mm diameter to form a monolayer granular pack in a circular Hele-Shaw cell that is initially filled with a viscous fluid. The key distinct feature of our system is that, with spherical particles, the granular pack has a connected pore space, thus allowing for pore-pressure diffusion and the study of effective stress in coupled poromechanical processes. We inject air into the fluid-filled photoelastic granular pack, varying the initial packing density and confining weight. With our recently developed experimental technique, photoporomechanics, we find two different modes of fluid invasion: fracturing in fluid-filled elastic media (with strong photoelastic response) and viscous fingering in frictional fluids (with weak or negligible photoelastic response). We directly visualize the evolving effective stress field and discover an effective stress shadow behind the propagating fracture tips, where the granular pack exhibits undrained behavior. We conceptualize the behavior of the system by means of a mechanistic model for a wedge of the granular pack bounded by two growing fractures. The model captures the pore-pressure build-up inside the stress shadow region and the grain compaction in the annular region outside. Our model reveals that a jamming transition determines the distinct rheological behavior of the wet granular pack, from a friction-dominated to an elasticity-dominated response.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Potential of hotspot solar‐induced chlorophyll fluorescence for better tracking terrestrial photosynthesis

Abstract Remote sensing of solar‐induced fluorescence (SIF) opens a new window for quantifying a key ecological variable, the terrestrial ecosystem gross primary production (GPP), because of the revealed strong SIF–GPP correlation. However, similar to many other remotely sensed metrics, SIF observations suffer from the sun‐sensor geometry effects, which may have important impacts on the SIF–GPP relationship but remain poorly understood. Here we used remotely sensed SIF, globally distributed tower GPP data, and a mechanistic model to provide a systematic analysis. Our results reveal that leaf physiology, canopy structure, and sun‐sensor geometries all affect the SIF–GPP relationship. In particular, we found that SIF observations in the sun‐tracking hotspot direction can be a better proxy of GPP due to the similar responses of light use efficiency and SIF escaping probability in the hotspot direction to the increasing incoming solar radiation. Such conclusions are supported by a variety of modeling simulations and satellite observations over various plant function types, at different time scales and with satellite observational modes. This study demonstrates the potential and advantage of normalizing SIF observations to the hotspot direction for better global GPP estimations. This study also demonstrates the great potentials of current and future spaceborne sun‐tracking satellite missions for a significant improvement in measuring and monitoring, at a wide range of spatial and temporal scales, the changes in terrestrial ecosystem GPP in response to anticipated changes in the Earth's environmental conditions.

Hao, Dalei↗

Rising Water Levels and Vegetation Shifts Drive Substantial Reductions in Methane Emissions and Carbon Dioxide Uptake in a Great Lakes Coastal Freshwater Wetland

ABSTRACT Coastal freshwater wetlands are critical ecosystems for both local and global carbon cycles, sequestering substantial carbon while also emitting methane (CH 4 ) due to anoxic conditions. Estuarine freshwater wetlands face unique challenges from fluctuating water levels, which influence water quality, vegetation, and carbon cycling. However, the response of CH 4 fluxes and their drivers to altered hydrology and vegetation remains unclear, hindering mechanistic modeling. To address these knowledge gaps, we studied an estuarine freshwater wetland in the Great Lakes region, where rising water levels led to a vegetation shift from emergent Typha dominance in 2015–2016 to floating‐leaved species in 2020–2022. Using eddy covariance flux measurements during the peak growing season (June–September) of both periods, we observed a 60% decrease in CH 4 emissions, from 81 ± 4 g C m −2 in 2015–2016 to 31 ± 3 g C m −2 in 2020–2022. This decline was driven by two main factors: (1) higher water levels, which suppressed ebullitive fluxes via increased hydrostatic pressure and extended CH 4 residence time, enhancing oxidation potential in the water column; and (2) reduced CH 4 conductance through plants. Net carbon dioxide (CO 2 ) uptake decreased by 90%, from −267 ± 26 g C m −2 in 2015–2016 to −27 ± 49 g C m −2 in 2020–2022. Additionally, diel CH 4 flux patterns shifted, with a distinct morning peak observed in 2015–2016 but absent in 2020–2022, suggesting changes in plant‐mediated transport and a potential decoupling from photosynthesis. The dominant factors influencing CH 4 fluxes shifted from water temperature and gross primary productivity in 2015–2016 to atmospheric pressure in 2020–2022, suggesting an increased role of ebullition as a primary transport pathway. Our results demonstrate that changes in water levels and vegetation can substantially alter CH 4 and CO 2 fluxes in coastal freshwater wetlands, underscoring the critical role of hydrological shifts in driving carbon dynamics in these ecosystems.

54 ENVIRONMENTAL SCIENCES↗

Proteins associated with the Arabidopsis thaliana plastid rhomboid-like protein RBL10

Rhomboid-like proteins are intramembrane proteases with a variety of regulatory roles in cells. Though many rhomboid-like proteins are predicted in plants, their detailed molecular mechanisms or cellular functions are not yet known. Of the 13 predicted rhomboids in Arabidopsis thaliana, one, RBL10, affects lipid metabolism in the chloroplast, because in the respective rbl10 mutant the transfer of phosphatidic acid through the inner envelope membrane is disrupted. Here we show that RBL10 is part of a high-molecular-weight complex of 250 kDa or greater in size. Nine likely components of this complex are identified by two independent methods and include Acyl Carrier Protein 4 (ACP4) and Carboxyltransferase Interactor1 (CTI1), which have known roles in chloroplast lipid metabolism. The acp4 mutant has decreased C16:3 fatty acid content of monogalactosyldiacylglycerol, similar to the rbl10 mutant, prompting us to offer a mechanistic model of how an interaction between ACP4 and RBL10 might affect chloroplast lipid assembly. We also demonstrate the presence of a seventh transmembrane domain in RBL10, refining the currently accepted topology of this protein. Taken together, the identity of possible RBL10 complex components as well as insights into RBL10 topology and distribution in the membrane provide a stepping-stone towards a deeper understanding of RBL10 function in Arabidopsis lipid metabolism.

59 BASIC BIOLOGICAL SCIENCES↗

Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation

The extensive heterogeneity of biological data poses challenges to analysis and interpretation. Construction of a large-scale mechanistic model of Escherichia coli enabled us to integrate and cross-evaluate a massive, heterogeneous dataset based on measurements reported by various groups over decades. We identified inconsistencies with functional consequences across the data, including that the total output of the ribosomes and RNA polymerases described by data are not sufficient for a cell to reproduce measured doubling times, that measured metabolic parameters are neither fully compatible with each other nor with overall growth, and that essential proteins are absent during the cell cycle—and the cell is robust to this absence. Finally, considering these data as a whole leads to successful predictions of new experimental outcomes, in this case protein half-lives.

59 BASIC BIOLOGICAL SCIENCES↗

Data, figures, animations, and scripts associated with the manuscript "Integrated Effects of Site Hydrology and Vegetation on Exchange Fluxes and Carbon Cycling at the Coastal Terrestrial Aquatic Interface"

This package contains the data, figures, animations, and scripts used in "Integrated Effects of Site Hydrology and Vegetation on Exchange Fluxes and Carbon Cycling at the Coastal Terrestrial Aquatic Interface" (Li et al., 2023). This study examines the interactions between soil, vegetation and hydrologic conditions in coastal areas, with a focus on the Chesapeake Bay region. The researchers used a mechanistic model called ATS-PFLOTRAN to explore how these interactions affect exchange process in different regions and the carbon/nitrogen cycle across the terrestrial-aquatic interface (TAI). Simulation scenarios isolate the effects of control factors and reaction constants derived from laboratory experiments. The results show a carbon cycle "hot zone" in coastal wetlands and in the transition zone between wetlands and uplands. Transpiration enhances fluxes between the surface and subsurface domains and increases dissolved oxygen in TAI. The decomposition of leaf-derived organic carbon provides an additional source of carbon for aerobic respiration and denitrification in the TAI. Microbial activity plays a key role in controlling redox conditions and their variability. This modeling study improves the understanding of complex TAI interactions and facilitates the representation of coastal ecosystems in larger-scale Earth system models.Several files can be found from this data package.1. Readme,md: This file describe the Title, Target Journal, Target submission date, Co-author, Science Questions, Hypotheses, Key words, Key message, Model and Data, Repo Structure. The user can read this file first and then go to details.2. mesh.zip: This file contains the mesh file for simulation cases. 3. Figure.zip: This file contains figures used in the manuscript . 4. animation.zip: This file contains animations used in the manuscript . 5. Data.zip: This file contains all required input data, such as concentration and flow boundaries. Also, it contains the DEM and processes results on area fraction. 6. Simulation_setup_and_results.zip: This file contains setup of cases used in the manuscript . The result files are too large, if you need that data, please contact to the Author. 7. notebooks.zip: This file contains the Jupyter notebooks for performing sensitivity analysis and other pre-process and post-process analyses.

54 ENVIRONMENTAL SCIENCES↗

COMPASS-FME Synoptic Site Characterization

This dataset contains soil biogeochemical and physicochemical characterization data for the COMPASS-FME synoptic sites.This dataset also contains data for the paper Patel et al. 2025 "Transition zones at the changing coastal terrestrial-aquatic interface", https://doi.org/10.1029/2025JG008978.Coastal soils are a significant but highly uncertain component of global biogeochemical cycles. These systems experience unique spatial and temporal variability in biogeochemical processes, driven by wetland-to-upland gradients and hydrological fluctuations. We studied drivers of coastal soil variability (a) at regional scales and (b) across transects from upland forest to wetland, in two contrasting regions — Lake Erie, a freshwater lacustrine system, and Chesapeake Bay, a saltwater estuarine system. Salinity-related analytes were a key driver of soil variability, not just in the saltwater system, but surprisingly, also in the freshwater system. We had hypothesized linear trends in biogeochemical parameters along the TAI – however, contrary to expectations, transition soils were not consistently intermediate between upland and wetland endmembers; the non-monotonic trends of carbon, phosphorus, iron along our transects suggest that these are key analytes to study in our regions. Rapidly changing soil factors across coastal gradients provide insights into which soil processes may act as precursors to ecosystem shifts. Our comprehensive soil characterization across the coastal transects provides essential data for mechanistic modeling of ecosystem dynamics.The data are provided as processed, csv files. Raw data and processing scripts can be accessed on GitHub (https://github.com/COMPASS-DOE/cmps-soil_characterization).A note on the nomenclature: the experimental design represents three points along the coastal gradient -- upland, transition, and wetland. "wetland" is referred to as "marsh" in the corresponding paper. The two terms can be used interchangeably for the sites in this study.

54 ENVIRONMENTAL SCIENCES↗