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At least 1,729 records · Page 96

Spatio–Temporal Machine Learning for Regional to Continental Scale Terrestrial Hydrology

Integrated hydrologic models can simulate coupled surface and subsurface processes but are computationally expensive to run at high resolutions over large domains. Here we develop a novel deep learning model to emulate subsurface flows simulated by the integrated ParFlow–CLM model across the contiguous US. We compare convolutional neural networks like ResNet and UNet run autoregressively against our novel architecture called the Forced SpatioTemporal RNN (FSTR). The FSTR model incorporates separate encoding of initial conditions, static parameters, and meteorological forcings, which are fused in a recurrent loop to produce spatiotemporal predictions of groundwater. We evaluate the model architectures on their ability to reproduce 4D pressure heads, water table depths, and surface soil moisture over the contiguous US at 1 km resolution and daily time steps over the course of a full water year. The FSTR model shows superior performance to the baseline models, producing stable simulations that capture both seasonal and event–scale dynamics across a wide array of hydroclimatic regimes. The emulators provide over 1,000× speedup compared to the original physical model, which will enable new capabilities like uncertainty quantification and data assimilation for integrated hydrologic modeling that were not previously possible. Our results demonstrate the promise of using specialized deep learning architectures like FSTR for emulating complex process–based models without sacrificing fidelity.

54 ENVIRONMENTAL SCIENCES↗

Data Imbalance, Uncertainty Quantification, and Transfer Learning in Data‐Driven Parameterizations: Lessons From the Emulation of Gravity Wave Momentum Transport in WACCM

Abstract Neural networks (NNs) are increasingly used for data‐driven subgrid‐scale parameterizations in weather and climate models. While NNs are powerful tools for learning complex non‐linear relationships from data, there are several challenges in using them for parameterizations. Three of these challenges are (a) data imbalance related to learning rare, often large‐amplitude, samples; (b) uncertainty quantification (UQ) of the predictions to provide an accuracy indicator; and (c) generalization to other climates, for example, those with different radiative forcings. Here, we examine the performance of methods for addressing these challenges using NN‐based emulators of the Whole Atmosphere Community Climate Model (WACCM) physics‐based gravity wave (GW) parameterizations as a test case. WACCM has complex, state‐of‐the‐art parameterizations for orography‐, convection‐, and front‐driven GWs. Convection‐ and orography‐driven GWs have significant data imbalance due to the absence of convection or orography in most grid points. We address data imbalance using resampling and/or weighted loss functions, enabling the successful emulation of parameterizations for all three sources. We demonstrate that three UQ methods (Bayesian NNs, variational auto‐encoders, and dropouts) provide ensemble spreads that correspond to accuracy during testing, offering criteria for identifying when an NN gives inaccurate predictions. Finally, we show that the accuracy of these NNs decreases for a warmer climate (4 × CO 2 ). However, their performance is significantly improved by applying transfer learning, for example, re‐training only one layer using ∼1% new data from the warmer climate. The findings of this study offer insights for developing reliable and generalizable data‐driven parameterizations for various processes, including (but not limited to) GWs.

54 ENVIRONMENTAL SCIENCES↗

Harnessing the Power of Machine Learning and Omics to Identify Environmental Regulation on Microbial Functional Composition for Soil C, N, and P Cycling

Microbial enzyme-mediated soil organic matter (SOM) decomposition regulates many key ecosystem functions, such as elemental cycling, soil carbon sequestration, and soil fertility. However, representing microbial processes in Earth system models (ESMs) remains challenging due to a limited understanding of the spatial patterns of diverse microbial functions responsible for soil carbon (C), nitrogen (N), and phosphorus (P) cycling as well as the underlying mechanisms regulating their relative abundances across various environments. We collected published metagenomics data across the continental US (CONUS) to identify hundreds of microbial genes involved in soil C, N, and P cycling and grouped them into eight enzyme functional classes (EFCs). Each EFC represented a group of gene-encoded potential enzymes that decompose similar soil compounds. By integrating the abundances of omics-informed EFCs with the corresponding environmental information, we trained a machine learning (ML) model to identify key edaphic, climate, and vegetation factors regulating the abundances of each EFC. Quantitative analysis of effects of these factors revealed that the spatial distribution of eight EFCs for soil C, N, and P cycling across CONUS reflected potential resource optimization strategies of microbial communities under nutrient limitation, preferential organic-mineral associations, and climatological stresses. This insight, together with the interpreted ML tool and the CONUS-level benchmark for EFCs abundances, paves the way for parameterizing environmental-regulated microbial functional dynamics in biogeochemical models.

machine learning↗

Simulating Atmospheric Processes in Earth System Models and Quantifying Uncertainties With Deep Learning Multi‐Member and Stochastic Parameterizations

Abstract Deep learning is a powerful tool to represent subgrid processes in climate models, but many application cases have so far used idealized settings and deterministic approaches. Here, we develop stochastic parameterizations with calibrated uncertainty quantification to learn subgrid convective and turbulent processes and surface radiative fluxes of a superparameterization embedded in an Earth System Model (ESM). We explore three methods to construct stochastic parameterizations: (a) a single Deep Neural Network (DNN) with Monte Carlo Dropout; (b) a multi‐member parameterization; and (c) a Variational Encoder Decoder with latent space perturbation. We show that the multi‐member parameterization improves the representation of convective processes, especially in the planetary boundary layer, compared to individual DNNs. The respective uncertainty quantification illustrates that methods (b) and (c) are advantageous compared to a dropout‐based DNN parameterization regarding the spread of convective processes. Hybrid simulations with our best‐performing multi‐member parameterizations remained challenging and crash within the first days. Therefore, we develop a pragmatic partial coupling strategy relying on the superparameterization for condensate emulation. Partial coupling reduces the computational efficiency of hybrid Earth‐like simulations but enables model stability over 5 months with our multi‐member parameterizations. However, our hybrid simulations exhibit biases in thermodynamic fields and differences in precipitation patterns. Despite this, the multi‐member parameterizations enable improvements in reproducing tropical extreme precipitation compared to a traditional convection parameterization. Despite these challenges, our results indicate the potential of a new generation of multi‐member machine learning parameterizations leveraging uncertainty quantification to improve the representation of stochasticity of subgrid effects.

Behrens, Gunnar [Deutsches Zentrum für Luft‐ und R↗

Learning Constitutive Relations From Soil Moisture Data via Physically Constrained Neural Networks

Abstract The constitutive relations of the Richardson‐Richards equation encode the macroscopic properties of soil water retention and conductivity. These soil hydraulic functions are commonly represented by models with a handful of parameters. The limited degrees of freedom of such soil hydraulic models constrain our ability to extract soil hydraulic properties from soil moisture data via inverse modeling. We present a new free‐form approach to learning the constitutive relations using physically constrained neural networks. We implemented the inverse modeling framework in a differentiable modeling framework, JAX, to ensure scalability and extensibility. For efficient gradient computations, we implemented implicit differentiation through a nonlinear solver for the Richardson‐Richards equation. We tested the framework against synthetic noisy data and demonstrated its robustness against varying magnitudes of noise and degrees of freedom of the neural networks. We applied the framework to soil moisture data from an upward infiltration experiment and demonstrated that the neural network‐based approach was better fitted to the experimental data than a parametric model and that the framework can learn the constitutive relations.

54 ENVIRONMENTAL SCIENCES↗

Combined Meteorological and Hydrologic Uncertainties Shape Projections of Future Soil Moisture in the Eastern United States

Physical hazards pose risks to many critical systems. Designing adaptive measures to mitigate these risks is challenging due to large uncertainties in modeling future hazards and the associated sectoral responses. Here, we help address this challenge in a hydrologic context by examining the combined role of meteorological forcing and hydrologic parameter uncertainties in shaping projections of future soil moisture. By encoding a simple conceptual water balance model in a differentiable programming framework, we facilitate fast runtimes and an efficient calibration, enabling an improved uncertainty analysis. We characterize uncertainty in model parameters by calibrating against different target data sets and by using several loss functions. We then convolve the resulting parameter ensemble with a set of Earth system model projections to produce a large ensemble (2,340 members) of daily soil moisture simulations. Focusing on the eastern United States, we find that most ensemble members project a drying of soils across the region, although some simulate wetter conditions throughout this century. Our ensemble shows an increase in the frequency and intensity of dry extremes while there is less agreement for wet extremes. We conduct sensitivity analyses on several soil moisture signatures to measure the relative influence of meteorological and hydrologic uncertainties across space and time. Both meteorological and hydrologic factors contribute consistently to uncertainty surrounding long-term trends, while changes to both wet and dry soil extremes are typically more sensitive to hydrologic parameter uncertainty. Our results underscore the need to account for varied sources of uncertainty when developing long-term hydrometeorological projections.

Lafferty, David C. [University of Illinois Urbana‐↗

Seismic Tremors From Sea‐Landfast Ice Interactions Near Utqiaġvik, Alaska

The mechanical state of Arctic landfast sea ice remains poorly constrained due to limited observations. This study investigates interactions between drifting sea ice and the coastal landfast ice near Utqiaġvik, Alaska by integrating data from broadband seismometer, Distributed Acoustic Sensing, and marine radar. We find that decreases in sea ice velocity, marking transitions from drift to compressive contact, coincide with increased seismic energy. Tremor characteristics vary seasonally with ice conditions. In January, dense ice packs produced sustained harmonic tremors with gliding and U-shaped spectral features, consistent with repetitive stick-slip motion at the ice–ice or ice–ground interface under velocity-weakening friction. In April, smaller fragmented floes generated short-lived, chaotic tremors linked to brittle failure and spatially dispersed impacts. These findings demonstrate that seismic tremors encode the mechanical properties of interacting ice, offering a new tool to distinguish ice regimes and monitor evolving Arctic coastal dynamics under climate change.

58 GEOSCIENCES↗

Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters

Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria, or in unclassified archaeal viruses predicted to infect Thaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mercury methylation by metabolically versatile and cosmopolitan marine bacteria

Microbes transform aqueous mercury (Hg) into methylmercury (MeHg), a potent neurotoxin that accumulates in terrestrial and marine food webs, with potential impacts on human health. This process requires the gene pair hgcAB, which encodes for proteins that actuate Hg methylation, and has been well described for anoxic environments. However, recent studies report potential MeHg formation in suboxic seawater, although the microorganisms involved remain poorly understood. In this study, we conducted large-scale multi-omic analyses to search for putative microbial Hg methylators along defined redox gradients in Saanich Inlet, British Columbia, a model natural ecosystem with previously measured Hg and MeHg concentration profiles. Analysis of gene expression profiles along the redoxcline identified several putative Hg methylating microbial groups, including Calditrichaeota, SAR324 and Marinimicrobia, with the last the most active based on hgc transcription levels. Marinimicrobia hgc genes were identified from multiple publicly available marine metagenomes, consistent with a potential key role in marine Hg methylation. Computational homology modelling predicts that Marinimicrobia HgcAB proteins contain the highly conserved amino acid sites and folding structures required for functional Hg methylation. Furthermore, a number of terminal oxidases from aerobic respiratory chains were associated with several putative novel Hg methylators. Our findings thus reveal potential novel marine Hg-methylating microorganisms with a greater oxygen tolerance and broader habitat range than previously recognized.

59 BASIC BIOLOGICAL SCIENCES↗

Evidence for methanobactin “Theft” and novel chalkophore production in methanotrophs: impact on methanotrophic-mediated methylmercury degradation

Abstract Aerobic methanotrophy is strongly controlled by copper, and methanotrophs are known to use different mechanisms for copper uptake. Some methanotrophs secrete a modified polypeptide—methanobactin—while others utilize a surface-bound protein (MopE) and a secreted form of it (MopE*) for copper collection. As different methanotrophs have different means of sequestering copper, competition for copper significantly impacts methanotrophic activity. Herein, we show that Methylomicrobium album BG8, Methylocystis sp. strain Rockwell, and Methylococcus capsulatus Bath, all lacking genes for methanobactin biosynthesis, are not limited for copper by multiple forms of methanobactin. Interestingly, Mm. album BG8 and Methylocystis sp. strain Rockwell were found to have genes similar to mbnT that encodes for a TonB-dependent transporter required for methanobactin uptake. Data indicate that these methanotrophs “steal” methanobactin and such “theft” enhances the ability of these strains to degrade methylmercury, a potent neurotoxin. Further, when mbnT was deleted in Mm. album BG8, methylmercury degradation in the presence of methanobactin was indistinguishable from when MB was not added. Mc. capsulatus Bath lacks anything similar to mbnT and was unable to degrade methylmercury either in the presence or absence of methanobactin. Rather, Mc. capsulatus Bath appears to rely on MopE/MopE* for copper collection. Finally, not only does Mm. album BG8 steal methanobactin, it synthesizes a novel chalkophore, suggesting that some methanotrophs utilize both competition and cheating strategies for copper collection. Through a better understanding of these strategies, methanotrophic communities may be more effectively manipulated to reduce methane emissions and also enhance mercury detoxification in situ.

59 BASIC BIOLOGICAL SCIENCES↗

Microbial drivers of methane emissions from unrestored industrial salt ponds

Wetlands are important carbon (C) sinks, yet many have been destroyed and converted to other uses over the past few centuries, including industrial salt making. A renewed focus on wetland ecosystem services (e.g., flood control, and habitat) has resulted in numerous restoration efforts whose effect on microbial communities is largely unexplored. We investigated the impact of restoration on microbial community composition, metabolic functional potential, and methane flux by analyzing sediment cores from two unrestored former industrial salt ponds, a restored former industrial salt pond, and a reference wetland. We observed elevated methane emissions from unrestored salt ponds compared to the restored and reference wetlands, which was positively correlated with salinity and sulfate across all samples. 16S rRNA gene amplicon and shotgun metagenomic data revealed that the restored salt pond harbored communities more phylogenetically and functionally similar to the reference wetland than to unrestored ponds. Archaeal methanogenesis genes were positively correlated with methane flux, as were genes encoding enzymes for bacterial methylphosphonate degradation, suggesting methane is generated both from bacterial methylphosphonate degradation and archaeal methanogenesis in these sites. These observations demonstrate that restoration effectively converted industrial salt pond microbial communities back to compositions more similar to reference wetlands and lowered salinities, sulfate concentrations, and methane emissions.

59 BASIC BIOLOGICAL SCIENCES↗

Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium

Abstract In many anoxic environments, syntrophic acetate oxidation (SAO) is a key pathway mediating the conversion of acetate into methane through obligate cross-feeding interactions between SAO bacteria (SAOB) and methanogenic archaea. The SAO pathway is particularly important in engineered environments such as anaerobic digestion (AD) systems operating at thermophilic temperatures and/or with high ammonia. Despite the widespread importance of SAOB to the stability of the AD process, little is known about their in situ physiologies due to typically low biomass yields and resistance to isolation. Here, we performed a long-term (300-day) continuous enrichment of a thermophilic (55 °C) SAO community from a municipal AD system using acetate as the sole carbon source. Over 80% of the enriched bioreactor metagenome belonged to a three-member consortium, including an acetate-oxidizing bacterium affiliated with DTU068 encoding for carbon dioxide, hydrogen, and formate production, along with two methanogenic archaea affiliated with Methanothermobacter_A. Stable isotope probing was coupled with metaproteogenomics to quantify carbon flux into each community member during acetate conversion and inform metabolic reconstruction and genome-scale modeling. This effort revealed that the two Methanothermobacter_A species differed in their preferred electron donors, with one possessing the ability to grow on formate and the other only consuming hydrogen. A thermodynamic analysis suggested that the presence of the formate-consuming methanogen broadened the environmental conditions where ATP production from SAO was favorable. Collectively, these results highlight how flexibility in electron partitioning during SAO likely governs community structure and fitness through thermodynamic-driven mutualism, shedding valuable insights into the metabolic underpinnings of this key functional group within methanogenic ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗

Sequence-selective dynamic covalent assembly of information-bearing oligomers

Relatively robust dynamic covalent interactions have been employed extensively to mediate molecular self-assembly reactions; however, these assembly processes often do not converge to a thermodynamic equilibrium, instead yielding mixtures of kinetically-trapped species. Here, we report a dynamic covalent self-assembly process that mitigates kinetic trapping such that multiple unique oligomers bearing covalently coreactive pendant groups are able to undergo simultaneous, sequence-selective hybridization with their complementary strands to afford biomimetic, in-registry molecular ladders with covalent rungs. Analogous to the thermal cycling commonly employed for nucleic acid melting and annealing, this is achieved by raising and lowering the concentration of a multi-role reagent to effect quantitative dissociation and subsequently catalyze covalent bond rearrangement, affording selective assembly of the oligomeric sequences. The hybridization specificity afforded by this process further enabled information encoded in oligomers to be retrieved through selective hybridization with complementary, mass-labeled sequences.

36 MATERIALS SCIENCE↗

Structural basis of RNA cap modification by SARS-CoV-2

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19 illness, has caused millions of infections worldwide. In SARS coronaviruses, the non-structural protein 16 (nsp16), in conjunction with nsp10, methylates the 5'-end of virally encoded mRNAs to mimic cellular mRNAs, thus protecting the virus from host innate immune restriction. We report here the high-resolution structure of a ternary complex of SARS-CoV-2 nsp16 and nsp10 in the presence of cognate RNA substrate analogue and methyl donor, S-adenosyl methionine (SAM). The nsp16/nsp10 heterodimer is captured in the act of 2'-O methylation of the ribose sugar of the first nucleotide of SARS-CoV-2 mRNA. We observe large conformational changes associated with substrate binding as the enzyme transitions from a binary to a ternary state. This induced fit model provides mechanistic insights into the 2'-O methylation of the viral mRNA cap. We also discover a distant (25 Å) ligand-binding site unique to SARS-CoV-2, which can alternatively be targeted, in addition to RNA cap and SAM pockets, for antiviral development.

59 BASIC BIOLOGICAL SCIENCES↗

An epigenetic gene silencing pathway selectively acting on transgenic DNA in the green alga Chlamydomonas

Abstract Silencing of exogenous DNA can make transgene expression very inefficient. Genetic screens in the model alga Chlamydomonas have demonstrated that transgene silencing can be overcome by mutations in unknown gene(s), thus producing algal strains that stably express foreign genes to high levels. Here, we show that the silencing mechanism specifically acts on transgenic DNA. Once a permissive chromatin structure has assembled, transgene expression can persist even in the absence of mutations disrupting the silencing pathway. We have identified the gene conferring the silencing and show it to encode a sirtuin-type histone deacetylase. Loss of gene function does not appreciably affect endogenous gene expression. Our data suggest that transgenic DNA is recognized and then quickly inactivated by the assembly of a repressive chromatin structure composed of deacetylated histones. We propose that this mechanism may have evolved to provide protection from potentially harmful types of environmental DNA.

Neupert, Juliane↗

Moiré metrology of energy landscapes in van der Waals heterostructures

The emerging field of twistronics, which harnesses the twist angle between two-dimensional materials, represents a promising route for the design of quantum materials, as the twist-angle-induced superlattices offer means to control topology and strong correlations. At the small twist limit, and particularly under strain, as atomic relaxation prevails, the emergent moiré superlattice encodes elusive insights into the local interlayer interaction. Here we introduce moiré metrology as a combined experiment-theory framework to probe the stacking energy landscape of bilayer structures at the 0.1 meV/atom scale, outperforming the gold-standard of quantum chemistry. Through studying the shapes of moiré domains with numerous nano-imaging techniques, and correlating with multi-scale modelling, we assess and refine first-principle models for the interlayer interaction. We document the prowess of moiré metrology for three representative twisted systems: bilayer graphene, double bilayer graphene and H-stacked MoSe 2 /WSe 2 . Moiré metrology establishes sought after experimental benchmarks for interlayer interaction, thus enabling accurate modelling of twisted multilayers.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Structural understanding of non-nucleoside inhibition in an elongating herpesvirus polymerase

All herpesviruses encode a conserved DNA polymerase that is required for viral genome replication and serves as an important therapeutic target. Currently available herpesvirus therapies include nucleoside and non-nucleoside inhibitors (NNI) that target the DNA-bound state of herpesvirus polymerase and block replication. Here we report the ternary complex crystal structure of Herpes Simplex Virus 1 DNA polymerase bound to DNA and a 4-oxo-dihydroquinoline NNI, PNU-183792 (PNU), at 3.5 Å resolution. PNU bound at the polymerase active site, displacing the template strand and inducing a conformational shift of the fingers domain into an open state. These results demonstrate that PNU inhibits replication by blocking association of dNTP and stalling the enzyme in a catalytically incompetent conformation, ultimately acting as a nucleotide competing inhibitor (NCI). Sequence conservation of the NCI binding pocket further explains broad-spectrum activity while a direct interaction between PNU and residue V823 rationalizes why mutations at this position result in loss of inhibition.

59 BASIC BIOLOGICAL SCIENCES↗

Ecology and molecular targets of hypermutation in the global microbiome

Abstract Changes in the sequence of an organism’s genome, i.e., mutations, are the raw material of evolution. The frequency and location of mutations can be constrained by specific molecular mechanisms, such as diversity-generating retroelements (DGRs). DGRs have been characterized from cultivated bacteria and bacteriophages, and perform error-prone reverse transcription leading to mutations being introduced in specific target genes. DGR loci were also identified in several metagenomes, but the ecological roles and evolutionary drivers of these DGRs remain poorly understood. Here, we analyze a dataset of >30,000 DGRs from public metagenomes, establish six major lineages of DGRs including three primarily encoded by phages and seemingly used to diversify host attachment proteins, and demonstrate that DGRs are broadly active and responsible for >10% of all amino acid changes in some organisms. Overall, these results highlight the constraints under which DGRs evolve, and elucidate several distinct roles these elements play in natural communities.

59 BASIC BIOLOGICAL SCIENCES↗