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DOE OSTI2022

microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes

Remote sensing approaches have revolutionized the study of macroorganisms, allowing theories of population and community ecology to be tested across increasingly larger scales without much compromise in resolution of biological complexity. In microbial ecology, our remote window into the ecology of microorganisms is through the lens of genome sequencing. For microbial organisms, recent evidence from genomes recovered from metagenomic samples corroborate a highly complex view of their metabolic diversity and other associated traits which map into high physiological complexity. Regardless, during the first decades of this omics era, microbial ecological research has primarily focused on taxa and functional genes as ecological units, favoring breadth of coverage over resolution of biological complexity manifested as physiological diversity. Recently, the rate at which provisional draft genomes are generated has increased substantially, giving new insights into ecological processes and interactions. From a genotype perspective, the wide availability of genome-centric data requires new data synthesis approaches that place organismal genomes center stage in the study of environmental roles and functional performance. Extraction of ecologically relevant traits from microbial genomes will be essential to the future of microbial ecological research. Here, we present microTrait , a computational pipeline that infers and distills ecologically relevant traits from microbial genome sequences. microTrait maps a genome sequence into a trait space, including discrete and continuous traits, as well as simple and composite. Traits are inferred from genes and pathways representing energetic, resource acquisition, and stress tolerance mechanisms, while genome-wide signatures are used to infer composite, or life history, traits of microorganisms. This approach is extensible to any microbial habitat, although we provide initial examples of this approach with reference to soil microbiomes.

Karaoz, Ulas↗

DOE OSTI2022

Geographic patterns and determinants of antibiotic resistomes in coastal sediments across complex ecological gradients

Coastal areas are highly influenced by terrestrial runoffs and anthropogenic disturbances, commonly leading to ecological gradients from bay, nearshore, to offshore areas. Although the occurrence and distribution of sediment antibiotic resistome are explored in various coastal environments, little information is available regarding geographic patterns and determinants of coastal sediment antibiotic resistomes across ecological gradients at the regional scale. Here, using high-throughput quantitative PCR, we investigated the geographic patterns of 285 antibiotic resistance genes (ARGs) in coastal sediments across a ~ 200 km scale in the East China Sea. Sediment bacterial communities and physicochemical properties were characterized to identify the determinants of sediments antibiotic resistome. Higher richness and abundance of ARGs were detected in the bay samples compared with those in nearshore and offshore samples, and significant negative correlations between the richness and/or abundance of ARGs and the distance to coastline (DTC) were identified, whereas different types of ARGs showed inconsistency in their relationships with DTC. The composition of antibiotic resistome showed significant correlations with nutrition-related variables (including NH 4 + -N, NO 3 − -N, and total phosphorus) and metals/metalloid (including As, Cu, Ni, and Zn), suggesting that terrestrial disturbances largely shape the antibiotic resistome. The Bipartite network showed strong associations between ARGs and mobile genetic elements (MGEs), and Partial Least Squares Path Modeling further revealed that terrestrial disturbance strength (as indicated by DTC) directly affected abiotic environmental conditions and bacterial community composition, and indirectly affected antibiotic resistome via MGEs. These findings provide insights into regional variability of sediment antibiotic resistome and its shaping path across complex ecological gradients, highlighting terrestrial disturbances as determinative forces in shaping coastal sediment antibiotic resistomes.

Xiong, Shangling↗

DOE OSTI2024

Growth and Stability of Stratiform Carrollite (CuCo2S4) in the Tenke-Fungurume Ore District, Central African Copperbelt

Abstract Carrollite (CuCo2S4) is the main ore mineral of the critical battery metal cobalt, yet, surprisingly, detailed characterization of its thermodynamic properties and of its trace element contents remain sparse in the scientific literature. To fill these knowledge gaps, we generated the first thermodynamic data set for carrollite using well-characterized samples obtained from the stratiform sulfide mineralization style at Fungurume 88 deposit in the Democratic Republic of Congo. Detailed mineralogical investigation of these same samples suggests that carrollite has limited ability to incorporate other ‘sweetener’ elements (except Cu and Ni) by substitution mechanisms. Modeling using CHNOSZ 2.0.0. software and an integrated Cu-Co-S-O thermodynamic data set provides insights into the stability of carrollite relative to other Co-bearing minerals under physicochemical conditions relevant to the Central African Copperbelt. Further exploration of these models indicates that dropping redox potential in the mineralizing system is insufficient to explain the mineral-scale and deposit-scale zonation patterns commonly observed in Cu-Co deposits of the Central African Copperbelt. Instead, factors such as increasing pH, decreasing T, decreasing sulfur activity, or some combination of changing physicochemical parameters may need to be invoked to explain these zonation trends. At the Fungurume 88 deposit, the absence of linnaeite (Co3S4) suggests that ore precipitation occurred at temperatures cooler than 211 °C. From our pH-logfO2 diagrams, and relative to higher temperatures, such a lower T regime is marked by a greater degree of offset between the modeled Cu and Co solubility contours, thus facilitating a more differentiated and zoned distribution of these two metals at the deposit scale. Our models are offered to the geoscience community as exceptionally useful tools for modeling and visualizing the Cu-Co-S-O systematics and may be applied to a variety of geological and geometallurgical questions in the Central African Copperbelt and other deposits elsewhere.

Mineralogy↗

DOE OSTI2020

Multi-Scale Modeling Framework for Mercury Biogeochemistry

Multi-Scale modeling of mercury (Hg) geochemical speciation and reactions has been performed by integrating atomistic quantum chemical calculations with continuum scale speciation models. Major progress has been made in the improvement of quantum chemical models to calculate critical thermodynamic data for Hg complexes in aquatic environments. Rapid and reliable quantum chemical approaches have been developed for calculating acid dissociation constants (pK a ) and stability constants (log K), with calculated mean unsigned errors of 0.5 and 1.5 log units, respectively for ligand molecules and Hg complexes. At the continuum scale, systematic analysis of uncertainty propagation in mercury (Hg) speciation modeling has been conducted and was used to identify environmental conditions under which thermodynamic constant uncertainties are significant and recommended to be accounted for. The integrated framework for multi-scale modeling of mercury geochemistry is open to the research community through the web-based multiscale modeling aqueous speciation resource, AQUA-MER. The improved quantum chemical approaches for thermodynamic constant calculations are accessible through AQUA-MER and can be used to provide the missing constants in the continuum scale speciation calculations. In addition to low molecular mass Hg complex speciation, modeling natural aquatic environments also involve the transport of high molecular weight dissolved organic matter (DOM) in reactive flows simultaneously with equilibrium and kinetic reactions. To this end, atomistic MD simulations were performed to capture the details of aggregation, mechanisms and distribution of functional groups in DOM at the molecular level. The elemental composition and calculated bulk properties of the DOM models are in close agreement with experimental measurements. A travel-time based reactive transport model in the hyporheic zone of stream corridors was established for the multicomponent Hg-DOM-S system and implemented through PFLOTRAN.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Geochemical and microbial characteristics of seepage water and mineral precipitates in a radwaste disposal facility impacted by seawater intrusion and high alkalinity

The construction of an underground facility can dramatically change the quality, flow direction, and level of groundwater. It may also impact subsurface microbial composition and activity. Groundwater quality was monitored over eight years in two observational wells near an underground disposal facility on the east coast of South Korea. The results showed dramatic increases in dissolved ions such as O 2 , Na, Ca, Mg, and SO 4 during facility construction. Seepage water samples downgradient from the silos and tunnels, and precipitates deposited along the seepage water flow path were collected to determine the impact inside the disposal facility. X-ray analysis (powder X-ray diffraction (pXRD) and X-ray absorption fine structure (XAFS)) were used to characterize the mineral precipitates. Microbial community composition was determined by 16S rRNA gene sequencing. The seepage water composition was of two types: Ca-Cl and Ca-Na-HCO 3 . The ratio of Cl and δ 18 O showed that the Ca-Cl type seepage water was influenced by groundwater mixed with seawater ranging from 2.7% to 15.1%. Various sulfate-reducing bacteria were identified in the Ca-Cl type seepage water, exhibiting relatively high sulfate content from seawater intrusion. Samples from the Ca-Na-HCO 3 type seepage water had an extremely high pH (>10) and abundance of Hydrogenophaga. The precipitates observed along the flow path of the seepage water included calcite, ferrihydrite, green rust, and siderite, depending on seepage water chemistry and microbial activity. This study suggests that the construction of underground structures creates distinct, localized geochemical conditions (e.g., high alkalinity, high salinity, and oxic conditions), which may impact microbial communities. These biogeochemical changes may have undesirable large-scale impacts such as water pump clogging. Overall, an understanding of the process and long-term monitoring are essential to assess the safety of underground facilities.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Unexpected Changes of Aerosol Burdens With Decreased Convection in the Context of Scale-Aware Convection Schemes

Atmospheric aerosols in global climate models (GCMs) can be removed by both large-scale and convective precipitation. As the horizontal resolution of GCMs increases, it is expected that large-scale precipitation increases and convective precipitation decreases if scale-aware convection schemes are well developed. Here, to explore its impact on aerosol burdens, this study develops a novel method and applies it to the National Center for Atmospheric Research Community Atmosphere Model version 5.3 to mimic the behavior of scale-aware convective schemes. Surprisingly, it is found that aerosol burden increases globally as convective precipitation decreases and large-scale precipitation increases, which can be attributed to the reduced light rain. In the light-rain intensity category, the decreased frequency of convective precipitation is not offset by the increased frequency of large-scale precipitation. Therefore, for aerosol simulations in high-resolution GCMs using scale-aware convection schemes, subgrid convection and large-scale condensation should be coordinated to assure light rain stays the same.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Novel Approaches Toward Scalable Composable Workflows in Hyper-Heterogeneous Computing Environments

The annual Workshop on Workflows in Support of Large-Scale Science (WORKS) is a premier venue for the scientific workflow community to present the latest advances in research and development on the many facets of scientific workflows throughout their life-cycle. The Lightning Talks at WORKS focus on describing a novel tool, scientific workflow, or concept, which are work-in-progress and address emerging technologies and frameworks to foster discussion in the community. This paper summarizes the lightning talks at the 2023 edition of WORKS, covering five topics: leveraging large language models to build and execute workflows; developing a common workflow scheduler interface; scaling uncertainty workflow applications on exascale computing systems; evaluating a transcriptomics workflow for cloud vs. HPC systems; and best practices in migrating legacy workflows to workflow management systems.

Titov, Mikhail↗

DOE OSTI2022

Continuous Fiber Bath Treatments at Pilot Scale: A Novel Testbed System

The technical demands on high performance textiles continues to expand, and the research community has answered the call with innovative fiber bath treatments for enhanced properties and sizings for improved composites. However, little translation to greater scale has been demonstrated. To fill this gap, a novel, multifunctional system has been developed to explore polymer fiber treatment methods, the deployment of nanoadditive coatings and other sizings, and smart processing methods at the pilot scale. Continuous tows of fibers can be passed through a temperature-controlled, crossflow bath with an immersion residence time exceeding 2 hours. The modular system is resistant to corrosive solutions, includes additional inline stations for washing and drying after processing, is equipped with a bevy of sensors, pumps, and valves monitored and controlled by a LabView program, and can be fully contained in a standard lab fume hood. This new testbed system, when coupled with high fidelity materials characterization methods, will enable rapid evaluation of new fiber treatment methods at pilot-scale.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Plankton energy flows using a global size-structured and trait-based model

Plankton community models are critical tools for understanding the processes that shape marine plankton communities, how plankton communities impact biogeochemical cycles, and the feedbacks between community structure and function. Here, using the flexible Marine Biogeochemistry Library (MARBL), we present the Size-based Plankton ECological TRAits (MARBL-SPECTRA) model, which is designed to represent a diverse plankton community while remaining computationally tractable. MARBL-SPECTRA is composed of nine phytoplankton and six zooplankton size classes represented using allometric scaling relationships for physiological traits and interactions within multiple functional types. MARBL-SPECTRA is embedded within the global ocean component of the Community Earth System Model (CESM) and simulates large-scale, emergent patterns in phytoplankton growth limitation, plankton phenology, plankton generation time, and trophic transfer efficiency. The model qualitatively reproduces observed global patterns of surface nutrients, chlorophyll biomass, net primary production, and the biogeographies of a range of plankton size classes. In addition, the model simulates how predator:prey dynamics and trophic efficiency vary across gradients in total ecosystem productivity. Shorter food chains that export proportionally more carbon from the surface to the ocean interior occur in productive, eutrophic regions, whereas in oligotrophic regions, the food chains are relatively long and export less organic matter from the surface. The union of functional type modeling with size-resolved, trait-based modeling approaches allows MARBL-SPECTRA to capture both large-scale elemental cycles and the structure of planktonic food webs affecting trophic transfer efficiency.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Assessment of the ParFlow–CLM CONUS 1.0 integrated hydrologic model: evaluation of hyper-resolution water balance components across the contiguous United States

Abstract. Recent advancements in computational efficiency and Earth system modeling have awarded hydrologists with increasingly high-resolution models of terrestrial hydrology, which are paramount to understanding and predicting complex fluxes of moisture and energy. Continental-scale hydrologic simulations are, in particular, of interest to the hydrologic community for numerous societal, scientific, and operational benefits. The coupled hydrology–land surface model ParFlow–CLM configured over the continental United States (PFCONUS) has been employed in previous literature to study scale-dependent connections between water table depth, topography, recharge, and evapotranspiration, as well as to explore impacts of anthropogenic aquifer depletion to the water and energy balance. These studies have allowed for an unprecedented process-based understanding of the continental water cycle at high resolution. Here, we provide the most comprehensive evaluation of PFCONUS version 1.0 (PFCONUSv1) performance to date by comparing numerous modeled water balance components with thousands of in situ observations and several remote sensing products and using a range of statistical performance metrics for evaluation. PFCONUSv1 comparisons with these datasets are a promising indicator of model fidelity and ability to reproduce the continental-scale water balance at high resolution. Areas for improvement are identified, such as a positive streamflow bias at gauges in the eastern Great Plains, a shallow water table bias over many areas of the model domain, and low bias in seasonal total water storage amplitude, especially for the Ohio, Missouri, and Arkansas River basins. We discuss several potential sources for model bias and suggest that minimizing error in topographic processing and meteorological forcing would considerably improve model performance. Results here provide a benchmark and guidance for further PFCONUS model development, and they highlight the importance of concurrently evaluating all hydrologic components and fluxes to provide a multivariate, holistic validation of the complete modeled water balance.

O'Neill, Mary M. F. (ORCID:0000000221455165)↗

DOE OSTI2023

ResStock: Annual Baseline Results with Component Loads

The ResStock Analysis Tool was developed by NREL with support from the U.S. Department of Energy to provide a new approach to large-scale residential analysis by combining large public and private data sources, statistical sampling, detailed sub hourly building simulations, and high-performance computing. This combination achieves unprecedented granularity and accuracy in modeling the diversity of the housing stock and the distributional impacts of building technologies in different communities. The annual baseline energy results from a national-scale ResStock run use typical meteorological year 3 (TMY3) files for energy simulations. Results include heating and cooling loads for individual components of each building. Component loads describe the heating/cooling load that can be attributed to specific elements of a home, such as heat transfer through walls or internal gains. Additionally, these results include the standard ResStock outputs for housing characteristics and numerous energy outputs by end-use and fuel. A snapshot of the ResStock version used to produce this data, including a configuration file for the run can be found using the Source Code resource link.

Array↗

DOE OSTI2025

Characterizing How Meteorological Forcing Selection and Parameter Uncertainty Influence Community Land Model Version 5 Hydrological Applications in the United States

Despite the increasing use of large-scale Land Surface Models (LSMs) in predicting hydrological responses in extreme conditions, there's a critical gap in understanding the uncertainties in these predictions. This study addresses this gap through a detailed diagnostic evaluation of the uncertainties arising from meteorological forcing selection and model parametrization in hydrological simulations of the Community Land Model version 5 (CLM5). CLM5 is configured at a spatial scale of about 12-km to simulate runoff processes for 464 headwater watersheds, selected from the Catchment Attributes for Large-Sample Studies (CAMELS) dataset to be representative of physiographic and climatic gradients across the conterminous United States. For each watershed, CLM5 is driven by five commonly used gridded forcing datasets in combination with a large ensemble (> 1200) of key CLM5 hydrologic parameters. Our results suggest that uncertainty in CLM5 runoff simulations resulting from both forcing and parametric sources is markedly higher in arid regions, e.g., Great Plains and Midwest regions. Uncertainty in low flow is dominated by parametric uncertainty, while the selection of meteorological forcing contributes more dominantly to high flow and seasonal flows during fall and spring. Our analysis also demonstrates that the selection of forcing datasets and the metrics used to calibrate CLM5 significantly impact the model’s predictive accuracy in extreme event severity for both floods and droughts. Overall, the results from this study highlight the need to understand and account for forcing and parametric uncertainties in CLM5 simulations, particularly for hazard and risk assessments addressing hydrologic extremes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Process-oriented evaluation of quasi-stationary Rossby waves and their impact on surface air temperature extremes in dynamical downscaling over North America

Quasi-stationary Rossby waves are a crucial component of the general circulation and play a significant role in regional water and energy cycles, as well as in extreme events. However, process-oriented evaluation for Rossby waves is rarely performed for dynamical downscaling simulations. To close this gap, we evaluate three classes of dynamical downscaling approaches, with a focus on quasi-stationary Rossby waves and their impact on surface air temperature over North America during Northern Hemisphere summer. The three classes of models differ in the way large-scale forcing is provided: a limited-area model (LAM) constrained only by lateral boundary conditions, represented by RegCM4 from the North American branch of the Coordinated Regional Downscaling Experiment (NA-CORDEX), a LAM with spectral nudging to maintain consistency in large-scale dynamics with the forcing data, represented by the Weather Research and Forecasting (WRF) model simulation in NA-CORDEX, and a global variable-resolution model with smoothly varying grid spacings, represented by the Community Atmosphere Model version 5.4, with the Model for Prediction Across Scales (MPAS) as its dynamical core (CAM-MPAS). With no constraints on the atmospheric dynamics, CAM-MPAS exhibits several mean biases in the upper-level circulations over the Pacific Coast region: a weaker subtropical jet, a northward-shifted mid-latitude jet, and an overestimated southerly flow. With the lateral boundary constraint alone, RegCM4 also exhibits weaker jets and overestimated southerly winds off the West Coast. Rossby ray theory reveals that those wind biases direct incoming Rossby waves northward. The erroneously routed Rossby waves distort the relationship between the accumulation of wave activity over the US West Coast and surface temperature anomalies over the Southern Great Plains, which emerges approximately 4 d after the convergence of wave-activity flux in the ERA-Interim reanalysis. Furthermore, the response of heatwaves to the extreme wave activity flux is not reproduced by the two models, a serious drawback as a dynamical downscaling framework is expected to connect large-scale forcing to local-scale phenomena. The WRF model employing spectral nudging is largely free from the aforementioned problems. A pair of sensitivity simulations suggests that spectral nudging is the key to improving the dynamics of quasi-stationary Rossby waves and their impact on surface air temperature. Our results also demonstrate the effectiveness of Rossby wave diagnostics that allow for realistic background flows for assessing the credibility of dynamical downscaling over North America, where incoming Rossby waves propagate through complex circulation patterns before traveling across the continent.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Potential Challenges of HyBlend Storage in a Methane Reservoir Located in Southwestern United States

Hydrogen has been identified as a flexible energy carrier with zero or negative emissions across multiple energy systems. It is possible to utilize hydrogen by storing Hyblend, or hydrogen gas blended with methane, in existing natural gas infrastructure. However, the compatibility of adapting the current CH4 storage strategies to include H2 injection has not been fully demonstrated. It is essential that we understand the impact of H2 gas on the naturally occurring microbial community of subsurface storage reservoirs before deploying large-scale H2-CH4 storage. We designed a series of experiments that allowed us to identify potential geochemical and microbial challenges of HyBlend Storage in existing methane reservoirs. First, we collected and characterized field fluid samples from a methane reservoir located in southwestern United States. Next, we used these field fluid samples to complete a series of short-term reactor experiments at reservoir conditions (80 °C and ~1,000 psi) for a natural gas (100% CH4) and HyBlend(80% CH4/20% H2) storage environment to measure the transformation of gas content. We conducted both biotic and abiotic (sterilized) measurements to accurately understand and decouple abiotic and microbially driven processes. Overall, we found that our field sample was characterized by a diverse microbial community with the metabolic capacity for sulfur reduction, iron reduction, and acetogenesis. Across our reactors, there was minimal change in geochemistry.

hydrogen storage↗

DOE OSTI2025

Ecological acclimation: A framework to integrate fast and slow responses to climate change

Ecological responses to climate change occur across vastly different time-scales, from minutes for physiological plasticity to decades or centuries for community turnover and evolutionary adaptation. Accurately predicting the range of ecosystem trajectories will require models that incorporate both fast processes that may keep pace with climate change and slower ones likely to lag behind and generate disequilibrium dynamics. However, the knowledge necessary for this integration is currently fragmented across disciplines. We develop ‘ecological acclimation’ as a unifying framework to emphasize the similarity of dynamics driven by processes operating on dramatically different time-scales and levels of biological organization. The framework focuses on ecoclimate sensitivities, measured as the change in an ecological response variable per unit of climate change. Acclimation processes acting at different time-scales cause these sensitivities to shift in magnitude and even direction over time. We highlight shifting ecoclimate sensitivities in case studies from diverse ecosystems, including terrestrial plant communities, coral reefs and soil microbiomes. Models predicting future ecosystem states inevitably make assumptions about acclimation processes; these assumptions must be explicit for users to evaluate whether a model is appropriate for a given forecast horizon. Similarly, decision frameworks that clearly account for multiple acclimation processes and their distinct time-scales will help natural resource managers plan for ecological impacts of climate change from years to many decades into the future. We outline a synthetic research programme focused on the time-scales of ecological acclimation to reduce uncertainty in ecological forecasts.

climate adaptation↗

DOE OSTI2024

Changes in microbial community and network structure precede shrub degradation in a desert ecosystem

Large-scale restoration is intended to promote ecological recovery. Improvements in plant and microbial conditions, however, may slow or even reverse in late succession. To better understand long-term restoration outcomes and underlying drivers of successional pathways, we tracked plant, bacterial and fungal, and soil conditions across a 40-year shrub plantation that was intended to stabilize desertified land in northern China. Here, we found that planted Haloxylon ammodendron shrubs developed and then subsequently became degraded after 30–40 years. Bacterial abundance and α-diversity were much higher than those of fungi, but no significant differences in composition and structure were found in different plantation ages. In contrast, the dominant taxa of fungal communities shifted from symbiotroph and saprotroph species towards pathotroph species with increased soil nutrients in the plantation chronosequence after two decades. The changes in fungal dominant species led to a transition in microbial network structure and function, with an increase in negative linkages among taxa that began in the middle stages of succession. Changes in fungal community structure had direct and indirect negative effects on shrub leaf physiology, root activity, and biomass. Our results highlight the preceding role of a breakdown in soil microbial community composition and network structure on the degradation of shrub performance in long-term desert succession. Our study emphasizes the importance of understanding soil-microbial-plant linkages on restoration outcomes, and mechanisms that can slow or reverse the recovery of ecosystems.

Bacterial and fungal community composition↗

DOE OSTI2025

Implementation of Sub‐Grid Scale Temperature Perturbations Induced by Non‐Orographic Gravity Waves in WACCM6

Abstract Atmospheric gravity waves can play a significant role on atmospheric chemistry through temperature fluctuations. A recent modeling study introduced a method to implement subgrid‐scale orographic gravity‐wave‐induced temperature perturbations in the Whole Atmosphere Community Climate Model (WACCM). The model with a wave‐induced temperature parameterization was able to reproduce for example, the influence of mountain wave events on atmospheric chemistry, as highlighted in previous literature. Here we extend the subgrid‐scale wave‐induced temperature parameterization to also include non‐orographic gravity waves arising from frontal activity and convection. We explore the impact of these waves on middle atmosphere chemistry, particularly focusing on reactions that are strongly sensitive to temperature. The non‐orographic gravity waves increase the variability of chemical reaction rates, especially in the lower mesosphere. As an example, we show that this, in turn, leads to increases in the daytime ozone variability. To demonstrate another impact, we briefly investigate the role of non‐orographic gravity waves in cirrus cloud formation in this model. Consistent with findings from the previous study focusing on orographic gravity waves, non‐orographic waves also enhance homogeneous nucleation and increase cirrus clouds. The updated method used enables the global chemistry‐climate model to account for both orographic and non‐orographic gravity‐wave‐induced subgrid‐scale dynamical perturbations in a consistent manner.

Yook, Simchan [Department of Earth Atmospheric and↗

DOE OSTI2024

Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study

There is limited data on human immunodeficiency virus (HIV) evolutionary trends in African populations. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a 24-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based HIV surveillance cohort. Gag (p24) and env (gp41) HIV data were generated from people living with HIV (PLHIV) in 31 inland semi-urban trading and agrarian communities (1994–2018) and four hyperendemic Lake Victoria fishing communities (2011–2018) under continuous surveillance. HIV subtype was assigned using the Recombination Identification Program with phylogenetic confirmation. Inter-subtype diversity was evaluated using the Shannon diversity index, and intra-subtype diversity with the nucleotide diversity and pairwise TN93 genetic distance. Genetic divergence was measured using root-to-tip distance and pairwise TN93 genetic distance analyses. Demographic history of HIV was inferred using a coalescent-based Bayesian Skygrid model. Evolutionary dynamics were assessed among demographic and behavioral population subgroups, including by migration status. 9931 HIV sequences were available from 4999 PLHIV, including 3060 and 1939 persons residing in inland and fishing communities, respectively. In inland communities, subtype A1 viruses proportionately increased from 14.3% in 1995 to 25.9% in 2017 (P < .001), while those of subtype D declined from 73.2% in 1995 to 28.2% in 2017 (P < .001). The proportion of viruses classified as recombinants significantly increased by nearly four-fold from 12.2% in 1995 to 44.8% in 2017. Inter-subtype HIV diversity has generally increased. While intra-subtype p24 genetic diversity and divergence leveled off after 2014, intra-subtype gp41 diversity, effective population size, and divergence increased through 2017. Intra- and inter-subtype viral diversity increased across all demographic and behavioral population subgroups, including among individuals with no recent migration history or extra-community sexual partners. This study provides insights into population-level HIV evolutionary dynamics following the scale-up of HIV prevention and treatment programs. Continued molecular surveillance may provide a better understanding of the dynamics driving population HIV evolution and yield important insights for epidemic control and vaccine development.

60 APPLIED LIFE SCIENCES↗