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DOE OSTI2025

Community‐Level Metabolic Shifts Following Land Use Change in the Amazon Rainforest Identified by a Supervised Machine Leaning Approach

ABSTRACT The Amazon rainforest has been subjected to high rates of deforestation, mostly for pasturelands, over the last few decades. This change in plant cover is known to alter the soil microbiome and the functions it mediates, but the genomic changes underlying this response are still unresolved. In this study, we used a combination of deep shotgun metagenomics complemented by a supervised machine learning approach to compare the metabolic strategies of tropical soil microbial communities in pristine forests and long‐term established pastures in the Amazon. Machine learning‐derived metagenome analysis indicated that microbial community structures (bacteria, archaea and viruses) and the composition of protein‐coding genes were distinct in each plant cover type environment. Forest and pasture soils had different genomic diversities for the above three taxonomic groups, characterised by their protein‐coding genes. These differences in metagenome profiles in soils under forests and pastures suggest that metabolic strategies related to carbohydrate and energy metabolisms were altered at community level. Changes were also consistent with known modifications to the C and N cycles caused by long‐term shifts in aboveground vegetation and were also associated with several soil physicochemical properties known to change with land use, such as the C/N ratio, soil temperature and exchangeable acidity. In addition, our analysis reveals that these alterations in land use can also result in changes to the composition and diversity of the soil DNA virome. Collectively, our study indicates that soil microbial communities shift their overall metabolic strategies, driven by genomic alterations observed in pristine forests and long‐term established pastures with implications for the C and N cycles.

carbon and nitrogen cycles↗

DOE OSTI2025

Multivariate environmental and trait-based controls of transpiration in the Central Amazon Rainforest

Tropical forest tree mortality is increasing due to more severe droughts, yet our understanding of how tree traits and life strategies are linked to drought stress has been limited by measurement scarcity. The BIONTE (BIOmass and NuTrient Experiment) near Manaus, Brazil hosts one of the world’s largest sap flow installations, with sensors in 90 canopy trees across a wood density gradient monitored since June 2022. The 2023 El Niño drought provided a unique opportunity to evaluate how water availability impacts tree transpiration. An interpretable machine learning framework was used to study the complex interactions between transpiration and multiple environmental variables such as soil water availability and vapor pressure deficit (VPD), and how these interactions vary with wood density and individual trees. We found varying responses of transpiration from different trees during the El Niño drought. Transpiration generally increased with temperature, with stronger effects in wetter areas and in trees with low to medium wood density. However, this response was modulated by stomatal sensitivity to VPD, which constrained transpiration under high atmospheric demand, particularly in intermediate-moisture area. The inflection in transpiration rate at high temperatures (>32°C) underscores the role of stomatal and hydraulic regulation in limiting water loss and protecting trees from excessive evaporative demand. Analysis of soil water contribution to transpiration revealed unimodal patterns in wetter area, with peak contributions near 0.45 cm 3 cm -3 of surface soil water and declining or flat responses beyond that threshold, suggesting a shift from water- to energy-limited transpiration. In contrast, drier areas exhibited limited transpiration sensitivity to soil water conditions and minimal trait-based variation in VPD responses, indicating supply-limited conditions. Despite higher wood density trees being generally more resilient, this study shows diverse tree drought resilience, prompting further investigation into the specific traits and dynamics between environmental variables in regulating transpiration and other physiological processes in trees.

Drought↗

DOE OSTI2025

Weak influence of anthropogenic emissions on aerosol, cloud, and rain in the wet season of the Amazon rainforest

Anthropogenic emissions have been shown to affect new particle formation, aerosol concentrations, and clouds. Such effects vary with region, environmental conditions, and cloud types. In the wet season of Amazonia, anthropogenic emissions emitted from Manaus, Brazil, can significantly increase the cloud condensation nuclei (CCN) concentrations compared to the background of mainly natural aerosols. However, the regional response of cloud and rain to anthropogenic emissions in Amazonia remains very uncertain. Here, we aim to quantify how aerosol concentration, cloud, and rain respond to changes in anthropogenic emissions through parameterized new particle formation and primary aerosol emission in the Manaus region and to understand the underlying mechanisms. We ran the atmosphere-only configuration of the HadGEM3 climate model with a nested regional domain that covers most of the rainforest region (720 km by 1200 km with 3 km resolution) under scaled regional emissions. The 7 d simulations show that, in the areas that are affected by anthropogenic emissions, when aerosol and precursor gas emissions are doubled from the baseline emission inventories, aerosol number concentrations increase by 13 %. The nucleation rate that involves sulfuric acid and biogenic compounds generally increases with pollution levels. However, nucleation is suppressed very close to the pollution source, resulting in lower nucleation and soluble Aitken mode aerosol number concentrations. We also found that doubling the anthropogenic emission can increase the cloud droplet number concentrations ( N d ) by 9 %, but cloud water and rain mass mixing ratios do not change significantly. Even very strong reductions in aerosol number concentrations by a factor of 4, which is an unrealistic condition, cause only a 4 % increase in rain over the domain. If we assume our simulation has a fine enough grid resolution and an accurate representation of the relevant atmospheric processes, the simulated weak and non-linear response of cloud and rain properties to linearly scaled anthropogenic emissions suggests that the interactions among aerosol, cloud, and precipitation in the Amazonian convective environment are buffered by microphysical processes. It also implies that the convective environment is resilient to the changes in Nd that occur in response to localized anthropogenic aerosol perturbations.

Wang, Xuemei [University of Leeds (United Kingdom)↗

DOE OSTI2026

Final DOE-ASR Report for the Project “Using LASSO to bridge the gap between model and observations and to learn about atmospheric convection”

Atmospheric convection spans a wide range of spatial and temporal scales and involves complex interactions with the surrounding dynamic and thermodynamic environment, particularly over tropical continental regions. These processes remain a major source of uncertainty in weather and climate models, including persistent biases in the diurnal cycle of convective precipitation that directly affect estimates of climate sensitivity. Addressing these challenges requires the combined use of high-resolution observations and cloud-resolving modeling frameworks. In this context, the DOE Atmospheric Radiation Measurement (ARM) program’s Large-Eddy Simulation ARM Symbiotic Simulation and Observation (LASSO) activity provides a powerful platform that pairs comprehensive observations with numerical simulations to enable process-level understanding of atmospheric convection. Within this context, this Research and Development Partnership Pilot (RDPP) project was designed to initiate and expand DOE ARM/ASR research capacity at minority-serving institutions, while advancing scientific understanding of convective processes over the Amazon rainforest. Consistent with the RDPP mission, the project emphasized partnership development, training, and workforce capacity building alongside exploratory research activities. On the scientific side, the project produced two peer-reviewed journal articles, and one manuscript currently under review (see list in section 3.1). Together, these studies combine long-term ARM observations and cloud-resolving and convection-permitting modeling to investigate the environmental controls on the shallow-to-deep convective transition during the Amazon wet season. The results demonstrate the central role of early-day moisture preconditioning and large-scale dynamical forcing in regulating isolated deep convection, provide mechanistic insight into convective evolution, and establish physically informed modeling frameworks for future sensitivity experiments. These scientific outcomes are described in sections 2.1 to 2.3 and were disseminated in 8 conference presentations (see section 3.2) and 5 invited talks (see section 3.3), reflecting broad engagement with our community. Equally important, the project achieved its RDPP capacity-building objectives (see section 2.4). A sustained research partnership was established among the University of Maryland, Baltimore County (UMBC), Morgan State University (MSU), and Howard University (HU), and extended to include collaboration with Pacific Northwest National Laboratory (PNNL). The project organized multiple multi-day training events focused on ARM data, LASSO simulations, and quantitative analysis methods, directly engaging students, postdoctoral researchers, and faculty across institutions. These activities broadened participation in ASR research and led to independent adoption of LASSO workflows by students beyond the immediate project team. Finally, the project successfully positioned the participating institutions to pursue future DOE research. Preliminary scientific results, coupled with strengthened partnerships and technical capacity, enabled the submission of follow-on proposals to DOE ASR funding opportunities. In this way, the project fulfilled the RDPP goal of seeding durable research capacity and laying the foundation for larger-scale, sustained engagement with DOE ARM and ASR programs.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Quantifying and Modeling the Impact of Phase State on the Ice Nucleation Abilities of 2-Methyltetrols as a Key Component of Secondary Organic Aerosol Derived from Isoprene Epoxydiols

Organic aerosols (OAs) may serve as ice-nucleating particles (INPs), impacting the formation and properties of cirrus clouds when their phase state and viscosity are in the semisolid to glassy range. However, there is a lack of direct parameterization between aerosol viscosity and their ice nucleation capabilities. In this study, we experimentally measured the ice nucleation rate of 2-methyltetrols (2-MT) aerosols, a key component of isoprene-epoxydiol-derived secondary organic aerosols (IEPOX-SOA), at different viscosities. These results demonstrate that the phase state has a significant impact on the ice nucleation abilities of OA under typical cirrus cloud conditions, with the ice nucleation rate increasing by 2 to 3 orders of magnitude when the phase state changes from liquid to semisolid. An innovative parametric model based on classical nucleation theory was developed to directly quantify the impact of viscosity on the heterogeneous nucleation rate. This model accurately represents our laboratory measurement and can be implemented into climate models due to its simple, equation-based form. Based on data collected from the ACRIDICON-CHUVA field campaign, our model predicts that the INP concentration from IEPOX-SOA can reach the magnitude of 1 to tens per liter in the cirrus cloud region impacted by the Amazon rainforest, consistent with recent field observations and estimations. This novel parameterization framework can also be applied in regional and global climate models to further improve representations of cirrus cloud formation and associated climate impacts.

2-methyltetrol↗

DOE OSTI2026

GPM IMERG V07B and V06B: Evaluation Using Ground-Based Radar Observations and Application in Global Mesoscale Convective System Tracking

This study evaluates the latest Global Precipitation Measurement (GPM) Integrated Multi-satellitE Retrievals for GPM (IMERG V07B) against its predecessor V06B, for studying mesoscale convective systems (MCSs). Both versions are compared using ground-based radar and rain gauge data from five meteorologically diverse regions: the contiguous United States (including eastern coastlines), Amazon rainforest, central Argentina mountains, equatorial Indian Ocean, and northern Australia across multiple temporal (0.5–6 hours) and spatial scales (0.1°–0.25°). An updated global MCS tracking dataset is developed by integrating satellite-observed infrared brightness temperature with IMERG V07B. Comparation of IMERG against radar observations reveals that IMERG demonstrates better performance in capturing the probability distribution and quantitative contributions of rainfall (from no-rain to intense-rain conditions) over tropical oceans than over land, with marked improvements in IMERG V07B for heavy-to-intense rain (> 10 mm h-1). Over land, systematic biases persist: IMERG tends to overestimate light-to-moderate rain (1–10 mm h-1) while underestimating heavy-to-intense rain. Additionally, aggregating IMERG to coarser resolutions (3-hourly or 0.25°) improves consistency with radar observations, outperforming the 1-hourly/0.1° resolution. The new IMERG V07B-based global MCS dataset exhibits consistent statistical characteristics with the V06B-based dataset, despite lower mean rain rates and reduced heavy precipitation contributions. These findings offer valuable insights for utilizing IMERG V07B in global precipitation studies, MCS characterization, and model evaluation.

Zhang, Sihan↗

DOE OSTI2024

Observational evidence for Criegee intermediate oligomerization reactions relevant to aerosol formation in the troposphere

Criegee intermediates are reactive intermediates that are implicated in transforming the composition of Earth’s troposphere and in the formation of secondary organic aerosol, impacting Earth’s radiation balance, air quality and human health. Yet, direct identification of their signatures in the field remains elusive. Here, from particulate and gas-phase mass-spectrometric measurements in the Amazon rainforest, we identify sequences of masses consistent with the expected signatures of oligomerization of the CH 2 OO Criegee intermediate, a process implicated in ozonolysis-driven aerosol formation. In this study, we assess the potential contributions of oligomerization through laboratory ozonolysis experiments, direct kinetic studies of Criegee intermediate reactions, and high-level theoretical calculations. Global atmospheric models built on these kinetics results indicate that Criegee intermediate chemistry may play a larger role in altering the composition of Earth’s troposphere than is captured in current atmospheric models, especially in areas of high humidity. However, the models still capture only a relatively small fraction of the observed signatures, suggesting considerable underestimates of Criegee intermediate concentrations and reactivity and/or the dominance of other, presently uncharacterized, oxidation mechanisms. Resolving the remaining uncertainties in emission inventories and the effects of atmospheric water vapour on key chemical reactions will be required to definitively assess the role of Criegee intermediate oligomerization reactions.

58 GEOSCIENCES↗

DOE OSTI2026

Amazonian fog harbors viable microbes

Fog formation over tropical forests remains poorly characterized, despite its potential role in bioaerosol dispersion and ecosystem processes. Here, we analyzed fog samples collected at the Amazon Tall Tower Observatory using flow cytometry and culture-based techniques to characterize viable microbial communities. Microbial cell concentrations varied over an order of magnitude across 13 fog events, reaching up to 8 × 104 cells per ml of fog water. Flow cytometry consistently detected metabolically active cells, while culturing and mass spectrometry-based identification yielded eight viable bacterial species and seven fungal taxa. The bacteria Serratia marcescens, Ralstonia pickettii and Sphingomonas paucimobilis exhibited seasonal variations in prevalence. The fungal species identified were primarily mesophilic saprophytes and endophytes, commonly associated with soil and plant surfaces. Our findings indicate that fog harbors viable microbes, including Serratia marcescens and Ralstonia pickettii, which may imply a relevance of fog for microbial dispersal, colonization and nutrient cycling in the Amazon rainforest.

Godoi, Ricardo H. (ORCID:0000000247744870)↗

DOE OSTI2026

A multi‐variable framework for selecting WRF physics configurations at convection‐permitting scales: An Amazon wet‐season case study

Tropical convection over rainforests modulates atmospheric circulation and the energy and hydrological cycles across multiple scales. However, the scarcity of observations still limits our understanding of these processes. Although numerical models are utilized to investigate atmospheric physical processes, their performance depends on the choice of parameterizations and grid resolution. Here, in this work, we introduce and apply a multi‐variable, multi‐physics framework to evaluate and rank the Advanced Research Weather Research and Forecasting (WRF–ARW) configurations at 1‐km resolution over the central Amazon during the wet season. A 48‐member ensemble combines three land‐surface models (LSMs), four planetary boundary layer (PBL), and four microphysics (MP) schemes. Model performance for seven convection‐related near‐surface and boundary‐layer variables is assessed using Taylor diagrams and the Taylor skill score (TSS), analysis of variance (ANOVA)‐based sensitivity metrics, and non‐parametric rank tests. We then construct a combined, weighted TSS to identify configurations that are comparatively robust across variables. Results showed that most configurations reproduce near‐surface temperature, sensible and latent heat fluxes, and boundary‐layer height reasonably well, whereas humidity and rainfall remain challenging. LSM choice has the strongest impact on the surface fluxes and a secondary influence on near‐surface temperature and humidity, PBL schemes dominate boundary‐layer height, and MP schemes exert the largest control on rainfall. No single configuration is optimal for all variables, but the combination of Noah (LSM), Yonsei University (PBL), and Morrison (MP) emerges as the most robust configuration for this case, with the WRF single‐moment six‐class scheme (WSM6) providing a competitive, computationally cheaper MP alternative. The framework is general and can be applied to other regions, seasons, and convective regimes.

Amazon rainforest↗

DOE OSTI2025

Seasonal investigation of ultrafine-particle organic composition in an eastern Amazonian rainforest

Abstract. Reports on the composition of ultrafine particles (<100 nm in diameter) in the Amazon are scarce, due in part to the fact that new-particle formation has rarely been observed near ground level. Ultrafine particles near the surface have nevertheless been observed, leaving open questions regarding the sources and chemistry of their formation and growth, particularly as these vary across seasons. Here, we present measurements of the composition of ultrafine particles collected in the Tapajós National Forest (2.857° S, 54.959° W) during three different seasonal periods: 10–30 September 2016 (SEP), 18 November–23 December 2016 (DEC), and 22 May–21 June 2017 (JUN). Size-selected (5–70 nm) particles were collected daily (for 22 h each day) using an offline sampler. Samples collected during the three time periods were compiled and analyzed using liquid chromatography coupled with Orbitrap high-resolution mass spectrometry. Our findings suggest a sustained influence of isoprene organosulfate chemistry on ultrafine particles from the different periods. We present chemical evidence that indicates that biological-spore fragmentation impacted ultrafine-particle composition during the late wet season (JUN), while chemical markers for biomass burning and secondary chemistry peaked during the dry season (SEP and DEC). Higher oxidation states and degrees of unsaturation were observed for organics in the dry season (SEP and DEC), suggesting greater extents of aerosol aging. Finally, applying a volatility parameterization to the observed compounds suggests that organic sulfur species are likely key drivers of new-particle growth in the region due to their low volatility compared to other species.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Factors Controlling Precipitation Onset and Maintenance: Inferences From Large Eddy Simulations of Two Afternoon Deep Convective Regimes Over Amazon

To investigate the environmental factors controlling the onset and maintenance of afternoon precipitation over tropical rainforests, two contrasting cases are created for large eddy simulations (LES) using GoAmazon observations: one features a single-pulse rain dissipating quickly in earlier afternoon, while the other shows double pulses lasting until evening. For these two specific cases under consideration, LES confirms that early-morning relative humidity dominates afternoon rain patterns. The attributed impacts are distinct: moisture determines the rain onset timing while temperature affects the peak rain intensity. Single-pulse day observes one round of strong precipitation and cold pools, which further suppresses convection. On double-pulse day, the first precipitation peak results from an intermediate development of congestus clouds, whose detrainment leads to a gradual moistening of the lower-to-middle troposphere. This behavior of convection favors a second pulse of stronger precipitation with more convective organization, whose development decouples from surface fluxes and sustains until evening.

Amazon↗

DOE OSTI2025

The ATTO-Campina site: A new observatory for tropical convection and gas-aerosol-cloud-precipitation interactions in the Amazon

We present results from ATTO-Campina, a new permanent observational site in central Amazon, about 4 km from the ATTO towers. Operational since 2020, ATTO-Campina characterizes atmospheric, cloud and rainfall properties through remote sensing. The goal is to provide continuous, complementary measurements to the ATTO towers, addressing the rainforest’s complex gas-aerosol-cloud-precipitation dynamics. Using a 3.5-year dataset, we classified convective clouds into three types: shallow cumulus (ShCu), congestus (Con) or (Deep) clouds. The shallow-to-deep transition takes about three hours, starting with ShCu formation at 11:00 local time. The accumulated rainfall peak follows at about 16:00. Only weak downdrafts are present in the upper troposphere where previous studies indicate new particle formation (NPF) occurrence. Strong downdrafts are mostly limited to heights below 5 km. Con and Deep convective days have higher concentrations of ultrafine aerosol and lower concentrations of accumulation-mode particles compared to ShCu. Convective clouds also significantly modify gas mixing ratios. Deep convective clouds are associated with high near-surface O3, consistent with downward transport from the midtroposphere. Our results showcase the added detail achieved by integrating data from the ATTO towers and ATTO-Campina sites. Together, these sites support better understanding of interconnected gas-aerosol-cloud-precipitation processes in the Amazon and their evolution under climate change.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Hot droughts in the Amazon provide a window to a future hypertropical climate

Tropical forests represent the warmest and wettest of Earth’s biomes, but with continued anthropogenic warming, they will be pushed to climate states with no current analogue. Droughts in the tropics are already becoming more intense as they occur at successively higher temperatures. Here, in this study, we synthesize multiple datasets to assess the effects of hot droughts on a central Amazon forest. First, a more than 30-year record of annually resolved forest demographic data from a selective logging experiment showed higher tree mortality during intense droughts, particularly among fast-growing pioneer species with low wood density. Second, analysis of ecophysiological field measurements from the 2015 and 2023 El Niño droughts identified a soil moisture threshold beyond which transpiration rates rapidly declined. As rainless days beyond this threshold continued, drought conditions intensified, increasing the potential for tree mortality from hydraulic failure and carbon starvation. Third, analyses from the Coupled Model Intercomparison Project Phase 6 demonstrated that under high-emission scenarios, a large area of tropical forest will shift to a hotter ‘hypertropical’ climate by 2100. Last, under a hypertropical climate, temperature and moisture conditions during typical dry season months will more frequently exceed identified drought mortality thresholds, elevating the risk of forest dieback. Present-day hot droughts are harbingers of this emerging climate, offering a window for studying tropical forests under expected extreme future conditions.

drought↗