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At least 55 records · Page 3

Species‐Specific Epigenetic Signature Associates With Heat Stress Tolerance in the Perennial Tree Species Populus

Epigenetic regulation in annual plants is recognized as a key component of recurring stress acclimation and adaptation, but reports on perennial tree species are limited. In this study, two contrasting tree species, Populus trichocarpa and Populus deltoides, and an F1 hybrid cross between them showed species-specific epigenetic and physiological responses to heat stress (42°C) following priming (35°C). By analyzing whole-genome methylation, transcriptomics, proteomics, metabolomics, and photosynthesis parameters, we found that P. deltoides expresses specific epigenetic signatures in response to heat, resulting in improved photosynthetic efficiency compared to P. trichocarpa. Conversely, P. trichocarpa displayed stress signaling and defense mechanisms that could not sustain a net assimilation rate despite maintaining higher gas exchange. Heat stress following priming in hybrid plants increased transcript levels of thermotolerance-related transcription factors, such as SPL12. Selected regions in the promoter of SPL12 showed differential methylation between direct heat stress and priming followed by heat stress. As a result, upregulation of downstream genes and associated increases in protein and metabolite abundance for stress adaptation were exhibited. Consequently, hybrid plants showed enhanced photosynthesis and gas exchange rates, a trait lacking in P. trichocarpa. These results imply that priming may not be universally effective in enhancing plant performance under stress, particularly in perennial tree species. However, priming can acclimate the perennial tree species P. deltoides to withstand elevated temperature stress better. Our study has demonstrated that priming-based stress adaptation is species-specific but can be attained through crossbreeding, indicating its potential use in breeding programs.

DNA methylation↗

Tree drought physiology: critical research questions and strategies for mitigating climate change effects on forests

Droughts of increasing severity and frequency are a primary cause of forest mortality associated with climate change. Yet, fundamental knowledge gaps regarding the complex physiology of trees limit the development of more effective management strategies to mitigate drought effects on forests. Here, in this work, we highlight some of the basic research needed to better understand tree drought physiology and how new technologies and interdisciplinary approaches can be used to address them. Our discussion focuses on how trees change wood development to mitigate water stress, hormonal responses to drought, genetic variation underlying adaptive drought phenotypes, how trees ‘remember’ prior stress exposure, and how symbiotic soil microbes affect drought response. Next, we identify opportunities for using research findings to enhance or develop new strategies for managing drought effects on forests, ranging from matching genotypes to environments, to enhancing seedling resilience through nursery treatments, to landscape-scale monitoring and predictions. We conclude with a discussion of the need for co-producing research with land managers and extending research to forests in critical ecological regions beyond the temperate zone.

54 ENVIRONMENTAL SCIENCES↗

Crash–and–dash: a new era in tree genome editing

In less than a decade since the first demonstrations of CRISPR genome editing of agronomic genes in several tree species (Zhou et al., 2015; Jia et al., 2016; Ren et al., 2016), this disruptive technology has been deployed for a growing number of traits in both basic and applied research. The precision and efficiency of CRISPR editing allow for the recovery of null mutants in the first generation (Zhou et al., 2015; Elorriaga et al., 2018; Muhr et al., 2018), which is a significant benefit for perennial trees with long generation times. The stability of editing outcomes over multiple years or clonal propagation cycles (Bewg et al., 2022; Chen et al., 2023; Goralogia et al., 2024) is another key advantage since most woody perennials are vegetatively propagated in commercial operations. However, in many countries, gene-edited trees with stably integrated T-DNA face the same regulatory hurdles as traditional transgenics, slowing field trial characterization and the integration of transgenesis with conventional breeding (Boerjan & Strauss, 2024). In an article recently published in New Phytologist, Hoengenaert et al. (2025; doi: 10.1111/nph.20415) demonstrate transgene-free editing in poplar (Populus tremula × alba) that shows promise for wide adoption. The CRISPR-edited, transgene-free canker-resistant citrus (Citrus sinensis) trees (Su et al., 2023) have recently been approved by USDA-APHIS and are exempt from regulation by the US Environmental Protection Agency (EPA) for commercial production. The work by Hoengenaert et al. (2025) suggests a similar path could be followed for purpose-grown plantations for bioenergy, bioproducts, and biomaterials.

59 BASIC BIOLOGICAL SCIENCES↗

Tree root nutrient uptake kinetics vary with nutrient availability, environmental conditions, and root traits: a global analysis

Summary: Root nutrient uptake by trees is a critical process that couples carbon and nutrient cycling in forest ecosystems. Yet, root nutrient uptake traits are poorly constrained, and the dynamics of this process are often not represented in models reflecting sparse measurements and understanding of root nutrient uptake physiology that lags those of aboveground physiology in forest ecosystems. Here, we present a global dataset of published nutrient uptake capacity and affinity values for tree species, with the goal of describing global patterns and evaluating responses to environmental drivers and associations with root traits. Furthermore, the dataset contains observations for ammonium, nitrate, and phosphate uptake spanning 77 tree species. Nutrient uptake capacity and affinity varied by more than an order of magnitude for each nutrient. Notably, tropical forests are underrepresented in these observations. Nutrient uptake capacity was generally diminished under nutrient enrichment but enhanced with soil warming and root–mycorrhizal colonization. The magnitude and direction of these effects can depend on the duration of exposure to a given treatment. Species with thinner roots had a tendency toward greater uptake capacity and affinity. Overall, root nutrient uptake traits are highly variable across tree species, yet they depend on environmental drivers and life-history strategies.

Km↗

Response of ectomycorrhizal fungi to full and selective removal of an invasive tree in riparian woodland

The Brazilian pepper tree ( Schinus terebinthifolius ) is an invasive species that requires significant disturbance to eradicate. Previous studies have identified associations between the Brazilian pepper tree and ectomycorrhizal fungi (EMF). However, limited research has explored the connection between disturbance from removal and the effect on EMF. This study investigated the sensitivity of EMF and the broader fungal community to the full and selective removal of the Brazilian pepper tree. During the selective removal of Brazilian pepper tree, we examined the mycorrhizal community of the Arroyo willow ( Salix lasiolepis ) to assess the influence of the restoration disturbance on native species. We used ITS2 sequencing to identify the EMF present during the restoration. Our expectation was that both removal efforts would reduce the presence of EMF. Contrary to our predictions, full removal increased EMF richness and relative abundance in the soil. As anticipated, selective removal reduced the richness and relative abundance of EMF associated with soil. Selective removal led to a decrease in the richness of EMF in arroyo willow roots with no effect on relative abundance. Moreover, fungal community composition in soil and roots shifted significantly during selective and full removal. However, the community composition of EMF, specifically, remained constant across treatment types. During full removal efforts, the application of organic soil amendments may have contributed to the increase in the diversity and relative abundance of EMF. Selective removal will require additional measures, such as soil amendments, to curtail the loss of EMF.

Environmental Sciences & Ecology↗

Orchard: Heterogeneous Parallelism and Fine-grained Fusion for Complex Tree Traversals

Many applications are designed to perform traversals ontree-likedata structures. Fusing and parallelizing these traversals enhance the performance of applications. Fusing multiple traversals improves the locality of the application. The runtime of an application can be significantly reduced by extracting parallelism and utilizing multi-threading. Prior frameworks have tried to fuse and parallelize tree traversals using coarse-grained approaches, leading to missed fine-grained opportunities for improving performance. Other frameworks have successfully supported fine-grained fusion on heterogeneous tree types but fall short regarding parallelization. We introduce a new frameworkOrchardbuilt on top ofGrafter.Orchard’s novelty lies in allowing the programmer to transform tree traversal applications by automatically applyingfine-grainedfusion and extractingheterogeneousparallelism.Orchardallows the programmer to write general tree traversal applications in a simple and elegant embedded Domain-Specific Language (eDSL). We show that the combination of fine-grained fusion and heterogeneous parallelism performs better than each alone when the conditions are met.

Computer Science↗

COMPASS-FME Synoptic Site Tree Greenhouse Gas Concentrations

These data are tree stem greenhouse gas concentrations collected from tree gas wells at some of the COMPASS-FME (Coastal Observations, Mechanisms, and Predictions Across Systems and Scales; see https://compass.pnnl.gov/) 'synoptic' sites in the Chesapeake Bay region: Moneystump (MSM), Goodwin Islands (GWI), and GCReW (GCW). The sap flow monitoring trees at these sites in the Upland (UP) and Transition (TR) zones were cored and had gas wells installed at breast height. There were also some dead standing trees cored, gas well installed, and sampled at MSM and GWI. The GCW UP samples overlap with the TEMPEST experiment control plot, so the GCW UP data was pulled from the TEMPEST page and included here. These data provide crucial information about possible pathways for the greenhouse gas (carbon dioxide and methane, CO2 and CH4 respectively) production and emission (or in the case of CH4, perhaps taken up from) the atmosphere.All data are plain text CSV (comma separated value) files and require no special software to read.Updated 2025-10-09 to fix two missing dates (lines 77 and 78 in the data file).

54 ENVIRONMENTAL SCIENCES↗

Leaf functional traits highlight phenotypic variation of two tree species in the urban environment

Urbanization is transforming landscapes globally, altering environmental conditions that affect ecosystem functioning, particularly in urban areas where trees are crucial for regulating microclimates, improving air quality, and sustaining biodiversity. This study investigates the environmental differences and tree leaf structure and morphology in urban and suburban sites in the Chicago Metropolitan Region. The leaf functional traits of Norway Maple and Little − leaved Linden were studied in three locations in the summer of 2023: an urban park (University of Illinois Chicago, Chicago, IL), a suburban park (Morton Arboretum, Lisle, IL), and a suburban residential site (Lombard, IL). The urban site had higher daytime and nighttime air, and land surface temperatures compared to the suburban sites with significant fluctuations observed across the sites. Cumulative growing degree days, a measure of potential photosynthetically active days, were also higher in the urban park than in the suburban sites between March and August. Norway Maple trees growing in the urban site displayed higher specific leaf area (SLA) and lower leaf dry matter content (LDMC) than in the suburban sites, resulting in thinner leaves. Similarly, Little−leaved Linden trees in the suburban residential site displayed higher SLA and lower LDMC than those in the suburban park. The values of gas exchange traits − namely photosynthetic assimilation, transpiration rates, and stomatal conductance − of Norway Maple were higher at the urban site compared to suburban sites as temperatures increased during the summer. Norway Maple gas exchange values decreased as the growing season progressed, as expected by ontogeny. In contrast, Little−leaved Linden maintained similar leaf gas exchange values throughout the growing season. Both species in the urban site exhibited lower instantaneous water use efficiency and reduced LDMC, suggesting greater water loss in response to elevated temperatures compared to suburban park and residential sites. Comparisons with existing global trait databases emphasize the need for localized data to accurately capture site−specific responses. Although some traits aligned with database values, others deviated significantly, underscoring the importance of comprehensive, site−specific datasets for robust ecosystem modeling and management strategies.

Cho, Ahram↗

A minor respiratory process with major global implications: is atmospheric methane oxidation in tree stems driven by stem respiration rather than microbial methanotrophy?

Tree stem surfaces are widely recognized as sites of carbon dioxide (CO₂) efflux and oxygen (O₂) influx, reflecting the dynamics of aerobic respiration of photosynthate substrates, such as sugars, delivered via the phloem. Stems are also largely considered passive conduits for methane (CH₄) produced in anoxic soils via microbial methanogenesis, where CH₄ is thought to be transported upward through the transpiration stream and/or diffusion and emitted through stem surfaces and the canopy. However, recent observations from dynamic stem chambers suggest that stems may also act as active sinks for atmospheric CH₄. Despite these findings, the extent and drivers of stem CH₄ consumption remain poorly characterized across biomes, species, and environmental gradients, and its quantitative relationship to stem respiration has not been established. Moreover, previous studies captured only snapshot fluxes, leaving diurnal patterns of CH₄ exchange uncharacterized. Here, we address these limitations by combining real-time measurements of stem CH₄ and O₂ uptake under ambient conditions in a California cherry tree, using a dynamic stem gas exchange system with three chambers receiving a continuous flow of ambient air and automated chamber and reference air sampling every 10 min. Our results confirm that stems of upland trees can actively consume both atmospheric CH₄ and O₂, but with decreasing temperature sensitivity as daily temperatures increase. Early mornings were marked by rapid influxes of both gases, followed by declining uptake as temperatures rose further. Methane uptake was tightly coupled with O₂ influx and represented a minor (0.012% ± 0.002%) fraction of stem respiratory activity, as determined by concurrent O₂ uptake. These findings suggest that while atmospheric CH₄ oxidation is a minor respiratory process in stems, it is strongly linked with stem physiological activity. This challenges the current assumption that terrestrial CH₄ uptake is driven solely by microbial methanotrophy and raises the possibility that living stem tissues may contribute to CH₄ oxidation through an as-yet-unidentified plant-based mechanism.

Atmospheric greenhouse gases↗

Tree-ring evidence marks year 2022 as the driest spring season in nearly four centuries in the Western Himalayas

The Hindukush-Karakoram-Himalayan region is a crucial freshwater source for billions across South Asia, yet its climate remains poorly understood due to limited long-term records. Winter and spring precipitation govern snow accumulation and downstream water availability in dry months particularly across the Western Himalayas (WH), but recent decades show intensifying droughts with unclear long-term context. Here, we have reconstructed a nearly four-century-long spring i.e. February to May (FMAM) precipitation for the Lahaul region of the (WH), an area dominated by the Western Disturbances. This record was developed using moisture-sensitive Cedrus deodara (Deodar) tree-rings from three high-elevation sites. A regional composite tree-ring-width chronology, developed through a Nested Principal Component Analysis and modeled with a nonlinear Generalized Additive Model (GAM) that explains 71 % of the variance during the calibration period. We identified the last two decades as the most precipitation deficit phase and the year 2022 showing the driest FMAM on record. The observed rise in the FMAM dry episodes post 1999 CE in our reconstruction, corresponds to the meteorological records. This recent drying is linked to a northward shift of the subtropical westerly jet and reduced moisture transport, both associated with unusual sea surface temperature patterns in the tropical Indian Ocean and the Western Pacific Ocean. Our results provide compelling evidence of long-term hydroclimatic instability in the WH and emphasize the value of tree-ring records in extending precipitation histories beyond the instrumental observations. Such reconstructions can be benchmarks to validate high-resolution climate models and formulate adaptation policies to mitigate future risks.

Cedrus deodara↗

COMPASS-FME Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) Experiment Tree Inventory

This is the tree inventory (diameter, species, and live/dead status) data from the Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) experimental site. This manipulative, ecosystem-scale TEMPEST experiment is part of the COMPASS-FME (Coastal Observations, Mechanisms, and Predictions Across Systems and Scales: Field Measurements and Experiments; see https://compass.pnnl.gov/FME/COMPASSFME) project. It addresses the potential for freshwater and estuarine-water disturbance events to alter tree function, species composition, and ecosystem processes in a deciduous coastal forest in eastern Maryland, USA. The experiment uses a large-unit (2000 m2), un-replicated experimental design, with three 50 m × 40 m plots serving as control, freshwater, and estuarine-water treatments.This dataset includes:- An overall dataset README file.- The tree inventory data in both "wide" and "long" forms. These contain the same information but are structured differently, with the former more useful for human viewers and the latter more amenable for programmatic analyses.- A key to the species/genus codes used, which follow the U.S. Department of Agriculture's PLANTS schema (https://plants.usda.gov/).- A copy of the R code used to generate the wide- and long-form data files.All files are comma-separated value (CSV) and no special software is required to read them.

54 ENVIRONMENTAL SCIENCES↗

Eucalyptus – An Analysis Suite for Fault Trees with Uncertainty Quantification

Eucalyptus is a novel code developed at Lawrence Livermore National Laboratory to incorporate uncertainty quantification into Fault Tree Analysis (FTA). This tool addresses the challenge of imperfect knowledge in “grey-box” systems by allowing analysts to incorporate and propagate uncertainty from component-level assessments to system-level effects. Eucalyptus facilitates a consistent evaluation of the impact of subject matter expert judgment and knowledge gaps on overall system response by Monte Carlo generation of possible system fault trees, sampling probabilities of the existence of subsystems and components. Here, the code supports the specification of fault trees through text and allows export to various formats, including auto-generated images, easing analysis and reducing errors. It has undergone extensive verification testing, demonstrating its reliability and readiness for deployment, and leverages on-node parallelism for rapid analysis. Example analyses are shown that include the identification of system failure paths and quantification of the value of further information about system components.

Fault Tree Analysis↗

Coastal groundwater salinization impairs tree carbon–water balance

How coastal forest productivity varies with local nutrient availability and water supply remains a knowledge gap under climate change. In a two-decade field experiment manipulating fertilization and density in coastal pine forests, we show that a decade of growth enhancement by simulated sedimentary nutrient inputs has resulted in a striking reversal in growth and increased mortality risk as drought and sea level rise progressed. Recent groundwater salinization has further triggered a shift from nutrient to water limitation, causing severe stomatal closure and decoupling of tree carbon–water balance, which induces a negative intrinsic water use efficiency (iWUE)–growth relationship. Higher tree iWUE predicted sharper tree growth declines, and both nutrient enrichment and high stand density amplified this feedback, increasing the risk of hydraulic failure and mortality. These results suggest that a transient nutrient-stimulatory effect could drive further coastal forest degradation due to heightened belowground saltwater stress under sea-level rise.

Climate-change ecology↗

Photosynthetic capacity is reduced by warming but unaffected by elevated CO2 in seedlings of five boreal tree species

Abstract Increasing atmospheric CO2 concentrations fuel global warming, with boreal regions warming at a faster rate than many other areas. Boreal forests are an important component of the global carbon cycle, yet we have little data on photosynthetic responses of boreal trees to elevated CO2 (EC) and warming. We grew seedlings of 5 widespread North American boreal tree species (from Betula, Larix, Picea, and Pinus) under current (410 ppm) or elevated (750 ppm) CO2 and either ambient (+0 °C) or increased (+4 °C or +8 °C) temperature, then measured photosynthetic traits over a range of leaf temperatures. Our results were generally consistent across species: photosynthetic capacity (maximum rates of Rubisco carboxylation, Vcmax, and electron transport, Jmax) was unaffected by EC but decreased under +8 °C warming. Accordingly, net photosynthesis measured at the growth CO2 concentration (Agrowth) was reduced under warming and increased under EC. The thermal optimum for Agrowth (ToptA) increased by ∼1.8 °C with EC but increased with warming in only two species. In contrast, the activation energies and thermal optima for Vcmax and Jmax, which are used to estimate photosynthesis in Earth System Models, were unaffected by growth environment. There were a few interactions between growth, CO2, and warming. These results suggest increased photosynthesis of widespread boreal tree species under EC may be offset by future reductions in photosynthetic capacity related to warming. We also show that the temperature sensitivities of parameters used to estimate global photosynthesis in large-scale models are generally unaffected by simulated climate change in these species.

Plant Sciences↗

Growth–Mortality Coordination Differs Among Xerophytic Versus Mesophytic Tree Species During Severe Drought

ABSTRACT Forest composition is changing, yet the consequences for terrestrial carbon cycling are unclear. In the eastern United States, water‐demanding “mesophytic” tree species are replacing “xerophytic” oaks (Quercusspp.) and hickories (Caryaspp.), raising concerns that forest productivity will become increasingly sensitive to more frequent and severe drought conditions predicted for the region. However, we have a limited understanding of the extent to which the mortality risk of xerophytes versus mesophytes is coordinated with their growth sensitivity during drought. Here, we evaluated growth and mortality dynamics for 20 abundant eastern United States tree species following a severe drought in the summer of 2012. We synthesized data from ~4500 forest inventory plots and used an approach that quantified relative drought responses between co‐located trees to minimize impacts from environmental heterogeneity. We found that mesophytes were just as likely to perish as co‐occurring xerophytes but were more sensitive to drought in terms of diminished growth. These findings suggest that xerophytic decline is likely to lead to reduced carbon uptake during drought and that management efforts to conserve oak‐hickory stands will be decisive to sustain the carbon mitigation potential of these forests. However, we also found that growth‐mortality relationships differed between functional groups. Among xerophytes, growth and survival during drought were decoupled. Among mesophytes, there was a high degree of coordination, where species that experienced greater mortality also experienced greater growth reductions. Therefore, mesophytes with high growth sensitivity to water deficits are likely to be the most vulnerable to drought‐driven die‐off events moving forward.

Biodiversity & Conservation↗

Data for “Tree root nutrient uptake kinetics vary with nutrient availability, environmental conditions, and root traits: A global analysis”

This data package contains data and code used in the paper “Tree root nutrient uptake kinetics vary with nutrient availability, environmental conditions, and root traits: A global analysis”. The central product is a global dataset of root inorganic nutrient uptake rates and kinetics parameters covering temperate, boreal, and sub/tropical tree species, representing a collection of nutrient uptake data from published studies. This dataset enables tree investigation of root nutrient uptake rates across species, space, and experimental conditions. The data can also be combined with supplementary data on root and soil traits or with external datasets (e.g. R scripts contained within use data from FRED 3.0; (Iversen et al., 2021)). Contained within is the main nutrient data “uptake_data.csv” as well as 4 additional .csv files that link uptake data to supplementary measurements, source references, taxonomic information, and additional nutrient uptake measurements across nutrient gradients, and 1 .csv file that records meta-analysis results for plotting with the R scripts. There are seven R scripts that support data analysis and creation of the figures in the related publication.

54 ENVIRONMENTAL SCIENCES↗

Remote Sensing Approach for Monitoring Tree Health Adjacent to Transmission Corridors

This study presents an initial proof-of-concept for a satellite-based remote sensing approach to identify and monitor potential areas of poor tree health across the entire BPA service territory on an annual basis. We tested three variants of “delta peak NDVI” ( ΔPN ) change detection metrics that express interannual variation in primary productivity relative to a baseline by comparing ΔPN values for known insect/disease disturbances and nearby reference locations. All three metrics showed promise for detecting poor tree health in the year during disturbance, but the metric based on the difference from the long-term (2016-2024) median ( Δ Med PN ) was preferred due to its responsiveness to change in the years during and after disturbance, resilience to interannual variation, and ease of interpretation as being above or below normal. Comparison of Δ Med PN grouped by relative severity of disturbance indicated it was not sensitive enough to detect “low” severity disturbances, as mapped by USGS’s LANDFIRE program, but could distinguish “moderate” and “high” severity disturbances from reference locations. These findings informed selection of a threshold for Δ Med PN , which was combined with areas exhibiting negative NDVI to map potential areas of concern. Visual inspection of before/after high-resolution imagery and NDVI time series showed that many areas of concern aligned with visible signs of defoliation and die-off as well as other types of disturbance (e.g., landslides, logging, road grading, flooding). Some areas of concern are thought to be false detections caused by persistent shadow, and some could not be explained with visual inspection due to spatiotemporal limitations of before/after imagery. In summary, our approach shows promise for large-scale monitoring of tree health adjacent to BPA transmission lines, but additional work is recommended to improve model sophistication and remove noise.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Research Development and Partnership Pilot (RDPP): Developing plans and partnerships for incorporating tree reproduction to understand Earth system change

The goals for this Research Development and Partnership Pilot (RDPP) proposal were to i) learn about Department of Energy (DOE) research and use the PI’s expertise on patterns and environmental drivers of tree reproduction as a basis to make connections with individuals and research groups at DOE National Laboratories, and ii) to develop plans and form partnerships that will both enhance the PI’s research. The objectives of the proj ect were for the PI to i) participate in the Department of Energy's Office of Science program in Biological and Environmental Research training and outreach activities, ii) conduct directed fact-finding on Earth and Environmental Systems Sciences Division (EESSD) research projects and new partnerships with individuals and groups at National Laboratories, ii) conduct meetings with potential collaborators at National Laboratories to discuss EESSD-relevant research ideas, and iv) to develop a plan for future research efforts. During the period of the award, the objectives of the proposal were met, as the PI attended Environmental System Sciences meetings, American Geophysical Union meetings, SPRUCE experiment meetings, and visited the Oak Ridge National Lab. These activities led to increased understanding of the research being conducted by DOE scientists and the PI had meetings with potential collaborators to develop future research plans that leverage expertise at DOE and the research interests of the PI to increase understanding of the role of tree reproduction in future carbon allocation and in tree regeneration models in boreal ecosystems.

54 ENVIRONMENTAL SCIENCES↗