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DOE OSTI2025

Enrichment of root-associated Streptomyces strains in response to drought is driven by diverse functional traits and does not predict beneficial effects on plant growth

The genus Streptomyces has consistently been found enriched in drought-stressed plant root microbiomes, yet the ecological basis and functional variation underlying this enrichment at the strain and isolate level remain unclear. Using two 16S rRNA sequencing methods with different levels of taxonomic resolution, we confirmed drought-associated enrichment (DE) of Streptomyces in field-grown sorghum roots and identified five closely related but distinct amplicon sequence variants (ASVs) belonging to the genus with variable drought enrichment patterns. From a culture collection of sorghum root endophytes, we selected 12 Streptomyces isolates representing these ASVs for phenotypic and genomic characterization. Whole-genome sequencing revealed substantial variation in gene content, even among closely related isolates, and exometabolomic profiling showed distinct metabolic responses to media supplemented with drought- versus well-watered root tissue. Traits linked to drought survival, including osmotic stress tolerance, siderophore production, and carbon utilization, varied widely among isolates and were not phylogenetically conserved. Using a broader panel of 48 Streptomyces, we demonstrate that DE scores, determined through mono-association experiments in gnotobiotic sorghum systems, showed high variability and lacked correlation with plant growth promotion. Pangenome-wide association identified orthogroups involved in osmolyte transport (e.g., proP) and membrane biosynthesis (e.g., fabG) as positively associated with DE, though most associations lacked phylogenetic signal. Collectively, these results demonstrate that Streptomyces DE is not a conserved genus-level trait but is instead strain-specific and functionally heterogeneous. Furthermore, DE in the root microbiome was shown not to predict beneficial effects on plant growth. This work underscores the need to resolve functional traits at the strain level and highlights the complexity of microbe-host-environment interactions under abiotic stress.

Fonseca-Garcia, Citlali↗

DOE OSTI2023

Microbial Drivers of Plant Performance during Drought Depend upon Community Composition and the Greater Soil Environment

The increasing occurrence of drought is a global challenge that threatens food security through direct impacts to both plants and their interacting soil microorganisms. Plant growth promoting microbes are increasingly being harnessed to improve plant performance under stress. However, the magnitude of microbiome impacts on both structural and physiological plant traits under water limited and water replete conditions are not well-characterized. Using two microbiomes sourced from a ponderosa pine forest and an agricultural field, we performed a greenhouse experiment that used a crossed design to test the individual and combined effects of the water availability and the soil microbiome composition on plant performance. Specifically, we studied the structural and leaf functional traits of maize that are relevant to drought tolerance. We further examined how microbial relationships with plant phenotypes varied under different combinations of microbial composition and water availability. We found that water availability and microbial composition affected plant structural traits. Surprisingly, they did not alter leaf function. Maize grown in the forest-soil microbiome produced larger plants under well-watered and water-limited conditions, compared to an agricultural soil community. Although leaf functional traits were not significantly different between the watering and microbiome treatments, the bacterial composition and abundance explained significant variability in both plant structure and leaf function within individual treatments, especially water-limited plants. Our results suggest that bacteria-plant interactions that promote plant performance under stress depend upon the greater community composition and the abiotic environment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Fostering Peat Moss Feedbacks to Accelerate Peatland Restoration

Extensive knowledge exists on plant-species traits and functions, but we understand less about how population- or community-level emergent traits influence ecosystem functioning. This knowledge gap is important for ecosystems like peatlands, arid drylands, salt marshes, seagrass meadows and mangroves, where emergent traits of plant communities can create plant-environment feedbacks that amplify or dampen ecosystem processes. Recent insights from restoration ecology suggest that these feedbacks can critically influence restoration success. Despite growing recognition of emergent trait-driven feedbacks in other ecosystems, they remain underexplored in peatland restoration, world’s most carbon-dense ecosystem. Here, we review emergent self-amplifying and self-dampening feedbacks with net positive effects for peat moss-dominated systems. We show how these feedbacks can promote key physical, chemical, and biological processes that enhance peat moss growth, increase water retention, and reduce microbial decomposition of organic matter. Understanding and fostering these feedbacks offers a promising framework to accelerate peatland restoration across diverse degradation states.

Sphagnum↗

DOE OSTI2020

Methods and compositions for obtaining useful plant traits

The present invention provides methods for obtaining plants that exhibit useful traits by perturbation of plastid function in plant rootstocks and grafting the rootstocks to scions. Methods for identifying genetic loci that provide for useful traits in plants and plants produced with those loci are also provided. In addition, plants that exhibit the useful traits, parts of the plants including seeds, and products of the plants are provided as well as methods of using the plants. Recombinant DNA vectors and transgenic plants comprising those vectors that provide for plastid perturbation are also provided.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Methods and compositions for obtaining useful plant traits

Mackenzie, Sally↗

DOE OSTI2021

Fine-root functional trait responses to experimental warming: a global meta-analysis

Whether and how warming alters functional traits of absorptive plant roots remains to be answered across the globe. Tackling this question is crucial to better understanding terrestrial responses to climate change as fine-root traits drive many ecosystem processes. In this work, we carried out a detailed synthesis of fine-root trait responses to experimental warming by performing a meta-analysis of 964 paired observations from 177 publications. Warming increased fine-root biomass, production, respiration and nitrogen concentration as well as decreased root carbon : nitrogen ratio and nonstructural carbohydrates. Warming effects on fine-root biomass decreased with greater warming magnitude, especially in short-term experiments. Furthermore, the positive effect of warming on fine-root biomass was strongest in deeper soil horizons and in colder and drier regions. Total fine-root length, morphology, mortality, life span and turnover were unresponsive to warming. Our results highlight the significant changes in fine-root traits in response to warming as well as the importance of warming magnitude and duration in understanding fine-root responses. These changes have strong implications for global soil carbon stocks in a warmer world associated with increased root-derived carbon inputs into deeper soil horizons and increases in fine-root respiration.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

The three major axes of terrestrial ecosystem function

The leaf economics spectrum and the global spectrum of plant forms and functions revealed fundamental axes of variation in plant traits, which represent different ecological strategies that are shaped by the evolutionary development of plant species. Ecosystem functions depend on environmental conditions and the traits of species that comprise the ecological communities. However, the axes of variation of ecosystem functions are largely unknown, which limits our understanding of how ecosystems respond as a whole to anthropogenic drivers, climate and environmental variability. Here we derive a set of ecosystem functions from a dataset of surface gas exchange measurements across major terrestrial biomes. We find that most of the variability within ecosystem functions (71.8%) is captured by three key axes. The first axis reflects maximum ecosystem productivity and is mostly explained by vegetation structure. The second axis reflects ecosystem water-use strategies and is jointly explained by variation in vegetation height and climate. The third axis, which represents ecosystem carbon-use efficiency, features a gradient related to aridity, and is explained primarily by variation in vegetation structure. We show that two state-of-the-art land surface models reproduce the first and most important axis of ecosystem functions. However, the models tend to simulate more strongly correlated functions than those observed, which limits their ability to accurately predict the full range of responses to environmental changes in carbon, water and energy cycling in terrestrial ecosystems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Leaf nonstructural carbohydrate residence time, not concentration, correlates with leaf functional traits following the leaf economic spectrum in woody plants

Nonstructural carbohydrate (NSC) concentrations might reflect the strategies described in the leaf economic spectrum (LES) due to their dependence on photosynthesis and respiration. Here, we examined if NSC concentrations correlate with leaf structure, chemistry, and physiology traits for 114 species from 19 sites and 5 biomes around the globe. Total leaf NSC concentrations varied greatly from 16 to 199 mg g -1 dry mass and were mostly independent of leaf gas exchange and the LES traits. By contrast, leaf NSC residence time was shorter in species with higher rates of photosynthesis, following the fast-slow strategies in the LES. An average leaf held an amount of NSCs that could sustain one night of leaf respiration and could be replenished in just a few hours of photosynthesis under saturating light, indicating that most daily carbon gain is exported. Our results suggest that NSC export is clearly linked to the economics of return on resource investment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Maps of plant functional type (PFT), PFT fractional cover, and uncertainty derived from AVIRIS-NG data, 2019, Seward Peninsula

Remote sensing maps of plant functional type (PFT), PFT fractional cover (fCover), and fCover uncertainty maps derived from NASA’s Airborne Visible / Infrared Imaging Spectrometer – Next Generation (AVIRIS-NG). The AVIRIS-NG imaging spectroscopy data (380 ~ 2510 nm) was collected as a part of the collaboration between NASA’s Arctic-Boreal Vulnerability Experiment (ABoVE; Miller et al., 2019) and DOE’s Next Generation Ecosystem Experiment in the Arctic (NGEE-Arctic). This package includes maps for flights over Teller, Kougarok, and Council watersheds created using eight AVIRIS-NG imagery collected in July, 2019. The map data and metadata are provided as image (ENVI, *.png) and text (*.txt, *hdr) formats. Additional supporting map quicklooks are provided as GIS *.kml files. Detailed description of the methods for each map are provided in Yang et al., (2023). These datasets are provided in support of Yang et al., (In revision) “Topography and Functional Traits Control the Distribution of Key Shrub Plant Functional Types in Low-Arctic Tundra”.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Large Divergence of Projected High Latitude Vegetation Composition and Productivity Due To Functional Trait Uncertainty

Abstract Vegetation distribution and composition are expected to change in northern high latitudes under rapid warming, which regulates ecosystem functions but remains challenging to predict. Vegetation change arises from the interplay of chronic climate trends such as warming and transient demographic processes of recruitment, growth, competition, and mortality. Most predictive models overlooked the role of demographic dynamics controlled by plant traits. Here, we simulate vegetation dynamics at the Kougarok Hillslope site in Alaska under historical and future climates using the E3SM Land Model coupled to the Functionally Assembled Terrestrial Simulator (ELM‐FATES). To evaluate the roles of plant traits, we parameterize the model with 5,265 trait configurations representing diverse physiological and demographic strategies. Results show current modeled biomass, composition, and productivity are most sensitive to traits controlling photosynthetic capacity, carbon allocation, allometry, and phenology. Among all trait configurations, ∼5% reproduce in situ biomass and plant functional type (PFT) composition measured in 2016, that are indistinguishable from these two observed ecosystem states. Notably, these same trait configurations produce diverging biomass, composition, and productivity under future climate, where the uncertainty attributable to traits is twice the change attributable to climate change. The variation of projected productivity arises from emerging PFT composition under novel climate regimes, primarily explained by traits controlling cold‐induced mortality, recruitment, and allometry. Our findings highlight the importance and uncertainty of demographic dynamics and its interaction with climate change in shaping Arctic vegetation change. Improved model predictions will likely benefit from explicit consideration of vegetation demography and better constraints of critical traits.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Different model assumptions about plant hydraulics and photosynthetic temperature acclimation yield diverging implications for tropical forest gross primary production under warming

Tropical forest photosynthesis can decline at high temperatures due to (1) biochemical responses to increasing temperature and (2) stomatal responses to increasing vapor pressure deficit (VPD), which is associated with increasing temperature. It is challenging to disentangle the influence of these two mechanisms on photosynthesis in observations, because temperature and VPD are tightly correlated in tropical forests. Nonetheless, quantifying the relative strength of these two mechanisms is essential for understanding how tropical gross primary production (GPP) will respond to climate change, because increasing atmospheric CO 2 concentration may partially offset VPD-driven stomatal responses, but is not expected to mitigate the effects of temperature-driven biochemical responses. We used two terrestrial biosphere models to quantify how physiological process assumptions (photosynthetic temperature acclimation and plant hydraulic stress) and functional traits (e.g., maximum xylem conductivity) influence the relative strength of modeled temperature versus VPD effects on light-saturated GPP at an Amazonian forest site, a seasonally dry tropical forest site, and an experimental tropical forest mesocosm. By simulating idealized climate change scenarios, we quantified the divergence in GPP predictions under model configurations with stronger VPD effects compared with stronger direct temperature effects. Assumptions consistent with stronger direct temperature effects resulted in larger GPP declines under warming, while assumptions consistent with stronger VPD effects resulted in more resilient GPP under warming. Furthermore, our findings underscore the importance of quantifying the role of direct temperature and indirect VPD effects for projecting the resilience of tropical forests in the future, and demonstrate that the relative strength of temperature versus VPD effects in models is highly sensitive to plant functional parameters and structural assumptions about photosynthetic temperature acclimation and plant hydraulics.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Ectomycorrhizal Plant-Fungal Co-invasions as Natural Experiments for Connecting Plant and Fungal Traits to Their Ecosystem Consequences

Introductions and invasions by fungi, especially pathogens and mycorrhizal fungi, are widespread and potentially highly consequential for native ecosystems, but may also offer opportunities for linking microbial traits to their ecosystem functions. In particular, treating ectomycorrhizal (EM) invasions, i.e., co-invasions by EM fungi and their EM host plants, as natural experiments may offer a powerful approach for testing how microbial traits influence ecosystem functions. Forests dominated by EM symbiosis have unique biogeochemistry whereby the secretions of EM plants and fungi affect carbon (C) and nutrient cycling; moreover, particular lineages of EM fungi have unique functional traits. EM invasions may therefore alter the biogeochemistry of the native ecosystems they invade, especially nitrogen (N) and C cycling. By identifying “response traits” that favor the success of fungi in introductions and invasions (e.g., spore dispersal and germination) and their correlations with “effect traits” (e.g., nutrient-cycling enzymes) that can alter N and C cycling (and affect other coupled elemental cycles), one may be able to predict the functional consequences for ecosystems of fungal invasions using biogeochemistry models that incorporate fungal traits. Here, we review what is already known about how EM fungal community composition, traits, and ecosystem functions differ between native and exotic populations, focusing on the example of EM fungi associated with species of Pinus introduced from the Northern into the Southern Hemisphere. We develop hypotheses on how effects of introduced and invasive EM fungi may depend on interactions between soil N availability in the exotic range and EM fungal traits. We discuss how such hypotheses could be tested by utilizing Pinus introductions and invasions as a model system, especially when combined with controlled laboratory experiments. Finally, we illustrate how ecosystem modeling can be used to link fungal traits to their consequences for ecosystem N and C cycling in the context of biological invasions, and we highlight exciting avenues for future directions in understanding EM invasion.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Sap flow data from San Lorenzo, Panama (PA-SLZ), 2019

This data package contains sap flow data from the NGEE Tropics site in San Lorenzo, Panama (PA-SLZ) from 22 January 2019 to 31 December 2019. Sap flow measurements quantify plant-level transpiration, which varies across spatial and temporal scales. It is a key trait in understanding plant hydraulic functioning. Here sap flow was measured using ‘Granier-type’ thermal dissipation probes. Raw data downloaded from each data logger are in the 'Raw data' folder as CSV files, along with the Campbell data logger programs which can be read when opened with a text editor. The data was processed using the AquaFlux package in R. R code for preparing the data for use in AquaFlux is in the 'R code for pre-processing data folder'; it is saved as a text file that can be copy and pasted into R. The processed data for each data logger is in the 'Processed data' folder as CSV files. Documentation for the Granier sensors and AquaFlux package is in the ‘Manuals’ folder as PDF files.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Data for Impact of Vertical and Seasonal Variation in Leaf Traits on Simulating Soybean Canopy Photosynthesis via 1D and 3D Modeling

Accurate modeling of photosynthesis is crucial for predicting crop productivity and quantifying the carbon cycle in agroecosystems. Leaf traits are essential inputs for modeling canopy photosynthesis. Yet, many existing models still use fixed plant functional type (PTF)-based values to parameterize leaf traits under a big-leaf or two-big-leaf assumption, neglecting their vertical profiles and seasonal changes. This simplification may introduce significant uncertainties in estimating gross primary productivity (GPP). In this study, we simulated soybean GPP and tested the effects of vertical and seasonal variation in three key leaf photosynthetic traits: the maximum carboxylation rate at 25 °C (Vcmax25), leaf chlorophyll content (LCC), and leaf mass per area (LMA) in the 1D-SCOPE and 3D-Helios models. Weekly field measurements were conducted during the growing season of 2024 to support the simulation. We designed ten leaf trait parameterization schemes by incorporating different combinations of vertical profiles and seasonal changes, while assuming homogeneous canopy architecture in both models. Our results revealed that Vcmax25 vertical and seasonal variation had the strongest influence on simulated GPP in both 1D and 3D models, while LCC and LMA effects were minimal. Particularly, the scheme with an empirically parameterized Vcmax25 profile achieved comparable performance to the scheme with the measured Vcmax25 profile. Both 1D-SCOPE and 3D-Helios accurately modeled GPP (SCOPE: R2 = 0.87, Bias = 0.55 µmol m⁻² s⁻¹; Helios: R2 = 0.9, Bias = 0.22 µmol m⁻² s⁻¹) under the most complex scheme, and their responses to vertical and seasonal variation in leaf traits were consistent, demonstrating the robustness of our findings. Based on our findings, we propose a scalable framework for parameterizing leaf traits to improve GPP simulations. This study contributes to improving the representation of leaf trait dynamics in canopy-level photosynthesis models, potentially enhancing our ability to predict crop productivity and understand agroecosystem carbon dynamics.

Photosynthesis↗

DOE OSTI2022

Increasing Functional Diversity in a Global Land Surface Model Illustrates Uncertainties Related to Parameter Simplification

Abstract Simulations of the land surface carbon cycle typically compress functional diversity into a small set of plant functional types (PFT), with parameters defined by the average value of measurements of functional traits. In most earth system models, all wild plant life is represented by between five and 14 PFTs and a typical grid cell (≈100 × 100 km) may contain a single PFT. Model logic applied to this coarse representation of ecological functional diversity provides a reasonable proxy for the carbon cycle, but does not capture the non‐linear influence of functional traits on productivity. Here we show through simulations using the Energy Exascale Land Surface Model in 15 diverse terrestrial landscapes, that better accounting for functional diversity markedly alters predicted total carbon uptake. The shift in carbon uptake is as great as 30% and 10% in boreal and tropical regions, respectively, when compared to a single PFT parameterized with the trait means. The traits that best predict gross primary production vary based on vegetation phenology, which broadly determines where traits fall within the global distribution. Carbon uptake is more closely associated with specific leaf area for evergreen PFTs and the leaf carbon to nitrogen ratio in deciduous PFTs.

58 GEOSCIENCES↗

DOE OSTI2023

JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom

Abstract Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Root exudation links root traits to soil functioning in agroecosystems

Root exudation is a key process for plant nutrient acquisition, but the controls on root exudation and its relationship to soil C and N processes in agroecosystems are unclear. We hypothesized that root exudation rates would be related to root morphological traits, N fertilization, and soil moisture. We also anticipated that root exudation would be correlated with bulk soil enzyme activity. Root exudation, root traits, and bulk soil extracellular enzyme activity were assessed in maize (Zea mays L.), soybean (Glycine max (L.) Merr.), biomass sorghum (Sorghum bicolor (L.) Moench), giant miscanthus (Miscanthus × giganteus), and switchgrass (Panicum virgatum L.). Measurements were taken in situ during two growing seasons with contrasting precipitation regimes, and N fertilization rate was varied in sorghum during one year. Specific root exudation (per unit root surface area) was negatively related to root diameter and was generally higher in annuals than perennials. Sorghum N fertilization did not affect root exudation rates, and soil moisture regime had no effect on annual root exudation rates within maize, sorghum, and miscanthus. Specific root exudation was negatively related to bulk soil C- and N-degrading soil enzyme activities. Intrinsic plant characteristics appeared more important than environmental variables in controlling in situ root exudation rates. The relationships between root diameter, root exudation, and soil C and N processes link root morphological traits to soil functions and demonstrate the potential tradeoffs among plant nutrient acquisition strategies in agroecosystems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Data for Root Exudation Links Root Traits to Soil Functioning in Agroecosystems

Biomass Analytics↗