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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Engineering custom morpho- and chemotypes of Populus for sustainable production of biofuels, bioproducts, and biomaterials

Humans have been modifying plant traits for thousands of years, first through selection (i.e., domestication) then modern breeding, and in the last 30 years, through biotechnology. These modifications have resulted in increased yield, more efficient agronomic practices, and enhanced quality traits. Precision knowledge of gene regulation and function through high-resolution single-cell omics technologies, coupled with the ability to engineer plant genomes at the DNA sequence, chromatin accessibility, and gene expression levels, can enable engineering of complex and complementary traits at the biosystem level. Populus spp., the primary genetic model system for woody perennials, are among the fastest growing trees in temperate zones and are important for both carbon sequestration and global carbon cycling. Ample genomic and transcriptomic resources for poplar are available including emerging single-cell omics datasets. To expand use of poplar outside of valorization of woody biomass, chassis with novel morphotypes in which stem branching and tree height are modified can be fabricated thereby leading to trees with altered leaf to wood ratios. These morphotypes can then be engineered into customized chemotypes that produce high value biofuels, bioproducts, and biomaterials not only in specific organs but also in a cell-type-specific manner. For example, the recent discovery of triterpene production in poplar leaf trichomes can be exploited using cell-type specific regulatory sequences to synthesize high value terpenes such as the jet fuel precursor bisabolene specifically in the trichomes. By spatially and temporally controlling expression, not only can pools of abundant precursors be exploited but engineered molecules can be sequestered in discrete cell structures in the leaf. The structural diversity of the hemicellulose xylan is a barrier to fully utilizing lignocellulose in biomaterial production and by leveraging cell-type-specific omics data, cell wall composition can be modified in a tailored and targeted specific manner to generate poplar wood with novel chemical features that are amenable for processing or advanced manufacturing. Precision engineering poplar as a multi-purpose sustainable feedstock highlights how genome engineering can be used to re-imagine a crop species.

09 BIOMASS FUELS↗
DOE OSTI2023

Modeling strategies and data needs for representing coastal wetland vegetation in land surface models

Vegetated coastal ecosystems sequester carbon rapidly relative to terrestrial ecosystems. Coastal wetlands are poorly represented in land surface models, but work is underway to improve process-based, predictive modeling of these ecosystems. Here, in this work, we identify guiding questions, potential simulations, and data needs to make progress in improving representation of vegetation in terrestrial–aquatic interfaces, with a focus on coastal and estuarine ecosystems. We synthesize relevant plant traits and environmental controls on vegetation that influence carbon cycling in coastal ecosystems. We propose that models include separate plant functional types (PFTs) for mangroves, graminoid salt marshes, and succulent salt marshes to adequately represent the variation in aboveground and belowground productivity between common coastal wetland vegetation types. We also discuss the drivers and carbon storage consequences of shifts in dominant PFTs. We suggest several potential approaches to represent the diversity in vegetation tolerance and adaptations to fluctuations in salinity and water level, which drive key gradients in coastal wetland ecosystems. Finally, we discuss data needs for parameterizing and evaluating model implementations of coastal wetland vegetation types and function.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Long-term, large-scale experiment reveals the effects of seed limitation, climate, and anthropogenic disturbance on restoration of plant communities in a biodiversity hotspot

Ecological restoration is essential for maintaining biodiversity in the face of dynamic, global changes in climate, human land use, and disturbance regimes. Effective restoration requires understanding bottlenecks in plant community recovery that exist today, while recognizing that these bottlenecks may relate to complex histories of environmental change. Such understanding has been a challenge because few long-term, well-replicated experiments exist to decipher the demographic processes influencing recovery for numerous species against the backdrop of multiyear variation in climate and management. Here we address this challenge through a long-term and geographically expansive experiment in longleaf pine savannas, an imperiled ecosystem and biodiversity hotspot in the southeastern United States. Using 48 sites at three locations spanning 480 km, the 8-y experiment manipulated initial seed arrival for 24 herbaceous plant species and presence of competitors to evaluate the impacts of climate variability and management actions (e.g., prescribed burning) on plant establishment and persistence. Adding seeds increased plant establishment of many species. Cool and wet climatic conditions, low tree density, and reduced litter depth also promoted establishment. Once established, most species persisted for the duration of the 8-y experiment. Plant traits were most predictive when tightly coupled to the process of establishment. Our results illustrate how seed additions can restore plant diversity and how interannual climatic variation affects the dynamics of plant communities across a large region. The significant effects of temperature and precipitation inform how future climate may affect restoration and conservation via large-scale changes in the fundamental processes of establishment and persistence.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Enhancing climate-smart crop performance in arid agrivoltaics systems: effects of photovoltaic shading and soil amendments on tepary bean growth, yield, and associated soil microbiome

As climate change expands the world’s arid and semiarid regions, sustainable systems that integrate food and energy production are becoming increasingly critical. Agrivoltaics—co-locating crops with photovoltaic (PV) panels—offers a dual land-use strategy that mitigates environmental stress by shading crops, conserving soil moisture, and enhancing PV efficiency. While climate-smart crops like the tepary bean ( Phaseolus acutifolius ) are well adapted to heat and drought, little is known about how these crops and their associated soil microbiomes respond to the unique microclimates created by PV shading. This study evaluated tepary bean performance and plant–microbial interactions under PV-shade vs. no shade across three soil amendment treatments at two experimental sites. We assessed plant traits including germination, phenology, biomass, height, as well as yield and bean morphology, alongside shifts in soil microbial composition and functional potential. Plants grown under PV-shade were generally taller, with extended reproductive periods and higher yields: 42% of shaded plants produced beans compared to only 8% under full sun. Shaded plants also produced rounder, higher-quality beans, whereas non-shaded plants yielded flatter, less developed beans. Microbial community composition was more strongly influenced by amendment and site conditions than by shading alone. Key microbial taxa (e.g., Glomeromycetes, Desulfobacterota ) and predicted functions (e.g., denitrification, nitrogen-respiration, sulfate reduction) were associated with differences in plant performance. Finally, combining agrivoltaic systems with targeted soil amendments can enhance crop yield and soil microbial functionality—offering a promising strategy for sustainable agriculture in arid landscapes.

14 SOLAR ENERGY↗
DOE OSTI2023

Latent Dirichlet Allocation modeling of environmental microbiomes

Interactions between stressed organisms and their microbiome environments may provide new routes for understanding and controlling biological systems. However, microbiomes are a form of high-dimensional data, with thousands of taxa present in any given sample, which makes untangling the interaction between an organism and its microbial environment a challenge. Here we apply Latent Dirichlet Allocation (LDA), a technique for language modeling, which decomposes the microbial communities into a set of topics (non-mutually-exclusive sub-communities) that compactly represent the distribution of full communities. LDA provides a lens into the microbiome at broad and fine-grained taxonomic levels, which we show on two datasets. In the first dataset, from the literature, we show how LDA topics succinctly recapitulate many results from a previous study on diseased coral species. We then apply LDA to a new dataset of maize soil microbiomes under drought, and find a large number of significant associations between the microbiome topics and plant traits as well as associations between the microbiome and the experimental factors, e.g. watering level. This yields new information on the plant-microbial interactions in maize and shows that LDA technique is useful for studying the coupling between microbiomes and stressed organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

PhytoOracle: Scalable, modular phenomics data processing pipelines

As phenomics data volume and dimensionality increase due to advancements in sensor technology, there is an urgent need to develop and implement scalable data processing pipelines. Current phenomics data processing pipelines lack modularity, extensibility, and processing distribution across sensor modalities and phenotyping platforms. To address these challenges, we developed PhytoOracle (PO), a suite of modular, scalable pipelines for processing large volumes of field phenomics RGB, thermal, PSII chlorophyll fluorescence 2D images, and 3D point clouds. PhytoOracle aims to ( i ) improve data processing efficiency; ( ii ) provide an extensible, reproducible computing framework; and ( iii ) enable data fusion of multi-modal phenomics data. PhytoOracle integrates open-source distributed computing frameworks for parallel processing on high-performance computing, cloud, and local computing environments. Each pipeline component is available as a standalone container, providing transferability, extensibility, and reproducibility. The PO pipeline extracts and associates individual plant traits across sensor modalities and collection time points, representing a unique multi-system approach to addressing the genotype-phenotype gap. To date, PO supports lettuce and sorghum phenotypic trait extraction, with a goal of widening the range of supported species in the future. At the maximum number of cores tested in this study (1,024 cores), PO processing times were: 235 minutes for 9,270 RGB images (140.7 GB), 235 minutes for 9,270 thermal images (5.4 GB), and 13 minutes for 39,678 PSII images (86.2 GB). These processing times represent end-to-end processing, from raw data to fully processed numerical phenotypic trait data. Repeatability values of 0.39-0.95 (bounding area), 0.81-0.95 (axis-aligned bounding volume), 0.79-0.94 (oriented bounding volume), 0.83-0.95 (plant height), and 0.81-0.95 (number of points) were observed in Field Scanalyzer data. We also show the ability of PO to process drone data with a repeatability of 0.55-0.95 (bounding area).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Future climate doubles the risk of hydraulic failure in a wet tropical forest

Summary Future climate presents conflicting implications for forest biomass. We evaluate how plant hydraulic traits, elevated CO 2 levels, warming, and changes in precipitation affect forest primary productivity, evapotranspiration, and the risk of hydraulic failure. We used a dynamic vegetation model with plant hydrodynamics (FATES‐HYDRO) to simulate the stand‐level responses to future climate changes in a wet tropical forest in Barro Colorado Island, Panama. We calibrated the model by selecting plant trait assemblages that performed well against observations. These assemblages were run with temperature and precipitation changes for two greenhouse gas emission scenarios (2086–2100: SSP2‐45, SSP5‐85) and two CO 2 levels (contemporary, anticipated). The risk of hydraulic failure is projected to increase from a contemporary rate of 5.7% to 10.1–11.3% under future climate scenarios, and, crucially, elevated CO 2 provided only slight amelioration. By contrast, elevated CO 2 mitigated GPP reductions. We attribute a greater variation in hydraulic failure risk to trait assemblages than to either CO 2 or climate. Our results project forests with both faster growth (through productivity increases) and higher mortality rates (through increasing rates of hydraulic failure) in the neo‐tropics accompanied by certain trait plant assemblages becoming nonviable.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Switchgrass-associated soil microbes have subtle but distinct effects on germination vs. growth under drought

Soil microbial communities can play a large role in plant fitness, including plants’ response to drought. How microbes mediate drought response may also differ across the plants’ life stage, but studies rarely study causal effects of microbes on plant fitness at multiple stages. We conducted a greenhouse experiment on switchgrass (Panicum virgatum L.) to investigate how microbial presence (sterile bulk vs. live bulk soils) and microbial source (communities from bulk vs. rhizosphere soil) affect germination and seedling growth (life-stage) during drought. We also investigated how drought and life-stage alter the assembly of the inoculated communities. Both drought conditions and the absence of microbes reduced germination (49% and 50% fewer seedlings, respectively, p < 0.05), but there were few effects of microbial presence on older seedlings. In addition, microbial source had no effect on the evaluated plant traits, but interestingly, the initially similar bulk and rhizosphere communities became compositionally distinct after 34 days with germinating seeds, but not with seedlings. Therefore, it may be that the plants did respond to microbial source through changes in seed or root exudates, and calls for further study. Finally, while sometimes microbes did benefit plants under drought, we did not find evidence that they are especially beneficial in this condition. We suggest that microbes’ effects differ across plant life stage, and may be both positive and negative. Further research should advance understanding of plant stress tolerance within a framework of plant-microbiome co-development.

drought↗
DOE OSTI2025

TARP Identifying Critical Thresholds for Acute Response of Plants and Ecosystems to Water Stress at Walker Branch Watershed, 2002-2005

This dataset contains data from a manipulative field study aimed at identifying critical thresholds for acute response of plants and ecosystems to water stress (TARP) that took place at Walker Branch Watershed in Oak Ridge, Tennessee from 2002-2005 (2002-06-20 to 2005-12-16). The study used understory tents for the removal of 100% of the growing-season throughfall and stem flow, to provide data on the impact of acute drought on mechanisms responsible for growth and mortality of deciduous forest canopy trees representative of common plant functional types (Liriodendron and Quercus). Through three years of manipulation (2003, 2004 and 2005; pretreatment measurements in 2002) various measures of tree response to surface moisture deficits were recorded including root and leaf traits, plant nonstructural carbohydrates status, hourly sapflow, basal area, and periodic observations of foliar photosynthesis and conductance. Additionally, environmental data such as air and soil temperature, soil water content, and soil matric potential were recorded. This dataset contains data 16 files in comma-separate (*.csv) format. Additional metadata are provided: 16 data dictionaries and a file-level metadata file in comma separate (*.csv) format and a user guide in PDF (*.pdf) format.

basal area↗
DOE OSTI2023

Root traits of perennial C 4 grasses contribute to cultivar variations in soil chemistry and species patterns in particulate and mineral‐associated carbon pool formation

Abstract Recent studies have indicated that the C 4 perennial bioenergy crops switchgrass ( Panicum virgatum ) and big bluestem ( Andropogon gerardii ) accumulate significant amounts of soil carbon (C) owing to their extensive root systems. Soil C accumulation is likely driven by inter‐ and intraspecific variability in plant traits, but the mechanisms that underpin this variability remain unresolved. In this study we evaluated how inter‐ and intraspecific variation in root traits of cultivars from switchgrass (Cave‐in‐Rock, Kanlow, Southlow) and big bluestem (Bonanza, Southlow, Suther) affected the associations of soil C accumulation across soil fractions using stable isotope techniques. Our experimental field site was established in June 2008 at Fermilab in Batavia, IL. In 2018, soil cores were collected (30 cm depth) from all cultivars. We measured root biomass, root diameter, specific root length, bulk soil C, C associated with coarse particulate organic matter (CPOM) and fine particulate organic matter plus silt‐ and clay‐sized fractions, and characterized organic matter chemical class composition in soil using high‐resolution Fourier‐transform ion cyclotron resonance mass spectrometry. C 4 species were established on soils that supported C 3 grassland for 36 years before planting, which allowed us to use differences in the natural abundance of stable C isotopes to quantify C 4 plant‐derived C. We found that big bluestem had 36.9% higher C 4 plant‐derived C compared to switchgrass in the CPOM fraction in the 0–10 cm depth, while switchgrass had 60.7% higher C 4 plant‐derived C compared to big bluestem in the clay fraction in the 10–20 cm depth. Our findings suggest that the large root system in big bluestem helps increase POM‐C formation quickly, while switchgrass root structure and chemistry build a mineral‐bound clay C pool through time. Thus, both species and cultivar selection can help improve bioenergy management to maximize soil carbon gains and lower CO 2 emissions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Incorporating the Acclimation of Photosynthesis and Leaf Respiration in the Noah‐MP Land Surface Model: Model Development and Evaluation

Abstract Realistic simulation of leaf photosynthetic and respiratory processes is needed for accurate prediction of the global carbon cycle. These two processes systematically acclimate to long‐term environmental changes by adjusting photosynthetic and respiratory traits (e.g., the maximum photosynthetic capacity at 25°C ( V cmax,25 ) and the leaf respiration rate at 25°C ( R 25 )) following increasingly well‐understood principles. While some land surface models (LSMs) now account for thermal acclimation, they do so by assigning empirical parameterizations for individual plant functional types (PFTs). Here, we have implemented an Eco‐Evolutionary Optimality (EEO)‐based scheme to represent the universal acclimation of photosynthesis and leaf respiration to multiple environmental effects, and that therefore requires no PFT‐specific parameterizations, in a standard version of the widely used LSM, Noah MP. We evaluated model performance with plant trait data from a 5‐year experiment and extensive global field measurements, and carbon flux measurements from FLUXNET2015. We show that observed R 25 and V cmax,25 vary substantially both temporally and spatially within the same PFT ( C.V. >20%). Our EEO‐based scheme captures 62% of the temporal and 70% of the spatial variations in V cmax,25 (73% and 54% of the variations in R 25 ). The standard scheme underestimates gross primary production by 10% versus 2% for the EEO‐based scheme and generates a larger spread in r (correlation coefficient) across flux sites (0.79 ± 0.16 vs. 0.84 ± 0.1, mean ± S.D.). The standard scheme greatly overestimates canopy respiration (bias: ∼200% vs. 8% for the EEO scheme), resulting in less CO 2 uptake by terrestrial ecosystems. Our approach thus simulates climate‐carbon coupling more realistically, with fewer parameters.

Ren, Yanghang [Department of Earth System Science ↗
DOE OSTI2021

Decadal changes in fire frequencies shift tree communities and functional traits

Global change has resulted in chronic shifts in fire regimes. Variability in the sensitivity of tree communities to multi-decadal changes in fire regimes is critical to anticipating shifts in ecosystem structure and function, yet remains poorly understood. Here, we address the overall effects of fire on tree communities and the factors controlling their sensitivity in 29 sites that experienced multi-decadal alterations in fire frequencies in savanna and forest ecosystems across tropical and temperate regions. Fire had a strong overall effect on tree communities, with an average fire frequency (one fire every three years) reducing stem density by 48% and basal area by 53% after 50 years, relative to unburned plots. Here, the largest changes occurred in savanna ecosystems and in sites with strong wet seasons or strong dry seasons, pointing to fire characteristics and species composition as important. Analyses of functional traits highlighted the impact of fire-driven changes in soil nutrients because frequent burning favoured trees with low biomass nitrogen and phosphorus content, and with more efficient nitrogen acquisition through ectomycorrhizal symbioses. Taken together, the response of trees to altered fire frequencies depends both on climatic and vegetation determinants of fire behaviour and tree growth, and the coupling between fire-driven nutrient losses and plant traits.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Embolism resistance explains mortality and recovery of five subtropical evergreen broadleaf trees to persistent drought

Subtropical evergreen broadleaf forest (SEBF) is experiencing and expected to suffer more frequent and severe drought events. However, how the hydraulic traits directly link to the mortality and recovery of SEBF trees remains unclear. In this study, we conducted a drought-rewatering experiment on tree seedlings of five dominant species to investigate how the hydraulic traits were related to tree mortality and the resistance and recovery of photosynthesis (A) and transpiration (E) under different drought severities. Species with greater embolism resistance (P 50 ) survived longer than those with the weaker P 50 . However, there was no general hydraulic threshold associated with tree mortality, with the lethal hydraulic failure varying from 64% to 93% loss of conductance. Further, the photosynthesis and transpiration of tree species with greater P 50 were more resistant to and recovered faster from drought than those with lower P 50 . Other plant traits could not explain the interspecific variation in tree mortality and drought resistance and recovery. These results highlight the unique importance of embolism resistance in driving carbon and water process under persistent drought across different trees in SEBF. The absence of multiple efficient drought strategies in SEBF seedlings implies the difficulty of natural seedling regeneration under future droughts, which often occurs after destructive disturbances (e.g., extreme drought events and typhoon), suggesting that this biome may be highly vulnerable to co-occurring climate extremes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Modeling the Joint Effects of Vegetation Characteristics and Soil Properties on Ecosystem Dynamics in a Panama Tropical Forest

Abstract In tropical forests, both vegetation characteristics and soil properties are important not only for controlling energy, water, and gas exchanges directly but also determining the competition among species, successional dynamics, forest structure and composition. However, the joint effects of the two factors have received limited attention in Earth system model development. Here we use a vegetation demographic model, the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) implemented in the Energy Exascale Earth System Model (E3SM) Land Model (ELM), ELM‐FATES, to explore how plant traits and soil properties affect tropical forest growth and composition concurrently. A large ensemble of simulations with perturbed vegetation and soil hydrological parameters is conducted at the Barro Colorado Island, Panama. The simulations are compared against observed carbon, energy, and water fluxes. We find that soil hydrological parameters, particularly the scaling exponent of the soil retention curve ( B sw ), play crucial roles in controlling forest diversity, with higher B sw values (>7) favoring late successional species in competition, and lower B sw values (1 ∼ 7) promoting the coexistence of early and late successional plants. Considering the additional impact of soil properties resolves a systematic bias of FATES in simulating sensible/latent heat partitioning with repercussion on water budget and plant coexistence. A greater fraction of deeper tree roots can help maintain the dry‐season soil moisture and plant gas exchange. As soil properties are as important as vegetation parameters in predicting tropical forest dynamics, more efforts are needed to improve parameterizations of soil functions and belowground processes and their interactions with aboveground vegetation dynamics.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRSDate not supplied

Remote Sensing of Lineage Functional Types for Modeling and Monitoring Biodiversity

Hyperspectral remote sensing has the potential to continuously scale plant function and plant diversity information from landscape to global extents. Numerous studies have indicated that VSWIR (400-2500 nm) reflectance properties of vegetation capture evolutionarily conserved biochemical, structural, and other functional attributes of plant species. Spectral properties conserved in plants provide the opportunity to both 1) aggregate species into lineages with improved classification accuracy and 2) link those lineages directly to plant traits. Full realization of this goal will enable parameterization of Land Surface Models (LSMs) with remotely sensed information, e.g., canopy nitrogen, and better representations of biodiversity and functional diversity in biogeographic studies. In this study, we use hyperspectral AVIRIS data from the 2013 HyspIRI campaign over the Southern Sierra Nevada, California flight box to investigate the potential for incorporating evolutionary thinking into landcover classification. We link the airborne hyperspectral data with vegetation plot data from roughly 1372 surveys and a phylogeny representing 1361 species. We aggregate species into lineages ranging from species level groups down to similar number of Plant Functional Types as often used in LSMs. We assessed the ability of Random Forest and Partial Least Squares Discriminant Analysis to discriminate across these different phylogenetic scales and determine the optimal number of lineages to classify. Although there are some temporal and spatial differences in our training data, our best approaches achieved moderate classification accuracy (Kappa > 0.65). Given an optimal number of lineages, we explored approaches to improve classifications including machine learning and unmixing approaches. This work suggests that lineage-based methods may be a promising way to leverage the huge amounts of data that will come from high resolution and high return interval hyperspectral data planned for the Surface Biology and Geology mission with sparsely sampled existing ground-based ecological data.

Hyperspectral↗
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↗