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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

The importance of independent replication of treatments in plant science

Among other foci, the Journal of Experimental Botany aims to advance understanding of plant environment interactions, including abiotic stress, mineral nutrition, and the response of plants to global change. Advancing understanding in these areas often requires manipulation of the growth environment. Experiments range in scale and include: growth chambers (Yiotis et al., 2020), glasshouses (Rho et al., 2019), whole plant chambers (Sharwood et al., 2017), and open-air field experiments (Ruiz-Vera et al., 2020). The application of environmental manipulations can be constrained by available resources, operational costs, and time. In designing experiments, researchers attempt to balance logistical challenges with the desire to address scientific questions and maximize statistical power.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

The Global Spectra-Trait Initiative: A database of paired leaf spectroscopy and functional traits associated with leaf photosynthetic capacity (v1.0.0)

The Global Spectra-Trait Initiative (GSTI) aims to generate generalizable spectra trait models using reflectance data to predict leaf traits associated with the photosynthesis capacity of leaves. It comprises a synthesized dataset of leaf trait data, input datasets and code. Leaf traits include the maximum carboxylation rate of rubisco (Vcmax), the maximum electron transport rate (Jmax), the dark respiration, as well as the prediction of leaf nitrogen, leaf mass per area (LMA), and leaf water content (LWC). The dataset comprises >7500 paired observations from around 400 species from a broad range of biomes. This dataset comprises a zip file of the GSTI GitHub repository (https://github.com/plantphys/gsti), the synthesized database (.csv) and database metadata files. This dataset was updated on 2025-12-12 with minor edits to mirror the accepted manuscript version and GitHub release (Version 1.0.0 (ESSD accepted version)). Edits included minor changes to the project documentation on GitHub and removal of 12 duplicate entries from the database.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Root and Leaf Traits of Alfalfa Exhibit Distinct Responses to Soil Microbial Communities and Environmental Stresses

Ongoing climate change is negatively impacting crop productivity globally. Past research has highlighted that a diverse soil microbial community and variation in plant traits for resource acquisition can mitigate the negative impacts of climate change factors on crop productivity. This study investigates the effects of two major environmental stressors—drought and salinity stress, on plant productivity, biomass allocation, and root and leaf trait responses under distinct soil microbial diversities. Our results showed that salinity stress had stronger negative impacts on plant productivity than drought stress. Shoot biomass decreased by 30% and 32.5% under drought and salinity stress, respectively, whereas the root biomass decreased by 32% only under salinity stress. Soil microbial diversity did not affect plant productivity. Next, root traits were mainly impacted by drought and salinity stress, whereas leaf traits were impacted by both environmental stresses and soil microbial diversity. Specific root length and specific root area decreased under drought, and root tissue density was minimal under salinity stress. Root traits were not affected by soil microbial communities. In contrast, the leaf nitrogen content increased, whereas pheophytin content (a breakdown product of chlorophyll) decreased when plants were grown in diverse microbial communities under environmental stresses, especially drought. These results highlight the importance of soil microbial diversity in impacting plant traits in response to environmental stresses. We showed that the soil microbial diversity influences both aboveground and belowground plant traits, indicating the need for better management practices to conserve and promote soil microbial diversity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Short-term warming increased soil heterotrophic respiration due to enhanced active microbial community

Soil microbes, particularly active microbes, play a crucial role in conserving soil carbon under climate change, especially in forest ecosystems, constituting over 50% of global soil organic carbon. Nevertheless, the response mechanisms of active microbial community to climate warming and their subsequent impacts on soil heterotrophic respiration (Rh) remain insufficiently understood. To resolve this mechanistic uncertainty, we implemented a 3-year soil translocation experiment to investigate soil warming effects on active microbial community and Rh. We used 16S rRNA gene amplicon sequencing, Metatranscriptomics sequencing, coupled with correlation analyses to explore the linkages between warming-induced shifts in Rh and the active microbial community. Our results demonstrated that warming of soil induced a 55% enhancement in Rh. Concurrently, the Shannon index and Richness of active microbial community increased by 20% and 117%, respectively. Warming significantly altered active microbial community composition, inducing a compositional shift characterized by 0.5-to 2-fold increases in the abundances of Proteobacteria, Chloroflexi, and Actinobacteria. Our study also revealed 92–100% increases in the abundance of C-degradation functional genes encoding starch, cellulose, and lignin decomposition pathways within active microbial community under warming. Statistical analyses identified significant positive correlations between Rh and the abundance of Proteobacteria and Actinobacteria, as well as expression levels of functional genes associated with lignin and cellulose decomposition pathways. Furthermore, our results suggested that short-term warming increased Rh through altering diversity, species composition, and C degradation functional genes of active microbial community providing insights into the influence of microbial communities on soil C-climate feedbacks under climate warming.

Active microbial community↗
DOE OSTI2025

Earthworms significantly enhance the temperature sensitivity of soil organic matter decomposition: Insights into future soil carbon budgeting

How and what soil fauna influence the soil organic matter (SOM) decomposition rate (Rs) and its temperature sensitivity (Q 10 ) have been largely ignored, although this is a crucial matter, especially under the scenario of global change. Further, in this study, a novel approach was adopted with a continuous changing-temperature incubation (daytime, from 7 °C to 22 °C; nighttime, from 22 °C to 7 °C) with rapid and continuous measurement, to examine the effect of soil macrofauna (specifically, earthworms) on Rs and Q 10 with three densities (no addition, low density, and high density). According to the results, the earthworms accelerated Rs. Furthermore, Rs with earthworm addition had a symmetrical pattern during daytime and nighttime cycles, which is contrary to traditional soil incubation, with only soil microbe as asymmetrical. More importantly, earthworm addition increased Q 10 markedly, ranging from 48% to 67%. Overall, the findings highlight the pivotal role of earthworms as soil macrofauna that regulating soil carbon release, and their effects should be integrated into process-based ecological models in future.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Phosphate amendment drives bloom of RNA viruses after soil wet-up

Soil rewetting after a dry period results in a surge of activity and succession in both microbial and DNA virus communities. Less is known about the response of RNA viruses to soil rewetting—while they are highly diverse and widely distributed in soil, they remain understudied. We hypothesized that RNA viruses would show temporal succession following rewetting and that phosphate amendment would influence their trajectory, as viral proliferation may cause phosphorus limitation. Using 39 time-resolved metatranscriptomes and amplicon data, 2190 RNA viral populations were identified across five phyla, with 26 % of these predicted to infect bacteria, and 11 % fungi. Only 1.2 % of viral populations had annotated capsid genes, suggesting most persist via intracellular replication without a free virion phase. Phosphate amendment altered RNA viral community composition within the first week and amended vs. unamended communities remained distinguishable for up to three weeks. While the overall host community remained stable, certain bacterial populations showed reduced abundance in phosphate-amended soils, likely due to increased viral lysis, as RNA bacteriophages proliferated significantly. Notably, 60 % of the viruses with increased abundance under phosphate amendment belonged to basal Lenarviricota clades rather than well-known groups like Leviviricetes. We estimate RNA bacteriophage infections may affect 10 7 –10 9 bacteria per gram of soil, aligning with the total bacterial population (10 7 –10 10 g -1 soil), suggesting that RNA phages significantly influence bacterial communities post-wet-up, with phosphorus availability modulating this effect.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The temperature sensitivity of soil: microbial biodiversity, growth, and carbon mineralization

Abstract Microorganisms drive soil carbon mineralization and changes in their activity with increased temperature could feedback to climate change. Variation in microbial biodiversity and the temperature sensitivities (Q10) of individual taxa may explain differences in the Q10 of soil respiration, a possibility not previously examined due to methodological limitations. Here, we show phylogenetic and taxonomic variation in the Q10 of growth (5–35 °C) among soil bacteria from four sites, one from each of Arctic, boreal, temperate, and tropical biomes. Differences in the temperature sensitivities of taxa and the taxonomic composition of communities determined community-assembled bacterial growth Q10, which was strongly predictive of soil respiration Q10 within and across biomes. Our results suggest community-assembled traits of microbial taxa may enable enhanced prediction of carbon cycling feedbacks to climate change in ecosystems across the globe.

Wang, Chao (ORCID:0000000257567505)↗
DOE OSTI2024

Integrating viruses into soil food web biogeochemistry

The soil microbiome is recognized as an essential component of healthy soils. Viruses are also diverse and abundant in soils, but their roles in soil systems remain unclear. Here we argue for the consideration of viruses in soil microbial food webs and describe the impact of viruses on soil biogeochemistry. The soil food web is an intricate series of trophic levels that span from autotrophic microorganisms to plants and animals. Each soil system encompasses contrasting and dynamic physicochemical conditions, with labyrinthine habitats composed of particles. Conditions are prone to shifts in space and time, and this variability can obstruct or facilitate interactions of microorganisms and viruses. Because viruses can infect all domains of life, they must be considered as key regulators of soil food web dynamics and biogeochemical cycling. Finally, we highlight future research avenues that will enable a more robust understanding of the roles of viruses in soil function and health.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Nutrient and moisture limitations reveal keystone metabolites linking rhizosphere metabolomes and microbiomes

Plants release a wealth of metabolites into the rhizosphere that can shape the composition and activity of microbial communities in response to environmental stress. The connection between rhizodeposition and rhizosphere microbiome succession has been suggested, particularly under environmental stress conditions, yet definitive evidence is scarce. In this study, we investigated the relationship between rhizosphere chemistry, microbiome dynamics, and abiotic stress in the bioenergy crop switchgrass grown in a marginal soil under nutrient-limited, moisture-limited, and nitrogen (N)-replete, phosphorus (P)-replete, and NP-replete conditions. We combined 16S rRNA amplicon sequencing and LC-MS/MS-based metabolomics to link rhizosphere microbial communities and metabolites. We identified significant changes in rhizosphere metabolite profiles in response to abiotic stress and linked them to changes in microbial communities using network analysis. N-limitation amplified the abundance of aromatic acids, pentoses, and their derivatives in the rhizosphere, and their enhanced availability was linked to the abundance of bacterial lineages from Acidobacteria, Verrucomicrobia, Planctomycetes, and Alphaproteobacteria. Conversely, N-amended conditions increased the availability of N-rich rhizosphere compounds, which coincided with proliferation of Actinobacteria. Treatments with contrasting N availability differed greatly in the abundance of potential keystone metabolites; serotonin and ectoine were particularly abundant in N-replete soils, while chlorogenic, cinnamic, and glucuronic acids were enriched in N-limited soils. Serotonin, the keystone metabolite we identified with the largest number of links to microbial taxa, significantly affected root architecture and growth of rhizosphere microorganisms, highlighting its potential to shape microbial community and mediate rhizosphere plant–microbe interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Molecular mechanisms underlying host-induced gene silencing

Abstract Host-induced gene silencing (HIGS) refers to the silencing of genes in pathogens and pests by expressing homologous double-stranded RNAs (dsRNA) or artificial microRNAs (amiRNAs) in the host plant. The discovery of such trans-kingdom RNA silencing has enabled the development of RNA interference-based approaches for controlling diverse crop pathogens and pests. Although HIGS is a promising strategy, the mechanisms by which these regulatory RNAs translocate from plants to pathogens, and how they induce gene silencing in pathogens, are poorly understood. This lack of understanding has led to large variability in the efficacy of various HIGS treatments. This variability is likely due to multiple factors, such as the ability of the target pathogen or pest to take up and/or process RNA from the host, the specific genes and target sequences selected in the pathogen or pest for silencing, and where, when, and how the dsRNAs or amiRNAs are produced and translocated. In this review, we summarize what is currently known about the molecular mechanisms underlying HIGS, identify key unanswered questions, and explore strategies for improving the efficacy and reproducibility of HIGS treatments in the control of crop diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The Chlamydomonas Genome Project, version 6: reference assemblies for mating type plus and minus strains reveal extensive structural mutation in the laboratory

Five versions of the Chlamydomonas reinhardtii reference genome have been produced over the last two decades. Here we present version 6, bringing significant advances in assembly quality and structural annotations. PacBio-based chromosome-level assemblies for two laboratory strains, CC-503 and CC-4532, provide resources for the plus and minus mating type alleles. We corrected major misassemblies in previous versions and validated our assemblies via linkage analyses. Contiguity increased over ten-fold and >80% of filled gaps are within genes. We used Iso-Seq and deep RNA-seq datasets to improve structural annotations, and updated gene symbols and textual annotation of functionally characterized genes via extensive manual curation. We discovered that the cell wall-less classical reference strain CC-503 exhibits genomic instability potentially caused by deletion of the helicase RECQ3, with major structural mutations identified that affect >100 genes. We therefore present the CC-4532 assembly as the primary reference, although this strain also carries unique structural mutations and is experiencing rapid proliferation of a Gypsy retrotransposon. We expect all laboratory strains to harbor gene-disrupting mutations, which should be considered when interpreting and comparing experimental results. Collectively, the resources presented here herald a new era of Chlamydomonas genomics and will provide the foundation for continued research in this important reference organism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Plants use molecular mechanisms mediated by biomolecular condensates to integrate environmental cues with development

This review highlights recent literature on biomolecular condensates in plant development and discusses challenges for fully dissecting their functional roles. Plant developmental biology has been inundated with descriptive examples of biomolecular condensate formation, but it is only recently that mechanistic understanding has been forthcoming. Here, we discuss recent examples of potential roles biomolecular condensates play at different stages of the plant life cycle. We group these examples based on putative molecular functions, including sequestering interacting components, enhancing dwell time, and interacting with cytoplasmic biophysical properties in response to environmental change. We explore how these mechanisms could modulate plant development in response to environmental inputs and discuss challenges and opportunities for further research into deciphering molecular mechanisms to better understand the diverse roles that biomolecular condensates exert on life.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

VipariNama: RNA viral vectors to rapidly elucidate the relationship between gene expression and phenotype

Synthetic transcription factors have great promise as tools to help elucidate relationships between gene expression and phenotype by allowing tunable alterations of gene expression without genomic alterations of the loci being studied. However, the years-long timescales, high cost, and technical skill associated with plant transformation have limited their use. In this work, we developed a technology called VipariNama (ViN) in which vectors based on the tobacco rattle virus are used to rapidly deploy Cas9-based synthetic transcription factors and reprogram gene expression in planta. We demonstrate that ViN vectors can implement activation or repression of multiple genes systemically and persistently over several weeks in Nicotiana benthamiana, Arabidopsis (Arabidopsis thaliana), and tomato (Solanum lycopersicum). By exploring strategies including RNA scaffolding, viral vector ensembles, and viral engineering, we describe how the flexibility and efficacy of regulation can be improved. We also show how this transcriptional reprogramming can create predictable changes to metabolic phenotypes, such as gibberellin biosynthesis in N. benthamiana and anthocyanin accumulation in Arabidopsis, as well as developmental phenotypes, such as plant size in N. benthamiana, Arabidopsis, and tomato. These results demonstrate how ViN vector-based reprogramming of different aspects of gibberellin signaling can be used to engineer plant size in a range of plant species in a matter of weeks. In summary, ViN accelerates the timeline for generating phenotypes from over a year to just a few weeks, providing an attractive alternative to transgenesis for synthetic transcription factor-enabled hypothesis testing and crop engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A small molecule antagonizes jasmonic acid perception and auxin responses in vascular and nonvascular plants

The phytohormone jasmonoyl-L-isoleucine (JA-Ile) regulates many stress responses and developmental processes in plants. A co-receptor complex formed by the F-box protein Coronatine Insensitive 1 (COI1) and a Jasmonate (JA) ZIM-domain (JAZ) repressor perceives the hormone. JA-Ile antagonists are invaluable tools for exploring the role of JA-Ile in specific tissues and developmental stages, and for identifying regulatory processes of the signaling pathway. Using two complementary chemical screens, we identified three compounds that exhibit a robust inhibitory effect on both the hormone-mediated COI–JAZ interaction and degradation of JAZ1 and JAZ9 in vivo. One molecule, J4, also restrains specific JA-induced physiological responses in different angiosperm plants, including JA-mediated gene expression, growth inhibition, chlorophyll degradation, and anthocyanin accumulation. Interaction experiments with purified proteins indicate that J4 directly interferes with the formation of the Arabidopsis (Arabidopsis thaliana) COI1–JAZ complex otherwise induced by JA. The antagonistic effect of J4 on COI1–JAZ also occurs in the liverwort Marchantia polymorpha, suggesting the mode of action is conserved in land plants. Besides JA signaling, J4 works as an antagonist of the closely related auxin signaling pathway, preventing Transport Inhibitor Response1/Aux–indole-3-acetic acid interaction and auxin responses in planta, including hormone-mediated degradation of an auxin repressor, gene expression, and gravitropic response. However, J4 does not affect other hormonal pathways. Altogether, our results show that this dual antagonist competes with JA-Ile and auxin, preventing the formation of phylogenetically related receptor complexes. J4 may be a useful tool to dissect both the JA-Ile and auxin pathways in particular tissues and developmental stages since it reversibly inhibits these pathways. One-sentence summary: A chemical screen identified a molecule that antagonizes jasmonate perception by directly interfering with receptor complex formation in phylogenetically distant vascular and nonvascular plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

X-ray microscopy enables multiscale high-resolution 3D imaging of plant cells, tissues, and organs

Capturing complete internal anatomies of plant organs and tissues within their relevant morphological context remains a key challenge in plant science. While plant growth and development are inherently multiscale, conventional light, fluorescence, and electron microscopy platforms are typically limited to imaging of plant microstructure from small flat samples that lack a direct spatial context to, and represent only a small portion of, the relevant plant macrostructures. We demonstrate technical advances with a lab-based X-ray microscope (XRM) that bridge the imaging gap by providing multiscale high-resolution three-dimensional (3D) volumes of intact plant samples from the cell to the whole plant level. Serial imaging of a single sample is shown to provide sub-micron 3D volumes co-registered with lower magnification scans for explicit contextual reference. High-quality 3D volume data from our enhanced methods facilitate sophisticated and effective computational segmentation. Advances in sample preparation make multimodal correlative imaging workflows possible, where a single resin-embedded plant sample is scanned via XRM to generate a 3D cell-level map, and then used to identify and zoom in on sub-cellular regions of interest for high-resolution scanning electron microscopy. In total, we present the methodologies for use of XRM in the multiscale and multimodal analysis of 3D plant features using numerous economically and scientifically important plant systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Laisk measurements in the nonsteady state: Tests in plants exposed to warming and variable CO2 concentrations

Abstract Light respiration (RL) is an important component of plant carbon balance and a key parameter in photosynthesis models. RL is often measured using the Laisk method, a gas exchange technique that is traditionally employed under steady-state conditions. However, a nonsteady-state dynamic assimilation technique (DAT) may allow for more rapid Laisk measurements. In 2 studies, we examined the efficacy of DAT for estimating RL and the parameter Ci* (the intercellular CO2 concentration where Rubisco's oxygenation velocity is twice its carboxylation velocity), which is also derived from the Laisk technique. In the first study, we compared DAT and steady-state RL and Ci* estimates in paper birch (Betula papyrifera) growing under control and elevated temperature and CO2 concentrations. In the second, we compared DAT-estimated RL and Ci* in hybrid poplar (Populus nigra L. × P. maximowiczii A. Henry “NM6”) exposed to high or low CO2 concentration pre-treatments. The DAT and steady-state methods provided similar RL estimates in B. papyrifera, and we found little acclimation of RL to temperature or CO2; however, Ci* was higher when measured with DAT compared to steady-state methods. These Ci* differences were amplified by the high or low CO2 pre-treatments. We propose that changes in the export of glycine from photorespiration may explain these apparent differences in Ci*.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A century of studying plant secondary metabolism—From “what?” to “where, how, and why?”

Abstract Over the past century, early advances in understanding the identity of the chemicals that collectively form a living plant have led scientists to deeper investigations exploring where these molecules localize, how they are made, and why they are synthesized in the first place. Many small molecules are specific to the plant kingdom and have been termed plant secondary metabolites, despite the fact that they can play primary and essential roles in plant structure, development, and response to the environment. The past 100 yr have witnessed elucidation of the structure, function, localization, and biosynthesis of selected plant secondary metabolites. Nevertheless, many mysteries remain about the vast diversity of chemicals produced by plants and their roles in plant biology. From early work characterizing unpurified plant extracts, to modern integration of ‘omics technology to discover genes in metabolite biosynthesis and perception, research in plant (bio)chemistry has produced knowledge with substantial benefits for society, including human medicine and agricultural biotechnology. Here, we review the history of this work and offer suggestions for future areas of exploration. We also highlight some of the recently developed technologies that are leading to ongoing research advances.

54 ENVIRONMENTAL SCIENCES↗