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30 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Wildfire impact on soil microbiome life history traits and roles in ecosystem carbon cycling

Abstract Wildfires, which are increasing in frequency and severity with climate change, reduce soil microbial biomass and alter microbial community composition and function. The soil microbiome plays a vital role in carbon (C) and nitrogen (N) cycling, but its complexity makes it challenging to predict post-wildfire soil microbial dynamics and resulting impacts on ecosystem biogeochemistry. The application of biogeochemically relevant conceptual trait-based frameworks to the soil microbiome can distill this complexity, enabling enhanced predictability of soil microbiome recovery following wildfire and subsequent impacts to biogeochemical cycles. Conceptual frameworks that have direct links to soil C and N cycling have been developed for the soil microbiome; the Y-A-S framework overviews soil microbiome life history strategies that have tradeoffs with one another and others have proposed frameworks specific to wildfire. Here, we aimed to delineate post-wildfire changes of bacterial traits in western US coniferous forests to inform how severe wildfire influences soil microbiome recovery and resultant biogeochemical cycling. We utilized a comprehensive metagenome-assembled genome catalog from post-wildfire soils representing 1 to 11 years following low- and high-severity burning to identify traits that enable the persistence of microbial taxa in burned soils and influence ecosystem C and N cycling. We found that high-severity wildfire initially selects for fast growers and, up to a decade post-fire, taxa that invest in genes for acquiring diverse resources from the external environment, which in combination could increase soil C losses. This work begins to disentangle how climate change–induced shifts in wildfire behavior might alter microbially mediated soil biogeochemical cycling.

Nelson, Amelia R.↗
DOE OSTI2022

Dissecting the Genetic Architecture of Carbon Partitioning in Sorghum Using Multiscale Phenotypes

Carbon partitioning in plants may be viewed as a dynamic process composed of the many interactions between sources and sinks. The accumulation and distribution of fixed carbon is not dictated simply by the sink strength and number but is dependent upon the source, pathways, and interactions of the system. As such, the study of carbon partitioning through perturbations to the system or through focus on individual traits may fail to produce actionable developments or a comprehensive understanding of the mechanisms underlying this complex process. Using the recently published sorghum carbon-partitioning panel, we collected both macroscale phenotypic characteristics such as plant height, above-ground biomass, and dry weight along with microscale compositional traits to deconvolute the carbon-partitioning pathways in this multipurpose crop. Multivariate analyses of traits resulted in the identification of numerous loci associated with several distinct carbon-partitioning traits, which putatively regulate sugar content, manganese homeostasis, and nitrate transportation. Using a multivariate adaptive shrinkage approach, we identified several loci associated with multiple traits suggesting that pleiotropic and/or interactive effects may positively influence multiple carbon-partitioning traits, or these overlaps may represent molecular switches mediating basal carbon allocating or partitioning networks. Conversely, we also identify a carbon tradeoff where reduced lignin content is associated with increased sugar content. The results presented here support previous studies demonstrating the convoluted nature of carbon partitioning in sorghum and emphasize the importance of taking a holistic approach to the study of carbon partitioning by utilizing multiscale phenotypes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Fine-root traits from common tree species in Puerto Rico before and after Hurricane María (2017-2018)

This dataset is a compilation of root trait measurements from common tree species in the Luquillo Experimental Forest in Puerto Rico taken in February 2017 (before Hurricane María), and in February 2018 (after the hurricane). This dataset is being used on a publication called "Tradeoffs in phosphorus acquisition strategies of five tree species in a tropical forest of Puerto Rico", where we describe belowground P-acquisition strategies of five common tree species (two pioneers and three non-pioneers) growing in the lowland tropical wet forests of Puerto Rico. Additionally, we used the unique opportunity of two consecutive hurricanes that passed over the island (Irma and Maria) to compare root traits before and after the hurricanes to determine which traits were the most responsive and whether such disturbance affected root trait relationships and trade-offs. For this, we sampled trees from EV1, SB2, and NGEE Tropics' plots EVV and EVR in 2017 (before hurricanes) and 2018 (after hurricanes). Morphological fine-root traits include root length, diameter, and SRL. Root architectural traits includes root branching ratio and intensity. Root physiological trait measured includes phosphatase activity, and root microbial association trait measured includes percentage mycorrhizal colonization. Chemistry data includes root phosphorus concentration, soil available, and organic phosphorus.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Propelling sustainable energy: Multi-omics analysis of pennycress FATTY ACID ELONGATION1 knockout for biofuel production

Abstract The aviation industry’s growing interest in renewable jet fuel has encouraged the exploration of alternative oilseed crops. Replacing traditional fossil fuels with a sustainable, domestically sourced crop can substantially reduce carbon emissions, thus mitigating global climate instability. Pennycress (Thlaspi arvense L.) is an emerging oilseed intermediate crop that can be grown during the offseason between maize (Zea mays) and soybean (Glycine max) to produce renewable biofuel. Pennycress is being domesticated through breeding and mutagenesis, providing opportunities for trait enhancement. Here, we employed metabolic engineering strategies to improve seed oil composition and bolster the plant's economic competitiveness. FATTY ACID ELONGATION1 (FAE1) was targeted using CRISPR-Cas 9 gene editing to eliminate very long chain fatty acids (VLCFAs) from pennycress seed oil, thereby enhancing its cold flow properties. Through an integrated multiomics approach, we investigated the impact of eliminating VLCFAs in developing and mature plant embryos. Our findings revealed improved cold-germination efficiency in fae1, with seedling emergence occurring up to 3 d earlier at 10 °C. However, these alterations led to a tradeoff between storage oil content and composition. Additionally, these shifts in lipid biosynthesis were accompanied by broad metabolic changes, such as the accumulation of glucose and ADP-glucose quantities consistent with increased starch production. Furthermore, shifts to shorter FA chains triggered the upregulation of heat shock proteins, underscoring the importance of VLCFAs in stress signaling pathways. Overall, this research provides crucial insights for optimizing pennycress seed oil while preserving essential traits for biofuel applications.

Rasoul, Amira (ORCID:0009000714290175)↗
DOE OSTI2021

Pantropical tropical tree xylem hydraulic functional traits, 1991 - 2013

This data package contains xylem hydraulic properties data, both newly extracted from publications plus tropics-specific data extracted from the "Xylem Functional Traits Database" (Choat et al., 2012; Gleason et al., 2016), which is available on TRY (www.try-db.org). Choat, B., Jansen, S., et al: Global convergence in the vulnerability of forests to drought, Nature, doi: 10.1038/nature11688, 2012. 2012. Gleason, S. M., Westoby, M., Jansen, S., Choat, B., et al.: Weak tradeoff between xylem safety and xylem-specific hydraulic efficiency across the world's woody plant species, New Phytologist, 209, 123-136, 2016. Measurements include xylem hydraulic conductivity per unit sapwood (Ks) and per unit leaf (Kl) area, water potential at 12%, 50%, and 88% loss of conductivity (P12, P50, and P88, respectively), leaf mass per area, wood density, and maximum rate of photosynthesis. Data span both natural tropical forests and plantations and rainfall gradients from deciduous dry tropical forests to everwet tropical forests, and come from countries all across the pantropics. Data is included in the attached zip file as three CSV files.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

A Pleiotropic Flowering Time QTL Exhibits Gene-by-Environment Interaction for Fitness in a Perennial Grass

Appropriate flowering time is a crucial adaptation impacting fitness in natural plant populations. Although the genetic basis of flowering variation has been extensively studied, its mechanisms in nonmodel organisms and its adaptive value in the field are still poorly understood. Here, we report new insights into the genetic basis of flowering time and its effect on fitness in Panicum hallii, a native perennial grass. Genetic mapping in populations derived from inland and coastal ecotypes identified flowering time quantitative trait loci (QTL) and many exhibited extensive QTL-by-environment interactions. Patterns of segregation within recombinant hybrids provide strong support for directional selection driving ecotypic divergence in flowering time. A major QTL on chromosome 5 (q-FT5) was detected in all experiments. Fine-mapping and expression studies identified a gene with orthology to a rice FLOWERING LOCUS T-like 9 (PhFTL9) as the candidate underlying q-FT5. We used a reciprocal transplant experiment to test for local adaptation and the specific impact of q-FT5 on performance. We did not observe local adaptation in terms of fitness tradeoffs when contrasting ecotypes in home versus away habitats. However, we observed that the coastal allele of q-FT5 conferred a fitness advantage only in its local habitat but not at the inland site. Sequence analyses identified an excess of low-frequency polymorphisms at the PhFTL9 promoter in the inland lineage, suggesting a role for either selection or population expansion on promoter evolution. Together, our findings demonstrate the genetic basis of flowering variation in a perennial grass and provide evidence for conditional neutrality underlying flowering time divergence.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Tradeoffs between phenotypic plasticity and local adaptation influence the ecophysiology of the moss, Sphagnum magellanicum

Bryophytes are a diverse plant group and are functionally different from vascular plants. Yet, their peculiarities are rarely considered in the theoretical frameworks for plants. Currently, we lack information about the magnitude and the importance of intraspecific variability in the ecophysiology of bryophytes and how these might translate to local adaptation—a prerequisite for adaptive evolution. Capitalizing on two ecologically distinct (hummock and hollow) phenotypes of Sphagnum magellanicum, we explored the magnitude and pattern of intraspecific variability in this species and asked whether the environmental-mediated changes in shoot and physiological traits are due to phenotypic plasticity or local adaptation. Size, pigmentation, and habitat type that distinguished the phenotypes in the field did not influence the trait responses under a transplant and factorial experiment. In addition, the magnitude and pattern of trait variability (e.g., branch, stem and capitulum mass) changed with the treatments, which suggest that trait responses were due largely to phenotypic plasticity. The trait responses also suggest that the ecophysiological needs for mosses to grow in clumps, where they maintain a uniform growth may have an overriding effect over the potential for a fixed adaptive response to environmental heterogeneity, which would constrain local adaptation. In this paper, we conclude that extending the trait-based framework to mosses or making comparisons between mosses and vascular plants under any theoretical framework would only be meaningful to the extent that growth form and dispersal strategies are considered.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The xylem of anisohydric Quercus alba L. is more vulnerable to embolism than isohydric codominants

Abstract The coordination of plant leaf water potential (Ψ L ) regulation and xylem vulnerability to embolism is fundamental for understanding the tradeoffs between carbon uptake and risk of hydraulic damage. There is a general consensus that trees with vulnerable xylem more conservatively regulate Ψ L than plants with resistant xylem. We evaluated if this paradigm applied to three important eastern US temperate tree species, Quercus alba L., Acer saccharum Marsh. and Liriodendron tulipifera L., by synthesizing 1600 Ψ L observations, 122 xylem embolism curves and xylem anatomical measurements across 10 forests spanning pronounced hydroclimatological gradients and ages. We found that, unexpectedly, the species with the most vulnerable xylem ( Q. alba ) regulated Ψ L less strictly than the other species. This relationship was found across all sites, such that coordination among traits was largely unaffected by climate and stand age. Quercus species are perceived to be among the most drought tolerant temperate US forest species; however, our results suggest their relatively loose Ψ L regulation in response to hydrologic stress occurs with a substantial hydraulic cost that may expose them to novel risks in a more drought‐prone future.

Benson, Michael C.↗
NASA NTRSDate not supplied

The Pheno-Evo Model: Evolution of Microbial Phenotypic Diversity in 2D Space

Biologists appreciate microbes for their simplicity and predictability: we assume that a population of genetically identical cells in a uniform environment will all behave the same way. While this assumption is often useful, it is also often wrong. Not only might microbes in a clonal population act differently from one another, the differences may be categorical (growing v. non-growing; toxin-sensitive v. tolerant), and this diversity might be an evolved trait conferring increased fitness on the population. How does such phenotypic heterogeneity evolve? And how does a population find the optimal distribution of phenotypes for a given environment? Efforts at modeling microbial phenotypic heterogeneity often focus on populations with two discrete phenotypic types; phenotypes in continuous distributions remain poorly explored. To address this gap and to explore the role of spatial relationships, we use agent-based modeling to simulate a phenotypically diverse population of microbial cells evolving in the presence of periodic toxic stress. Cells on patches in a 2D grid may degrade toxin, suffer damage from toxin, switch phenotype, and reproduce. An individual's phenotype its toxin degradation rate-- for which there is a tradeoff with reproduction-- and the genotype encodes the distribution of phenotypic values in the population. The rate of toxin diffusion determines how individuals influence their neighbors' environments. We examine the effects of toxin concentration, diffusion rate, and environmental predictability on the survival success of populations with different phenotype distributions, and populations' evolutionary trajectories when phenotype distribution is allowed to evolve. We conduct all simulations on the platform NetLogo, which provides a friendly interface allowing users of any experience level to tweak parameters and run their own simulations. We have also created custom tools in R for analyzing and visualizing the results of multiple runs.

microbial evolution↗
DOE OSTI2022

MYC transcription factors coordinate tryptophan–dependent defence responses and compromise seed yield in Arabidopsis

Robust plant immunity negatively affects other fitness traits, including growth and seed production. Jasmonate (JA) confers broad-spectrum protection against plant consumers by stimulating the degradation of JASMONATE ZIM-DOMAIN (JAZ) proteins, which in turn relieves repression on transcription factors (TFs) coincident with reduced growth and fecundity. The molecular mechanisms underlying JA-mediated decreases in fitness remain largely unknown. To assess the contribution of MYC TFs to growth and reproductive fitness at high levels of defence, we mutated three MYC genes in a JAZ-deficient mutant (jazD) of Arabidopsis thaliana that exhibits strong defence and low seed yield. Genetic epistasis analysis showed that de-repression of MYC TFs in jazD not only conferred strong resistance to insect herbivory but also reduced shoot and root growth, fruit size and seed yield. We also provided evidence that the JAZ–MYC module coordinates the supply of tryptophan with the production of indole glucosinolates and the proliferation of endoplasmic reticulum bodies that metabolise glucosinolates through the action of b-glucosidases. Our results establish MYCs as major regulators of growth- and reproductive–defence tradeoffs and further indicate that these factors coordinate tryptophan availability with the production of amino acid-derived defence compounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Climate adaptation and sustainability in switchgrass: exploring plant-microbe-soil interactions across continental scale environmental gradients

Less carbon-intensive energy sources are needed to reduce greenhouse gas emissions and their predicted role in climate change. There is growing interest in the potential of biofuels for meeting this need. A critical question is whether large-scale biofuel production can be sustainable over the time scales needed to mitigate our carbon debt from fossil fuel consumption. The carbon balance and ultimately the sustainability of biofuel feedstock production is the result of complex climate-coupled interactions between carbon fixation, sequestration, and release through combustion. Similarly, the long-term productivity of biofuels depends on the environmental factors limiting plant growth. These factors are often related to soil resources which involve complex interactions at the plant-microbe-soil interface impacting their availability and cycling. Our collaborative project addressed sustainable switchgrass (Panicum virgatum) production by exploring Plant Systems, Plant-Microbiome Interactions, and Ecosystem Processes through the integrating lens of Multi-Scale Modeling. Our research was based on detailed characterization of genetically diverse switchgrass genotypes planted in common gardens across a continental latitudinal gradient. The underlying theme of our Plant Systems research was the use of locally adapted plant material to explore plant function, to understand the mechanistic basis of environmental interactions, and to discover the plant genes important for adaptation and sustainability in the face of climate change. Our Plant-Microbiome Interaction project characterized the microbial communities associated with switchgrass using genomic tools. Our Ecosystem Processes research focused on carbon cycle responses at the ecosystem level using stand level plantings. Finally, our Multi-Scale Modeling helped to define conditions of a sustainable biofuel system and identify key tradeoffs between genetic diversity, productivity, and ecosystem services. Genome-wide association analyses were used to identify alleles that contribute to successful establishment and biomass production across North America. Together, our work provided a baseline analyses of the potential of switchgrass as a biofuel feedstock. Our project resulted in a number of successful outcomes. First, we were successful in collecting switchgrass germplasm across the species range, propagating the material, and establishing common garden experiments across the species range. In collaboration with DOE JGI, we successfully assembled the first tetraploid switchgrass genome and published this resource with an analyses of the genetic basis local adaptation from our gardens (Lowry et al. 2019, Lovell et al. 2021). The gardens were used to characterize the genetic architecture for a number of important plant phenotypes. Our project also conducted extensive sampling and sequencing to characterize the bacterial and fungal associates of switchgrass roots and leaves. We showed that host genotype, location, and harvesting practices can play a role in microbiome assembly (Singer et al. 2019 & 2022, Van Wallendael et al. 2020 & 2022, Edwards et al. 2023). Our ecosystem processes work created baseline dataset of carbon and nutrient cycling in realistic stand plantings of switchgrass. Data from this experiment provided new insight into the role of plant traits, phenology, and local environments in ecosystem processes like soil respiration, net-ecosystem exchange, and dynamics of soil and plant nutrients (Ricketts et al. 2023). Finally, our crop modelling experiments help to characterize the sensitivity of common modeling frameworks to parameters, identify key limiters of productivity across large geographic scales, and leverage patterns of local adaptation in prediction. Ultimately, these studies help to identify critical plant-microbe-soil traits that may be manipulated, through breeding or agronomic management, to improve the sustainability of biofuel feedstocks.

09 BIOMASS FUELS↗
DOE OSTI2022

Plant carbohydrate storage: intra- and inter-specific trade-offs reveal a major life history trait

Trade-offs among carbon sinks constrain how trees physiologically, ecologically, and evolutionarily respond to their environments. These trade-offs typically fall along a productive growth to conservative, bet-hedging continuum. How nonstructural carbohydrates (NSCs) stored in living tree cells (known as carbon stores) fit in this trade-off framework is not well understood. Here, we examined relationships between growth and storage using both within species genetic variation from a common garden, and across species phenotypic variation from a global database. We demonstrate that storage is actively accumulated, as part of a conservative, bet-hedging life history strategy. Storage accumulates at the expense of growth both within and across species. Within the species Populus trichocarpa, genetic trade-offs show that for each additional unit of wood area growth (in cm 2 yr –1 ) that genotypes invest in, they lose 1.2 to 1.7 units (mg g –1 NSC) of storage. Across species, for each additional unit of area growth (in cm 2 yr –1 ), trees, on average, reduce their storage by 9.5% in stems and 10.4% in roots. Our findings impact our understanding of basic plant biology, fit storage into a widely used growth-survival trade-off spectrum describing life history strategy, and challenges the assumptions of passive storage made in ecosystem models today.

59 BASIC BIOLOGICAL SCIENCES↗