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At least 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Arabidopsis Dehiscence Zone Polygalacturonase 1 (ADPG1) releases latent defense signals in stems with reduced lignin content

There is considerable interest in engineering plant cell wall components, particularly lignin, to improve forage quality and biomass properties for processing to fuels and bioproducts. However, modifying lignin content and/or composition in transgenic plants through down-regulation of lignin biosynthetic enzymes can induce expression of defense response genes in the absence of biotic or abiotic stress. Arabidopsis thaliana lines with altered lignin through down-regulation of hydroxycinnamoyl CoA:shikimate/quinate hydroxycinnamoyl transferase (HCT) or loss of function of cinnamoyl CoA reductase 1 (CCR1) express a suite of pathogenesis-related (PR) protein genes. The plants also exhibit extensive cell wall remodeling associated with induction of multiple cell wall-degrading enzymes, a process which renders the corresponding biomass a substrate for growth of the cellulolytic thermophile Caldicellulosiruptor bescii lacking a functional pectinase gene cluster. The cell wall remodeling also results in the release of size- and charge-heterogeneous pectic oligosaccharide elicitors of PR gene expression. Genetic analysis shows that both in planta PR gene expression and release of elicitors are the result of ectopic expression in xylem of the gene Arabidopsis Dehiscence Zone Polygalacturonase 1 (ADPG1), which is normally expressed during anther and silique dehiscence. These data highlight the importance of pectin in cell wall integrity and the value of lignin modification as a tool to interrogate the informational content of plant cell walls.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Seismic refraction tracks porosity generation and possible CO 2 production at depth under a headwater catchment

Significance To understand groundwater in weathered bedrock aquifers, we explore (bio)geochemical reactions using geophysical measurements. The result leads to a conceptual model for the three-dimensional distribution of geochemical alteration in the subsurface—well beyond the typical approach of inferring (bio)geochemical reactions in the subsurface from pits, boreholes, and outcrops. With this geophysical technique we discovered the prevalence of gas beneath the water table at this site. This geophysical viewing of the subsurface highlights patterns of water movement, reactions of clays, and microbial and abiotic gas-producing reactions recorded in the subsurface and thus illuminates storage, flow, and reactions of groundwater in bedrock systems. Protecting the groundwater resource beneath our feet will rely on such enhanced capacities to see into the subsurface.

58 GEOSCIENCES↗
DOE OSTI2021

Large ecosystem-scale effects of restoration fail to mitigate impacts of land-use legacies in longleaf pine savannas

Ecological restoration is a global priority, with potential to reverse biodiversity declines and promote ecosystem functioning. Yet, successful restoration is challenged by lingering legacies of past land-use activities, which are pervasive on lands available for restoration. Although legacies can persist for centuries following cessation of human land uses such as agriculture, we currently lack understanding of how land-use legacies affect entire ecosystems, how they influence restoration outcomes, or whether restoration can mitigate legacy effects. Using a large-scale experiment, we evaluated how restoration by tree thinning and land-use legacies from prior cultivation and subsequent conversion to pine plantations affect fire-suppressed longleaf pine savannas. In this work, we evaluated 45 ecological properties across four categories: 1) abiotic attributes, 2) organism abundances, 3) species diversity, and 4) species interactions. The effects of restoration and land-use legacies were pervasive, shaping all categories of properties, with restoration effects roughly twice the magnitude of legacy effects. Restoration effects were of comparable magnitude in savannas with and without a history of intensive human land use; however, restoration did not mitigate numerous legacy effects present prior to restoration. As a result, savannas with a history of intensive human land use supported altered properties, especially related to soils, even after restoration. The signature of past human land-use activities can be remarkably persistent in the face of intensive restoration, influencing the outcome of restoration across diverse ecological properties. Understanding and mitigating land-use legacies will maximize the potential to restore degraded ecosystems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Predicting transcriptional responses to cold stress across plant species

Although genome-sequence assemblies are available for a growing number of plant species, gene-expression responses to stimuli have been cataloged for only a subset of these species. Many genes show altered transcription patterns in response to abiotic stresses. However, orthologous genes in related species often exhibit different responses to a given stress. Accordingly, data on the regulation of gene expression in one species are not reliable predictors of orthologous gene responses in a related species. Here, we trained a supervised classification model to identify genes that transcriptionally respond to cold stress. A model trained with only features calculated directly from genome assemblies exhibited only modest decreases in performance relative to models trained by using genomic, chromatin, and evolution/diversity features. Models trained with data from one species successfully predicted which genes would respond to cold stress in other related species. Cross-species predictions remained accurate when training was performed in cold-sensitive species and predictions were performed in cold-tolerant species and vice versa. Models trained with data on gene expression in multiple species provided at least equivalent performance to models trained and tested in a single species and outperformed single-species models in cross-species prediction. These results suggest that classifiers trained on stress data from well-studied species may suffice for predicting gene-expression patterns in related, less-studied species with sequenced genomes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Transcription factor bHLH121 regulates root cortical aerenchyma formation in maize

Root anatomical phenotypes present a promising yet underexploited avenue to deliver major improvements in yield and climate resilience of crops by improving water and nutrient uptake. For instance, the formation of root cortical aerenchyma (RCA) significantly increases soil exploration and resource capture by reducing the metabolic costs of root tissue. A key bottleneck in studying such phenotypes has been the lack of robust high-throughput anatomical phenotyping platforms. We exploited a phenotyping approach based on laser ablation tomography, termed Anatomics , to quantify variation in RCA formation of 436 diverse maize lines in the field. Results revealed a significant and heritable variation for RCA formation. Genome-wide association studies identified a single-nucleotide polymorphism mapping to a root cortex-expressed gene-encoding transcription factor bHLH121. Functional studies identified that the bHLH121 Mu transposon mutant line and CRISPR/Cas9 loss-of-function mutant line showed reduced RCA formation, whereas an overexpression line exhibited significantly greater RCA formation when compared to the wild-type line. Characterization of these lines under suboptimal water and nitrogen availability in multiple soil environments revealed that bHLH121 is required for RCA formation developmentally as well as under studied abiotic stress. Overall functional validation of the bHLH121 gene’s importance in RCA formation provides a functional marker to select varieties with improved soil exploration and thus yield under suboptimal conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Mitigating drought mortality by incorporating topography into variable forest thinning strategies

Abstract Drought-induced productivity reductions and tree mortality have been increasing in recent decades in forests around the globe. Developing adaptation strategies hinges on an adequate understanding of the mechanisms governing the drought vulnerability of forest stands. Prescribed reduction in stand density has been used as a management tool to reduce water stress and wildfire risk, but the processes that modulate fine-scale variations in plant water supply and water demand are largely missing in ecosystem models. We used an ecohydrological model that couples plant hydraulics with groundwater hydrology to examine how within-stand variations in tree spatial arrangements and topography might mitigate forest vulnerability to drought at individual-tree and stand scales. Our results demonstrated thinning generally ameliorated plant hydraulic stress and improved carbon and water fluxes of the remaining trees, although the effectiveness varied by climate and topography. Variable thinning that adjusted thinning intensity based on topography-mediated water availability achieved higher stand productivity and lower mortality risk, compared to evenly-spaced thinning at comparable intensities. The results from numerical experiments provided mechanistic evidence that topography mediates the effectiveness of thinning and highlighted the need for an explicit consideration of within-stand heterogeneity in trees and abiotic environments when designing forest thinning to mitigate drought impacts.

Environmental Sciences & Ecology↗
DOE OSTI2026

Bioproduction, bioprotection, and biocontainment in multi-kingdom microbial systems with 3D spatial control

Engineered living materials (ELMs) are a class of hybrid materials that include engineered microbes encapsulated by a polymer matrix. The biotic and abiotic components define the ELMs design space and can be altered to improve performance and function. While current synthetic materials in the field display robust biocompatibility with both native and engineered living systems, we have a limited understanding of how to leverage three-dimensional (3D) form factors to spatially organize and control microbial dynamics within the material. Motivated by this knowledge gap, we employed extrusion-based 3D printing to fabricate multi-kingdom hydrogel constructs for the encapsulation of both single and multi-kingdom microbial systems. Core–shell cubic constructs enabled the spatial organization of a constitutive multi-kingdom system of levodopa (L-DOPA)-producing E. coli and betaxanthins (BXN)-producing S. cerevisiae. This spatial organization in 3D materials can introduce precise control over bioproduction, bioprotection, and biocontainment features that are critical to the efficacy of current ELMs. The relative spatial organization of the organisms, as well as the surface area-to-volume ratio were investigated to determine how these design elements impact microbial behavior (metabolite production, growth, expression, and cell distribution) over time. We demonstrated that F127-bis-urethane methacrylate (F127-BUM) core–shell geometries enable the hierarchical 3D printing of multi-kingdom constructs, offering customizable control over bioproduction, bioprotection, and biocontainment. With the optimization of these core–shell structures for continuous bioproduction, these ELMs could be deployed as compact and sustainable bioreactors in remote environments.

additive manufacturing↗
DOE OSTI2025

Pollinator habitat in solar facilities has potential to support high diversity of bee species

Conversion of agricultural and degraded lands to solar energy production provides opportunities to support diverse bee communities—and their pollination services—by creating habitat at solar facilities. Habitat restoration for bees at solar facilities follows the general principle of installing a diverse flowering plant community and assuming bees will come. However, selecting seed mixes for solar facilities is challenging because selected plants need to establish in the unique abiotic conditions of solar facilities and not interfere with solar energy production (tall plants may shade panels). Recent research tested commercially available and bespoke pollinator mixes for establishment success in Minnesota solar facilities and identified 14 forb species that established successfully over three years of the experiment. We ask an important follow-up question: how many native bee species, and which bee species, are these 14 plant species capable of supporting? We used a plant-bee interaction data set from Minnesota to calculate the number of bee species that would be supported by the 14 plant species for the duration of their flight seasons using a published bee species richness function. We found 122 unique bee species (24% of Minnesota diversity) may be supported for their entire flight seasons by the 14 focal plants.

14 SOLAR ENERGY↗
DOE OSTI2026

Accounting for linkages between wildfire-driven shifts in plant-microbial interactions and soil carbon dynamics in Arctic tundra

Increasing wildfire regimes in the rapidly changing Arctic tundra are altering the soil carbon budget through increased permafrost degradation, shrubs expansion, and shifts in microbial activities. Whether future arctic wildfires will result in net C losses or gains in the future will depend on complex biotic and abiotic interactions that regulate belowground C biogeochemical processes, including linkages among biotic communities. One important linkage is plant-microbe interactions. While these interactions are likely shaped or altered by wildfires, they remain little explored in the context of successional trajectories. Yet, incorporating plant-microbe interactions in frameworks for defining and understanding post-fire soil C trajectories is critical to predict belowground C responses to future tundra wildfires. Here, we provide examples of and discuss how fire-mediated changes in plant-soil-microbe (PSM) interactions can impact soil C dynamics in the Arctic tundra. We consider different impacts of wildfires on PSM interactions and their implications to soil C dynamics, as well as the nuances associated with particular wildfire regimes (severity and intensity) and successional timescales. We suggest that accounting for plant-microbial linkages in future wildfire-succession interactions frameworks can inform future experimental designs and reduce uncertainties in our ability to predict the net effect of Arctic wildfires on ecosystem C.

fungi, bacteria↗
DOE OSTI2025

A multi-model assessment of global freshwater temperature and thermoelectric power supply under climate change

Water temperature is a key abiotic factor influencing aquatic ecosystem health and the services provided to both nature and humans. Global water temperature models offer possibilities to improve our understanding of water temperature regimes, which is increasingly important against the backdrop of climate change. Yet, existing studies have predominantly relied on a single model, which can lead to an incomplete representation of uncertainty and potential biases, in addition to limited insight into the range of possible future conditions, which ultimately reduces the robustness of climate impact assessments. Here, we provide a comprehensive assessment of surface freshwater temperature changes from various river and lake models for both past conditions and under future scenarios of climate change. Global models consistently simulate that surface water temperatures are currently 0.5 °C–0.8 °C higher than at the turn of the century (i.e. 1981–2000), and that warming will extend and intensify with future global change throughout the 21st century. While the strength of warming is highly sensitive to the different water temperature models, emissions scenarios and global climate models, our multi-model ensemble shows a global average annual water temperature rise of between +1.3 °C and +4.1 °C by the end of the century. To illustrate a potential societal impact of our results, we evaluate how future changes in discharge and water temperature may affect existing thermoelectric power plants, estimating average annual reductions of 1.5%–6% in global usable capacity by the end of the century. However, with river water temperatures projected to exhibit more pronounced seasonal patterns in the future—especially under the more extreme climate change scenarios and during summer months in the Northern Hemisphere—intra-annual reductions in usable capacity can be much more severe. Given the challenges associated with (large-scale) adaptation to control water temperature regimes, strong climate change mitigation is crucial for minimising water temperature rises and its associated negative impacts on humankind and ecosystems.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2024

Chapter 8: Searching for Life Beyond Earth

The search for life beyond Earth necessitates a rigorous and comprehensive examination of biosignatures, the types of observable imprints that life produces. These imprints and our ability to detect them with advanced instrumentation hold the key to our understanding of the presence and abundance of life in the universe. Biosignatures are the chemical or physical features associated with past or present life and may include the distribution of elements and molecules, alone or in combination, as well as changes in structural components or physical processes that would be distinct from an abiotic background. The scientific and technical strategies used to search for life on other planets include those that can be conducted in situ to planetary bodies and those that could be observed remotely. Here this chapter discusses numerous strategies that can be employed to look for biosignatures directly on other planetary bodies using robotic exploration including those that have been deployed to other planetary bodies, are currently being developed for flight, or will become a critical technology on future missions. Search strategies for remote observations using current and planned ground-based and space-based telescopes are also described. Evidence from spectral absorption, emission, or transmission features can be used to search for remote biosignatures and technosignatures. Improving our understanding of biosignatures, their production, transformation, and preservation on Earth can enhance our search efforts to detect life on other planets.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Divergent selection and climate adaptation fuel genomic differentiation between sister species of Sphagnum (peat moss)

Abstract Background and Aims New plant species can evolve through the reinforcement of reproductive isolation via local adaptation along habitat gradients. Peat mosses (Sphagnaceae) are an emerging model system for the study of evolutionary genomics and have well-documented niche differentiation among species. Recent molecular studies have demonstrated that the globally distributed species Sphagnum magellanicum is a complex of morphologically cryptic lineages that are phylogenetically and ecologically distinct. Here, we describe the architecture of genomic differentiation between two sister species in this complex known from eastern North America: the northern S. diabolicum and the largely southern S. magniae. Methods We sampled plant populations from across a latitudinal gradient in eastern North America and performed whole genome and restriction-site associated DNA sequencing. These sequencing data were then analyzed computationally. Key Results Using sliding-window population genetic analyses we find that differentiation is concentrated within ‘islands’ of the genome spanning up to 400 kb that are characterized by elevated genetic divergence, suppressed recombination, reduced nucleotide diversity and increased rates of non-synonymous substitution. Sequence variants that are significantly associated with genetic structure and bioclimatic variables occur within genes that have functional enrichment for biological processes including abiotic stress response, photoperiodism and hormone-mediated signalling. Demographic modelling demonstrates that these two species diverged no more than 225 000 generations ago with secondary contact occurring where their ranges overlap. Conclusions We suggest that this heterogeneity of genomic differentiation is a result of linked selection and reflects the role of local adaptation to contrasting climatic zones in driving speciation. This research provides insight into the process of speciation in a group of ecologically important plants and strengthens our predictive understanding of how plant populations will respond as Earth’s climate rapidly changes.

58 GEOSCIENCES↗
DOE OSTI2025

The genome of the polyextremophilic yeast, Naganishia friedmannii, reveals adaptations involved in stress response pathways, carbohydrate metabolism expansion, and a limited DNA repair repertoire

Here we report the draft genome sequence of Naganishia friedmannii (formerly Cryptococcus friedmannii) isolate, a Basidiomycota yeast commonly found in some of the most extreme environments of the Earth's cryosphere. We isolated N. friedmannii strain Llullensis from soils at 6000 m above sea level on Volcán Llullaillaco, Argentina. The genome was 22.2 Mb with 6251 identified protein coding genes. Proteins known to be associated with thermal, osmotic, and radiation stress were identified in the genome. Comparative analysis with seven other Naganishia genomes revealed unique features underlying its polyextremophilic lifestyle. Naganishia friedmannii showed an expansion of genes involved in breaking down plant-derived carbohydrates, supporting the hypothesis that it survives at high elevations by metabolizing wind-deposited organic matter. Surprisingly, many genes involved in cell-cycle checkpoints and DNA repair were missing, as in several other Naganishia species. This extensive loss may be adaptive in extreme environments prone to abiotic stress, where a high mutation rate could generate advantageous traits, and reduced cell-cycle control may allow for faster reproduction that would be advantageous for rapid growth during brief periods of soil wetting following rare snow events.

Vimercati, Lara↗
DOE OSTI2021

Genomic patterns of structural variation among diverse genotypes of Sorghum bicolor and a potential role for deletions in local adaptation

Genomic structural mutations, especially deletions, are an important source of variation in many species and can play key roles in phenotypic diversification and evolution. Previous work in many plant species has identified multiple instances of structural variations (SVs) occurring in or near genes related to stress response and disease resistance, suggesting a possible role for SVs in local adaptation. Sorghum [Sorghum bicolor (L.) Moench] is one of the most widely grown cereal crops in the world. It has been adapted to an array of different climates as well as bred for multiple purposes, resulting in a striking phenotypic diversity. In this study, we identified genome-wide SVs in the Biomass Association Panel, a collection of 347 diverse sorghum genotypes collected from multiple countries and continents. Using Illumina-based, short-read whole-genome resequencing data from every genotype, we found a total of 24,648 SVs, including 22,359 deletions. The global site frequency spectrum of deletions and other types of SVs fit a model of neutral evolution, suggesting that the majority of these mutations were not under any types of selection. Clustering results based on single nucleotide polymorphisms separated the genotypes into eight clusters which largely corresponded with geographic origins, with many of the large deletions we uncovered being unique to a single cluster. Even though most deletions appeared to be neutral, a handful of cluster-specific deletions were found in genes related to biotic and abiotic stress responses, supporting the possibility that at least some of these deletions contribute to local adaptation in sorghum.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Characterization of a novel polyextremotolerant fungus, Exophiala viscosa , with insights into its melanin regulation and ecological niche

Black yeasts are polyextremotolerant fungi that contain high amounts of melanin in their cell wall and maintain a primary yeast form. These fungi grow in xeric, nutrient depletes environments which implies that they require highly flexible metabolisms and have been suggested to contain the ability to form lichen-like mutualisms with nearby algae and bacteria. However, the exact ecological niche and interactions between these fungi and their surrounding community are not well understood. We have isolated 2 novel black yeasts from the genus Exophiala that were recovered from dryland biological soil crusts. Despite notable differences in colony and cellular morphology, both fungi appear to be members of the same species, which has been named Exophiala viscosa (i.e. E. viscosa JF 03-3 Goopy and E. viscosa JF 03-4F Slimy). A combination of whole genome sequencing, phenotypic experiments, and melanin regulation experiments have been performed on these isolates to fully characterize these fungi and help decipher their fundamental niche within the biological soil crust consortium. Our results reveal that E. viscosa is capable of utilizing a wide variety of carbon and nitrogen sources potentially derived from symbiotic microbes, can withstand many forms of abiotic stresses, and excretes melanin which can potentially provide ultraviolet resistance to the biological soil crust community. Besides the identification of a novel species within the genus Exophiala, our study also provides new insight into the regulation of melanin production in polyextremotolerant fungi.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

A small secreted protein serves as a plant-derived effector mediating symbiosis between Populus and Laccaria bicolor

Beneficial symbiotic fungi colonize plant tissues, delivering crucial ecosystem services such as carbon sequestration and plant fertilization. Specifically, trees that form a nutrient-acquiring symbiosis with mutualistic ectomycorrhizal (ECM) fungi gain advantages from these associations by experiencing enhanced growth rates and increased resilience to both biotic and abiotic stresses. Despite the vital role ECM fungi play in the nutrition and well-being of trees, identifying key regulators participating in the molecular communication between plant and fungal cells is still in its early stages. The mutualistic relationship between Laccaria bicolor and Populus spp. has been utilized as a model system for investigating ECM symbiosis at the molecular level. It has been demonstrated that the fungus L. bicolor secretes Mycorrhiza-induced Small Secreted Proteins (MiSSPs) required for ECM development. Meanwhile, we have previously shown that P. trichocarpa small, secreted proteins (PtSSPs) are highly induced during mutualistic symbiosis and some of them can enter, via in-vitro feeding, L. bicolor hyphae affecting their growth and morphology. However, the exact role and mode of action of PtSSPs in mutualistic symbiosis remain unknown. Because previous study showed that PtSSP1 is taking up by fungal cell and then localize in fungal cells, we decide to dig further on its putative role in fungal cells and also by overexpressing it in poplar because it is not technically possible yet to overexpress poplar protein in Laccaria bicolor hyphae. Here, we further characterized the function of PtSSP1(Potri.009G063200) in ectomycorrhization, which accumulates in the nucleus of L. bicolor in an in-vitro feeding experiment. Our results provide new knowledge for the genetic engineering of plants to control associated microbes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Rapid Shifts in the Temperature Dependence of Locomotor Performance in an Invasive Frog, Xenopus laevis , Implications for Conservation

Abstract Temperature is a critical abiotic factor impacting all aspects of the biology of organisms, especially in ectotherms. As such, it is an important determinant of the potential invasive ability of organisms and may limit population expansion unless organisms can physiologically respond to changes in temperature either through plasticity or by adapting to their novel environment. Here, we studied the African clawed frog, Xenopus laevis, which has become invasive on a global scale. We compared adults from an invasive population of western France with individuals from two populations in the native range in South Africa. We measured the thermal dependence of locomotor performance in adults given its relevance to dispersal, predator escape, and prey capture. Our results show significant differences in the limits of the 80% performance breadth interval for endurance with the French population showing a left shift in its limits congruent with the colder climate experienced in France. The French invasive population was introduced only about 40 years ago suggesting a rapid shift in the thermal physiology. Given that all individuals were acclimated under laboratory conditions at 23°C for 2 months this suggests that the invasive frogs have adapted to their new environment. These data may allow the refinement of physiologically informed species distribution models permitting better estimates of future ranges at risk of invasion.

Araspin, Laurie↗
DOE OSTI2024

Viral niche-partitioning: comparative genomics of giant viruses across environmental gradients in a high Arctic freshwater-saltwater lake

Giant viruses (GVs; Nucleocytoviricota) impact the biology and ecology of a wide range of eukaryotic hosts, with implications for global biogeochemical cycles. Here, we investigated GV niche separation in highly stratified Lake A at the northern coast of Ellesmere Island, Nunavut, Canada. This lake is composed of a layer of ice-covered freshwater that overlies saltwater derived from the ancient Arctic Ocean, and it therefore provides a broad gradient of environmental conditions and ecological habitats, each with a distinct protist community and rich assemblages of associated GVs. The upper layer (mixolimnion) had measurable light and oxygen, and contained diverse GVs linked to photosynthetic protists, indicating adaptation to surface biotic and abiotic conditions. In contrast, the saline lower layer (monimolimnion), lacking oxygen and light, hosted GVs associated with predicted heterotrophic protists, some of which are known for a predatory lifestyle, and with several viral genes suggesting adaptation to deep-water anaerobic conditions. Our observations underscore the coupling between physical and chemical gradients, microeukaryotes and their associated GVs in Lake A, and provide insight into the potential for GVs to directly and indirectly impact host metabolism. There were similarities between the genetic composition of GVs and the metabolic processes of their potential hosts, implying co-evolution and niche-adaptation within the lake habitats. Notably, we found a greater presence of viral rhodopsins in deeper water layers, suggesting an evolutionary relationship with potential hosts capable of supplementing their energetic needs to thrive in low energy, anoxic conditions.

59 BASIC BIOLOGICAL SCIENCES↗