Transcriptional, metabolic, physiological and developmental responses to nitrogen limitation in switchgrass (Panicum virgatum)
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Environmental Sciences & Ecology↗
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Transgenic manipulation of triacylglycerol biosynthetic enzymes in B. napus alters lipid-associated gene expression and lipid metabolism
Abstract Oilseed rape ( Brassica napus ) is an important crop that is cultivated for the oil (mainly triacylglycerol; TAG) it produces in its seeds. TAG synthesis is controlled mainly by key enzymes in the Kennedy pathway, such as glycerol 3-phosphate acyltransferase (GPAT), lysophosphatidate acyltransferase (LPAT) and diacylglycerol acyltransferase (DGAT) but can also be produced from phosphoglycerides such as phosphatidylcholine (PC) by the activity of the enzyme phospholipid: diacylglycerol acyltransferase (PDAT). To evaluate the potential for these enzymes to alter oil yields or composition, we analysed transgenic B. napus lines which overexpressed GPAT, LPAT or PDAT using heterologous transgenes from Arabidopsis and Nasturtium and examined lipid profiles and changes in gene expression in these lines compared to WT. Distinct changes in PC and TAG abundance and spatial distribution in embryonic tissues were observed in some of the transgenic lines, together with altered expression of genes involved generally in acyl-lipid metabolism. Overall our results show that up-regulation of these key enzymes differentially affects lipid composition and distribution as well as lipid-associated gene expression, providing important information which could be used to improve crop properties by metabolic engineering.
59 BASIC BIOLOGICAL SCIENCES↗
Isolation and characterization of an anti-proliferative polysaccharide from the North American fungus Echinodontium tinctorium
Abstract A novel polysaccharide EtGIPL1a was purified from fruiting bodies of Echinodontium tinctorium , a fungus unique to western North America. EtGIPL1a has an estimated weight average molecular weight of 275 kDa and is composed of glucose (54.3%), galactose (19.6%), mannose (11.1%), fucose (10.3%), glucuronic acid (4%), and rhamnose (0.6%). It has multiple glycosidic linkages, with 3-Glc p (28.9%), 6-Glc p (18.3%), 3,6-Glc p (13%), 4-Glc p A (9.2%), 6-Gal p (3.9%), 2,6-Gal p (2.6%), 3-Fuc p (2.5%), 6-Man p (2.4%) being the most prominent, and unsubstituted glucose (15.3%), mannose (1.3%) and fucose (0.9%) as major terminal sugars. EtGIPL1a has a backbone containing mostly 3-substituted β -glucopyranose with 4-substituted glucopyranosyluronic acid. EtGIPL1a showed anti-proliferative activity against multiple cancer cell lines, with IC 50 ranging from 50.6 to 1446 nM. Flow cytometry analyses confirmed that apoptosis induction is one mechanism for its anti-proliferative activity. EtGIPL1a should be further investigated for its potential anti-cancer activity in animal models, and for its possible utility in differentiation cancer therapy.
59 BASIC BIOLOGICAL SCIENCES↗
Mycorrhizal effects on decomposition and soil CO 2 flux depend on changes in nitrogen availability during forest succession
Not provided.
Environmental Sciences & Ecology↗
A common resequencing‐based genetic marker data set for global maize diversity
SUMMARY Maize ( Zea mays ssp. mays ) populations exhibit vast ranges of genetic and phenotypic diversity. As sequencing costs have declined, an increasing number of projects have sought to measure genetic differences between and within maize populations using whole‐genome resequencing strategies, identifying millions of segregating single‐nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). Unlike older genotyping strategies like microarrays and genotyping by sequencing, resequencing should, in principle, frequently identify and score common genetic variants. However, in practice, different projects frequently employ different analytical pipelines, often employ different reference genome assemblies and consistently filter for minor allele frequency within the study population. This constrains the potential to reuse and remix data on genetic diversity generated from different projects to address new biological questions in new ways. Here, we employ resequencing data from 1276 previously published maize samples and 239 newly resequenced maize samples to generate a single unified marker set of approximately 366 million segregating variants and approximately 46 million high‐confidence variants scored across crop wild relatives, landraces as well as tropical and temperate lines from different breeding eras. We demonstrate that the new variant set provides increased power to identify known causal flowering‐time genes using previously published trait data sets, as well as the potential to track changes in the frequency of functionally distinct alleles across the global distribution of modern maize.
59 BASIC BIOLOGICAL SCIENCES↗
Better Plants Resources for Achieving Science Based Targets
The US Department of Energy’s (DOE’s) Better Buildings, Better Plants Program is a voluntary initiative that works with leading manufacturers to showcase leadership and drive deep energy savings in the U.S. industrial sector. Partners agree to set ambitious sustainability goals and in return receive robust technical assistance, national recognition, facilitated peer-to-peer learning opportunities, and access to innovation. Many Better Plants partners are looking to translate their energy intensity progress towards carbon reduction goals and exploring if setting a Science-Based Target (SBT) is right for their organization. This document provides an overview of the SBT initiative and compares it to the offerings of the Better Plants program. To help companies who are participating in both initiatives, DOE tools and resources are highlighted and discussed.
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
Impact of Grazing Duration and Environment on Soil Carbon in Reclaimed Uranium Mines Tailings: A Region Specific Study
ABSTRACT Grassland ecosystems, which cover over one‐third of the Earth's land area, store 10%–30% of global soil carbon (C). However, these ecosystems face substantial impacts from human activities, including mining. This study investigates the spatial distribution of soil C and related environmental factors in reclaimed grasslands on former uranium mine sites in Wyoming. We hypothesized that grazing duration and environmental factors would influence soil C levels. Interactions between topography, vegetation diversity, soil properties, and soil C in the context of grazing management in both natural and reclaimed grasslands from a wide range of periods from 1 year to 100 years were analyzed using geographically weighted regression models. Data collected from 2022 to 2023 showed that total carbon was consistently higher in natural grasslands (1.2%–4.9%) than in reclaimed grasslands (0.8%–1.3%). Additionally, soil C was significantly higher in natural grasslands grazed for 1 year compared to those grazed for 100 years. In contrast, reclaimed grasslands had lower soil C in areas grazed for 1 year compared to those grazed for 7 or 14 years. The absolute values of coefficients from environmental covariates indicated that areas grazed for a shorter duration (~1 year) were more influenced by biotic and abiotic factors than areas grazed for longer periods (> 7 years). Our findings show moderate grazing increases the resiliency of grassland ecosystems when grazed 7 years or longer and acknowledge the roles of topographic, soil, and vegetative factors in enhancing soil C concentration and developing sustainable land management practices in rangeland conditions.
Shilpakar, Chandan [Department of Plant Sciences U↗
Supporting Information for manuscript: “A latitudinal gradient in S/G lignin monomer ratio driven by laccase in natural poplar variants”
Lignin composition plays a crucial role in plant structural integrity and environmental adaptation. However, the genetic and molecular mechanisms underlying natural variation in lignin composition remain poorly understood. This study investigates the syringyl-to-guaiacyl (S/G) lignin monomer ratio across a natural population of Populus trichocarpa spanning a latitudinal gradient along the Northwest coast of North America. By integrating biochemical, genomic, and geographic analysis, we identify key gene variants associated with S/G ratio differences. These datasets provide valuable insights into the evolutionary and functional genomics of lignin composition and serve as a resource for developing poplar variants optimized for forestry and bioenergy applications.
Poplar, lignin composition, laccases, latitude, ad↗
Predicting plant attractiveness to coccinellids with plant trait profiling, citizen science, and common garden surveys
Lady beetles are key predators in agricultural systems and their impact can be enhanced by plant resources. Facilitation of lady beetles is a potentially effective pest management strategy but a lack of data on which plant species attract and nurture them limits implementation. Here we investigate which plant species might optimize lady beetle impact by developing a profile of plant characteristics most likely to attract lady beetles and testing if the subset of “potentially preferred” plant families exhibiting those characteristics are significantly more attractive to lady beetles than other families. This testing encompassed a combination of observations submitted to a citizen science program, the Lost Ladybug Project, and two repeated site surveys. Traits reported to be most attractive to lady beetles included the presence of trichomes that provide protection from predation, nutritional resources such as nectar or prey, and visual or chemical cues associated with those traits. Significantly more lady beetles were observed on the three plant families which most often exhibit these traits, Apiaceae, Asteraceae, and Rosaceae, than on other families. Furthermore, strategies for incorporating plants from these families into production systems to attract lady beetles and limit pest damage are discussed.
59 BASIC BIOLOGICAL SCIENCES↗
Jasmonate primes plant responses to extracellular ATP
SUMMARYExtracellular ATP (eATP) signaling in Arabidopsis thaliana is mediated by the purinoceptor P2K1. Previous studies have clarified that the downstream transcriptional responses to eATP involve jasmonate (JA)‐based signaling components such as the JA receptor (COI1) and JA‐responsive bHLH transcription factors (MYCs). However, the specific contributions of JA itself on eATP signaling are unexplored. Here, we report that JA primes plant responses to eATP through P2K1. Our findings show that JA treatment significantly upregulates P2K1 transcription, corroborating our observation that JA facilitates eATP‐induced cytosolic calcium elevation and transcriptional reprogramming in a JA signaling‐dependent manner. Additionally, we find that salicylic acid pre‐treatment represses eATP‐induced plant response. These results suggest that JA accumulation during biotic or abiotic stresses potentiates eATP signaling, enabling plants to better cope with subsequent stress events.
Jewell, Jeremy B. [Institute of Biological Chemist↗
Understanding local plant extinctions before it is too late: bridging evolutionary genomics with global ecology
Understanding evolutionary genomic and population processes within a species range is key to anticipating the extinction of plant species before it is too late. However, most models of biodiversity risk under global change do not account for the genetic variation and local adaptation of different populations. Population diversity is critical to understanding extinction because different populations may be more or less susceptible to global change and, if lost, would reduce the total diversity within a species. Here, two new modeling frameworks advance our understanding of extinction from a population and evolutionary angle: Rapid climate change-driven disruptions in population adaptation are predicted from associations between genomes and local climates. Furthermore, losses of population diversity from global land-use transformations are estimated by scaling relationships of species' genomic diversity with habitat area. Overall, these global eco-evolutionary methods advance the predictability – and possibly the preventability – of the ongoing extinction of plant species.
60 APPLIED LIFE SCIENCES↗
The end game(s) of photosynthetic carbon metabolism
Abstract The year 2024 marks 70 years since the general outline of the carbon pathway in photosynthesis was published. Although several alternative pathways are now known, it is remarkable how many organisms use the reaction sequence described 70 yrs ago, which is now known as the Calvin–Benson cycle or variants such as the Calvin–Benson–Bassham cycle or Benson–Calvin cycle. However, once the carbon has entered the Calvin–Benson cycle and is converted to a 3-carbon sugar, it has many potential fates. This review will examine the last stages of photosynthetic metabolism in leaves. In land plants, this process mostly involves the production of sucrose provided by an endosymbiont (the chloroplast) to its host for use and transport to the rest of the plant. Photosynthetic metabolism also usually involves the synthesis of starch, which helps maintain respiration in the dark and enables the symbiont to supply sugars during both the day and night. Other end products made in the chloroplast are closely tied to photosynthetic CO2 assimilation. These include serine from photorespiration and various amino acids, fatty acids, isoprenoids, and shikimate pathway products. I also describe 2 pathways that can short circuit parts of the Calvin–Benson cycle. These final processes of photosynthetic metabolism play many important roles in plants.
59 BASIC BIOLOGICAL SCIENCES↗
Rational engineering to enhance C8-fatty acid biosynthesis in Picosynechococcus sp. PCC 7002
Medium-chain fatty acids (e.g., C8-C14) are important biofuel precursors that can be produced from CO2 by cyanobacteria and other photoautotrophs. However, cyanobacteria naturally direct a relatively small fraction of fixed carbon to lipid synthesis, primarily producing long-chain membrane-bound fatty acids. We investigated whether mitigating kinetic bottlenecks within the fatty acid biosynthesis (FAB) pathway could enhance flux to free fatty acid (FFA) production in Picosynechococcus sp. PCC 7002. Previous in vitro studies proposed that the FAB initiating enzyme FabH is the primary rate-controlling enzyme in PCC 7002. We hypothesized that enhancing fatty acid initiation could increase in vivo FFA production while shifting the kinetic bottleneck further downstream in the pathway. We enabled C8-FFA accumulation by knocking out the native acyl-acyl carrier protein synthetase gene (aas) and expressing the highly active Cuphea palustris-derived mutant thioesterase CpFatB1.2-M4-287 (CupTE), which selectively catalyzes C8 chain termination. We then expressed the diatom-derived Chaetoceros sp. GSL56 FabH ortholog (chKASIII), to enhance initiation, and a medium-chain selective E. coli ketosynthase ecFabF[I108F] (ecFabF∗), to enhance elongation. When expressed individually or in combination with ecFabF∗, chKASIII slowed growth and decreased net carbon fixation rates relative to the parental Δaas-CupTE strain. However, co-expression of chKASIII, ecFabF∗, and CupTE redirected a larger fraction of fixed carbon toward FFA production, increasing relative carbon flux to C8-FFA and decreasing the projected minimum selling price by four-fold. This work demonstrates how systems metabolic engineering can be applied to enhance C8-FFA production in cyanobacteria while highlighting the unpredictable physiological consequences of host metabolic burden.
09 BIOMASS FUELS↗
No evidence for transient transformation via pollen magnetofection in several monocot species
Abstract not provided.
59 BASIC BIOLOGICAL SCIENCES↗
Phytohormones in a universe of regulatory metabolites: lessons from jasmonate
Small-molecule phytohormones exert control over plant growth, development, and stress responses by coordinating the patterns of gene expression within and between cells. Increasing evidence indicates that currently recognized plant hormones are part of a larger group of regulatory metabolites that have acquired signaling properties during the evolution of land plants. This rich assortment of chemical signals reflects the tremendous diversity of plant secondary metabolism, which offers evolutionary solutions to the daunting challenges of sessility and other unique aspects of plant biology. A major gap in our current understanding of plant regulatory metabolites is the lack of insight into the direct targets of these compounds. Here, we illustrate the blurred distinction between classical phytohormones and other bioactive metabolites by highlighting the major scientific advances that transformed the view of jasmonate from an interesting floral scent to a potent transcriptional regulator. Lessons from jasmonate research generally apply to other phytohormones and thus may help provide a broad understanding of regulatory metabolite–protein interactions. In providing a framework that links small-molecule diversity to transcriptional plasticity, we hope to stimulate future research to explore the evolution, functions, and mechanisms of perception of a broad range of plant regulatory metabolites.
59 BASIC BIOLOGICAL SCIENCES↗
Plant Design for a Developing Bioeconomy Workshop Report: Frontier Science for the Bioeconomy Workshop Series
Recent advances in fundamental plant biology research, synthetic biology, and artificial intelligence (AI) are unlocking powerful new capabilities in plant biodesign, offering unprecedented potential to reimagine plants as programmable platforms for resource-efficient production of bioenergy, biomaterials, chemicals, and more. The U.S. Department of Energy (DOE) convened the Plant Design for a Developing Bioeconomy virtual workshop on March 12 through 14, 2025, to bring together leaders across plant science, engineering, and computation to assess the current landscape and define a bold vision for future research. Discussions during the workshop built upon findings included in DOE’s Biological and Environmental Research (BER) workshop report Overcoming Barriers in Plant Transformation: A Focus on Bioenergy Crops (U.S. DOE 2024; genomicscience. energy.gov/plant-transformation). Participants identified critical knowledge gaps, technical barriers, and emerging opportunities in the design and engineering of plant systems to support a robust, resilient domestic bioeconomy aligned with DOE’s mission.
09 BIOMASS FUELS↗
Drought Drives Spatial Variation in the Millet Root Microbiome
Efforts to boost crop yield and meet global food demands while striving to reach sustainability goals are hindered by the increasingly severe impacts of abiotic stress, such as drought. One strategy for alleviating drought stress in crops is to utilize rootassociated bacteria, yet knowledge concerning the relationship between plant hosts and their microbiomes during drought remain under-studied. One broad pattern that has recently been reported in a variety of monocot and dicot species from both native and agricultural environments, is the enrichment of Actinobacteria within the drought-stressed root microbiome. In order to better understand the causes of this phenomenon, we performed a series of experiments in millet plants to explore the roles of drought severity, drought localization, and root development in provoking Actinobacteria enrichment within the root endosphere. Through 16S rRNA ampliconbased sequencing, we demonstrate that the degree of drought is correlated with levels of Actinobacterial enrichment in four species of millet. Additionally, we demonstrate that the observed drought-induced enrichment of Actinobacteria occurs along the length of the root, but the response is localized to portions of the root experiencing drought. Finally, we demonstrate that Actinobacteria are depleted in the dead root tissue of Japanese millet, suggesting saprophytic activity is not the main cause of observed shifts in drought-treated root microbiome structure. Collectively, these results help narrow the list of potential causes of drought-induced Actinobacterial enrichment in plant roots by showing that enrichment is dependent upon localized drought responses but not root developmental stage or root death.
59 BASIC BIOLOGICAL SCIENCES↗
Genetic variation in Zea mays influences microbial nitrification and denitrification in conventional agroecosystems
Nitrogenous fertilizers provide a short-lived benefit to crops in agroecosystems, but stimulate nitrification and denitrification, processes that result in nitrate pollution, N 2 O production, and reduced soil fertility. Recent advances in plant microbiome science suggest that genetic variation in plants can modulate the composition and activity of rhizosphere N-cycling microorganisms. Here we attempted to determine whether genetic variation exists in Zea mays for the ability to influence the rhizosphere nitrifier and denitrifier microbiome under “real-world” conventional agricultural conditions. To capture an extensive amount of genetic diversity within maize we grew and sampled the rhizosphere microbiome of a diversity panel of germplasm that included ex-PVP inbreds (Z. mays ssp. mays), ex-PVP hybrids (Z. mays ssp. mays), and teosinte (Z. mays ssp. mexicana and Z. mays ssp. parviglumis). From these samples, we characterized the microbiome, a suite of microbial genes involved in nitrification and denitrification and carried out N-cycling potential assays. Here we are showing that populations/genotypes of a single species can vary in their ecological interaction with denitrifers and nitrifers. Some hybrid and teosinte genotypes supported microbial communities with lower potential nitrification and potential denitrification activity in the rhizosphere, while inbred genotypes stimulated/did not inhibit these N-cycling activities. These potential differences translated to functional differences in N 2 O fluxes, with teosinte plots producing less GHG than maize plots. Taken together, these results suggest that Zea genetic variation can lead to changes in N-cycling processes that result in N leaching and N 2 O production, and thereby are selectable targets for crop improvement. Understanding the underlying genetic variation contributing to belowground microbiome N-cycling into our conventional agricultural system could be useful for sustainability.
59 BASIC BIOLOGICAL SCIENCES↗