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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Scripting a new dialogue between diazotrophs and crops

Diazotrophs are bacteria and archaea that can reduce atmospheric dinitrogen (N 2 ) into ammonium. Plant–diazotroph interactions have been explored for over a century as a nitrogen (N) source for crops to improve agricultural productivity and sustainability. This scientific quest has generated much information about the molecular mechanisms underlying the function, assembly, and regulation of nitrogenase, ammonium assimilation, and plant–diazotroph interactions. This review presents various approaches to manipulating N fixation activity, ammonium release by diazotrophs, and plant–diazotroph interactions. Here, we discuss the research avenues explored in this area, propose potential future routes, emphasizing engineering at the metabolic level via biorthogonal signaling, and conclude by highlighting the importance of biocontrol measures and public acceptance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Seasonal activities of the phyllosphere microbiome of perennial crops

Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on replicated plots of field-grown switchgrass and miscanthus, and to quantify their activities over two growing seasons for switchgrass. We use metagenome and metatranscriptome sequencing and curate 40 medium- and high-quality metagenome-assembled-genomes (MAGs). We find that classes represented by these MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) are active in the late season, and upregulate transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase. Stress-associated pathways are expressed for most MAGs, suggesting engagement with the host environment. We also detect seasonally activated biosynthetic pathways for terpenes and various non-ribosomal peptide pathways that are poorly annotated. Our findings support that leaf-associated bacterial populations are seasonally dynamic and responsive to host cues.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Emissions leakage and economic losses may undermine deforestation-linked oil crop import restrictions

Import restrictions on deforestation-linked commodities are being considered strategies to reduce global deforestation and emissions. However, limited market share of importers imposing such restrictions and the potential for emissions leakage could reduce their effectiveness. Moreover, they could result in negative economic implications for producers and consumers. We quantify future emissions and economic implications of oil palm and soybean import restrictions. Current EU restrictions will likely have minimal impact due to the EU’s otherwise small and diminishing share of global palm and soy demand. If extended beyond the EU, such import restrictions could drive reductions in cumulative LUC emissions by 2050 in key oil crop exporting regions— up to 0.9% in Indonesia, 1.5% in the rest of Southeast Asia, 3.8% in Argentina and 6.7% in Brazil, relative to a scenario with no import restrictions. However, these key exporters could also face losses ranging $\$$4.1-$\$$61 billion in cumulative agricultural production revenue by 2050.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2020

Netting and pan traps fail to identify the pollinator guild of an agricultural crop

Pollinator decline is expected to cause significant reductions in food production and plant reproduction. Quantifying the impact of pollinator decline on food production requires survey methods that can identify insect and bee species responsible for pollination of specific crops. To address this issue, we compared the effectiveness of two survey methods, netting and pan traps, at capturing the pollinators of alfalfa, Medicago sativa. Alfalfa is a major component of forage for cows and an important ingredient in chicken feed. We also examined bee species richness and diversity with these two survey methods, and compared these measures among three different colors of pan traps. Netting was more effective at capturing known pollinators of alfalfa, especially those belonging to the Bombus and Apis genera. Pan traps captured a higher bee diversity relative to netting and, like previous studies, each survey method and each trap color was more efficient at capturing certain bee genera. However, without a priori knowledge of pollinators, neither survey method could identify which of the bee species captured could pollinate alfalfa. We therefore recommend direct observations when the goal of a study is to identify pollinators or link pollinator decline to food production.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Influence of soil heterogeneity on soybean plant development and crop yield evaluated using time-series of UAV and ground-based geophysical imagery

Understanding the interactions among agricultural processes, soil, and plants is necessary for optimizing crop yield and productivity. This study focuses on developing effective monitoring and analysis methodologies that estimate key soil and plant properties. These methodologies include data acquisition and processing approaches that use unmanned aerial vehicles (UAVs) and surface geophysical techniques. In particular, we applied these approaches to a soybean farm in Arkansas to characterize the soil–plant coupled spatial and temporal heterogeneity, as well as to identify key environmental factors that influence plant growth and yield. UAV-based multitemporal acquisition of high-resolution RGB (red–green–blue) imagery and direct measurements were used to monitor plant height and photosynthetic activity. We present an algorithm that efficiently exploits the high-resolution UAV images to estimate plant spatial abundance and plant vigor throughout the growing season. Such plant characterization is extremely important for the identification of anomalous areas, providing easily interpretable information that can be used to guide near-real-time farming decisions. Additionally, high-resolution multitemporal surface geophysical measurements of apparent soil electrical conductivity were used to estimate the spatial heterogeneity of soil texture. By integrating the multiscale multitype soil and plant datasets, we identified the spatiotemporal co-variance between soil properties and plant development and yield. Our novel approach for early season monitoring of plant spatial abundance identified areas of low productivity controlled by soil clay content, while temporal analysis of geophysical data showed the impact of soil moisture and irrigation practice (controlled by topography) on plant dynamics. Our study demonstrates the effective coupling of UAV data products with geophysical data to extract critical information for farm management.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Anti-fungal bioactive terpenoids in the bioenergy crop switchgrass (Panicum virgatum) may contribute to ecotype-specific microbiome composition

Abstract Plant derived bioactive small molecules have attracted attention of scientists across fundamental and applied scientific disciplines. We seek to understand the influence of these phytochemicals on rhizosphere and root-associated fungi. We hypothesize that – consistent with accumulating evidence that switchgrass genotype impacts microbiome assembly – differential terpenoid accumulation contributes to switchgrass ecotype-specific microbiome composition. An initial in vitro Petri plate-based disc diffusion screen of 18 switchgrass root derived fungal isolates revealed differential responses to upland- and lowland-isolated metabolites. To identify specific fungal growth-modulating metabolites, we tested fractions from root extracts on three ecologically important fungal isolates – Linnemania elongata, Trichoderma sp. and Fusarium sp. Saponins and diterpenoids were identified as the most prominent antifungal metabolites. Finally, analysis of liquid chromatography-purified terpenoids revealed fungal inhibition structure – activity relationships (SAR). Saponin antifungal activity was primarily determined by the number of sugar moieties – saponins glycosylated at a single core position were inhibitory whereas saponins glycosylated at two core positions were inactive. Saponin core hydroxylation and acetylation were also associated with reduced activity. Diterpenoid activity required the presence of an intact furan ring for strong fungal growth inhibition. These results inform future breeding and biotechnology strategies for crop protection with reduced pesticide application.

09 BIOMASS FUELS↗
DOE OSTI2026

Urban agrivoltaics enhance crop resilience and food-energy synergies in a changing climate

Urban agrivoltaics, the synergistic integration of solar photovoltaics with urban agriculture, offers a transformative solution to food and energy insecurity, which are major barriers to sustainable urban development, especially in low-income urban areas facing intensified heat and water stress due to climate change. With 70% of the global population projected to live in cities by 2050, maximizing underutilized urban spaces is critical. Our study presents the first evaluation of ground-based agrivoltaics in an urban context, demonstrating that, while early-season yields may decline due to light reduction in temperate climates, productivity rebounds during periods of extreme heat, extending harvest windows and enhancing crop resilience. As cities seek climate-adaptive infrastructure, converting just a fraction of vacant land and rooftops to urban agrivoltaics can yield significant co-benefits such as generating renewable energy for thousands of households while supplying fresh produce to help alleviate food deserts.

14 SOLAR ENERGY↗
DOE OSTI2023

Application of Time-Domain 1 H NMR for Investigating Dynamics of Vegetative Lipids in Bioenergy Crops at Different Developmental Stages

Sweet sorghum is typically cultivated for the food and fodder market. Recently, sweet sorghum varieties are being metabolically transitioned to enhance energy density by accumulating oil droplets in their vegetative tissues for bioenergy applications. Owing to the high biomass yield of sorghum, the transgenic lines can compete with oil-seed crops for biodiesel yield per unit area. In the initial phase of transgenic development, a high-throughput phenotyping method can bridge the gap between the production pipeline and analysis to improve the efficiency of the process. To meet the requirement, the present study extends the application of time-domain 1 H-NMR spectroscopy for rapid quantification and characterization of the total in-situ lipids of sweet sorghum ‘ramada’ to lay the groundwork for analyzing the upcoming large quantity of transgenic samples. NMR technology has been successfully established for analyzing lipid contents of vegetative tissues of non-transgenic variety. The multiexponential analysis of spin-lattice (T 1 ) relaxation spectra obtained from TD-NMR aided the investigation of the dynamics of the free and bound lipid fraction with plant development. The total lipid concentration of bagasse and leaves of non-transgenic sweet sorghum remained unchanged throughout the plant development. Leaves displayed a higher percentage of bound lipids as compared to bagasse. Here, a significant variation in the lipid concentration of juice was observed at the different growth stages with a maximum lipid accumulation of 1.21 ± 0.04% w/w at the boot stage that decreased with further maturity of the plant.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Natural variation and improved genome annotation of the emerging biofuel crop field pennycress ( Thlaspi arvense )

The Brassicaceae family comprises more than 3,700 species with a diversity of phenotypic characteristics, including seed oil content and composition. Recently, the global interest in Thlaspi arvense L. (pennycress) has grown as the seed oil composition makes it a suitable source for biodiesel and aviation fuel production. However, many wild traits of this species need to be domesticated to make pennycress ideal for cultivation. Molecular breeding and engineering efforts require the availability of an accurate genome sequence of the species. Here, we describe pennycress genome annotation improvements, using a combination of long- and short-read transcriptome data obtained from RNA derived from embryos of 22 accessions, in addition to public genome and gene expression information. Our analysis identified 27,213 protein-coding genes, as well as on average 6,188 biallelic SNPs. In addition, we used the identified SNPs to evaluate the population structure of our accessions. The data from this analysis support that the accession Ames 32872, originally from Armenia, is highly divergent from the other accessions, while the accessions originating from Canada and the United States cluster together. When we evaluated the likely signatures of natural selection from alternative SNPs, we found 7 candidate genes under likely recent positive selection. These genes are enriched with functions related to amino acid metabolism and lipid biosynthesis and highlight possible future targets for crop improvement efforts in pennycress.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Biostimulation of Salicornia europaea L. crops with plant growth-promoting bacteria in laboratory and field conditions: effects on growth and metabolite profile

Abstract Aim The objective of the work was to assess the effect of biostimulation with selected plant growth-promoting bacteria on growth and metabolite profile of Salicornia europaea. Methods and results Salicornia europaea seeds were inoculated with different combinations of plant growth-promoting bacteria Brevibacterium casei EB3, Pseudomonas oryzihabitans RL18, and Bacillus aryabhattai SP20. Plants germinated from inoculated seeds were grown either in laboratory conditions or in a saline crop field. Fresh and dry weight were determined at the end of the experiment, for biomass quantification. The microbiological quality of fresh shoots for human consumption as salad greens was assessed, and the persistence of the inoculated strains in the plant rhizosphere was confirmed by next-generation sequencing (Illumina) of the 16S rDNA gene. The primary metabolite profile of biostimulated plants was characterized by GC–TOF-MS. In laboratory conditions, inoculation with the two strains Br. casei EB3 and Ps. oryzihabitans RL18 caused the most significant increase in biomass production (fresh and dry weight), and caused a shift in the central metabolic pathways of inoculated plants toward amino acid biosynthesis. In the field experiment, no significant biostimulation effect was detected with any of the tested inoculants. Seed inoculation had no significant effect on the microbiological quality of the edible parts. The persistence of inoculants was confirmed in both experiments. Conclusions Manipulation of the plant microbiome can trigger primary metabolic reconfiguration and modulate the plant metabolism while promoting plant growth.

Ferreira, Maria J.↗
DOE OSTI2024

Nitrogen acquisition and retention pathways in sustainable perennial bioenergy grass cropping systems

Abstract Perennial tall grasses show promise as bioenergy crops due to high productivity and efficient nutrient use. Ongoing research on bioenergy grasses seeks to reduce their reliance on synthetic nitrogen (N) fertilizer, the manufacture of which relies on fossil fuel combustion. Excessive use of fertilizers also causes adverse environmental consequences and leads to the evolutionary loss of plant traits beneficial to sustainable N cycle. Notably, perennial tall grasses have exhibited the potential to maintain high biomass yield without the need for N fertilizer or causing soil N depletion. Perennial grasses can be adept at interacting with their microbial partners to facilitate N acquisition and retention via mechanisms such as biological N fixation and nitrification inhibition. These inherent N management traits should be preserved and optimized at the this early stage of bioenergy grass breeding programs. This review examines the impact of external N on bioenergy grass production and explores the potential of leveraging advantageous N‐cycling attributes of perennial tall grasses, laying groundwork for future management and research efforts. With minimized dependency on external N input, the cultivation of perennial energy grasses will pave the way toward more resilient agricultural systems and play a significant role in addressing key global energy and environmental challenges.

Agriculture↗
DOE OSTI2024

Genetic Basis of Non–Photochemical Quenching and Photosystem II Efficiency Responses to Chilling in the Biomass Crop Miscanthus

Miscanthus holds a promise as a biocrop due to its high yield, perenniality and ability to grow on infertile soils. However, the current commercial biomass production of Miscanthus is mostly limited to a single sterile triploid clone of M. × giganteus. Nevertheless, parental species of M. × giganteus, Miscanthus sacchariflorus and Miscanthus sinensis contain vast genetic diversity for crop improvement. With M. sacchariflorus having a natural geographic distribution in cold-temperate northeast China and eastern Russia, we hypothesised that it has substantial variation in physiological response to chilling. Using a semi-high-throughput method, we phenotyped 209 M. sacchariflorus genotypes belonging to six genetic groups for non-photochemical quenching (NPQ) and photosystem II efficiency (ΦPSII) kinetics under warm and chilling treatments in three growing seasons. In response to the chilling treatment, all genetic groups exhibited an increase in NPQ induction rate indicating faster activation of NPQ in light. Notably, under chilling, the Korea/NE China/Russia 2x and N China 2x groups stood out for the highest NPQ rate in light and the highest steady-state NPQ in light. This NPQ phenotype may contribute adaptation to chilling during bright, cold mornings of spring and early autumn in temperate climates, when faster NPQ would better protect from oxidative stress. Such enhanced adaptation could expand the growing season and thus productivity at a given location or expand the range of economically viable growing locations to higher latitudes and altitudes. A genome-wide association study identified 126 unique SNPs associated with NPQ and ΦPSII traits. Among the identified candidate genes were enzymes involved in the ascorbate recycle and shikimate pathway, gamma-aminobutyric acid and cation efflux transporters. Identifying natural variation and genes involved in NPQ and ΦPSII kinetics considerably enlarges the toolbox for breeding and/or engineering Miscanthus with optimised photosynthesis under warm and chilling conditions for sustainable feedstock production for bioenergy.

09 BIOMASS FUELS↗
DOE OSTI2022

Chromosome‐level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

Summary Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field‐based model species for genetics and epigenetics. The availability of a high‐quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome‐level genome assembly of var. MN106‐Ref with improved gene annotation and use it to investigate gene structure differences between two accessions (MN108 and Spring32‐10) that are highly amenable to genetic transformation. We describe non‐coding RNAs, pseudogenes and transposable elements, and highlight tissue‐specific expression and methylation patterns. Resequencing of forty wild accessions provided insights into genome‐wide genetic variation, and QTL regions were identified for a seedling colour phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Source:sink imbalance detected with leaf and canopy-level spectroscopy in a field-grown crop

The finely-tuned balance between sources and sinks determines plant resource partitioning and regulates growth and development. Understanding and measuring metabolic indicators of source or sink limitation forms a vital part of global efforts to increase crop yield for future food security. Here, we measured metabolic profiles of Cucurbita pepo (zucchini) grown in the field under carbon sink limitation and control conditions. We demonstrate that these profiles can be measured non-destructively using hyperspectral reflectance at both leaf and canopy scales. Total non-structural carbohydrates (TNC) increased 82% in sink-limited plants; leaf mass per unit area (LMA) increased 38%; free amino acids increased 22%. Partial least-squares regression models link these measured functional traits with reflectance data, enabling high-throughput estimation of traits comprising the sink limitation response. Leaf- and canopy-scale models for TNC had R 2 values of 0.93 and 0.64 and %RMSE of 13% and 38% respectively. For LMA, R 2 values were 0.91 and 0.60 and %RMSE 7% and 14%; for free amino acids, R 2 was 0.53 and 0.21 with %RMSE 20% and 26%. Remote sensing can enable accurate, rapid detection of sink limitation in the field at the leaf and canopy scale, greatly expanding our ability to understand and measure metabolic responses to stress.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

The recent evolutionary rescue of a staple crop depended on over half a century of global germplasm exchange

Rapid environmental change can lead to population extinction or evolutionary rescue. The global staple crop sorghum (Sorghum bicolor) has recently been threatened by a global outbreak of an aggressive new biotype of sugarcane aphid (SCA; Melanaphis sacchari). We characterized genomic signatures of adaptation in a Haitian breeding population that had rapidly adapted to SCA infestation, conducting evolutionary population genomics analyses on 296 Haitian lines versus 767 global accessions. Genome scans and geographic analyses suggest that SCA adaptation has been conferred by a globally rare East African allele of RMES1, which spread to breeding programs in Africa, Asia, and the Americas. De novo genome sequencing revealed potential causative variants at RMES1. Markers developed from the RMES1 sweep predicted resistance in eight independent commercial and public breeding programs. These findings demonstrate the value of evolutionary genomics to develop adaptive trait technology and highlight the benefits of global germplasm exchange to facilitate evolutionary rescue.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Framework For Spatial Agricultural Crop Yield Prediction Model Development

This framework was developed to provide data preprocessing for spatiotemporal agricultural yield data and remote sensing data for modelling using artificial neural networks (ANNs) to predict subfield crop yield estimates. The software includes methods to train, validate, and test ANN models. It also include methods to infer on new remote sensing data.

Griffel, LloydM.↗
DOE OSTI2024

DAWN: Dashboard for Agricultural Water Use and Nutrient Management—A Predictive Decision Support System to Improve Crop Production in a Changing Climate

Abstract Climate change presents huge challenges to the already-complex decisions faced by U.S. agricultural producers, as seasonal weather patterns increasingly deviate from historical tendencies. Under USDA funding, a transdisciplinary team of researchers, extension experts, educators, and stakeholders is developing a climate decision support Dashboard for Agricultural Water use and Nutrient management (DAWN) to provide Corn Belt farmers with better predictive information. DAWN’s goal is to provide credible, usable information to support decisions by creating infrastructure to make subseasonal-to-seasonal forecasts accessible. DAWN uses an integrated approach to 1) engage stakeholders to coproduce a decision support and information delivery system; 2) build a coupled modeling system to represent and transfer holistic systems knowledge into effective tools; 3) produce reliable forecasts to help stakeholders optimize crop productivity and environmental quality; and 4) integrate research and extension into experiential, transdisciplinary education. This article presents DAWN’s framework for integrating climate–agriculture research, extension, and education to bridge science and service. We also present key challenges to the creation and delivery of decision support, specifically in infrastructure development, coproduction and trust building with stakeholders, product design, effective communication, and moving tools toward use.

Meteorology & Atmospheric Sciences↗