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At least 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

PhytoOracle: Scalable, modular phenomics data processing pipelines

As phenomics data volume and dimensionality increase due to advancements in sensor technology, there is an urgent need to develop and implement scalable data processing pipelines. Current phenomics data processing pipelines lack modularity, extensibility, and processing distribution across sensor modalities and phenotyping platforms. To address these challenges, we developed PhytoOracle (PO), a suite of modular, scalable pipelines for processing large volumes of field phenomics RGB, thermal, PSII chlorophyll fluorescence 2D images, and 3D point clouds. PhytoOracle aims to ( i ) improve data processing efficiency; ( ii ) provide an extensible, reproducible computing framework; and ( iii ) enable data fusion of multi-modal phenomics data. PhytoOracle integrates open-source distributed computing frameworks for parallel processing on high-performance computing, cloud, and local computing environments. Each pipeline component is available as a standalone container, providing transferability, extensibility, and reproducibility. The PO pipeline extracts and associates individual plant traits across sensor modalities and collection time points, representing a unique multi-system approach to addressing the genotype-phenotype gap. To date, PO supports lettuce and sorghum phenotypic trait extraction, with a goal of widening the range of supported species in the future. At the maximum number of cores tested in this study (1,024 cores), PO processing times were: 235 minutes for 9,270 RGB images (140.7 GB), 235 minutes for 9,270 thermal images (5.4 GB), and 13 minutes for 39,678 PSII images (86.2 GB). These processing times represent end-to-end processing, from raw data to fully processed numerical phenotypic trait data. Repeatability values of 0.39-0.95 (bounding area), 0.81-0.95 (axis-aligned bounding volume), 0.79-0.94 (oriented bounding volume), 0.83-0.95 (plant height), and 0.81-0.95 (number of points) were observed in Field Scanalyzer data. We also show the ability of PO to process drone data with a repeatability of 0.55-0.95 (bounding area).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Agriculture’s Potential Regional Economic Contributions to the United States Economy When Supplying Feedstock to the Bio-Economy

The economic impact of obtaining biomass could become significant to U.S. rural economies via the establishment of a bioeconomy. In 2023, the Bioenergy Technologies Office (BETO) and Oak Ridge National Laboratory provided a road map to obtain over a billion tons of biomass for conversion to bioenergy and other products. Using information from this roadmap, this study estimates the potential positive and negative economic impacts that occur because of land use change, along with increased technological advances. This is achieved by using the input–output model, IMPLAN, and impacting 179 Bureau of Economic Analysis regions in the conterminous United States. Biomass included in the analysis comprises dedicated energy crops, crop residues, and forest residues. The analysis found that managing pastures more intensively could result in releasing land to produce dedicated energy crops on 30.8 million hectares, resulting in the production of 361 million metric tons of biomass. This, coupled with crop residues from barley, corn, oats, sorghum, and wheat (162 million metric tons), plus forest residues (41 million metric tons), provide 564 million dry metric tons of biomass. Assuming the price for biomass in 2023 dollars was USD 77 per dry metric-ton, this additional production results in an economic benefit for the nation of USD 619 billion, an increase from the Business As Is scenario (Baseline) of almost USD 100 billion per year, assuming a mature biomass industry. An additional 700,000 jobs are required to grow, harvest/collect, and transport the biomass material from the land.

ForSEAM↗
DOE OSTI2022

A Chemical-Free Pretreatment for Biosynthesis of Bioethanol and Lipids from Lignocellulosic Biomass: An Industrially Relevant 2G Biorefinery Approach

A wide range of inorganic and organic chemicals are used during the pretreatment and enzymatic hydrolysis of lignocellulosic biomass to produce biofuels. Developing an industrially relevant 2G biorefinery process using such chemicals is challenging and requires more unit operations for downstream processing. A sustainable process has been developed to achieve industrially relevant titers of bioethanol with significant ethanol yield. The pretreatment of sorghum biomass was performed by a continuous pilot-scale hydrothermal reactor followed by disk milling. Enzymatic hydrolysis was performed without washing the pretreated biomass. Moreover, citrate buffer strength was reduced to 100-fold (50 mM to 0.5 mM) during the enzymatic hydrolysis. Enzymatic hydrolysis at 0.5 mM citrate buffer strength showed that significant sugar concentrations of 222 ± 2.3 to 241 ± 2.3 g/L (glucose + xylose) were attained at higher solids loadings of 50 to 60% (w/v). Furthermore, hydrolysates were fermented to produce bioethanol using two different xylose-fermenting Saccharomyces cerevisiae strains and a co-culture of xylose-fermenting and non-GMO yeast cultures. Bioethanol titer of 81.7 g/L was achieved with an ethanol yield of 0.48 gp/gs. Additionally, lipids were produced using the oleaginous yeast Rhodosporidium toruloides, yielding 13.2 g/L lipids with cellular lipid accumulation of 38.5% w/w from 100 g/L of sugar concentration. In summary, reducing the strength of the citrate buffer during enzymatic hydrolysis and omitting inorganic chemicals from the pretreatment process enhances the fermentability of hydrolysates and can also reduce operating costs.

Deshavath, Narendra Naik↗
DOE OSTI2021

New Orthophoto Generation Strategies from UAV and Ground Remote Sensing Platforms for High-Throughput Phenotyping

Remote sensing platforms have become an effective data acquisition tool for digital agriculture. Imaging sensors onboard unmanned aerial vehicles (UAVs) and tractors are providing unprecedented high-geometric-resolution data for several crop phenotyping activities (e.g., canopy cover estimation, plant localization, and flowering date identification). Among potential products, orthophotos play an important role in agricultural management. Traditional orthophoto generation strategies suffer from several artifacts (e.g., double mapping, excessive pixilation, and seamline distortions). The above problems are more pronounced when dealing with mid- to late-season imagery, which is often used for establishing flowering date (e.g., tassel and panicle detection for maize and sorghum crops, respectively). In response to these challenges, this paper introduces new strategies for generating orthophotos that are conducive to the straightforward detection of tassels and panicles. The orthophoto generation strategies are valid for both frame and push-broom imaging systems. The target function of these strategies is striking a balance between the improved visual appearance of tassels/panicles and their geolocation accuracy. The new strategies are based on generating a smooth digital surface model (DSM) that maintains the geolocation quality along the plant rows while reducing double mapping and pixilation artifacts. Moreover, seamline control strategies are applied to avoid having seamline distortions at locations where the tassels and panicles are expected. The quality of generated orthophotos is evaluated through visual inspection as well as quantitative assessment of the degree of similarity between the generated orthophotos and original images. Several experimental results from both UAV and ground platforms show that the proposed strategies do improve the visual quality of derived orthophotos while maintaining the geolocation accuracy at tassel/panicle locations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

CAZyme domain architectures suggest fine-scale functional differentiation among anaerobic fungi and bacteria during lignocellulose conversion to volatile fatty acids

Anaerobic fermentation with microbial communities (microbiomes) is an emerging platform for conversion of lignocellulosic biomass to biofuels and bioproducts. The process relies on diverse anaerobic microbes that interact to deconstruct and convert lignocellulosic biomass into a range of products, such as volatile fatty acids (VFAs), which can be achieved by arresting methanogenesis during fermentation. However, defining the distinct functional roles played by various fungi and bacteria during anaerobic biodegradation remains poorly understood. Here, we performed parallel enrichment experiments from cow faeces, goat faeces, and anaerobic digester sludge, selecting for fungal or bacterial dominated communities that convert sorghum biomass into VFAs. Subsequently we reconstructed metabolic networks across these enrichments based on recovered bacterial metagenome-assembled genomes (MAGs) and fungal isolate genomes and profiled their metabolic activity using metatranscriptomics to identify potential functional niches. Our findings implicate diverse bacteria affiliated with the Bacteroidales and Lachnospiraceae in the direct conversion of lignocellulosic biomass to propionate and butyrate, respectively, whereas Neocallimastix-dominated fungal enrichments converted lignocellulose to lactate, acetate and formate. Analysis of carbohydrate-active enzymes (CAZymes) revealed fine-scale differences between microbes that expressed unique multi-functional enzymes linking two or more CAZymes together with distinct carbohydrate binding motifs, implicating lignocellulose structure as a key driver of selection and niche differentiation. Most of these multi-functional enzymes localized complementary degradation functions together, likely conferring synergistic degradation effects within and between microbiome members. We anticipate that these findings will help inform efforts to develop synthetic microbiomes with tailored functionality for low-cost conversion of lignocellulosic biomass to fuels and bio-based chemicals.

Lawson, Christopher E [University of Toronto;]↗
NASA NTRS1973

Reflectance of vegetation, soil, and water

The author has identified the following significant results. A ratio of MSS channels 5 and 7 (5/7) and 5 to 6 (5/6) signals resulted in a correct recognition of 86.9% of the members of representative crop and soil conditions, compared with recognitions of 60.0, 64.1, 74.1, and 81.4% for channels 4, 5, 6, and 7 taken individually. Based on this result a satellite channel ratio procedure has been developed that enhances line printer gray maps for more efficient experimental test site location in the CCT data. Because independent estimates are not available to judge acreage estmates derived from ERTS-1 data against, except for a few crops, an interpenetrating sample constituting 3.5% of the county is ground truthed periodically. The crop of land uses and their acreages, respectively, as estimated from the interpenetrating samples, are: cotton, 129, 714; sorghum, 182,783; mixed citrus, 53,954; oranges, 16,929; grapefruit, 13,863; rangeland, 137,845; and, improved pastures, 57.169.

Wiegand, C. L.↗
NASA NTRS1973

Temporal analysis of multispectral scanner data.

Multispectral scanner reflectance data were sampled for bare soil, cotton, sorghum, corn, and citrus at four dates during a growing season (April, May, June, and July 1969) to develop a time-dependent signature for crop and soil discrimination. Discrimination tests were conducted for single-date and multidate formats using training and test data sets. For classifications containing several crops, the multidate or temporal approach improved discrimination compared with the single-date approach. The multidate approach also preserved recognition accuracy better in going from training fields to test fields than the single-date analysis. The spectral distinctiveness of bare soil versus vegetation resulted in essentially equal discrimination using single-date versus multidate data for those two categories.

Richardson, A. J.↗
NASA NTRS1974

Reflectance of vegetation, soil, and water

The author has identified the following significant results. Reflectance of crop residues, that are important in reducing wind and water erosion, was more often different from bare soil in band 4 than in bands 5, 6, or 7. The plant parameters leaf area index, plant population, plant cover, and plant height explained 95.9 percent of the variation in band 7 (reflective infrared) digital counts for cotton and 78.2 percent of the variation in digital counts for the combined crops sorghum and corn; hence, measurable plant parameters explain most of the signal variation recorded for corpland. Leaf area index and plant population are both highly correlated with crop yields; since plant population can be readily measured (or possibly inferred from seeding rates), it is useful measurement for calibrating ERTS-type MSS digital data in terms of yield.

Wiegand, C. L.↗
NASA NTRS1974

Reflectance of vegetation, soil, and water

The author has identified the following significant results. The Kubelka-Munk model, a regression model, and a combination of these models were used to extract plant, soil, and shadow reflectance components of vegetated surfaces. The combination model was superior to the others; it explained 86% of the variation in band 5 reflectance of corn and sorghum, and 90% of the variation in band 6 reflectance of cotton. A fractional shadow term substantially increased the proportion of the digital count sum of squares explained when plant parameters alone explained 85% or less of the variation. Overall recognition of 94 agricultural fields using simultaneously acquired aircraft and spacecraft MSS data was 61.8 and 62.8%, respectively; recognition of vegetable fields larger than 10 acres and taller than 25 cm, rose to 88.9 and 100% for aircraft and spacecraft, respectively. Agriculture and rangeland, were well discriminated for the entire county but level 2 categories of vegetables, citrus, and idle cropland, except for citrus, were not.

Wiegand, C. L.↗
NASA NTRS1974

Crop identification and acreage measurement utilizing ERTS imagery

The Statistical Reporting Service of the U.S. Department of Agriculture is evaluating ERTS-1 imagery as a potential tool for estimating crop acreage. A main data source for the estimates is obtained by enumerating small land parcels that have been randomly selected from the total U.S. land area. These small parcels are being used as ground observations in this investigation. The test sites are located in Missouri, Kansas, Idaho, and South Dakota. The major crops of interest are wheat, cotton, corn, soybeans, sugar beets, potatoes, oats, alfalfa, and grain sorghum. Some of the crops are unique to a given site while others are common in two or three states. This provides an opportunity to observe crops grown under different conditions. Results for the Missouri test site are presented. Results of temporal overlays, unequal prior probabilities, and sample classifiers are discussed. The amount of improvement that each technique contributes is shown in terms of overall performance. The results show that useful information for making crop acreage estimates can be obtained from ERTS-1 data.

Wigton, W. H.↗
NASA NTRS1975

The use of ERTS-1 multispectral imagery for crop identification in a semi-arid climate

Crop identification using multispectral satellite imagery and multivariate pattern recognition was used to identify wheat accurately in Greeley County, Kansas. A classification accuracy of 97 percent was found for wheat and the wheat estimate in hectares was within 5 percent of the USDA's Statistical Reporting Service estimate for 1973. The multispectral response of cotton and sorghum in Texas was not unique enough to distinguish between them nor to separate them from other cultivated crops.

Stockton, J. G.↗
NASA NTRS1980

Houston area multicrop inspection trips

The phenology of crops such as corn, cotton, soybeans, sorghum, sunflowers, and rice and their observed signatures on LANDSAT imagery was studied. This was accomplished by photographing the various crops in segments 275 and 276 located in Wharton County, Texas and comparing those photographs with LANDSAT imagery of the same dates. These comparisons gave insight as to why a particular crop growth stage appeared as a definite signature on LANDSAT and how the percentage of ground cover of various crops affected the signatures on LANDSAT imagery. Numerous crop growth stages could not be directly compared due to cloud cover during several LANDSAT overpasses.

Dunham, E. W.↗
NASA NTRS1980

Spatial variability of surface temperature as related to cropping practice with implications for irrigation management

Crop stress measured using thermal infrared emission is evaluated with the stress-degree-day (SDD) concept. Throughout the season, the accumulation of SDD during the reproductive stage of growth is inversely related to yield. This relationship is shown for durum wheat, hard red winter wheat, barley, grain sorghum and soybeans. It is noted that SDD can be used to schedule irrigations for maximizing yields and for applying remotely sensed data to management of water resources. An airborne flight with a thermal-IR scanner was used to examine the variability in temperature that may exist from one field to another and to determine realistic within-field temperature variations. It was found that the airborne and the ground-based data agreed very well and that there was less variability in the fields that were completely covered with crops than those of bare soil.

Hatfield, J. L.↗
NASA NTRS1980

A model of plant canopy polarization response

Sensors to remotely measure the linear polarization of ground scenes have been proposed for the Multispectral Resource Sampler (MRS), a satellite sensor system proposed to complement the Thematic Mapper. At present justification for a sensor on MRS to measure scene polarization is limited. This paper discusses a model for the amount of linearly polarized light reflected by the shiny leaves of such crops as wheat, corn, and sorghum. The theory demonstrates that, potentially, measurements of the linearly polarized light from a crop canopy may be used as an additional feature to discriminate between crops. Examination of the model suggests that, potentially, satellite polarization measurements may be used to monitor crop development stage, leaf water content, leaf area index, hail damage, and certain plant diseases. The model adds to the understanding of the potential information content of scene polarization measurements acquired by future satellite sensor systems such as MRS.

Vanderbilt, V. C.↗
NASA NTRS1982

Optical parameters of leaves of seven weed species

Absorption coefficient (k), infinite reflectance (R inf.) and scattering coefficient (s) were tabulated for five wavelengths and analyzed for statistical differences for seven weed species. The wavelengths were: 0.55, 0.65, 0.85, 1.65, and 2.20 microns. The R inf. of common lambsquarters (Chenopodium album L.), johnsongrass (Sorghum halepense L. Pers.), and annual sowthistle (Sonchus oleraceus L.) leaves at the 0.85 micron wavelength were significantly (p = 0.05) higher than for sunflower (Helianthus annuus L.), ragweed parthenium (parthenium hysterophorus L.), or London rocket (Sisymbrium irio L.). Annual sowthistle had the largest k value, and Palmer amaranth (Amaranthus palmeri S. Wats.) had the smallest k value at the 0.65 micron chlorophyll absorption wavelength. In general, johnsongrass, ragweed parthenium, and London rocket had the largest s values among the five wavelengths, whereas annual sowthistle and Palmer amaranth were usually lowest.

Gausman, H. W.↗
NASA NTRS1982

Optical parameters of leaves of seven weed species

The absorption coefficient (k), infinite reflectance (R), and scattering coefficient (s) were tabulated for five wavelengths and analyzed for statistical differences for seven weed species. The wavelengths were: 0.55-micrometer, 0.65-micrometers, 0.85-micrometer, 1.65-micrometers, and 2.20-micrometer. The R of common lambsquarters (Chenopodium album L.), Johnsongrass (Sorghum halepense (L.) Pers.), and annual sowthistle (Sonchus oleraceus L.) leaves at the 0.85-micrometer wavelength were significantly (p=0.05) higher than for sunflower (Heliantus annus L.), ragweed parthenium (Parthenium hysterophorus L.), or London rocket (Sisymbrium irio L.). Annual sowthistle had the largest k value, and Plamer amaranth (Amaranthus palmer S. Wats.) had the smallest k value at the 0.65 approximately chlorophyll absorption wavelength. In general, john-songress, ragweed parthenium, or London rocket had the largest s values among the five wavelengths, wereas annual sowthistle and plamar amaranth were usually lowest.

Gausman, H. W.↗