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At least 55 records · Page 3

Scaling Spectroradiometric Monitoring to an Algal Factory Farm

This report briefly summarizes the spectroradiometric approach adapted and deployed as part of Task 4.2 within the BETO-funded D evelopment of I ntegrated S creening, C ultivar O ptimization, and V erification R esearch (DISCOVR) project, specifically task 4, “Increase crop protection and culture stability.” The goals of this subtask were to monitor ponds cultivating a variety of DISCOVR strains at the Arizona Center for Algae Technology and Innovation (AzCATI) with spectroradiometric technology to: • Predict biomass concentrations with high temporal frequency. • Optimize automated analysis methods that enabled feedback for pond automation strategies • Identify pond crash indicators from primary (pest/predator) and indirect (change in algal host) spectroscopic signals with potential for early treatment/intervention • Provide recommendations for technology deployment at scale. This report fulfills the deliverable requirement for the final bullet “provide recommendations for technology deployment at scale”.

09 BIOMASS FUELS↗

Abiotic and Biotic Damage of Microalgae Generate Different Volatile Organic Compounds (VOCs) for Early Diagnosis of Algal Cultures for Biofuel Production

Open microalgal ponds used in industrial biomass production are susceptible to a number of biotic and abiotic environmental stressors (e.g., grazers, pathogens, pH, temperature, etc.) resulting in pond crashes with high economic costs. Identification of signature chemicals to aid in rapid, non-invasive, and accurate identification of the stressors would facilitate targeted and effective treatment to save the algal crop from a catastrophic crash. Specifically, we were interested in identifying volatile organic compounds (VOCs) that can be used to as an early diagnostic for algal crop damage. Cultures of Microchloropsis gaditana were subjected to two forms of algal crop damage: (1) active grazing by the marine rotifer, Brachionus plicatilis, or (2) repeated freeze–thaw cycles. VOCs emitted above the headspace of these algal cultures were collected using fieldable solid phase microextraction (SPME) fibers. An untargeted analysis and identification of VOCs was conducted using gas chromatography-mass spectrometry (GC-MS). Diagnostic VOCs unique to each algal crop damage mechanism were identified. Active rotifer grazing of M. gaditana was characterized by the appearance of carotenoid degradation products, including β-cyclocitral and various alkenes. Freeze–thaw algae produced a different set of VOCs, including palmitoleic acid. Both rotifer grazing and freeze–thawed algae produced β-ionone as a VOC, possibly suggesting a common stress-induced cellular mechanism. Importantly, these identified VOCs were all absent from healthy algal cultures of M. gaditana. Early detection of biotic or abiotic environmental stressors will facilitate early diagnosis and application of targeted treatments to prevent algal pond crashes. Thus, our work further supports the use of VOCs for monitoring the health of algal ponds to ultimately enhance algal crop yields for production of biofuel.

09 BIOMASS FUELS↗

Data for Miscanthus giganteus Biolistic Transformation Using the Visible RUBY Red Marker Gene to Monitor Transformation Efficiency

Miscanthus × giganteus ( M × g ) is a high- yielding perennial C4 bioenergy crop, but genetic improvement by breeding is constrained by triploid sterility and clonal propagation. Improving genetic transformation methods for M × g would provide opportunities for advantageous trait introgression. Use of an easy to phenotype reporter gene is a promising strategy to improve transformation processes and efficiency. This study presents an efficient novel method for biolistic transformation of inflorescence- derived callus in M × g and demonstrates its efficacy using RUBY, a betalain-based noninvasive reporter that is visible throughout the transformation process. RUBY expression ( Zea mays codon optimized) was visible from callus stage through plantlet development into maturity. RUBY expressing independently transformed plants were confirmed by hygromycin phosphotransferase ELISA and by genomic PCR demonstrating that the RUBY phenotype is sufficient for screening transformants. The Zea mays codon optimized hygromycin selection marker was driven by previously established promoters for Miscanthus, ZmUBI and 2×35S, while the RUBY gene expression was controlled by a known Zea mays C4 promoter, Brachypodium UBI10, newly employed in Miscanthus. The construct containing the 2×35S promoter for hygromycin had a 15.1% transformation efficiency while the ZmUBI promoter had a 20.5% transformation efficiency. This study provides a novel, highly efficient protocol for successful biolistic transformation of M × g for stable expression. This study also demonstrates that RUBY expression can be used as a convenient and powerful monitor of transformation in ongoing and future work to engineer M × g into an improved bioproduct feedstock. **NOTE: in "TableS2_ProtocolComparison.csv", the data from row 665 to 971 should be removed.

Gene Editing↗

Accuracy, Bias, and Improvements in Mapping Crops and Cropland across the United States Using the USDA Cropland Data Layer

The U.S. Department of Agriculture’s (USDA) Cropland Data Layer (CDL) is a 30 m resolution crop-specific land cover map produced annually to assess crops and cropland area across the conterminous United States. Despite its prominent use and value for monitoring agricultural land use/land cover (LULC), there remains substantial uncertainty surrounding the CDLs’ performance, particularly in applications measuring LULC at national scales, within aggregated classes, or changes across years. To fill this gap, we used state- and land cover class-specific accuracy statistics from the USDA from 2008 to 2016 to comprehensively characterize the performance of the CDL across space and time. We estimated nationwide area-weighted accuracies for the CDL for specific crops as well as for the aggregated classes of cropland and non-cropland. We also derived and reported new metrics of superclass accuracy and within-domain error rates, which help to quantify and differentiate the efficacy of mapping aggregated land use classes (e.g., cropland) among constituent subclasses (i.e., specific crops). We show that aggregate classes embody drastically higher accuracies, such that the CDL correctly identifies cropland from the user’s perspective 97% of the time or greater for all years since nationwide coverage began in 2008. We also quantified the mapping biases of specific crops throughout time and used these data to generate independent bias-adjusted crop area estimates, which may complement other USDA survey- and census-based crop statistics. Our overall findings demonstrate that the CDLs provide highly accurate annual measures of crops and cropland areas, and when used appropriately, are an indispensable tool for monitoring changes to agricultural landscapes.

54 ENVIRONMENTAL SCIENCES↗

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↗

Miscanthus giganteus Biolistic Transformation Using the Visible RUBY Red Marker Gene to Monitor Transformation Efficiency

Miscanthus × giganteus ( M × g ) is a high-yielding perennial C4 bioenergy crop, but genetic improvement by breeding is constrained by triploid sterility and clonal propagation. Improving genetic transformation methods for M × g would provide opportunities for advantageous trait introgression. Use of an easy to phenotype reporter gene is a promising strategy to improve transformation processes and efficiency. This study presents an efficient novel method for biolistic transformation of inflorescence-derived callus in M × g and demonstrates its efficacy using RUBY, a betalain-based noninvasive reporter that is visible throughout the transformation process. RUBY expression ( Zea mays codon optimized) was visible from callus stage through plantlet development into maturity. RUBY expressing independently transformed plants were confirmed by hygromycin phosphotransferase ELISA and by genomic PCR demonstrating that the RUBY phenotype is sufficient for screening transformants. The Zea mays codon optimized hygromycin selection marker was driven by previously established promoters for Miscanthus, ZmUBI and 2×35S, while the RUBY gene expression was controlled by a known Zea mays C4 promoter, Brachypodium UBI10, newly employed in Miscanthus. The construct containing the 2×35S promoter for hygromycin had a 15.1% transformation efficiency while the ZmUBI promoter had a 20.5% transformation efficiency. This study provides a novel, highly efficient protocol for successful biolistic transformation of M × g for stable expression. This study also demonstrates that RUBY expression can be used as a convenient and powerful monitor of transformation in ongoing and future work to engineer M × g into an improved bioproduct feedstock.

RUBY↗

Deep Convolutional Neural Networks Exploit High-Spatial- and -Temporal-Resolution Aerial Imagery to Phenotype Key Traits in Miscanthus

Miscanthus is one of the most promising perennial crops for bioenergy production, with high yield potential and a low environmental footprint. The increasing interest in this crop requires accelerated selection and the development of new screening techniques. New analytical methods that are more accurate and less labor-intensive are needed to better characterize the effects of genetics and the environment on key traits under field conditions. We used persistent multispectral and photogrammetric UAV time-series imagery collected 10 times over the season, together with ground-truth data for thousands of Miscanthus genotypes, to determine the flowering time, culm length, and biomass yield traits. We compared the performance of convolutional neural network (CNN) architectures that used image data from single dates (2D-spatial) versus the integration of multiple dates by 3D-spatiotemporal architectures. The ability of UAV-based remote sensing to rapidly and non-destructively assess large-scale genetic variation in flowering time, height, and biomass production was improved through the use of 3D-spatiotemporal CNN architectures versus 2D-spatial CNN architectures. The performance gains of the best 3D-spatiotemporal analyses compared to the best 2D-spatial architectures manifested in up to 23% improvements in R2, 17% reductions in RMSE, and 20% reductions in MAE. The integration of photogrammetric and spectral features with 3D architectures was crucial to the improved assessment of all traits. In conclusion, our findings demonstrate that the integration of high-spatiotemporal-resolution UAV imagery with 3D-CNNs enables more accurate monitoring of the dynamics of key phenological and yield-related crop traits. This is especially valuable in highly productive, perennial grass crops such as Miscanthus, where in-field phenotyping is especially challenging and traditionally limits the rate of crop improvement through breeding.

47 OTHER INSTRUMENTATION↗

Marine Renewable Energy Applications for Restorative Ocean Farming: Kelp

Kelp farming and kelp forest restoration have both been proposed as a solution to locally decrease the impacts of ocean acidification and eutrophication, often with co-benefits to other forms of aquaculture and mariculture. Compared to global markets, the kelp industry in the United States is still in its early phases, with the first commercial kelp farm founded in Casco Bay, Maine in 2010. Since then, interest and effort in kelp production has been increasing, with farms now present in Maine, New Hampshire, Connecticut, Rhode Island, Massachusetts, New York, Washington, and Alaska. Many research projects are underway in the United States to explore benefits of 3D ocean farming, tackle logistical problems of working in the ocean, autonomous farming, and explore viable end uses for kelp products. In seaweed farming, to remove the stored carbon or excess nutrients from the system, the biomass needs to be harvested at the optimal time to avoid the release of CO 2 that comes with decomposition. Timing of the harvest is also important for maximum crop yield, which can vary based on the final product. Additional monitoring needs can include a variety of water quality metrics, growth measurements, and visuals to ensure the health of the farm, comply with permits, support operations and maintenance functions. The variables measured may vary by desired end use of the product, location of farm, and operational design. Monitoring all of these parameters requires specialized devices that can be costly and challenging to maintain. Monitoring devices often face power and logistical constraints that could prevent kelp farmers from adopting these technologies or receiving accurate, efficient monitoring to assess ecosystem benefits and valuation. Marine energy has been identified as a possible power source for these devices. This project investigates the power needs for conducting kelp farm environmental monitoring compared with the available marine energy resource to evaluate if locally generated ocean energy could provide a solution to these monitoring challenges and benefit kelp farmers. This process was structured as follows: 1. Define what data is needed for farmers and their communities through desk research and interviews with end users. 2. Identify sensors and power requirements currently in use or available for commercial purchase. 3. Analyze current kelp and other mariculture farm locations for the potential marine energy resource. 4. Analyze farm designs and associated structures to make recommendations for marine energy design. 5. Quantify value that investment in sensors could provide in terms of carbon credit possibilities.

09 BIOMASS FUELS↗

Ecovoltaic solar energy development can promote grassland bird communities

Ecologically informed photovoltaic (PV) developments that co-prioritize PV electricity generation with ecosystem function (‘ecovoltaics’) have emerged as a promising land sharing strategy to minimize ecological conflicts associated with PV solar energy development. While habitat-focused ecovoltaic designs can conceptually benefit biodiversity by offsetting or enhancing impacts of PV development, foundational field research is needed to examine how wildlife respond to these novel ecosystems. We conducted passive acoustic monitoring (PAM) in 2023 and 2024 at 13 solar facilities and paired control sites to investigate avian community responses to ecovoltaic facilities in the Midwestern United States. Compared to control sites (row crop agricultural fields), we found that ecovoltaic sites supported more grassland bird species throughout a 17-week monitoring period between May and September. Grassland bird communities on ecovoltaic sites were also more stable than on agricultural controls, as measured by the Jaccard dissimilarity index. We also used PAM-based weekly species occurrences in an occupancy-modelling framework to investigate the influence of PV development and other landscape variables on grassland bird occupancy. 10 out of 13 modelled grassland bird species had greater predicted occupancy probabilities (ψ) on PV sites than control sites. Synthesis and applications. Our findings suggest that properly sited and developed ecovoltaic solar facilities in human altered landscapes can improve habitat for birds and other wildlife, but further research is needed to understand which species may benefit most from these novel ecosystems.

14 SOLAR ENERGY↗

Grazer-induced changes in molecular signatures of cyanobacteria

Algal biomass production is an emerging renewable source of fuels, nutrients, manufacturing materials, and pharmaceuticals. Industrial-scale production is predominantly performed in open raceway ponds that are inexpensive to build, operate, and maintain compared to closed bioreactors. However, these open pond systems suffer from increased opportunities for biological contamination from predators, pathogens, and competitors, which result in reduced biomass quality and yields and often the complete destruction of the crop over a short period of time. Early detection of contaminants is a necessary step of integrated pest management for triggering and informing interventions to prevent crop losses. To develop a sensitive method of detection utilizing mass spectrometry (MS), we used three methods – imaging mass spectrometry (imaging MS), liquid chromatography MS/MS (LC-MS/MS) combined with molecular networking, and gas chromatography MS/MS (GC–MS/MS) – to observe and identify molecular signatures from a model predator-prey system of the heterolobosean amoeba HGG1 preying on the filamentous cyanobacterium Anabaena sp. PCC 7120. Imaging MS enabled the association of molecules with the crop, the predator, or the activity of protozoan grazing, while LC-MS/MS-based molecular networking identified a subset of the grazing-specific signals as the chlorophyll breakdown products pyropheophytin, pheophorbide A, and pyropheophorbide. Application of MS techniques to other amoebacyanobacterial predator-prey pairs allowed categorization of grazing signatures as universal or specific to the species of prey, predator, or the prey-predator pairing, indicating that MS-based techniques can distinguish crops from competitors and potentially identify predators. Finally, GCMS/MS was shown to be capable of monitoring novel volatile organic compounds (VOCs), including those predicted to be released through chlorophyll breakdown, in the headspace over algal cultures under predation. Furthermore, these results demonstrate that the combination of multiple MS technologies creates a predictive framework to identify and catalog relevant molecular signatures for informing crop protection strategies.

09 BIOMASS FUELS↗

Predicting Short-Term Deformation in the Central Valley Using Machine Learning

Land subsidence caused by excessive groundwater pumping in Central Valley, California, is a major issue that has several negative impacts such as reduced aquifer storage and damaged infrastructures which, in turn, produce an economic loss due to the high reliance on crop production. This is why it is of utmost importance to routinely monitor and assess the surface deformation occurring. Two main goals that this paper attempts to accomplish are deformation characterization and deformation prediction. The first goal is realized through the use of Principal Component Analysis (PCA) applied to a series of Interferomtric Synthetic Aperture Radar (InSAR) images that produces eigenimages displaying the key characteristics of the subsidence. Water storage changes are also directly analyzed by the use of data from the Gravity Recovery and Climate Experiment (GRACE) twin satellites and the Global Land Data Assimilation System (GLDAS). The second goal is accomplished by building a Long Short-Term Memory (LSTM) model to predict short-term deformation after developing an InSAR time series using LiCSBAS, an open-source InSAR time series package. The model is applied to the city of Madera and produces better results than a baseline averaging model and a one dimensional convolutional neural network (CNN) based on a mean squared error metric showing the effectiveness of machine learning in deformation prediction as well as the potential for incorporation in hazard mitigation models. The model results can directly aid policy makers in determining the appropriate rate of groundwater withdrawal while maintaining the safety and well-being of the population as well as the aquifers’ integrity.

58 GEOSCIENCES↗

Agricultural Management Affects the Active Rhizosphere Bacterial Community Composition and Nitrification

Cropping system diversity provides yield benefits that may result from shifts in the composition of root-associated bacterial and fungal communities, which either enhance nutrient availability or limit nutrient loss. We investigated whether temporal diversity of annual cropping systems (four versus two crops in rotation) influences the composition and metabolic activities of root-associated microbial communities in maize at a developmental stage when the peak rate of nitrogen uptake occurs. We monitored total (DNA-based) and potentially active (RNA-based) bacterial communities and total (DNA-based) fungal communities in the soil, rhizosphere, and endosphere. Cropping system diversity strongly influenced the composition of the soil microbial communities, which influenced the recruitment of the resident microbial communities and, in particular, the potentially active rhizosphere and endosphere bacterial communities. The diversified cropping system rhizosphere recruited a more diverse bacterial community (species richness), even though there was little difference in soil species richness between the two cropping systems. In contrast, fungal species richness was greater in the conventional rhizosphere, which was enriched in fungal pathogens; the diversified rhizosphere, however, was enriched in Glomeromycetes. While cropping system influenced endosphere community composition, greater correspondence between DNA- and RNA-based profiles suggests a higher representation of active bacterial populations. Cropping system diversity influenced the composition of ammonia oxidizers, which coincided with diminished potential nitrification activity and gross nitrate production rates, particularly in the rhizosphere. The results of our study suggest that diversified cropping systems shift the composition of the rhizosphere’s active bacterial and total fungal communities, resulting in tighter coupling between plants and microbial processes that influence nitrogen acquisition and retention.

60 APPLIED LIFE SCIENCES↗

Feedstock Carbon Intensity Calculator (FD-CIC): Users’ Manual and Technical Documentation

The carbon intensities (CIs) of biofuels are determined with the life cycle analysis (LCA) technique, which accounts for the energy/material uses and emissions during the complete supply chain of biofuel including feedstock production and fuel conversion stages. Regulatory agencies such as California Air Resources Board (CARB) adopts LCA to calculate biofuel CIs. The Low Carbon Fuel Standard (LCFS) program developed by CARB allows individual biofuel conversion facilities to submit their own biofuel CIs with their facility input data and incentivizes the reduction in the CI specific to that particular facility compared to a reference fuel’s CI (Liu et al 2020). Such an incentive program has driven innovations in biorefineries to reduce their greenhouse gas (GHG) emissions by linking their revenue directly to its CI score through LCFS credit trading. Besides the biofuel conversion stage, different farming practices for feedstock growth can result in significant CI variations for feedstocks, thus for biofuels. To provide evidence-based research findings, the U.S. Department of Energy’s Advanced Research Projects Agency–Energy (ARPA-E) has supported the Systems Assessment Center of the Energy Systems and Infrastructure Analysis Division at Argonne National Laboratory to examine CI variations of different farming practices to grow agricultural crops for biofuel production. Meanwhile, the ARPA-E has launched the Systems for Monitoring and Analytics for Renewable Transportation Fuels from Agricultural Resources and Management (SMARTFARM) program to develop technologies and data platforms that enable an accurate measurement of key farming parameters that can help robust accounting of the GHG benefits of sustainable, low-carbon agronomic practices at farm level.

54 ENVIRONMENTAL SCIENCES↗

Assessing Nutrient and Carbon Responses to Agricultural Conservation Practices in Two Midwest Watersheds

The United States is undertaking efforts to transition to a low-carbon economy in response to the heightened impacts of climate change, which are largely attributed to decades of carbon-intensive development. A concerted effort by the energy sector to achieve net-zero carbon emissions is aimed at strategically reducing the carbon footprint of the energy supply chain, particularly in the production of feedstocks for biofuels. The production of biofuels relies heavily on land use and management practices in biomass cultivation. Among other factors, soil organic carbon (SOC) plays a crucial role in the biofuel carbon cycle, impacting land productivity, greenhouse gas emissions, and water quality. The process of carbon drawdown during plant growth and storage helps to mitigate the release of carbon dioxide (CO 2 ) into the atmosphere. Another key parameter is the release of nitrous oxide (N 2 O) — a potent greenhouse gas with a global warming potential 273 times that of CO 2 — from soil. While prioritizing low-carbon production, sustainable bioenergy also necessitates improved water quality and ecosystem services. Agricultural conservation practices can contribute to enhanced soil health and reduce nutrient and sediment loss into streams. However, studies that explore the broader impact of these practices on soil carbon storage and N 2 O emissions at a watershed scale are limited. Specifically, our understanding of how low-carbon feedstock production and management affect nutrient cycle dynamics is incomplete. This study assesses watershed responses to land management practices in two agriculturally dominant watersheds: the Raccoon River watershed and the Southfork of Iowa River watershed. The study focuses on carbon and nutrient dynamics, characterizing spatial and temporal variations in SOC, N 2 O, and nutrient loadings to examine the relationship between nutrient and carbon responses and agricultural conservation practices. The study employs the newly developed Soil Water Analysis Tool for Carbon (SWAT-C) model, calibrated using 20 years’ of climate and water monitoring data, to simulate and evaluate two agricultural conservation practices: no-till and crop residue harvest with cover crop planting. We compared the calibrated SWAT-C model with a historical baseline model, which allowed us to analyze various aspects of the watershed, including stream flow, suspended sediments, nitrogen, phosphorus, organic carbon, SOC at different depths, and N 2 O emissions from topsoil. Our SWAT-C modeling results indicate that, compared with results from the historical baseline model, no-till practices are positively correlated with SOC accumulation, reduced N 2 O emissions, and decreased soil loss. We also observed no change or slightly increased nitrogen and phosphorus loss to water bodies in the watersheds compared with the baseline. Conversely, crop residue harvest with cover crop planting improved water quality by reducing nutrient and soil losses but also increased N 2 O emissions. This SWAT-C modeling study establishes the groundwork for further smaller-scale and/or sub-basin-level assessments of nitrogen, phosphorus, and carbon cycles. It provides valuable science-based insights to inform policy decisions — particularly in the context of transitioning to biofuel feedstock production in these watersheds — by addressing concerns about nutrient exports to local water bodies and, ultimately, the Mississippi River.

54 ENVIRONMENTAL SCIENCES↗

Utility of near‐surface phenology in estimating productivity and evapotranspiration across diverse ecosystems

Abstract Agroecosystems, which include row crops, pasture, and grass and shrub grazing lands, are sensitive to changes in management, weather, and genetics. To better understand how these systems are responding to changes, we need to improve monitoring and modeling carbon and water dynamics. Vegetation Indices (VIs) are commonly used to estimate gross primary productivity (GPP) and evapotranspiration (ET), but these empirical relationships are often location and crop specific. There is a need to evaluate if VIs can be effective and, more general, predictors of ecosystem processes through time and across different agroecosystems. Near‐surface photographic (red‐green‐blue) images from PhenoCam can be used to calculate the VI green chromatic coordinate (G CC ) and offer a pathway to improve understanding of field‐scale relationships between VIs and GPP and ET. We synthesized observations spanning 76 site‐years across 15 agroecosystem sites with PhenoCam G CC and GPP or ET estimates from eddy covariance (EC) to quantify interannual variability (IAV) in the relationship between GPP and ET and G CC across. We uncovered a high degree of variability in the strength and slopes of the G CC ∼ GPP and ET relationships (R 2 = 0.1 ‐ 0.9) within and across production systems. Overall, G CC is a better predictor of GPP than ET (R 2 = 0.64 and 0.54, respectively), performing best in croplands (R 2 = 0.91). Shrub‐dominated systems exhibit the lowest predictive power of G CC for GPP and ET but have less IAV in slope. We propose that PhenoCam estimates of G CC could provide an alternative approach for predictions of ecosystem processes.

Environmental Sciences & Ecology↗

Vehicle Tracking with Crop-based Detection

End-to-end production of vehicle tracking data from video in real-time and with high accuracy remains a challenging problem due to the computational cost of object detection on each frame. In this work we present Tracking with Crop-based Detection, a method for speeding object tracking in constrained contexts (with stable cameras and relatively-predictable object motion) such as vehicle traffic monitoring. We leverage this context to provide a strong prior for object locations, which we use to 1.) boost detection speed by detecting objects only in regions corresponding to object priors on most frames and 2.) inform the selection of the detector output for each object. We evaluate Crop-based Detection as an extension to the KIOU object tracker (Crop-KIOU) on the UA-DETRAC dataset. The proposed tracker outperforms all other reported algorithms in terms of PR-MOTA, PR-MOTP, and mostly tracked objects on the UA-DETRAC benchmark, establishing a new state-of-the-art. Relative to tracking by detection with KIOU, Crop-KIOU achieves a 26% higher frame-rate and increases accuracy. Furthermore, Tracking with Crop-based Detection can be combined with frame skipping; we show a 149% increase in framerate relative to KIOU with no decrease in accuracy using this combination of methods.

Gloudemans, Derek↗

Subfield crop yields and temporal stability in thousands of US Midwest fields

Understanding subfield crop yields and temporal stability is critical to better manage crops. Several algorithms have proposed to study within-field temporal variability but they were mostly limited to few fields. In this study, a large dataset composed of 5520 yield maps from 768 fields provided by farmers was used to investigate the influence of subfield yield distribution skewness on temporal variability. The data are used to test two intuitive algorithms for mapping stability: one based on standard deviation and the second based on pixel ranking and percentiles. The analysis of yield monitor data indicates that yield distribution is asymmetric, and it tends to be negatively skewed (p < 0.05) for all of the four crops analyzed, meaning that low yielding areas are lower in frequency but cover a larger range of low values. The mean yield difference between the pixels classified as high-and-stable and the pixels classified as low-and-stable was 1.04 Mg ha –1 for maize, 0.39 Mg ha –1 for cotton, 0.34 Mg ha –1 for soybean, and 0.59 Mg ha —1 for wheat. The yield of the unstable zones was similar to the pixels classified as low-and-stable by the standard deviation algorithm, whereas the two-way outlier algorithm did not exhibit this bias. Furthermore, the increase in the number years of yield maps available induced a modest but significant increase in the certainty of stability classifications, and the proportion of unstable pixels increased with the precipitation heterogeneity between the years comprising the yield maps.

59 BASIC BIOLOGICAL SCIENCES↗

Development of a field-deployable qPCR assay for real-time pest monitoring in algal cultivation systems

Outdoor cultivation is commonly used to produce algal biomass for a variety of bioproducts including food, feed, fuel, pharmaceuticals, and nutraceuticals. Outdoor cultivation ponds are highly susceptible to pest pressures that may lead to periods of low productivity or even entire loss of the algal crop. Consequently, there is a need for rapid, real-time tracking of pests for early intervention to mitigate crop loss. In this work, we describe the development of a field deployable, low-cost qPCR assay for detecting both known and novel pests of a farmed eukaryotic alga species, Nannochloropsis sp. We performed a proximity guided metagenome deconvolution approach (ProxiMeta™) to discover novel pests that temporally correspond to periods of reduced pond productivity. This approach provided high-quality metagenome assemblies that were used to design qPCR probes to detect specific pests of interest. The portable qPCR assay, designed to be deployed at remote field locations, enables low-cost surveillance with a rapid (2 h) turn-around time. Frequent sampling allows for early detection and prompts intervention strategies to remedy infected ponds to minimize crop loss. The qPCR assay was used to successfully detect a known predatory bacterium within the order Bdellovibrionales both in the lab and at a remote field location. Furthermore, we assembled the genome of two novel, site-specific pests in the Saprospiraceae family and successfully designed qPCR probes that differentially detected their presence in two different pond locations. Ultimately, this assay has the potential to monitor multiple pests simultaneously and tailor targets to match likely pest infections that differ across geographical locations, helping to mitigate crop loss on a large scale.

59 BASIC BIOLOGICAL SCIENCES↗