Open Access Publications

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Open access publications by faculty, postdocs, and graduate students in the Department of Plant and Soil Sciences.

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A suite of agronomic factors can offset the effects of climate variability on rainfed maize production in Kenya
(Scientific Reports, 2022-10-03) Oluoch, Kevin Ong'are; De Groote, Hugo; Gitonga, Zachary M.; Jin, Zhenong; Davis, Kyle Frankel
Achieving food security in sub-Saharan Africa (SSA) is a multidimensional challenge. SSA reliance on food imports is expected to grow in the coming decades to meet the population's demand, projected to double to over 2 billion people by 2050. In addition, climate change is already affecting food production and supply chains across the region. Addressing these multiple food security challenges will necessitate rapid enhancements in agricultural productivity, which is influenced by a host of demographic, agronomic, and climatic factors. We use statistical approaches to examine rainfed maize in Kenya, where maize cultivation and consumption are widespread and central to livelihoods and national food security. We find that improving a suite of agronomic factors, such as applying fertilizer, planting certified seeds, and extension services, will have a greater effect on rainfed maize productivity than demographics and can offset the effects of climate change. These findings could also offer insights into similar challenges for other crops in Kenya and other SSA countries.
Aggregation-induced emission of 5-(benzylidene)pyrimidine-2,4,6-triones
(Bulletin of the University of Karaganda – Chemistry, 2022-03-30) Mendigalieva, S. S.; Birimzhanova, D. A.; Irgibaeva, I. S.; Barashkov, N. N.; Sakhno, Y. E.
5-(Benzylidene)pyrimidine-2,4,6-triones with different substituents on the phenyl rings: 5-(4’-dimethylaminobenzylidene) barbituric acid and 5-(4’-methoxybenzylidene) barbituric acid were synthesized, and their spectral-luminescent properties were investigated. A decreasing fluorescence efficiency in the solid-state is general and is mainly attributed to the intermolecular vibronic interactions, which induce the nonradiative deactivation process. Whereas the isolated dye molecules are virtually non-luminescent in dilute solutions, they become highly emissive upon solution thickening or aggregation in poor solvents or in the solid-state, show an increase of luminescence intensity, the phenomenon of the aggregation-induced emission (AIE phenomenon). The development of efficient luminescent materials is a topic of great current interest. The emission color is changed from red (maximum at 630 nm) to green (maximum at 540 nm) by varying the substituent on the phenyl ring from dimethylamino to the methoxy group. Theoretical calculation shows that the dye molecules' aggregation-induced emission characteristics result from intermolecular interactions. Utilizing such features, the molecules can be employed as fluorescent probes for the detection of the ethanol content in aqueous solutions.
Backed-Up, Saturated, and Stagnant: Effect of Milldams on Upstream Riparian Groundwater Hydrologic and Mixing Regimes
(Water Resources Research, 2022-09-28) Sherman, Melissa; Hripto, Johanna; Peck, Erin K.; Gold, Arthur J.; Peipoch, Marc; Imhoff, Paul; Inamdar, Shreeram
How milldams alter riparian hydrologic and groundwater mixing regimes is not well understood. Understanding the effects of milldams and their legacies on riparian hydrology is key to assessing riparian pollution buffering potential and for making appropriate watershed management decisions. We examined the spatiotemporal effects of milldams on groundwater gradients, flow directions, and mixing regime for two dammed sites on Chiques Creek, Pennsylvania (2.4 m tall milldam), and Christina River, Delaware (4 m tall dam), USA. Riparian groundwater levels were recorded every 30 min for multiple wells and transects. Groundwater mixing regime was characterized using 30-min specific conductance data and selected chemical tracers measured monthly for about 2 years. Three distinct regimes were identified for riparian groundwaters—wet, dry, and storm. Riparian groundwater gradients above the dam were low but were typically from the riparian zone to the stream. These flow directions were reversed (stream to riparian) during dry periods due to riparian evapotranspiration losses and during peak stream flows. Longitudinal (parallel to the stream) riparian flow gradients and directions also varied across the hydrologic regimes. Groundwater mixing varied spatially and temporally between storms and seasons. Near-stream groundwater was poorly flushed or mixed during storms whereas that in the adjacent swales revealed greater mixing. This differential groundwater behavior was attributed to milldam legacies that include: berm and swale topography that influenced the routing of surface waters, varying riparian legacy sediment depths and hydraulic conductivities, evapotranspiration losses from riparian vegetation, and runoff input from adjoining roads. Key Points: - Milldams raise riparian groundwater levels, decrease hydraulic gradients, and cause reversals in groundwater flow - Milldam legacies contribute to reduced groundwater mixing in near-stream sediments - Altered groundwater regimes due to milldams could affect riparian water quality processes Plain Language Summary: Riparian zones can buffer streams from upland nitrogen pollution and are thus considered as important water quality management practices. How the presence of milldams affects groundwater flow paths and their buffering capacity is not known. This study showed that milldams back up stream water above dams, reduce the groundwater gradients from the upland to the stream, and also result in their reversal during summer dry conditions and floods. Milldams reduced the mixing of groundwaters for near-stream sediments. This response was attributed to the topographic and sediment conditions associated with the milldams.
Building Trust in Earth Science Findings through Data Traceability and Results Explainability
(IEEE Transactions on Parallel and Distributed Systems, 2022-11-08) Olaya, Paula; Kennedy, Dominic; Llamas, Ricardo; Valera, Leobardo; Vargas, Rodrigo; Lofstead, Jay; Taufer, Michela
To trust findings in computational science, scientists need workflows that trace the data provenance and support results explainability. As workflows become more complex, tracing data provenance and explaining results become harder to achieve. In this paper, we propose a computational environment that automatically creates a workflow execution's record trail and invisibly attaches it to the workflow's output, enabling data traceability and results explainability. Our solution transforms existing container technology, includes tools for automatically annotating provenance metadata, and allows effective movement of data and metadata across the workflow execution. We demonstrate the capabilities of our environment with the study of SOMOSPIE, an earth science workflow. Through a suite of machine learning modeling techniques, this workflow predicts soil moisture values from the 27 km resolution satellite data down to higher resolutions necessary for policy making and precision agriculture. By running the workflow in our environment, we can identify the causes of different accuracy measurements for predicted soil moisture values in different resolutions of the input data and link different results to different machine learning methods used during the soil moisture downscaling, all without requiring scientists to know aspects of workflow design and implementation.
Cereal rye seeding rate does not affect magnitude of weed suppression when planting green within Mid-Atlantic United States
(Weed Technology, 2022-12-12) Ficks, Teala S.; VanGessel, Mark J.; Wallace, John M.
In the Mid-Atlantic United States, there is increasing interest in delaying cereal rye termination until after soybean planting (i.e., planting green). Improved understanding of cereal rye seeding rate effects is needed to balance weed and agronomic management goals. We investigated the effects of cereal rye seeding rates on weed control and crop performance when planting green in complementary experiments in two Mid-Atlantic regions. The Pennsylvania experiment was replicated at three site-years and the Delaware experiment at two site-years. In both experiments, population-level weed responses were evaluated across four cereal rye seeding rates: 0, 51, 101, and 135 kg ha−1. The Delaware experiment also implemented a nitrogen treatment factor (0 and 34 kg N ha−1; spring applied). Both experiments showed that integrating cereal rye in the fall significantly improved winter- and summer-annual weed suppression compared with the fallow control, but no differences in total cereal rye biomass production or weed suppression were found among alternative cereal rye seeding rates (51 to 135 kg ha−1). Soybean yield did not differ among treatments in any of the studies. These results show there is no reason to increase cereal rye seeding rates for weed suppression services or to decrease seeding rates for agronomic reasons (i.e., soybean population and yield) when employing planting-green tactics in no-till soybean production within the Mid-Atlantic region of the United States.
Characterization of integration sites and transfer DNA structures in Agrobacterium-mediated transgenic events of maize inbred B104
(G3: Genes | Genomes | Genetics, 2023-07-31) Neelakandan, Anjanasree K.; Kabahuma, Mercy; Yang, Qin; Lopez, Miriam; Wisser, Randall J.; Balint-Kurti, Peter; Lauter, Nick
In maize, the community-standard transformant line B104 is a useful model for dissecting features of transfer DNA (T-DNA) integration due to its compatibility with Agrobacterium-mediated transformation and the availability of its genome sequence. Knowledge of transgene integration sites permits the analysis of the genomic environment that governs the strength of gene expression and phenotypic effects due to the disruption of an endogenous gene or regulatory element. In this study, we optimized a fusion primer and nested integrated PCR (FPNI-PCR) technique for T-DNA detection in maize to characterize the integration sites of 89 T-DNA insertions in 81 transformant lines. T-DNA insertions preferentially occurred in gene-rich regions and regions distant from centromeres. Integration junctions with and without microhomologous sequences as well as junctions with de novo sequences were detected. Sequence analysis of integration junctions indicated that T-DNA was incorporated via the error-prone repair pathways of nonhomologous (predominantly) and microhomology-mediated (minor) end-joining. This report provides a quantitative assessment of Agrobacterium-mediated T-DNA integration in maize with respect to insertion site features, the genomic distribution of T-DNA incorporation, and the mechanisms of integration. It also demonstrates the utility of the FPNI-PCR technique, which can be adapted to any species of interest.
Crop harvests for direct food use insufficient to meet the UN’s food security goal
(Nature Food, 2022-05-12) Ray, Deepak K.; Sloat, Lindsey L.; Garcia, Andrea S.; Davis, Kyle F.; Ali, Tariq; Xie, Wei
Rising competition for crop usage presents policy challenges exacerbated by poor understanding of where crops are harvested for various uses. Here we create high-resolution global maps showing where crops are harvested for seven broad use categories—food, feed, processing, export, industrial, seed and losses. Yields for food crops are low relative to other crop-use categories. It is unlikely, given current trends, that the minimum calorie requirement to eliminate projected food undernourishment by 2030 will be met through crops harvested for direct food consumption, although enough calories will be harvested across all usages. Sub-Saharan African nations will probably fall short of feeding their increased population and eliminating undernourishment in 2030, even if all harvested calories are used directly as food.
Culturally appropriate shifts in staple grain consumption can improve multiple sustainability outcomes
(Environmental Research Letters, 2021-11-24) Wei, Dongyang; Davis, Kyle Frankel
Diets exercise great influence over both human and environmental health. While numerous efforts have sought to define and identify sustainable diets, there remains a poor understanding of the extent to which such shifts are feasible when taking into account local dietary preferences. Accounting for 40% of dietary calories and 46% of global cropland, cereals offer an important food group by which culturally appropriate dietary shifts may achieve large sustainability benefits. Here we combine country-specific information on dietary cereal supply with nutrient content values, CO2 nutrient penalties, and environmental footprints to quantify the outcomes of adopting two feasible dietary shifts—maximizing the share of C4 cereals (e.g. maize, millet, sorghum) based on historical shares and increasing the share of whole grains. Our results show that increasing the share of whole grains can increase nutrient supply (+7% protein, +37% iron, +42% zinc) and overcome the nutrient-depleting effects of elevated CO2 (eCO2) and that maximizing the share of C4 cereals can substantially reduce environmental burden (−12% greenhouse gas emissions, −11% blue water demand), particularly in Africa and the Middle East. We also find that a combination of the two strategies would likely produce strong co-benefits between increased nutrient supply and reduced environmental impacts with mixed outcomes for offsetting the effects of eCO2. Such simultaneous improvements are particularly important for food insecure regions such as West Africa and Southeast Asia. These findings demonstrate important opportunities to identify sustainable diets that incorporate local preferences and cultural acceptability. Such considerations are essential when developing demand-side solutions to achieve more sustainable food systems.
Day-extension Blue Light Inhibits Flowering of Chrysanthemum When the Short Main Photoperiod Includes Far-red Light
(Journal of the American Society for Horticultural Science, 2023-03-16) Kohler, Annika E.; Birtell, Eva M.; Runkle, Erik S.; Meng, Qingwu
Chrysanthemum (Chrysanthemum ×morifolium) is a common ornamental crop with a qualitative short-day flowering response. Extending a short day with moderate blue [B (400–500 nm)] light inhibits flowering in greenhouse conditions with sunlight but does not indoors (without sunlight) under B + red [R (600–700 nm)] light or white light. We postulated that the contrasting responses to B light as a day extension depended on far-red [FR (700–800 nm)] light during the day, which is plentiful under sunlight but lacking indoors under B+R or white light-emitting diodes. To study this response in three chrysanthemum cultivars, we delivered indoor lighting treatments at two locations with an 11-hour main photoperiod of B, green [G (500–600 nm)], R, and FR light, where subscript values indicate the photon flux density (in µmol·m−2·s−1) of each waveband: B60R120, B60G60R60, and B60R60FR60. After each short main photoperiod, plants received 0 or 4 hours of day-extension lighting of 60 µmol·m−2·s−1 of B light (B60). Under all treatments except B60R60FR60 with day-extension B60, it took ‘Chelsey Pink’, ‘Gigi Gold’, and ‘Gigi Yellow’ 13 to 17 days to reach the first visible inflorescence and 42 to 51 days to the first open flower. In contrast, plants grown under B60R60FR60 with day-extension B60 took 41 to 67 days to reach the first visible inflorescence with few plants developing open flowers. Plants were tallest at the first open flower and after 9 weeks of treatments when grown under B60R60FR60 with day-extension B60. These results indicate that the inclusion of FR light, but not G light, in the main photoperiod is necessary for day-extension B light to inhibit flowering in chrysanthemum. On the basis of these results and those of other studies, we postulate that the spectral dependence of flowering in chrysanthemum depends on whether and how the phytochrome photoequilibrium changes during the day. In particular, a sufficiently high daytime phytochrome photoequilibrium (e.g., under B+R and B+G+R light) could establish a predominant mode of floral signaling that prevents perception of subsequent B light as a long day.
Distribution of urban green spaces: Comparative analysis between cities in different countries
(Ornamental Horticulture, 2020-11-04) Garcia, Cecília Souza Gontijo; Paiva, Patrícia Duarte de Oliveira; Bruck, Jules; Sousa, Rafael de Brito
The presence of urban green spaces (UGS) increases the human’s contact with nature and provides numerous benefits to the society and the local environment. In this way, analyzing, planning and stimulating the implementation of UGS in cities is a fundamental action to improve the life quality of urban society. In this context, the aim was to analyze the situation and distribution of the green spaces of the universities cities of Lavras, Minas Gerais State (Brazil) and Newark, Delaware (USA). For data collection, researches performed field visits and used aerial photography to survey and analysis before calculating indicators including green area index (GAI) and green space ratio (GSR). The city of Lavras has a GAI of 0.54 m2 inh-1. The GSR value was 0.29%, not meeting the minimum of 5% required by local municipal law. Furthermore, there is a bad distribution of UGSs in the urban framework. However, in Newark, the distribution of UGSs is homogeneous and covers all regions of the city. The calculated GAI was 50.2 m² inh-1 and the GSR has met the 7% minimum required by its Newark Municipal Law. When comparing the two cities, in different countries and conditions it is concluded that Newark (DE) presents UGS indicators, GAI (m² inh-1) and GSR (%), higher than the values obtained in Lavras (MG), indicating the need for Government actions to increase these values. Resumo As áreas verdes públicas urbanas (AVPs) concebem um importante tema, pois sua presença nas cidades, ampliando o contato do homem com a natureza, além dos efeitos ambientais geram inúmeros benefícios. Dessa maneira, analisar, planejar e estimular a implantação das AVPs nas cidades é ação fundamental para a melhoria da qualidade de vida da sociedade urbana. Nesse contexto objetivou-se analisar a situação e distribuição das áreas verdes das cidades universitárias de Lavras, estado de Minas Gerais, Brasil e Newark, estado de Delaware, EUA. Para a coleta de dados foram realizadas visitas a campo e o levantamento de áreas das AVPs por meio da análise de imagens de satélite utilizando o software ArcGIS e calculados os indicadores, índice de áreas verdes (IAV) e percentual de áreas verdes (PAV). A cidade de Lavras possui um IAV de 0,54m² hab-1. O valor de PAV foi de 0,29%, não cumprindo o mínimo de 5% exigido pela lei municipal local. Além disto, existe uma má distribuição das AVPs na malha urbana. Já em Newark, a distribuição das AVPs é homogênea abrangendo todas as regiões da cidade. O IAV calculado foi de 50,2m² hab-1 e o PAV cumpriu o mínimo de 7% exigido pela sua Lei municipal de Newark. Ao comparar as duas cidades, conclui-se que Newark (DE) apresenta indicadores sobre as áreas verdes públicas, IAV (m² hab-1) e PAV (%) superiores em comparação aos valores obtidos em Lavras (MG), indicando a necessidade de ações governamentais para ampliar esses valores.
Downscaling satellite soil moisture for landscape applications: A case study in Delaware, USA
(Journal of Hydrology: Regional Studies, 2021-10-15) Warner, Daniel L.; Guevara, Mario; Callahan, John; Vargas, Rodrigo
Study region: Delaware, USA and its surrounding watersheds. Study focus: An ensemble using multiple Kernel K-nearest neighbors (KKNN) models was trained to predict daily grids of SSM at 100-meter resolution based on SSM estimates from the European Space Agency’s Climate Change Initiative Soil Moisture Product, terrain data, soil maps, and local meteorological network data. Estimated SSM was evaluated against independent in situ SSM observations and were investigated for relationships with land cover class and vegetation phenology (i.e., NDVI). New hydrological insights for the region Downscaled daily mean SSM estimates had lower error in space (27%) and greater predictive performance over time compared to the raw, coarse resolution remotely sensed SSM dataset when calibrated to field observed values. Downscaled SSM identified stronger and more widespread temporal relationships with NDVI than other estimation methods. However, both coarse and fine resolution datasets greatly underestimated SSM in wetland areas. The findings highlight the need for enhanced in situ SSM monitoring across diverse settings to improve landscape-level downscaled SSM. The downscaling methodology developed in this study was able to produce daily SSM estimates, providing a framework that can support future SSM modeling efforts, hydroecological investigations, and agricultural studies in this and other regions around the world when used in conjunction with ground-based monitoring networks.
Effect of core cultivation, fertility, and plant growth regulators on recovery of voided creeping bentgrass greens canopies following annual bluegrass control via methiozolin
(Weed Technology, 2023-04-13) Venner, Katelyn A.; Ervin, Erik; Koo, Suk-Jin; Peppers, John M.; Askew, Shawn D.
Methiozolin is commonly used for the safe and selective removal of annual bluegrass from creeping bentgrass golf greens. Studies were conducted in 2013 and 2014 with the objective of assessing fertility programs consisting of synthetic fertilizers and biostimulants, with and without the plant growth regulator trinexapac-ethyl, to aid putting green canopy recovery following annual bluegrass removal via methiozolin. Additional studies were conducted to compare recovery of creeping bentgrass following an aggressive core aerification event with fertility programs with and without methiozolin. In all cases, the addition of 7 kg ha−1 of N-P-K from fertilizer or biostimulant biweekly to greens increased turfgrass recovery time by 1 to 3 wk compared to a standard green’s fertility program alone. Creeping bentgrass treated with biostimulants recovered equivalent to or quicker than creeping bentgrass treated with synthetic fertilizer (SF) in all cases. In the presence of methiozolin treatments, trinexapac-ethyl reduced time to 90% recovery (T90) by 0.25 to 0.5 wk at two locations, and increased T90 recovery time by 0.1 wk at one location. Otherwise, plots treated with SF plus trinexapac-ethyl were equivalent to plots treated with SF only. Methiozolin slowed turfgrass recovery time at one location where severe drought stress occurred but not at the other location that did not experience drought stress. These results suggest that turf managers should increase fertilizer treatments but will not need to discontinue trinexapac-ethyl use to maximize creeping bentgrass recovery following annual bluegrass control with methiozolin. These data also suggest that methiozolin has the potential to negatively affect creeping bentgrass recovery when drought stress is experienced.
Evaluation of Brace Root Parameters and Its Effect on the Stiffness of Maize
(in silico Plants, 2022-05-12) Obayes, Shaymaa K.; Timber, Luke; Head, Monique; Sparks, Erin E.
Plant mechanical failure (lodging) causes significant yield loss for crops such as maize. Understanding this failure has relied on static measurements of plant biomechanics. In this study, digital image correlation techniques are used to capture dynamic motion to understand the plant mechanical behavior of maize stalks in the presence and absence of brace roots, which are stem-borne aerial roots known to stabilize the maize stalks. The data show that brace roots function to secure the maize stalk, limiting both deflection and uplift. A finite element (FE) model is developed using ABAQUS software to validate the non-contact, video-based measured deflections captured by the dynamic motion and confirm the linear elastic behavior of the stem, following fundamental principles of engineering mechanics. Good agreement is found between the field data captured using video-based measurements and the physics-based FE model when a rotational connector element is connected at the base to quantify the 1) relative contribution and moment resistance provided by the root system, 2) displacement at any location along the stalk, and 3) flexural rigidity of the brace-stem system, where the rigidity can be associated with various phenotypes to design plant systems that are more resilient to lateral loading.
Evaluation of quantitative synchrotron radiation micro-X-ray fluorescence in rice grain
(Journal of Synchrotron Radiation, 2023-03-15) Limmer, Matt A.; Webb, Samuel M.; Seyffertha, Angelia L.
Concentrations of nutrients and contaminants in rice grain affect human health, specifically through the localization and chemical form of elements. Methods to spatially quantify the concentration and speciation of elements are needed to protect human health and characterize elemental homeostasis in plants. Here, an evaluation was carried out using quantitative synchrotron radiation microprobe X-ray fluorescence (SR-µXRF) imaging by comparing average rice grain concentrations of As, Cu, K, Mn, P, S and Zn measured with rice grain concentrations from acid digestion and ICP-MS analysis for 50 grain samples. Better agreement was found between the two methods for high-Z elements. Regression fits between the two methods allowed quantitative concentration maps of the measured elements. These maps revealed that most elements were concentrated in the bran, although S and Zn permeated into the endosperm. Arsenic was highest in the ovular vascular trace (OVT), with concentrations approaching 100 mg kg−1 in the OVT of a grain from a rice plant grown in As-contaminated soil. Quantitative SR-µXRF is a useful approach for comparison across multiple studies but requires careful consideration of sample preparation and beamline characteristics.
Facilitating viral vector movement enhances heterologous protein production in an established plant system
(Plant Biotechnology Journal, 2023-01-04) Wang, Xu; Prokhnevsky, Alexei I.; Skarjinskaia, Marina; Razzak, Md Abdur; Streatfield, Stephen J.; Lee, Jung-Youn
Molecular farming technology using transiently transformed Nicotiana plants offers an economical approach to the pharmaceutical industry to produce an array of protein targets including vaccine antigens and therapeutics. It can serve as a desirable alternative approach for those proteins that are challenging or too costly to produce in large quantities using other heterologous protein expression systems. However, since cost metrics are such a critical factor in selecting a production host, any system-wide modifications that can increase recombinant protein yields are key to further improving the platform and making it applicable for a wider range of target molecules. Here, we report on the development of a new approach to improve target accumulation in an established plant-based expression system that utilizes viral-based vectors to mediate transient expression in Nicotiana benthamiana. We show that by engineering the host plant to support viral vectors to spread more effectively between host cells through plasmodesmata, protein target accumulation can be increased by up to approximately 60%.
First report of Rhizoctonia solani AG 4 causing brown bean of lima bean in Delaware
(Plant Disease, 2022-06-11) Ginn, Adam Nicholas; Evans, Tom; Ernest, Emmalea; Koehler, Alyssa M.
Lima bean production has been an economically valuable staple in Delaware agriculture for almost a century, with annual revenue approaching 8 million dollars (USDA-NASS, 2019; Evans et al. 2007). From 2019-2021, lima beans displaying symptoms of brown discoloration, referred to as “brown bean” were observed in the green baby lima variety ‘Cypress’ across multiple commercial and research fields. Symptoms were present in approximately 1-5% of beans and not visible until pods were opened for harvest. Thirty-seven symptomatic beans were collected and surface disinfested in 0.85% sodium hypochlorite for 30 s, rinsed in sterile deionized water for 30 s, sectioned into four pieces and plated onto potato dextrose agar (PDA) amended with 50 µg/ml penicillin G and streptomycin sulfate. Petri dishes were incubated at 23ºC and observed for colony morphology. Pure cultures were obtained with tan colonies that had mycelia with right angle branching and septations near the branch, consistent with the description of Rhizoctonia solani Kuhn (Sneh et al. 1991). DNA extraction and pathogen identification was confirmed by sequencing of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA using primers ITS4/ITS5 (White et al. 1990) for thirty-seven isolates collected in 2019 and 2020. Isolates were identified as Rhizoctonia solani AG 4 (99.9% sequence identity with GenBank Accession [MN106359.1].) A representative isolate was selected to complete Koch’s postulates and the sequence was deposited in GenBank as accession number MW560551. To observe colonization ability, 10 detached pods were sterilized in 75% EtOH for 60 s, then rinsed in Milli-Q water. The detached pods were divided among two 150 mm Petri dishes containing a single 150 mm filter paper saturated with Milli-Q water. Five 1 mm2 agar plugs colonized with the representative R. solani isolate were placed 0.5 cm apart along the length of the pod. Plates were sealed with parafilm and left at room temperature. Control pods were kept in identical conditions but inoculated using clean agar plugs. The trial was repeated and a second trial was conducted on 12 attached asymptomatic pods from C-Elite Select lima bean plants at the succulent seed stage to complete Koch’s Postulates. Pods were surface disinfested with 70% ethanol. Three attached pods were wounded with the tip of a sterile scalpel blade where a colonized agar plug was placed and loosely wrapped with a thin parafilm layer to maintain contact. Three attached pods not wounded were also inoculated with a colonized agar plug and wrapped by parafilm. Three wounded and non-wounded pods received clean agar plug controls. Both attached and detached pods were kept at room temperature for one week until symptoms began to manifest on the pod surfaces, at which point the beans from infected pods were removed and placed on PDA, three to a plate. In the attached assay, all beans of both wounded and non-wounded pods developed symptoms. The plates were stored in identical conditions and monitored for 5 days until tan colonies were observed. Culture morphology was consistent with the original isolate in all beans. Sequencing of the ITS region confirmed identity as R. solani AG-4. No symptoms were observed on control pods or seeds. Rhizoctonia solani is most frequently associated with symptoms of root rot (Sharma-Poudyal et al. 2015), but no stem symptoms are associated with the late season “brown bean” that has been observed throughout production in recent years. To our knowledge, this is the first report of Rhizoctonia solani AG 4 causing symptoms of brown bean of lima bean in Delaware. In preliminary observations, symptoms seem to be worse in pods that could have had contact with the soil directly or via rain splash. This disease cannot be detected until pods are split open, which has potential to reduce lima bean quality at harvest. Further monitoring should be conducted to quantify yield impacts and develop appropriate preventative and curative techniques.
FLUXNET-CH4: a global, multi-ecosystem dataset and analysis of methane seasonality from freshwater wetlands
(Earth System Science Data, 2021-07-29) Delwiche, Kyle B.; Knox, Sara Helen; Malhotra, Avni; Fluet-Chouinard, Etienne; et al.
Methane (CH4) emissions from natural landscapes constitute roughly half of global CH4 contributions to the atmosphere, yet large uncertainties remain in the absolute magnitude and the seasonality of emission quantities and drivers. Eddy covariance (EC) measurements of CH4 flux are ideal for constraining ecosystem-scale CH4 emissions due to quasi-continuous and high-temporal-resolution CH4 flux measurements, coincident carbon dioxide, water, and energy flux measurements, lack of ecosystem disturbance, and increased availability of datasets over the last decade. Here, we (1) describe the newly published dataset, FLUXNET-CH4 Version 1.0, the first open-source global dataset of CH4 EC measurements (available at https://fluxnet.org/data/fluxnet-ch4-community-product/, last access: 7 April 2021). FLUXNET-CH4 includes half-hourly and daily gap-filled and non-gap-filled aggregated CH4 fluxes and meteorological data from 79 sites globally: 42 freshwater wetlands, 6 brackish and saline wetlands, 7 formerly drained ecosystems, 7 rice paddy sites, 2 lakes, and 15 uplands. Then, we (2) evaluate FLUXNET-CH4 representativeness for freshwater wetland coverage globally because the majority of sites in FLUXNET-CH4 Version 1.0 are freshwater wetlands which are a substantial source of total atmospheric CH4 emissions; and (3) we provide the first global estimates of the seasonal variability and seasonality predictors of freshwater wetland CH4 fluxes. Our representativeness analysis suggests that the freshwater wetland sites in the dataset cover global wetland bioclimatic attributes (encompassing energy, moisture, and vegetation-related parameters) in arctic, boreal, and temperate regions but only sparsely cover humid tropical regions. Seasonality metrics of wetland CH4 emissions vary considerably across latitudinal bands. In freshwater wetlands (except those between 20∘ S to 20∘ N) the spring onset of elevated CH4 emissions starts 3 d earlier, and the CH4 emission season lasts 4 d longer, for each degree Celsius increase in mean annual air temperature. On average, the spring onset of increasing CH4 emissions lags behind soil warming by 1 month, with very few sites experiencing increased CH4 emissions prior to the onset of soil warming. In contrast, roughly half of these sites experience the spring onset of rising CH4 emissions prior to the spring increase in gross primary productivity (GPP). The timing of peak summer CH4 emissions does not correlate with the timing for either peak summer temperature or peak GPP. Our results provide seasonality parameters for CH4 modeling and highlight seasonality metrics that cannot be predicted by temperature or GPP (i.e., seasonality of CH4 peak). FLUXNET-CH4 is a powerful new resource for diagnosing and understanding the role of terrestrial ecosystems and climate drivers in the global CH4 cycle, and future additions of sites in tropical ecosystems and site years of data collection will provide added value to this database. All seasonality parameters are available at https://doi.org/10.5281/zenodo.4672601 (Delwiche et al., 2021). Additionally, raw FLUXNET-CH4 data used to extract seasonality parameters can be downloaded from https://fluxnet.org/data/fluxnet-ch4-community-product/ (last access: 7 April 2021), and a complete list of the 79 individual site data DOIs is provided in Table 2 of this paper.
Heterogeneity in soil chemistry relates to urbanization while soil homogeneity relates to plant invasion in small temperate deciduous forests
(Landscape Ecology, 2022-02-07) Trammell, Tara L. E.; Pouyat, Richard V.; D ’Amico, Vince III
Context: Soil heterogeneity versus homogeneity patterns are observed within and across urban landscapes at multiple scales. To fully evaluate human-mediated influences on soil properties and processes, we need to understand spatial patterns and variation in soil characteristics within a single ecosystem patch type (e.g., forests) in and near cities. Objectives: Our research objectives were to: (1) identify soil characteristics important in driving variation in soil chemistry within urban forests, and (2) examine whether urbanization and invasion gradients were related to variation in soil chemistry within these forests. Methods: We measured soil chemical properties within 36 forests across the U.S. mid-Atlantic. The forests are spatially distributed across an urbanization gradient and comprise a gradient of non-native plant invasion. Results: Urbanization was related to more variation in soil chemistry, whereas plant invasion was related to less variation in soil chemistry within our forests. Soil Ca and Mg concentrations increase with plant invasion yet are less variable within invaded forests most likely due to invasive plants taking up and concentrating these elements. Soil pH, Ca, Mg, Zn, and Cu increase in forests surrounded by greater urbanization, however, these elements are more variable within urban forests likely due to edge effects altering element deposition. Conclusions: Our results demonstrate that while urbanization and invasion can increase soil chemical concentrations, they differentially alter variation in soil chemistry within urban forests. Plant invasion and urban environmental conditions need separate consideration in future conceptual models of urban ecological theory since non-native invasive plants influence soil chemistry independent of other urban factors.
Human-mediated dispersal drives the spread of the spotted lanternfly (Lycorma delicatula)
(Scientific Reports, 2023-01-19) Ladin, Zachary S.; Eggen, Donald A.; Trammell, Tara L. E.; D’Amico, Vincent
The spotted lanternfly (Lycorma delicatula) is a novel invasive insect from Asia now established and spreading throughout the United States. This species is of particular concern given its ability to decimate important crops such as grapes, fruit trees, as well as native hardwood trees. Since its initial detection in Berks County, Pennsylvania in 2014, spotted lanternfly infestations have been detected in 130 counties (87 under quarantine) within Connecticut, Delaware, Indiana, Maryland, New Jersey, New York, Ohio, Virginia, and West Virginia. Compounding this invasion is the associated proliferation and widespread distribution of the spotted lanternfly’s preferred host plant, the tree-of-heaven (Ailanthus altissima). While alternate host plant species have been observed, the tree-of-heaven which thrives in disturbed and human-dominated areas (e.g., along roads and railways) is likely facilitating the population growth rates of spotted lanternfly. We simulated the population and spread dynamics of the spotted lanternfly throughout the mid-Atlantic USA to help determine areas of risk and inform continued monitoring and control efforts. We tested the prediction that spotted lanternfly spread is driven by human-mediated dispersal using agent-based models that incorporated information on its life-history traits, habitat suitability, and movement and natural dispersal behavior. Overwhelmingly, our results suggest that human-mediated dispersal (e.g., cars, trucks, and trains) is driving the observed spread dynamics and distribution of the spotted lanternfly throughout the eastern USA. Our findings should encourage future surveys to focus on human-mediated dispersal of egg masses and adult spotted lanternflies (e.g., attachment to car or transported substrates) to better monitor and control this economically and ecologically important invasive species.
Hydrologic Control on Arsenic Cycling at the Groundwater–Surface Water Interface of a Tidal Channel
(Environmental Science and Technology, 2023-01-10) Yu, Xuan; LeMonte, Joshua J.; Li, Junxia; Stuckey, Jason W.; Sparks, Donald L.; Cargill, John G.; Russoniello, Christopher J.; Michael, Holly A.
Historical industrial activities have resulted in soil contamination at sites globally. Many of these sites are located along coastlines, making them vulnerable to hydrologic and biogeochemical alterations due to climate change and sea-level rise. However, the impact of hydrologic dynamics on contaminant mobility in tidal environments has not been well studied. Here, we collected data from pressure transducers in wells, multi-level redox sensors, and porewater samplers at an As-contaminated site adjacent to a freshwater tidal channel. Results indicate that sharp redox gradients exist and that redox conditions vary on tidal to seasonal timescales due to sub-daily water level fluctuations in the channel and seasonal groundwater–surface water interactions. The As and Fe2+ concentrations decreased during seasonal periods of net discharge to the channel. The seasonal changes were greater than tidal variations in both Eh and As concentrations, indicating that impacts of the seasonal mechanism are stronger than those of sub-daily water table fluctuations. A conceptual model describing tidal and seasonal hydro-biogeochemical coupling is presented. These findings have broad implications for understanding the impacts of sea-level rise on the mobility of natural and anthropogenic coastal solutes.

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