Department of Plant and Soil Sciences

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https://udspace.udel.edu/handle/19716/24268

The Department of Plant and Soil Sciences has excellent teaching, research, and outreach programs in the areas of plant biology (cellular, genetics, genomics, microbial, molecular and physiology), agronomy (including pathology, soil management, and weed science), horticulture (sustainable landscapes, fruits, and vegetables), landscape architecture, and environmental soil sciences (biogeochemistry, hydrology, and plant-soil interactions). We have a distinguished faculty, known nationally and internationally for their research and outreach, and within the University of Delaware for their excellence in teaching, advising, and mentoring students.

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Now showing 1 - 20 of 165

A Bacillus velezensis strain shows antimicrobial activity against soilborne and foliar fungi and oomycetes
(Frontiers in Fungal Biology, 2024-02-23) Wockenfuss, Anna; Chan, Kevin; Cooper, Jessica G.; Chaya, Timothy; Mauriello, Megan A.; Yannarell, Sarah M.; Maresca, Julia A.; Donofrio, Nicole M.
Biological control uses naturally occurring antagonists such as bacteria or fungi for environmentally friendly control of plant pathogens. Bacillus spp. have been used for biocontrol of numerous plant and insect pests and are well-known to synthesize a variety of bioactive secondary metabolites. We hypothesized that bacteria isolated from agricultural soil would be effective antagonists of soilborne fungal pathogens. Here, we show that the Delaware soil isolate Bacillus velezensis strain S4 has in vitro activity against soilborne and foliar plant pathogenic fungi, including two with a large host range, and one oomycete. Further, this strain shows putative protease and cellulase activity, consistent with our prior finding that the genome of this organism is highly enriched in antifungal and antimicrobial biosynthetic gene clusters. We demonstrate that this bacterium causes changes to the fungal and oomycete hyphae at the inhibition zone, with some of the hyphae forming bubble-like structures and irregular branching. We tested strain S4 against Magnaporthe oryzae spores, which typically form germ tubes and penetration structures called appressoria, on the surface of the leaf. Our results suggest that after 12 hours of incubation with the bacterium, fungal spores form germ tubes, but instead of producing appressoria, they appear to form rounded, bubble-like structures. Future work will investigate whether a single antifungal molecule induces all these effects, or if they are the result of a combination of bacterially produced antimicrobials.
A Green Future: Scranton PA
(2023-05) Welsh, Mike
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.
Adaptive Reuse Exploration Goodstay Gardens
(2020-12) Armstrong, Connor
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.
Area of Reflection for Enslaved Peoples
(2021-05) Moore, Brandon
Area of Reflection for Enslaved Peoples at the John Dickinson Plantation
(2021-05) Fleming, Hunter
Area of Reflection for John Dickinson Plantation
(2021-05) Niu, HaoChen
ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis
(Public Library of Science (PLoS), 2017-02-23) Yu, Yu; Ji, Lijuan; Le, Brandon H.; Zhai, Jixian; Chen, Jiayi; Lusche, Elizabeth; Gao, Lei; Liu, Chunyan; Cao, Xiaofeng; Mo, Beixin; Ma, Jinbiao; Meyers, Blake C.; Chen, Xuemei; Yu Yu, Lijuan Ji, Brandon H. Le, Jixian Zhai, Jiayi Chen, Elizabeth Luscher, Lei Gao, Chunyan Liu, Xiaofeng Cao, Beixin Mo, Jinbiao Ma, Blake C. Meyers, Xuemei Chen; Zhai, Jixian; Meyers, Blake C.
The degradation of small RNAs in plants and animals is associated with small RNA 30 truncation and 30 uridylation and thus relies on exonucleases and nucleotidyl transferases. ARGONAUTE (AGO) proteins associate with small RNAs in vivo and are essential for not only the activities but also the stability of small RNAs. AGO1 is the microRNA (miRNA) effector in Arabidopsis, and its closest homolog, AGO10, maintains stem cell homeostasis in meristems by sequestration of miR165/6, a conserved miRNA acting through AGO1. Here, we show that SMALL RNA DEGRADING NUCLEASES (SDNs) initiate miRNA degradation by acting on AGO1-bound miRNAs to cause their 30 truncation, and the truncated species are uridylated and degraded. We report that AGO10 reduces miR165/6 accumulation by enhancing its degradation by SDN1 and SDN2 in vivo. In vitro, AGO10-bound miR165/6 is more susceptible to SDN1-mediated 30 truncation than AGO1-bound miR165/ 6. Thus, AGO10 promotes the degradation of miR165/6, which is contrary to the stabilizing effect of AGO1. Our work identifies a class of exonucleases responsible for miRNA 30 truncation in vivo and uncovers a mechanism of specificity determination in miRNA turnover. This work, together with previous studies on AGO10, suggests that spatially regulated miRNA degradation underlies stem cell maintenance in plants.
Assessing relationships of cover crop biomass and nitrogen content to multispectral imagery
(Agronomy Journal, 2024-02-29) Miller, Jarrod O.; Shober, Amy L.; Taraila, Jamie
Cover crops provide valuable roles in sustainable agriculture, provided they produce enough biomass. To accurately measure their services to field management, spatial estimates would be useful to producers. This study used multispectral drone imagery to produce maps of normalized difference vegetation index (NDVI), normalized difference red edge index (NDRE), and a digital surface model (DSM) of cover crop plots on sandy, Mid-Atlantic soils. Cover crops included cereal rye (Secale cereale), mixtures of rye and crimson clover (Trifolium incarnatum), and mixtures of rye and hairy vetch (Vicia villosa). Their biomass was sampled in the spring of 2019, 2020, and 2021, dried, weighed, and analyzed for total nitrogen (N) content. Measurements of NDVI became saturated (i.e., reached a linear plateau) at 3.86 Mg biomass ha−1, NDRE at 5.72 Mg biomass ha−1, and the DSM at 5.11 Mg biomass ha−1. The measured N content became saturated at 80.9, 139.1, and 75 kg N ha−1 for NDVI, NDRE, and the DSM, respectively. Based on log transformations, NDVI was a stronger predictor of biomass and N, but not C:N. The NDRE was important for biomass, N, and C:N, while the DSM interactions with cover crop species helped predict both the N content and C:N of cover crop tissues. Accumulated growing degree days was important as an individual variable for biomass and N and as an interaction with cover crop species. Abbreviations DSM digital surface model GDD growing degree days NDRE normalized difference red edge index NDVI normalized difference vegetation index
The Awakening
(2021-05) Stewart, Charlye
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.
Birch Street Art Corridor
(2020-06) Bonura, Christopher
Blue Photons from Broad-Spectrum LEDs Control Growth, Morphology, and Coloration of Indoor Hydroponic Red-Leaf Lettuce
(Plants, 2023-03-02) Meng, Qingwu; Runkle, Erik S.
For indoor crop production, blue + red light-emitting diodes (LEDs) have high photosynthetic efficacy but create pink or purple hues unsuitable for workers to inspect crops. Adding green light to blue + red light forms a broad spectrum (white light), which is created by: phosphor-converted blue LEDs that cast photons with longer wavelengths, or a combination of blue, green, and red LEDs. A broad spectrum typically has a lower energy efficiency than dichromatic blue + red light but increases color rendering and creates a visually pleasing work environment. Lettuce growth depends on the interactions of blue and green light, but it is not clear how phosphor-converted broad spectra, with or without supplemental blue and red light, influence crop growth and quality. We grew red-leaf lettuce ‘Rouxai’ in an indoor deep-flow hydroponic system at 22 °C air temperature and ambient CO2. Upon germination, plants received six LED treatments delivering different blue fractions (from 7% to 35%) but the same total photon flux density (400 to 799 nm) of 180 μmol·m−2·s−1 under a 20 h photoperiod. The six LED treatments were: (1) warm white (WW180); (2) mint white (MW180); (3) MW100 + blue10 + red70; (4) blue20 + green60 + red100; (5) MW100 + blue50 + red30; and (6) blue60 + green60 + red60. Subscripts denote photon flux densities in μmol·m−2·s−1. Treatments 3 and 4 had similar blue, green, and red photon flux densities, as did treatments 5 and 6. At the harvest of mature plants, lettuce biomass, morphology, and color were similar under WW180 and MW180, which had different green and red fractions but similar blue fractions. As the blue fraction in broad spectra increased, shoot fresh mass, shoot dry mass, leaf number, leaf size, and plant diameter generally decreased and red leaf coloration intensified. Compared to blue + green + red LEDs, white LEDs supplemented with blue + red LEDs had similar effects on lettuce when they delivered similar blue, green, and red photon flux densities. We conclude that the blue photon flux density in broad spectra predominantly controls lettuce biomass, morphology, and coloration.
Brandywine Summit Camp Meeting Revitalizing a Summer Camp Through Sustainable Ecosystem Services
(2023-05) Davis, Elisabeth
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.
Carrcroft Elementary School Mindfulness Trail
(2019-12) Yang, Peiyuan
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.
Common ragweed (Ambrosia artemisiifolia L.) accessions in the Mid-Atlantic region resistant to ALS-, PPO-, and EPSPS-inhibiting herbicides
(Weed Technology, 2024-03-08) D’Amico Jr. , Frank; Besanҫon, Thierry; Koehler, Alyssa; Shergill, Lovreet; Ziegler, Melissa; VanGessel, Mark
Common ragweed is a troublesome weed in many crops. Farmers and crop advisors in the coastal Mid-Atlantic region have reported inadequate control of common ragweed in soybean fields with glyphosate and other herbicide modes of action. To determine whether herbicide resistance was one of the causes of poor herbicide performance, 29 accessions from four states (Delaware, Maryland, New Jersey, and Virginia) where common ragweed plants survived herbicide applications and produced viable seeds were used for greenhouse screening. Common ragweed seedlings from those accessions were treated with multiple rates of cloransulam, fomesafen, or glyphosate, applied individually postemergence (POST). All accessions except one demonstrated resistance to at least one of the herbicides applied at twice the effective rate (2×), 17 accessions were two-way resistant (to glyphosate and cloransulam, or to glyphosate and fomesafen), and three-way resistance was present in eight accessions collected from three different states. Based on the POST study, five accessions were treated preemergence (PRE) with herbicides that inhibit acetolactate synthase (ALS), and two accessions were treated with herbicides that inhibit protoporphyrinogen oxidase (PPO). All accessions treated PRE with the ALS inhibitors chlorimuron or cloransulam demonstrated resistance at the 2× rates. Both accessions treated PRE with the PPO inhibitor sulfentrazone had survivors at the 2× rate. When the same accessions were treated PRE with fomesafen, one had survivors at the 2× rate, and one had survivors at the 1× rate. Results from these tests confirmed common ragweed with three-way resistance to POST herbicides is widespread in the region. In addition, this is the first confirmation that common ragweed accessions in the region are also resistant to ALS- or PPO-inhibiting herbicides when applied PRE.

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