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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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Item 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.Item 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 FrankelAchieving 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.Item 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.Item 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.Item Assessing relationships of cover crop biomass and nitrogen content to multispectral imagery(Agronomy Journal, 2024-02-29) Miller, Jarrod O.; Shober, Amy L.; Taraila, JamieCover 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 indexItem 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, ShreeramHow 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.Item 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.Item 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, MichelaTo 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.Item 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.Item 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, NickIn 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.Item 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, MarkCommon 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.Item Continuous light can promote growth of baby greens over diurnal light under a high daily light integral(Environmental and Experimental Botany, 2024-02-23) Meng, Qingwu; Severin, Stefanie N.Sole-source lighting with light-emitting diodes (LEDs) incurs high operating expenditure in indoor vertical farms, where crops are typically grown under diurnal light at a fixed photosynthetic photon flux density (PPFD). Under the same daily light integral (DLI), continuous light lowers the needed PPFD, thereby decreasing the initial capital investment on high-output LEDs and operating expenditure by lighting in the nighttime, when electricity rates are lower than in the daytime in some areas. However, little is known about how temporal light patterns influence baby green growth at varying DLIs. We performed an indoor experiment on baby greens of lettuce (Lactuca sativa) ‘Rouxai’, kale (Brassica oleracea var. acephala) ‘Red Russian’, and arugula (Eruca sativa) ‘Astro’ at ≈ 21 ºC air temperature and ≈ 70% relative humidity. At each of two DLIs (8.64 and 17.28 mol∙m–2∙d–1), each crop was grown under warm-white LEDs with three light patterns [100%, 75%, and 50% daytime DLI (first half of a 24-hour cycle), followed by 0%, 25%, and 50% nighttime DLI, respectively]. The 0% nighttime DLI treatments delivered diurnal light with a 12-h photoperiod, whereas the 25% and 50% nighttime DLI treatments delivered alternating light and continuous light, respectively, both with a 24-h photoperiod. Lettuce and kale generally had more pronounced growth responses to the light pattern under the higher DLI, whereas arugula growth was unaffected by the light pattern. Compared to diurnal light, continuous light increased lettuce shoot mass at both DLIs, but increased kale shoot mass only under the higher DLI. Compared to continuous light, alternating light decreased lettuce shoot mass only under the higher DLI, but did not influence most parameters of kale or arugula. Doubling the DLI increased the shoot dry mass of all crops by 44–150% and the shoot fresh mass of arugula by 38–73% across light patterns. The shoot fresh mass of lettuce and kale increased with an increasing DLI under continuous or diurnal light. We conclude that the light pattern and DLI had interactive and crop-specific effects on the growth of baby greens. Under the same DLI, continuous light can increase growth of lettuce and kale, but not arugula, baby greens over diurnal light, especially under a high DLI.Item Contrasting roles of rice root iron plaque in retention and plant uptake of silicon, phosphorus, arsenic, and selenium in diverse paddy soils(Plant and Soil, 2024-02-20) Linam, Franklin A.; Limmer, Matt A.; Seyfferth, Angelia L.Background and aims Iron (Fe) plaque on rice roots is a mixture of Fe oxide and oxyhydroxide minerals thought to protect rice from high levels of arsenic (As) in flooded paddy soils. Silicon (Si), phosphorus (P), and selenium (Se) also exist as oxyanions in rice paddies, but the impacts of Fe plaque on uptake of these nutrients are unknown. Methods We used natural variation in paddy soil chemistry to test how Si, P, As, and Se move from porewater to plaque to plant via multiple techniques. In a pot study, we monitored Fe plaque deposition and porewater chemistry in 5 different soils over time and measured plaque/plant chemistry and Fe plaque mineralogy at harvest. We normalized oxyanion concentrations by Fe to determine the preferential retention on plaque or plant uptake. Results Low phosphorus availability increased root Fe-oxidizing activity, while Fe, Si, P, As, and Se concentrations in plaque were strongly correlated with porewater. Plaque did not appreciably retain Si and Se, and the oxyanions did not compete for adsorption sites on the Fe plaque. Conclusion Root Fe plaque seems to protect rice from As uptake, does not interfere with Si and Se uptake, and roots adapt to maintain P nutrition even with retention of porewater P on plaque.Item 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, WeiRising 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.Item Culturally appropriate shifts in staple grain consumption can improve multiple sustainability outcomes(Environmental Research Letters, 2021-11-24) Wei, Dongyang; Davis, Kyle FrankelDiets 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.Item 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, QingwuChrysanthemum (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.Item Distinct and Cooperative Activities of HESO1 and URT1 Nucleotidyl Transferases in MicroRNA Turnover in Arabidopsis(PLOS (Public Library of Science), 2015-04-30) Tu, Bin; Liu, Li; Xu, Chi; Zhai, Jixian; Li, Shengben; Lopez, Miguel A.; Zhao, Yuanyuan; Yu, Yu; Ramachandran, Vanitharani; Ren, Guodong; Yu, Bin; Li, Shigui; Meyers, Blake C.; Mo, Beixin; Chen, Xuemei; Bin Tu1, Li Liu, Chi Xu, Jixian Zhai, Shengben Li, Miguel A. Lopez, Yuanyuan Zhao, Yu Yu, Vanitharani Ramachandran, Guodong Ren, Bin Yu, Shigui Li, Blake C. Meyers, Beixin Mo, Xuemei Chen; Zhai, Jixian; Meyers, Blake C.3’ uridylation is increasingly recognized as a conserved RNA modification process associated with RNA turnover in eukaryotes. 2’-O-methylation on the 3’ terminal ribose protects micro(mi)RNAs from 3’ truncation and 3’ uridylation in Arabidopsis. Previously, we identified HESO1 as the nucleotidyl transferase that uridylates most unmethylated miRNAs in vivo, but substantial 3’ tailing of miRNAs still remains in heso1 loss-of-function mutants. In this study, we found that among nine other potential nucleotidyl transferases, UTP:RNA URIDYLYLTRANSFERASE 1 (URT1) is the single most predominant nucleotidyl transferase that tails miRNAs. URT1 and HESO1 prefer substrates with different 3’ end nucleotides in vitro and act cooperatively to tail different forms of the same miRNAs in vivo. Moreover, both HESO1 and URT1 exhibit nucleotidyl transferase activity on AGO1-bound miRNAs. Although these enzymes are able to add long tails to AGO1-bound miRNAs, the tailed miRNAs remain associated with AGO1. Moreover, tailing of AGO1-bound miRNA165/6 drastically reduces the slicing activity of AGO1-miR165/6, suggesting that tailing reduces miRNA activity. However, monouridylation of miR171a by URT1 endows the miRNA the ability to trigger the biogenesis of secondary siRNAs. Therefore, 3’ tailing could affect the activities of miRNAs in addition to leading to miRNA degradation.Item 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 BritoThe 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.Item 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, RodrigoStudy 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.Item Dynamics of short-term ecosystem carbon fluxes induced by precipitation events in a semiarid grassland(Biogeosciences, 2023-06-22) Delgado-Balbuena, Josué; Loescher, Henry W.; Aguirre-Gutiérrez, Carlos A.; Alfaro-Reyna, Teresa; Pineda-Martínez, Luis F.; Vargas, Rodrigo; Arredondo, TulioInfrequent and small precipitation (PPT) events characterize PPT patterns in semiarid grasslands; however, plants and soil microorganisms are adapted to use the unpredictable small pulses of water. Several studies have shown short-term responses of carbon and nitrogen mineralization rates (called the “priming effect” or the Birch effect) stimulated by wet–dry cycles; however, dynamics, drivers, and the contribution of the priming effect to the annual C balance are poorly understood. Thus, we analyzed 6 years of continuous net ecosystem exchange measurements to evaluate the effect of the PPT periodicity and magnitude of individual PPT events on the daily/annual net ecosystem C exchange (NEE) in a semiarid grassland. We included the period between PPT events, previous daytime NEE rate, and previous soil moisture content as the main drivers of the priming effect. Ecosystem respiration (ER) responded within a few hours following a PPT event, whereas it took 5–9 d for gross ecosystem exchange (GEE; where −NEE = GEE + ER) to respond. Precipitation events as low as 0.25 mm increased ER, but cumulative PPT > 40 mm infiltrating deep into the soil profile stimulated GEE. Overall, ER fluxes following PPT events were related to the change in soil water content at shallow depth and previous soil conditions (e.g., previous NEE rate, previous soil water content) and the size of the stimulus (e.g., PPT event size). Carbon effluxes from the priming effect accounted for less than 5 % of ecosystem respiration but were significantly high with respect to the carbon balance. In the long term, changes in PPT regimes to more intense and less frequent PPT events, as expected due to the effects of climate change, could convert the semiarid grassland from a small C sink to a C source.