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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Unwrapping the Native Plant Black Box: Consumer Perceptions and Segments for Target Marketing Strategies
(HortTechnology, 2024-05-23) Rihn, Alicia L.; Torres, Ariana; Behe, Bridget K.; Barton, Sue
The increasing demand for sustainable products has helped spur demand for native plants. This study used an online survey of 2066 US consumers, a factor analysis, and Ward’s linkage cluster analysis to identify unique customer segments in the native plant marketplace. The following three clusters were identified: native averse (31.6%), native curious (35.7%), and native enthusiast (32.7%). The native enthusiast cluster agreed strongly with positive statements related to native plant perceptions and attributes. The native averse cluster exhibited the lowest level of agreement with these items and the greatest level of agreement with negative or neutral statements about native plants. The native curious cluster was intermediate between the other clusters but generally agreed with positive attributes. Demographic characteristics impacted cluster membership. The marketing implications are discussed.
Varietal Tolerance of Cucurbitaceous Crops with S-metolachlor Applied Postemergence
(HortTechnology, 2024-06-01) Vollmer, Kurt M.; Lynn M. Sosnoskie; VanGessel, Mark J.; Besançon, Thierry E.
Cucurbit crops comprise ∼25% of the vegetable acreage in the mid-Atlantic and Northeastern United States. However, options for postemergence weed control in these crops are limited. Overlapping herbicides is a technique that involves sequential applications of soil-applied residual herbicides to lengthen herbicidal activity before the first herbicide dissipates. Residual herbicides such as S-metolachlor will not control emerged weeds, but weed control efficacy may be extended if these herbicides are applied after crop emergence, but before weed emergence occurs. Currently S-metolachlor is not labeled for broadcast applications over cucurbit crops. Greenhouse studies were conducted to evaluate pumpkin, cucumber, and summer squash variety response to varying S-metolachlor rates. S-metolachlor was applied at 1.42 and 2.85 lb/acre at the two-leaf stage of pumpkin and 0.71, 1.42, 2.85, and 5.7 lb/acre at the two-leaf stage of cucumber and summer squash. Cucumber showed a greater response to S-metolachlor with up to 67% injury observed at 5.70 lb/acre. S-metolachlor applications to pumpkin and summer squash resulted in less than 6% injury, regardless of application rate or crop variety. S-metolachlor applied at 2.85 lb/acre reduced pumpkin and cucumber dry weight 6% and 19%, respectively, but did not reduce squash dry weight. S-metolachlor reduced cucumber dry weight 78% for all varieties. Pumpkin varieties ‘Munchkin’ and ‘Baby Bear’ exhibited a 23% difference in dry weight, but no other differences were observed among other varieties because of S-metolachlor applications. Summer squash varieties ‘Respect’ and ‘Golden Glory’ exhibited a 31% difference in dry weight, but no other differences were observed among other varieties. Results show that pumpkin and summer squash demonstrated good crop safety when S-metolachlor was applied as a broadcast treatment after crop emergence. However, caution should be urged when applying this herbicide to cucumber.
Role of Bacillus subtilis exopolymeric genes in modulating rhizosphere microbiome assembly
(Environmental Microbiome, 2024-05-14) Nishisaka, Caroline Sayuri; Ventura, João Paulo; Bais, Harsh P.; Mendes, Rodrigo
Background Bacillus subtilis is well known for promoting plant growth and reducing abiotic and biotic stresses. Mutant gene-defective models can be created to understand important traits associated with rhizosphere fitness. This study aimed to analyze the role of exopolymeric genes in modulating tomato rhizosphere microbiome assembly under a gradient of soil microbiome diversities using the B. subtilis wild-type strain UD1022 and its corresponding mutant strain UD1022eps−TasA, which is defective in exopolysaccharide (EPS) and TasA protein production. Results qPCR revealed that the B. subtilis UD1022eps−TasA− strain has a diminished capacity to colonize tomato roots in soils with diluted microbial diversity. The analysis of bacterial β-diversity revealed significant differences in bacterial and fungal community structures following inoculation with either the wild-type or mutant B. subtilis strains. The Verrucomicrobiota, Patescibacteria, and Nitrospirota phyla were more enriched with the wild-type strain inoculation than with the mutant inoculation. Co-occurrence analysis revealed that when the mutant was inoculated in tomato, the rhizosphere microbial community exhibited a lower level of modularity, fewer nodes, and fewer communities compared to communities inoculated with wild-type B. subtilis. Conclusion This study advances our understanding of the EPS and TasA genes, which are not only important for root colonization but also play a significant role in shaping rhizosphere microbiome assembly. Future research should concentrate on specific microbiome genetic traits and their implications for rhizosphere colonization, coupled with rhizosphere microbiome modulation. These efforts will be crucial for optimizing PGPR-based approaches in agriculture.
Efficacy and Optimal Timing of Warm-white or Red + Far-red LED Lamps in Regulation of Flowering in Long-day Ornamentals
(HortScience, 2024-04-30) Meng, Qingwu; Kelly, Ian
When natural days are short, photoperiodic lighting at the end or beginning of the day (day extension) or in the middle of the night (night break) promotes flowering of long-day plants. The objective of this study was to compare broad-spectrum warm-white light-emitting diodes (LEDs) and red (R) + far-red (FR) LEDs at flowering regulation when delivered at different timings in the night period. We performed a greenhouse experiment on four long-day ornamentals [coreopsis (Coreopsis grandiflora) ‘Early Sunrise’, snapdragon (Antirrhinum majus) ‘Liberty Classic Yellow’, petunia (Petunia ×hybrida) ‘Easy Wave Burgundy Star’, and petunia ‘Wave Purple Improved’]. We grew plants under a truncated 8-hour photoperiod with or without low-intensity (∼2 μmol·m−2·s−1) nighttime lighting from warm-white or R+FR LEDs. For each light quality, we delivered four timings: 1) 8 hours after dusk; 2) 8 hours before dawn; 3) 4 hours after dusk + 4 hours before dawn; and 4) 4-hour night break. The effectiveness of floral promotion was determined by time from the treatment onset to the first open flower. Coreopsis flowered similarly under all lighting treatments, irrespective of light quality and timing, but did not flower under the short-day treatment by the end of the experiment. At flowering, coreopsis was 18% to 19% shorter under white than R+FR LEDs. In contrast, snapdragon flowered 9 to 20 days later under white than R+FR LEDs, when delivered for 8 hours at night, but flowered similarly under these two lamp types as a 4-hour night break. Compared with the short-day treatment, white and R+FR LEDs promoted flowering of both petunia cultivars, although flowering generally occurred later under white than R+FR LEDs. Snapdragon and petunia ‘Easy Wave Burgundy Star’ developed 30% to 122% more lateral branches under white than R+FR LEDs, when delivered for 8 hours at night. The effectiveness of warm-white LEDs was generally unaffected by timing, although it was most promotive of flowering in snapdragon when delivered for 8 hours before dawn. For R+FR LEDs, 8-hour day-extension lighting was generally more effective than 4-hour night-break lighting, irrespective of timing. We conclude when delivered for 8 hours at night, warm-white LEDs are generally less effective than R+FR LEDs at promoting flowering of long-day ornamentals but similarly effective as 4-hour night-break lighting. The effectiveness of day-extension lighting is generally independent of timing, although for R+FR LEDs, 8 hours after-dusk and/or before-dawn lighting was generally more effective than 4-hour night-break lighting.
Improvements in viral gene annotation using large language models and soft alignments
(BMC Bioinformatics, 2024-04-25) Harrigan, William L.; Ferrell, Barbra D.; Wommack, K. Eric; Polson, Shawn W.; Schreiber, Zachary D.; Belcaid, Mahdi
Background The annotation of protein sequences in public databases has long posed a challenge in molecular biology. This issue is particularly acute for viral proteins, which demonstrate limited homology to known proteins when using alignment, k-mer, or profile-based homology search approaches. A novel methodology employing Large Language Models (LLMs) addresses this methodological challenge by annotating protein sequences based on embeddings. Results Central to our contribution is the soft alignment algorithm, drawing from traditional protein alignment but leveraging embedding similarity at the amino acid level to bypass the need for conventional scoring matrices. This method not only surpasses pooled embedding-based models in efficiency but also in interpretability, enabling users to easily trace homologous amino acids and delve deeper into the alignments. Far from being a black box, our approach provides transparent, BLAST-like alignment visualizations, combining traditional biological research with AI advancements to elevate protein annotation through embedding-based analysis while ensuring interpretability. Tests using the Virus Orthologous Groups and ViralZone protein databases indicated that the novel soft alignment approach recognized and annotated sequences that both blastp and pooling-based methods, which are commonly used for sequence annotation, failed to detect. Conclusion The embeddings approach shows the great potential of LLMs for enhancing protein sequence annotation, especially in viral genomics. These findings present a promising avenue for more efficient and accurate protein function inference in molecular biology.
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
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.
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.
U.S. cereal rye winter cover crop growth database
(Scientific Data, 2024-02-13) Huddell, Alexandra M.; Thapa, Resham; Marcillo, Guillermo S.; Abendroth, Lori J.; et. al
Winter cover crop performance metrics (i.e., vegetative biomass quantity and quality) affect ecosystem services provisions, but they vary widely due to differences in agronomic practices, soil properties, and climate. Cereal rye (Secale cereale) is the most common winter cover crop in the United States due to its winter hardiness, low seed cost, and high biomass production. We compiled data on cereal rye winter cover crop performance metrics, agronomic practices, and soil properties across the eastern half of the United States. The dataset includes a total of 5,695 cereal rye biomass observations across 208 site-years between 2001–2022 and encompasses a wide range of agronomic, soils, and climate conditions. Cereal rye biomass values had a mean of 3,428 kg ha−1, a median of 2,458 kg ha−1, and a standard deviation of 3,163 kg ha−1. The data can be used for empirical analyses, to calibrate, validate, and evaluate process-based models, and to develop decision support tools for management and policy decisions.
Early-season biomass and weather enable robust cereal rye cover crop biomass predictions
(Agricultural & Environmental Letters, 2024-02-13) Huddell, Alexandra; Needelman, Brian; Law, Eugene P.; Ackroyd, Victoria J.; Bagavathiannan, Muthukumar V.; Bradley, Kevin; Davis, Adam S.; Evans, Jeffery A.; Everman, Wesley Jay; Flessner, Michael; Jordan, Nicholas; Schwartz-Lazaro, Lauren M.; Leon, Ramon G.; Lindquist, John; Norsworthy, Jason K.; Shergill, Lovreet S.; VanGessel, Mark; Mirsky, Steven B.
Farmers need accurate estimates of winter cover crop biomass to make informed decisions on termination timing or to estimate potential release of nitrogen from cover crop residues to subsequent cash crops. Utilizing data from an extensive experiment across 11 states from 2016 to 2020, this study explores the most reliable predictors for determining cereal rye cover crop biomass at the time of termination. Our findings demonstrate a strong relationship between early-season and late-season cover crop biomass. Employing a random forest model, we predicted late-season cereal rye biomass with a margin of error of approximately 1,000 kg ha−1 based on early-season biomass, growing degree days, cereal rye planting and termination dates, photosynthetically active radiation, precipitation, and site coordinates as predictors. Our results suggest that similar modeling approaches could be combined with remotely sensed early-season biomass estimations to improve the accuracy of predicting winter cover crop biomass at termination for decision support tools. Core Ideas - Cereal rye winter cover crop biomass modeled on data from 35 site-years. - We found a strong relationship between early and late-season biomass. - Random forest model with early-season biomass and weather data performed well. - Similar approach could improve decision support tools for cover crop management. Graphical Abstract available at: https://doi.org/10.1002/ael2.20121 Effect size estimates from the generalized linear mixed effects model prediction late-season cereal rye cover crop biomass. All covariates were standardized, and significant relationships are indicated by *p < 0.05, **p < 0.01, and ***p < 0.001. Abbreviations CGDD cumulative growing degree days GLMM generalized linear mixed effects model PAR photosynthetically active radiation
Post-harvest drone flights to measure weed growth and yield associations
(Agricultural & Environmental Letters, 2022-06-14) Miller, Jarrod O.; Shober, Amy L.; VanGessel, Mark J.
Drone flights are often only performed during the growing season, with no data collected once harvest has been completed, although they could be used to measure winter annual weed growth. Using a drone mounted with a multispectral sensor, we flew small plot corn (Zea mays L.) fertility, cover crop, and population studies at black layer and 0–14 d after harvest (DAH). Yields had positive correlations to normalized difference vegetation index (NDVI) at black layer but often had negative correlations to corn yields 0–14 DAH. After harvest, NDVI could be associated with weed growth, and negative correlations to yield could point to reduced corn canopy allowing light to reach late-season weeds. In fertility studies, excess nitrogen appears to increase weed biomass after harvest, which can be easily identified through drone imagery. Flights should be performed after corn harvest as weed growth may provide additional insight into management decisions. Core Ideas: - Corn yields can be correlated to post-harvest weed biomass by using NDVI. - Drone flights efficiently mapped weeds and made correlations to yield and management. - Fall weed control can be prioritized using drone mapping. Abbreviations: DAH days after harvest LAI leaf area index NDVI normalized difference vegetation index
Monitoring winter wheat growth at different heights using aerial imagery
(Agronomy Journal, 2021-02-09) Miller, Jarrod O.; Adkins, James
Drones (unmanned aerial vehicles) provide another system to mount sensors for measuring plant characteristics. For winter wheat (Triticum aestivum) this can include evaluating stands and making nitrogen (N) recommendations. Timing these flights and adequate camera resolution (based on flying height), must be known before applying tasks. This study observed six winter wheat planting populations (222, 297, 371, 445, 494, and 544 seeds m–2) at three different heights above ground level (30, 60, and 120 m) over three growing seasons. Plant populations could be separated at all growth stages and heights flown but were easier to separate right after emergence (GS11). In the spring, additional tillering caused the higher populations (371–544 seeds m–2) to have similar normalized difference vegetative index (NDVI), much like the final yields. Comparing changes in NDVI between flights was also successful in separating high and low planting populations, with inverse relationships in the fall and spring. A random forest classification of tiller counts by NDVI measurements ranked change in NDVI between stages as the most important compared to single flights. As separation and classification was successful at the lowest camera resolution (120 m), it can be possible for scouts to collect whole field imagery for analyses prior to deciding on split N applications.
Sensor-based measurements of NDVI in small grain and corn fields by tractor, drone, and satellite platforms
(Crop and Environment, 2024-02-01) Miller, Jarrod O.; Mondal, Pinki; Sarupria, Manan
The use of sensors for variable rate nitrogen (VRN) applications is transitioning from equipment-based to drone and satellite technologies. However, regional algorithms, initially designed for proximal active sensors, require evaluation for compatibility with remotely sensed reflectance and N-rate predictions. This study observed normalized difference vegetation index (NDVI) data from six small grain and two corn fields over three years. We employed three platforms: tractor-mounted active sensors (T-NDVI), passive multispectral drone (D-NDVI), and satellite (S-NDVI) sensors. Averaged NDVI values were extracted from the as-applied equipment polygons. Correlations between NDVI values from the three platforms were positive and strong, with D-NDVI consistently recording the highest values, particularly in areas with lower plant biomass. This was attributed to D-NDVI's lower soil reflectance and its ability to measure the entire biomass within equipment polygons. For small grains, sensors spaced on equipment booms might not capture accurate biomass in poor-growing and low NDVI regions. Regarding VRN, S-NDVI and D-NDVI occasionally aligned with T-NDVI recommendations but often suggested half the active sensor rate. Final yields showed some correlation with landscape variables, irrespective of N application. This finding suggests the potential use of drone or satellite imagery to provide multiple NDVI maps before application, incorporating expected landscape responses and thereby enhancing VRN effectiveness.
How manganese affects rice cadmium uptake and translocation in vegetative and mature plants
(Plant and Soil, 2024-04-19) Hu, Ruifang; Limmer, Matthew A.; Seyfferth, Angelia L.
Background and aims Rice is prone to Cd uptake under aerobic soil conditions primarily due to the OsNramp5 Mn transport pathway. Unlike Cd, Mn availability in rice paddies decreases as redox potential increases. We tested whether increasing Mn concentrations in solution would decrease Cd accumulation in rice through competition between Mn and Cd for uptake and/or suppression of OsNramp5 expression. Methods Rice was grown to maturity under Mn concentrations that spanned three orders of magnitude (0.30 to 37 μM) that corresponded to free Mn2+ activities of 10–7.9 to 10–5.0 M while free Cd2+ activity was held as constant as achievable (10–10.2 to 10–10.4 M). Plant biomass and elemental concentrations were measured in roots and shoots at each stage. Fold changes in the expression of OsNramp5, OsCd1, OsHMA3, OsCCX2, and OsYSL6 genes in vegetative and grain-filling stages of rice plants were determined. Results Competition between Mn and Cd for root uptake and accumulation in shoots was observed at the highest concentration of Mn tested. OsNramp5 expression was significantly higher in rice plants at the vegetative stage compared to the grain-filling stage, while OsCd1 and OsHMA3 showed the opposite. Solution Mn concentrations previously thought to be tolerable by rice grown to the vegetative stage led to Mn toxicity as plants matured. Conclusions Mn competes with Cd during uptake into rice with OsNramp5 expression unaffected. Different translocation paths may occur for Mn and Cd within the rice plant and over the rice life cycle, with OsCCX2 correlated with shoot Cd concentration.
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.
The unexplored role of preferential flow in soil carbon dynamics
(Soil Biology and Biochemistry, 2021-08-28) Franklin, Shane M.; Kravchenko, Alexandra N.; Vargas, Rodrigo; Vasilas, Bruce; Fuhrmann, Jeffry J.; Jin, Yan
Water is a crucial factor controlling the fate and processing of soil organics. Water commonly flows through the vadose zone via preferential flow pathways, resulting in nonuniform and rapid infiltration. Hence, a large portion of the soil matrix is bypassed. Preferential flow paths, often associated with well-connected macropore networks (>300 μm Ø), offer a unique balance between water availability, nutrient delivery, and re-oxygenation upon drainage. The heightened concentrations of moisture, nutrients, and oxygen make these locations optimal for high rates of microbial activity. Flow paths often display temporal stability. This stability results in repeated wetting and biogeochemical reactivation through time creating a lasting impact on micro-environmental conditions relevant to microbial functioning and carbon cycling in soil. Despite decades of research on preferential flow, there is still a need to link flow paths and the resultant heterogeneous moisture distributions to soil function. In this review, we discuss how preferential flow can serve as a framework of reference for the spatially and temporally heterogeneous biogeochemical cycling of soil carbon. We highlight the importance of combining current knowledge of pore-scale carbon dynamics with an appreciation of connected networks of hydraulically active pores/paths within the soil profile. Such combination opens new possibilities for upscaling pore-scale processes with the inclusion of resource heterogeneity at the macroscale. Working within this hydraulically connected framework can provide insight for the mechanistic representation of hot moments, which are temporally isolated large pulses of CO2 after rewetting or thawing events. We conclude with suggestions on knowledge gaps and stress the critical need of linking soil physics with biology to mechanistically understand soil functions. Highlights • Preferential flow paths play a key role in soil carbon dynamics. • Pore-scale carbon dynamics could be upscaled using hydraulic connectivity. • A conceptual model is presented that considers how soil pores function from hydrological and microbial perspectives.
Soil nitrogen cycling in forests invaded by the shrub Rosa multiflora: importance of soil moisture and invasion density
(Biogeochemistry, 2024-03-23) Moore, Eric R.; Pouyat, Richard V.; Trammell, Tara L. E.
Invasive plants often alter ecosystem function and processes, especially soil N cycling. In eastern United States forests, the shrub Rosa multiflora (“rose”) is a dominant invader, yet potential effects on N cycling are poorly understood. Moreover, invasive plant management can impact soil N cycling by decreasing plant N uptake and disturbing the soil. The objectives of this study were to evaluate N cycling along a gradient of rose invasion (observational) and investigate potential changes to N cycling (manipulative) under four different management strategies: (1) do nothing (the control), (2) invasive plant removal, (3) removal followed by native seed mix addition, (4) removal, native seed mix, and chipped rose stem addition. We selected three forest sites experiencing a Low, Medium, or High amount of shrub invasion, and measured N cycling in the early (June) and late (September) growing seasons. We found N was immobilized in June and mineralized in September. One year after experimental management, removal alone had no effect on N cycling compared to control plots, but addition of native seed mix and chipped stems reduced early-season nitrification in our Medium invasion site. Our findings suggest that rose invasion may increase N cycling rates when soils are dry, which may occur more frequently with future climate change. In addition, N cycling responds differentially to management in the year following invasive plant removal, but most noticeably under moderate rose invasion.
Far-red Light and Nitrogen Concentration Elicit Crop-specific Responses in Baby Greens under Superelevated CO2 and Continuous Light
(Journal of the American Society for Horticultural Science, 2024-03-05) Kennebeck, Emily J.; Meng, Qingwu
Baby greens are becoming increasingly popular in the consumer market because of their desired flavor and leaf size. The short life cycles and fast response times to environmental stimuli make baby greens ideal for testing environmental conditions for space crop production. Additionally, far-red (FR) light has been used for microgreen and baby green research to enhance stem elongation, leaf expansion, and biomass; however, how it interacts with nutrient solution nitrogen (N) concentrations remains unclear. During this ground-based study, we characterized how FR light and N concentrations influenced the growth and morphology of Chinese cabbage (Brassica rapa var. chinensis cv. Tokyo Bekana) and kale (Brassica oleracea var. sabellica cv. Red Russian) baby greens under similar superelevated CO2 and low relative humidity to levels observed in spaceflight. Plants were subject to combinations of four sole-source light spectra and three N concentrations (75, 125, and 175 mg⋅L−1). At the same total photon flux density (PFD) of 200 μmol⋅m−2⋅s−1, we maintained the same blue and green PFDs at 25 μmol⋅m−2⋅s−1 each; the remaining 150 μmol⋅m−2⋅s−1 comprised four red (R) and FR PFD combinations (FR: 0, 25, 50, and 75 μmol⋅m−2⋅s−1). Increasing the FR PFD enhanced the typical shade-avoidance morphology of Chinese cabbage ‘Tokyo Bekana’ and kale ‘Red Russian’, exhibiting leaf length increases of 20% to 26% and 31% to 61%, respectively. Edible biomass did not increase with increasing FR PFDs for either species, regardless of the N concentration. Increasing the N concentration increased the Chinese cabbage ‘Tokyo Bekana’ fresh mass and dry mass by 32% to 59% and 37% to 74%, respectively, except under 25 μmol⋅m−2⋅s−1 of FR light, with which shoot fresh mass increased by 55% with an increasing N concentration from 75 to 125 mg⋅L−1; however, the shoot dry mass was unaffected. Increasing the N concentration did not affect kale ‘Red Russian’ growth under various FR PFDs. We conclude that partially substituting incremental FR light for R light elicits the shade-avoidance response, with little influence on the growth, of Chinese cabbage ‘Tokyo Bekana’ and kale ‘Red Russian’ baby greens under superelevated CO2 and continuous light, and that the former, but not the latter, crop can benefit from increased N fertilization.
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.
Mustard ‘Amara’ Benefits from Superelevated CO2 While Adapting to Far-red Light Over Time
(HortScience, 2024-01-05) Kennebeck, Emily J.; Meng, Qingwu
Compared with the ambient Earth carbon dioxide concentration (≈415 μmol⋅mol–1), the International Space Station has superelevated carbon dioxide (≈2800 μmol⋅mol–1), which can be a stressor to certain crops. Far-red light can drive plant photosynthesis and increase extension growth and biomass. However, the effects of far-red light under superelevated carbon dioxide are unclear. We grew hydroponic mustard (Brassica carinata) ‘Amara’ seedlings in four growth chambers using a randomized complete block design with two carbon dioxide concentrations (415 and 2800 μmol⋅mol–1), two lighting treatments, and two blocks at temperature and relative humidity set points of 22 °C and 40%, respectively. Each growth chamber had two lighting treatments at the same total photon flux density of 200 μmol⋅m–2⋅s–1. Under the same blue and green light at 50 μmol⋅m–2⋅s–1 each, plants received either red light at 100 μmol⋅m–2⋅s–1 or red + far-red light at 50 μmol⋅m–2⋅s–1 each. At day 15 after planting, far-red light did not influence shoot fresh or dry mass at 415 μmol⋅mol–1 carbon dioxide, but decreased both parameters by 22% to 23% at 2800 μmol⋅mol–1 carbon dioxide. Increasing the carbon dioxide concentration increased shoot fresh and dry mass 27% to 49%, regardless of the lighting treatment. Far-red light decreased leaf area by 16% at 2800 μmol⋅mol–1 carbon dioxide, but had no effect at 415 μmol⋅mol–1 carbon dioxide. Increasing the carbon dioxide concentration increased leaf area by 21% to 33%, regardless of far-red light. Regardless of the carbon dioxide concentration, far-red light promoted stem elongation and decreased chlorophyll concentrations by 39% to 42%. These responses indicate far-red light elicited a crop-specific shade avoidance response in mustard ‘Amara’, increasing extension growth but decreasing leaf area, thereby reducing light interception and biomass. In addition, carbon dioxide enrichment up to 2800 μmol⋅mol–1 increased the biomass of mustard ‘Amara’ but decreased the biomass of other crops, indicating crop-specific tolerance to superelevated carbon dioxide. In conclusion, mustard ‘Amara’ seedlings benefit from superelevated carbon dioxide, but exhibit growth reduction under far-red light under superelevated carbon dioxide.

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