Soil and Crop Sciences Research

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Crop and Soil Sciences Research. Submission are by authorized individuals, only.

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Data from "Phylogenetic relatedness can influence cover crop-based weed suppression"
Menalled, Uriel D.; Smith, Richard G.; Cordeau, Stephane; DiTommaso, Antonio; Pethybridge, Sarah J.; Ryan, Matthew R. (2023-10-17)
These files contain data that Menalled et al. (2023) used to test how the relatedness between cover crops and weeds affects weed suppression and community assembly. The data was generated through winter and summer field experiments replicated for four site-years. Each site-year consisted of four cover crop treatments and one tilled control, replicated in four blocks for a total of 20 plots per site-year. Plant biomass was sampled at the end of the cover crop growing season in two 0.25 m2 (76 cm × 33 cm) quadrats randomly placed in each plot. During sampling, each quadrat was placed perpendicularly over four crop rows to ensure a consistent proportion of crop row and interrow area. To avoid pseudoreplication, samples were summed at the plot level. The samples were dried at 60 °C for at least 2 weeks before obtaining dry weight for analysis. Results show that cover crops can modify weed community structure by suppressing phylogenetically related weed species more intensely than phylogenetically unrelated weeds. All analyses and results are reported and discussed in Menalled et al. (2023): “Phylogenetic relatedness can influence cover crop-based weed suppression.”
S Krishna Kumar 2023 PhD Thesis Supplementary Tables
Kumar, Shanthanu Krishna; Peck, Gregory (2023-08-09)
These data files are a supplement in support of a thesis with the following abstract: Methods for processing the data: Pooled libraries were sequenced using HiSeqX 150 bp Pair End sequencing (Psomagen Inc, Rockville MD). Raw RNA-Seq reads were processed to remove adaptors and low-quality sequences using Trimmomatic (version 0.36; Bolger et al. 2014) with parameters ‘SLIDINGWINDOW:4:20 LEADING:3 TRAILING:3 MINLEN:40’ and to remove polyA/T tails using PRINSEQ++ [v1.2; (Cantu et. al. 2019) with parameters ‘-min_len 40 -trim_tail_left 10 -trim_tail_right 10’]. The remaining cleaned reads were aligned to the ribosomal RNA database (Quast et al. 2013) using Bowtie (version 1.1.2; Langmead, 2010) allowing up to three mismatches, and those aligned were discarded. The final cleaned reads were aligned to the ‘Golden Delicious’ double haploid (GDDH13) genome (v1.1; Daccord et al. 2017) using HISAT2 (version 2.1.0; Kim et al. 2019) with default parameters. Based on the alignments, raw read counts for each gene were calculated and then normalized to fragments per kilobase of exon model per million mapped fragments (FPKM). Raw read counts were then fed to DESeq2 to identify differentially expressed genes (DEGs) using a cutoff of adjusted P value < 0.05 and fold change ≥ 2. Gene ontology terms enriched in the lists of genes were identified using Blast2GO (Conesa et al. 2005) with a cutoff of adjusted P value < 0.05. Transcription factors were identified by using the blast tool in the genome database for Rosaceae and homolog comparisons with the Arabidopsis genome (Sook et al. 2018).
Data from: Fertility and tillage intensity affect weed community diversity and functional structure in long-term organic systems
Allen, Jake; Menalled, Uriel D.; Adeux, Guillaume; Pelzer, Christopher J.; Wayman, Sandra; Jernigan, Ashley B.; Cordeau, Stéphane; DiTommaso, Antonio; Ryan, Matthew R. (2023-03-13)
These files contain data supporting all results reported in Allen et al., which tested the effects of fertility and tillage intensity gradients on weed communities in long-term organic cropping systems. This study assessed the seed banks and weed communities of a long-term experiment initiated in 2005, which compared four organic systems differing in nutrient inputs and soil disturbance. The high fertility (HF) system received high-rate nutrient applications, low fertility (LF) received low-rate applications, enhanced weed management (EWM) focused on weed control through frequent soil disturbance, and reduced tillage (RT) prioritized soil health with less intense or frequent soil disturbance. Soil samples for greenhouse germination assays were collected at the beginning (2017) and end (2022) of the experiment’s last crop rotation cycle to explore how these four systems influenced seed bank dynamics over time. Weed community biomass was also sampled in each crop. Treatment effects on weed abundance, taxonomic diversity, and community-weighted means and functional dispersion of weed traits were analyzed with generalized mixed effect models. The RT system had the highest weed seed bank taxonomic diversity and EWM had the lowest. RT and LF had higher functional dispersion of traits than HF in the seed bank. Weed seed bank communities in HF and RT were characterized by short, small-seeded, and early germinating weed species. However, seed banks were also labile: differences between systems in seed density and mean trait values were dependent on the crop which preceded seed bank sampling. Likewise, while the traits of emergent weed communities differed in the four system treatments, they depended on an interaction between crop species and their planting year. Results suggest that resource availability and intensity of disturbance act as weed community assembly filters in organic cropping systems. Organic growers seeking to design systems that balance weed management and production goals can use relatively low soil disturbance and nutrient application to increase weed community taxonomic or functional diversity without necessarily increasing weed biomass or seed bank density.
Data from: Adverse effects of inbreeding on the transgenerational expression of herbivore-induced defense traits in Solanum carolinense
Nihranz, Chad; Helms, Anjel; Tooker, John; Mescher, Mark; De Moraes, Consuelo; Stephenson, Andrew G. (2022-09-14)
These files contain data supporting all results reported in Nihranz et al. "Adverse effects of inbreeding on the transgenerational expression of herbivore-induced defense traits in Solanum carolinense". In Nihranz et al. we found: We found that feeding by Manduca sexta caterpillars on maternal Solanum carolinense plants had a positive influence on trichome and spine production in offspring and that caterpillar development on offspring of herbivore- damaged maternal plants was delayed relative to that on offspring of undamaged plants. Offspring of inbred maternal plants had reduced spine production, compared to those of outbred plants, and caterpillars performed better on these plants. Both herbivory and inbreeding in the maternal generation altered volatile emissions of offspring. In general, maternal plant inbreeding dampened transgenerational effects of herbivory on offspring defensive traits and herbivore resistance. Taken together, this study demonstrates that inducible defenses in S. carolinense can persist across generations and that inbreeding compromises transgenerational resistance in S. carolinense.
Data from: Cereal rye mulch biomass and crop density affect weed suppression and community assembly in no-till planted soybean: A species and trait-based analysis
Menalled, Uriel D.; Adeux, Guillaume; Cordeau, Stéphane; Smith, Richard G.; Mirsky, Steven B.; Ryan, Matthew R. (2022-04-15)
These files contain data that Menalled et al. (2022) used to test the effects of crop density and mulch biomass on weed suppression and community assembly. The data was generated through a field experiment replicated for four site-years. In each site-year, soybean was planted at five rates from 0 to 74 seeds m-2, and five cereal rye mulch levels were established from 0 to 2 times the ambient cereal rye biomass within each site-year for 25 unique treatments. All treatments were replicated in four blocks for 100 plots per site-year. Approximately 15 weeks after soybean planting, weed biomass, soybean density, and mulch biomass were sampled in each plot. Changes in weed biomass and species abundance were used to assess weed suppression and community composition. We assessed treatment effects on weed life cycle, emergence timing, seed weight, height, and specific leaf area using trait data for each species. Results show that multi-tactic weed management can enhance weed suppression and promote the management of diverse weed functional groups. All analyses and results are reported and discussed in Menalled et al. (2022): “Cereal rye mulch biomass and crop density affect weed suppression and community assembly in no-till planted soybean.”
Data from: The Physiological Basis for Estimating Photosynthesis from Chlorophyll a Fluorescence
Han, Jimei; Gu, Lianhong; Zhang, Yongjiang; Sun, Ying (2022-02-17)
These files contain data supporting all results reported in Han et. al. The Physiological Basis for Estimating Photosynthesis from Chlorophyll a Fluorescence. In Han et al. we found: The availability of Solar-Induced chlorophyll Fluorescence (SIF) offers potential to curb large uncertainties in estimating photosynthesis across biomes, climates, and scales. However, it remains unclear how SIF should be used to mechanistically estimate photosynthesis. This study built a quantitative framework to estimate photosynthesis, based on a mechanistic light reaction model with chlorophyll a fluorescence from PSII (SIFPSII) as an input (MLR-SIF). Utilizing 29 C3 and C4 plant species representative of major plant biomes across the globe, we verified such a framework at the leaf level. MLR-SIF is capable of accurately reproducing photosynthesis for all C3 and C4 species under diverse light, temperature, and CO2 conditions. We further tested the robustness of MLR-SIF using Monte Carlo simulations, and found that the estimated photosynthesis is much less sensitive to parameter uncertainties relative to the conventional Farquhar, von Caemmerer, Berry (FvCB) model because of additional independent information contained in SIFPSII. SIFPSII, once inferred from direct observables of SIF, provides “parameter savings” to the MLR-SIF as compared to the mechanistically equivalent FvCB and thus shortcuts the uncertainties propagated from imperfect model parameterization. Our findings set the stage for future efforts employing SIF mechanistically to improve photosynthesis estimation across scales, functional groups, and environmental conditions.
Data From: Unpacking the drivers of diurnal dynamics of sun-induced chlorophyll fluorescence (SIF): Canopy structure, plant physiology, instrument configuration and retrieval methods
Chang, Christine Y.; Sun, Ying; Gu, Lianhong; Wood, Jeffrey D. (2022-02-09)
Data in support of research: Sun-induced chlorophyll fluorescence (SIF) from spaceborne sensors is a promising tool for global carbon cycle monitoring, but its application is constrained by insufficient understanding of the drivers underlying diurnal SIF dynamics. SIF measurements from ground-based towers can reveal diurnal SIF dynamics across biomes and environmental conditions; however, meaningful interpretation of diurnal variations requires disentangling impacts from canopy structure, plant physiology, instrument configuration and retrieval methods, which often interact with and confound each other. This study aims to unpack these drivers using 1) concurrent ground and airborne canopy-scale and leaf-scale measurements at a corn field, 2) a mechanistic SIF model that explicitly considers the dynamics of photochemistry (via the fraction of open photosystem II reaction centers, qL) and photoprotection (via nonphotochemical quenching, NPQ) as well as their interactive dependence on the sub-canopy light environment, and 3) cross-comparison of SIF instrument configurations and retrieval methods. We found that crop row orientations and sun angles can introduce a distinctive midday dip in SIF in absence of stress, due to a midday drop of absorbed photosynthetically active radiation (APAR) when crop rows are north-south oriented. Canopy structure caused distinctive responses in both qL and NPQ at different positions within the vertical canopy that collectively influenced fluorescence quantum yield (ΦF) at the leaf scale. Once integrated at the canopy scale, diurnal dynamics of both APAR and canopy escape probability (ε) are critical for accurately shaping diurnal SIF variations. While leaf-level qL and NPQ exhibited strong diurnal dynamics, their influence was attenuated at the canopy scale due to opposing effects on SIF at different canopy layers. Furthermore, different system configurations (i.e., bi-hemispherical vs. hemispherical-conical) and retrieval methods can bias the SIF magnitude and distort its diurnal shapes, therefore confounding the interpretation of inherent strength and dynamics of SIF emission. Our findings demonstrate the importance of crop row structures, interactive variations in canopy structure and plant physiology, instrument configuration, and retrieval method in shaping the measured dynamics of diurnal SIF. This study highlights the necessity to account for these factors to accurately interpret satellite SIF, and informs future synthesis work with different SIF instrumentation and retrieval methods across sites.
Data From: Co-precipitation Induces Changes to Iron and Carbon Chemistry and Spatial Distribution at the Nanometer Scale
Possinger, Angela R.; Zachman, Michael J.; Dynes, James J.; Regier, Tom Z.; Kourkoutis, Lena F.; Lehmann, Johannes (2021-09-24)
Data in support of research on: Association of organic matter (OM) with mineral phases via co-precipitation is expected to be a widespread process in environments with high OM input and frequent mineral dissolution and re-precipitation. In contrast to surface area-limited adsorption processes, co-precipitation may allow for greater carbon (C) accumulation. However, the potential sub-micrometer scale structural and compositional differences that affect the bioavailability of co-precipitated C are largely unknown. In this study, we used a combination of high-resolution analytical electron microscopy and bulk spectroscopy to probe interactions between a mineral phase (ferrihydrite, nominally Fe2O3•0.5H2O) and organic soil-derived water-extractable OM (WEOM). In co-precipitated WEOM-Fe, nanometer-scale scanning transmission electron microscopy with electron energy loss spectroscopy (STEM-EELS) revealed increased Fe(II) and less Fe aggregation relative to adsorbed WEOM-Fe. Spatially distinct lower- and higher-energy C regions were detected in both adsorbed and co-precipitated WEOM-Fe. In co-precipitates, lower-energy aromatic and/or substituted aromatic C was spatially associated with reduced Fe(II), but higher-energy oxidized C was enriched at the oxidized Fe(III) interface. Therefore, we show that co-precipitation does not constitute a non-specific physical encapsulation of C that only affects Fe chemistry and spatial distribution, but may cause a bi-directional set of reactions that lead to spatial separation and transformation of both Fe and C forms. In particular, we propose that abiotic redox reactions between Fe and C via substituted aromatic groups (e.g., hydroquinones) play a role in creating distinct co-precipitate composition, with potential implications for its mineralization.
Data from: Finding the right mix: a framework for selecting seeding rates for cover crop mixtures
Bybee-Finley, K. Ann; Cordeau, Stéphane; Yvoz, Séverin; Mirsky, Steven B.; Ryan, Matthew R. (2021-07-09)
This dataset consists of experiment data that was used to design a framework for constructing cover crop mixtures and validation data that was used to test the effectiveness of the models within the framework. The framework was developed using data from a field experiment, which included six response surface designs of two-species mixtures, as well as a factorial replacement design of three- and four-species mixtures. We quantified intra- and interspecific competition among two grasses and two legume cover crop species with grass and legume representing two functional groups: pearl millet [Pennisetum glaucum (L.) R. Br.], sorghum sudangrass [Sorghum bicolor (L.) Moench × S. sudanense (Piper) Stapf], sunn hemp (Crotalaria juncea L.), and cowpea [Vigna unguiculata (L.) Walp]. Yield-density models were fit to estimate intra- and interspecific competition coefficients for each species in biculture. Competition coefficients were used to build models that estimated the biomass of each cover crop species in three- and four-species mixtures. The competition coefficients and models were validated with an additional nine site-years testing the same cover crop mixtures. Accounting for competition when constructing cover crop mixtures can improve the ecosystem services provided, and such an advancement would likely lead to greater farmer adoption.
Data from: Plants and mycorrhizal symbionts acquire substantial soil nitrogen from gaseous ammonia transport
Hestrin, Rachel; Weber, Peter; Pett-Ridge, Jennifer; Lehmann, Johannes (2021)
data in support of research on 1) Nitrogen (N) is an essential nutrient that limits plant growth in many ecosystems. Here we investigate an overlooked component of the terrestrial N cycle—subsurface ammonia (NH3) gas transport and its contribution to plant and mycorrhizal N acquisition. 2) We used controlled mesocosms, soil incubations, stable isotopes, and imaging to investigate edaphic drivers of NH3 gas efflux, track lateral subsurface N transport originating from 15NH3 gas or 15N-enriched organic matter, and assess plant and mycorrhizal N assimilation from this gaseous transport pathway. 3) NH3 is released from soil organic matter, travels below ground, and contributes to root and fungal N content. Abiotic soil properties (pH and texture) influence the quantity of NH3 available for subsurface transport. Mutualisms with arbuscular mycorrhizal (AM) fungi can substantially increase plant NH3-N uptake. The grass Brachypodium distachyon acquired 6-9% of total plant N from organic matter-N that traveled as a gas below ground. Colonization by the AM fungus Rhizophagus irregularis was associated with a twofold increase in total plant N acquisition from subsurface NH3 gas. 4) NH3 gas transport and uptake pathways may be fundamentally different from those of more commonly studied soil N species and warrant further research.

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