School of Plant and Environmental Sciences
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SPES was formed in 2017 from three departments: Crop and Soil Environmental Sciences; Horticulture; and Plant Pathology, Physiology, and Weed Science.
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Browsing School of Plant and Environmental Sciences by Department "Biological Systems Engineering"
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- AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadataLiang, Xiao; Akers, Kyle; Keenum, Ishi M.; Wind, Lauren L.; Gupta, Suraj; Chen, Chaoqi; Aldaihani, Reem; Pruden, Amy; Zhang, Liqing; Knowlton, Katharine F.; Xia, Kang; Heath, Lenwood S. (2021-03-10)Background Metagenomics is gaining attention as a powerful tool for identifying how agricultural management practices influence human and animal health, especially in terms of potential to contribute to the spread of antibiotic resistance. However, the ability to compare the distribution and prevalence of antibiotic resistance genes (ARGs) across multiple studies and environments is currently impossible without a complete re-analysis of published datasets. This challenge must be addressed for metagenomics to realize its potential for helping guide effective policy and practice measures relevant to agricultural ecosystems, for example, identifying critical control points for mitigating the spread of antibiotic resistance. Results Here we introduce AgroSeek, a centralized web-based system that provides computational tools for analysis and comparison of metagenomic data sets tailored specifically to researchers and other users in the agricultural sector interested in tracking and mitigating the spread of ARGs. AgroSeek draws from rich, user-provided metagenomic data and metadata to facilitate analysis, comparison, and prediction in a user-friendly fashion. Further, AgroSeek draws from publicly-contributed data sets to provide a point of comparison and context for data analysis. To incorporate metadata into our analysis and comparison procedures, we provide flexible metadata templates, including user-customized metadata attributes to facilitate data sharing, while maintaining the metadata in a comparable fashion for the broader user community and to support large-scale comparative and predictive analysis. Conclusion AgroSeek provides an easy-to-use tool for environmental metagenomic analysis and comparison, based on both gene annotations and associated metadata, with this initial demonstration focusing on control of antibiotic resistance in agricultural ecosystems. Agroseek creates a space for metagenomic data sharing and collaboration to assist policy makers, stakeholders, and the public in decision-making. AgroSeek is publicly-available at https://agroseek.cs.vt.edu/ .
- Changes in Fluvial Erosion of Cohesive Streambank Soils with Stream ChemistryThompson, Theresa M.; Akinola, Akinrotimi I.; Hoomehr, Siavash; Eick, Matthew J. (2018-06-01)The goal of this study was to quantify changes in fluvial erosion rates with changes in stream chemistry.
- Characterizing glucose, illumination, and nitrogen-deprivation phenotypes of Synechocystis PCC6803 with Raman spectroscopyTanniche, Imen; Collakova, Eva; Denbow, Cynthia J.; Senger, Ryan S. (2020-03-30)Background. Synechocystis sp. PCC6803 is a model cyanobacterium that has been studied widely and is considered for metabolic engineering applications. Here, Raman spectroscopy and Raman chemometrics (Rametrix (TM)) were used to (i) study broad phenotypic changes in response to growth conditions, (ii) identify phenotypic changes associated with its circadian rhythm, and (iii) correlate individual Raman bands with biomolecules and verify these with more accepted analytical methods. Methods. Synechocystis cultures were grown under various conditions, exploring dependencies on light and/or external carbon and nitrogen sources. The Rametrix (TM) LITE Toolbox for MATLAB (R) was used to process Raman spectra and perform principal component analysis (PCA) and discriminant analysis of principal components (DAPC). The Rametrix (TM) PRO Toolbox was used to validate these models through leave-oneout routines that classified a Raman spectrum when growth conditions were withheld from the model. Performance was measured by classification accuracy, sensitivity, and specificity. Raman spectra were also subjected to statistical tests (ANOVA and pairwise comparisons) to identify statistically relevant changes in Synechocystis phenotypes. Finally, experimental methods, including widely used analytical and spectroscopic assays were used to quantify the levels of glycogen, fatty acids, amino acids, and chlorophyll a for correlations with Raman data. Results. PCA and DAPC models produced distinct clustering of Raman spectra, representing multiple Synechocystis phenotypes, based on (i) growth in the presence of 5 mM glucose, (ii) illumination (dark, light/dark [12 h/12 h], and continuous light at 20 mE), (iii) nitrogen deprivation (0-100%NaNO3 of native BG-11 medium in continuous light), and (iv) throughout a 24 h light/dark (12 h/12 h) circadian rhythm growth cycle. Rametrix (TM) PRO was successful in identifying glucose-induced phenotypes with 95.3% accuracy, 93.4% sensitivity, and 96.9% specificity. Prediction accuracy was above random chance values for all other studies. Circadian rhythm analysis showed a return to the initial phenotype after 24 hours for cultures grown in light/dark (12 h/12 h) cycles; this did not occur for cultures grown in the dark. Finally, correlation coefficients (R > 0.7) were found for glycogen, all amino acids, and chlorophyll a when comparing specific Raman bands to other experimental results.
- Characterizing metabolic stress-induced phenotypes of Synechocystis PCC6803 with Raman spectroscopyTanniche, Imen; Collakova, Eva; Denbow, Cynthia J.; Senger, Ryan S. (2020-03-30)Background. During their long evolution, Synechocystis sp. PCC6803 developed a remarkable capacity to acclimate to diverse environmental conditions. In this study, Raman spectroscopy and Raman chemometrics tools (Rametrix (TM)) were employed to investigate the phenotypic changes in response to external stressors and correlate specific Raman bands with their corresponding biomolecules determined with widely used analytical methods. Methods. Synechocystis cells were grown in the presence of (i) acetate (7.5-30 mM), (ii) NaCl (50-150 mM) and (iii) limiting levels of MgSO4 (0-62.5 mM) in BG-11 media. Principal component analysis (PCA) and discriminant analysis of PCs (DAPC) were performed with the Rametrix (TM) LITE Toolbox for MATLABR (R). Next, validation of these models was realized via Rametrix (TM) PRO Toolbox where prediction of accuracy, sensitivity, and specificity for an unknown Raman spectrum was calculated. These analyses were coupled with statistical tests (ANOVA and pairwise comparison) to determine statistically significant changes in the phenotypic responses. Finally, amino acid and fatty acid levels were measured with well-established analytical methods. The obtained data were correlated with previously established Raman bands assigned to these biomolecules. Results. Distinguishable clusters representative of phenotypic responses were observed based on the external stimuli (i.e., acetate, NaCl, MgSO4, and controls grown on BG-11 medium) or its concentration when analyzing separately. For all these cases, Rametrix (TM) PRO was able to predict efficiently the corresponding concentration in the culture media for an unknown Raman spectra with accuracy, sensitivity and specificity exceeding random chance. Finally, correlations (R > 0.7) were observed for all amino acids and fatty acids between well-established analytical methods and Raman bands.
- Facilitated iron reduction as a possible means of rejuvenating phosphorus removal performance of filtration substratesRosenquist, Shawn E.; Levy, C. L.; Sell, S. T.; Hession, W. Cully; Eick, Matthew J.; Vaughan, David H. (American Society of Agricultural and Biological Engineers, 2011)In order to mitigate nutrient pollution in surface runoff more sustainably, the finite capacity for phosphorus (P) sequestration in best management practices (BMP) that rely heavily on sorption processes must be addressed. These BMP include sand filters, bioretention cells, and several types of constructed wetland. This study investigated facilitated microbial reduction of iron-based filtration substrates to promote controlled release of P previously sequestered by the BMP, P harvest for recycling, and rejuvenation of the substrate sorption capacity. Total dissolved P was well correlated with total dissolved iron during the reduction process, indicating that microbial iron reduction was capable of releasing previously sequestered P from substrates. Furthermore, results indicated that a sufficient carbon source was necessary but addition of a microbial culture was not necessary to facilitate iron reduction. While a large percentage of the previously sequestered P was removed, the process was much slower than initial sequestration of P by adsorption, and further research is needed to promote a more rapid release of P in order to optimize the rejuvenation process for field application.
- Feedstock Contract Considerations for a Piedmont BiorefineryCundiff, John S.; Grisso, Robert D.; Fike, John H. (MDPI, 2020-12-14)A biorefinery purchasing feedstock (perennial grass) must offer contracts that provide the same opportunity to earn a profit for a feedstock contractor located 50 or 5 km from the biorefinery. The business plan presented here specifies that the biomass is purchased in satellite storage locations (SSLs), and the load-out and hauling costs are paid by the biorefinery. Contracts can be offered for harvest in September, October, and November, a three-month harvest window, or the harvest window can be extended to December, January, and February, a six-month harvest window. Required total storage capacity is 75% of annual consumption for the three-month window and 50% for the six-month window, a significant difference in total storage capacity (cost). The storage cost difference paid by the biorefinery is 5.27 and 3.52 USD/Mg for the three-month and six-month, respectively. Several issues must be addressed in the feedstock contracts: (1) earlier harvest, before plant senescence, means less nutrients are translocated back into the soil and more are removed at harvest; (2) harvest losses are higher for all harvests after the September harvest; and (3) storage losses increase with storage time in the SSL. Time of removal from the SSL is dictated by the biorefinery; thus, the feedstock contractor must be compensated. The contracts paid by the biorefinery, averaged across the entire annual consumption, were about the same for the three-month window, and six-month window. This result was obtained because fertilizer cost decreases and harvest losses increase as the harvest date increases; thus, the two factors tend to offset. Using a 77 USD/Mg base cost, representative feedstock payment at the SSL (no storage losses included) for contractors with various month contracts are September (84.30), October (85.54), November (86.72), December 88.63), January (89.98), and February (90.58). Subsequent compensation for storage losses depends on the amount of time the particular unit of biomass is in storage before shipment.
- A mycotoxin transporter (4D) from a library of deoxynivalenol-tolerant microorganismsJimenez-Sanchez, Celia; Wilson, Nina M.; McMaster, Nicole J.; Gantulga, Dash; Freedman, Benjamin G.; Senger, Ryan S.; Schmale, David G. III (Elsevier, 2020-03-01)New strategies are needed to mitigate the mycotoxin deoxynivalenol (DON) in feed and food products. Microbial DNA fragments were generated from a library of DON-tolerant microorganisms. These fragments were screened in DON-sensitive yeast strains for their ability to modify or transport DON. Fragments were cloned into a PCR8/TOPO vector, and recombined into the yeast vector, pYES-DEST52. Resulting yeast transformants were screened in the presence of 100 ppm DON. Transformants that were able to grow in the presence of DON were plated on a selective medium, and the cloned microbial DNA fragments were sequenced. BLAST queries of one microbial DNA fragment (4D) showed a high degree of similarity to an ABC transporter. A series of screening and inhibition assays were conducted with a transport inhibitor (propanol), to test the hypothesis that 4D is a mycotoxin transporter. DON concentrations did not change for yeast transformants expressing 4D. The ability of yeast transformants expressing 4D to transport DON was inhibited by the addition of propanol. Moreover, yeast transformants expressing a known efflux pump (PDR5) showed similar trends in propanol transport inhibition compared to 4D. Future work should consider mycotoxin transporters such as 4D to the development of transgenic plants to limit DON accumulation in seeds.
- Overcoming Biomass Recalcitrance by Combining Genetically Modified Switchgrass and Cellulose Solvent-Based Lignocellulose PretreatmentSathitsuksanoh, Noppadon; Xu, Bin; Zhao, Bingyu Y.; Zhang, Y. H. Percival (2013-09-27)Decreasing lignin content of plant biomass by genetic engineering is believed to mitigate biomass recalcitrance and improve saccharification efficiency of plant biomass. In this study, we compared two different pretreatment methods (i.e., dilute acid and cellulose solvent) on transgenic plant biomass samples having different lignin contents and investigated biomass saccharification efficiency. Without pretreatment, no correlation was observed between lignin contents of plant biomass and saccharification efficiency. After dilute acid pretreatment, a strong negative correlation between lignin content of plant samples and overall glucose release was observed, wherein the highest overall enzymatic glucan digestibility was 70% for the low-lignin sample. After cellulose solvent- and organic solvent-based lignocellulose fractionation pretreatment, there was no strong correlation between lignin contents and high saccharification efficiencies obtained (i.e., 80-90%). These results suggest that the importance of decreasing lignin content in plant biomass to saccharification was largely dependent on pretreatment choice and conditions.
- Overexpression of AtLOV1 in Switchgrass Alters Plant Architecture, Lignin Content, and Flowering TimeXu, Bin; Sathitsuksanoh, Noppadon; Tang, Yuhong; Udvardi, Michael K.; Zhang, Ji-Yi; Shen, Zhengxing; Balota, Maria; Harich, Kim; Zhang, Y. H. Percival; Zhao, Bingyu Y. (2012-12-26)Background: Switchgrass (Panicum virgatum L.) is a prime candidate crop for biofuel feedstock production in the United States. As it is a self-incompatible polyploid perennial species, breeding elite and stable switchgrass cultivars with traditional breeding methods is very challenging. Translational genomics may contribute significantly to the genetic improvement of switchgrass, especially for the incorporation of elite traits that are absent in natural switchgrass populations. Methodology/Principal Findings: In this study, we constitutively expressed an Arabidopsis NAC transcriptional factor gene, LONG VEGETATIVE PHASE ONE (AtLOV1), in switchgrass. Overexpression of AtLOV1 in switchgrass caused the plants to have a smaller leaf angle by changing the morphology and organization of epidermal cells in the leaf collar region. Also, overexpression of AtLOV1 altered the lignin content and the monolignol composition of cell walls, and caused delayed flowering time. Global gene-expression analysis of the transgenic plants revealed an array of responding genes with predicted functions in plant development, cell wall biosynthesis, and flowering. Conclusions/Significance: To our knowledge, this is the first report of a single ectopically expressed transcription factor altering the leaf angle, cell wall composition, and flowering time of switchgrass, therefore demonstrating the potential advantage of translational genomics for the genetic improvement of this crop.
- Perspectives on Harmful Algal Blooms (HABs) and the Cyberbiosecurity of Freshwater SystemsSchmale, David G. III; Ault, Andrew P.; Saad, Walid; Scott, Durelle T.; Westrick, Judy A. (Frontiers, 2019-06-04)Harmful Algal Blooms (HABs) have been observed in all 50 states in the U.S., ranging from large freshwater lakes, such as the Great Lakes, to smaller inland lakes, rivers, and reservoirs, as well as marine coastal areas and estuaries. In 2014, a HAB on Lake Erie containing microcystin (a liver toxin) contaminated the municipal water supply in Toledo, Ohio, providing non-potable water to 400,000 people. Studying HABs is complicated as different cyanobacteria produce a range of toxins that impact human health, such as microcystins, saxitoxin, anatoxin-a, and cylindrospermopsin. HABs may be increasing in prevalence with rising temperatures and higher nutrient runoff. Consequently, new tools and technology are needed to rapidly detect, characterize, and respond to HABs that threaten our water security. A framework is needed to understand cyber threats to new and existing technologies that monitor and forecast our water quality. To properly detect, assess, and mitigate security threats on water infrastructure, it is necessary to envision water security from the perspective of a cyber-physical system (CPS). In doing so, we can evaluate risks and research needs for cyber-attacks on HAB-monitoring networks including data injection attacks, automated system hijacking attacks, node forgery attacks, and attacks on learning algorithms. Herein, we provide perspectives on the research needed to understand both the threats posed by HABs and the coupled cyber threats to water security in the context of HABs.
- Precision Farming Tools. Soil Electrical ConductivityGrisso, Robert D.; Alley, Marcus M.; Holshouser, David L.; Thomason, Wade E. (Virginia Cooperative Extension, 2005-09-01)Soil electrical conductivity (EC) is one of the simplest, least expensive soil measurements available to precision farmers today. Soil EC measurement can provide more measurements in a shorter amount of time than traditional grid soil sampling.
- Precision Farming Tools: Variable-Rate ApplicationGrisso, Robert D.; Alley, Marcus M.; Thomason, Wade E.; Holshouser, David L.; Roberson, Gary T. (Virginia Cooperative Extension, 2011-08-01)Discusses the two basic variable-rate application technologies, map-based and sensor-based, for fertilizer, lime, weed control, and seed.
- River Birch, Betula nigraNiemiera, Alexander X. (Virginia Cooperative Extension, 2012-02-27)This publication covers the physical and main features, plant needs, functions, care, and additional information for River Birch, Betula nigra.
- Salt dilution and flushing dynamics of an impaired agricultural−urban streamLakoba, Vasiliy T.; Wind, Lauren L.; DeVilbiss, Stephen; Lofton, Mary E.; Bretz, Kristen; Weinheimer, Alaina R.; Moore, Chloe; Baciocco, Colin; Hotchkiss, Erin R.; Hession, W. Cully (2020-11-09)Anthropogenic freshwater salinization is increasing with global change. Rising freshwater salinity threatens ecosystem biodiversity, health, and services via toxicity to organisms and mobilization of nutrients and metals. Brining roads is one major source of freshwater salinization that continues to grow with rising urbanization. While the detrimental effects of salinization in streams are well-documented, high-frequency, temporal patterns in salt transport, particularly during winter road de-icing in mixed land use landscapes, are less understood. To address this knowledge gap, we analyzed high-frequency specific conductance as a proxy for salinity across 114 high-flow events from 2013 to 2018 in an impaired stream draining mixed agriculture−urban land use. The specific conductance was highest in winter (median = 947 μS cm−1) and decreased with first-order kinetics up to 90 days after brining (β1 = −0.003), suggesting lasting impacts of road de-icing on water quality. Although hysteresis patterns suggested a transition from distal to proximal salt sources, they showed no clear correlation of flushing versus dilution to brining events. While seasonal brining increased salinity in receiving streams, unpredictable transport dynamics reduced the efficacy of hysteresis in characterizing salt transport dynamics. Thus, the complexity of mixed land use watersheds requires more spatially and temporally explicit monitoring to characterize stream salinization dynamics.