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 "Civil and Environmental 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/ .
- Coordinated Sampling of Microorganisms Over Freshwater and Saltwater Environments Using an Unmanned Surface Vehicle (USV) and a Small Unmanned Aircraft System (sUAS)Powers, Craig W.; Hanlon, Regina; Grothe, Hinrich; Prussin, Aaron J. II; Marr, Linsey C.; Schmale, David G. III (Frontiers, 2018-08-15)Biological aerosols (bioaerosols) are ubiquitous in terrestrial and aquatic environments and may influence cloud formation and precipitation processes. Little is known about the aerosolization and transport of bioaerosols from aquatic environments. We designed and deployed a bioaerosol-sampling system onboard an unmanned surface vehicle (USV; a remotely operated boat) to collect microbes and monitor particle sizes in the atmosphere above a salt pond in Falmouth, MA, United States and a freshwater lake in Dublin, VA, United States. The bioaerosol-sampling system included a series of 3D-printed impingers, two different optical particle counters, and a weather station. A small unmanned aircraft system (sUAS; a remotely operated airplane) was used in a coordinated effort with the USV to collect microorganisms on agar media 50 m above the surface of the water. Samples from the USV and sUAS were cultured on selective media to estimate concentrations of culturable microorganisms (bacteria and fungi). Concentrations of microbes from the sUAS ranged from 6 to 9 CFU/m3 over saltwater, and 12 to 16 CFU/m3 over freshwater (over 10-min sampling intervals) at 50 m above ground level (AGL). Concentrations from the USV ranged from 0 (LOD) to 42,411 CFU/m3 over saltwater, and 0 (LOD) to 56,809 CFU/m3 over freshwater (over 30-min sampling intervals) in air near the water surface. Particle concentrations recorded onboard the USV ranged from 0 (LOD) to 288 μg/m3 for PM1, 1 to 290 μg/m3 for PM2.5, and 1 to 290 μg/m3 for PM10. A general trend of increasing concentration with an increase in particle size was recorded by each sensor. Through laboratory testing, the collection efficiency of the 3D-printed impingers was determined to be 75% for 1 μm beads and 99% for 3 μm beads. Additional laboratory tests were conducted to determine the accuracy of the miniaturized optical particle counters used onboard the USV. Future work aims to understand the distribution of bioaerosols above aquatic environments and their potential association with cloud formation and precipitation processes.
- Diversity and Ice Nucleation Activity of Microorganisms Collected With a Small Unmanned Aircraft System (sUAS) in France and the United StatesJimenez-Sanchez, Celia; Hanlon, Regina; Aho, Ken A.; Powers, Craig W.; Morris, Cindy E.; Schmale, David G. III (Frontiers, 2018-08-15)Many microbes relevant to crops, domestic animals, and humans are transported over long distances through the atmosphere. Some of these atmospheric microbes catalyze the freezing of water at higher temperatures and facilitate the onset of precipitation. We collected microbes from the lower atmosphere in France and the United States with a small unmanned aircraft system (sUAS). 55 sampling missions were conducted at two locations in France in 2014 (an airfield in Pujaut, and the top of Puy de Dôme), and three locations in the U.S. in 2015 (a farm in Blacksburg, Virginia, and a farm and a lake in Baton Rouge, Louisiana). The sUAS was a fixed-wing electric drone equipped with a remote-operated sampling device that was opened once the aircraft reached the desired sampling altitude (40–50 meters above ground level). Samples were collected on agar media (TSA, R4A, R2A, and CA) with and without the fungicide cycloheximide. Over 4,000 bacterial-like colonies were recovered across the 55 sUAS sampling missions. A positive relationship between sampling time and temperature and concentrations of culturable bacteria was observed for sUAS flights conducted in France, but not for sUAS flights conducted in Louisiana. A droplet freezing assay was used to screen nearly 2,000 colonies for ice nucleation activity, and 15 colonies were ice nucleation active at temperatures warmer than −8◦C. Sequences from portions of 16S rDNA were used to identify 503 colonies from 54 flights to the level of genus. Assemblages of bacteria from sUAS flights in France (TSA) and sUAS flights in Louisiana (R4A) showed more similarity within locations than between locations. Bacteria collected with sUAS on TSA in France and Virginia were significantly different across all levels of classification tested (P < 0.001 for class, order, family, and genus). Principal Coordinates Analysis showed a strong association between the genera Curtobacterium, Pantoea, and Pseudomonas from sUAS flights in Virginia, and Agrococcus, Lysinibacillus, and Paenibacillus from sUAS flights in France. Future work aims to understand the potential origin of the atmospheric microbial assemblages collected with sUAS, and their association with mesoscale atmospheric processes.
- Effect of composting and soil type on dissipation of veterinary antibiotics in land-applied manuresChen, Chaoqi; Ray, Partha P.; Knowlton, Katharine F.; Pruden, Amy; Xia, Kang (2018)The objective of this study was to determine the fate of commonly used veterinary antibiotics in their naturally excreted form when manure-based amendments are applied to soil. Beef cattle were administered sulfamethazine, tylosin, and chlortetracycline and dairy cows were treated with pirlimycin. The resulting manure was composted for 42 d under static or turned conditions and applied at agronomic N rates to sandy, silt, and silty clay loam soils and compared with amendment with corresponding raw manures in sacrificial microcosms over a 120-day period. Antibiotic dissipation in the raw manure-amended soils followed bi-phasic first order kinetics. The first phase half-lives for sulfamethazine, tylosin, chlortetracycline, and pirlimycin ranged from 6.0 to 18, 2.7 to 3.7, 23 to 25, and 5.5–8.2 d, respectively. During the second phase, dissipation of sulfamethazine was negligible, while the half-lives for tylosin, chlortetracycline, and pirlimycin ranged from 41 to 44, 75 to 144, and 87–142 d, respectively. By contrast, antibiotic dissipation in the compost-amended soils followed single-phase first order kinetics with negligible dissipation of sulfamethazine and half-lives of tylosin and chlortetracycline ranging from 15 to 16 and 49–104 d, respectively. Pirlimycin was below the detection limit in the compost-amended soils. After incubating 120 d, antibiotics in compost-amended soils (up to 3.1 μg kg−1) were significantly lower than in manure-amended soils (up to 19 μg kg−1, p < .0001), with no major effect of soil type on the dissipation. Risk assessment suggested that composting can reduce antibiotic resistance selection potential in manure-amended soils.
- Intercomparison of Small Unmanned Aircraft System (sUAS) Measurements for Atmospheric Science during the LAPSE-RATE CampaignBarbieri, Lindsay; Kral, Stephan T.; Bailey, Sean C. C.; Frazier, Amy E.; Jacob, Jamey D.; Reuder, Joachim; Brus, David; Chilson, Phillip B.; Crick, Christopher; Detweiler, Carrick; Doddi, Abhiram; Elston, Jack; Foroutan, Hosein; González-Rocha, Javier; Greene, Brian R.; Guzman, Marcelo I.; Houston, Adam L.; Islam, Ashraful; Kemppinen, Osku; Lawrence, Dale; Pillar-Little, Elizabeth A.; Ross, Shane D.; Sama, Michael P.; Schmale, David G. III; Schuyler, Travis J.; Shankar, Ajay; Smith, Suzanne W.; Waugh, Sean; Dixon, Cory; Borenstein, Steve; de Boer, Gijs (MDPI, 2019-05-10)Small unmanned aircraft systems (sUAS) are rapidly transforming atmospheric research. With the advancement of the development and application of these systems, improving knowledge of best practices for accurate measurement is critical for achieving scientific goals. We present results from an intercomparison of atmospheric measurement data from the Lower Atmospheric Process Studies at Elevation—a Remotely piloted Aircraft Team Experiment (LAPSE-RATE) field campaign. We evaluate a total of 38 individual sUAS with 23 unique sensor and platform configurations using a meteorological tower for reference measurements. We assess precision, bias, and time response of sUAS measurements of temperature, humidity, pressure, wind speed, and wind direction. Most sUAS measurements show broad agreement with the reference, particularly temperature and wind speed, with mean value differences of 1.6 ± 2.6 ∘ C and 0.22 ± 0.59 m/s for all sUAS, respectively. sUAS platform and sensor configurations were found to contribute significantly to measurement accuracy. Sensor configurations, which included proper aspiration and radiation shielding of sensors, were found to provide the most accurate thermodynamic measurements (temperature and relative humidity), whereas sonic anemometers on multirotor platforms provided the most accurate wind measurements (horizontal speed and direction). We contribute both a characterization and assessment of sUAS for measuring atmospheric parameters, and identify important challenges and opportunities for improving scientific measurements with sUAS.
- MetaCompare: a computational pipeline for prioritizing environmental resistome riskOh, Min; Pruden, Amy; Chen, Chaoqi; Heath, Lenwood S.; Xia, Kang; Zhang, Liqing (2018-07)The spread of antibiotic resistance is a growing public health concern. While numerous studies have highlighted the importance of environmental sources and pathways of the spread of antibiotic resistance, a systematic means of comparing and prioritizing risks represented by various environmental compartments is lacking. Here, we introduce MetaCompare, a publicly available tool for ranking 'resistome risk', which we define as the potential for antibiotic resistance genes (ARGs) to be associated with mobile genetic elements (MGEs) and mobilize to pathogens based on metagenomic data. A computational pipeline was developed in which each ARG is evaluated based on relative abundance, mobility, and presence within a pathogen. This is determined through the assembly of shotgun sequencing data and analysis of contigs containing ARGs to determine if they contain sequence similarity to MGEs or human pathogens. Based on the assembled metagenomes, samples are projected into a 3-dimensionalhazard space and assigned resistome risk scores. To validate, we tested previously published metagenomic data derived from distinct aquatic environments. Based on unsupervised machine learning, the test samples clustered in the hazard space in a manner consistent with their origin. The derived scores produced a well-resolved ascending resistome risk ranking of: wastewater treatment plant effluent, dairy lagoon, and hospital sewage.
- Modification of the Mycotoxin Deoxynivalenol Using Microorganisms Isolated from Environmental SamplesWilson, Nina M.; McMaster, Nicole J.; Gantulga, Dash; Soyars, Cara L.; McCormick, Susan P.; Knott, Ken; Senger, Ryan S.; Schmale, David G. III (MDPI, 2017-04-01)The trichothecene mycotoxin deoxynivalenol (DON) is a common contaminant of wheat, barley, and maize. New strategies are needed to reduce or eliminate DON in feed and food products. Microorganisms from plant and soil samples collected in Blacksburg, VA, USA, were screened by incubation in a mineral salt media containing 100 μg/mL DON and analysis by gas chromatography mass spectrometry (GC/MS). Two mixed cultures derived from soil samples consistently decreased DON levels in assays using DON as the sole carbon source. Nuclear magnetic resonance (NMR) analysis indicated that 3-keto-4-deoxynivalenol was the major by-product of DON. Via 16S rRNA sequencing, these mixed cultures, including mostly members of the genera Acinetobacter, Leadbetterella, and Gemmata, were revealed. Incubation of one of these mixed cultures with wheat samples naturally contaminated with 7.1 μg/mL DON indicated nearly complete conversion of DON to the less toxic 3-epimer-DON (3-epi-DON). Our work extends previous studies that have demonstrated the potential for bioprospecting for microorganisms from the environment to remediate or modify mycotoxins for commercial applications, such as the reduction of mycotoxins in fuel ethanol co-products.
- Remote collection of microorganisms at two depths in a freshwater lake using an unmanned surface vehicle (USV)Powers, Craig W.; Hanlon, Regina; Schmale, David G. III (PeerJ, 2018-01-26)Microorganisms are ubiquitous in freshwater aquatic environments, but little is known about their abundance, diversity, and transport. We designed and deployed a remote-operated water-sampling system onboard an unmanned surface vehicle (USV, a remote-controlled boat) to collect and characterize microbes in a freshwater lake in Virginia, USA. The USV collected water samples simultaneously at 5 and 50 cm below the surface of the water at three separate locations over three days in October, 2016. These samples were plated on a non-selective medium (TSA) and on a medium selective for the genus Pseudomonas (KBC) to estimate concentrations of culturable bacteria in the lake. Mean concentrations ranged from 134 to 407 CFU/mL for microbes cultured on TSA, and from 2 to 8 CFU/mL for microbes cultured on KBC. There was a significant difference in the concentration of microbes cultured on KBC across three sampling locations in the lake (P = 0.027), suggesting an uneven distribution of Pseudomonas across the locations sampled. There was also a significant difference in concentrations of microbes cultured on TSA across the three sampling days (P = 0.038), demonstrating daily fluctuations in concentrations of culturable bacteria. There was no significant difference in concentrations of microbes cultured on TSA (P = 0.707) and KBC (P = 0.641) across the two depths sampled, suggesting microorganisms were well-mixed between 5 and 50 cm below the surface of the water. About 1 percent (7/720) of the colonies recovered across all four sampling missions were ice nucleation active (ice+) at temperatures warmer than — 10 °C. Our work extends traditional manned observations of aquatic environments to unmanned systems, and highlights the potential for USVs to understand the distribution and diversity of microbes within and above freshwater aquatic environments.
- Scavenging of Sub-Micron to Micron-Sized Microbial Aerosols during Simulated RainfallMoore, Rachel A.; Hanlon, Regina; Powers, Craig W.; Schmale, David G. III; Christner, Brent C. (MDPI, 2020-01-09)The processes removing aerosols from the atmosphere during rainfall are generically referred to as scavenging. Scavenging influences aerosol distributions in the atmosphere, with consequent effects on cloud properties, radiative forcing, and human health. In this study, we investigated the below-cloud scavenging process, specifically focusing on the scavenging of 0.2 to 2 µm-sized microbial aerosols by populations of water drops with average diameters of 3.0 and 3.6 mm. Rainfall was simulated in convective boundary layer air masses by dispensing the water drops from a 55 m bridge and collecting them at ground level. Particles and microbial cells scavenged by the water drops were visualized, enumerated, and sized using scanning electron and epifluorescence microscopy. Aerosolized particles and DNA-containing microbial cells of 2 µm diameter were scavenged at efficiencies similar to those reported previously in empirical studies; however, the efficiencies derived for smaller aerosols were significantly higher (one to three orders of magnitude) than those predicted by microphysical modeling. Application of the derived scavenging efficiencies to cell data from rainfall implies that, on average, approximately 50 to 70% of the 1 µm microbial cells in the precipitation originated from within the cloud. Further study of submicron to micron-sized aerosol scavenging over a broader raindrop size distribution would improve fundamental understanding of the scavenging process and the capacity to estimate (bio)aerosol abundances in the source cloud through analysis of rainfall.
- A System to Automatically Classify and Name Any Individual Genome-Sequenced Organism Independently of Current Biological Classification and NomenclatureMarakeby, Haitham; Badr, Eman; Torkey, Hanaa; Song, Yuhyun; Leman, Scotland C.; Monteil, Caroline L.; Heath, Lenwood S.; Vinatzer, Boris A. (PLOS, 2014-02-21)A broadly accepted and stable biological classification system is a prerequisite for biological sciences. It provides the means to describe and communicate about life without ambiguity. Current biological classification and nomenclature use the species as the basic unit and require lengthy and laborious species descriptions before newly discovered organisms can be assigned to a species and be named. The current system is thus inadequate to classify and name the immense genetic diversity within species that is now being revealed by genome sequencing on a daily basis. To address this lack of a general intra-species classification and naming system adequate for today’s speed of discovery of new diversity, we propose a classification and naming system that is exclusively based on genome similarity and that is suitable for automatic assignment of codes to any genome-sequenced organism without requiring any phenotypic or phylogenetic analysis. We provide examples demonstrating that genome similarity-based codes largely align with current taxonomic groups at many different levels in bacteria, animals, humans, plants, and viruses. Importantly, the proposed approach is only slightly affected by the order of code assignment and can thus provide codes that reflect similarity between organisms and that do not need to be revised upon discovery of new diversity. We envision genome similarity-based codes to complement current biological nomenclature and to provide a universal means to communicate unambiguously about any genome-sequenced organism in fields as diverse as biodiversity research, infectious disease control, human and microbial forensics, animal breed and plant cultivar certification, and human ancestry research.
- Wind-driven spume droplet production and the transport of Pseudomonas syringae from aquatic environmentsPietsch, Renee B.; Grothe, Hinrich; Hanlon, Regina; Powers, Craig W.; Jung, Sunghwan; Ross, Shane D.; Schmale, David G. III (PeerJ, 2018-09-26)Natural aquatic environments such as oceans, lakes, and rivers are home to a tremendous diversity of microorganisms. Some may cross the air-water interface within droplets and become airborne, with the potential to impact the Earth’s radiation budget, precipitation processes, and spread of disease. Larger droplets are likely to return to the water or adjacent land, but smaller droplets may be suspended in the atmosphere for transport over long distances. Here, we report on a series of controlled laboratory experiments to quantify wind-driven droplet production from a freshwater source for low wind speeds. The rate of droplet production increased quadratically with wind speed above a critical value (10-m equivalent 5.7 m/s) where droplet production initiated. Droplet diameter and ejection speeds were fit by a gamma distribution. The droplet mass flux and momentum flux increased with wind speed. Two mechanisms of droplet production, bubble bursting and fragmentation, yielded different distributions for diameter, speed, and angle. At a wind speed of about 3.5 m/s, aqueous suspensions of the ice-nucleating bacterium Pseudomonas syringae were collected at rates of 283 cells m−2 s−1 at 5 cm above the water surface, and at 14 cells m−2 s−1 at 10 cm above the water surface. At a wind speed of about 4.0 m/s, aqueous suspensions of P. syringae were collected at rates of 509 cells m−2 s−1 at 5 cm above the water surface, and at 81 cells m−2 s−1 at 10 cm above the water surface. The potential for microbial flux into the atmosphere from aquatic environments was calculated using known concentrations of bacteria in natural freshwater systems. Up to 3.1 × 104 cells m−2 s−1 of water surface were estimated to leave the water in potentially suspended droplets (diameters <100 µm). Understanding the sources and mechanisms for bacteria to aerosolize from freshwater aquatic sources may aid in designing management strategies for pathogenic bacteria, and could shed light on how bacteria are involved in mesoscale atmospheric processes.