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 Sciences"
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- An aeroponic culture system for the study of root herbivory on Arabidopsis thalianaVaughan, Martha M.; Tholl, Dorothea; Tokuhisa, James G. (Biomed Central, 2011-03-10)Background Plant defense against herbivory has been studied primarily in aerial tissues. However, complex defense mechanisms have evolved in all parts of the plant to combat herbivore attack and these mechanisms are likely to differ in the aerial and subterranean environment. Research investigating defense responses belowground has been hindered by experimental difficulties associated with the accessibility and quality of root tissue and the lack of bioassays using model plants with altered defense profiles. Results We have developed an aeroponic culture system based on a calcined clay substrate that allows insect herbivores to feed on plant roots while providing easy recovery of the root tissue. The culture method was validated by a root-herbivore system developed for Arabidopsis thaliana and the herbivore Bradysia spp. (fungus gnat). Arabidopsis root mass obtained from aeroponically grown plants was comparable to that from other culture systems, and the plants were morphologically normal. Bradysia larvae caused considerable root damage resulting in reduced root biomass and water absorption. After feeding on the aeroponically grown root tissue, the larvae pupated and emerged as adults. Root damage of mature plants cultivated in aeroponic substrate was compared to that of Arabidopsis seedlings grown in potting mix. Seedlings were notably more susceptible to Bradysia feeding than mature plants and showed decreased overall growth and survival rates. Conclusions A root-herbivore system consisting of Arabidopsis thaliana and larvae of the opportunistic herbivore Bradysia spp. has been established that mimics herbivory in the rhizosphere. Bradysia infestation of Arabidopsis grown in this culture system significantly affects plant performance. The culture method will allow simple profiling and in vivo functional analysis of root defenses such as chemical defense metabolites that are released in response to belowground insect attack.
- Analysis of T-DNA alleles of flavonoid biosynthesis genes in Arabidopsis ecotype ColumbiaBowerman, Peter A.; Ramirez, Melissa V.; Price, Michelle B.; Helm, Richard F.; Winkel, Brenda S. J. (2012-09-04)BACKGROUND: The flavonoid pathway is a long-standing and important tool for plant genetics, biochemistry, and molecular biology. Numerous flavonoid mutants have been identified in Arabidopsis over the past several decades in a variety of ecotypes. Here we present an analysis of Arabidopsis lines of ecotype Columbia carrying T-DNA insertions in genes encoding enzymes of the central flavonoid pathway. We also provide a comprehensive summary of various mutant alleles for these structural genes that have been described in the literature to date in a wide variety of ecotypes. FINDINGS: The confirmed knockout lines present easily-scorable phenotypes due to altered pigmentation of the seed coat (or testa). Knockouts for seven alleles for six flavonoid biosynthetic genes were confirmed by PCR and characterized by UPLC for altered flavonol content. CONCLUSION: Seven mutant lines for six genes of the central flavonoid pathway were characterized in ecotype, Columbia. These lines represent a useful resource for integrating biochemical and physiological studies with genomic, transcriptomic, and proteomic data, much of which has been, and continues to be, generated in the Columbia background.
- Assessing age, breeding stage, and mating activity as drivers of variation in the reproductive microbiome of female tree swallowsHernandez, Jessica; Hucul, Catherine; Reasor, Emily; Smith, Taryn; McGlothlin, Joel W.; Haak, David C.; Belden, Lisa K.; Moore, Ignacio T. (Wiley, 2021-07)Sexually transmitted microbes are hypothesized to influence the evolution of reproductive strategies. Though frequently discussed in this context, our understanding of the reproductive microbiome is quite nascent. Indeed, testing this hypothesis first re-quires establishing a baseline understanding of the temporal dynamics of the reproductive microbiome and of how individual variation in reproductive behavior and age influence the assembly and maintenance of the reproductive microbiome as a whole. Here, we ask how mating activity, breeding stage, and age influence the reproductive microbiome. We use observational and experimental approaches to explain variation in the cloacal microbiome of free- living, female tree swallows (Tachycineta bicolor). Using microsatellite- based parentage analyses, we determined the number of sires per brood (a proxy for female mating activity). We experimentally increased female sexual activity by administering exogenous 17ß-estradiol. Lastly, we used bacterial 16S rRNA amplicon sequencing to characterize the cloacal microbiome. Neither the number of sires per brood nor the increased sexual activity of females significantly influenced female cloacal microbiome richness or community structure. Female age, however, was positively correlated with cloacal microbiome richness and influenced overall community structure. A hypothesis to explain these patterns is that the effect of sexual activity and the number of mates on variation in the cloacal microbiome manifests over an individual's lifetime. Additionally, we found that cloacal microbiome alpha diversity (Shannon Index, Faith's phylogenetic distance) decreased and community structure shifted between breeding stages. This is one of few studies to document within-individual changes and age- related differences in the cloacal microbiome across successive breeding stages. More broadly, our results contribute to our understanding of the role that host life history and behavior play in shaping the cloacal microbiomes of wild birds.
- Candidate Gene Sequence Analyses toward Identifying Rsv3-Type Resistance to Soybean Mosaic VirusRedekar, Neelam R.; Clevinger, Elizabeth M.; Laskar, M. A.; Biyashev, Ruslan M.; Ashfield, Tom; Jensen, Roderick V.; Jeong, Soon-Chun; Tolin, Sue A.; Saghai-Maroof, Mohammad A. (Crop Science Society of America, 2016-05-13)Rsv3 is one of three genetic loci conferring strain-specific resistance to Soybean mosaic virus (SMV). The Rsv3 locus has been mapped to a 154-kb region on chromosome 14, containing a cluster of five nucleotide-binding leucine-rich repeat (NB-LRR) resistance genes. High sequence similarity between the Rsv3 candidate genes challenges fine mapping of the locus. Among the five, Glyma14g38533 showed the highest transcript abundance in 1 to 3 h of SMV-G7 inoculation. Comparative sequence analyses were conducted with the five Rsv3 candidate NB-LRR genes from susceptible (rsv-type) soybean [Glycine max (L.) Merr.] cultivar Williams 82, resistant (Rsv3-type) cultivar Hwangkeum, and resistant lines L29 and RRR. Sequence comparisons revealed that Glyma14g38533 had far more polymorphisms than the other candidate genes. Interestingly, Glyma14g38533 gene from Rsv3-type lines exhibited 150 single-nucleotide polymorphism (SNP and six insertion–deletion (InDel) markers relative to rsv-type line, Furthermore, the polymorphisms identified in three Rsv3-type lines were highly conserved. Several polymorphisms were validated in 18 Rsv3-type resistant and six rsv-type susceptible lines and were found associated with their disease response. The majority of the polymorphisms were located in LRR domain encoding region, which is involved in pathogen recognition via protein–protein interactions. These findings associating Glyma14g38533 with Rsv3-type resistance to SMV suggest it is the most likely candidate gene for Rsv3.
- Diversity and Abundance of Ice Nucleating Strains of Pseudomonas syringae in a Freshwater Lake in Virginia, USAPietsch, Renee B.; Vinatzer, Boris A.; Schmale, David G. III (Frontiers, 2017-03-09)
- Genome-Wide Assessment of Efficiency and Specificity in CRISPR/Cas9 Mediated Multiple Site Targeting in ArabidopsisPeterson, Brenda A.; Haak, David C.; Nishimura, Marc T.; Teixeira, Paulo J. P. L.; James, Sean R.; Dangl, Jeffery L.; Nimchuk, Zachary L. (PLOS, 2016-09-13)Simultaneous multiplex mutation of large gene families using Cas9 has the potential to revolutionize agriculture and plant sciences. The targeting of multiple genomic sites at once raises concerns about the efficiency and specificity in targeting. The model Arabidopsis thaliana is widely used in basic plant research. Previous work has suggested that the Cas9 off-target rate in Arabidopsis is undetectable. Here we use deep sequencing on pooled plants simultaneously targeting 14 distinct genomic loci to demonstrate that multiplex targeting in Arabidopsis is highly specific to on-target sites with no detectable off-target events. In addition, chromosomal translocations are extremely rare. The high specificity of Cas9 in Arabidopsis makes this a reliable method for clean mutant generation with no need to enhance specificity or adopt alternate Cas9 variants.
- Genome-wide transcriptome analyses of developing seeds from low and normal phytic acid soybean linesRedekar, Neelam R.; Biyashev, Ruslan M.; Jensen, Roderick V.; Helm, Richard F.; Grabau, Elizabeth A.; Saghai-Maroof, Mohammad A. (2015-12-18)Background Low phytic acid (lpa) crops are potentially eco-friendly alternative to conventional normal phytic acid (PA) crops, improving mineral bioavailability in monogastric animals as well as decreasing phosphate pollution. The lpa crops developed to date carry mutations that are directly or indirectly associated with PA biosynthesis and accumulation during seed development. These lpa crops typically exhibit altered carbohydrate profiles, increased free phosphate, and lower seedling emergence, the latter of which reduces overall crop yield, hence limiting their large-scale cultivation. Improving lpa crop yield requires an understanding of the downstream effects of the lpa genotype on seed development. Towards that end, we present a comprehensive comparison of gene-expression profiles between lpa and normal PA soybean lines (Glycine max) at five stages of seed development using RNA-Seq approaches. The lpa line used in this study carries single point mutations in a myo-inositol phosphate synthase gene along with two multidrug-resistance protein ABC transporter genes. Results RNA sequencing data of lpa and normal PA soybean lines from five seed-developmental stages (total of 30 libraries) were used for differential expression and functional enrichment analyses. A total of 4235 differentially expressed genes, including 512-transcription factor genes were identified. Eighteen biological processes such as apoptosis, glucan metabolism, cellular transport, photosynthesis and 9 transcription factor families including WRKY, CAMTA3 and SNF2 were enriched during seed development. Genes associated with apoptosis, glucan metabolism, and cellular transport showed enhanced expression in early stages of lpa seed development, while those associated with photosynthesis showed decreased expression in late developmental stages. The results suggest that lpa-causing mutations play a role in inducing and suppressing plant defense responses during early and late stages of seed development, respectively. Conclusions This study provides a global perspective of transcriptomal changes during soybean seed development in an lpa mutant. The mutants are characterized by earlier expression of genes associated with cell wall biosynthesis and a decrease in photosynthetic genes in late stages. The biological processes and transcription factors identified in this study are signatures of lpa-causing mutations.
- Phyllopshere Bacterial Community Structure of Spinach (Spinacia oleracea) as Affected by Cultivar and Environmental Conditions at Time of HarvestLopez-Velasco, Gabriela; Welbaum, Gregory E.; Falkinham, Joseph O. III; Ponder, Monica A. (MDPI, 2011-12-20)Modern molecular ecology techniques were used to demonstrate the effects of plant genotype and environmental conditions prior to harvest on the spinach epiphytic bacterial community. Three cultivars of spinach with different leaf topographies were collected at three different periods during the fall growing season. Leaf surface topography had an effect on diversity and number of culturable bacteria on the phylloepiphtyic community of spinach. Savoy cultivars, which had larger surface area and more stomata and glandular trichomes, where bacterial aggregates were observed, featured more diverse communities with increased richness and larger bacterial populations compared to flat-leaved cultivars. Bacterial community richness was compared using denaturant gradient gel electrophoresis (DGGE), while abundance was quantified using 16s rRNA primers for major phyla. The most diverse communities, both in richness and abundance, were observed during the first sampling period, immediately following a period of rapid spinach growth. Exposure to lower air and soil temperatures and decreased precipitation resulted in significantly reduced bacterial population size and bacterial community richness in November and December. This study describes the effect of the plant characteristics and environmental conditions that affect spinach microbiota population size and diversity, which might have implications in the survival of food and plant bacterial pathogens.
- Rethinking Biological Invasions as a Metacommunity ProblemBrown, Bryan L.; Barney, Jacob (2021-01-13)Perhaps more than any other ecological discipline, invasion biology has married the practices of basic science and the application of that science. The conceptual frameworks of population regulation, metapopulations, supply-side ecology, and community assembly have all to some degree informed the regulation, management, and prevention of biological invasions. Invasion biology needs to continue to adopt emerging frameworks and paradigms to progress as both a basic and applied science. This need is urgent as the biological invasion problem continues to worsen. The development of metacommunity theory in the last two decades represents a paradigm-shifting approach to community ecology that emphasizes the multi-scale nature of community assembly and biodiversity regulation. Work on metacommunities has demonstrated that even relatively simple processes at local scales are often heavily influenced by regional-scale processes driven primarily by the dispersal of organisms. Often the influence of dispersal interacts with, or even swamps, the influence of local-scale drivers like environmental conditions and species interactions. An emphasis on dispersal and a focus on multi-scale processes enable metacommunity theory to contribute strongly to the advancement of invasion biology. Propagule pressure of invaders has been identified as one of the most important drivers facilitating invasion, so the metacommunity concept, designed to address how dispersal-driven dynamics affect community structure, can directly address many of the central questions of invasion biology. Here we revisit many of the important concepts and paradigms of biological invasions-propagule pressure, biotic resistance, enemy release, functional traits, neonative species, human-assisted transport,-and view those concepts through the lens of metacommunity theory. In doing so, we accomplish several goals. First, we show that work on metacommunities has generated multiple predictions, models, and the tools that can be directly applied to invasion scenarios. Among these predictions is that invasibility of a community should decrease with both local controls on community assembly, and the dispersal rates of native species. Second, we demonstrate that framing biological invasions in metacommunity terms actually unifies several seemingly disparate concepts central to invasion biology. Finally, we recommend several courses of action for the control and management of invasive species that emerge from applying the concepts of metacommunity theory.
- A Rootstock Provides Water Conservation for a Grafted Commercial Tomato (Solanum lycopersicum L.) Line in Response to Mild-Drought Conditions: A Focus on Vegetative Growth and Photosynthetic ParametersNilsen, Erik T.; Freeman, Joshua H.; Grene, Ruth; Tokuhisa, James G. (Public Library of Science, 2014-12-22)The development of water stress resistant lines of commercial tomato by breeding or genetic engineering is possible, but will take considerable time before commercial varieties are available for production. However, grafting commercial tomato lines on drought resistant rootstock may produce drought tolerant commercial tomato lines much more rapidly. Due to changing climates and the need for commercial production of vegetables in low quality fields there is an urgent need for stress tolerant commercial lines of vegetables such as tomato. In previous observations we identified a scion root stock combination (‘BHN 602’ scion grafted onto ‘Jjak Kkung’ rootstock hereafter identified as 602/Jjak) that had a qualitative drought-tolerance phenotype when compared to the non-grafted line. Based on this initial observation, we studied photosynthesis and vegetative above-ground growth during mild-drought for the 602/Jjak compared with another scion-rootstock combination (‘BHN 602’ scion grafted onto ‘Cheong Gang’ rootstock hereafter identified as 602/Cheong) and a non-grafted control. Overall above ground vegetative growth was significantly lower for 602/Jjak in comparison to the other plant lines. Moreover, water potential reduction in response to mild drought was significantly less for 602/Jjak, yet stomatal conductance of all plant-lines were equally inhibited by mild-drought. Light saturated photosynthesis of 602/Jjak was less affected by low water potential than the other two lines as was the % reduction in mesophyll conductance. Therefore, the Jjak Kkung rootstock caused aboveground growth reduction, water conservation and increased photosynthetic tolerance of mild drought. These data show that different rootstocks can change the photosynthetic responses to drought of a high yielding, commercial tomato line. Also, this rapid discovery of one scion-rootstock combination that provided mild-drought tolerance suggests that screening more scion-rootstock combination for stress tolerance may rapidly yield commercially viable, stress tolerant lines of tomato.
- 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.
- Single Cell RNA-Seq and Machine Learning Reveal Novel Subpopulations in Low-Grade Inflammatory Monocytes With Unique Regulatory CircuitsLee, Jiyoung; Geng, Shuo; Li, Song; Li, Liwu (2021-02-23)Subclinical doses of LPS (SD-LPS) are known to cause low-grade inflammatory activation of monocytes, which could lead to inflammatory diseases including atherosclerosis and metabolic syndrome. Sodium 4-phenylbutyrate is a potential therapeutic compound which can reduce the inflammation caused by SD-LPS. To understand the gene regulatory networks of these processes, we have generated scRNA-seq data from mouse monocytes treated with these compounds and identified 11 novel cell clusters. We have developed a machine learning method to integrate scRNA-seq, ATAC-seq, and binding motifs to characterize gene regulatory networks underlying these cell clusters. Using guided regularized random forest and feature selection, our method achieved high performance and outperformed a traditional enrichment-based method in selecting candidate regulatory genes. Our method is particularly efficient in selecting a few candidate genes to explain observed expression pattern. In particular, among 531 candidate TFs, our method achieves an auROC of 0.961 with only 10 motifs. Finally, we found two novel subpopulations of monocyte cells in response to SD-LPS and we confirmed our analysis using independent flow cytometry experiments. Our results suggest that our new machine learning method can select candidate regulatory genes as potential targets for developing new therapeutics against low grade inflammation.
- Soil Bacterial and Fungal Communities Exhibit Distinct Long-Term Responses to Disturbance in Temperate ForestsOsburn, Ernest D.; McBride, Steven Glynn II; Aylward, Frank O.; Badgley, Brian D.; Strahm, Brian D.; Knoepp, Jennifer D.; Barrett, John E. (2019-12-11)In Appalachian ecosystems, forest disturbance has long-term effects on microbially driven biogeochemical processes such as nitrogen (N) cycling. However, little is known regarding long-term responses of forest soil microbial communities to disturbance in the region. We used 16S and ITS sequencing to characterize soil bacterial (16S) and fungal (ITS) communities across forested watersheds with a range of past disturbance regimes and adjacent reference forests at the Coweeta Hydrologic Laboratory in the Appalachian mountains of North Carolina. Bacterial communities in previously disturbed forests exhibited consistent responses, including increased alpha diversity and increased abundance of copiotrophic (e.g., Proteobacteria) and N-cycling (e.g., Nitrospirae) bacterial phyla. Fungal community composition also showed disturbance effects, particularly in mycorrhizal taxa. However, disturbance did not affect fungal alpha diversity, and disturbance effects were not consistent at the fungal class level. Co-occurrence networks constructed for bacteria and fungi showed that disturbed communities were characterized by more connected and tightly clustered network topologies, indicating that disturbance alters not only community composition but also potential ecological interactions among taxa. Although bacteria and fungi displayed different long-term responses to forest disturbance, our results demonstrate clear responses of important bacterial and fungal functional groups (e.g., nitrifying bacteria and mycorrhizal fungi), and suggest that both microbial groups play key roles in the long-term alterations to biogeochemical processes observed following forest disturbance in the region.
- 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.