Browsing by Author "Barney, Jacob"

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    Adaptation of an invasive grass to agriculture: ecological and genomic evidence
    Smith, Alyssa Laney (Virginia Tech, 2017-06-06)
    Species vary phenotypically and genetically across their environmental range limits, and this variation can influence ecological processes. Ecologically meaningful intraspecific variation might be particularly important in the context of agricultural weeds and exotic invaders, because intraspecific variation in these species might allow them to rapidly adapt to their unusually dynamic and variable environments. In a greenhouse study, we explored intraspecific variation in the size, rhizome production, and competitive ability of the global invader, Johnsongrass (Sorghum halepense), representing populations from agricultural and non-agricultural habitats across its introduced North American range. We also used these populations to explore the relationship between phenotypic variation and genomic endoreduplication responses to the common stresses herbicides, competition, and clipping. Endoreduplication occurs when plants increase their genome size by increasing their nuclear chromosome number, with some evidence showing correlations with stress response. We found that Johnsongrass plants from agricultural habitats were larger than plants from non-agricultural habitats, but there was no difference between habitats in either rhizome production or competitive ability. Two of the five herbicides we tested, primisulfuron and imazethapyr, had the strongest suppressive effects on Johnsongrass, and also stimulated the greatest rates of endoreduplication. Furthermore, agricultural populations showed higher levels of endoreduplication. We found no overall effect of competition on endoreduplication, although endoreduplication was higher for non-agricultural populations than agricultural populations. When competing with corn, but not with conspecifics, Johnsongrass roots increased endoreduplication by 13%. Clipping induced substantial endoreduplication, but there was no difference between agricultural and non-agricultural populations. Our results suggest that endoreduplication may play a role in some, but not all, stress responses in Johnsongrass. Furthermore, our results indicate that Johnsongrass has adapted in some phenotypic and genomic ways to agricultural habitats in North America. Such adaptation may play a role in this species' success as both an agricultural weed and an exotic invader.
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    Best Management Practices for Bioenergy Crops: Reducing the Invasion Risk
    Barney, Jacob (Virginia Cooperative Extension, 2012-01-05)
    Best practices for selection, field management, harvest, transport, and storage of bioenergy crops to minimize spread of invasive species such as noxious weeds.
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    Biological control of the invasive Ailanthus altissima (tree-of-heaven) in Virginia using naturally occurring Verticillium wilt fungi
    Brooks, Rachel Keys (Virginia Tech, 2020-06-08)
    The invasive tree-of-heaven, Ailanthus altissima (Miller) Swingle, is widespread and damaging throughout North America. Verticillium wilt disease is emerging as a potentially exciting biological control option for this difficult to control tree. In Virginia, Verticillium nonalfalfae has been confirmed causing significant mortality to A. altissima, while V. dahliae is suspected to be present and causing lower levels of disease. Little else is known regarding these two fungal species in this state. The purpose of this research was to gain a better understanding of how Verticillium wilt impacts A. altissima and its potential as a biological control agent. We first confirmed V. dahliae's presence in Virginia and its pathogenicity to A. altissima using Koch's postulates. We then completed a regional field-inoculation experiment to show that V. nonalfalfae effectively kills and spreads to adjacent A. altissima, regardless of V. dahliae presence or other climate and stand variables. Additionally, we showed that V. dahliae causes lower levels of disease than V. nonalfalfae, and does not spread rapidly. Next, we surveyed all Virginia A. altissima stands known to be naturally infected with V. nonalfalfae to determine whether V. nonalfalfae persists long-term, that it considerably reduces A. altissima numbers, and that its local prevalence may be higher than initially suspected. However, we were unable to infect A. altissima seedlings using soil collected at these infested sites, suggesting that V. nonalfalfae's survival within field soil may be limited. Lastly, using paired A. altissima invaded-uninvaded sites, we found that A. altissima presence is associated with a decreased proportion of native plants and species in the woody and herbaceous understory, but not the germinable seedbank. Furthermore, we found that this impact on the woody understory appears to increase over time, supporting early management actions and helping us predict post-management restoration needs. We conclude that V. nonalfalfae has a high potential of successfully limiting A. altissima throughout Virginia, supporting its registration as a biopesticide.
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    Biotic Interaction of Invasive, Early-Succession Trees and Their Effects on Community Diversity: a Multi-Scale Study Using the Exotic Invasive Ailanthus altissima and the Native Robinia pseudoacacia in the Mid-Appalachian Forest of Eastern United States
    Bao, Zhe (Virginia Tech, 2015-04-28)
    Invasive plants can displace native species, deteriorate native forest, and change plant communities and ecosystem functions. Native plant populations are fundamentally impacted by invasive species because of the interactions between invasive species and native plants. This study focuses on understanding the extent, mechanisms and consequences of interaction between a non-indigenous invader Ailanthus altissima and its functionally similar native species Robinia pseudoacacia in the Mid-Appalachian region, from an individual scale to a regional scale. These two subject species are common and coexist in early-successional eastern deciduous forest. The interactions between these two common species are important to community structure and canopy tree regeneration. To address the type and extent of interactions of these two species, a greenhouse experiment utilizing various species proportions, nutrient levels and seed sources was performed. In addition, a common-garden experiment with various species densities and proportions over three consecutive growing seasons was performed in a more natural condition than that of the greenhouse experiment. We found at the seedling stage, the dominant interaction was competition, and R. pseudoacacia was the winner both above- and belowground. The allelopathic compounds of A. altissima may have inhibited nodulation of R. pseudoacacia. Ailanthus altissima seedlings from its native region had slightly stronger competitive abilities compared with the seedlings from its invaded range. In the common garden experiment, R. pseudoacacia plants grew quicker than A. altissima, but A. altissima inhibited the growth of R. pseudoacacia by interspecific competition. The negative impact of A. altissima on R. pseudoacacia became larger as time progressed. To assess the community-level consequences of the two species, we conducted a forest mapping and a complete target-tree-based forest survey, and analyzed regional-scale data from the Forest Inventory Analysis Data Base. The two target species were significantly associated with themselves and with each other. Community species composition and diversity were significantly different across sites. A negative impact of both species on the understory community diversity and tree regeneration at the neighborhood scale was detected; while at a regional level, tree diversity in the FIA plots with either A. altissima or R. pseudoacacia was higher than the reference plots.
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    Characterizing Oxadiazon Resistance and Improving Postemergence Control Programs for Goosegrass (Eleusine indica) in Bermudagrass (Cynodon spp.)
    Cox, Michael Christopher (Virginia Tech, 2014-04-16)
    Goosegrass is a problematic weed of golf courses, sports fields, and residential lawns that decreases playability and aesthetic quality of turf. With the recent banning of MSMA in sports fields and intensive restrictions in golf and sod production, turfgrass managers are seeking alternatives for postemergence goosegrass control and how to utilize currently labeled goosegrass control products more effectively. Studies were conducted to investigate a suspected-resistant (SR) goosegrass accession in Richmond, VA and characterize the resistance mechanism if present. The SR accession showed a hypersensitive response to oxadiazon treatment and reached maximum electrolyte leakage quicker than the susceptible (S) accession, but had significantly lower electrolyte leakage indicating less tissue damage and suggesting there is a physiological resistance mechanism within the SR accession. In absorption and translocation studies, percent oxadiazon absorption and translocation was not significantly affected by goosegrass biotype. Roots of both the S and resistant (R) biotypes contained over 95% of total detected oxadiazon, while the plant tissue above the treated foliage only contained small quantities. These results suggest that absorption or translocation is not the mechanism conferring oxadiazon resistance in the goosegrass biotype from Richmond, VA. Greenhouse and field trials were conducted to determine the lowest rate at which topramezone, with or without the addition of triclopyr, controls goosegrass while maintaining commercially-acceptable bermudagrass quality. In field trials, topramezone rate did not significantly affect goosegrass cover at 56 and 70 days after initial treatment (DAIT). All treatments reduced goosegrass cover below 3 and 7% with and without the addition of triclopyr, respectively at 70 DAIT. A significant herbicide effect on bermudagrass cultivar showed higher injury from topramezone within three weeks of application, but injury persisted longer from treatments containing triclopyr. Bermudagrass cultivars completely recovered by 4 weeks after treatment (WAT) from all treatments. Greenhouse trials were conducted to determine if goosegrass growth stage affects efficacy of nine postemergent herbicides or programs documented to have goosegrass activity. As goosegrass growth stage increased from four- to five-leaf to greater than eight-tiller stage, goosegrass control and biomass reduction decreased among all of the herbicides except topramezone and MSMA plus metribuzin at 4 and 8 WAT. These data suggest that one application of sulfentrazone is only effective for seedling stage (pre-tiller) goosegrass control; foramsulfuron, topramezone, and metribuzin suppress all growth stages of goosegrass; and diclofop, sulfentrazone plus metribuzin, fenoxaprop, and metamifop control up to three-tiller stage goosegrass.
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    Chemical and biological control of silvery threadmoss on creeping bentgrass putting greens
    Post, Angela R. (Virginia Tech, 2013-07-31)
    Silvery threadmoss is a problematic weed of golf putting greens, growing interspersed with turf, decreasing aesthetic quality and playability.  Moss is typically controlled postemergence and currently only one herbicide, carfentrazone, is registered for silvery threadmoss control on greens.  Carfentrazone controls moss up to 75% applied at a three week interval throughout the growing season.  Alternatives providing longer residual or more effective control are desirable.  Studies were conducted to examine the growth of moss gametophytes from spores and bulbils and to evaluate turf protection products for pre and postemergence moss control.  Moss gametophytes develop best from spores at 30"aC and from bulbils at 23"aC.  Products which control moss equivalent to carfentrazone (>70%) both pre and postemergent include sulfentrazone, saflufenacil, flumioxazin, oxadiazon, and oxyfluorfen.  Fosamine and fosetyl-Al alone controlled moss equivalent to carfentrazone post-, but not preemergent.  14C glyphosate absorption and translocation through moss colonies was examined from 12 to 192 hours after treatment (HAT) to understand how herbicides are absorbed by silvery threadmoss.  It appears that 14C reaches equilibrium by 24 HAT in capillary water of the moss colony and inside moss tissues.  Subsequently, 14C is lost to the system presumably through microorganism degradation of 14C glyphosate in capillary water.  The final objective of this work was to identify and evaluate two fungal organisms observed to cause disease of silvery threadmoss on putting greens in efforts to develop a biological control.  The organisms were identified by morphology and ITS sequence as Alternaria sp. and Sclerotium rolfsii.  Alternaria sp. causes a leaf disease of silvery threadmoss and Sclerotium rolfsii causes Southern blight of silvery threadmoss.  Host specificity testing demonstrated moderate pathogenicity of S. rolfsii to annual bluegrass but not to "¥Penn A4"" creeping bentgrass.  Both organisms have potential to be effective biological controls for silvery threadmoss; however, host specificity indicates Alternaria sp. may be a better choice.  Data from these experiments suggest herbicides in two chemical classes control mosses both pre and postemergence, and sulfentrazone, fosetyl-Al, and Alternaria sp. may be new alternatives to carfentrazone for use on golf putting greens.  
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    Choosing Plant Species for Reclamation to Better Resist Invasion from Exotic, Invasive Plants
    Barney, Jacob; Franke, Morgan (Virginia Tech. Powell River Project, 2017)
    Post‐mining landscapes are currently reclaimed using the Forestry Reclamation Approach (FRA) developed at Virginia Tech that seeks to achieve high hardwood tree canopy cover following establishment of “tree‐compatible groundcover”. FRA has been successful in advancing development of ecosystem structure (e.g., ground cover, species diversity, stem density). However, as Dr. Burger and colleagues pointed out in 2010, FRA results in more bare ground, which “allows more invasion by plant species from nearby areas.” They point out this is often from adjacent native species from natural dispersal or by animals. However, the gaps left by FRA leave much of the ground open to invasion by exotic plants as well, that may have negative impacts to desirable vegetation and ecosystem function. Exotic invasive plants are known to have negative impacts to ecosystem structure and function in a wide range of systems. However, the effect of these exotic plants can be especially problematic on reclaimed mine sites due to the harsh growing environment.
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    Climatic niche shifts are common in introduced plants
    Atwater, Daniel Z.; Ervine, Carissa; Barney, Jacob (Nature, 2017-12-04)
    Our understanding of how climate influences species distributions and our ability to assess the risk of introduced species depend on the assumption that species’ climatic niches remain stable across space and time. While niche shifts have been detected in individual invasive species, one assessment of ~50 plants in Europe and North America concluded that niche shifts were rare, while another concluded the opposite. These contradictory findings, limited in species number and geographic scope, leave open a need to understand how often introduced species experience niche shifts and whether niche shifts can be predicted. We found evidence of climatic niche shifts in 65–100% of 815 terrestrial plant species introduced across five continents, depending on how niche shifts were measured. Individual species responses were idiosyncratic, but we generally saw that niche shifts reflected changes in climate availability at the continent scale and were largest in long-lived and cultivated species. Smaller intercontinental niche shifts occurred within species’ native ranges. Overall, the climatic niches of terrestrial plant species were not conserved as they crossed continents. These results have major consequences for applying environmental niche models to assess the risk of invasive species and for predicting species responses to climate change. Our findings challenge the tenet that species’ niches are conserved aspects of their ecology.
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    Conservation Programs and White-tailed Deer Ecology
    Royeen, David D. (Virginia Tech, 2019-05-07)
    White-tailed deer have reached historical numbers since nearly being wiped out due to overhunting and habitat loss. This paper seeks to review the rebound of white-tailed deer populations, specifically analyzing the role conservation practice and habitat management have played. A brief history of private land contracts in the United States is established before relating deer ecology to habitat availability. The importance of deer from the perspective of humans as well as the ecosystem is highlighted in an effort to encourage and promote conservation and habitat preservation efforts. This work seeks to answer the question “How do conservation programs influence white-tailed deer behavior and what steps can land managers take to protect wildlife on their property?”. A list of recommendations for land owners is given to share best-practice policies for governing a healthy population of white-tailed deer. Lastly, study limitations and constraints of this paper are analyzed to promote transparency and identify areas of concern with data collection.
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    Cool Temperature Effects on Productivity and Photosynthesis of Two Biomass Fuel Species: Switchgrass (Panicum virgatum) and  Miscanthus (Miscanthus x giganteus)
    Mitchell, Jackson Lee Bean (Virginia Tech, 2013-01-14)
    The world\'s highest yielding crops are C4 plants due to their higher water use efficiency, nitrogen use efficiency, and productivity compared with C3 plants.  With an increasing demand for renewable resources as a result of the decreasing global supplies of fossil fuels, we need to improve our understanding of the limitations of biomass fuel feedstock to improve yields and better satisfy energy requirements.  The ability to attain the goal feedstock production in the US is limited by available arable land and cool temperatures.  This study investigates the effects of cool temperatures on the productivity and photosynthesis of the two species with the highest potential for feedstock production in the US: switchgrass (Panicum virgatum) cv. Alamo and miscanthus (Miscanthus × giganteus).  At 14/12"C and a 14/10 hour light/dark photoperiod, switchgrass showed lower productivity and light saturated photosynthetic rates (Amax=10.3 "mol m-2s-1) compared with 28/25"C and the same photoperiod (Amax=18.8 "mol m-2s-1).  Miscanthus has demonstrated cold tolerance in previous studies, and here showed no significant decrease in the productivity or photosynthetic rates in cool, compared with warm, growing conditions (Amax=8.2 "mol m-2s-1 and 7.0 "mol m-2s-1 for warm and cool conditions, respectively). Also, this study examines the potential limitations of C4 photosynthesis by the enzyme pyruvate phosphate dikinase (PPDK) under the same cool conditions, transgenic switchgrass cv. Alamo were created with the insertion of the miscanthus PPDK gene. Productivity and photosynthetic responses of the transgenic plants were evaluated in cool and warm growth temperatures.  Of the two transgenic events tested here, line S(1) displayed cold tolerance, as seen in no loss of both carboxylation efficiency and the ratio of CO2 assimilation to electron transport (Asat/Jmax).  These results indicate that PPDK may pose a significant limitation to C4 photosynthesis in cool conditions and there is a possibility that cold season photosynthesis of switchgrass cv. Alamo could be improved.
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    The Curious Poisoned Weed: Poison Ivy Ecology and Physiology
    Dickinson, Christopher Cody (Virginia Tech, 2019-07-11)
    Poison ivy (Toxicodendron radicans (L.) Kuntze) is a native perennial liana widely recognized for the production of urushiol, and the associated contact dermatitis it causes in humans. Poison ivy is predicted to become both more prevalent and more noxious in response to projected patterns of global change. Moreover, poison ivy is an important food source for avian species, and urushiol has numerous applications as a high-value engineering material. Thus, this curious weed has many avenues for future concern, and promise. Here, I address gaps in knowledge about poison ivy ecology and physiology so that we may better understand its weediness and utilize its benefits. I address three core areas: poison ivy establishment patterns; biotic interactions with multiple taxa; and the development of molecular tools for use in poison ivy. I found that the early life stage of seedling emergence is a critical linchpin in poison ivy establishment due largely to herbivore pressure from large grazers. I also describe the multifaceted relationship between poison ivy and avian frugivores that not only disperse the drupes of poison ivy but also aid in reduction of fungal endophytic phytopathogens. A survey of poison ivy urushiols yielded that while variation in urushiol congeners was high across individuals, relative congener levels were stable within individuals over a two month period. Lastly I demonstrate best practices for introducing and transiently expressing recombinant DNA in poison ivy as a step towards future reverse genetic procedures.
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    Detection of a Surrogate Biological Threat Agent (Bacillus globigii) with a Portable Surface Plasmon Resonance Biosensor
    Adducci, Benjamin Augustus (Virginia Tech, 2015-06-08)
    New methods and technology are needed to detect biological agents that threaten the health of humans and domestic animals. The bacterium Bacillus anthracis, causal agent of anthrax, has been used as a biological warfare agent. Here, we extend the work of Chinowksy et al. (2007) to the detection of a surrogate of B. anthracis, B. globigii (also known as B. atrophaeus, B. subtilis var. niger, B. subtilis var. subtilis) in a mixed sample containing two different species of Bacillus using a portable surface plasmon resonance (SPR) biosensor (SPIRIT 4.0, Seattle Sensor Systems). Two methods (direct capture and antibody injection) were used to determine the limit of detection for spores of B. globigii and to detect spores of B. globigii in a mixed sample containing at least one other Bacillus spp. Spores of B. globigii were detected on freshly coated sensors (not previously exposed to spores) with direct capture at a minimum concentration of 10^7 spores/mL, and with antibody injection at a concentration of 10^5 spores/mL. Spores of B. globigii were also detected when mixed with B. pumilus spores in the same sample at equal concentrations (107 spores/mL) using antibody injection. An SPR method using synthetic miRNA was adapted to the portable SPR unit (SPIRIT), and preliminary experiments suggested that the target sequence could be detected. SPR methods using nucleic acids have an exciting future in the detection of biological agents, such as B. anthracis. With the availability of portable instrumentation to accurately detect biological warfare agents such as B. anthracis, emergency responders can implement emergency protocols in a timely fashion, limiting the amount of people and domestic animals exposed.
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    Ecology and niche characterization of the invasive ornamental grass Miscanthus sinensis
    Dougherty, Ryan Fitzgerald (Virginia Tech, 2013-06-12)
    The recent trend in bioenergy feedstock development focuses on the use of large-statured perennial grasses that pose a relatively high risk of becoming invasive species due to the similarity in desirable agronomic traits with those of many of our worst invaders. Thus, it would be prudent to evaluate the potential ecological benefits and consequences of widespread cultivation of potentially invasive species. Miscanthus sinensis and its sterile daughter species, Miscanthus × giganteus, are two prominent bioenergy feedstock candidates due to their low input requirements and significant biomass production in a broad range of growing conditions. Despite being an extremely popular ornamental grass, and naturalizing in over half of US states, little is actually known about the biology, ecology and niche requirements of M. sinensis. Thus, the objective of our research is to characterize extant M. sinensis populations, and evaluate the niche requirements, especially in terms of the commonly limiting resources of light and soil moisture. In order to better assess the risk of M. sinensis (and subsequently M. × giganteus) cultivation, we surveyed 18 naturalized populations across the east coast to characterize habitat preferences, population structure, and plant performance across a latitudinal gradient. We found the vast majority of M. sinensis populations occurred in areas of high and low resource availability (e.g. soil nutrients and light) along roadsides and forest edges, with outlier individuals found in forest understories. We conducted a greenhouse study to compare shade and soil moisture tolerance among common ornamental cultivars and naturalized populations, where we found enhanced plant growth and vigor in naturalized biotypes compared to ornamentals across varying levels of shade. We also found that both naturalized and ornamental biotypes were not significantly affected by soil moisture stress, and thus express significant drought tolerance. Finally, we investigated the temperature and moisture requirements of M. sinensis seeds and determined a base temperature of approximately 8"C, as well as variable moisture and time to germination requirements between varieties and seed sources. These basic ecological studies will help refine and support future evaluations and weed risk assessments of both Miscanthus sinensis and M. × giganteus, which is critical in prevention of major ecological invasions.
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    Ecotypic Variation in Johnsongrass in Its Invaded U.S. Range
    Lakoba, Vasiliy T. (Virginia Tech, 2021-05-28)
    Biological invasions have been observed throughout the world for centuries, often with major consequences to biodiversity and food security. Tying invasion to species identity and associated traits has led to numerous hypotheses on why, and where, some species are invasive. In recent decades, attention to intraspecific variation among invaders has produced questions about their adaptation to climate, land use, and environmental change. I examined the intraspecific variation of invasive Johnsongrass's (Sorghum halepense (L.) Pers.) seedling stress response, propagule cold tolerance, and large-scale niche dynamics for correlation with populations' climatic and ecotypic (i.e., agricultural vs. non-agricultural) origin. Overall, I found a greater number of home climate effects than ecotypic effects on various traits. Non-agricultural seed from cold climates and agricultural seed from warm climates germinated more and faster, while non-agricultural seedlings showed uniform chlorophyll production regardless of home soil carbon origin, unlike their agricultural counterparts. Neither seedling stress response nor propagule cold tolerance interacted with ecotype identity; however, drought stress varied with population origins' aridity and soil fertility, and seed from warm/humid and cold/dry climates was most germinable. Comparison of seed and rhizome cold tolerance also suggested that the latter is a conserved trait that may be limiting S. halepense poleward range expansion. This physiological limit, an unchanged cold temperature niche boundary between continents and ecotypes, and a narrowed niche following transition to non-agricultural lands all imply low likelihood of spread based on climatic niche shift. Instead, evidence points to range expansion driven primarily by climate change and highlights agriculture's role in facilitating invasibility. This tandem approach to climate and land use as drivers of intraspecific variation is transferable to other taxa and can help refine our conception of and response to invasion in the Anthropocene.
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    The effects of wildflower plots and diverse landscapes on ecosystem services, bee communities, and on-farm tick abundance
    McCullough, Christopher T. (Virginia Tech, 2020-06-03)
    Conservation of natural habitats and planting wildflower plots are two commonly promoted tactics to enhance pollination services and biological control of crop pests, which are ecosystem services that can improve agricultural outputs. There are several programs at various levels of government in the United States that landowners can use to defray the costs of implementing these conservation strategies. Studies of European Agricultural Environmental Schemes have shown these tactics to have positive outcomes for crop production. However, real-world applications of cost-sharing programs have not been evaluated in the United States on pollination services and biological control. Furthermore, these tactics may inadvertently perform ecosystem disservices, like increasing crop pests or creating habitat for disease vectors. In this study, we evaluated the effects of natural habit and wildflower plots on biological control, pollination services, bee communities, and tick populations in Eastern Virginia and Maryland. This research was conducted on 22 farms. 10 of these farms had wildflower plots that were designed by Natural Resource Conservation Service personnel, and implemented by cooperating farmers. Collards, strawberries, tomatoes, and squash were used as model systems. We measured pest density, sentinel egg predation, crop damage, seed pollination, biomass production, marketable crop yield, sampled the bee community, and recorded tick abundance in wildflower plots. Many of the measures of biological control and pollination services had idiosyncratic results in regards to the wildflower plots and natural habit in the landscape. However, the proportion of high quality yield for all four crops increased with increasing natural habitat in the landscape. Bee communities between sites with and without wildflower plots were not different. Bee abundance did increase at wildflower sites when natural habitat comprised a certain proportion of the habitat around the site. Ticks were sampled from wildflower plantings, but not in greater abundance compared to field margins. In this study, the effects of wildflower plots were overshadowed by the landscape effects of natural habitat. Government personnel that oversee these programs may need to consider the surrounding landscape when helping implement on-farm conservation measure like wildflower plots. Such measures, do not perform an ecosystem disservice in regards to ticks.
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    Epigenetic Responses of Arabidopsis to Abiotic Stress
    Laliberte, Suzanne Rae (Virginia Tech, 2023-03-17)
    Weed resistance to control measures, particularly herbicides, is a growing problem in agriculture. In the case of herbicides, resistance is sometimes connected to genetic changes that directly affect the target site of the herbicide. Other cases are less straightforward where resistance arises without such a clear-cut mechanism. Understanding the genetic and gene regulatory mechanisms that may lead to the rapid evolution of resistance in weedy species is critical to securing our food supply. To study this phenomenon, we exposed young Arabidopsis plants to sublethal levels of one of four weed management stressors, glyphosate herbicide, trifloxysulfuron herbicide, mechanical clipping, and shading. To evaluate responses to these stressors we collected data on gene expression and regulation via epigenetic modification (methylation) and small RNA (sRNA). For all of the treatments except shade, the stress was limited in duration, and the plants were allowed to recover until flowering, to identify changes that persist to reproduction. At flowering, DNA for methylation bisulfite sequencing, RNA, and sRNA were extracted from newly formed rosette leaf tissue. Analyzing the individual datasets revealed many differential responses when compared to the untreated control for gene expression, methylation, and sRNA expression. All three measures showed increases in differential abundance that were unique to each stressor, with very little overlap between stressors. Herbicide treatments tended to exhibit the largest number of significant differential responses, with glyphosate treatment most often associated with the greatest differences and contributing to overlap. To evaluate how large datasets from methylation, gene expression, and sRNA analyses could be connected and mined to link regulatory information with changes in gene expression, the information from each dataset and for each gene was united in a single large matrix and mined with classification algorithms. Although our models were able to differentiate patterns in a set of simulated data, the raw datasets were too noisy for the models to consistently identify differentially expressed genes. However, by focusing on responses at a local level, we identified several genes with differential expression, differential sRNA, and differential methylation. While further studies will be needed to determine whether these epigenetic changes truly influence gene expression at these sites, the changes detected at the treatment level could prime the plants for future incidents of stress, including herbicides.
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    The Evolution of an Invasive Plant, Sorghum halepense L. ('Johnsongrass')
    Paterson, Andrew H.; Kong, Wenqian; Johnston, Robyn M.; Nabukalu, Pheonah; Wu, Guohong; Poehlman, William L.; Goff, Valorie H.; Isaacs, Krista; Lee, Tae-Ho; Guo, Hui; Zhang, Dong; Sezen, U. Uzay; Kennedy, Megan; Bauer, Diane; Feltus, Frank A.; Weltzien, Eva; Rattunde, Henry Frederick; Barney, Jacob; Barry, Kerrie; Cox, T. Stan; Scanlon, Michael J. (Frontiers, 2020-05-14)
    From noble beginnings as a prospective forage, polyploid Sorghum halepense (‘Johnsongrass’) is both an invasive species and one of the world’s worst agricultural weeds. Formed by S. bicolor x S. propinquum hybridization, we show S. halepense to have S. bicolor-enriched allele composition and striking mutations in 5,957 genes that differentiate it from representatives of its progenitor species and an outgroup. The spread of S. halepense may have been facilitated by introgression from closely-related cultivated sorghum near genetic loci affecting rhizome development, seed size, and levels of lutein, a photochemical protectant and abscisic acid precursor. Rhizomes, subterranean stems that store carbohydrates and spawn clonal propagules, have growth correlated with reproductive rather than other vegetative tissues, and increase survival of both temperate cold seasons and tropical dry seasons. Rhizomes of S. halepense are more extensive than those of its rhizomatous progenitor S. propinquum, with gene expression including many alleles from its non-rhizomatous S. bicolor progenitor. The first surviving polyploid in its lineage in ∼96 million years, its post-Columbian spread across six continents carried rich genetic diversity that in the United States has facilitated transition from agricultural to non-agricultural niches. Projected to spread another 200–600 km northward in the coming century, despite its drawbacks S. halepense may offer novel alleles and traits of value to improvement of sorghum.
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    Germination niche of an emergent invasive grass, Arthraxon hispidus
    Beall, Michael Christian (Virginia Tech, 2022-07-01)
    Joint-head grass (Arthraxon hispidus) is a widespread nonindigenous plant species in the eastern United States. It is observed forming large monodominant patches that impact native and managed grassland systems. With such little understanding of its foundational biology or ecological impacts, leaving land managers desperate for effective control measures to manage A. hispidus invasion. We conducted a series of complementary experiments on six populations of A. hispidus to better understand how environmental factors affect seed germination. Germination is a critical life stage that allows a species to disperse. Freshly harvested seeds germinated effectively within 14 days of imbibition in the dark at 23°C, exhibiting little to no dormancy or influence by light. A pH range of 5 - 10 resulted in ≥ 80% germination, suggesting that pH will not limit colonization in other portions of the United States. Arthaxon hispidus was tolerant to abiotic stressors such as salinity and osmotic potential. The concentration required to limit germination to 50% (LD50) in the populations tested surpassed soil salinity found in the contiguous United States and some tidal systems (Frederick, MD = 354; Lincoln, MO = 354; Williamsburg, VA = 298 mM NaCl). While drought adversely affects A. hispidus germination, the LD50 occurred in moderate to more severe osmotic potentials (Frederick, MD = -0.67; Lincoln, MO = -0.37; Williamsburg, VA = -0.25 MPa) making A. hispidus expansion more likely in wetter years and regions. Constant temperature treatments resulted in germination percentages across a range of temperatures (8 - 37°C), and A. hispidus is well distributed in several major temperature regimes found in the United States. Finally, emergence greatly decreased with burial depth. Emergence occurred at ≥ 43% at 1 - 2 cm, decreasing to 5% at 6 cm, and 0% at 8-cm depths. With adequate soil moisture, a broad range of germination temperatures, and a decreased emergence rate with depth, we believe A. hispidus is unlikely to develop a seed bank. These initial studies on A. hispidus' germination posit a broad range of environmental tolerances; although, it may be limited by other life stages.
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    Global Climate Niche Estimates for Bioenergy Crops and Invasive Species of Agronomic Origin: Potential Problems and Opportunities
    Barney, Jacob; DiTomaso, Joseph M. (PLOS, 2011-03-09)
    The global push towards a more biomass-based energy sector is ramping up efforts to adopt regionally appropriate high-yielding crops. As potential bioenergy crops are being moved around the world an assessment of the climatic suitability would be a prudent first step in identifying suitable areas of productivity and risk. Additionally, this assessment also provides a necessary step in evaluating the invasive potential of bioenergy crops, which present a possible negative externality to the bioeconomy. Therefore, we provide the first global climate niche assessment for the major graminaceous (9), herbaceous (3), and woody (4) bioenergy crops. Additionally, we contrast these with climate niche assessments for North American invasive species that were originally introduced for agronomic purposes as examples of well-intentioned introductions gone awry. With few exceptions (e.g., Saccharum officinarum, Pennisetum purpureum), the bioenergy crops exhibit broad climatic tolerance, which allows tremendous flexibility in choosing crops, especially in areas with high summer rainfall and long growing seasons (e.g., southeastern US, Amazon Basin, eastern Australia). Unsurprisingly, the invasive species of agronomic origin have very similar global climate niche profiles as the proposed bioenergy crops, also demonstrating broad climatic tolerance. The ecoregional evaluation of bioenergy crops and known invasive species demonstrates tremendous overlap at both high (EI≥30) and moderate (EI≥20) climate suitability. The southern and western US ecoregions support the greatest number of invasive species of agronomic origin, especially the Southeastern USA Plains, Mixed Woods Plains, and Mediterranean California. Many regions of the world have a suitable climate for several bioenergy crops allowing selection of agro-ecoregionally appropriate crops. This model knowingly ignores the complex biotic interactions and edaphic conditions, but provides a robust assessment of the climate niche, which is valuable for agronomists, crop developers, and regulators seeking to choose agro-ecoregionally appropriate crops while minimizing the risk of invasive species.
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    Global Invader Impact Network (GIIN): toward standardized evaluation of the ecological impacts of invasive plants
    Barney, Jacob; Tekiela, Daniel R.; Barrios-Garcia, Maria Noelia; Dimarco, Romina D.; Hufbauer, Ruth A.; Leipzig-Scott, Peter; Nuñez, Martin A.; Pauchard, Aníbal; Pyšek, Petr; Vítková, Michaela; Maxwell, Bruce D. (Wiley, 2015-06-30)
    Terrestrial invasive plants are a global problem and are becoming ubiquitous components of most ecosystems. They are implicated in altering disturbance regimes, reducing biodiversity, and changing ecosystem function, sometimes in profound and irreversible ways. However, the ecological impacts of most invasive plants have not been studied experimentally, and most research to date focuses on few types of impacts, which can vary greatly among studies. Thus, our knowledge of existing ecological impacts ascribed to invasive plants is surprisingly limited in both breadth and depth. Our aim was to propose a standard methodology for quantifying baseline ecological impact that, in theory, is scalable to any terrestrial plant invader (e.g., annual grasses to trees) and any invaded system (e.g., grassland to forest). The Global Invader Impact Network (GIIN) is a coordinated distributed experiment composed of an observational and manipulative methodology. The protocol consists of a series of plots located in (1) an invaded area; (2) an adjacent removal treatment within the invaded area; and (3) a spatially separate uninvaded area thought to be similar to pre-invasion conditions of the invaded area. A standardized and inexpensive suite of community, soil, and ecosystem metrics are collected allowing broad comparisons among measurements, populations, and species. The method allows for one-time comparisons and for long-term monitoring enabling one to derive information about change due to invasion over time. Invader removal plots will also allow for quantification of legacy effects and their return rates, which will be monitored for several years. GIIN uses a nested hierarchical scale approach encompassing multiple sites, regions, and continents. Currently, GIIN has network members in six countries, with new members encouraged. To date, study species include representatives of annual and perennial grasses; annual and perennial forbs; shrubs; and trees. The goal of the GIIN framework is to create a standard yet flexible platform for understanding the ecological impacts of invasive plants, allowing both individual and synthetic analyses across a range of taxa and ecosystems. If broadly adopted, this standard approach will offer unique insight into the ecological impacts of invasive plants at local, regional, and global scales.