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148 results for “plant performance”
Plant virus SNP prediction artificial dataset Performance Study
<p>Recent developments in high-throughput sequencing (HTS) technologies and bioinformatics have drastically changed research on viral pathogens, especially for virus discovery and monitoring. Indeed, proper monitoring of the viral population requires information on the different isolates circulating in the studied area. For this purpose, HTS technologies have greatly facilitated the generation of new genomes of the detected viruses and their comparison. Nevertheless, the bioinformatics analyses allowing the reconstruction of genomes and the detection of Single Nucleotide Polymorphisms (SNPs) can potentially create bias, although it has not been widely addressed so far. </p> <p>Therefore, more knowledge is required on the limitation and possibility of predicting SNPs based on HTS-generated sequence datasets. To address this issue, we compared the ability of 14 plant virology laboratories, each employing a different bioinformatics pipeline, to detect 21 variants of pepino mosaic virus (PepMV) through large-scale Performance Testing (PT) using three artificially designed datasets. The bioinformatics analyses were divided into three key steps: reads pre-processing (quality trimming, merging …), virus identification (assembly, alignment, mapping …) and variant calling. Each step was evaluated independently through an original, step-by-step PT design with iteration between participants. </p> <p>Overall, this work underlines key parameters in SNP detection and proposes recommendations for reliable variant calling for plant viruses. The identification of the closest reference, mapping parameters and manual validation of the prediction were the most impactful analysis step for the success or failure of the predictions. Strategies to improve SNPs prediction are also discussed. </p>
Does a history of population co-occurrence predict plant performance, community productivity, or invasion resistance?
<p>A history of species co-occurrence in plant communities is hypothesized to lead to greater niche differentiation, more efficient resource partitioning, and more productive, resistant communities as a result of evolution in response to biotic interactions. A similar question can be asked of co-occurring populations: do individual species or community responses differ when communities are founded with plants sharing a history of population co-occurrence (sympatric) or originating from different locations (allopatric)? Using shrub, grass, and forb species from six locations in the western Great Basin, USA, we compared establishment, productivity, reproduction, phenology, and resistance to invaders for experimental communities with either sympatric or allopatric population associations. Each community type was planted with six taxa in outdoor mesocosms, measured over three growing seasons, and invaded with the annual grass <em>Bromus tectorum</em> in the final season. For most populations, the allopatric or sympatric status of neighbors was not important. However, in some cases, it was beneficial for some species from some locations to be planted with allopatric neighbors, while others benefited from sympatric neighbors, and some of these responses had large effects. For instance, the <em>Elymus</em> population that benefited the most from allopatry grew 50% larger with allopatric neighbors than in single origin mesocosms. This response affected invasion resistance, as <em>B. tectorum</em> biomass was strongly affected by productivity and phenology of <em>Elymus</em> spp., as well as <em>Poa secunda</em>. Our results demonstrate that while community composition can affect plant performance in semi-arid plant communities, assembling communities from sympatric populations is not sufficient to ensure high productivity and invasion resistance. Instead, we observed an idiosyncratic interaction between sampling effects and evolutionary history, with the potential for seed source of individual populations to have community-level effects.</p>
Nutrient supply and accessibility in plants: Effect of protein and carbohydrates on Australian plague locust (Chortoicetes terminifera) preference and performance
<p>In contrast to predictions from nitrogen limitation theory, recent studies have shown that herbivorous migratory insects tend to be carbohydrate (not protein) limited, likely due to increased energy demands, leading them to preferentially feed on high carbohydrate plants. However, additional factors such as mechanical and chemical defenses can also influence host plant choice and nutrient accessibility. In this study, we investigated the effects of plant protein and carbohydrate availability on plant selection and performance for a migratory generalist herbivore, the Australian plague locust, <em>Chortoicetes</em> <em>terminifera</em>. We manipulated the protein and carbohydrate content of seedling wheat (<em>Triticum</em> <em>aestivum</em> L.) by two means: 1) we increased the protein:carbohydrate ratio using nitrogen (N) fertilizer, 2) we sought to increase carbohydrate accessibility by grinding cell walls after drying the plants. Using a full factorial design, we ran both choice and no-choice experiments to measure preference and performance. We confirmed locust preference for plants with a lower protein-carbohydrate ratio (unfertilized plants). Unlike previous studies with mature wild grass species, we found that intact plants supported better performance than dried and ground plants, suggesting that cell wall removal may only improve performance for tougher or more carbohydrate-rich plants. These results add to the growing body of evidence suggesting that several migratory herbivorous species perform better on plants with a lower protein:carbohydrate ratio. </p>
Data from: Planting design influences green infrastructure performance: Plant species identity and complementarity in rain gardens
<p>Green infrastructure's capacity to mitigate urban environmental problems, like heat island effects and excessive stormwater runoff, is partially governed by its plant community. Traditionally, green infrastructure design has focused on engineered aspects, such as substrate and drainage, rather than on the properties of its living components. Since the functioning of these plant assemblages is controlled by ecophysiological processes which differ by species, the identity and relative abundance of the species used will influence green infrastructure performance. We used trait-based modeling to derive principles for the effective composition of green infrastructure plant assemblages, parameterizing our model using the vegetation and ecophysiological traits of the species within New York City rain gardens. Focusing on two plant traits that influence rain garden performance, leaf surface temperature and stomatal conductance, we simulated the cumulative temperature and transpiration for plant communities of differing species composition and diversity. The outcomes of the model demonstrate that plant species composition, species identity, selection effects, and interspecific complementarity increase green infrastructure performance much the way biodiversity affects ecosystem functioning in natural systems. More diverse assemblages resulted in more consistent transpiration and surface temperatures, with the former showing a positive, saturating curve as diversity increased. While the dominant factors governing individual species' leaf temperature were abiotic, transpiration was more influential at the community level, suggesting that plants within diverse communities may be cooler in aggregate than any individual species on its own. This implies green infrastructure should employ a variety of vegetation; particularly plants with different statures and physical attributes, such as low-growing ground covers, erect herbaceous perennials, and shrubs.</p>
The plant toxin 4-methylsulfinylbutyl isothiocyanate decreases herbivore performance and modulate cellular and humoral immunity
<p class="MsoNormal"><span>Insect herbivores frequently encounter plant defense molecules, but the physiological and ecological consequences for their immune systems are not fully understood. The majority of studies attempting to relate levels of plant defensive chemistry to herbivore immune responses have used natural population or species-level variation in plant defensive chemistry. Yet, this potentially confounds the effects of plant defense chemistry with other potential traits that may affect the expression of herbivore immunity such as development time and nutritional quality. We have used an artificial diet containing known quantities of a plant toxin (4-methylsulfinylbutyl isothiocyanate; 4MSOB-ITC or ITC), an isothiocyanate present in many plants in the genus <em>Brassica</em>, to explicitly explore the effects of a plant toxin on the cellular and humoral immune responses of the generalist herbivore <em>Trichoplusia ni</em> (Lepidoptera: Noctuidae) that frequently feeds on glucosinolate-containing plants. Caterpillars feeding on diets with high concentrations of ITC experienced reduced survivorship and growth rates. High concentrations of ITC suppressed the appearance of several types of hemocytes and melanization activity, which are critical defenses against parasitic Hymenoptera and microbial pathogens. In terms of </span><em><span>T. ni</span></em><span> humoral immunity, only </span><span>the antimicrobial peptide (AMP) genes <em>lebocin</em> and <em>gallerimycin </em>were significantly upregulated in caterpillars fed on diets </span><span>containing high levels of 4MSOB-ITC relative to caterpillars that were provided with ITC-free diet</span><span>. Surprisingly, challenging </span><span>caterpillars</span><span> </span><span>with a non-pathogenic strain of </span><em><span>Escherichia coli</span></em><span> resulted in the upregulation of the AMP gene <em>cecropin</em>. Feeding on high concentrations of plant toxins hindered caterpillar development and decreased cellular immunity but conferred mixed effects on humoral immunity. Our findings provide novel insights into the effects of herbivore diet composition on insect performance demonstrating the role of specific plant defense toxins that shape herbivore immunity and trophic interactions. </span></p>
Dataset and R-script for Article: Increased heat tolerance of geothermal plants comes at the cost of reduced performance under cooler conditions
<p>Dataset and R-script for Article</p> <p>"Increased heat tolerance of geothermal plants comes at the cost of reduced performance under cooler conditions"</p> <p>to be published in the Journal "Ecology and Evolution"</p>
Performance and preference of four above- and below-ground invertebrate and generalist herbivores on regionally and locally rare plant species
<ol> <li>Rare plant species are suggested to be less resistant to herbivores than common species. Their lower apparency and the fact that they often live in isolated populations, resulting in fewer herbivore encounters, might have led to the evolution of reduced defences. Moreover, their frequently lower levels of genetic diversity compared with common species could negatively affect their resistance against enemies. However, the hypothesis that plant resistance depends on plant regional and local rarity, independently of habitat and competitive and growth strategy, lacks evidence.</li> <li>To test this hypothesis, we assessed the performance and preference of one belowground and three aboveground generalist invertebrate herbivores from different taxonomic groups as indicators of plant resistance. Herbivores were fed a total of 62 regionally and locally rare and common plant species from Switzerland. We accounted for differences in a plant's growth and competitive strategy and habitat resource availability.</li> <li>We found that regionally and locally rare and common plant species did not generally differ in their resistance to most generalist herbivores. However, one herbivore species even performed better and preferred locally and regionally common plant species over rarer ones, indicating that common species are not more resistant, but tend to be less resistant. We also found that all herbivore species consistently performed better on competitive and large plant species, although different herbivore species generally preferred and performed better on different plant species. The latter indicates that the use of generalist herbivores as indicators of plant-resistance levels can be misleading.</li> <li> <em>Synthesis</em>: Our results show that rare plant species are not inherently less resistant than common ones to herbivores. Instead, our results suggest that the ability of plants to allocate resources away from defence towards enhancing their competitive ability might have allowed plants to tolerate herbivory, and to become locally and regionally common.</li> </ol>
Data from: Photodegradation modifies microplastic effects on soil properties and plant performance
<p>Microplastics in soil affect plant-soil systems depending on their shape and polymer type. However, previous research has not yet considered the effects of degraded plastics, which are the plastic materials actually present in the environment. We selected 8 microplastics representing different shapes (fibers, films and foams) and polymer types, and exposed them to UV-C degradation. Each microplastic was mixed with soil at a concentration of 0.4% (w/w). The phytometer Daucus carota grew in each pot. At harvest, soil properties and plant biomass were measured.</p> <p>Photodegradation altered microplastics physical and chemical properties, impacting plant-soil systems. Microplastics degradation effects on plant and soil were observed with fibers and foams, but there were negligible effects with films. The latter could be explained by the polymer structure of films and manufacturer's additives, potentially delaying their degradation.</p> <p>Degraded fibers increased soil respiration more than their non-degraded counterparts, as photodegradation increased the positive effects of fibers on soil water retention. The emergence of oxygenated groups during degradation may have increased the hydrophilicity of fibers, enhancing their ability to retain water. Degraded foams increased soil respiration, which could be related to the possible leaching of organic substances with lower partition coefficients, which may promote soil microbial activity.</p> <p>By contrast, degraded foams decreased soil aggregation, likely as degradation produced larger holes increasing their permeability. Also, the increase of hydrophilic molecules could have decreased soil particle cohesiveness. Degraded fibers and foams increased shoot and root mass as a result of microplastic effects on soil properties. Photodegraded microplastics affected root traits, which could be linked to microplastic effects on soil water status and plant coping strategies.</p>
Artificial light at night (ALAN) decreases plant diversity and performance in experimental grassland communities – Data on species biomass and traits
<p>Artificial light at night (ALAN) affects many areas of the world and is increasing globally. To date, there has been limited and inconsistent evidence regarding the consequences of ALAN on plant communities as well as the fitness of their constituent species. ALAN could be beneficial for plants as they need light as an energy source, but they also need darkness for regeneration and growth. We created model communities composed of 16 plant species sown, exposed to a gradient of ALAN ranging from 'moonlight only' to conditions like situations typically found directly underneath a streetlamp. We measured plant community composition and its production (biomass), as well as functional traits of three plant species from different functional groups (grasses, herbs, legumes) in two separate harvests. We found that biomass was reduced by 33% in the highest ALAN treatment compared to the control, Shannon diversity decreased by 43% and Evenness by 34% in the first harvest. Some species failed to establish in the second harvest. Specific leaf area, leaf dry matter content and leaf hairiness responded to ALAN. These responses suggest that plant communities will be sensitive to increasing ALAN, and they flag a need for plant conservation activities that consider impending ALAN scenarios.</p>
Specialist herbivore performance on introduced plants during native host decline
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Optical traits perform equally well as directly-measured functional traits in explaining the impact of an invasive plant on litter decomposition
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Interplay between native plant performance and environment shapes resistance to aquatic plant invasion
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Nutrient supply and accessibility in plants: Effect of protein and carbohydrates on Australian plague locust (Chortoicetes terminifera) preference and performance
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Data from: Plant performance was greater in the soils of more distantly related plants for an herbaceous understory species
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Data from: Planting design influences green infrastructure performance: Plant species identity and complementarity in rain gardens
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Does a history of population co-occurrence predict plant performance, community productivity, or invasion resistance?
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Nitrogen fertilization and high plant growing temperature increase herbivore performance
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Data from: Functional traits underlying performance variations in the overwintering of the cosmopolitan invasive plant water hyacinth (Eichhornia crassipes) under climate warming and water drawdown
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Effect of green infrastructure on restoration of pollination networks and plant performance in semi-natural dry grasslands across Europe
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Data related to Oriental armyworm performance in silicon-supplemented maize plants.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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