Find research datasets worth reusing

opencc-zeroMay 2023View details →

Data on the association between garlic mustard and the plant community from a long-term observational dataset in Illinois, U.S.A.

The impact of a biological invasion on native communities is expected to be uneven across invaded landscapes due to differences in local abiotic conditions, invader abundance, and traits and composition of the native community. One way to improve predictive ability about the impact of an invasive species given variable conditions is to exploit known mechanisms driving invasive species' success. Invasive plants frequently exhibit allelopathic traits, which can be directly toxic to plants or indirectly impact them via disruption of root symbionts, including mycorrhizal fungi. The indirect mechanism – mutualism disruption – is predicted to impact plants that rely on mycorrhizas but not affect non-mycorrhizal plant species. To assess whether invader-driven mutualism disruption explains observed changes in native plant communities, we analyzed long-term (1998–2018) plant cover data from forest plots across the state of Illinois. We evaluated native plant communities experiencing a range of abundance of invasive allelopathic garlic mustard (Alliaria petiolata) and varying environmental conditions. Consistent with the mutualism disruption hypothesis, we showed that as garlic mustard abundance increased over time in 0.25 m2 sampling quadrats, the abundance of mycorrhizal plant species decreased, but non-mycorrhizal plant species did not. Over space and time, garlic mustard abundance predicted plant abundances and diversity at the quadrat level, but this relationship was not present at a larger scale when quadrats were aggregated within sites. Garlic mustard's impact on the plant community was highly localized, yet it was as important as abiotic variables for predicting local plant diversity. We showed that garlic mustard abundance was a key predictor of patterns of plant diversity across invasion intensity and environmental heterogeneity in a way that is consistent with mutualism disruption. Our work indicates that the mutualism disruption hypothesis can provide generalizable predictions of the impacts of allelopathic invasive plants that are evident at a broad spatial scale.

opencc-by-4.0May 2023View details →

Datasets related to the Eggsplorer rapid plant–insect resistance determination tool, using an automated whitefly egg quantification algorithm

These datasets support the data provided directly in the scientific publication titled "Eggsplorer: a rapid plant–insect resistance determination tool using an automated whitefly egg quantification algorithm", published in the <a href="https://plantmethods.biomedcentral.com/articles/10.1186/s13007-023-01027-9#Abs1">BMC Plant Methods journal</a>.  The figures and tables included in the datasets highlight various materials and methods employed to build a proof-of-concept of the Eggsplorer tool. These included whitefly assays, leaf image acquisitions, an automatic egg quantification algorithm, image pre-processing, object detection and image stitching, detection post-processing, algorithm evaluation and software programming. The provided figures and tables in the datasets are further discussed and interpreted in detail, as well as their subsequent results, in the scientific publication. This research was conducted within the VIRTIGATION project, which is part of the EU Open Research Data pilot. This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 101000570.

opencc-zeroMay 2023View details →

Cactus height increases the modularity of a plant-frugivore network in the Caatinga dry forest

Cacti fruits are key resources to many frugivorous animals in Neotropical arid and semiarid regions. However, most studies have focused on a particular animal group or cacti species, but few have explored the overall interactions of such species at the community level. Here we monitored frugivory on five cacti species using camera traps that sampled diurnal and nocturnal interactions. We investigated the structure of interactions with bird, mammal, and reptile frugivores in the Brazilian Caatinga dry forest. We hypothesized that the height of cacti limit interactions with different types of frugivores, which would result in highly structured and modular interaction networks. In 2,929 camera-days, we recorded 23 vertebrate species feeding on cacti fruits, including seven new records, all determined to be primary seed dispersers. As predicted, the cacti-frugivore network was modular and non-nested, with the two shortest cacti species grouped in a module dominated by interactions with reptiles and non-flying mammals. The tallest cacti species were dominated by frugivory interactions with birds and had comparatively less interaction diversity than shorter cacti species. Our results support the contention that cacti are keystone species in semiarid ecosystems where they produce small-seeded fleshy fruits year-round.

opencc-zeroMay 2023View details →

Plant productivity response to inter- and intra-symbiont diversity: mechanisms, manifestations, and meta-analyses

Symbiont diversity can have large effects on plant growth but the mechanisms generating this relationship remain opaque. We identify three potential mechanisms underlying symbiont diversity-plant productivity relationships: provisioning with complementary resources, differential impact of symbionts of varying quality, and interference between symbionts. We connect these mechanisms to descriptive representations of plant responses to symbiont diversity, develop analytical tests differentiating these patterns, and test them using meta-analysis. We find generally positive symbiont diversity-plant productivity relationships, with relationship strength varying with symbiont type. Inoculation with symbionts from different guilds (e.g. mycorrhizal fungi and rhizobia) yields strongly positive relationships, consistent with complementary benefits from functionally distinct symbionts. In contrast, inoculation with symbionts from the same guild yields weak relationships, with co-inoculation not consistently generating greater growth than the best individual symbiont, consistent with sampling effects. The statistical approaches we outline, along with our conceptual framework, can be used to further explore plant productivity and community responses to symbiont diversity, and we identify critical needs for additional research to explore context-dependency in these relationships.

opencc-by-4.0May 2023View details →

Dataset - Fast mechanical and biochemical cell wall dynamics underlie plant nutation

Dataset and codes (Python and Matlab) used to produce the figures in the article "Fast mechanical and biochemical cell wall dynamics underlie plant nutation".

opencc-by-4.0May 2023View details →

Data for: The need to decipher plant drought stress along the soil-plant-atmosphere continuum

Dataset and R-Script accompanying the in OIKOS published manuscript: Schweiger et al. (2023) - The need to decipher plant drought stress along the soil-plant-atmosphere continuum Article DOI: 10.1111/oik.10136   All data is provided within one excel file. Please, pay attention to the provided ReadMe sheet for information on the dataset. The R-Script allows to reproduce the presented results with the provided data.

Effects of plant traits and ecosystem properties on wave attenuation and soil carbon content

Understanding the relationships among the environment, species traits and ecosystem properties is important for developing management measures that optimize the delivery of ecosystem services (ESs). Here, we identify the most important relationships responsible for the delivery of two key ESs provided by tidal marshes: (1) nature-based shoreline protection through wave attenuation and (2) mitigation of climate change through soil carbon storage. In two tidal zones below and above the mean high water (MHW, Elbe Estuary, Germany) level, we measured environmental parameters, such as soil salinity and inundation, as well as plant traits representing adaptations to hydrodynamic stress and strongly influencing decomposition rates. Multiple linear regression results showed that wave attenuation rates were positively related to aboveground community biomass and stem bending resistance, and soil organic carbon was positively related to stem-specific density (below the MHW level). In the tidal zone above the MHW level, soil carbon density was governed by inundation duration and decomposition rates. Our study highlights that (1) ES delivery is not equally spread across tidal marshes and (2) ecosystem management should stimulate the development and persistence of habitat diversity (here, low and high marsh zones) to maximize ES delivery potential. Securing the delivery of the two studied ESs under climate change will depend on providing suitable (landward) space to sustain the functioning of the two marsh zones. In the studied marshes, these services are highly dependent on a few species (i.e., wave attenuation on Schoenoplectus tabernaemontani and Bolboschoenus maritimus and carbon storage on Phragmites australis), and as such, current and future ESs strongly depend on specific species' responses to changing environmental conditions.

opencc-by-4.0Jun 2023View details →

Vascular variants in seed plants – a developmental perspective

Over centuries of plant morphological research, biologists have enthusiastically explored how distinct vascular arrangements have diversified. These investigations have focused on the evolution of steles and secondary growth and examined the diversity of vascular tissues (xylem and phloem), including atypical developmental pathways generated through modifications to the typical development of ancestral ontogenies. A shared vernacular has evolved for communicating on the diversity of alternative ontogenies in seed plants. Botanists have traditionally used the term “anomalous secondary growth” which was later renamed to “cambial variants” by late Dr. Sherwin Carlquist (1988). However, the term “cambial variants” can be vague in meaning since it is applied for developmental pathways that do not necessarily originate from cambial activity. Here, we review the “cambial variants” concept and propose the term “vascular variants” as a more inclusive overarching framework to interpret alternative vascular ontogenies in plants. In this framework, vascular variants are defined by their developmental origin (instead of anatomical patterns), allowing the classification of alternative vascular ontogenies into three categories: (1) procambial variants, (2) cambial variants and (3) ectopic cambia. Each category includes several anatomical patterns. Vascular variants, which represent broader developmental-based groups, can be applied to both extant and fossil plants, and thereby offer a more adequate term from an evolutionary perspective. An overview of the developmental diversity and phylogenetic distribution of vascular variants across selected seed plants is provided. Finally, the evolutionary implications of vascular variants are discussed.

Ecological consequences of plant genotypic diversity within a foundation plant, Spartina alterniflora, are pervasive but not universal across multiple stress gradients

<ol> <li>Plant genotypic diversity can influence population- and community-level processes, yet we have a limited understanding of how these effects vary across environmental gradients that are ubiquitous in nature. </li> <li>We conducted a 2-year field experiment manipulating plant (Spartina alterniflora) genotypic diversity across a natural stress gradient in tidal elevation, both with and without the addition of nutrients. </li> <li> Spartina diversity increased stem production, but the magnitude of this effect was reduced at both the most stressful and most benign endpoints of the combined elevation and nutrient gradient, consistent with recent species diversity studies. Complementarity among individuals likely underpins the observed benefit of Spartina diversity. </li> <li> Spartina diversity also affected the associated marsh community, with higher consumer (Littoraria irrorata) abundance in more diverse plots, owing to both greater Spartina density and increased variation in Spartina traits.</li> <li> Synthesis: The positive effects of Spartina diversity on population- and community-level responses under most environmental conditions highlights the ecological importance of plant genotypic diversity for the maintenance of function across the marsh landscape. </li> </ol>

opencc-by-4.0Jun 2023View details →

A decade of cumulative radiocesium testing data for foodstuffs throughout Japan after the 2011 Fukushima Daiichi Nuclear Power Plant accident

Updated dataset.

Fitness and niche differences are both important in explaining responses of plant diversity to nutrient addition

Plant species loss due to eutrophication is a common phenomenon in temperate perennial grasslands. It occurs in a non-random fashion and is usually explained by increased competitive size asymmetry between co-occurring winner (tall species with optima in productive habitats) and loser species (small-statured plants typical for unproductive habitats). It remains unclear why nutrient addition decreases diversity in communities consisting of losers only, whereas it has little effect on winner-only communities. Here, I used the framework of modern coexistence theory to explore fertilization-driven changes in fitness and niche differences between different combinations of field-identified winner (W) and loser (L) species. I experimentally estimated competition parameters for plant species pairs constructed from a pool of eight species, including pairs of species from the same (WW, LL) and different species categories (LW) grown for approximately two years in control and fertilized conditions. Concurrently, I also followed plant species diversity in mesocosm communities constructed from the same species pool (four-species communities including winners, losers, or both) exposed to control and nutrient addition. I found that nutrient addition can reduce but, unexpectedly, also promote species coexistence depending on the type of species pairs. Whereas nutrient addition eroded coexistence of losers with winners, but also with other losers, treatment had the opposite effect on the persistence of winner species. Fertilization induced large fitness differences between species in loser-winner and loser-loser combinations, but had little effect on the fitness differences of species within the winner-winner combination. In addition, the persistence of winner pairs was promoted by larger niche differences compared to loser species, irrespective of soil nutrients. The differences in how nutrient addition modified coexistence at the pairwise level were reflected by differences in evenness of multispecies communities assembled from the corresponding species categories. These results suggest that the effect of eutrophication on plant species richness cannot simply be explained by an increased competitive asymmetry. To fully understand the effect of fertilization on the diversity of temperate grasslands, interspecific and intraspecific interactions should be explored while considering differences in species' ecological optima.

Data for: Honey bees (Apis mellifera) modify plant-pollinator network structure, but do not alter wild species' interactions

Honey bees (Apis mellifera) are widely used for honey production and crop pollination, raising concern for wild pollinators, as honey bees may compete with wild pollinators for floral resources. The first sign of competition, before changes appear in wild pollinator abundance or diversity, may be changes to wild pollinator interactions with plants. Such changes for a community can be measured by looking at changes to metrics of resource use overlap in plant-pollinator interaction networks. Studies of honey bee effects on plant-pollinator networks have usually not distinguished whether honey bees alter wild pollinator interactions, or if they merely alter total network structure by adding their own interactions. To test this question, we experimentally introduced honey bees to a Canadian grassland and measured plant-pollinator interactions at varying distances from the introduced hives. We found that honey bees increased the network metrics of pollinator and plant functional complementarity and decreased interaction evenness. However, in networks constructed from just wild pollinator interactions, honey bee abundance did not affect any of the metrics calculated. Thus, all network structural changes to the full network (including honey bee interactions) were due only to honey bee-plant interactions, and not to honey bees causing changes in wild pollinator-plant interactions. Given widespread and increasing use of honey bees, it is important to establish whether they affect wild pollinator communities. Our results suggest that honey bees did not alter wild pollinator foraging patterns in this system, even in a year that was drier than the 20-year average.

Data from: Positive plant diversity effects on soil microbial drought resistance are linked to variation in labile carbon and microbial community structure

Biodiversity loss and drought are substantially altering both above-and belowground terrestrial ecosystem functioning, but mechanistic understanding of plant diversity effects on the drought resistance of soil microbial biomass remains limited. We designed a mesocosm experiment to examine drought resistance of soil microbial biomass along a plant species richness gradient (five plant species richness levels based on old-field communities). We calculated resistance of microbial biomass to drought and recorded key belowground properties which may influence microbial resistance to drought (i.e., microbial diversity, microbial community structure, soil carbon stocks and root biomass). Plant species richness had a positive effect on microbial resistance to drought. Variation in microbial resistance to drought was linked to properties of the fungal community in ambient soil (Shannon diversity, arbuscular mycorrhizal fungal richness and abundance) but not soil bacterial diversity. Moreover, microbial resistance to drought increased with increasing root biomass and dissolved organic carbon recorded under ambient conditions. These results highlight the importance of plant diversity for microbial biomass stability in our old-field study system with implications for biogeochemical cycling, and suggest that indirect effects of plant species richness on labile soil carbon and soil fungi may drive resistance of soil microbial biomass to drought.

Compositional shifts of alpine plant communities across the High Andes

Aim: Climate change is transforming mountain summit plant communities worldwide, but we know little about such changes in the High Andes. Understanding large-scale patterns of vegetation changes across the Andes, and the factors driving these changes, is fundamental to predicting the effects of global warming. We assessed trends in vegetation cover, species richness (SR) and community-level thermal niches (CTN) and tested whether they are explained by summits' climatic conditions and soil temperature trends. Location: High Andes Time period: Between 2011/2012 and 2017/2019 Major taxa studied: Vascular plants Methods: Using permanent vegetation plots placed on 45 mountain summits and soil temperature loggers situated along a ~6,800 km N-S gradient, we measured species and their percentage cover and estimated CTN in two surveys (intervals between 5-8 years). We then estimated the annual rate of changes for the three variables and used generalized linear models to assess their relationship with rates of change in the locally recorded soil temperatures, annual precipitation, and the minimum air temperatures of each summit. Results: Over time, there was an average loss of vegetation cover (mean = -0.26 %/yr), and a gain in SR across summits (mean = 0.38 species m2/yr), but most summits had significant increases in SR and vegetation cover. Changes in SR were positively related to minimum air temperature and soil temperature rate of change. Most plant communities experienced shifts in their composition by including greater abundances of species with broader thermal niches and higher optima. However, the measured changes in soil temperature did not explain the observed changes in CTN. Main conclusions: High-Andean vegetation is changing in cover and SR and is shifting towards species with wider thermal niche breadths. The weak relationship with soil temperature trends could have resulted from the short study period that only marginally captures changes in vegetation through time.

Data from: Planting design influences green infrastructure performance: Plant species identity and complementarity in rain gardens

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.

Data from: Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis

Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here, we generated a chromosome-scale genome assembly of the Asian pitcher plant Nepenthes gracilis to analyze how its novel traits (dioecy and carnivorous pitcher leaves) are linked to genomic evolution. We found a decaploidal karyotype with a complete set of syntenic chromosomes (2n=10x=80) yet with a clear indication of subgenome dominance and highly diploidized gene contents. The male-linked and pericentromerically located region on the putative sex chromosome was identified in a recessive subgenome and harbored three transcription factors involved in flower and pollen development, including a likely neofunctionalized LEAFY duplicate. Transcriptomic and syntenic analyses suggested that the paleopolyploidization events seeded genes that subsequently formed tandem clusters in recessive subgenomes with the specific expression in the digestive zone, where specialized cells digest prey and absorb derived nutrients. Novel gene evolution in recessive subgenomes is likely to be prevalent there because duplicates were enriched with Nepenthes-specific genes with tissue-specific expression, including those expressed in pitcher-specific tissues. Thus, subgenome dominance likely contributed to evolutionary novelty by allowing recessive subgenomes to serve as a preferred host of novel tissue-specific duplicates. Our results provide insight into how polyploids, which may frequently be evolutionary dead-ends, have given rise to novel traits in exceptionally thriving high-ploidy lineages.

opencc-by-4.0Aug 2021View details →

[DATASET 9] - PLANT-ROBOT INTERFACES FOR ENERGY HARVESTING

In the framework of GrowBot project, task 7.2 aims at developing bio-hybrid energy harvesting systems based on the triboelectric effect. The energy conversion occurs at plant leaves level during mechanical stimulation (i.e., wind, rain, etc.). Two main components have been developed in GrowBot: - Flexible artificial “leaves” (flexible electrodes covered with tailored materials) to enhance mechanical impacts with the plant leaves and further enhance power output. - Minimal-invasive electrodes that establish electrical contact between GrowBots and real plants. DS9 aims at collecting all the experimental data gathered during these activities.

Ecosystem stability is determined by plant defense functional traits and population stability under mowing in a semi-arid temperate steppe

<ol> <li>As a common grassland management practice in many high-latitude regions worldwide, mowing has great impacts on grassland functioning and stability. Species richness, species asynchrony and species stability have been suggested as central in responses to environmental change. Mowing can evoke plant defense systems due to physical damages to plants. However, no studies have comprehensively evaluated the role of plant defense functional traits, species richness, species asynchrony and stability in ecosystem functioning under mowing regimes across time-scales. </li> <li> In the present study, we set up short-term (4-years) and long-term (16-years) mowing experiments with three stubble heights (control, 10 cm, 2 cm) in a temperate steppe of Inner Mongolia. We investigated the effects of mowing-induced changes in distribution metrics associated with plant defense traits, i.e. mean, variance, skewness and kurtosis of trait distribution, on ecosystem stability of grassland communities using structural equation modeling. </li> <li>We found that grassland ecosystem stability was enhanced by increasing mowing duration and decreasing stubble height. Mowing-induced increases in abundance and diversity of plant defense traits contributed to greater ecosystem stability by enhancing species asynchrony and population stability. Moreover, we found that mowing enhanced the abundance and diversity of plant defense traits of dominant species and contributed to population stability and species asynchrony, thus enhancing temporal stability of grassland ecosystems. </li> <li>These results demonstrate the important roles of plant defense traits in maintaining stability of grasslands under mowing, and highlight that, in addition to species richness, asynchrony and population stability, plant functional defense trait act in stabilizing ecosystem functions under human-induced environmental changes.</li> </ol>

opencc-by-4.0Jul 2023View details →

The positive effect of plant diversity on soil carbon depends on climate

The three files contain all data (Data S1) and all R code to produce all tables and figures of the manuscript entitled "The positive effect of plant diversity on soil carbon depends on climate".