Find research datasets worth reusing

Effects of disturbance on plant regrowth along snow pack gradients in alpine habitats

Human disturbance in alpine habitats is expected to increase, and improved knowledge of short-term recovery after disturbance events is necessary to interpret vegetation responses and formulate planning and mitigation efforts. The ability of a plant community to return to its original state after a disturbance (community resilience) depends on species composition and environmental conditions. The aim of this study is to analyze initial short-term effects of disturbance in alpine plant communities in contrasting climates (oceanic vs. continental; central Norway). We used a nested block-design to examine vegetative regrowth and seedling recruitment after experimental perturbation. Three plant community types along the snow pack gradient were exposed to (1) no disturbance, (2) clipping, and (3) clipping and uprooting. Slow vegetative regrowth and low seedling establishment rates were found in dry alpine ridges and late-melting oceanic snowbed communities. Leeside habitats with intermediate snow conditions were found more resilient. The difference was related to growth form and species diversity. Woody species, which dominated in ridges and oceanic snowbeds, showed the most negative response to disturbance. Species-rich plant communities dominated by graminoids and herbs showed higher rates of regrowth. Species richness seems to cause resilience to the plant communities through higher response diversity. Plant communities at the extreme ends of abiotic gradients, ridges and late-melting snowbeds, will be most sensitive to both disturbance and environmental change. In an up-scaled human-used landscape disturbance effects will be amplified and further limit recovery to a pre-disturbance state.

opencc-zeroDec 2021View details →

Data from: A trait‒environment relationship approach to participatory plant breeding for organic agriculture

The extent of intraspecific variation in trait‒environment relationships is an open question with limited empirical support in crops. In organic agriculture, with high environmental heterogeneity, this knowledge could guide breeding programs to optimize crop attributes. We propose a three-dimensional framework involving crop performance, crop traits, and environmental axes to uncover the multidimensionality of trait‒environment relationships within a crop. We modeled instantaneous photosynthesis (Asat) and water-use efficiency (WUE) as functions of four phenotypic traits, three soil variables, five carrot (D. carota) varieties, and their interactions in a national participatory plant breeding program involving a suite of farms across Canada. We used these interactions to describe the resulting 12 trait‒environment relationships across varieties. We found one significant trait‒environment relationship for Asat (taproot tissue density‒soil phosphorus), which was consistent across varieties. For WUE, we found that three relationships (petiole diameter‒soil nitrogen, petiole diameter‒soil phosphorus, and leaf area‒soil phosphorus) varied significantly across varieties. As a result, WUE was maximized by different combinations of trait values and soil conditions depending on the variety. Our three-dimensional framework supports the identification of functional traits behind the differential responses of crop varieties to environmental variation and thus guides breeding programs to optimize crop attributes from an eco-evolutionary perspective.

opencc-zeroDec 2021View details →

Plastic mulch film residues in agriculture: impact on soil suppressiveness, plant growth, and microbial communities

Plastic mulch film residues have been accumulating in agricultural soils for decades, but so far, little is known about its consequences on soil microbial communities and functions. Here, we tested the effects of plastic residues of low-density polyethylene and biodegradable mulch films on soil suppressiveness and microbial community composition. We investigated how plastic residues in a Fusarium culmorum suppressive soil affect the level of disease suppressiveness, plant biomass, nutrient status, and microbial communities in rhizosphere using a controlled pot experiment. The addition of 1% plastic residues to the suppressive soil did not affect the level of suppression and the disease symptoms index. However, we did find that plant biomasses decreased, and that plant nutrient status changed in the presence of plastic residues. No significant changes in bacterial and fungal rhizosphere communities were observed. Nonetheless, bacterial and fungal communities closely attached to the plastisphere were very different from the rhizosphere communities with overrepresentation of potential plant pathogens. The plastisphere revealed a high abundance of specific bacterial phyla (Actinobacteria, Bacteroidetes, and Proteobacteria) and fungal genera (Rhizoctonia and Arthrobotrys). Our work revealed new insights and raises emerging questions for further studies on the impact of microplastics on the agroecosystems.

Mating and fitness consequences of variation in male allocation in a wind pollinated plant

In hermaphrodites, the allocation of resources to each sex function can influence fitness through mating success. A prediction that arises from sex allocation theory is that in wind-pollinated plants, male fitness should increase linearly with investment of resources into male function but there have been few empirical tests of this prediction. In a field experiment we experimentally manipulated allocation to male function in Ambrosia artemisiifolia (common ragweed) and measured mating success in contrasting phenotypes using genetic markers. We investigated the effects of morphological traits and flowering phenology on male siring success, and on the diversity of mates. Our results provide evidence for a linear relation between allocation to male function, mating and fitness. We find earlier onset of male flowering time increases reproductive success, whereas later flowering increases the probability of mating with diverse individuals. Our study is among the first empirical studies testing the prediction of linear male fitness returns in wind pollinated plants and emphasize the importance of a large investment into male function by wind pollinated plants and mating consequences of temporal variation in sex allocation.

Positive allometric growth explains the positive effect of foliar fungal pathogens on plant coexistence

The data was collected in the northeastern Qinghai-Tibetan Plateau, Qinghai Province, China (101° 18′ 57″ E, 37° 36′ 50″ N; 3 221 m a.s.l.) in 2019 and 2020, including the species-specific growth allometry (scaling exponent and intercept) fitted by the allometric equation under each treatment in a population-level experiment, i.e., control, fungicide application, neighbor removal (removal), fungicide application × neighbor removal, and the community-level mean and dispersion of the growth allometry (CWM and FDis of growth scaling exponent and intercept, respectively) weighted by the species cover for each plot in a community-level fungicide application experiment.

opencc-zeroDec 2021View details →

Phenological status of plants in the very tropical dry forests of Curaçao

Tropical dry plant formations comprise diverse forests found in areas that experience pronounced seasonal changes in precipitation. Across broad regions, variation in the amount and distribution of precipitation determine the availability of water, and thus differences in species composition and phenology. Within any given region hydrology and topographic position, and geologic substrate may underlie additional differences in forest attributes. Of these three factors, geologic substrate is the least understood but it has been suggested that its influence on tropical dry forests, and more broadly speaking tropical forests, results from a combination of mechanisms regulating the use of water and nutrients. Phenological studies at population, community, and system levels acknowledge the significance of plan phenology for different ecological processes. Thus, characterizing phenological patterns at multiple levels of biological organization as a function of geologic substrate is important to assess the diversity of behaviors, and ultimately vulnerability of tropical dry forests to climate change. A study conducted in Curaçao between September of 1992 to February of 1995 at three sites underlaing by different geologies provided a unique opportunity to investigate the extent to which plant phenology diverges in regions underlain by different geologies.

Robustness of organ morphology is associated with modules of co-expressed genes related to plant cell wall

Reproducibility in organ size and shape is a fundamental trait of living organisms. The mechanisms underlying such robustness remain, however, to be elucidated. In the manuscript <a href="https://www.biorxiv.org/content/10.1101/2022.04.26.489498v1">"Robustness of organ morphology is associated with modules of co-expressed genes related to plant cell wall", doi: https://doi.org/10.1101/2022.04.26.489498</a>, we took the sepal of Arabidopsis as a model, and we investigated whether variability of gene expression plays a role in variation of organ morphology. To address this question, we produced a dataset composed of both transcriptomic and morphological information obtained from 27 individual sepals from wild-type plants. This repository contains the raw confocal image of 30 sepals used as starting point for the analysis, as well as their extracted contours as binary images. These images were used to recover the 3D shape of the sepals. The 30 abaxial sepals were collected at early stage 11, from three different Col-0 wild-type plants, labeled D, E and F, grown simultaneously in experimentally controlled standard conditions. Each sepal was imaged under a confocal microscope using autofluorescence. Immediately following imaging, the sepal was frozen in liquid nitrogen for RNA extraction, on which an RNA-seq analysis was performed. Related informations : <ul> <li>The repository of the numerical tools used for 3D shape extraction as well as the results of geometrical measurements is <a href="http://forge.cbp.ens-lyon.fr/redmine/projects/florivar">here</a>.</li> <li>The repository of RNA-Seq analysis results of these same sepals is here.</li> <li>And the analysis tools used to relate geometrical measurements to RNA-seq data are here.</li> </ul>

Nitrogen availability and plant functional composition modify biodiversity-multifunctionality relationships

The ability of an ecosystem to deliver multiple functions at high levels (multifunctionality) typically increases with biodiversity but there is substantial variation in the strength and direction of biodiversity effects, suggesting context-dependency. A better understanding of the drivers of this context dependency is essential to predict effects of global change on ecosystems. To determine how different factors modulate the effect of diversity on multifunctionality, we established a large grassland experiment with 216 communities, crossing a manipulation of plant species richness (1, 4, 8, 20 species) with manipulations of resources (nitrogen enrichment), plant functional composition (gradient in mean specific leaf area [SLA] to manipulate abundances of exploitative, fast-growing vs. conservative, slow-growing species), plant functional diversity (variance in SLA) and enemy abundance (foliar fungal pathogen removal). We measured ten above- and belowground functions, related to productivity, nutrient cycling and energy transfer between trophic levels, and calculated ecosystem multifunctionality. Plant species richness and functional diversity both increased multifunctionality, but their effects were context dependent. Species richness increased multifunctionality only when communities were assembled with fast growing (high SLA) species. This was because slow species were more redundant in their functional effects, whereas different fast species tended to promote different functions. Functional diversity also increased multifunctionality but this effect was dampened by nitrogen enrichment. However, unfertilised, functionally diverse communities still delivered more functions than low diversity, fertilised communities. Our study suggests that a shift towards fast-growing exploitative communities will not only alter ecosystem functioning but also the strength of biodiversity-functioning relationships, which highlights the potentially complex effects of global change on multifunctionality.

Data from: The hydrochorous dispersal of plant propagules in a giant river reservoir: implications for restoration of riparian vegetation

The riparian vegetation of many rivers around the world is impacted by flow regulation for hydropower. Water levels behind dams are being raised to generate electric energy, forming river reservoirs. River regulation has a large impact on the riparian vegetation which influences both the adjacent aquatic and terrestrial ecosystems. Therefore, restoration of degraded riparian vegetation in river reservoirs has been of increasing research interest. Propagules dispersed from connected tributaries via water (hydrochory) are considered a vital source for the recovery of riparian vegetation in regulated rivers. However, the hydrochorous dispersal of plant propagules in river reservoirs is unclear. We explored the dispersal distance and deposition patterns of hydrochorous propagule mimics in three tributaries that are regulated by the Three Gorges Reservoir (TGR) in China. In eight out of nine release experiments, 95% of propagule mimics were found within 3 km downstream from the release points. Cumulative wind speed was the most important factor affecting the dispersal distance of propagule mimics in the TGR. However, the dispersal distance of propagule mimics was not significantly affected by water-level variation and channel sinuosity. Variations in water level strongly affected the deposition pattern of propagule mimics, with only 6.6% of the propagule mimics stranding on the riparian zones under raised water level and 83.8% stranding under declined water levels. The majority of stranded propagule mimics were deposited at gentle slopes (0‒20°). Synthesis and applications. Our results suggest that the majority of propagules that enter river reservoirs via water would be retained within the first few kilometers. Wind and water level variation are the main factors determining the dispersal distance and deposition pattern of propagules. Our findings have applications for riparian vegetation restoration in river reservoirs. The vegetation in steep riparian zones distant from free-flowing tributaries should be the priority for restoration actions because these areas receive limited hydrochorous propagules. The plant biodiversity and hydrological connectivity of connected tributaries, which is an important propagule sources for riparian vegetation along river reservoirs, should be protected. The seasonal dominant wind pattern should be considered when evaluating the importance of tributaries as the source of hydrochorous propagules for river reservoirs.

Climate influence on plant–pollinator interactions in the keystone species Vaccinium myrtillus

Background: Climate change is altering the world's ecosystems through direct effects of climate warming and precipitation changes, but also indirectly through changes in biotic interactions. For instance, climate-driven changes in plant and/or insect communities may alter plant-pollinator interactions, thereby influencing plant reproductive success and ultimately population dynamics of insect-pollinated plants. Methods: To better understand how the importance of insect pollination for plant fruit set varies with climate, we experimentally excluded pollinators from the partly selfing key-stone species Vaccinium myrtillus along elevational gradients in the forest-tundra ecotone in central Norway. The study comprised three mountain areas, seven elevational gradients spanning from the climatically relatively benign birch forest to the colder alpine areas above the tree line, and 180 plots of 1 x 1 m, with experimental treatments allocated randomly to plots within sites. Within the experimental plots we counted the number of flowers of V. myrtillus and counted and weighted all fruits, as well as seeds for a selection of fruits. Results: Excluding pollinators resulted in lower fruit production, as well as reduced fruit and seed mass of Vaccinium myrtillus. In the alpine sites pollinator exclusion resulted in 84 % fewer fruits, 50 % lower fruit weight and 50 % lower seed weight compared to control conditions. Contrary to our expectations, the negative effect of pollinator exclusion was less pronounced in forest compared to alpine sites, suggesting that the importance of insect pollination for seed production is lower at low elevation. Conclusions: Our findings indicate that the keystone species Vaccinium myrtillus is relatively robust to changes in the pollinator community in a warmer climate, thereby making it less vulnerable to climate-driven changes in plant-pollinator interactions.

Flower plantings support wild bee reproduction and may also mitigate pesticide exposure effects

1. Sustainable agriculture relies on pollinators, and wild bees benefit yield of multiple crops. However, the combined exposure to pesticides and loss of flower resources, driven by agricultural intensification, contribute to declining diversity and abundance of many bee taxa. Flower plantings along the margins of agricultural fields offer diverse food resources not directly treated with pesticides. 2. To investigate the potential of flower plantings to mitigate bee pesticide exposure effects and support bee reproduction, we selected replicated sites in intensively farmed landscapes where half contained flower plantings. We assessed solitary bee Osmia lignaria and bumble bee Bombus vosnesenskii nesting and reproduction throughout the season in these landscapes. We also quantified local and landscape flower resources and used bee-collected pollen to determine forage resource use and pesticide exposure and risk. 3. Flower plantings, and their local flower resources, increased O. lignaria nesting probability. Bombus vosnesenskii reproduction was more strongly related to landscape than local flower resources. 4. Bees at sites with and without flower plantings experienced similar pesticide risk, and the local flowers, alongside flowers in the landscape, were sources of pesticide exposure particularly for O. lignaria. However, local flower resources mitigated negative pesticide effects on B. vosnesenskii reproduction. 5. Synthesis and applications. Bees in agricultural landscapes are threatened by pesticide exposure and loss of flower resources through agricultural intensification. Therefore, finding solutions to mitigate negative effects of pesticide use and flower deficiency is urgent. Our findings point towards flower plantings as a potential solution to support bee populations by mitigating pesticide exposure effects and providing key forage. Further investigation of the balance between forage benefits and added pesticide risk is needed to reveal contexts where net benefits occur.

Data supporting "Stems Matter: Xylem Physiological Limits Are an Accessible and Critical Improvement to Models of Plant Gas Exchange in Deep Time"

Model outputs from from Paleo-BGC and Paleo-BGC+. Code detailing data structure and allowing reproduction of analysis can be found at github.com/wjmatthaeus

Water availability dictates how plant traits predict demographic rates

A major goal in ecology is to make generalizable predictions of organism responses to environmental variation based on their traits. However, straightforward relationships between traits and fitness are rare and likely vary with environmental context. Characterizing how traits mediate demographic responses to the environment may enhance predictions of organism responses to global change. We synthesized 15 years of demographic data and species-level traits in a shortgrass steppe to determine whether the effects of leaf and root traits on growth and survival depend on seasonal water availability. We predicted that (1) species with drought-tolerant traits, such as lower leaf turgor loss point (TLP) and higher leaf and root dry matter content (LDMC and RDMC), would be more likely to survive and grow in drier years due to higher wilting resistance, (2) these traits would not predict fitness in wetter years, and (3) traits that more directly measure physiological mechanisms of water use such as TLP would best predict demographic responses. We found that graminoids with more negative TLP and higher LDMC and RDMC had higher survival rates in drier years. Forbs demonstrated similar yet more variable responses. Graminoids grew larger in wetter years, regardless of traits. However, in both wet and dry years, graminoids with more negative TLP and higher LDMC and RDMC grew larger than less negative TLP and low LDMC and RDMC species. Traits significantly mediated the impact of drought on survival, but not growth, suggesting survival could be a stronger driver of species' drought response in this system. TLP predicted survival in drier years, but easier-to-measure LDMC and RDMC were equal or better predictors. These results advance our understanding of the mechanisms by which drought drives population dynamics, and show that abiotic context determines how traits drive fitness.

Annotated compounds in extracts from alpine aromatic and medicinal plants grown in an aeroponics system

The compounds were annotated by comparing the experimental HRMS/MS spectra of the samples with an in silico MS/MS spectral database of natural products.

Historical context modifies plant diversity–community productivity relationships in alpine grassland

While most studies yield positive relationships between biodiversity (B) and ecosystem functioning (EF), awareness is growing that BEF relationships can vary with ecological context. The awareness has led to increased efforts to understand how contemporary environmental context modifies BEF relationships, but the role of historical context, and the mechanisms by which it may influence biodiversity effects, remains poorly understood. We examined how historical context alters plant diversity‒community productivity relationships via plant species interactions in alpine grassland. We also tested how historical context modifies interactions between plants and arbuscular mycorrhizal (AM) fungi, which can potentially mediate the above processes. We studied biodiversity effects on plant community productivity at two grassland sites with different histories related to grazing intensity — heavy versus light livestock grazing — but similar current management. We assembled experimental communities of identical species composition with plants from each of the two sites in disturbed soil from a contemporary heavily grazed grassland, ranging in species richness from one to two, three and six species. Moreover, we carried out a mycorrhizal hyphae-exclusion experiment to test how plant interactions with AM fungi influence plant responses to historical context. We detected a significantly positive diversity‒productivity relationship that was driven by complementarity effects in communities composed of plants from the site without heavy-grazing history, but no such relationship in plant communities composed of plants from the site with heavy-grazing history. Plants from the site with heavy-grazing history had increased competitive ability and increased yields in low-diversity communities but disrupted complementarity effects in high-diversity communities. Moreover, plants of one species from the site with heavy-grazing history benefitted more from AM fungal communities than did plants from the site without such history. Synthesis: Using the same experimental design and species, communities assembled by plants from two sites with different historical contexts showed different plant diversity‒community productivity relationships. Our results suggest that historical context can alter plant diversity‒community productivity relationships via plant species interactions and potentially plant‒soil interactions. Therefore, considering historical contexts of ecological communities is of importance for advancing our understanding of long-term impacts of anthropogenic disturbance on ecosystem functioning.

X-ray driven peanut trait estimation-Plant Methods paper

The ground-truth dataset linked to the research article "X-ray driven peanut trait estimation: Computer vision aided agri-system transformation" of Plant Methods is available in this data repository. Description of the headers: <ol> <li>Peanut variety name [39 peanut varieties were used]</li> <li>Variety number [number linked to variety]</li> <li>Variety Type [Breeding lines, Released popular cultivar, or Farmers' produce]</li> <li>Rep [number of replicates per sample used in the study]</li> <li>Corresponding TIFF image number</li> <li>kernel_weight_(g) [unit = g]</li> <li>shell_weight_(g) [unit = g]</li> <li>percentage_shelling_(%) [unit = %]</li> </ol> For additional information please contact the corresponding author Jana Kholova (j.kholova@cgiar.org)

opencc-zeroJun 2022View details →

Data supporting: Drivers of individual-based, antagonistic interaction networks during plant range expansion

1. Range expansion in plant populations, especially at the colonization front, can be either limited by disproportionately large effects of antagonistic interactions or facilitated by their release. How the strength of antagonistic interactions changes along successional gradients during range expansion is still poorly documented, especially when diverse assemblages of plant antagonists (rodents, invertebrates, and birds) combine within interaction networks. 2. We study the changes in individual-based, predispersal seed-pulp predator networks along a colonization gradient in a rapidly-expanding Juniperus phoenicea population in Doñana National Park (SW Spain). Additionally, we analysed the role of individual plant traits and neighbourhood attributes in network configuration by using Exponential Random Graph Models. 3. Seven seed-pulp consumer animal species varied significantly in their frequency of interaction and prevalence. While invertebrate species were well established in old and intermediately mature stands, greenfinch (Chloris chloris) was dominant at the colonization front. Variable species roles and spread of interactions among individual plants generated changes in the configuration of interactions during plant expansion. 4. Individual plant traits strongly determined the topology of these networks, although with differences between stands. Increasing individual crop size and seeds per cone increased the interaction odds of individual plants, while seed viability showed the opposite effect. The network topology at the colonization front appeared less driven by individual traits, possibly because of the short interaction history of this recently established area. The disproportionately large effect of C. chloris in these recently established stands, potentially resulted in large seed losses during range expansion. 5. Synthesis. Turnover of antagonistic interactions, characterized the colonization front, resulting in more heterogeneous interaction strengths among individual plants. We found no evidence for a complete or sizeable antagonistic release of J. phoenicea at the colonization front promoting this rapid expansion. It becomes necessary to explore interactions with seed dispersers to understand how antagonistic and mutualistic plant-animal interactions balance during range expansion. Our study highlights the importance of an individual-based approach in understanding how interactions are structured and driven in natural changing landscapes.

opencc-by-4.0Jun 2022View details →

Quantification of SARS-CoV-2 RNA in Wastewater Treatment Plants Mirrors the Pandemic Trend in Hong Kong

The dataset included the SARS-CoV-2 and PMMoV virus concentration of WWTPs from December 24, 2020 to June 30, 2021 in Hong Kong, China.

opencc-zeroJun 2022View details →

Experimental comparison of fish mortality and injuries at innovative and conventional small hydropower plants - raw data

Resolving the controversy about hydropower is only possible based on reliable data on its ecological effects, particularly fish welfare. Herein, we propose a comprehensive assessment of conventional and innovative hydropower using a data set of 52 250 fish. The effects of hydropower on fish were most harmful at sites with Kaplan turbines, showing £ 83% mortality. Innovative hydropower, often termed 'fish-friendly', caused £ 64% mortality. Our findings suggested that the runner peripheral speed, number of turbine blades, turbulence and gas oversaturation at turbine outlets were the most important factors. Synthesis and Applications: To reduce the impact of hydropower on fish, site-specific characteristics such as head drop, bypass options and river-specific species composition need to be more intensively considered in optimal turbine technologies and operation modes.