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22,710 results for “Plant”
Canopy Trimming Experiment (CTE) plant seedling measurements
Seedlings were measured before and after treatments to determine how alterations in canopy openness and detritus affect seedling densities and life histories (growth, mortality, recruitment). It was predicted that plots experiencing canopy openness with detritus removed would have the quickest increase in seedlings (recruitment and growth), especially of early successional (light demanding) species, such as Cecropia. Seedlings in plots that received no canopy manipulation but had detritus deposited is predicted to have near-total mortality initially (low light and high physical inhibition due to detritus). Treatment plots experiencing both canopy manipulation and addition of detritus would initially experience near-total mortality, with some light demanding seedlings establishing and growing through detritus with time. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Canopy Trimming Experiment (CTE) plants greater than 1 centimeter diameter at breast height (DBH)
Plant diameters and growth measurements were taken both before and after treatments to determine how alterations in canopy openness and detritus affect measures of growth, mortality, and production. Both types of trimmed plots are predicted to have relatively quick evidence of re-sprouting (1-3 months; based on Hurricane Hugo studies), especially palms. Because essentially complete defoliation to the canopy took place in the trim plots, the large stems that were trimmed should experience delayed growth and higher mortality than those in non-trimmed plots. The understory vegetation, or otherwise those that were not trimmed (i.e., stems <10cm at dbh) should experience increased growth in both trim plots as a result of increased light. Some nutrient immobilization may occur in the detritus addition plots, but this is predicted to affect belowground processes most. Little influence on aboveground processes from detritus addition might occur and cause some stunted growth rates of stems. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Soil factors predict initial plant colonization on Puerto Rican landslides
Tropical storms are the principal cause of landslides in montane rainforests, such as the Luquillo Experimental Forest (LEF) of Puerto Rico . A storm in 2003 caused 30 new landslides in the LEF that we used to examine prior hypotheses that slope stability and organically enriched soils are prerequisites for plant colonization. We measured slope stability and litterfall in 1 m2 plots 8-13 months following landslide formation. At 13 months we also measured microtopography, soil characteristics (organic matter, particle size, total nitrogen, and water holding capacity), elevation, distance to forest edge, and canopy cover, as well as plant aboveground biomass, plant cover, and root biomass. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Plant Apparency data - Habitat selection/Caracolus caracolla and other snails (2019 Ongoing)
Various habitat characteristics are presented, as well as the apparency of common plant taxa at 7 heights (every 0.5 m from ground level to 3 m). The files are divided because variables measured varied by year. This is Version 2020 of these data. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
N and P fertilization experiment plant phenology data for South of saddle, 1993-1994
The effects of nitrogen, phosphorus, and nitrogen+phosphorus fertilization on phenology of alpine plants was examined. This was a preliminary study to determine if the phenologies of dry meadow plants were affected by nutrient amendments, and if they were, which species responded most to the treatments. Times of emergence, senescence, and other key vegetative and reproductive "events" were recorded.
N fertilization and recovery experiment (2-4-6) plant species composition data for East of Tvan from 1997 to 2017, yearly
The realization that anthropogenic nitrogen (N) deposition is causing significant environmental change in many ecosystems has led to lower emissions of reactive N and deposition rates in many regions. However, the impacts of N deposition on terrestrial ecosystems can be long-lasting, with significant inertia in the return of the biota and biogeochemical processes to baseline levels. To better understand patterns of recovery and the factors that may contribute to slow or no responses following declines in N deposition, we followed plant species composition, microbial abundance, N cycling rates, soil pH, and pools of NO3- and extractable cations in an impacted alpine ecosystem following cessation of 12-year experiment increasing N deposition rates by 0, 20, 40, and 60 kg N/ha/yr. Simulated N deposition had resulted in a tripling in the cover of the nitrophilic species Carex rupestris, while the dominant sedge Kobresia myosuroides had decreased by more than half at the highest N input level. In addition nitrification rates were elevated, soil extractable magnesium (Mg2+) and pH decreased, and aluminum (Al3+) and manganese (Mn2+) were elevated at the highest N treatment inputs. Over the nine years following cessation of N additions to the impacted plots only the cover of the nitrophilic C. rupestris showed any recovery to prior levels. Abundances of both bacteria and fungi were lower with N addition in both treatment and recovery plots. Rates of nitrification and pools of NO3- remained elevated in the recovery plots, likely contributing to the lack of biotic response to the cessation of N inputs. In addition, nutrient base cations (Ca2+ and Mg2+) and soil pH remained depressed, and the toxic metal cations (Al3+ and Mn2+) remained elevated in recovery plots, also potentially influencing biotic recovery. These results emphasize the importance of considering long-term environmental impacts of N deposition associated with legacy effects, such as elevated N cycling and losse
Alpine soil islands plant and soil microbial community composition, 2024.
High alpine ecosystems are particularly sensitive to climate-driven change, with vegetation expansion increasingly observed in historically barren soils. In late August and early September 2024, we revisited 50 previously established vegetation plots in Green Lakes Valley (Niwot Ridge LTER) to evaluate patterns of plant colonization and community change over time. Using legacy vegetation data from 2008 and 2015, we assessed changes in plant cover and composition in relation to microtopography and prior plant occurrence. Concurrently, we collected soil samples for 16S and 18S rRNA gene sequencing to characterize bacterial, archaeal, and eukaryotic microbial communities associated with these plots. Vegetation was resampled using spatially referenced 1-meter radius surveys, estimating species incidence and cover and documenting moss, lichen, sedge, and grass diversity. Together, these above- and belowground data provide insight into how priority effects, fine-scale environmental variation, and plant–microbe interactions influence alpine community dynamics, and may inform predictive models of ecosystem responses to ongoing climatic shifts.
Niwot plant functional traits, 2008 - 2018.
Globally, human activities are altering environmental conditions through changes to disturbance regimes, climate, and primary productivity. Attempts to generalize changes in biodiversity in response to altered environmental conditions have had mixed success and the mechanisms that causes differences in responses are poorly understood. These contingent responses represent one of the largest obstacles to synthesis in community ecology and global change biology. Over the past decade, much progress has been made in resolving these ecological contingencies by shifting from a taxonomic perspective on community assembly and global change to a focus on functional traits. Functional traits are any morphological, physiological, or phenological characteristic of a species linked to fitness and have proven to be effective for understanding species interactions, biogeographic processes, and environmental change. Between 2008 and 2018, we measured plant height, specific leaf area, leaf size, chlorophyll content, stomatal conductance, leaf dry matter content, and leaf chemical composition (nitrogen, carbon, δ13C, δ15N) on 2689 individual plants from 141 species (not all traits on all individuals or species). These measurements were collected to capture intraspecific trait variation among the key habitat types on Niwot Ridge and to examine how species traits respond to global change in the ITEX experiment.
Plant & lichen species composition data for Saddle Nodal Plots, 1971 - ongoing.
To study long-term changes in alpine tundra plant communities, thirty permanently marked plots were surveyed in 1971. These same plots were surveyed at twenty, thirty, forty and fifty year intervals from the initial sampling date; in 1991, 2001, 2011, and 2021. Due to covid and other events, data for the 50-year time point was collected over three summers, from 2021-2023. Plots are one by ten meters, divided into ten subplot quadrats, and marked with rebar. The presence or absence of each vascular plant species was recorded per plot. The cover was recorded for each species that appeared in a one meter by ten centimeter strip at the base of each quadrat within each plot. The cover of non-vascular plants, soil, rocks, and lichens was also recorded within the strip in most sampling years. Lichen were also surveyed in 1971 and 2021.These data have been used to study the changes in vascular plant and lichen communities and cover across habitats following a moisture gradient on the saddle portion of Niwot Ridge; these habitats include dry fellfield, dry meadow, moist meadow, wet meadow, snow bank, and shrub tundra. While we have observed some changes in species richness and cover in the plots, overall the plant communities seem fairly stable over time. Lichen species richness has increased in some habitats, while some lichen species have been disappearing from others.
Presence or absence of marsh plant species along transects through a nutrient enriched marsh receiving wastewater effluent and a reference (unenriched) marsh, Plum Island Ecosystems LTER.
Presence or absence of marsh plant species along transects through a nutrient enriched marsh receiving wastewater effluent and a reference (unenriched) marsh. Nutrient enrichment comes from the Ipswich Wastewater Treatment Facility on Greenwood Creek in Ipswich. The marsh around Clubhead Creek, Rowley, MA was used as a reference.
Context dependency of effect of fungal connections between plants and biocrusts
Conceptual context: Species interactions may couple the resource dynamics of different primary producers and may enhance productivity by reducing loss from the system. In low-resource systems, this biotic control may be especially important for maintaining productivity. In drylands, the activities of vascular plants and biological soil crusts can be decoupled in space because biocrusts grow on the soil surface but plant roots are underground, and decoupled in time due to biocrusts activating with smaller precipitation events than plants. Soil fungi are hypothesized to functionally couple the plants and biocrusts by transporting nutrients. We studied whether disrupting fungi between biocrusts and plants reduces nitrogen transfer and retention and decreases primary production as predicted by the fungal loop hypothesis. Additionally, we compared varying precipitation regimes that can drive different timing and depth of biological activities. Methodological approach: We used field mesocosms in which the potential for fungal connections between biocrusts and roots remained intact or were impeded by mesh. We imposed a precipitation regime of small, frequent or large, infrequent rain events. We used 15N to track fungal-mediated nitrogen (N) transfer. We quantified microbial carbon use efficiency and plant and biocrust production and N content.
Sevilleta Plant Species Sensitivity of Dryland Plant Allometry to Climate
Patterns of plant biomass partitioning are fundamental to estimates of primary productivity and ecosystem process rates. Allometric relationships between aboveground plant biomass and non-destructive measures of plant size, such as cover, volume, or stem density are widely used in plant ecology. Such size-biomass allometry is often assumed to be invariant for a given plant species, plant functional group, or ecosystem type. Allometric adjustments may be an important component of the short- or long-term responses of plants to abiotic conditions. We used 18 years of size-biomass data describing 85 plant species to investigate the sensitivity of allometry to precipitation, temperature, or drought across two seasons and four ecosystems in central New Mexico, USA. Our results demonstrate that many plant species adjust patterns in the partitioning of aboveground biomass under different climates and highlight the importance of long-term data for understanding functional differences among plant species.
SEV-LTER Mean - Variance Experiment Quadrat Plant Species Cover and Height
We designed novel field experimental infrastructure to resolve the relative importance of changes in the climate mean and variance in regulating the structure and function of dryland populations, communities, and ecosystem processes. The Mean - Variance Climate Experiment (MVE) adds three novel elements to prior designs that have manipulated interannual variance in climate in the field (Gherardi & Sala, 2013) by (i) determining interactive effects of mean and variance with a factorial design that crosses reduced mean with increased variance, (ii) studying multiple dryland biomes to compare their susceptibility to transition under interactive climate drivers, and (iii) adding stochasticity to our treatments to permit the antecedent effects that occur under natural climate variability. This new infrastructure enables direct experimental tests of the hypothesis that interactions between the mean and variance of precipitation will have larger ecological impacts than either the mean or variance in precipitation alone. This dataset includes plant species cover and height data measured in 1 m x 1 m quadrats at all Mean - Variance experiment sites. Quadrat locations span five important ecosystems of the American southwest: blue grama-dominated Plains grassland (est. fall 2019), black grama-dominated Chihuahuan Desert grassland (est. fall 2020), creosotebush dominated Chihuahuan Desert shrubland (est. fall 2021), juniper savanna (est. fall 2022) and pinon-juniper woodland (est. fall 2023). Data on plant cover and height for each plant species are collected per individual plant or patch (for clonal plants) within 1 m x 1 m quadrats. These data inform population dynamics of foundational and rare plant species. The cover and height of individual plants or patches are sampled twice yearly (spring and fall) in permanent 1m x 1m plots within each site or experiment. This data package includes plant cover and height only -- for species biomass estimates per quad see package knb-lte
Rapid root to leaf uptake of inorganic and amino acid nitrogen in three dryland plant species.
Our aim was to quantify inorganic and organic nitrogen (N) uptake and compare short-term nutrient acquisition patterns among three dryland plant species: Bouteloua eriopoda, Achnatherum hymenoides, and Gutierrezia sarothrae collected from a mixed grassland community in the Northern Chihuahuan Desert to better understand how asynchronous resource availability may influence biotic interactions and nutrient retention in these ecosystems. We collected living plants from two locations within the Sevilleta National Wildlife Refuge and transplanted them into pots maintained in the greenhouse with supplemental light and water for two months. We then conducted a greenhouse experiment using these species to compare nutrient uptake of 15N-labeled ammonium (NH4+), nitrate (NO3-), and glutamate (an amino acid) over 12 to 48 hours. Our study examined three main questions: (1) How rapidly do these dryland plants take up available soil N?, (2) Does leaf uptake differ among inorganic and amino acid N forms?, and (3) Do plant species differ in the speed or form of short-term N uptake?. In the greenhouse, we applied one of three isotopic 15N tracers directly to plant roots and quantified N uptake and recovery in leaves after 12, 24, and 48 hours. We found that plants took up inorganic and amino acid N to leaves as rapidly as 12 h following application, and N uptake more than doubled between 24 and 48 h. Inorganic N uptake was 3-4x higher than organic N uptake in all three species, and plants took up ammonium and nitrate at 2-3x faster rates than glutamate. On average, B. eriopoda had higher inorganic N recovery and uptake speeds, while G. sarothrae had the highest organic N uptake over time. A. hymenoides root to leaf uptake was ~50% lower than the other two species after 48 h. Plants showed similar patterns of short-term foliar uptake and recovery indicating a lack of niche partitioning by N form among the three dryland species measured. Our results suggest that soil inorganic N, par
Biomass and Plant Species Composition on Hog and Metompkin Islands, 2020-2022
Beginning in 2020, annual plant surveys were conducted along 3 cross-shore transects on Hog and Metompkin Islands along the Atlantic coast of Virginia. Transects were established starting at the high water mark, and continuing inland until reaching a shrub thicket. Plots were placed 10m apart in beach and swale habitats, and 5m apart across dunes. At each plot, percent composition was measured within a 0.25m^2 quadrat. Aboveground biomass was also obtained within a randomly placed 10x100cm^2 quadrat. Biomass was then dried and weighed. Due to logistical constraints, biomass was not collected in 2022.
Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis
<p>Six centaury transcriptomes (embryogenic calli, globular somatic embryos, cotyledonary somatic embryos, adventitious buds, leaves and roots of <em>in vitro</em> grown plants) were sequenced and <em>de novo</em> assembled using <a href="https://github.com/trinityrnaseq/trinityrnaseq/wiki">Trinity</a> .</p> <p><a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/CE_Assembly.tar.gz">CE_Assembly.tar.gz</a> - Centaury referent transcriptome comprises of 160.839 Trinity transcripts grouped in 105.726 Trinity genes.</p> <p><a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/CE_Assembly_fpkm.tar.gz">CE_Assembly_fpkm.tar.gz</a> - fpkm normalized read counts of the assembled transcripts in the six sequenced centaury tissues.</p> <p><a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/nt.db_CE_assembly.tar.gz">nt.db_CE_assembly.tar.gz</a> - annotation of assembled transcripts by mapping them against NCBI nucleotide (NT) database using BLASTn . The obtained results were filtered with E-value E ≤ 10<sup>-3</sup>.</p> <p><a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/swissprot.db_CE_assembly.tar.gz">swissprot.db_CE_assembly.tar.gz</a> - annotation of assembled transcripts by mapping them against NCBI nucleotide (<a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/swissprot.db_CE_assembly.tar.gz">s</a>wissprot) database using BLASTx . The obtained results were filtered with E-value E ≤ 10<sup>-3</sup>.</p> <p><a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/pfam30.db_CE_assembly.tar.gz">pfam30.db_CE_assembly.tar.gz</a> - annotation of assembled transcripts by mapping them against Pfam30 domain database using hmmer3. The obtained results were filtered with independent E-value E ≤ 10<sup>-3</sup>.</p>
Urbanization drives an early spring for plants but not for pollinators
<p>These files include data and code used in the article titled: "Urbanization drives an early spring for plants but not for pollinators". Data files are .txt with tab-separated values, and include abundances of pollinators captured and total floral cover estimated in each site (1-12) at each sampling event (6 events), in the three urban classes (low, medium, high).</p>
Modifications of the plant-pollinator network structure and species' roles along a gradient of urbanization
<p>This file includes data and codes used in the article titled: " Modifications of the plant-pollinator network structure and species’ roles along a gradient of urbanization".</p> <p>Data include plant-pollinator interactions sampled in each site (1-12) at each sampling event (6 events) in the three urbanization classes (low, medium, high). Each row is a single insect pollinator X plant interaction. Full species names and abbreviations used in figures in the Supplementary Information are reported.<br> The data file is .txt with tab-separated values.</p>
Eyebright species maintenance (scripts and data accompanying Becher et al., Plant Communications)
<p><strong>This gzipped TAR ball contains data and scripts related to the study on Fair Isle eyebrights by Hannes Becher, Max R. Brown, Gavin Powell, Chris Metherell, Nick J. Riddiford, and Alex D. Twyford, submitted to Plant Communications.</strong></p> <p>Data: genome assembly of<em> Euphrasia arctica</em>, variant call files of the "tetraploid" and "conserved" sets of scaffolds, per-individual k-mer spectra, mapping depths, etc.</p> <p>Scripts: R scripts for the analysis of plant trait data, heterozygosity, ect.; an ipython notebook for the analysis of variant data, and a Mathematica notebook with the derivation of the formulae used to fit pop gen parameters to k-mer spectra.</p>
Scored protein-protein interactions accompanying "A pan-plant protein complex map reveals deep conservation and novel assemblies"
<p><a href="http://plants.proteincomplexes.org/static/data/panplant_cfms_scores_annot.txt.gz">All scored pairwise protein-protein interactions with CF-MS scores (3,076,999 unique pairwise interactions)</a></p> <ul> <li>Description: Scores between Orthogroups with the corresponding CF-MS score and eggNOG generated orthogroup descriptions.</li> <li>Note: Only the highest scoring pairs are considered significant. A CF-MS score >= 0.509 corresponds to 10% FDR, >= 0.207 corresponds to 50% FDR</li> <li>Format: OrthogroupID1 [tab] OrthogroupID2 [tab] Score [tab] Annotation1 [tab] Annotation2</li> </ul>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.