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445 results for “abiotic”
Biomass and abiotic variable data in the study of the ecosystem engeneering effect of oysters on Suaeda linearis distribution in Georgia salt marshes (2008-2009)
Oysters are ecosystem engineers in marine ecosystems, but the functions of oyster shell deposits in intertidal salt marshes are not well understood. The annual plant Suaeda linearis is associated with oyster shell deposits in Georgia salt marshes. We hypothesized that oyster shell deposits promoted the distribution of Suaeda linearis by engineering soil conditions unfavorable to dominant salt marsh plants of the region (the shrub Borrichia frutescens, the rush Juncus roemerianus and the grass Spartina alterniflora). We tested this hypothesis using common garden pot experiments and field transplant experiments. Suaeda linearis thrived in Borrichia frutescens stands in the absence of neighbors, but was suppressed by Borrichia frutescens in the with-neighbor treatment, suggesting that Suaeda linearis was excluded from Borrichia frutescens stands by interspecific competition. Suaeda linearis plants all died in Juncus roemerianus and Spartina alterniflora stands, indicating that Suaeda linearis is excluded from these habitats by physical stress (likely water-logging). In contrast, Borrichia frutescens, Juncus roemerianus and Spartina alterniflora all performed poorly in Suaeda linearis stands regardless of neighbor treatments, probably due to physical stresses such as low soil water content and low organic matter content. Thus, oyster shell deposits play an important ecosystem engineering role in influencing salt marsh plant communities by providing a unique niche for Suaeda linearis, which otherwise would be rare or absent in salt marshes in the southeastern US. Since the success of Suaeda linearis is linked to the success of oysters, efforts to protect and restore oyster reefs may also benefit salt marsh plant communities.
Cover and frequency of biological soil crust community types, moss species, vascular plants, and abiotic land surface features, on gypsum & non-gypsum soils from the Chihuahuan and Mojave Deserts in 2023
This dataset contains raw and calculated percent cover and frequency data for biological soil crust (hereafter biocrust) functional groups, vascular plant functional groups, and abiotic land surface features on and off gypsum soils in the northern Chihuahuan and eastern Mojave Deserts. Abundance data were obtained from 20 study sites total, 10 located on soils derived from gypsum parent material and 10 located on soils derived from non-gypsum parent materials. Sites were grouped into 10 pairs, in which every gypsum site was partnered with a non-gypsum site located in the same region. Apart from soil type, partnered-site characteristics (topography, climate, elevation, slope, aspect, and presence of biocrusts) were held relatively constant. At each site, cover and frequency assessments were made using the line-point intercept method (LPI) and frequency quadrats (1.0 m^2), respectively. Biocrust functional groups included the following crusts: lichen, moss, incipient algal, light algal, dark algal, unknown photosynthetic crust, and vagrant cyanobacteria. Vascular plant categories included: perennial forbs, perennial graminoids, annual forbs, annual graminoids, subshrub, shrub, Yucca, and cacti. Abiotic land surface features included: woody litter, herbaceous litter, bare soil, rock, bedrock, and animal feces. Moss crusts identified within cover and frequency analyses were sampled, and classified to species level via microscopy. The resulting percent cover and frequency data was used to understand differences in biocrust and moss species abundance and diversity on and off gypsum soils; furthermore, how biocrust and moss species abundance was associated with the measured environmental variables. Soil physical and chemical data from this study can be accessed at knb-lter-jrn.210616002. This study and dataset are complete.
Supplementary material to: Long-term (bio)deterioration of Fe-containing and Fe-depleted sandstones: An experimental insight into biotic and abiotic interactions.
<p>This dataset includes: micorphotographs, scanning electron microscope images and related EDS spectra, thermal analysis (DSC-TG), grain size distribution. Abbreviations used in the supplementary file names refer to: GMB (growth medium inoculated with the bacteria, Pseudomonas fluorescens), GM (sterile growth medium), ARE (artificial root exudates), H2O (water), NR (Sample Nowa Ruda), Z (Sample Żerkowice ŻR).</p>
The Blue Carbon of Southern South West Atlantic salt marshes and their biotic and abiotic drivers
<p>Organic carbon stocks, salt marsh plant biomass, crab burrow abundances and diameters. This data was generated by sampling at 11 salt marsh sites along 3000 km of coastal line in southern SW Atlantic coast in South America. Organic carbon stocks and burial rates extarcted from other publications and used to update global estimates are also included with their respective references. Values of biotic and abiotic drivers included in the Structural Equation Model (SEM) to evaluate their roles in belowground organic carbon stocks.</p>
Abrupt and Gradual Salt Application Mesocosm Experiment Zooplankton, Phytoplankton, Periphyton and Abiotic Data, Troy, NY, 2018.
Increasing chloride concentrations from road salt applications are an emerging threat to freshwater diversity in cold weather regions. Few studies have focused on how road salt affects freshwater biota and even fewer have focused on how the rate of exposure alters organism responses. We hypothesized that road salt concentrations delivered gradually would result in slower population declines and more rapid rebounds due to evolved tolerance. To test this hypothesis, we examined the responses of freshwater lake organisms to four environmentally relevant salt concentrations (100, 230, 860, and 1600 mg Cl−/L) that differed in application rate (abrupt vs. gradual). We used outdoor aquatic mesocosms containing zooplankton, filamentous algae, phytoplankton, periphyton, and macroinvertebrates. We found negative effects of road salt on zooplankton and macroinvertebrate abundance, but positive effects on phytoplankton and periphyton, likely resulting from reduced grazing. Only rarely did we detect a difference between abrupt vs gradual salt applications and the directions of those differences were not consistent. This affirms the need for additional research on how road salt pollution entering ecosystems at different frequencies and magnitudes will alter freshwater communities.
Abiotic monitoring of physical characteristics in porewaters and surface waters of mangrove forests from the Shark River Slough and Taylor Slough, Everglades National Park (FCE LTER), South Florida, USA, December 2000 - ongoing
Data on porewater salinity, temperature, conductivity, pH and redox have been collected to help explain patterns found in porewater nutrient concentrations that were sampled in the same plots. See knb-lter-fce.1171 (https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-fce&identifier=1171) for related porewater-nutrient-concentration data.
Percent cover, species richness, and canopy height data of seagrass communities in Shark Bay, Western Australia, with accompanying abiotic data, from October 2012 to July 2013
This dataset provides cover, canopy height, and species richness estimates for seagrass communities throughout Shark Bay, as well as ancilliary physical data. These data will be used to determine spatial patterns of seagrass loss and recovery, as well as recovery rates and succisional changes in community composition, if present.
Capture data for sharks caught in standardized drumline fishing in Shark Bay, Western Australia, with accompanying abiotic data, from February 2008 to July 2014.
This dataset provides data on large sharks captured during standardized drumline fishing and is used to monitor shark catch rates, sex ratios and size distributions in Shark Bay.
Capture data for sharks caught in standardized drumline fishing in Shark Bay, Western Australia, with accompanying abiotic data, from January 2012 to April 2014.
This file provides data on standardized drumline fishing effort (gear deployment data) targeting large elasmobranchs in Shark Bay, Western Australia between 2012 and 2014
GIS30 GIS Coverages Defining Sample Locations for Abiotic Datasets on Konza Prairie (1972-present)
These data show sample locations for various abiotic data collected on Konza Prairie (rain gauges, soil moisture, and stream data). Included in these data are the locations for 12 rain gauges (GIS300) on Konza Prairie. The Konza headquarters weather station formerly consisted of two gauges which were operated year-round. The Konza headquarters weather station currently consists of one Otto-Pluvio2 gauge which is operated year-round. The remaining Konza-operated gauges run from April 1 to November 1. These data are to be used in conjunction with the APT01 (precipitation) dataset. GIS305 defines the locations where measurements of soil moisture (%volume) are taken on Konza Prairie. These data are to be used in conjunction with the ASM01 (soil moisture) dataset. GIS309 defines the locations within watershed N4D of soil sampler nests. In Jan 2020, we separated the original GIS310 file 'Wells in N4D' into GIS310 'Wells in N4D' and GIS309 'Soil Sampler Nests'. Prior to then, soil sampler nests and wells were combined in GIS310. GIS310 defines the locations within watershed N4D where samples are taken for analyzing the belowground water chemistry of the watershed. These data are to be used in conjunction with the AGW01 dataset. GIS311 defines the locations of 14 wells at two sites along Kings Creek. Depth and nutrient content of groundwater is measured at these sites. These data are to be used in conjunction with the AGW02 dataset. GIS315 defines the locations of stream sampling stations within multiple Konza watersheds. These data are to be used in conjunction with the NWC, ASS, ASD, and ASW datasets. GIS320 defines the locations of the rainfall collectors used to collect the samples analyzed as a part of the National Atmospheric Deposition Program. These data are to be used in conjunction with the ANA01 dataset. These data are available to download as zipped shapefiles (.zip), compressed Google Earth KML layers (.kmz).
Effects of biotic (shrimp) and abiotic (discharge) factors on the depositional environment quantified in a montane stream in Puerto Rico. (Shrimp/Algae/Can J. Fish Aquat. Sci. (1994))
Effects of biotic (shrimp) and abiotic (discharge) factors on the depositional environment were quantified in a montane stream in Puerto Rico. Electricity was used experimentally to exclude large (approximately >1cm in length) biota without artificially increasing sedimentation as in cage enclosure/exclosure experiments in stream systems. Shrimp (>1cm in length) were excluded from substrata by semicircular fence hooked up to battery-powered fence chargers which emitted continuous pulses of electricity. Unelectrified control substrata had natural high densities of atyid shrimp. Significantly greater masses of total sediment, fine and large organic particles, and algal biovolume occurred in shrimp exclusion treatments relative to controls. Shrimp exclusion treatments experienced slow and steady accumulation of sediments under base flow conditions and a large stepwise increase in sediment following a storm. No measurable sediment accrued in the presence of natural densities of shrimp under base flow conditions. Shrimp rapidly removed sediments that accrued during the storm (440-620 g*m2 dry mass-1), decreasing sediment mass in control treatments to near prestorm levels (5-13 g*m2 dry mass-1) within 30 h. Atyid shrimp can significantly affect the accumulation of organic and inorganic materials on rock substrata in stream pools between high-discharge events. 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.
Phenology data set of plants and birds and other taxonomic groups, as well as agrarian activities and abiotic phenomena from Latvia, 1970-2018
<p>A data set of phenological observations of plants, birds, as well as agrarian activities and abiotic phenomena from Latvia, 1970-2018 is presented. The data include limited number of observations of insects, amphibians, mammals, mushrooms, mollusks and fishes as well. The data was collected by voluntary observers (citizen scientists) and published as paper based yearly bulletins. It includes almost 48 000 individual observations of 159 different phenological phases from 103 locations in Latvia. Each entry is comprised of following fields:</p> <ol> <li>Station: name of the observation station</li> <li>Year: year of observation</li> <li>Season: season of observation as indicated in the primary publication</li> <li>Species: English name of the species observed or description of phenomena observed in case of abiotic occurrences</li> <li>Species Latin: Latine name of the species observed</li> <li>Taxonomic_group: taxonomic group of the species observed or grouping of non-biological phases (“Abiotic” for meteorological phenomena and “Agrarian” for agrarian activities)</li> <li>Phenophase: description of phenological phase observed</li> <li>BBCH: attributed BBCH code for phenological phase observed, where applicable</li> <li>Date: date of the first observation of the phase</li> <li>DoY: day of the year of the first observation of the phase</li> <li>Implausible: flag indicating of the reported date of phenological phase is highly implausible (TRUE) or realistic (FALSE)</li> <li>Wrong_order: flag indicating if the order of the reported phases at a given station and year is not realistic (TRUE) or realistic (FALSE)</li> </ol>
Dataset for: Oxygen isotope fractionation of O2 consumption through abiotic photochemical singlet oxygen formation pathways
<p>Dataset containing raw and treated isotope-ratio mass spectrometry data as well as O2 concentration data, accompanying the manuscript "Oxygen isotope fractionation of O2 consumption through abiotic photochemical singlet oxygen formation pathways".</p>
Drone orthomosaics for 'Livestock impacts on an iconic Namib Desert plant are mediated by abiotic conditions'
<p>Drone orthomosaics used in the analyses and figures of: Livestock impacts on an iconic Namib Desert plant are mediated by abiotic conditions, accepted in Oecologia.</p> <p>These drone orthomosaics are a data supplement to the code and data repository here: https://github.com/jtkerb/Nara_Paper_Repo</p>
Supplementary material for "Patterns of high-flying insect abundance are shaped by landscape type and abiotic conditions"
<p><strong>Abstract</strong></p> <p>Insects are of increasing conservation concern as a severe decline of both biomass and biodiversity have been reported. At the same time, data on where and when they occur in the airspace is still sparse, and we currently do not know whether their density is linked to the type of landscape above which they occur. Here, we combine data of high-flying insect abundance from six locations across Switzerland representing rural, urban and mountainous landscapes, which was recorded using vertical-looking radar devices. We analysed the abundance of high-flying insects in relation to meteorological factors, daytime, and type of landscape. Air pressure was positively related to insect abundance, wind speed showed an optimum, and temperature and wind direction did not show a clear relationship. Mountainous landscapes showed a higher insect abundance than the other two landscape types. Insect abundance increased in the morning, decreased in the afternoon, had a peak after sunset, and then declined again, though the extent of this general pattern slightly differed between landscape types. We conclude that the abundance of high-flying insects is not only related to abiotic parameters, but also to the type of landscapes. Thus, conservation measures implemented on the ground should start to also account for the needs of high-flying insects.</p>
Data from "Grassland woody plant management rapidly changes woody vegetation persistence and abiotic habitat conditions but not herbaceous community composition"
These files contain microhabitat, soil, vegetation structure, and woody plant species data used in the paper "Grassland woody plant management rapidly changes woody vegetation persistence and abiotic habitat conditions but not herbaceous community composition". The project was conducted at seven publicly accessible remnant (i.e., unplowed or old-growth) tallgrass prairie within 100 miles of Madison, Wisconsin, United States starting in the 2020 growing season and commencing following the 2022 growing season. The goal was to assess the initial effects of different management interventions on woody vegetation persistence, abiotic habitat conditions, and herbaceous community composition, including physical and chemical management interventions and their combination.
Seed dispersal data for Warneke et al "Habitat fragmentation alters the distance of abiotic seed dispersal through edge effects and direction of dispersal"
This csv file contains seed dispersal data for five species (Carphephorus bellidifolius, Aristida beyrichiana, Liatris squarrulosa, Sorghastrum secundum, and Anthenantia villosa). Data were collected at the Savannah River Site, near Aiken, South Carolina, United States. Data were collected between November 17, 2009, to January 22, 2010 and were collected using the methods outlined in this document.
Luquillo Experimental Forest Canopy Trimming Experiment CTE2 2015-2020 30-minute abiotic data
The data archive is here: https://doi.org/10.2737/RDS-2021-0028 please use this DOI when citing this dataset. This data publication contains 30-minute values for abiotic field data from 3 treated and 3 control plots from the Canopy Trimming Experiment (CTE) located near El Verde Field Station in the Luquillo Experimental Forest (El Yunque National Forest), Puerto Rico collected from 2015 through 2020. In December of 2014 (CTE2), in 0.09 hectare (ha) square plots near the El Verde Field Station the forest canopy was trimmed and the canopy debris was littered to the forest floor. The plot size and trim amounts were based on the patch disturbance after the two most recent hurricanes before 2017, both category 3 hurricanes at the location of El Verde: Hugo in September 1989, and Georges in September 1998. Data were collected in the inner 0.04 ha quadrants of the 0.09 ha trimmed plots to minimize edge effects. Each plot was made up of 16 subplots with different data types collected in each subplot. There were 3 sets of control and treated plots, with each set near El Verde field station. Field data include 30-minute: solar radiation, soil profile volumetric water content, shallow soil volumetric water content, canopy leaf saturation, litter leaf saturation, air temperature, soil temperature, air relative humidity, vapor pressure, and throughfall. Field data were collected by one automatic sensor in each plot inside a designated subplot, except: soil profile volumetric water content, canopy leaf saturation, and litter leaf saturation; each were collected in three subplots. 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
Abiotic stress mediated modulation of chromatin landscape in Arabidopsis thaliana
<p>This dataset include figures and supplementary material for the manuscript entitled<strong> </strong>"Abiotic stress mediated modulation of chromatin landscape in <em>Arabidopsis thaliana" </em>to be published in Journal of Experimental Botany special issue focused on Chromatin.</p> <p><strong>Supplementary File 1:</strong> Table describing read count, mapping percentage and genome coverage from each sample in FAIRE-seq and DNase-seq.</p> <p><strong>Supplementary File 2:</strong> List of DHSs obtained from control and stress subjected samples.</p> <p><strong>Supplementary File 3:</strong> List of FIRs obtained from control and stress subjected samples.</p> <p><strong>Supplementary File 4:</strong> List of uniquely merged OCRs with respective chromatin accessibility score in cold, heat, salt and drought stress.</p> <p><strong>Supplementary File 5:</strong> List of GO terms enriched in nrOCRs, SRCRs, and SACRs.</p> <p><strong>Supplementary File 6:</strong> List of GO terms enriched in overlapping nrOCRs, SRCRs, and SACRs.</p> <p><strong>Supplementary File 7:</strong> List of digital footprints (DFPs) obtained from nrOCRs regions of control-cold, control-heat, control-salt and control-drought pairs.</p> <p><strong>Supplementary File 8: </strong>Annotation details of the chromatin regions which were either found to be in state of accessible (CAS > 0.2) or inaccessible (CAS < -0.2) upon exposure to all of the stresses studied (heat, cold, salt and drought stress).</p> <p><strong>Supplementary Fig S1: Overlap of DHSs in control sample of present study with previously published studies.</strong></p> <p>A Venn diagram showing overlap of DNase hypersensitive sites (DHSs) found in control sample of present study and Zhang et al 2010 (<strong>A</strong>) and Sullivan et al 2014 (<strong>B</strong>). The statistical significance of overlap is calculate using hypergeometric Fischer`s exact test.</p> <p><strong>Supplementary Fig S2: Genomic locations of DHSs and FIRs</strong></p> <p>A line diagram representing the genomic location of unique DHSs and FIRs over each chromosome. DHSs/FIRs identified from each sample were merged to generate unique non-redundant subset of DHSs/FIRs before plotting over genome.</p> <p><strong>Supplementary Fig S3: Validation of correlation between OCRs and gene expression using microarray.</strong></p> <p>Box plot representing expression of genes (log10(normalised expression)) whose various structual elements fall in OCRs.</p> <p><strong>Supplementary Fig S4: First exons are highly enriched in both DHSs and FIRs</strong></p> <p> A bar plot showing presence of uFIRs, uDHSs, and ovOCRs in various positions of exon in Arabidopsis genes. The X-axis represent the exon number whereas Y-axis represent the fraction of OCRs found in each exon number.</p> <p><strong>Supplementary Fig S5: Validation of correlation between Ha-SACRs/Ha-SRCRs and gene expression using microarray.</strong></p> <p>Relative expression of genes (log2 fold change) corresponding to Ha-SACRs (Top) and (Ha-SRCRs (bottom) in cold (A), heat (B), salt (C) and drought (D) stress are plotted as box plot (p- value from Mann-Whitney test). To further compare RNA-seq data of salt stress with microarray, RNA-seq data was down-sampled to include genes which were also present in microarray data (E).</p> <p><strong>Supplementary Fig S6: Genomic location of SACRs and SRCRs found in Drought sample.</strong></p> <p>A snapshot of Integrative Genome Viewer (IGV) showing genomic location of stress activated chromatin regions (SACRs) and stress repressed chromatin region (SRCRs) in drought sample. The location of the centromere on each chromosome is shown as green bar IGV track.</p>
Can root-associated fungi mediate the impact of abiotic conditions on the growth of a High Arctic herb?
<p>This is a dataset containing fragments of internal transcribed spacer 2 (ITS2) extracted from <em>Bistorta vivipara</em> root-associated fungi, sampled from snow fence experiment in Adventdalen, Svalbard. </p> <p>This dataset was used in Wutkowska et al., 2020, Can root-associated fungi mediate the impact of abiotic conditions on the growth of a High Arctic herb?Can root-associated fungi mediate the impact of abiotic conditions on the growth of a High Arctic herb? [available at biorXiv.org, DOI: 10.1101/2020.06.20.157099]</p> <p>Now the manuscript is available as a peer-reviewed paper:</p> <p>Wutkowska, Magdalena, Dorothee Ehrich, Sunil Mundra, Anna Vader, and Pernille Bronken Eidesen. 2021. ‘Can Root-Associated Fungi Mediate the Impact of Abiotic Conditions on the Growth of a High Arctic Herb?’ <em>Soil Biology and Biochemistry</em> 159:108284. doi: 10.1016/j.soilbio.2021.108284.</p> <p> </p> <p>All other corresponding data are available here: https://github.com/magdawutkowska/bistorta</p>
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OpenNeuro
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