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787 results for “Community Composition”
Zooplankton and macroinvertebrate size spectra, biomass, and community composition; and harvest of bigmouth buffalo and common carp in six shallow lakes in Iowa, USA (2018-2020)
This data product contains biological data collected within six shallow lakes in Iowa, USA between 2018 - 2020, where four lakes were undergoing targeted removals of common carp (Cyprinus carpio) and bigmouth buffalo (Ictiobus cyprinellus). Parts of these data were a portion of Albright et al. 2022 (https://doi.org/10.6073/pasta/1d3797fd573208bae6f78963479445a0), however the data herein include additional survey data from the Ambient Lake Monitoring network instituted through Iowa State University and the Iowa Department of Natural Resources (https://www.iowadnr.gov/environmental-protection/water-quality/water-monitoring/ambient-lake-monitoring#ambient-lake-monitoring-sampling-plan). Data are packaged and formatted specifically for size spectra analysis and compositional analysis.
Herbaceous Community Composition in CRUI Land Use Project at Harvard Forest 1996
Patterns of vascular plant species richness were investigated in six land use legacy sites (2 formerly plowed, 2 formerly pastured, and 2 permanent woodlot) in Prospect Hill to test predictions about the effects of disturbance, light and soil resources, and forest floor environmental heterogeneity on community composition. The occurrence of vascular taxa was recorded in each of the 60 5 m x 5 m contiguous plots within the 30 m x 50 m permanently gridded study plot in each land use legacy site in June 1996. Identification was made to species in most cases. Woodlots showed higher average species richness at the site level (53) than either pastured (52 species) or plowed (49) sites. However woodlots also show greater spatial variation in richness at the 5 m x 5 m resolution than either the plowed or pastured sites (in that order) as represented by the range, standard deviation, and coefficient of variation. Seasonally-averaged light levels at 50 cm are approximately twice as high in the plowed and pastured sites as in the woodlots, but the woodlots show significantly greater soil organic matter, carbon, nitrogen and water-holding capacity than the post-agricultural sites. These results suggest that soil resources may be more important than light in fostering higher herbaceous stratum richness. However, woodlot richness is also affected by the presence of taxa that are slow to re-colonize heavily disturbed sites (e.g., Epigaea repens) and to distinctive microsites that are less common in the plowed or pastured sites in the Harvard Forest system (e.g., exposed boulders). The greater spatial variation in woodlot richness is strongly influenced by both substrate diversity and by scattered hemlock trees, which substantially depress the herb stratum in localized patches.
Physical soil characteristics, microbial community composition, extracellular enzymatic activity, biologically based phosphorus (BBP) pools, and available phosphorus from two soil depths, four microhabitats, and four landforms at the Jornada Experimental Range, 2021.
This dataset contains physical soil characteristics, PLFA based microbial community composition, extracellular enzymatic activity, nitrate and ammonium activity, and phosphorus availability in various phosphorus pools (Biologically Based Phosphorus, potassium sulfate, Olsen-P). Soils were collected from two depths (0-2cm, 2-30 cm), four microhabitats (grass, shrub, biocrust, interspace), and four landforms (alluvial flat, alluvial fan remnant, erosional scarplet, fan piedmont – see coordinates) within the Jornada Experimental Range in July 2021 to answer questions about how these variables change across these spatial scales in drylands. This project was a collaboration between researchers at New Mexico State University and The University of Texas at El Paso as part of the Drylands Critical Zone Thematic Cluster within the Critical Zone Network. This dataset is complete.
Lake Mendota, Wisconsin, USA, Phytobenthos Abundance and Community Composition 2016-2018
We sampled the phytobenthos (epibenthic periphyton) of Lake Mendota from 2016-2018 to track impacts of invasive zebra mussels (Dreissena polymorpha) which were discovered in Lake Mendota in 2015 and grew exponentially to densities greater than 10,000 m-2 in shallow, rocky habitat by 2018. We sampled along three transects inherited from Karatayev et al. (2013) at five different depths (1, 3, 5, 8, and 10 m) twice a summer (June and August) from 2016-2018. A pared-down version of this routine sampling continued from 2019 onward but is not included here. This dataset complements zebra mussel and zoobenthos data collected according to the same routine sampling structure, for which data is also archived with EDI.
Lake Mendota, Wisconsin, USA, (Non-Dreissenid) Benthic Macroinvertebrate Abundance, Biomass, and Community Composition 2016-2018
We sampled the zoobenthos (macroinvertebrates of the benthos) of Lake Mendota from 2016-2018 to track impacts of invasive zebra mussels (Dreissena polymorpha) which were discovered in Lake Mendota in 2015 and grew exponentially to densities greater than 10,000 m-2 in shallow, rocky habitat by 2018. The data presented here exclude all zebra mussels, which are archived in a separate datset. We sampled along three transects inherited from Karatayev et al. (2013) at five different depths (1, 3, 5, 8, and 10 m) twice a summer (June and August) from 2016-2018. These data also contain some samples opportunistically taken from deeper depths along these transects that do not follow the routine sampling structure. A pared-down version of this routine sampling continued from 2019 onward but is not included here. This dataset complements zebra mussel and phytobenthos data collected according to the same routine sampling structure, for which data is also archived with EDI.
H2Ohio Wetland Monitoring Program Vegetation Community Composition, Biomass, and Nutrient Content across Ohio, USA (2021-2022)
This data package includes vegetation community composition, percent cover, biomass, and nutrient concentration data from wetland projects across Ohio, USA, monitored by the H2Ohio Wetland Monitoring Program. Monitoring began in July 2021 and is ongoing, with annual updates planned. While data collection varies by site, most wetlands are surveyed to characterize vegetation and estimate nutrient stocks through community composition assessments and biomass sampling. Sampling points are randomly generated within and up to 5 meters outside the approximated wetland boundary. Surveys are conducted at points where wetland species (FAC–OBL) are present using a 1×1 meter quadrat to record species composition and percent cover. At approximately half of these locations, a 0.25×0.25 meter quadrat is placed outside the northeast corner to collect vegetation samples for nutrient analysis. In these smaller quadrats, community composition and percent cover are recorded prior to sampling aboveground biomass and, at approximately one third of those sites, belowground biomass. Datasets collected by the H2Ohio Wetland Monitoring Program containing surface water and soil nutrient concentration from samples collected at Ohio wetlands during the 2021–2022 sampling period can be found in an accompanying data package (edi.2087) at https://doi.org/10.6073/pasta/297bd6d93b4fcc8416e4225834db380e.
Microbial Community Composition in Lakes - Taxonomic/Ecological characteristics of the sample at North Temperate Lakes LTER 2000 - 2007
Microbial community composition is inferred by a combination of automated ribosomal intergenic spacer analysis (ARISA) and PCR-generated clone library analysis. Clone libraries include both the 16S rRNA gene and the 16S-23S ribosomal intergenic spacer fragment. Phylogenetic assignments for individual ARISA fragments are obtained by comparing the ARISA fragment length from each clone to all of the profiles stored in our database. We have analyzed over 3900 clones obtained from 41 lakes that represent the range of trophic types found in temperate landscapes. Querying by a combination of taxonomic and ecological characteristics of the sample allows the user to retrieve sample information [sample IDs, sample dates, lake information (region, type, size, depth) and physical/chemical data (water temperature, clarity, pH, DOC, SUVA, TN, TP, nitrates/nitrites)] and clone information [clone IDs, sequence data, and characteristics of the sequence (length, chimera status, accession number, taxonomic affiliation)]. The data can be filtered by ecological characteristics of the sample [lake name, sample date, lake information (region, type, size, depth)] and taxonomic characteristics of the community members [clone ID, ARISA fragment length (raw or binned), and/or taxonomic characteristics (Phylum and Phylum-Class)]. The output can include links to individual sample records, which contain links to the taxonomic composition of the sample inferred by dynamically matching clones to ARISA fragments in the individual sample. The output can also include links to clone records directly (though this creates a very large number of lines in the output and is not recommended). Project ID's 30 Lakes - Survey of 30 lakes in northern and southern Wisconsin. June, August and October, 2002. See http://microbes.limnology.wisc.edu/lakes30.html. Lake Characteristics. CB0000 - Time series monitoring microbial community composition in Crystal Bog. 2000-2002. CBX_02 - Food web manipulation experiment i
Microbial Community Composition in lakes - Ecological characteristics of the sample at North Temperate Lakes LTER 2002 - 2007
Microbial community composition is inferred by a combination of automated ribosomal intergenic spacer analysis (ARISA) and PCR-generated clone library analysis. Clone libraries include both the 16S rRNA gene and the 16S-23S ribosomal intergenic spacer fragment. Phylogenetic assignments for individual ARISA fragments are obtained by comparing the ARISA fragment length from each clone to all of the profiles stored in our database. We have analyzed over 3900 clones obtained from 41 lakes that represent the range of trophic types found in temperate landscapes. Querying by ecological characteristics of the sample allows the user to retrieve sample IDs, sample dates, lake information (region, type, size, depth) and physical/chemical data (water temperature, clarity, pH, DOC, SUVA, TN, TP, nitrates/nitrites). The data can be filtered by lake name, sample date, lake information (region, type, size, depth), and physical/chemical data (water temperature, clarity, pH, DOC, SUVA, TN, TP, nitrates/nitrites). The output includes links to individual sample records, which contain links to the taxonomic composition of the sample inferred by dynamically matching clones to ARISA fragments in the individual sample
Microbial Community Composition in Lakes - Taxonomic characteristics of the clones at North Temperate Lakes LTER 2000 - 2007
Microbial community composition is inferred by a combination of automated ribosomal intergenic spacer analysis (ARISA) and PCR-generated clone library analysis. Clone libraries include both the 16S rRNA gene and the 16S-23S ribosomal intergenic spacer fragment. Phylogenetic assignments for individual ARISA fragments are obtained by comparing the ARISA fragment length from each clone to all of the profiles stored in our database. We have analyzed over 3900 clones obtained from 41 lakes that represent the range of trophic types found in temperate landscapes. Querying by taxonomic characteristics of the clone allows the user to retrieve clone IDs, sequence data, and characteristics of the sequence (length, chimera status, accession number, taxonomic affiliation). The data can be filtered by clone ID, ARISA fragment length (raw or binned), and/or taxonomic characteristics (Phylum and Phylum-Class). The output includes links to individual clone records, which contain more detailed information about how the clone was generated (researcher, library ID, project ID, primer sets used, etc.).
Zooplankton community composition and trait data for Green Lakes Valley, 2009 - ongoing.
Starting in 2012 zooplankton sampling at Green Lake 4 was included in the long term monitoring data set at Niwot Ridge. Immediately after the ice has completely melted from the lakes, zooplankton samples are taken once a week for six consecutive weeks at the deepest portion of the lake from an inflatable raft. Zooplankton were sampled at the deepest location of each lake by pulling a conical net (Wisconsin net) vertically through the water column (i.e., vertical tow sample). For each zooplankton sample obtained, adult organisms were identified to species, or lowest taxonomic level (Chydoridae sp. and Bosminidae sp.). Larvae of cladocerans were counted together as neonates; calanoid and cyclopoid copepodites were counted together as nauplii. Individual body lengths of the first 50 -100 (when possible) individuals of each taxon were recorded using a calibrated eyepiece micrometer and means reported.
Summer water chemistry, high frequency sensors, zooplankton and benthic macroinvertebrate community composition, periphyton, fish, and macrophyte biomass, along with lake metabolism and greenhouse gas dynamics in six experimental ponds in central Iowa, USA (2020)
This data product contains physical, chemical, and biological data ranging from the minute to daily to weekly scale in six artificial ponds (400 square meter surface area, 2m depth) in central Iowa (USA) 2020. Ponds were paired into three sets of treatment and reference with treatment ponds receiving two nutrient pulses designed to increase ambient phosphorus concentrations ~ 3 - 5%. Nitrogen and phosphorus were added as NH4NO3 and H3PO4, respectively, at a 24:1 molar ratio. The first nutrient pulse occurred on Julian day of year (DOY) 176 corresponding to a 3% increase and the second nutrient pulse occurred on DOY 211 to a 5% increase. Each treatment-reference set had a different food web structure established ranging between low, intermediate, and high complexity based on trophic connectivity and food chain length. Added to this data package is a document titled "2020 Iowa State University Horticultural Farm Experimental Ponds Nutrient Addition Experiment". For experimental set up, context, and a summary table of the data tables archived herein with available variables please review this document. It is added to aid in successful interpretation and to increase ease-of-use. Please email Tyler Butts (tyler.james.butts@gmail.com) for any and all questions regarding context or use of this dataset!
The Sierra Lakes Inventory Project: Non-Native fish and community composition of lakes and ponds in the Sierra Nevada, California
The Sierra Lakes Inventory Project (SLIP) was a research endeavor that ran from 1995-2002 and has supported research and management of Sierra Nevada aquatic ecosystems and their terrestrial interfaces. We described the physical characteristics of and surveyed aquatic communities for > 8,000 lentic water bodies in the southern Sierra Nevada, including lakes, ponds, marshes, and meadows. We also created digital map layers for these water bodies when such layers did not exist. The original objective of SLIP was to describe impacts of non-native fish on lake communities, but SLIP data has subsequently enabled study of additional ecological issues, including regional amphibian declines and their impacts on communities, and impacts of non-native fish on terrestrial species. In addition, these data are being used to develop fish removal efforts to restore aquatic ecosystems and recover endangered amphibians. The SLIP data is stored in a relational database that collectively describes water bodies (e.g., depth, elevation, location), surveys (conditions, effort), and communities (including approximately 170 fish, amphibian, reptile, benthic macroinvertebrate, and zooplankton taxa).
NGE01 Chronic Addition of Nitrogen Gradient Experiment (ChANGE): Assessing threshold responses of plant community composition and ecosystem processes at Konza Prairie
Chronic nutrient additions can lead to drastic shifts in the plant community through time, both within tallgrass prairie in other grassland ecosystems worldwide. Nutrient addition experiments have answered many questions about patterns of diversity loss and community shifts; however, the level of nutrients which must be added to cause community shifts is unknown. To date, all nitrogen (N) addition experiments at Konza have added 10 g m-2 (e.g., NutNet Plots; Phosphorus (P) Plots; Belowground Plots), yet current rates of N deposition are one-tenth of that level. Even predicted rates of future N deposition in grasslands are not expected to exceed 5 g m-2 by the year 2050 and will likely be around 2 g m-2 for most of the US. This mismatch begs the question will 10 g/m2 affect grasslands the same way 2 or 5 g m-2 will? There are two main goals for this long-term experiment (1) to identify the nutrient threshold needed to drive plant community change with nutrient additions, and (2) to determine what factors underlie those threshold responses (build up of nutrients, mycorrhizal loss, invertebrate herbivory). Konza ChANGE is part of a multi-site experiment spanning grasslands on two different continents: North America – tallgrass prairie (KNZ) and shortgrass steppe (SGS), and China – three sites in Inner Mongolia. By including multiple grasslands, we expand our ability to make generalizations about how grasslands are affected by N additions, and whether thresholds, if they exist, vary with precipitation, natural nutrient availability, and species identity/composition. Research Questions: (1) Do ecosystems have N tolerance thresholds above which community composition will change, and does that differ between grassland types (i.e. mesic and xeric grasslands)? (2) Does adding a large amount of nutrients in one season result in an equivalent community change as adding a small amount over multiple years? (For example does 5 g m-2 for 6 years create the same community change as
Artisanal and farmer bread making practices differently shape fungal species community composition in French sourdoughs
<p>Datasets describing the fungal species diversity, microbial density and acidity of French sourdoughs, phenotypic variation of Kazachstania bulderi and Kazachstania humilis strains as well as the diversity of bread-making practices of 40 bakers and farmers-bakers.The data were collected, analyzed, and reported within the following publication :</p> <p>Elisa Michel, Estelle Masson, Sandrine Bubbendorf, Léocadie Lapicque, Thibault Nidelet, Diego Segond, Stéphane Guézenec, Thérèse Marlin, Hugo deVillers, Olivier Rué, Bernard Onno, Judith Legrand, Delphine Sicard and the participating bakers: <strong>Artisanal and farmer bread making practices differently shape fungal species community composition in French sourdoughs</strong>. PCI Evol. Biol.</p> <p> </p>
AMBON diversity & community composition, data & code
<p>Data and R code for analyzing diversity and community composition of eight assemblages in the Northeast Chukchi Sea in 2015 and 2017. For details of the analysis, results and interpretation, see:</p> <p><em>Mueter, F.J., Iken, K., Cooper, L.W., Grebmeier, J.M., Kuletz, K.J., Hopcroft, R.R., Danielson, S.L., Collins, R.E., Cushing, D. Changes in diversity and species composition across multiple assemblages in the northeast Chukchi Sea during two contrasting years are consistent with borealization. Oceanography (In Press).</em></p>
Morpho-anatomical traits explain the effects of bacterial-feeding nematodes on soil bacterial community composition and plant growth and nutrition
<p>Soil Bacterial populations</p> <p>V3-V4, of the 16S rRNA gene using the primers 341F CCTAYGGGRBGCASCAG and 806R GGACTACNNGGGTATCTAAT.</p>
Summer water chemistry, phytoplankton and zooplankton community composition, size structure, and biomass in a shallow, hypereutrophic reservoir in southwestern Iowa, USA (2019).
This data product contains data for Green Valley Lake, a hypereutrophic reservoir in southwest Iowa (USA) from the summer of 2019. We sampled and quantified zooplankton, phytoplankton, and nutrient concentrations (total N, total P, soluble reactive P, nitrate) in the lake weekly with the primary aim of assessing consumer nutrient cycling, specifically zooplankton nutrient cycling, in a hypereutrophic reservoir. Weekly plankton sampling included quantifying zooplankton and phytoplankton biomass, community composition, and size structure. Phytoplankton size was measured as the greatest axial linear distance which would be approached by a zooplankton grazer. Allometric equations from the literature were applied to the zooplankton size measurements to estimate zooplankton community excretion of N and P. We found that the estimated contribution of zooplankton excretion to the dissolved P pool was substantial in the spring. Further, we found evidence that zooplankton affected phytoplankton size distributions through selective grazing of smaller phytoplankton cells likely affecting nutrient uptake and storage by phytoplankton.
The recovery of plant community composition following passive restoration across spatial scales, Cedar Creek Ecosystem Science Reserve, 1983-2016
1. Human impacts have led to dramatic biodiversity change which can be highly scale-dependent across space and time. A primary means to manage these changes is via passive (here, the removal of disturbance) or active (management interventions) ecological restoration. The recovery of biodiversity, following the removal of disturbance is often incomplete relative to some kind of reference target. The magnitude of recovery of ecological systems following disturbance depend on the landscape matrix, as well as the temporal and spatial scales at which biodiversity is measured. 2. We measured the recovery of biodiversity and species composition over 27 years in 17 temperate grasslands abandoned after agriculture at different points in time, collectively forming a chronosequence since abandonment from one to eighty years. We compare these abandoned sites with known agricultural land-use histories to never-disturbed sites as relative benchmarks. We specifically measured aspects of diversity at the local plot-scale (α-scale, 0.5m2) and site-scale (γ-scale, 10m2), as well as the within-site heterogeneity (β-diversity) and among-site variation in species composition (turnover and nestedness). 3. At our α-scale, sites recovering after agricultural abandonment only had 70% of the plant species richness (and ~30% of the evenness), compared to never-ploughed sites. Within-site β-diversity recovered following agricultural abandonment to around 90% after 80 years. This effect, however, was not enough to lead to recovery at our γ-scale. Richness in recovering sites was ~65% of that in remnant never-ploughed sites. The presence of species characteristic of the never disturbed sites increased in the recovering sites through time. Forb and legume cover declines in years since abandonment, relative to graminoid cover across sites. 4. Synthesis. We found that, during the 80 years after agricultural abandonment, old-fields did not recover to the level of biodiversity in remnant never-plough
Submersed aquatic vegetation community composition in the Sacramento-San Joaquin Delta integrated across four surveys
Submersed aquatic vegetation (SAV) has become widespread in the Sacramento-San Joaquin Delta (Delta), and the diverse SAV assemblage is dominated by non-native species. SAV negatively impacts this estuarine ecosystem by impeding flows needed for water delivery and flood control, degrading habitat needed by native species, increasing breeding habitat for disease-vectoring mosquitoes, harboring non-native predatory fish, and hindering water recreation. The goal of this published integrated dataset is to facilitate study of these impacts. This data set includes four surveys conducted in the region during 2008-2021. Two of these are short-term special studies that have been completed, and two are ongoing long-term annual surveys. The nearshore survey of SAV and largemouth bass was conducted by the University of California-Davis (UC-Davis) at sites across the Delta during 2008-2010. The Aquatic Weed Control Action was completed by the Department of Water Resources as part of the Delta Smelt Resiliency Strategy and included monthly surveys of four sites during 2017-2018. The ongoing survey of Franks Tract is conducted annually by the SePRO corporation and the Division of Boating and Waterways, and available data are from 2014-2021. The ongoing annual survey conducted by the UC-Davis Center for Spatial Technologies and Remote Sensing covers many areas of the Delta and spans 2007-2008 and 2014-2021. Additional data from these ongoing surveys and data from other surveys will be added in subsequent versions of this data set.
Crossing Treeline: Bacterioplankton community composition in alpine and subalpine lakes of the Rocky Mountain southern ecoregion and associated physical and chemical characteristics
This dataset includes lake water samples collected in the summer of 2016 from 16 different mountain lakes in the Rocky mountains in both Rocky Mountain National Park and the Snowy Range of southern Wyoming. Each lake was sampled twice: once in the early summer when hydrologic connections with the surrounding terrestrial environment were high and again in the late summer when hydrologic connections were low. The main goal of the study was to compare communities of bacterioplankton in alpine and subalpine lakes to determine if communities differed across treeline as soil microbes in the surrounding terrestrial environment were. To do so, we collected water samples from the deepest point of each lake, mixed it with a surface water sample and characterized bacterioplankton communities with 16S sequencing technology. Additionally, we wanted to identify abiotic factors that may correlate with community dissimilarity and characterized a suite of chemical attributes for each lake. Lake characteristics reported included surface temperature, soluble reactive phosphorous (SRP), ammonia (NH3+), pH, total dissolved nitrogen (TDN), total dissolved phosphorus (TDP), and total dissolved organic carbon (DOC), and chlorophyll a (chl-a).
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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.