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176 results for “Biological communities”
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.
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.
warmXtrophic: plant community responses to the individual and interactive effects of climate warming and herbivory across multiple years at Kellogg Biological Station Long-Term Ecological Research Sites (KBS LTER), Michigan, USA, and University of Michigan Biological Station (UMBS), Michigan, USA.
Climate change has both direct and indirect effects on ecological communities. Whereas most climate change ecology experiments manipulate abiotic drivers to measure direct effects of climate on species or communities, fewer quantify the indirect effects through biotic interactions, especially over multiple sites and years. In this factorial experiment we manipulate temperature through open-top chambers, and the level of insect herbivory through insecticide. At two early successional field sites separated by 3 degrees of latitude and 3°C of mean annual temperature (University of Michigan Biological Station, Pellston, MI and Kellogg Biological Station, Hickory Corners, MI), 6 replicate 1-m2 plots per treatment were installed in May 2015. 12 plots per site are at ambient temperature, 12 are warmed with year-round non-UV filtering polycarbonate and wood frame construction OTCs for tall-stature plants (Welshofer et al. 2018 MEE). Insecticide reduces insect herbivory in half the plots (Welshofer et al. 2018 Oecologia). Over the course of the experiment, OTCs warmed the plant communities by 1.9°C-3.0°C on average over the growing season. Each year, through 2021, plant traits and community responses were measured at the species level: plant phenology (green-up, flowering, flowering duration, seed set); plant percent cover (aerial % cover of the 1m2 plot); plant traits (specific leaf area, C and N content), herbivory damage to leaves, and plant species biomass (only in 2021). Further methodological details are found within each response variable metadata. This experiment is ongoing and further data package updates are planned. L0 data is available upon request. R scripts can be found here: https://github.com/SpaCE-Lab-MSU/warmXtrophic. The biotic and abiotic community context and relative strengths of direct vs. indirect effects may yield ecological surprises under climate change unless addressed together. Large-scale experiments like this one can improve our ability to unde
Plant Community and Ecosystem Responses to Long-term Fertilization & Disturbance at the Kellogg Biological Station, Hickory Corners, MI (1989 to 2019)
Dataset AbstractThis work is part of the long-term sampling and monitoring of successional dynamics in abandoned fields – and responses to N-fertilization. Data from this research has been, and will continue to, contribute to LTER cross-site analysis of plant community dynamics, diversity-productivity, and responses to fertilization and disturbance.N-fertilized and tilled (disturbed) microplots are located in the NW corner of all treatment 7 (early successional communities) on the LTER main site. Experimental treatments are: 1) Nitrogen addition vs. no nitrogen addition and 2) Annual disturbance vs. undisturbedoriginal data source http://lter.kbs.msu.edu/datasets/60
Testing a biological mechanism of the insurancehypothesis in experimental aquatic communities - Data Deposit
<p>1.The insurance hypothesis predicts a stabilizing effect of increasing species richness on commu-nity and ecosystem properties. Difference among species’ responses to environmental fluctuationsprovides a general mechanism for the hypothesis. Previous experimental investigations of theinsurance hypothesis have not examined this mechanism directly.</p> <p>2.First, responses to temperature of four protist species were measured in laboratory microcosms.For each species, we measured the response of intrinsic rate of increase (r) and carrying capacity(K) to temperature.</p> <p>3.Next, communities containing pairs of species were exposed to temperature fluctuations. Com-munity biomass varied less when correlation inKbetween species (but notr) was more negative,and this resulted from more negative covariances in population sizes, as predicted. Results werecontingent on species identity, with findings differing between analyses including or not includingcommunities containing one particular species.</p> <p>4.These findings provide the clearest support to date for this mechanism of the insurance hypo-thesis. Biodiversity, in terms of differences in species’ responses to environmental fluctuations (i.e.functional response diversity) stabilizes community dynamics.</p>
Community-level flowering & fitness data across an elevational gradient, Rocky Mountain Biological Lab, 2021-2022
We collected data at three sites in Washington Gulch near the Rocky Mountain Biological Laboratory (RMBL, Gothic, Colorado, USA) from June to August 2021 and 2022. RMBL is located in the East River valley of the West Elk mountains, approximately 10 kilometers from Crested Butte, Colorado. Study sites were located at 2815 m (38°53'50"N, 106°58'43"W), 3165 m (38°57'38"N, 107°01'53"W) and 3380 m (38°58'10"N, 107°01'53"W) in elevation. All sites are approximately 50 m2 and have similar slope and aspect (Sloat et al. 2015). We randomly defined five 1.2 m x 1.2 m plots within each site. Within the plots, we marked all newly open flowering units once per week from early June to mid-August. We counted flowering units as either a single flower (most species), a flowering head (Asteraceae), or an umbel (Apiaceae). We only counted flowering units once as they opened, so counts were not cumulative. We quantified fitness as successful fruit and seed development at the end of the season. When flowers began to produce fruits, we counted the number of units with fruit, the number of developed fruits produced by each flowering unit, and the number of seeds per fruit. We also recorded the week of flowering for each fruit. We could not count fruits and seeds for all species because they disappeared, were consumed too quickly, or did not produce seeds during our field season.
Range size and local abundance data for angiosperm communities across an elevation gradient, Rocky Mountain Biological Lab, 2021-2022
This dataset contains abundance and range size data for angiosperm communities at three sites in Washington Gulch near the Rocky Mountain Biological Laboratory (RMBL, Gothic, Colorado, USA) for 2021 and 2022. RMBL is located in the East River valley of the West Elk mountains, approximately 10 kilometers from Crested Butte, Colorado. Study sites were located at 2815 m (38°53'50"N, 106°58'43"W), 3165 m (38°57'38"N, 107°01'53"W) and 3380 m (38°58'10"N, 107°01'53"W) in elevation, and contained five 1.2 m x 1.2 m plots each. We identified all vascular plants to species level. Each plot was sampled once per year near the peak of the growing season (approximately mid-July, depending on the year and elevation). In each plot, we counted all individuals of every species. To quantify abundance, we averaged local abundance across all five plots at each site and the two data collection years, and then ranked species by averaged abundance within each site (highest to lowest). We calculated range size as Extent of Occurrence (EOO) and Area of Occupancy (AOO). We calculated AOO and EOO with GBIF data using the ‘red’ package. We then ranked species by AOO within each site (largest to smallest).
MCR LTER: Coral Reef: Community structure outdoor flume data in support of Edmunds 2019 Marine Biology
This dataset contains data in support of Edmunds, P.J., S.S. Doo, R.C. Carpenter, 'Changes in coral reef community structure in response to year-long incubations under contrasting pCO2 regimes', Marine Biology, 2019, doi:10.1007/s00227-019-3540-2. Here, the effects of ocean acidification (OA) on back reef communities from Mo'orea, French Polynesia (17.492S, 149.826W), were tested from 12 November 2015 to 16 November 2016 in outdoor flumes maintained at various mean pCO2 levels. Change in mass and percent cover were recorded monthly. This material is based upon work supported by the U.S. National Science Foundation under Grant No. OCE 16-37396 (and earlier awards) as well as a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2018). This work represents a contribution of the Moorea Coral Reef (MCR) LTER Site.
Experimental evaluation of how biological invasions and climate change interact to alter the vertical assembly of an amphibian community
<ol> <li>While biotic-abiotic interactions are increasingly documented in nature, a process-based understanding of how such interactions influence community assembly is lacking in the ecological literature. Perhaps the most emblematic and pervasive example of such interactions is the synergistic threat to biodiversity posed by climate change and invasive species. Invasive species often out-compete or prey on native species. Despite this long-standing and widespread issue, little is known about how abiotic conditions, such as climate change, will influence the frequency and severity of negative biotic interactions that threaten the persistence of native fauna.</li> <li>Treefrogs are a globally diverse group of amphibians that climb to complete life-cycle processes, such as foraging and reproduction, as well as to evade predators and competitors, resulting in frog communities that are vertically partitioned. Furthermore, treefrogs adjust their vertical position to maintain optimal body temperature and hydration in response to environmental change. Here, utilizing this model group, we designed a novel experiment to determine how extrinsic abiotic and biotic factors (changes to water availability and an introduced predator, respectively) interact with intrinsic biological traits, such as individual physiology and behavior, to influence treefrogs’ vertical niche. </li> <li>Our study found that treefrogs adjusted their vertical niche through displacement behaviors in accordance with abiotic resources. However, biotic interactions resulted in native treefrogs distancing themselves from abiotic resources to avoid the non-native species. Importantly, under altered abiotic conditions, both native species avoided the non-native species – more than they avoided their native counterpart. Additionally, exposure to the non-native species resulted in native species altering their tree climbing behaviors by and becoming more vertically dynamic to avoid the non-native antagonist.</li> <li>Our experiment determined that vertical niche selection and community interactions were most accurately represented by a biotic-abiotic interaction model, rather than a model that considers these factors to operate in an isolated (singular) or even additive manner. Our study provides evidence that native species may be resilient to interacting disturbances via physiological adaptations to local climate and plasticity in space-use behaviors that mediate the impact of the introduced predator. </li> </ol>
Long Term Research in Environmental Biology (LTREB): California vernal pool plant community ecology and restoration, 2000-2017
This data set includes annual vegetation data and selected water depth data collected during the period 2000-2017 from vernal pool basins that were constructed in 1999 as part of a large-scale vernal pool mitigation effort at Travis Air Force Base, California. The constructed pools covered an area of about 15 Ha and were located adjacent to a complex of naturally-occurring pools, which were used as reference sites for comparison. Five plant species were intentionally seeded into the pools according to five seeding treatment protocols to assess the influence of order of colonization, frequency of colonization, and dispersal limitation on vernal pool plant community assembly. Because water depth was known to influence plant species distributions, water depth was recorded weekly during the winter wet season in selected years for each constructed and reference pool at the site. Seed plots were 50 cm x 50 cm and were permanently marked and used for repeated sampling of vegetation from 2000-2017. For each plant species that occurred in the plots, the frequency of occurrence was recorded as the number of squares out of a 100-cell grid laid over the plot in which that plant species appeared. For the five species that were planted into the plots, the frequency was recorded, as above, but in addition the number of individuals of that species in the plot was also recorded.
Habitat quality and biological community responses to innovative hydropower plant installations at transverse in-stream structures
<ol> <li>Ecological assessments of the effects of hydropower plants (HPPs) are often limited to aspects of entrainment, mortality, injuries, and passage of fish, whereas the effects on riverine habitats and biological communities in proximity to these structures are hardly documented.</li> <li>In this study, aquatic communities comprising fish, macroinvertebrates, macrophytes, and periphyton as well as physical and hydromorphological parameters were investigated in upstream and downstream river sections at five transverse structures at different seasons before and after the installation of an innovative HPP.</li> <li>At all study sites, significant differences in the aquatic community composition between the assessed upstream and downstream sections were found after HPP construction, indicating distinct serial discontinuity.</li> <li>Raising the damming target at the sites Großweil and Au deteriorated the habitat conditions in the upstream area close to the weir and presumably influenced in particular the macroinvertebrate community, where a significant decrease in the density of rheophilic mayfly, stonefly, and caddisfly larvae was observed after HPP construction.</li> <li> <em>Synthesis and applications</em>: The installation of different types of innovative HPPs has not improved the habitat conditions for rheophilic species, contrary to the promises raised by the developers of these concepts. Conversely, retrofitting existing weirs accompanied by further damming even significantly increased the effects of serial discontinuity and deteriorated the habitat conditions for rheophilic species in upstream sections. As evident from the findings of this study, habitat and biological community effects resulting from serial discontinuity should become better integrated into ecological assessments of HPP developments.</li> </ol>
Biological and biogeochemical responses of benthic communities to marine heatwaves - BioHeat
<p>The dataset presents data from a laboratory experiment exploring the effect of heatwaves of different intensities on benhic bioturbation, community excretion and biogeochemical cycling of solutes. <span>We tested the effects of short-term, moderate and strong marine heatwaves on macrofauna bioturbation and associated solute fluxes as examples of ecosystem functioning. We also measured macrofaunal excretion rates to assess effects of temperature on macrofauna metabolism. For this experiment, we used unmanipulated sediment cores with natural animal communities collected from a muddy location at 32 m depth in the northern Baltic Sea. Despite the mechanistic effect of bioturbation remaining unchanged between the treatments, there were significant differences in oxygen consumption, solute fluxes and excretion. Biogeochemical and biological processes were boosted by the moderate heatwave, whereas biogeochemical cycling seemed to decrease under a strong heatwave.</span></p>
Data from: Phenological mismatches mitigate the ecological impact of a biological invader on amphibian communities
<p>Data and code for the manuscript entitled "Phenological mismatches mitigate the ecological impact of a biological invader on amphibian communities" for Ecological Applications (2024). <br><br><br><br>The raw sequencing data was submitted to NCBI’s Sequence Read Archive (SRA) under BioProject number PRJNA1023717 (https://dataview.ncbi.nlm.nih.gov/object/PRJNA1023717?reviewer=rciv7kme2qq5vpcnqqog4vjioo). </p>
Dataset for manuscript entitled "The effects of a synthetic and biological surfactant on the community composition and metabolic activity of a freshwater biofilm"
<p>The following datasets were used for the 16s rRNA analysis in the manuscript entitled " The effects of a synthetic and biological surfactant on the community composition and metabolic activity of a freshwater biofilm". BZ2 files were obtained from next generation sequencing with the Illumina Mi-Seq. Mothur was used to analyze the BZ2 files, creating the listed excel documents.</p>
Resource competition shapes biological rhythms and promotes temporal niche differentiation in a community simulation
<p>This is the code and dataset for the article entitled "Resource competition shapes biological rhythms and promotes temporal niche differentiation in a community simulation," in the journal Ecology and Evolution.</p> <ul> <li>Competition for resources often contributes strongly to defining an organism's ecological niche. Endogenous biological rhythms are important adaptations to the temporal dimension of niches, but how other organisms influence such temporal niches have not been much studied, and the role of competition in particular has been even less examined. We investigated how interspecific and intraspecific competition for resources shape an organism's activity rhythms.</li> <li>To do this, we simulated communities of one or two species in an agent-based model. Individuals in the simulation move according to a circadian activity rhythm and compete for limited resources. Probability of reproduction is proportional to an individual's success in obtaining resources. Offspring may have variance in rhythm parameters, which allow for the population to evolve over time.</li> <li>We demonstrate that when organisms are arrhythmic, one species will always be competitively excluded from the environment, but the existence of activity rhythms allows niche differentiation and indefinite coexistence of the two species. Two species which are initially active at the same phase will differentiate their phase angle of entrainment over time to avoid each other. When only one species is present in an environment, competition within the species strongly selects for niche expansion through arrhythmicity, but the addition of an interspecific competitor facilitates evolution of increased rhythmic amplitude when combined with additional adaptations for temporal specialization. Finally, if individuals preferentially mate with others who are active at similar times of day, then disruptive selection by intraspecific competition can split one population into two reproductively isolated groups separated in activity time.</li> <li>These simulations suggest that biological rhythms are an effective method to temporally differentiate ecological niches, and that competition is an important ecological pressure promoting the evolution of rhythms and sleep. This is the first study to use ecological modeling to examine biological rhythms.</li> </ul>
Fire severity as a key determinant of aboveground and belowground biological community recovery in managed even-aged boreal forests
<p><span>Changes in fire regime of boreal forests in response to climate warming are expected to impact post-fire recovery. However, quantitative data on how managed forests sustain and recover from recent fire disturbance are limited. </span></p> <p><span>Two years after a large wildfire in managed even-aged boreal forests in Sweden,</span><span> we investigated how recovery of aboveground and belowground communities, i.e., understory vegetation and soil microbial and faunal communities, responded to variation in the severity of soil (i.e., consumption of soil organic matter) and canopy fires (i.e., tree mortality). </span></p> <p><span>While fire overall enhanced diversity of understory vegetation through colonization of fire adapted plant species, it reduced the abundance and diversity of soil biota. We observed contrasting effects of tree- and soil-related fire severity on survival and recovery of understory vegetation and soil biological communities. </span><span>Severe fires that killed overstory <em>Pinus sylvestris</em> promoted a successional stage dominated by the mosses <em>Ceratodon purpureus</em> and <em>Polytrichum juniperum</em>, but reduced regeneration of tree seedlings and disfavoured the ericaceous dwarf-shrub<em> Vaccinium vitis-idaea</em> and the grass<em> Deschampsia flexuos</em>a. Moreover, high tree mortality from fire reduced fungal biomass and changed fungal community composition, in particular that of ectomycorrhizal fungi, and reduced the fungivorous soil Oribatida. In contrast, soil-related fire severity had little impact on vegetation composition, fungal communities and soil animals. Bacterial communities responded to both tree- and soil-related fire severity. </span></p> <p><span>Synthesis: Our results two years post-fire suggest that a change in fire regime from a historically low-severity ground-fire regime, with fires that mainly burns into the soil organic layer, to a </span><span>stand-replacing </span><span>fire regime with a high degree of tree mortality, as may be expected with climate change, is likely to impact the short-term recovery of stand structure and above- and belowground species composition of even-aged <em>P. sylvestris</em> </span><span>boreal forests.</span></p>
Biological and biogeochemical responses of benthic communities to marine heatwaves - BioHeat
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Fire severity as a key determinant of aboveground and belowground biological community recovery in managed even-aged boreal forests
Open the record for dataset details and reuse information.
Resource competition shapes biological rhythms and promotes temporal niche differentiation in a community simulation
Open the record for dataset details and reuse information.
Habitat quality and biological community responses to innovative hydropower plant installations at transverse in-stream structures
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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.