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18 results for “microcosm experiment”
Erosion and biomass measurements from microcosm experiments, 2022
This dataset accompanies the manuscript: "Microalgae and meiofauna induce heterogeneous biostabilization in marine sediments". It includes erosion and biomass measurements from microcosm experiments, along with R and MATLAB scripts to reproduce the analyses and figures. Initial diatom cultures were collected from Dauphin Island Alabama during the spring of 2022. All experiments were conducted at the Navel Research lab in Stennis Space Center, Stennis MS. in the summer of 2022.
Data associated with a study on freshwater phenanthrene removal by three emergent wetland plants conducted in a microcosm experiment at the IISD Experimental Lakes Area, ON, Canada, in 2022.
The following package includes data from a study that evaluated the efficacy of three common wetland plants, Typha sp. (cattail), Carex utriculata (sedge a), and C. lasiocarpa (sedge b) in enhancing removal of phenanthrene (1 mg/L) from freshwater in a microcosm experiment conducted at the IISD Experimental Lakes Area, northwestern Ontario, Canada, in 2022. Over 21 days, microcosms were monitored for phenanthrene chemistry, basic water quality, plant growth metrics (height and final biomass), and root biofilm oxygen consumption (respirometry) and adenosine triphosphate (ATP). Data included in this package was first collected and used in the paper by Stanley et al., titled Freshwater Phenanthrene Removal by three Emergent Wetland Plants.
Figure 1 in Soil quality, leaf litter quality, and microbial biomass interactively drive soil respiration in a microcosm experiment
Figure 1. Principal components analysis of (A) soil quality and (B) leaf litter quality across the experimental treatments (Table S1-2). Soil quality was quantified as a combination of soil pH, C, N, and C:N; leaf litter quality was quantified as a combination of leaf Ca, C, lignin, Mg, N, P, C:N, C:P, and N:P. Soil and leaf litter were collected from Hainich National Park, Germany.
Data from: Effects of fungicides on aquatic fungi and bacteria: a comparison of morphological and molecular approaches from a microcosm experiment
<p>Data files and R code for the manuscript: Effects of fungicides on aquatic fungi and bacteria: a comparison of morphological and molecular approaches from a microcosm experiment. Published in Environmental Sciences Europe.</p>
Freeze-thaw microcosm experiment data 2021
Warmer winters with less snowfall are increasing the frequency of soil freeze-thaw cycles across temperate regions. Soil microbial responses to freeze-thaw cycles vary and some of this variation may be explained by microbial conditioning to prior winter conditions, yet such linkages remain largely unexplored. We investigated how differences in temperature history influenced microbial community composition and activity in response to freeze-thaw cycles. We collected soil microbial communities that developed under colder (high elevation) and warmer (low elevation) temperature regimes in spruce-fir forests, then added each of these soil microbial communities to a sterile bulk-soil in a laboratory microcosm experiment. The inoculated high-elevation cold and low-elevation warm microcosms were subjected to diurnal freeze-thaw cycles or constant above-freezing temperature for 9 days. Then, all microcosms were subjected to a 7-day above-freezing recovery period. Overall, we found that the high-elevation cold community had, relative to the low-elevation warm community, a smaller reduction in microbial respiration (CO2 flux) during freeze-thaw cycles. Further, the high-elevation cold community, on average, experienced lower freeze-thaw-induced bacterial mortality than the warm community and may have partly acclimated to freeze-thaw cycles via increased lipid membrane fluidity. Respiration of both microbial communities quickly recovered following the end of the freeze-thaw treatment period and there were no changes in soil extractable carbon or nitrogen. Our results provide evidence that past soil temperature conditions may influence the responses of soil microbial communities to freeze-thaw cycles. The microbial community that developed under a colder temperature regime was more tolerant of freeze-thaw cycles than the community that developed under a warmer temperature regime, although both communities displayed some level of resilience. Taken together, our data suggest that
Contrasting effects of indigenous arbuscular mycorrhizal fungi on nitrogen absorption of C3 and C4 grasses: Evidence from microcosm and 15N labeling experiments
<p><strong><em>Background and aims</em></strong></p> <p>Nitrogen (N) captured by arbuscular mycorrhizal (AM) symbiosis is a major pathway in the N uptake of host plants. However, the relative contribution of arbuscular mycorrhizal fungi (AMF) to N uptake in different plant functional types has not been well assessed.</p> <p><strong><em>Methods</em></strong></p> <p>Two dominant plant species in semiarid steppe ecosystems on the Mongolian plateau, i.e. <em>Leymus chinensis </em>(C<sub>3</sub> grass) and <em>Cleistogenes squarrosa</em> (C<sub>4</sub> grass), were selected in this study. We conducted a greenhouse manipulation experiment using novel microcosms combined with <sup>15</sup>N labeling techniques and investigated the effect of indigenous AMF on plant growth and quantified their relative contribution to N uptake under high and low levels of available soil N. </p> <p><strong><em>Results</em></strong></p> <p>Indigenous AMF contribute more to N uptake in C<sub>3</sub> grass than that in C<sub>4</sub> grass, and mycorrhizal partners act as parasites for C<sub>4</sub> plant growth. For <em>L. chinensis</em>, indigenous AM symbiosis suppressed plant growth under low soil N but improved plant growth under high soil N conditions. AMF contributed to <em>c.</em> 23% and 20% of the total plant N uptake under low and high soil N conditions, respectively. For <em>C. squarrosa</em>, indigenous AM symbiosis consistently inhibited plant growth under both low and high soil N conditions, and the percent contributions of AMF to N uptake were only <em>c.</em> 9% and 7%, respectively.</p> <p><strong><em>Conclusions</em></strong></p> <p>Our results demonstrate that indigenous AM symbiosis plays a vital role in N uptake by host plants, even in the absence of a positive growth response. AMF can modify the fitness of C<sub>3</sub> and C<sub>4</sub> grasses and thereby alter plant community composition and ecosystem N cycling, particularly under high N conditions. Our study has important implications for improving global N cycling models in the face of increasing global N deposition.</p>
Data from: Aquatic ecosystem responds differently to press and pulse nutrient disturbances as revealed by a microcosm experiment
<p><span>Due to climate change and increasing anthropogenic activities, lakes are disturbed frequently, usually by press (e.g., diffused pollution, rising temperatures) or pulse (e.g., storms, rainfall, pollution events) disturbances. Both press and pulse disturbances can affect abiotic and biotic environments, changing the structure of ecosystems and affecting ecosystem services. To confront with the effects of climate change and increasing anthropogenic activities, understanding the different effects of press and pulse disturbances on lake ecosystems is essential. This study assessed the effect of press and pulse disturbances of phosphorus on a microcosmic </span><span>aquatic </span><span>eco</span><span>system</span><span> by measuring the total phosphorus (TP), algae density, and physiological indicators of submerged macrophytes. We found that the microcosmic aquatic ecosystem responded differently to press and pulse disturbances. Our results suggested that it had a lower resistance to pulse phosphorus disturbances than to press phosphorus disturbances. There were significantly higher nutrient concentrations and algal densities in the pulse treatment than in the press treatment. Positive feedback was found between the biomass of submerged macrophytes and the water quality. There was a higher submerged macrophytes biomass at low TP concentration and algal density. In the context of climate change, press and pulse disturbances could have severe impacts on lake ecosystems. Our findings will provide some insight for further research and lake management.</span></p>
Data from: Fast drug rotation reduces bacterial resistance evolution in a microcosm experiment
<p><span>Drug rotation (cycling), in which multiple drugs are administrated alternatively, has the potential for limiting resistance evolution in pathogens. The frequency of drug alternation could be a major factor to determine the effectiveness of drug rotation. Drug rotation practices often have low frequency of drug alternation, with an expectation of resistance reversion. Here we, based on evolutionary rescue and compensatory evolution theories, suggest that fast drug rotation can limit resistance evolution in the first place. This is because fast drug rotation would give little time for the evolutionarily rescued populations to recover in population size and genetic diversity, and thus decrease the chance of future evolutionary rescue under alternate environmental stresses. We experimentally tested this hypothesis using the bacterium <em>Pseudomonas</em> <em>fluorescens</em> and two antibiotics (chloramphenicol and rifampin). Increasing drug rotation frequency reduced the chance of evolutionary rescue, and most of the final surviving bacterial populations are resistant to both drugs. Drug resistance incurred significant fitness costs, which did not differ among the drug treatment histories. A link between population sizes during the early stages of drug treatment and the end-point fates of populations (extinction versus survival) suggested that population size recovery and compensatory evolution before drug shift increase the chance of population survival. Our results therefore advocate fast drug rotation as a promising approach to reduce bacterial resistance evolution, which in particular could be a substitute for drug mixing when the latter has safety risks.</span></p>
Data from: Fast drug rotation reduces bacterial resistance evolution in a microcosm experiment
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Contrasting effects of indigenous arbuscular mycorrhizal fungi on nitrogen absorption of C3 and C4 grasses: Evidence from microcosm and 15N labeling experiments
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Data from: Aquatic ecosystem responds differently to press and pulse nutrient disturbances as revealed by a microcosm experiment
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Data from: The Metapopulation Microcosm Plate: a modified 96-well plate for use in microbial metapopulation experiments
1. Researchers in many sub-fields of ecology and evolutionary biology test hypotheses relating to metapopulation dynamics and landscape spatial structure. Key aspects of these hypotheses are often (a) large numbers of subpopulations and dispersal corridors and (b) their positions relative to each other. Testing such spatial hypotheses using traditional lab equipment and methods can be impractical, unwieldy, expensive, or impossible. 2. The Metapopulation Microcosm Plate (MMP) overcomes these difficulties. This device resembles a 96-well microtiter plate, but contains dispersal corridors between wells that can be modified in their spatial position to create various artificial landscapes, each with up to 96 habitat patches and hundreds of non-intersecting dispersal corridors of varying lengths. The device can be filled with nutrient broth and used to culture microbial metapopulations. 3. Here I describe how MMPs are designed, assembled, sterilized, and filled and demonstrate that MMPs can remain water tight and sterile with minimal evaporation for 5-7 days. 4. MMPs can be used to test many spatial hypotheses that have previously been prohibitively difficult to test. Further, by incorporating individual behavioral responses to within-patch conditions, MMPs can incorporate greater realism than do directed pipetting or other artificial dispersal methods.
Data from: A rapid and cost-effective quantitative microsatellite genotyping protocol to estimate intraspecific competition in protist microcosm experiments
High levels of intra-specific variation are commonly observed in natural microbial populations, yet the consequences of this variation for ecological and evolutionary processes remains poorly understood. Protists are excellent experimental models for investigating fundamental and applied questions in ecology and evolution, but studying intra-specific variation remains a challenge due to a lack of molecular resources to aid in quantifying and distinguishing strains during experiments. Here we present a molecular method, quantitative microsatellite genotyping, to accurately quantify strain specific frequencies from microcosm experiments of the marine flagellate Oxyrrhis marina, both between many pairs of strains and between strains in a multi-strain mixture. We find that for pairs of strains the method is effective for relative frequencies as low as 0.02 and with around 99% accuracy. The method is able to quantify four strains reasonably well, though less accurately than for pairs (range 92%-97% accuracy). This makes accessible a cheap and easy to implement method for quantifying strain (or allele) frequencies, and is suitable for use in a broad range of single celled eukaryotes (Protists) where copy number should correlate well with number of individuals (i.e. cells). This opens up the possibility of examining the role of intra-specific variation using experimental protist microcosms.
Data from: A rapid and cost-effective quantitative microsatellite genotyping protocol to estimate intraspecific competition in protist microcosm experiments
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Data from: The Metapopulation Microcosm Plate: a modified 96-well plate for use in microbial metapopulation experiments
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Raw data for: "Abrupt declines marine phytoplankton production driven by warming and biodiversity loss in a microcosm experiment"
<p><strong>Raw data for the article:</strong> Bestion, E, Barton, S, García, FC, Warfield, R, Yvon-Durocher, G (2020). Abrupt declines in marine phytoplankton production driven by warming and biodiversity loss in a microcosm experiment. Ecology Letters. 2020.</p> <p><br> <strong>This data should be cited as:</strong> Bestion, E, Barton, S, García, FC, Warfield, R, Yvon-Durocher, G (2020). Raw data for: "Abrupt declines marine phytoplankton production driven by warming and biodiversity loss in a microcosm experiment" [Data set]. Bestion et al 2020 Ecology Letters. Zenodo. http://doi.org/10.5281/zenodo.3555223<br> -----------------------------</p> <p><strong>The data is composed of two datasets:</strong><br> -----------------------------------------<br> - Biodiversity_ecosystem_function_data.csv<br> - Cell_traits_data.csv</p> <p> </p> <p><strong>Composition of the Biodiversity ecosystem function dataset</strong><br> ------------------------------------------------------------<br> The dataset contains 27 columns<br> - Temperature: the temperature treatment, either 15, 25or 30°C<br> - R: the community richness (1, 2, 4, 8 or 16 species)<br> - log2_R: the log2-scaled richness<br> - M: the community identity (e.g. ABCD is a community composed of 4 species, species A, B, C and D)<br> - P: the partition id (5 independent partitions of the species pool were drawn, following Bell et al 2009)<br> - Q: the partitioned species pool id (following Bell et al 2009)<br> - R: the replicate id (3 replicates per community within a partition, named 1 to 3)<br> - SA to SP: the species presence-absence status for each of the 16 species (species A to species P), with 1: species present within the community, 0: species absent<br> - Abundance: number of cells per ml at the end of the experiment<br> - ln_Abundance: log-transformed Abundance<br> - Chl_a : chlorophyll a content at the end of the experiment in pg ml-1<br> - ln_Chl_a : log-transformed chlorophyll a</p> <p><br> <strong>Composition of the Cell traits dataset</strong><br> -----------------------------------------<br> The dataset contains 9 columns<br> - Species_alpha: the alphanumeric id of the species used in the Biodiversity ecosystem function dataset<br> - Species_name: species identity<br> - Phylum: the phylum<br> - ln.c: the ln transformed metabolic rate b(Tc) at the reference temperature Tc = 293.15°K from the Sharpe-Schoolfield equation (eq. 4 in the article) in µgO2 cell-1 hour-1<br> - Ea: the activation energy (eV) from the Sharpe-Schoolfield equation<br> - Eh: the deactivation energy (eV) from the Sharpe-Schoolfield equation<br> - Th: the temperature at which half of the enzyme have become non functional (°K) from the Scharpe-Schoolfield equation<br> - Topt: the optimum temperature from differentiating the Sharpe-Schoolfield equation. It is presented in °C to be easier to link to the temperature treatments in the experiment<br> - cell_volume: the cell volume, in µm3</p>
Data from: Population responses to perturbations: the importance of trait-based analysis illustrated through a microcosm experiment
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Data from: Herbivores control effects of algal species richness on community biomass and stability in a laboratory microcosm experiment
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.