Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
104
datasets available to search
ShareScore release 0.9.0
Dataset results
104 results for “heterotrophs”
Automated total and heterotrophic soil respiration in semi-arid shrubland and annual invasive patches
<p>Soil respiration (Rs) is the largest terrestrial source of carbon (C) flux to the atmosphere but our understanding of Rs controls with shifts in plant-community composition remains limited. We used high frequency soil respiration measurements and root exclusion to evaluate how Rs component fluxes, autotrophic respiration (Ra) and heterotrophic respiration (Rh), vary between a perennial semi-arid shrub community and annual invasive community. </p>
Datasets associated with paper "Heterotrophic eukaryotes show a fast-slow continuum, not a gleaner-exploiter trade-off"
<p>This contains 6 data files used in the analysis of the paper "Heterotrophic eukaryotes show a fast-slow continuum, not a gleaner-exploiter trade-off", and one file describing their contents in detail. </p> <p>Kiorboe_and_Hirst_dataset_edited_2020_03_21.csv</p> <p>FoRAGE_dataset_edited_2020_03_21.csv</p> <p>FoRAGE_dataset_taxonomic_info_edited_2020_03_21</p> <p>FoRAGE_dataset_with_outliers_raw.csv</p> <p>Growth_ingestion_dataset_raw.csv</p> <p>Litchman_2007_phytoplankton_Vmax_and_affinity_data.csv<br> </p> <p>The primary contents of these files are compiled parameter estimates of the clearance, ingestion and growth rates of heterotrophic organisms. These have largely been taken from two published data compilations:</p> <p>Kiørboe T, Hirst AG (2014) Shifts in mass scaling of respiration, feeding, and growth rates across life-form transitions in marine pelagic organisms. Am Nat 183(4):E118-30. <a href="https://doi.org/10.1086/675241">https://doi.org/10.1086/675241</a></p> <p>Uiterwaal SF, Lagerstrom IT, Lyon SR, DeLong JP (2018) Data paper: FoRAGE (Functional Responses from Around the Globe in all Ecosystems) database: a compilation of functional responses for consumers and parasitoids. bioRxiv doi: <a href="https://doi.org/10.1101/503334">https://doi.org/10.1101/503334</a> <br> </p> <p>The data files are described in detail in 'Data description.txt'.</p> <p>Scripts to analyse this data can be found at <a href="https://doi.org/10.5281/zenodo.4002083">https://doi.org/10.5281/zenodo.4002083</a> . The paper associated with the data and scripts, will be linked to here when published. </p>
Data from: Necrobiome framework for bridging decomposition ecology of autotrophically and heterotrophically derived organic matter
Decomposition contributes to global ecosystem function by contributing to nutrient recycling, energy flow and limiting biomass accumulation. The decomposer organisms influencing this process form diverse, complex, and highly dynamic communities that often specialize on different plant or animal resources. Despite performing the same net role, there is a need to conceptually synthesize information on the structure and function of decomposer communities across the spectrum of dead plant and animal resources. A lack of synthesis has limited cross-disciplinary learning and research in important areas of ecosystem and community ecology. Here we expound on the 'necrobiome' concept and develop a framework describing the decomposer communities and their interactions associated with plant and animal resource types within multiple ecosystems. We outline the biotic structure and ecological functions of the necrobiome, along with how the necrobiome fits into a broader landscape and ecosystem context. The expanded necrobiome model provides a set of perspectives on decomposer communities across resource types, and conceptually unifies plant and animal decomposer communities into the same framework, while acknowledging key differences in processes and mechanisms. This framework is intended to raise awareness among researchers, and advance the construction of explicit, mechanistic hypotheses that further our understanding of decomposer community contributions to biodiversity, the structure and function of ecosystems and global nutrient recycling and energy flow.
Seasonal and interannual variability of soil heterotrophic respiration and autotrophic respiration in typical grassland of Inner Mongolia
Open the record for dataset details and reuse information.
Physiologic, Genomic and Electrochemical Characterization of two heterotrophic marine sediment microbes from the Idiomarina genus
<p><em>Idiomarina</em> strain S11 on ITO plated glass electrodes stained with a lipid stain (FM<sup>TM</sup> 4-64FX) and provided RedoxSensor<sup>TM</sup> Green (RSG). Video show back-to-back fixed location on the electrode with loose attachment of cells in clumpy biofilms. Each frame taken at 5 min intervals. As indicated in the video, voltage at the electrode is decreased from -400 mV vs. Ag/AgCl to a -600 mV Ag/AgCl, which qualitatively corresponds to an increase in RSG fluorescence, though this could not be accurately quantified given the shifting focal plane<strong>.</strong></p>
Observation‐based global soil heterotrophic respiration indicates underestimated turnover and sequestration of soil carbon by terrestrial ecosystem models
<p><span>Soil heterotrophic respiration (R<sub>h</sub>) refers to the flux of CO2 released from soil to atmosphere as a result of organic matter decomposition by soil microbes and fauna. As one of the major fluxes in the global carbon cycle, the estimation of global R<sub>h</sub> still exists large uncertainties, which further limited our current understanding of the carbon accumulation in soils. Here, we applied a Random Forest algorithm to create a global dataset of soil R<sub>h</sub>, by linking 761 field observations with both abiotic and biotic predictors. We estimated that the global R<sub>h</sub> was 48.8 ± 0.9 Pg C yr<sup>-1</sup> for 1982–2018, which was 16% less than the ensemble mean (58.6 ± 9.9 Pg C yr<sup>-1</sup>) of 16 terrestrial ecosystem models. By integrating our observational R<sub>h</sub> with independent soil carbon stock datasets, we obtained a global mean soil carbon turnover time of 38.3 ± 11 yr. Using observation-based turnover times as a constraint, we found that terrestrial ecosystem models simulated faster carbon turnovers, leading to a 30% (74 Pg C) underestimation of terrestrial ecosystem carbon accumulation for the past century, which was especially pronounced at high latitudes. This underestimation is equivalent to 45% of the total carbon emissions (164 Pg C) caused by global land use change at the same time. Our analyses highlight the need to constrain ecosystem models using observation-based and locally adapted R<sub>h</sub> values to obtain reliable predictions of the carbon sink capacity of terrestrial ecosystems. </span></p>
Abundances of Heterotrophic Bacteria, Prochlorococcus, Synnechococcus, and Picoeucaryotes during the PARAGON2 cruise
<p>This dataset is part of the 2022 SCOPE-PARAGON II (PARticles And Growth in the Oceanic Nutricline) research expedition (KM2209 aboard the R/V Kilo Moana), a coordinated effort to characterize particle dynamics and remineralization in the upper 500 m of the North Pacific Subtropical Gyre (more info here: http://scope.soest.hawaii.edu/data/scope2022/scope2022.html). Cruise date: Aug 4 - Aug 12 2022; Cruise location: 17-24N, ~154W. The cruise tracked a high chlorophyll feature close to the Hawaiian Islands. Particle abundances of three separate chlorophyll containing populations were enumerated by autofluorescence using a B/D Influx flow cytometer: Prochlorococcus, Synechococcus and the pico-Eukaryotes. Heterotrophic bacteria were enumerated using the DNA stain SYBR Green I and subtracting the previously obtained Prochlorococcus concentration from the DNA positive cells. Particles were collected in situ and preserved following standard protocols for analysis in the lab (~6 months after collection). 1 micrometer polystyrene beads were added to all samples as reference. Timestamp is in UTC.</p>
Data from: Global, satellite-driven estimates of heterotrophic respiration
While heterotrophic respiration (Rh) makes up about a quarter of gross global terrestrial carbon fluxes, it remains among the least observed carbon fluxes, particularly outside the mid-latitudes. In situ measurements collected in the Soil Respiration Database (SRDB) number only a few hundred worldwide. Similarly, only a single data-driven wall-to-wall estimate of annual average heterotrophic respiration exists, based on bottom-up upscaling of SRDB measurements using an assumed functional form to account for climate variability. In this study, we exploit recent advances in remote sensing of terrestrial carbon fluxes to estimate global variations in heterotrophic respiration in a top-down fashion at monthly temporal resolution and 4x5o spatial resolution. We combine net ecosystem productivity estimates from atmospheric inversions of the NASA Carbon Monitoring System- Flux (CMS-Flux) with an optimally-scaled gross primary productivity dataset based on satellite-observed solar-induced fluorescence variations to estimate total ecosystem respiration as a residual of the terrestrial carbon balance. The ecosystem respiration is then separated into autotrophic and heterotrophic components based on a spatially-varying carbon use efficiency retrieved in a model-data fusion framework (the CARbon DAta MOdel fraMework, CARDAMOM). The resulting dataset is independent of any assumptions about how heterotrophic respiration responds to climate or substrate variations. It estimates an annual average global average heterotrophic respiration flux of 43.6 ± 19.3 Pg C/yr. Sensitivity and uncertainty analyses showed that the top-down Rh are more sensitive to the choice of input GPP and NEP datasets than to the assumption of a static CUE value, with the possible exception of the wet tropics. These top-down estimates are compared to bottom-up estimates of annual heterotrophic respiration, with new uncertainty estimates that partially account for sampling and model errors. Top-down heterotrophic respiration estimates are higher than those from bottom-up upscaling everywhere except at high latitudes, and are 30% greater overall (43.6 Pg C/yr vs. 33.4 Pg C/yr). The uncertainty ranges of both methods are comparable, except poleward of 45 degrees North, where bottom-up uncertainties are greater. The ratio of top-down heterotrophic to total ecosystem respiration varies seasonally by as much as 0.6 depending on season and climate, illustrating the importance of studying the drivers of autotrophic and heterotrophic respiration separately, and thus the importance of data-driven estimates of Rh such as those estimated here.
Apparent thermal acclimation of soil heterotrophic respiration mainly mediated by substrate availability
<p><span>Multiple lines of existing evidence suggest that increasing CO<sub>2</sub> emission from soils</span> <span>in response to rising temperatures could accelerate global warming. However, in experimental studies, the initial positive response of soil heterotrophic respiration (</span><span>R</span><sub><span>H</span></sub><span>) to</span><span> warming often weakens over time (referred to apparent thermal acclimation). If the</span><span> decreased </span><span>R</span><span>H</span> <span>is driven by</span><span> the thermal adaptation of soil microbial community, the potential for soil carbon (C) losses would be reduced substantially. In the meanwhile, the response could </span><span>equally be caused by substrate depletion, and would then </span><span>reflect the gradual loss of soil C.</span> <span>To address uncertainties regarding the causes of apparent thermal acclimation, we carried out </span><span>sterilization and inoculation</span><span> experiments using the soil samples from an alpine meadow with 6-years of warming and nitrogen (N) addition. We demonstrate</span><span> that substrate depletion, rather than microbial adaptation, determined the response of R<sub>H</sub> to long-term warming. Furthermore, </span><span>N addition appeared to alleviate the apparent acclimation of </span><span>R</span><sub><span>H</span></sub><span> to warming. Our study provides strong empirical support for </span><span>substrate availability being the cause of the </span><span>apparent acclimation of soil </span><span>microbial respiration to temperature. Thus, t</span><span>hese mechanistic insights</span><span> could</span><span> facilitate efforts of biogeochemical modeling to accurately project soil C stocks in the future climate.</span></p>
Data from: Global, satellite-driven estimates of heterotrophic respiration
Open the record for dataset details and reuse information.
Apparent thermal acclimation of soil heterotrophic respiration mainly mediated by substrate availability
Open the record for dataset details and reuse information.
Observation‐based global soil heterotrophic respiration indicates underestimated turnover and sequestration of soil carbon by terrestrial ecosystem models
Open the record for dataset details and reuse information.
Automated total and heterotrophic soil respiration in semi-arid shrubland and annual invasive patches
Open the record for dataset details and reuse information.
Data from: Necrobiome framework for bridging decomposition ecology of autotrophically and heterotrophically derived organic matter
Open the record for dataset details and reuse information.
Net primary production, heterotrophic respiration, and net ecoystem production out from TEM outputs: 1899 - 2100
Output from TEM modeling in North American black spruce grid cells Data from the following manuscript Clein, J.S., A.D. McGuire, X. Zhang, D.W. Kicklighter, J.M. Melillo, S.C. Wofsy, P.G. Jarvis, and J. M. Massheder. 2002. Historical and projected carbon balance of mature black spruce ecosystems across North America: The role of carbon-nitrogen interactions. Plant and Soil 242:15-32.
Net primary production, heterotrophic respiration, and net ecoystem production out from TEM outputs compared with Tower data: 1899 - 2100
Net primary production, heterotrophic respiration, and net ecoystem production out from TEM outputs compared with Tower data: 1899 - 2100.
Cell counts (per liter) by size groups of diatoms, autotrophic and heterotrophic plankton, via epifluorescent microscopy (EPI) from CCE LTER process cruises in the California Current region, 2006 - 2016.
Microbial community assemblages of the California Current Ecosystem (CCE) are assessed for abundance of diatoms, autotrophic (dinoflagellate and other eukaryotes) and heterotrophic (dinoflagellate and other eukaryotes) plankton using high-throughput digital epifluorescence microscopy (EPI). Samples to estimate the nano- and microplankton (0.2-2.0-µm and 2.0-20-µm size, respectively) are collected at various depths, preserved, stained, and filtered onto a membrane filter and mounted on a glass microscope slide aboard the process cruises (since 2006, ongoing). Slides are then frozen at -80°C for subsequent imaging and analysis in the laboratory onshore.
Size group (pico, nano, micro) and group total carbon estimates from cell counts via epifluorescent microscopy (EPI) of heterotrophic and autotrophic plankton from CCE LTER process cruises in the California Current region, 2006 - 2016
Microbial community assemblages of the California Current Ecosystem (CCE) are assessed for biomass of heterotrophic (dinoflagellate and other eukaryotes) and autotrophic (dinoflagellate and other eukaryotes) plankton using high-throughput digital epifluorescence microscopy (EPI). Samples to estimate the nano- and microplankton (0.2-2.0-µm and 2.0-20-µm size, respectively) are collected at various depths, preserved, stained, and filtered onto a membrane filter and mounted on a glass microscope slide aboard the process cruises (since 2006, ongoing). Slides are then frozen at -80°C for subsequent imaging and analysis in the laboratory onshore. Carbon biomass is computed from cell biovolumes.
Size group (pico, nano, micro) and group total carbon estimates from cell counts via epifluorescent microscopy (EPI) of heterotrophic and autotrophic plankton from CCE-CalCOFI Augmented cruises in the California Current System, 2004 - 2011 (ongoing).
Microbial community assemblages of the California Current Ecosystem (CCE) are assessed for biomass of heterotrophic (dinoflagellate and other eukaryotes) and autotrophic (dinoflagellate and other eukaryotes) plankton using high-throughput digital epifluorescence microscopy (EPI). Samples to estimate the nano- and microplankton (0.2-2.0-µm and 2.0-20-µm size, respectively) are collected at various depths via Niskin bottles, preserved, stained, and filtered onto a membrane filter and mounted on a glass microscope slide aboard the quarterly CalCOFI survey cruises (since 2004, ongoing). Slides are then frozen at -80°C for subsequent imaging and analysis in the laboratory onshore. Carbon biomass is computed from cell biovolumes.
Cell counts (per liter) by size groups of diatoms, autotrophic and heterotrophic plankton, via epifluorescent microscopy (EPI) from CCE-CalCOFI Augmented cruises in the California Current System, 2004 - 2011 (ongoing).
Microbial community assemblages of the California Current Ecosystem (CCE) are assessed for abundance of diatoms, autotrophic (dinoflagellate and other eukaryotes) and heterotrophic (dinoflagellate and other eukaryotes) plankton using high-throughput digital epifluorescence microscopy (EPI). Samples to estimate the nano- and microplankton (0.2-2.0-µm and 2.0-20-µm size, respectively) are collected at various depths via Niskin bottles, preserved, stained, and filtered onto a membrane filter and mounted on a glass microscope slide aboard the quarterly CalCOFI survey cruises (since 2004, ongoing). Slides are then frozen at -80°C for subsequent imaging and analysis in the laboratory onshore.
ScienceDex guides
Understand access before you commit
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.