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.
105
datasets available to search
ShareScore release 0.7.1
Dataset results
105 results for “microbial activity”
Data collected for: The contrasted impacts of grasshoppers on soil microbial activities in function of ecosystem productivity and herbivore diet
Open the record for dataset details and reuse information.
Strong links between plant traits and microbial activities but different abiotic drivers in mountain grasslands
Open the record for dataset details and reuse information.
Inorganic nitrogen, microbial ecoenzymatic activities, and organic matter in soils collected from the Monsoon Rainfall Manipulation Experiment (MRME), Sevilleta National Wildlife Refuge, New Mexico during the 2014 growing season
Drylands are characterized by a pulse dynamics framework in which episodic rain events trigger brief pulses of biological activity and resource availability that regulate primary production in these ecosystems. Relatively small rain events can stimulate microbial processes like decomposition that release inorganic nitrogen needed by plant processes, which typically also depend on soil moisture received from larger rain events. Little is known how changes in rainfall patterns may affect plant available nitrogen in dryland soils, particularly across temporal scales. Therefore, we conducted a study to examine the daily and seasonal responses of plant available nitrogen to rain events that differed in size and frequency throughout a summer monsoon in a northern Chihuahuan Desert grassland located in the Sevilleta National Wildlife Refuge, New Mexico, USA. This data package, which accompanies an associated manuscript (Brown et al. 2022), contains measurements of inorganic nitrogen, nitrogen-acquiring microbial ecoenzymatic activities, and organic matter in soils collected from the Monsoon Rainfall Manipulation Experiment (MRME) during the 2014 summer growing season.
Soil microbial activity and abundance data in the rhizosphere and bulk soils of O horizon in the MELNHE study, 2014
The Multiple Element Limitation in Northern Hardwood Ecosystems (MELNHE) project studies N and P acquisition and limitation through a series of nutrient manipulations in northern hardwood forests. This data set includes rhizosphere processes and microbial abundance at the Bartlett Experimental Forest. Samples were collected once, in summer 2014, in the forth year of fertilization with N and P. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
Data from: Plant biodiversity responds more strongly to climate warming and anthropogenic activities than microbial biodiversity in the Qinghai-Tibetan alpine grasslands
<p>Biodiversity serves as the fundamental underpinning for ecosystem functions and services. As a result of human-induced global change, there is a growing awareness of the substantial alterations in terrestrial aboveground biodiversity, particularly within alpine regions. However, it remains uncertain whether belowground biodiversity will exhibit similar responses, both in terms of magnitude and manner, to anthropogenic global changes as aboveground biodiversity.</p> <p>Here, we conducted a meta-analysis to assess the impacts of warming, nutrient addition, and grazing on plant and soil microbial biodiversity in alpine grasslands on the Qinghai-Tibetan Plateau, which are known to be climate-sensitive and vulnerable. The analysis included 819 experimental observations from 152 studies, focusing on species richness, Shannon diversity, and Pielou's evenness.</p> <p>We found that plant biodiversity exhibited greater sensitivity to climate warming and anthropogenic activities compared to soil microbial biodiversity. Specifically, plant richness and Shannon diversity were reduced by warming and nutrient addition, while plant evenness was increased by grazing. However, only microbial richness was increased by grazing and microbial evenness was increased by warming slightly.</p> <p>The responses of biodiversity to climate warming and anthropogenic activities were modulated by multiple factors. Specifically, the negative effects of warming on plant biodiversity were more pronounced in long-term experiments under warmer or drier environmental conditions. The negative effects of nitrogen addition on biodiversity were enhanced by the intensity and duration of nitrogen treatment. Appropriate intensity and frequency of grazing were beneficial to sustaining plant biodiversity. Soil microbial biodiversity was weakly regulated, where bacterial Shannon diversity was more sensitive to nutrient addition, while fungal species richness was sensitive to grazing.</p> <p><strong>Synthesis: </strong>Our findings reveal a mismatch between aboveground plant and belowground microbial biodiversity in response to climate warming and anthropogenic activities in alpine grasslands, with plant biodiversity being more sensitive. In the context of future global change, plant biodiversity may be at greater risk than soil microbial biodiversity. In addition, biodiversity responses of different experimental and environmental conditions should be distinguished, and more attention is needed on biodiversity conservation in alpine steppe, or areas with warmer and drier environmental conditions, high-intensity fertilization or heavy grazing. </p>
Spatial patterns and effects of invasive plants on soil microbial activity and diversity along river corridors - raw data
<p>Dataset for the study</p> <p><strong><span>Spatial patterns and effects of invasive plants on soil microbial activity and diversity along river corridors</span></strong></p> <ol> <li>environmental variables of the research plots</li> <li>vascular plant species composition of the research plots</li> <li>mcirobial activity on the research plots</li> <li>CLPP profiles of the research plots</li> </ol>
Data from: Microbial metabolic activity in two basins of the Gulf of Mexico influenced by mesoscale structures
<p>Information on microbial metabolic activity is essential for quantifying carbon and energy flows through marine food webs. We quantified community (R<sub>com</sub>) and prokaryotic (R<sub>pro</sub>) respiration rates, bacterial production (BP), bacterial abundance (BA), and bacterial growth efficiencies (BGE) in the Perdido and Coatzacoalcos basins of the Gulf of Mexico (GOM) during summer and winter conditions in 2016. Our results showed seasonal, regional, and mesoscale eddy influences on those metabolic variables. R<sub>pro</sub> accounted for more than 60% of total respiration in both regions, being three times higher in stations influenced by a cyclonic eddy (CE) in September (24.1 μM O<sub>2</sub> d<sup>-1</sup>) than in stations affected by an anticyclonic eddy in March (7.2 μM O<sub>2</sub> d<sup>-1</sup>) within the Coatzacoalcos basin where the eddy-trapping mechanism advected biomass-enriched waters from the Bay of Campeche. The eddy-stirring mechanism produced horizontal and vertical dipole patterns of metabolic variables increasing up to one order of magnitude R<sub>com</sub> and R<sub>pro</sub> while decreasing BGE to 25-fold from the southeastern to the northwestern edges in CEs. This finding indicates that dissolved organic matter is more actively taken up to build bacterial biomass on the eastern edge of CEs in the GOM, while respiration rates increase on the western edges. Satellite integrated primary production was coupled with surface respiration rates at CEs and no eddies. Bacterial production was mainly regulated by CEs and was about 50% higher in the Coatzacoalcos basin (~0.03–0.14 µmol C L<sup>-1</sup> d<sup>-1</sup>). BP increased in zones with high respiration rates, suggesting that R<sub>com</sub> is associated with heterotrophic prokaryote activity in both basins. Bacterial growth efficiency was lower than 25% within the upper 500 m during both cruises, but the highest values were quantified in the euphotic zone and during the September cruise. Metabolic variables integrated over the water column showed that 40–80% of the activity occurred between the base of the euphotic zone and 150 m depth. Our findings contribute to a better understanding of the metabolic activity of the microbial communities in two regions of the GOM influenced by mesoscale eddies.</p>
Dataset for manuscript entitled: Switchgrass cropping systems affect soil carbon and nitrogen and microbial diversity and activity on marginal lands
<p class="MsoListParagraph">Switchgrass (<em>Panicum virgatum</em> L.),<span> </span>as a dedicated bioenergy crop, can provide cellulosic feedstock for biofuel production while improving or maintaining soil quality. However, comprehensive evaluations of how switchgrass cultivation and nitrogen (N) management impact soil and plant parameters remain incomplete. We conducted<span> </span>field trials in three years (2016–2018) at six locations in the North Central Great Lakes Region to evaluate the effects of cropping systems (switchgrass, restored prairie, undisturbed control) and N rates (0, 56 kg N ha<sup>-1</sup> yr<sup>-1</sup>) on biomass yield and soil physicochemical, microbial, and enzymatic parameters. Switchgrass cropping system yielded an aboveground biomass 2.9–3.3 times higher than the other two systems (Jayawardena et al., In submission) but our study found that this biomass accumulation didn't reduce soil dissolved organic C (DOC), total dissolved N (TDN), or bacterial diversity. The annual aboveground biomass removal for bioenergy feedstock, however, reduced soil microbial biomass C (MBC) and N (MBN) and bacterial richness in the 2<sup>nd</sup> and 3<sup>rd</sup> years; despite this, continuous monocropping of switchgrass improved soil TDN, inorganic N, bacterial diversity, and shoot biomass in the 2<sup>nd</sup> and/or 3<sup>rd</sup> years when compared to the 1<sup>st</sup> year. N fertilization increased aboveground biomass yield by 1.2 times and significantly increased soil TDN, MBN, and the shoot biomass of switchgrass when compared to the unfertilized control. Locations with higher C and N contents and lower C:N ratio had higher aboveground biomass, MBC, MBN, and the activity of BG, CBH, and UREA enzymes; by contrast, locations with higher pH had higher soil TDN and activity of NAG and LAP enzymes. Our research demonstrates that switchgrass cultivation could improve or maintain soil N content and N fertilization can increase plant biomass yield. The comprehensive data also can inform future biogeochemical models to successfully implement switchgrass for bioenergy production.</p>
Dataset from Microbial bile salt hydrolase activity influences gene expression profiles and gastrointestinal maturation in infant mice
<p>Files from Intestinal Alkaline Phosphatase, Ki-67, and apoptosis (TUNEL) from colon samples. RT-qPCR dCT values of genes analyzed in colon, small intestine, liver and colon organoids</p>
Data and metadata of soil microbial community structure, enzyme activities, functional genes and earthworms derived from H2020 Diverfarming project
<p>Soil data and metadata of soil microbial community structure, enzyme activities (dehydrogenase, β-glucosidase, leucine-aminopeptidase, alkaline phosphatase and arylsusfatase activities), N functional genes and earthworms from the different cases studies and long terms from WP4 "Impact of crop diversification on biodiversity", derived from H2020 Diverfarming project. The main objective of workpackage is to provide a scientific understanding of the link between diversified cropping systems, above- and belowground biodiversity, and the resulting ecosystem services provided by soil microorganisms, soil invertebrates and vegetation in agro-ecosystems. Soil organisms contribute to all biogeochemical cycles, Soil organic matter mineralization and stabilization, shape soil structure and have associations with plant species promoting growth and development. http://www.diverfarming.eu.</p>
Biochar and nitrogen fertilizer promote rice yield by altering soil enzyme activity and microbial community structure
<p><span>Biochar can significantly change soil properties and improve soil quality.</span> <span>However, the effects of long-term combined application of biochar (B) and nitrogen (N) fertilizer on relationships between soil enzyme activity, microbial community structure and crop yield are still obscure. We characterized these relationships in a long-term (8 years) field experiment with rice, two biochar rates of 0 and 13.5 t ha<sup>-1</sup> year<sup>-1</sup> (B0 and B) and two N fertilizer rates of 0 and 300 kg N ha<sup>-1</sup> year<sup>-1</sup> (N0 and N).</span><span> The repeated, long-term combined applications of biochar and N fertilizer significantly increased microbial biomass carbon and nitrogen (MBC and MBN), but biochar decreased the abundance of total bacteria, fungi, actinomycetes, Gram-positive and Gram-negative bacteria as well as the amount of total phospholipid fatty acids. </span><span>The activity of leucine aminopeptidase (LAP) </span><span>decreased significantly in the biochar-amended and N fertilized treatment, but</span><span> the LAP activity either remained unchanged or increased with biochar amendment at N0. The relative abundance of bacterial phylum <em>Chloroflexi</em> was increased in the combined biochar and N fertilizer treatment. The changes in soil organic matter and the activity of α-1,4-xylosidase were the major properties influencing soil bacterial community composition, whereas the structure of fungal community was governed by MBC, MBN and LAP activity. In addition, long-term biochar and N fertilizer applied together significantly increased rice yield (more than biochar and nitrogen fertilizer applied alone). Yield</span> <span>was significantly positively correlated with LAP activity, but significantly negatively correlated with the relative abundance of Chloroflexi. In conclusion, long-term biochar and nitrogen fertilizer applications increased rice yield, which was associated with altered soil microbial community and enhanced activity of some enzymes.</span></p>
Data for Marshall et al, "Microbial metabolism disrupts cytokine activity to impact host immune response"
<p>Raw data for publication "Microbial metabolism disrupts cytokine activity to impact host immune response", Marshall EKP et al. The archive is organized into folders containing raw data pertaining to each figure.</p>
Imprint of tree species mycorrhizal association on microbial-mediated enzyme activity and stoichiometry
<p>1. Understanding the effects of tree species and their mycorrhizal association on soil processes is critical for predicting the ecosystem consequences of species shifts owing to global change and forest management decisions. While it is well established that forests dominated by different mycorrhizal types can vary in how they cycle carbon (C), nitrogen (N) and phosphorus (P), the degree to which these patterns are driven by microbial-mediated enzyme activity (EA) and ecoenzymatic stoichiometry (ES) remain elusive.</p> <p>2. Here, we synthesized the effects of mycorrhizal association on seven soil enzymes involved in microbial C, N and P acquisition and ES using data from 56 peer-reviewed papers.</p> <p>3. We found that relative to soil in ectomycorrhizal (EcM) trees, soil in arbuscular mycorrhizal (AM) trees exhibited greater activity of some C acquisition enzymes (e.g., beta-glucosidase; BG) and higher ecoenzymatic ratios of BG/NAG (N-acetyl-glucosaminidase) and BG/AP (acid phosphatase). These results supported that AM trees had rapid C and nutrient turnover rates, inorganic nutrient economics and high soil microbial C limitation. We also found evidence for an organic nutrient economy and greater soil microbial demand for nutrients in EcM trees compared to AM trees. In addition, the effect of mycorrhizal association on the activity of certain soil enzymes and enzymatic stoichiometry (i.e., BG and BG/NAG ratio) appeared to be associated with the differences in soil pH, phylogenetic group (i.e., conifers and broadleaves) and leaf habit (i.e., evergreen and deciduous) between AM and EcM trees.</p> <p>4. The results from the global meta-analysis suggested that soil EA and ES appear to play critical roles in shaping the differences in the nutrient economy between AM and EcM tree species, but leaf morphology and soil conditions should be considered in evaluations of soil processes in forests of different mycorrhizal associations. Given that most of the studies in the database were from the temperate and subtropical regions, further research in other biomes is needed to elucidate the underlying mechanisms driving the mycorrhizal effect at the global scale. </p>
Data from: Microbial activity contributes to spatial heterogeneity of wetland methane fluxes
<p>The emission of methane from wetlands is spatially heterogeneous, as concurrently measured surface fluxes can vary by orders of magnitude within the span of a few meters. Despite extensive study and the climatic significance of these greenhouse gas emissions, it remains unclear what drives these large within-site variations, creating a knowledge-gap that impedes a mechanistic understanding of wetland fluxes. While geophysical variables including water table depth (WTD) and soil temperature are known to correlate with CH<sub>4</sub> flux, measurable variance in these parameters declines as spatial and temporal scales become finer. Here, we leveraged depth-stratified gene abundance and gene expression measurements of methanogenesis and methanotrophy to investigate CH<sub>4</sub> flux variance at an ombrotrophic peat bog. Our results show that the flux variance was strongly correlated to methanogen abundance and that peat depth also exerted significant control over CH<sub>4</sub> flux, methanogen abundance, and the relationship between the two. Correlations between CH<sub>4</sub> flux and either WTD or soil temperature were absent or minimal. These findings suggest that microbial factors likely underlie localized variance in wetland CH<sub>4</sub> flux, and that a greater reliance on biological predictors could improve our ability to understand wetland methane fluxes at finer scales than is currently possible.</p>
Rifaximin as a Modulator of Microbial Translocation and Immune Activation
ClinicalTrials.gov study NCT01466595. IPD Sharing: Not stated. Countries: 2. Publications: 1.
Dataset for manuscript entitled: Switchgrass cropping systems affect soil carbon and nitrogen and microbial diversity and activity on marginal lands
Open the record for dataset details and reuse information.
Data from: Microbial metabolic activity in two basins of the Gulf of Mexico influenced by mesoscale structures
Open the record for dataset details and reuse information.
Plant invasions alter soil biota and microbial activities: A global meta-analysis
Open the record for dataset details and reuse information.
Data from: Microbial activity contributes to spatial heterogeneity of wetland methane fluxes
Open the record for dataset details and reuse information.
Data from: Plant biodiversity responds more strongly to climate warming and anthropogenic activities than microbial biodiversity in the Qinghai-Tibetan alpine grasslands
Open the record for dataset details and reuse information.
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.