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105 results for “microbial activity”
Temperature Sensitivity of Microbial Activity in Three Forest Soils at Harvard Forest 2010-2011
We evaluated possible seasonal variation in the temperature sensitivity of microbially mediated soil fluxes related to decomposition (net N mineralization, net nitrification, proteolysis, the maximum velocity (Vmax) of proteolysis, microbial respiration, and the Vmax of four soil exo-enzymes) across forests dominated by eastern hemlock (Tsuga canadensis), white ash (Fraxinus americana), and red oak (Quercus rubra) in Harvard Forest. We asked two simple questions: (1) do temperature sensitivities vary across forest types or different steps of the decomposition process, and (2) do temperature sensitivities display plasticity on a seasonal time frame?We observed substantial variation in temperature sensitivities (Q10 and R10 values) across the different fluxes and forest types. The ash soils exhibited the strongest temperature sensitivities and the mineral-N fluxes exhibited higher temperature sensitivities relative to the proteolytic fluxes or microbial respiration. The Vmax of soil exo-enzymes varied considerably in an interactive manner across forests and time, and the response of some enzymes was consistent with the thermal plasticity. The enzymatic kinetic properties Vmax and Km (half-saturation constant) were strongly correlated with slopes that differed across enzymes, reflecting an enzyme-specific tradeoff between maximum catalytic rate and substrate-binding efficiency. Generally, Q10 values were largely constant, but R10 values varied in a manner consistent with distinct seasonal plasticity. There was a consistent seasonal shift in R10 values coincident with snowmelt, suggesting that the time following snowmelt is a particularly interesting and dynamic period of microbial activity in these temperate forests.
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.
Effects of Warming on Soil Microbial Oxidative Activity at Harvard Forest 2013
As Earth’s climate warms, the massive stores of carbon found in soil are predicted to become depleted, and leave behind a smaller carbon pool that is less accessible to microbes. At a long-term forest soil-warming experiment in central Massachusetts, soil respiration and bacterial diversity have increased, while fungal biomass and microbially-accessible soil carbon have decreased. Here, we evaluate how warming has affected the microbial community’s capability to degrade chemically-complex soil carbon using lignin-amended BioSep beads. We profiled the bacterial and fungal communities using PCR-based methods and completed extracellular enzyme assays as a proxy for potential community function. We found that lignin-amended beads selected for a distinct community containing bacterial taxa closely related to known lignin degraders, as well as members of many genera not previously noted as capable of degrading lignin. Warming tended to drive bacterial community structure more strongly in the lignin beads, while the effect on the fungal community was limited to unamended beads. Of those bacterial operational taxonomic units (OTUs) enriched by the warming treatment, many were enriched uniquely on lignin-amended beads. These taxa may be contributing to enhanced soil respiration under warming despite reduced readily available C availability. In aggregate, these results suggest that there is genetic potential for chemically complex soil carbon degradation that may lead to extended elevated soil respiration with long-term warming.
North Temperate Lakes LTER: Summary of Microbial Activity 2000 - 2002
Summary of Microbial Observatory data from the bacterial production, planktonic respiration and alakline phosphatase activity databases, plus bacterial cell counts from epifluorescence microscopy using DAPI cell stain. Information on integrated sample depth and incubation temperature is also included Sampling Frequency: fortnightly during ice-free season - every 6 weeks during ice-covered season Number of sites: 4
Hubbard Brook Nitrogen Oligotrophication (HBNO): Microbial Biomass and Activity, 2021-2023
The goal of this project is to test the overarching hypothesis that positive feedback mechanisms involving changes in seasonal cycles that diminish N availability to plants such that plant N demand is not met by soil N availability in northern forests. Specifically, we hypothesize that increasing N demand by plants (induced by increasing temperatures, longer growing seasons, and other environmental changes) leads to greater N resorption by trees in autumn, increased C:N in litter, and greater net immobilization of N by soil microbes in the following spring. However, the timing of snowmelt and soil freezing in spring may further affect net mineralization and N availability for plants. These hypotheses are being tested with a combination of observational, experimental, and modeling approaches at Hubbard Brook Experimental Forest in New Hampshire: 1) measurements at 14 previously established sites along an elevation/aspect climate gradient; 2) litter and snow manipulation experiments at six sites along the climate gradient to create variation in soil climate conditions and microbial N immobilization during spring. We leveraged 14 sites previously established along an elevation and aspect-driven climate gradient at Hubbard Brook as a “natural climate experiment" to test our hypothesis that a positive feedback between N cycling during fall senescence and spring contributes to declining N availability in northern forests. This elevation gradient encompasses variation in mean annual air temperature of ~2.5 °C that is similar to the change projected to occur with climate change over the next 50–100 years in the northeastern U.S. There is relatively little variation in soils along the gradient. We are utilizing three sites at higher elevation (~550-660 m, north facing) and three sites at lower elevation (~375-500 m, south facing) for the litter and snow manipulation experiments to maximize the differences in temperature among the 14 sites. Litterbox manipulation: The objecti
Using the Tea Bag Index to unravel how interactions between an antibiotic (Trimethoprim) and endocrine disruptor (17a-estradiol) affect aquatic microbial activity: Supporting Dataset 1
<p>The constant release of complex mixture of pharmaceuticals, including antimicrobials and endocrine disruptors, into the aquatic environment. These have the potential to affect aquatic microbial metabolism and alter biogeochemical cycling of carbon and nutrients. We used the Tea Bag Index (TBI) for decomposition within a series of contaminant exposure experiments to test how interactions between an antibiotic (trimethoprim) and endocrine disruptor (17a-estradiol) affects microbial activity in an aquatic system. The TBI is a citizen science tool used to test microbial activity by measuring the differential degradation of green and rooibos tea as proxies for labile and recalcitrant organic matter decomposition. Here we present the raw data on pharmaceutical exposures and the mass loss of the Rooibos and Green tea bags within the experiment. From Tea Bag mass loss we then calculated the Stabilisation Factor (S) and Initial Decomposition Rate of the labile organic matter fraction.</p>
Long-term measurements of microbial biomass and activity at the Hubbard Brook Experimental Forest 1994 – ongoing
Long-term monitoring of soil nitrate (NO3-) and ammonium (NH4+) concentrations, microbial biomass carbon (C) and nitrogen (N) content, microbial respiration, potential nitrification and N mineralization rates, pH, and denitrification potential has been ongoing at the Hubbard Brook Experimental Forest since 1994. Samples have been collected in the Bear Brook Watershed (west of Watershed 6) beginning in 1994. In 1998, our sampling regime was extended to Watershed 1 in an effort to monitor and quantify microbial response to a whole-watershed calcium addition. 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.
Supplementary data to "Changing microbial activities during low salinity acclimation in the brown alga Ectocarpus subulatus"
<p>This data set contains supplementary data related to the paper: “Insights into the potential for mutualistic and harmful host–microbe interactions affecting brown alga freshwater acclimation”: https://onlinelibrary.wiley.com/doi/10.1111/mec.16766</p> <p>Metagenome.zip:<br>This archive contains the reconstructed genomes of the different bacterial bins. The ".gbk" file was used for the reconstruction of metabolic networks. The ".fsa" and ".gff" files were used for "read mapping".</p> <p>Metabolic_networks.zip:<br>This archive contains all bacterial networks in the "padmet" format (see Aite et al. 2018). Furthermore, there is one file containing all gene-reaction associations (for all bins).</p> <p>Expression_data.zip:<br>This file contains algal gene expression data, bacterial gene expression data (number of reads mapping to each feature in each sample), and, lastly, the summarized bacterial expression per metabolic reaction. </p>
Extracellular polymeric substances are closely related to land cover, microbial communities, and enzyme activity in tropical soils
<p>These are datasets and R codes linked to the paper: Extracellular polymeric substances are closely related to land cover, microbial communities, and enzyme activity in tropical soils. </p>
Soil redox potential vs. soil microbial activity and structure
<p>The dataset was collected as a part of the Carbon Action field experiment in 2021. The experiment had 100 farms testing carbon farming practices 2019-2023. These samples were from a subset of 20 farms, which were routinely sampled every year.</p> <p>I measured the following parameters</p> <ul> <li>redox potential Eh, with an ORP meter + electrode reference voltage at 50% pore filled moisture</li> <li> pH in distilled water 10:1 water:soil mixture</li> <li>VESS soil structure on the field</li> <li>CO2burst by rewetting dried soil and measuring how much CO2 was respired in 24 hours</li> </ul> <p>pH and Eh were used to calculate a rH2 hydrogen potential, which combines Eh and pH</p> <p>Background information for clay and organic matter content was determined separately</p> <p>the clay content was defined by sieving and the organic matter content by loss of ignition.</p> <p>The analysis of the results is published in Plant and Soil journal in 2023. </p> <p>Mattila, T.J., 2023. Redox potential as a soil health indicator - how does it compare to microbial activity and soil structure?</p> <p><a href="https://doi.org/10.1007/s11104-023-06305-y">https://doi.org/10.1007/s11104-023-06305-y</a></p>
Hubbard Brook Experimental Forest: microbial biomass and activity at Climate Change Across Seasons Experiment (CCASE) plots, 2015
This data set includes measurements of microbial biomass and activity measured on the Climate Change Across Seasons Experiment (CCASE) plots in May 2015. Reference (or control) plots are shared with the collaborating Northern Forest DroughtNet experiment. There are six plots total (each 11 x 14m). Two are warmed 5 degrees C throughout the growing season (Plots 3 and 4). Two others are warmed 5 degrees C in the growing season and have snow removed during winter to induce soil freeze/thaw cycles (Plots 5 and 6). Four kilometers (2.5 mi) of heating cable are buried in the soil to warm these four plots. Two additional plots serve as controls for our experiment (Plots 1 and 2). This data set includes measurements of microbial biomass and activity. 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.
Hubbard Brook Experimental Forest: microbial biomass and activity at climate gradient plots, 2010-2012
In October 2010, as part of a study of the relationships between snow depth, soil freezing and nutrient cycling (http://www.ecostudies.org/people_sci_groffman_snow_summary.html), we established 6 20 x 20 m plots (intensive plots) and 14 10 x 10-m plots (extensive plots) following an elevation gradient, with eight of the plots facing north and twelve facing south. Seasonal (spring, summer autumn) measurements of soil nitrate (NO3-) and ammonium (NH4+) concentrations, microbial biomass carbon (C) and nitrogen (N) content, microbial respiration, potential nitrification and N mineralization rates, and denitrification potential occurred from 2010 – 2012. 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.
Measurements of microbial biomass and activity in two snow manipulation experiments at Hubbard Brook Experimental Forest 1998 – 2004
In 1997, as part of a study of the relationships between snow depth, soil freezing and nutrient cycling (http://www.ecostudies.org/people_sci_groffman_snow_summary.html), we established eight 10 x 10-m plots located within four stands; two dominated (80%) by sugar maple and two dominated by yellow birch, with one snow reduction (freeze) and one reference plot in each stand. In 2001, we established eight new 10-m x 10-m plots (4 treatment, 4 reference) in four new sites; two high elevation, north facing and two low elevation, south facing maple-beech-birch stands. To establish plots for the “freeze” study, we cleared minor amounts of understory vegetation from all (both freeze and reference) plots (to facilitate shoveling). We then installed soil solution samplers (zero tension lysimeters), thermistors for soil temperature monitoring, water content (time domain) reflectometers (for measuring soil moisture), soil atmosphere sampling probes, minirhizotron access tubes, and trace gas flux measurement chambers (described below). All plots were equipped with dataloggers to allow for continuous monitoring of soil moisture and temperature. Treatments (keep plots snow free by shoveling through the end of January) were applied in the winters of 1997/98, 1998/99, 2002/2003 and 2003/2004. Measurements of soil nitrate (NO3 -) and ammonium (NH4 +) concentrations, microbial biomass carbon (C) and nitrogen (N) content, microbial respiration, potential nitrification and N mineralization rates, pH, and denitrification potential were measured on these plots at multiple time points during these studies. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES) using funding from the U.S. National Science Foundation. 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.
Hubbard Brook Experimental Forest: Soil Acid-Base Properties and Microbial Activity, Watershed 1 and West of Watershed 6 (2015-2016)
In summer 2015 and spring 2016, researchers collected soils from the CaSiO3-enriched watershed at Hubbard Brook (W1) and from a nearby site west of the reference watershed at Hubbard Brook (W6). These soils were sampled throughout the hardwood zone of each watershed, and the sampling scheme explicitly examined pit-and-mound microtopographic gradients. These soils were analyzed for acid-base properties, net and gross N cycling rates, microbial biomass, and C cycling rates. 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 US Forest Service, Northern Research Station.
In vitro antibacterial activity of microbial natural products against bacterial pathogens of veterinary and zoonotic relevance
<p>Supplemental material to the publication "<i>In vitro</i> antibacterial activity of microbial natural products against bacterial pathogens of veterinary and zoonotic relevance"</p>
Data from: Strong links between plant traits and microbial activities but different abiotic drivers in mountain grasslands
<p>This dataset contains data and code that support the results in Weil, S.-S., Martinez-Almoyna, C., Piton, G., Renaud, J., Boulangeat, L., Foulquier, A., ... & Thuiller, W. (2021) Strong links between plant traits and microbial activities but different abiotic drivers in mountain grasslands (accepted in Journal of Biogeography).</p> <p>We used an extensive plant-soil dataset that covers 14 elevational gradients (between 1500 and 2800 m of elevation) distributed over the whole French Alps to analyse the spatial co-dependencies between the plant and soil compartments. We ran a Graphical Lasso that extracts the direct and indirect linkages between plant functional composition, soil microbial activities, and environmental conditions (local climate and soil properties).</p> <p>Our main results are 1) that plant traits are tightly associated with microbial activities, the former being driven by climate and the latter by soil properties; 2) that the dominance of specific plant traits was more important than their diversity to determine plant-soil linkages; and 3) that soil microbes invested strongly in nutrient acquisition in sites with conservative plant traits and reduced organic matter quality.</p>
Data collected for: The contrasted impacts of grasshoppers on soil microbial activities in function of ecosystem productivity and herbivore diet
<p>Herbivory can have contrasted impacts on soil microbes and nutrient cycling, which has stimulated the development of conceptual frameworks exploring the links between below- and aboveground processes. The "productivity model" predicts that herbivores stimulate microbial activities and accelerate nutrient mineralization in productive ecosystems, while they have an opposite effect in less productive ecosystems. In parallel, the "diet model" predicts that herbivores feeding on conservative plants accelerate nutrient cycling while those feeding on exploitative plants decelerate nutrient cycling, due to changes in litter inputs. Since these two frameworks can lead to conflicting predictions in some cases, experimental evidence combining herbivore diet and productivity is required.</p> <p>During two consecutive years, we conducted an experiment controlling the presence of three grasshopper species consuming either grasses, forbs or both in twelve natural and managed alpine grasslands of contrasted productivities. In order to assess the effects of herbivory on soil microbes, we measured their enzymatic activities, their biomass and the soil potential nitrogen mineralization (PNM). Soil and vegetation characteristics were also determined in order to test if they modulated the effects of herbivory on microbes.</p> <p>Contrary to the predictions of the diet model, the effects of herbivory on microbial characteristics did not depend on the herbivores diet but relied on ecosystem productivity. The most productive sites were characterized by exploitative plant species which depleted N resources in the soil, and by microbes producing relatively few extracellular enzymes, leading to a lower PNM. Herbivory increased microbial biomass and decreased the production of extracellular enzymes in those sites, possibly through the stimulation of root exudates produced by exploitative species. The least productive sites were characterized by conservative plants, which led to the sequestration of soil C, and by microbes having a resource acquisition strategy (more extracellular enzymes, higher PNM). Herbivory decreased microbial biomass and increased the production of extracellular enzymes in those sites. This pattern can be explained by the loss of carbon associated with insect respiration, which increases the need for microbes to acquire resources and by a lower production of root exudates by conservative species. Therefore, the effects of two years of herbivory on soil microbes were at odds with the productivity model, which focuses instead on longer term effects corresponding to herbivory-induced changes in plant species composition. This highlights the multidimensional feature of the impacts of herbivory on ecosystem functioning, both in space and time.</p>
Electronic appendix to: Spectral Induced Polarization (SIP) of Denitrification-Driven Microbial Activity in Column Experiments Packed with Calcareous Aquifer Sediments
<p>This is the electronic appendix of the publication <br> C. Strobel, S. Abramov, J. A. Huisman, O.A. Cirpka, A. Mellage (2022): Spectral Induced Polarization (SIP) of Denitrification-Driven Microbial Activity in Column Experiments Packed with Calcareous Aquifer Sediments (submitted)</p>
A Hard Day's Night: Diel shifts in microbial eukaryotic activity in the North Pacific Subtropical Gyre
<p><strong>A Hard Day’s Night: Diel shifts in microbial eukaryotic activity in the North Pacific Subtropical Gyre </strong>(<em>submitted</em>)</p> <p><strong>Authors: </strong>Sarah K. Hu<sup>1</sup>*, Paige E. Connell<sup>1</sup>, Lisa Y. Mesrop<sup>1</sup>, & David A. Caron<sup>1</sup></p> <p><sup>1</sup>University of Southern California, Biological Sciences, Los Angeles, CA, USA</p> <p> </p> <p><strong>Abstract</strong></p> <p>Molecular analysis revealed diel rhythmicity in the metabolic activity of single-celled microbial eukaryotes (protists) at station ALOHA in the North Pacific Subtropical Gyre. Diel trends among different protistan taxonomic groups reflected distinct nutritional capabilities and temporal niche partitioning. Changes in relative metabolic activities among phototrophs corresponded to the light cycle, generally peaking in mid- to late-afternoon. Metabolic activities of protistan taxa with phagotrophic ability were higher at night, relative to daytime, potentially in response to increased availability of picocyanobacterial prey. Tightly correlated Operational Taxonomic Units throughout the diel cycle implicated the existence of parasitic and mutualistic relationships within the microbial eukaryotic community, underscoring the need to define and include these symbiotic interactions in marine food web descriptions. This study provided a new high-resolution view into the ecologically important interactions among primary producers and consumers that mediate the transfer of carbon to higher trophic levels. Characterizations of the temporal dynamics of protistan activities contribute knowledge for predicting how these microorganisms respond to environmental forcing factors.</p> <p> </p> <p><a href="https://github.com/shu251/18Sdiversity_diel">See github for additional information on data analysis.</a></p>
Energetic return on investment determines overall soil microbial activity.
<p><strong>Data</strong> and <strong>R codes</strong> used for the manuscript entitled " <strong>Energetic return on investment determines overall soil microbial activity."</strong></p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.