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74 results for “microbial biomass”
Macrophyte and microbial mat biomass co-variation along a hydrologic gradient and response to a removal experiment in temporary wetlands Everglades, FL, USA, February 2003 – November 2006
This data package encompasses hydrologic variables, soil depth, hydrologically-regulated macrophyte community types, macrophyte biomass and community structure, and microbial mat biomass that was collected in two observational surveys and one in-situ experimental manipulation in six temporary wetland regions located in the Everglades, FL, USA. The goal of this project was to examine the co-variation in macrophyte and microbial mat biomass along the hydrologic gradient present across wetland regions and to determine the type and strength of interactions occurring between the two communities, which was tested using a biomass (macrophyte or microbial mat) removal experiment. The census observational survey took place at 140 sites from 2003-04-09 to 2004-05-26, which were randomly distributed across the hydrologic gradient present across the six temporary wetland regions. The transect observational survey occurred along six transects and each was deliberately established along the present hydrologic gradient within each region; a total of 254 sites were sampled from 2003-02-19 to 2005-03-04. The experiment took place at three temporary wetland sites with contrasting hydroperiods (3 – 6 months), and four transects were established per site with 24 pairs of control and treatment plots per transect. The removal treatment occurred one year before data collection, and data collection occurred from 2004-06-20 to 2006-11-25. The package includes six datasets, one R code file, and two shape files associated with the R code. Data collection for all datasets is complete. FCE1274_Census_Survey includes hydrologically-regulated macrophyte community type classifications, macrophyte biomass, microbial mat ash-free dry mass, mean soil depth, water depth, mean annual hydroperiod, and vegetation-inferred hydroperiod; each site was sampled once during the survey period and a subset of sites were sampled each year. FCE1274_Transect_Survey includes macrophyte community type classifications
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
Microbial biomass and water-extractable carbon on Mt. Kilimanjaro
<p>This dataset presents the value of microbial biomass carbon (MBC) and water-extractable carbon (WOC) at study plots under KiLi project.</p> <p>Microbial biomass carbon (MBC) and water-extractable organic carbon (WOC) – as sensitive and important parameters for soil fertility and C turnover – are strongly affected by land-use changes all over the world. These effects are particularly distinct upon conversion of natural to agricultural ecosystems due to very fast carbon (C) and nutrient cycles and high vulnerability, especially in the tropics. The objective of this study was to use the unique advantage of Mt. Kilimanjaro – altitudinal gradient leading to different tropical ecosystems but developed all on the same soil parent material – to investigate the effects of land-use change and elevation on MBC and WOC contents during a transition phase from dry to wet season. Down to a soil depth of 50 cm, we compared MBC and WOC contents of 2 natural (<em>Ocotea</em> and <em>Podocarpus</em> forest), 3 seminatural (lower montane forest, grassland, savannah), 1 sustainably used (homegarden) and 2 intensively used (maize field, coffee plantation) ecosystems on an elevation gradient from 950 to 2850 m a.s.l.</p> <p>The KiLi project (2010-2018) is a German Science Foundation (DFG) funded research unit (DFG research unit FOR1246) that focuses on biodiversity and ecosystem processes along altitudinal and disturbance gradients on Mt. Kilimanjaro (Tanzania, Africa), capitalizing on its world-wide unique range of climatic and vegetation zones. The research unit comprises 2 central projects and 7 subprojects from various disciplines. On a total of 60 study sites in both natural and human-disturbed ecosystems biodiversity (e.g. plants, soil arthropods, ants, bees, frogs, lizards, bats, birds), related ecosystem processes (decomposition, seed dispersal, pollination, herbivory, predation), and biogeochemical processes and properties of ecosystems (climate, soil properties and nutrient status, regulation of water and carbon fluxes, trace gas emissions, primary productivity, functional diversity) are analyzed.</p>
Effects of Nitrogen Fertilization on Litter and Soil Decomposition: Microbial Biomass
The influence of inorganic nitrogen (N) inputs on decomposition is poorly understood. Some prior studies suggest that N may reduce the decomposition of substrates with high concentrations of lignin via inhibitory effects on the activity of lignin-degrading enzymes, although such inhibition has not always been demonstrated. The purpose of E145 was to study the effects of nitrogen (N) addition on decomposition of seven substrates ranging in initial lignin concentrations (from 7.4 - 25.6%) over five years in eight different grassland and forest sites in central Minnesota.
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.
OMB01 Microbial biomass in the Belowground Plot Experiment at Konza Prairie (1989-1999)
The purpose of this data set is to monitor long-term changes in microbial biomass on the belowground plots due to the effect on annual burning, mowing and nitrogen and phosphorus fertilization.
MRCE/LTER Soil and Microbial Biomass Nitrogen
The data reported here are only for tabonuco forest at El Verde. Following plot setup and one year of pre-treatment measurements, Hurricane Hugo struck before the first planned fertilization. Because a year and a half of annual above ground litter inputs of phosphorus were dropped onto the forest floor in the form of leaf litter, we added a debris removal treatment to the original two, fertilized and control.These data were used to determine the pools of readily available nitrogen in soil solution in debris removal and fertilizer treatments applied to tabonuco forest at El Verde immediately after Hurricane Hugo struck in September 1989. The treatments (complete removal of litter and woody debris, total fertilization, and control). Both ammonium and nitrate were low in the May 1990 samples. All samples had more KCl extractable ammonium in September, but negligible nitrate. Increases in ammonium were greatest in the fertilized and debris removal plots as compared to the control treatment. These results were positively correlated with litterfall production and canopy closure, with faster rates of recovery in the fertilized and debris removal treatments as compared to the control. Soil extractable (readily available) N was negatively correlated with microbial N in the samples collected one year after Hurricane Hugo, indicating microbial immobilization of N. Century modeling results were consistent with our observations and indicated that woody debris increased the input of low-nutrient substrate to the soil thereby stimulating microbial uptake/immobilization. Thus the soil microbes in the control plots outcompeted the trees for limiting N, thereby slowing their recovery. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Add
Deschampsia biomass, soil microbes and endophyte root colonization for snowmelt and microbial innoculation transplant experiment in the Green Lakes Valley, 2015-2018
As organisms shift their geographic distributions in response to climate change, biotic interactions have emerged as an important factor driving the rate and success of range expansions. Plant-microbe interactions are an understudied but potentially important factor governing plant range shifts. We studied the distribution and function of microbes present in high-elevation unvegetated soils, areas that plants are colonizing as climate warms, snow melts earlier and the summer growing season lengthens. Using a manipulative snowpack and microbial inoculation transplant experiment, we tested the hypothesis that growing season length and microbial community composition interact to control plant elevational range shifts. We predicted that a lengthening growing season combined with dispersal to patches of soils with more mutualistic microbes and fewer pathogenic microbes would facilitate plant survival and growth in previously unvegetated areas. We identified negative effects on survival of the common alpine bunchgrass Deschampsia cespitosa in both short and long growing seasons, suggesting an optimal growing season length for plant survival in this system that balances time for growth with soil moisture levels. Importantly, growing season length and microbes interacted to affect plant survival and growth, such that microbial community composition increased in importance in suboptimal growing season lengths. Further, plants grown with microbes from unvegetated soils grew as well or better than plants grown with microbes from vegetated soils. These results suggest that the rate and spatial extent of plant colonization of unvegetated soils in mountainous areas experiencing climate change could depend on both growing season length and soil microbial community composition, with microbes potentially playing more important roles as growing seasons lengthen.
VDMBC_vertical_distribution_soil_microbial_biomass_carbon
<p>Soil microbial biomass carbon (SMBC) is important in regulating soil organic carbon (SOC) dynamics along soil profiles by mediating the decomposition and formation of SOC. The dataset (VDMBC) is about the vertical distributions of SOC, SMBC, and soil microbial quotient (SMQ = SMBC/SOC) and their relations to environmental factors across five continents. Data were collected from literature, with a total of 289 soil profiles and 1040 observations in different soil layers compiled. The associated environment data collectd include climate, ecosystem types, and edaphic factors. We developed this dataset by searching the the Web of Sciene and the China National Knowledge Infrastructure from the year of 1970 to 2019. All the data in this dataset met two creteria: 1) there were at least three mineral soil layers along a soil profile, and 2) SMBC was measured using the fumigation extraction method. The data in tables and texts were obtained from literature directly, and the data in figures were extracted by using the GetData Graph digitizer software version 2.25. When climate and soil properties were not available from publications, we obtainted the data from the World Weather Information Service (https://worldweather.wmo.int/en/home.html) and SoilGrids at a spatial resolution of 250 meters (version 0.5.3, https://soilgrids.org).</p> <p>The units of all the variables were converted to the standard international units or commonly used ones and the values were converted correspondingly. For example, the value of soil organic matter (SOM) was converted to SOC using the equation (SOC = SOM × 0.58). Soil depth was calculated as the arithmetic mean value of the upper and lower boundaries for a given soil layer.</p> <p>This dataset can be used in predicting global SOC change along soil profiles using the multi-layer soil carbon models. It can also be used to analyse how soil microbial biomass changes with plant roots as well as the composition, structure, and functions of soil microbial communities along soil profiles at large spatial scales. This dataset offers opportunities to improve our prediction of SOC dynamics under global changes and to advance our understanding of the environmental controls.</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.
Algal microbial mat biomass measurements from the McMurdo Dry Valleys and Cape Royds, Antarctica (1994-2025, ongoing)
As part of the Long Term Ecological Research (LTER) project in the McMurdo Dry Valleys of Antarctica, a systematic sampling program has been undertaken to monitor the glacial meltwater streams in that region. This dataset contains microbial biomass concentrations found in algal mats located in streams throughout the McMurdo Dry Valleys as well as in ponds of the nearby Cape Royds. Microbial mat biomass has been collected as part of the McMurdo LTER since the 1993-1994 field season and measured as ash-free dry mass (AFDM) and chlorophyll-a (Chl-a).
Biomass, stoichiometry, and isotopic signatures of stream microbial mats, McMurdo Dry Valleys, Antarctica (2012-2013)
We conducted a field survey to quantify the biomass (chlorophyll-a and ash-free dry mass), nutrient ratios (molar C:N:P), and isotopic signatures (δ13C and δ15N) of four microbial mat types (green, orange, black, and red) in the glacial meltwater streams of the McMurdo Dry Valleys, Antarctica. All samples were taken from late December to late January during the 2011-2012 and 2012-2013 austral summers, and included sites from Taylor, Miers, Garwood, and Wright valleys. Most collection sites were located at the lake outlet of streams, but for a subset (e.g. Delta, Von Guerard, Onyx, Miers, and Canada) more than one sample site is included per stream system.
Squeegee: de novo identification of reagent and laboratory induced microbial contaminants in low biomass microbiomes, simulation dataset 0.25% spike-in contaminant sequences
<p>Computational analysis of host-associated microbiomes has opened the door to numerous discoveries relevant to human health and disease. However, contaminant sequences in metagenomic samples can potentially impact the interpretation of findings reported in microbiome studies, especially in low biomass environments. Our hypothesis is that contamination from DNA extraction kits or sampling lab environments will leave taxonomic "bread crumbs” across multiple distinct sample types, allowing for the detection of microbial contaminants when negative controls are unavailable. To test this hypothesis we implemented Squeegee, a de novo contamination detection tool. We tested Squeegee on simulated and real low biomass metagenomic datasets. On the low biomass samples, we compared Squeegee predictions to experimental negative control data and show that Squeegee accurately recovers known contaminants. We also analyzed 749 metagenomic datasets from the Human Microbiome Project and identified likely previously unreported kit contamination. Collectively, our results highlight that Squeegee can identify microbial contaminants with high precision.</p> <p> </p> <p>Simulation Dataset 0.25% contaminant spike-in.</p>
Squeegee: de novo identification of reagent and laboratory induced microbial contaminants in low biomass microbiomes, simulation dataset 1% spike-in contaminant sequences
<p>Computational analysis of host-associated microbiomes has opened the door to numerous discoveries relevant to human health and disease. However, contaminant sequences in metagenomic samples can potentially impact the interpretation of findings reported in microbiome studies, especially in low biomass environments. Our hypothesis is that contamination from DNA extraction kits or sampling lab environments will leave taxonomic "bread crumbs” across multiple distinct sample types, allowing for the detection of microbial contaminants when negative controls are unavailable. To test this hypothesis we implemented Squeegee, a de novo contamination detection tool. We tested Squeegee on simulated and real low biomass metagenomic datasets. On the low biomass samples, we compared Squeegee predictions to experimental negative control data and show that Squeegee accurately recovers known contaminants. We also analyzed 749 metagenomic datasets from the Human Microbiome Project and identified likely previously unreported kit contamination. Collectively, our results highlight that Squeegee can identify microbial contaminants with high precision.</p> <p> </p> <p>Simulation Dataset 1% contaminant spike-in.</p>
Data supporting the manuscript entitled: 'Intermittent soil water stress history favors microbial traits that better mitigate wheat biomass losses during subsequent water stress.'
<p>Data living in this data repository supports the scientific article entitled: Intermittent soil water stress history favors microbial traits that better mitigate wheat biomass losses during subsequent water stress.</p> <p> </p> <p> </p> <p> </p>
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.
Figure 1 in Building a global database of soil microbial biomass and function: a call for collaboration
Figure 1. Sampling locations and underrepresented environmental conditions in the dataset as of 19 November, 2019. For each pixel, we measured the percentage of environmental conditions (e.g. climate, soil characteristics, topographic information, vegetation indices) captured by the current dataset. Hot deserts, tropical rainforests and sub-Arctic regions are the least represented.
Fig. 8 in Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species
Fig. 8 | Total microbial diversity across vertebrate hindguts and within multi- plebodysites of fish. a Hindgutmicrobiotasamplesfrom 569 speciesof vertebrates were rarified to 5000 reads and unique or shared ASVs determined for each class. b The percentage of unique ASVs only found in a given class (not shared in other classes) as compared to the total ASVs within that class. c Rarefaction of cumulative gamma diversity as a function of unique vertebrate species. Included is a single fish species, S. japonicus, sampled over 3 years "black dots" and the unrarefied FMP samples which had detectable bacteria in all four body sites (gill, skin, midgut, and hindgut).d Gammadiversity of 68 fishspeciesacrossfour bodysites.e Percentageof unique ASVs associatedwitha given bodysiteacrossthe 68 fish species.f Rarefaction curve of increasing gamma diversity (inclusive of four body sites) as a function of increasing fish species. ASV amplified sequence variant, 5k 5000.
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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)
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DANDI Archive for NWB datasets
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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.