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174 results for “soil microbial community”
Effects of Warming on Soil Microbial Communities at Harvard Forest 2011
As Earth’s climate warms, soil carbon pools and the microbial communities that process them may change, altering the way in which carbon is recycled in soil. In this study, we used a combination of metagenomics and bacterial cultivation to evaluate the hypothesis that experimentally raising soil temperatures by 5°C for 5, 8, or 20 years increased the potential for temperate forest soil microbial communities to degrade carbohydrates. Warming decreased the proportion of carbohydrate-degrading genes in the organic horizon derived from eukaryotes and increased the fraction of genes in the mineral soil associated with Actinobacteria in all studies. Genes associated with carbohydrate degradation increased in the organic horizon after 5 years of warming but had decreased in the organic horizon after warming the soil continuously for 20 years. However, a greater proportion of the 295 bacteria from 6 phyla (10 classes, 14 orders, and 34 families) isolated from heated plots in the 20-year experiment were able to depolymerize cellulose and xylan than bacterial isolates from control soils. Together, these findings indicate that the enrichment of bacteria capable of degrading carbohydrates could be important for accelerated carbon cycling in a warmer world.
Soil Microbial Community Effects on Quercus Rubra Seedling Survival at Harvard Forest 2016-2017
Feedbacks between plants and their soil microbial communities often drive negative density dependence in tropical forests, but their importance for tree demographics in temperate forests remains unclear. Additionally, the relative contribution of intraspecific seedling competition and soil pathogens to density-dependent patterns has rarely been assessed. We assessed how the soil microbial community influenced Quercus rubra seedling survival by growing seedlings in a greenhouse inoculated with soil collected from beneath conspecific and heterospecific mature trees. We found that seedlings grown with soil from beneath conspecific adults had a higher mortality rate than seedlings grown with soil from beneath heterospecific adults; therefore adult plant-soil feedbacks decrease seedling survival in Q. rubra.
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.
Seasonal Soil Sampling of Grass-dominated, Mesquite-dominated, and Ecotone Sites at the Jornada Basin LTER site for the Analysis of Microbial Community Variance, 2022-2023
Fungal and bacterial soil communities were analyzed to assess the influence of woody shrub encroachment on soil microbial communities. Three study sites in the Jornada Long Term Ecological Research Site were selected to represent a grass-dominated site, a woody shrub dominated site, and an ecotone of woody shrubs and grass. The field sampling began in October 2022 and concluded in July 2023 with five sampling periods that aimed to capture seasonal variation: October 2022, January 2023, March 2023, May 2023, and July 2023. This dataset includes data pertaining to the soil microbial composition, environmental characteristics, microbial sequence processing, and documentation of the code utilized for data processing and statistical analyses. Data on soil microbial composition was collected from Phospholipid Fatty-Acid composition data from soil samples. Data on environmental characteristics were collected from on-site temperature probes, laboratory assessments of soil properties, and Jornada meteorological stations. Information pertaining to microbial sequence processing is included in the documented code as well as in the record of the primers utilized.
Alpine soil islands plant and soil microbial community composition, 2024.
High alpine ecosystems are particularly sensitive to climate-driven change, with vegetation expansion increasingly observed in historically barren soils. In late August and early September 2024, we revisited 50 previously established vegetation plots in Green Lakes Valley (Niwot Ridge LTER) to evaluate patterns of plant colonization and community change over time. Using legacy vegetation data from 2008 and 2015, we assessed changes in plant cover and composition in relation to microtopography and prior plant occurrence. Concurrently, we collected soil samples for 16S and 18S rRNA gene sequencing to characterize bacterial, archaeal, and eukaryotic microbial communities associated with these plots. Vegetation was resampled using spatially referenced 1-meter radius surveys, estimating species incidence and cover and documenting moss, lichen, sedge, and grass diversity. Together, these above- and belowground data provide insight into how priority effects, fine-scale environmental variation, and plant–microbe interactions influence alpine community dynamics, and may inform predictive models of ecosystem responses to ongoing climatic shifts.
Soil microbial community coupling network in response to diversified crop rotations
<p>Dataset of manuscript entitled “Soil microbial community coupling network in response to diversified crop rotations”. This manuscript includes the results of WP3 from the SOFT project (ref. 890874).</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 microbial community composition (16S) data from a laboratory redox fluctuation experiment conducted with an Oxisol and Mollisol
To test the response of microbial communities to periodic oxygen limitation, we conducted a laboratory experiment where two contrasting soils (a rainforest Oxisol from Puerto Rico, and an Iowa cropland Mollisol) were incubated under headspace treatments where oxygen availability varied cyclically over time. Treatments consisted of 0, 2, 4, 8, or 12 d of anoxic conditions (dinitrogen headspace) followed by 4 d of oxic conditions (i.e., ambient oxygen concentrations), and these treatments were repeated for a total of 384 d. At 0, 48, and 384 days, DNA was extracted from replicates from each treatment for sequencing of 16S rRNA amplicons. Companion biogeochemical measurements from this experiment were published previously by Huang et al. (2021a,b). These data support the Hall et al. (2022) manuscript published in Frontiers in Microbiology.
Soil geochemistry and microbial community data from glaciated and potential glacial refugia sites in the McMurdo Dry Valleys, Antarctica (1993-2019)
A study was conducted to examine soil microbial communities and associated geochemical parameters at potential glacial refugia and glaciated control sites throughout the McMurdo Dry Valleys region of Antarctica. Soil samples were collected as part of ongoing long-term monitoring efforts by the McMurdo Dry Valleys Long Term Ecological Research program (MCM LTER). The oldest samples used in this study were collected during the 1993-1994 austral summer, and the newest from the 2018-2019 austral summer. "Refugia" sites were selected based on geographical positions and elevations indicative of potential glacial refugia status. Each refugia site was paired with a lower elevation "glaciated" site in the same dry valley that was not likely to have functioned as a refugium. Six replicate soils per sampling site were sequenced with 16S primers following Earth Microbiome Project protocols, filtered using the DADA2 pipeline, and clustered to amplicon sequence variant using the SILVA reference database to generate the microbial classification table included herein. Soil samples were also analyzed for various geochemical parameters as part of this study, which include P, K, NO3-, gravimetric water content, percent organic matter, pH, and electroconductivity.
Impact of viruses on microbial communities and biogeochemical processes in agricultural soils
<p>The source data of microcosm experiment.</p>
Viroplant Project - Microcosm studies on the effect of bacteriophages used as plant protection products on soil microbial communities
<p>This file contains the description, data and DNA analyses on the effect of bacteriophages with a potential to be used as plant protecction products on the structure and function of soil microbial communities. The objective was to evaluate two different microcsom incubation systems with phages and microbial cells from soil, or soil itself and to analyses in a time dependent manner how the phages affect the natural soil microbiomes. The microbial communities were quantified with qPCR and their diversity analyzed with PCR amplified 16S rRNA gene sequences. Bioinformatic analyses were used to evaluate microbial community responses</p>
Plant management but not fertilization mediates soil carbon emission and microbial community composition in subtropical Eucalyptus plantations
<p><span>The diversity of </span><span>plant functional group</span><span>s</span><span> in plantations affects soil carbon, but we have limited understanding of the underlying mechanisms for how plant management affects soil carbon dynamics. Here, we conducted a 3-year manipulation experiment of plant functional groups that included understory removal, tree root trenching, and fertilization treatments in 2-year-old and 6-year-old <em>Eucalyptus</em> plantations in the subtropical region. The results showed that soil respiration was significantly suppressed by understory removal (-38%), tree root trenching (-41%), and their interactions (-54%), but that fertilization alone and in interactions had no significant effect. The Chao1 indices for soil bacterial and fungal diversity significantly decreased with understory removal in the 2-year-old plantation and with tree root trenching in the 6-year-old plantation. Soil bacterial and fungal communities were also affected by understory removal and tree root trenching. Soil respiration, physicochemical characteristics, microbial diversity, and community composition were significantly affected by plantation age. Reductions in soil carbon emissions were associated with reductions in plant functional groups and soil microbial groups, while increases in soil respiration were associated with soil physicochemical factors, soil temperature, and plantation age. Our findings highlight that plant managements are of great significance to the soil carbon emission processes in afforested plantations.</span></p>
Soil microbial communities from tropical forest and oil palm
<div> <h1>Description</h1> <p>A study examining the impact of selective logging and forest conversion to oil palm on soil microbial community composition. Soil samples were collected from old growth forest, selectively logged forest and oil palm plantations. Soil bacterial, protistan and fungal community composition were measured and summarised by calculating richness. </p> <h1>Projects</h1> <p> This dataset was collected as part of the following projects: </p><ul> <li><a href="https://safeproject.net/projects/project_view/124">https://safeproject.net/projects/project_view/124</a> </li> </ul> <p></p> <h1>Funding</h1> <p> These data were collected as part of research funded by: </p> <ul> <li>UK NERC-funded Biodiversity And Land-use Impacts on Tropical Ecosystem Function (BALI) consortium (Standard grant , NE/K016377/1 ) </li> </ul> <p></p> <p>This dataset is released under the CC-BY 4.0 licence, requiring that you cite the dataset in any outputs, but has the additional condition that you acknowledge the contribution of these funders in any outputs.</p> <h1>Permits</h1> <p>These data were collected under permit from the following authorities:</p> <ul> <li>Sabah Biodiversity Centre ( Research licence JKM/MBS.1000-2/2 JLD.5 (20))</li> <li>Sabah Biodiversity Centre ( Export licence JKM/MBS.1000-2/3 JLD.2 (70))</li> </ul> <p></p> <h1>Files</h1> <p>This dataset consists of 1 file: SAFE_Dataset_Richness.xlsx</p> <h2>SAFE_Dataset_Richness.xlsx</h2> <p>This file contains dataset metadata and 1 data tables:</p> <h3>Soil_Microbial_Communities</h3> <ul> <li>Worksheet: Soil_Microbial_Communities</li> <li>Description: Summary richness statistics from bacterial 16S, protistan 18S and fungal ITS biomarker microbial sequencing from DNA extracted from soils</li> <li>Number of fields: 10</li> <li>Number of data rows: 225</li> <ul> <li>PlotName: Plot name corresponding to the GEM Carbon plot where soils were sampled (type: id)</li> <li>ForestType: Old-growth, Logged or Oil palm (type: categorical)</li> <li>ForestPlotsCode: Plot name as listed in ForestPlots database (type: id)</li> <li>Replicate: replicate identifier for which soil core taken from each subplot (type: replicate)</li> <li>location_name: Name of subplot where soils were collected (type: location)</li> <li>Bacteria_Richness: Number of observed bacterial taxa from sequencing of 16S marker genes from soil samples (type: numeric)</li> <li>Protist_Richness: Number of observed protistan taxa from sequencing of 18S marker genes from soil samples (type: numeric)</li> <li>Fungal_Richness: Number of observed fungal taxa from sequencing of 16S marker genes from soil samples (type: numeric)</li> <li>EcM_Fungal_Richness: Number of observed Ectomycorrhizal fungal taxa from sequencing of ITS marker genes from soil samples (type: numeric)</li> <li>AMF_Fungal_Richness: Number of observed Arbuscular Mycorrhizal fungal taxa from sequencing of ITS marker genes from soil samples (type: numeric)</li> </ul> </ul> <h1>Extents</h1> <ul> <li>Date range: 2014-10-01 to 2018-09-01</li> <li>Latitudinal extent: 4.64° to 4.954°</li> <li>Longitudinal extent: 116.95° to 117.796°</li> </ul> </div>
Microbial community composition of earthworm-invaded and earthworm-free soils of the Canadian boreal forest
<p>Earthworm invasion in North American forests has the potential to greatly impact soil microbiomes by altering soil physicochemical properties. We characterized and compared microbial communities of earthworm-invaded and non-invaded soils in previously described sites across three major soil types found in the Canadian boreal forest using phospholipid fatty acid (PLFA) analysis and metabarcoding of the 16S rRNA gene (bacteria and archaea) and ITS2 region (fungi).</p>
Dataset for the article "Beyond PLFA: Concurrent extraction of neutral and glycolipid fatty acids provides new insights into soil microbial communities"
<p>The following are data and code used for statistical analysis and figure plotting in the manuscript</p> <p>Gorka et al. (2023) "Beyond PLFA: Concurrent extraction of neutral and glycolipid fatty acids provides new insights into soil microbial communities", Soil Biology and Biochemistry</p> <p>It contains the following files:</p> <p>1. Pure lipid standard data</p> <ul> <li>Total ion chromatogram (TIC) area data (<strong>area.csv</strong>)</li> <li>Assignment of lipids that the measured fatty acids originate from (<strong>LipidClass.csv</strong>)</li> <li>An R script reproducing the calculations and plotting for Fig. 2 and Fig. S1 (<strong>pure_lipids.R</strong>)</li> </ul> <p>2. Microbial pure culture fatty acid data data</p> <ul> <li>TIC area data of the PLFA, NLFA, and GLFA data from pure culture extracts (<strong>area.csv</strong>)</li> <li>Files needed for calculating the data and assigning taxonomic groups in the R code (<strong>weights.csv</strong>, <strong>C_atoms.csv</strong>, <strong>species_list.csv</strong>)</li> <li>An R script reproducing the calculations and plotting for Fig. 3, Fig. 4, Fig. S2, and Fig. S3 (<strong>pure_cultures.R</strong>)</li> </ul> <p>3. Soil fatty acid data</p> <ul> <li>Absolute abundance data in nmol C g<sup>-1</sup> dry weight of the PLFA, NLFA, and GLFA data from soil extracts (<strong>nmolC.csv</strong>)</li> <li>Taxonomic group assignments of fatty acids needed to run the R code (<strong>phylum.csv</strong>)</li> <li>An R script reproducing the calculations and plotting for Fig. 5, and Fig. S4 (<strong>soil.R</strong>)</li> </ul>
Data from: Plant, insect, and soil microbial communities vary across brome invasion gradients in northern mixed-grass prairies
Open the record for dataset details and reuse information.
Microbial community composition of earthworm-invaded and earthworm-free soils of the Canadian boreal forest
Open the record for dataset details and reuse information.
Plant management but not fertilization mediates soil carbon emission and microbial community composition in subtropical Eucalyptus plantations
Open the record for dataset details and reuse information.
Soil Microbial and N cycling data along a wetland plant community gradient
This dataset contains soil chemical and microbial data taken from surface soil cores (15cm) from the Black Spruce, Willow/Birch, Tussock, Emergent Fen, and Rich Fen plant communities along the APEX boardwalk. Data include DOC, soil C, potential nitrification, potential denitrification, soil DNA concentration, water content, ammonium concentration, nitrate concentration, archaea abundance, NirK functional gene abundance, ammonia oxidizing bacteria (AOB) abundance, ammonia oxidizing archaea (AOA) abundance, NosZ functional gene abundance, and eubacteria abundance.
Operational taxonomic unit (OTU) table characterizing water track and adjacent soil microbial communities in Taylor Valley, Antarctica during the 2012-13 austral summer
This data package includes the abundance of microbial operational taxonomic units (OTUs) for samples collected during the austral summer of 2012-2013 in the Lake Hoare and Goldman Glacier Basins of Taylor Valley, Antarctica. A total of twenty samples from on- and off-water track soils were collected and analyzed. Samples were collected from the Lake Hoare Basin on 27 December 2012 and from the Goldman Glacier Basin on 4 January 2013. The aim of the study was to identify how variation in the measured physical and chemical environment of water tracks within the two water track systems influenced soil microbial community structure and diversity. Soil bacterial biodiversity was assessed using cultivation independent 16S rRNA gene sequencing.
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