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51 results for “microbial community composition”
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.
Microbial Community Composition in Lakes - Taxonomic/Ecological characteristics of the sample at North Temperate Lakes LTER 2000 - 2007
Microbial community composition is inferred by a combination of automated ribosomal intergenic spacer analysis (ARISA) and PCR-generated clone library analysis. Clone libraries include both the 16S rRNA gene and the 16S-23S ribosomal intergenic spacer fragment. Phylogenetic assignments for individual ARISA fragments are obtained by comparing the ARISA fragment length from each clone to all of the profiles stored in our database. We have analyzed over 3900 clones obtained from 41 lakes that represent the range of trophic types found in temperate landscapes. Querying by a combination of taxonomic and ecological characteristics of the sample allows the user to retrieve sample information [sample IDs, sample dates, lake information (region, type, size, depth) and physical/chemical data (water temperature, clarity, pH, DOC, SUVA, TN, TP, nitrates/nitrites)] and clone information [clone IDs, sequence data, and characteristics of the sequence (length, chimera status, accession number, taxonomic affiliation)]. The data can be filtered by ecological characteristics of the sample [lake name, sample date, lake information (region, type, size, depth)] and taxonomic characteristics of the community members [clone ID, ARISA fragment length (raw or binned), and/or taxonomic characteristics (Phylum and Phylum-Class)]. The output can include links to individual sample records, which contain links to the taxonomic composition of the sample inferred by dynamically matching clones to ARISA fragments in the individual sample. The output can also include links to clone records directly (though this creates a very large number of lines in the output and is not recommended). Project ID's 30 Lakes - Survey of 30 lakes in northern and southern Wisconsin. June, August and October, 2002. See http://microbes.limnology.wisc.edu/lakes30.html. Lake Characteristics. CB0000 - Time series monitoring microbial community composition in Crystal Bog. 2000-2002. CBX_02 - Food web manipulation experiment i
Microbial Community Composition in lakes - Ecological characteristics of the sample at North Temperate Lakes LTER 2002 - 2007
Microbial community composition is inferred by a combination of automated ribosomal intergenic spacer analysis (ARISA) and PCR-generated clone library analysis. Clone libraries include both the 16S rRNA gene and the 16S-23S ribosomal intergenic spacer fragment. Phylogenetic assignments for individual ARISA fragments are obtained by comparing the ARISA fragment length from each clone to all of the profiles stored in our database. We have analyzed over 3900 clones obtained from 41 lakes that represent the range of trophic types found in temperate landscapes. Querying by ecological characteristics of the sample allows the user to retrieve sample IDs, sample dates, lake information (region, type, size, depth) and physical/chemical data (water temperature, clarity, pH, DOC, SUVA, TN, TP, nitrates/nitrites). The data can be filtered by lake name, sample date, lake information (region, type, size, depth), and physical/chemical data (water temperature, clarity, pH, DOC, SUVA, TN, TP, nitrates/nitrites). The output includes links to individual sample records, which contain links to the taxonomic composition of the sample inferred by dynamically matching clones to ARISA fragments in the individual sample
Microbial Community Composition in Lakes - Taxonomic characteristics of the clones at North Temperate Lakes LTER 2000 - 2007
Microbial community composition is inferred by a combination of automated ribosomal intergenic spacer analysis (ARISA) and PCR-generated clone library analysis. Clone libraries include both the 16S rRNA gene and the 16S-23S ribosomal intergenic spacer fragment. Phylogenetic assignments for individual ARISA fragments are obtained by comparing the ARISA fragment length from each clone to all of the profiles stored in our database. We have analyzed over 3900 clones obtained from 41 lakes that represent the range of trophic types found in temperate landscapes. Querying by taxonomic characteristics of the clone allows the user to retrieve clone IDs, sequence data, and characteristics of the sequence (length, chimera status, accession number, taxonomic affiliation). The data can be filtered by clone ID, ARISA fragment length (raw or binned), and/or taxonomic characteristics (Phylum and Phylum-Class). The output includes links to individual clone records, which contain more detailed information about how the clone was generated (researcher, library ID, project ID, primer sets used, etc.).
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 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.
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>
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>
Effects of parental care on skin microbial community composition in poison frogs
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Microbial community composition of earthworm-invaded and earthworm-free soils of the Canadian boreal forest
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Data from: Responses of subsoil organic carbon to climate warming and cooling is determined by microbial community rather than its molecular composition
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Plant management but not fertilization mediates soil carbon emission and microbial community composition in subtropical Eucalyptus plantations
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Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition
<ol> <li>Microbial communities are increasingly recognised as crucial for animal health. However, our understanding of how microbial communities are structured across wildlife populations is poor. Mechanisms such as interspecific associations are important in structuring free-living communities, but we still lack an understanding of how important interspecific associations are in structuring gut microbial communities in comparison to other factors such as host characteristics or spatial proximity of hosts.</li> </ol> <p> </p> <ol> <li>Here we ask how gut microbial communities are structured in a population of North American moose (<i>Alces alces</i>). We identify key microbial interspecific associations within the moose gut and quantify how important they are relative to key host characteristics, such as body condition, for predicting microbial community composition.</li> </ol> <p> </p> <ol> <li>We sampled gut microbial communities from 55 moose in a population experiencing decline due to a myriad of factors, including pathogens and malnutrition. We examined microbial community dynamics in this population utilizing novel graphical network models that can explicitly incorporate spatial information.</li> </ol> <p> </p> <ol> <li>We found that interspecific associations were the most important mechanism structuring gut microbial communities in moose and detected both positive and negative associations. Models only accounting for associations between microbes had higher predictive value compared to models including moose sex, evidence of previous pathogen exposure, or body condition. Adding spatial information on moose location further strengthened our model and allowed us to predict microbe occurrences with ~90% accuracy.</li> </ol> <p> </p> <ol> <li>Collectively, our results suggest that microbial interspecific associations coupled with host spatial proximity are vital in shaping gut microbial communities in a large herbivore. In this case, previous pathogen exposure and moose body condition were not as important in predicting gut microbial community composition. The approach applied here can be used to quantify interspecific associations and gain a more nuanced understanding of the spatial and host factors shaping microbial communities in non-model hosts.</li> </ol>
Data from: Do temperate tree species diversity and identity influence soil microbial community function and composition?
Studies of biodiversity-ecosystem function in treed ecosystems have generally focused on aboveground functions. The present study investigates inter-trophic links between tree diversity and soil microbial community function and composition.We examined how microbial communities in surface mineral soil responded to experimental gradients of tree species richness (SR), functional diversity (FD), community-weighted mean trait value (CWM) and tree identity. The site was a 4-yr-old common garden experiment near Montreal, Canada, consisting of deciduous and evergreen tree species mixtures. Microbial community composition, community-level physiological profiles (CLPP) and respiration were evaluated using phospholipid fatty acid (PLFA) analysis and the MicroRespTM system, respectively. The relationship between tree species richness and glucose induced respiration (GIR), basal respiration (BR), metabolic quotient (qCO2) followed a positive but saturating shape. Microbial communities associated with species mixtures were more active (basal respiration (BR)), with higher biomass (glucose induced respiration (GIR)), and used a greater number of carbon sources than monocultures. Communities associated with deciduous tree species used a greater number of carbon sources than those associated with evergreen species, suggesting a greater soil carbon storage capacity. There were no differences in microbial composition (PLFA) between monocultures and SR mixtures. The FD and the CWM of several functional traits affected both BR and GIR. In general, the CWM of traits had stronger effects than did FD, suggesting that certain traits of dominant species have more effect on ecosystem processes than does FD. Both the functions of GIR and BR were positively related to aboveground tree community productivity. Both tree diversity (SR) and identity (species and functional identity – leaf habit) affected soil microbial community respiration, biomass and composition. For the first time, we identified functional traits related to life history strategy, as well as root traits that influence another trophic level, soil microbial community function, via effects on BR and GIR.
Data from: Uniqueness of tree stand composition and soil microbial communities are related across urban spruce-dominated forests
<p>The dataset contains data obtained from urban spruce-dominated forests in southern Finland where we have measured tree stand composition, forest management history, soil chemical properties, and soil microbial communities. Data files include (1) microbial OTU tables describing microbial community composition (sequence read counts of Operational Taxonomic Units) across the study plots, (2) taxonomic assignments and other metadata related to OTUs, and (3) measured and calculated variables describing the characteristics of sites and their microbial assemblages (site metadata).</p>
Dataset - COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions
<p>Generated draft and consensus reconstructions for the manuscript "COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions" (Wendering & Nikoloski).</p>
Soil microbial diversity and community composition during conversion from conventional to organic agriculture
<p>It is generally assumed that the dependence of conventional agriculture on artificial fertilizers and pesticides strongly impacts the environment, while organic agriculture relying more on microbial functioning may mitigate these impacts. However, it is not well known how microbial diversity and community composition change in conventionally managed farmers' fields that are converted to organic management. Here, we sequenced bacterial and fungal communities of 34 organic fields on sand and marine clay soils in a time series (chronosequence) covering 25 years of conversion. Nearby conventional fields were used as references. We found that community composition of bacteria and fungi differed between organic and conventionally managed fields. In the organic fields, fungal diversity increased with time since conversion. However, this effect disappeared when the conventional paired fields were included. There was a relationship between pH and soil organic matter content and the diversity and community composition of bacteria and fungi. In marine clay soils, when time since organic management increased, fungal communities in organic fields became more dissimilar to those in conventional fields. We conclude that conversion to organic management in these Dutch farmers' fields did not increase microbial community diversity. Instead, we observed that in organic fields in marine clay when time since conversion increased soil fungal community composition became progressively dissimilar from that in conventional fields. Our results also showed that the paired sampling approach of organic and conventional fields was essential in order to control for environmental variation that was otherwise unaccounted for.</p>
Community assembly amplicon sequences, with pipeline to get asv table for "Spatial structure drives compositional convergence between nutrient environments in experimental microbial communities"
<p>Community assembly amplicon sequences, with pipeline to get asv table for "Spatial structure drives compositional convergence between nutrient environments in experimental microbial communities"</p> <p> </p> <p>compressed FASTA files for 16s amplicon sequences relating to two separate projects, "Spatial structure drives compositional convergence between nutrient environments in experimental microbial communities" and "Habitat filtering leads to phylogenetic clustering in synthetic microbial communities". DADA22 pipeline is included, which pools all samples for better accuracy. A Julia script bioinfo.jl is then used to select only the samples relevant to spatial structure project.</p> <p> </p> <p>All csv filenames are appended with "_q" indicating an increase in the stringency of quality filtering parameters (also increasing minimum hamming distance used in DADA2 algorithm to 5) to produce a taxa table with a sensible number of ASVs (given a known number of input strains) with each ASV uniquely aligning to an individual sequence from colony PCR of said input strains.</p> <p> </p>
Consistent predictors of microbial community composition across spatial scales in grasslands reveal low context-dependency
<p><span>Environmental circumstances shaping soil microbial communities have been studied extensively. However, due to disparate study designs, it has been difficult to resolve whether a globally consistent set of predictors exists, or context-dependency prevails. Here, we used a network of 18 grassland sites (11 of those containing regional plant productivity gradients) to examine i) if similar abiotic or biotic factors predict both large-scale (across sites) and regional-scale (within sites) patterns in bacterial and fungal community composition, and ii) if microbial community composition differs consistently at two levels of regional plant productivity (low vs high).</span><span> We found that </span><span>bacteria were consistently associated with certain soil properties and both bacteria and fungi were consistently associated with plant community composition within different sites. Moreover, there was a microbial community signal that clearly distinguished high and low-productivity soils that was shared across different grasslands independent of their location in the world.</span><span> In this study, we show that </span><span>there is high congruence between predictors of bacterial and fungal community composition at different spatial scales and that regional productivity differences are typified by characteristic soil microbial communities across the grassland biome. These results suggest that it might be feasible to predict the overall effects of global changes on soil microbial community composition in different grasslands, as well as to discriminate fertile from infertile systems using generally applicable microbial indicators.</span></p>
Data from: Community composition and physiological plasticity control microbial carbon storage across natural and experimental soil fertility gradients
<p>Data associated with 'Community composition and physiological plasticity control microbial carbon storage across natural and experimental soil fertility gradients' by Butler, Manzoni, and Warren, published in The ISME Journal (accepted 28/9/2023).</p>
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Allen Brain Atlas
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