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66 results for “soil microbiome”
Upcycling Human Excrement: The Gut Microbiome to Soil Microbiome Axis (supporting data)
<div> <div>This archive contains the supporting data and code for <a href="https://doi.org/10.1093/ismeco/ycaf089" target="_blank" rel="noopener">Meilander et al., 2024: <em>Upcycling Human Excrement: The Gut Microbiome to Soil Microbiome Axis</em></a>.</div> <div> </div> <div><strong>Clicking the links below will open the corresponding files using QIIME 2 View (<a href="https://view.qiime2.org" target="_blank" rel="noopener">https://view.qiime2.org</a>). </strong></div> <div> </div> <div> <div> <div>Summaries of master data files:</div> <div><a href="https://view.qiime2.org/visualization/?src=https://zenodo.org/api/records/13887457/files/asv-table.qzv/content" target="_blank" rel="noopener">Summary of master feature table (<code>asv-table.qzv</code>)</a></div> <div><a href="https://view.qiime2.org/visualization/?src=https://zenodo.org/api/records/13887457/files/sample-metadata.qzv/content">Tabulated view of sample metadata (<code>sample-metadata.qzv</code>)</a></div> <div><a href="https://view.qiime2.org/visualization/?src=https://zenodo.org/records/15390940/files/asv-seqs-ms10.qzv?download=1" target="_blank" rel="noopener">Summary of ASV sequences observed in at least 10 samples: (<code>asv-seqs-ms10.qzv</code>)</a></div> <div> </div> <div>PCoA plots:</div> <div><a href="https://view.qiime2.org/visualization/?src=https://zenodo.org/api/records/13887457/files/braycurtis.qzv/content" target="_blank" rel="noopener">Bray-Curtis Emperor plot (<code>braycurtis.qzv</code>)</a></div> <div><a href="https://view.qiime2.org/visualization/?src=https://zenodo.org/api/records/13887457/files/jaccard.qzv/content" target="_blank" rel="noopener">Jaccard Emperor plot (<code>jaccard.qzv</code>)</a></div> <div><a href="https://view.qiime2.org/visualization/?src=https://zenodo.org/api/records/13887457/files/unweighted_unifrac.qzv/content" target="_blank" rel="noopener">Unweighted UniFrac Emperor plot (<code>unweighted_unifrac.qzv</code>)</a></div> <div><a href="https://view.qiime2.org/visualization/?src=https://zenodo.org/api/records/13887457/files/weighted_unifrac.qzv/content" target="_blank" rel="noopener">Weighted UniFrac Emperor plot (<code>weighted_unifrac.qzv</code>)</a></div> <div> </div> <div>Taxonomy barplots:</div> <div> <div><a href="https://view.qiime2.org/visualization/?src=https://zenodo.org/records/15390940/files/taxa-bar-plots-bucket2-gtdb-r214.1-weighted-stool-taxonomy.qzv?download=1">Taxonomy bar plot for Bucket 2 only (<code>taxa-bar-plots-bucket2-gtdb-r214.1-weighted-stool-taxonomy.qzv</code>)</a></div> <div><a href="https://view.qiime2.org/visualization/?src=https://zenodo.org/records/15390940/files/taxa-bar-plots-bucket3-gtdb-r214.1-weighted-stool-taxonomy.qzv?download=1" target="_blank" rel="noopener">Taxonomy bar plot for Bucket 3 only (<code>taxa-bar-plots-bucket3-gtdb-r214.1-weighted-stool-taxonomy.qzv</code>)</a></div> <div><a href="https://view.qiime2.org/visualization/?src=https://zenodo.org/api/records/13887457/files/taxa-bar-plots-gtdb-r214.1-weighted-stool-taxonomy.qzv/content" target="_blank" rel="noopener">Taxonomy bar plot for all samples (<code>taxa-bar-plots-gtdb-r214.1-weighted-stool-taxonomy.qzv</code></a>)</div> </div> <div> </div> <div>q2-fmt "raincloud plots":</div> <div><a href="https://view.qiime2.org/visualization/?src=https://zenodo.org/api/records/13887457/files/hec-raincloud.qzv/content">Raincloud plot (<code>hec-raincloud.qzv</code>)</a></div> <div> </div> </div> </div> <div> </div> <div>The linked <code>.qzv</code> files are also contained in the <code>gut-to-soil-qiime2.zip</code> zip file, along with all relevant data artifacts (<code>.qza</code> files).</div> <div>The <code>.qzv</code> files are also maintained outside of the <code>.zip</code> file to facilitate their viewing with QIIME 2 View.</div> </div> <div> </div> <div> <div>Code for generating figures 1 and 2 (and corresponding supplemental figures):</div> <div><code>gut-to-soil-manuscript-figures-main.zip</code> (also see: <a href="https://github.com/caporaso-lab/gut-to-soil-manuscript-figures" target="_blank" rel="noopener">https://github.com/caporaso-lab/gut-to-soil-manuscript-figures</a>)</div> <div> </div> <div>Code for generating ridgeline plots (Figure S6):</div> <div><code>gut-to-soil-ridgeline-plots-main.zip</code> (also see: <a href="https://github.com/caporaso-lab/gut-to-soil-ridgeline-plots" target="_blank" rel="noopener">https://github.com/caporaso-lab/gut-to-soil-ridgeline-plots</a>)</div> </div> <div> <div> </div> </div>
Supplementary data: Winter cover cropping: Effect on soybean and synergistic implications on soil microbiome
<p>Supplementary data: (i) Agronomic and quality data of soybean (2 varieties) grown in 2 years (2020 & 2021) in two management systems (organic & low-input) with different cover crops; (ii) Soil microbiome analysis of the soybean field trials.</p>
Inventory of soil prokaryotic microbiome (via 16S based on rRNA gene amplicons) in freshwater and brackish water marshes following saltwater intrusion along Shark River Slough boundary, Everglades National Park (FCE LTER), Florida, USA, September 2018
Global sea-level rise is transforming coastal ecosystems, especially freshwater wetlands, in part due to increased episodic or chronic saltwater exposure, leading to shifts in microbial communities and related ecological services. Soil prokaryotes play a fundamental role in regulating important biogeochemical processes in coastal wetland ecosystem. Yet, it is still difficult to predict how soil prokaryotic communities respond to the saltwater exposure because of poorly understood prokaryotic sensitivity within complex wetland soil microbial communities, as well as the high heterogeneity of wetland soils and saltwater exposure. To address this, a four-year experimental simulation of saltwater intrusion in a pristine freshwater site and a previously saltwater-impacted site was conducted. The saltwater addition started in October 2014 on a monthly basis and continued through October 2018. The dataset contains amplicon sequencing date of 16S rRNA gene obtained from saltwater-exposed soils and unmanipulated native soils in both sites (collected in September 2018). The 2018 data are published in Zhao et al. 2023. A detailed list of sequence data and their accession numbers in GenBank is provided, and data collection is complete. This data package is an inventory of sequence read archive (SRA) entries available through GenBank BioProject PRJNA804545 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA804545). This data package is associated with the following publication: Zhao, J., Chakrabarti, S., Chambers, R., Weisenhorn, P., Travieso, R., Stumpf, S., Standen, E., Briceno, H., Troxler, T., Gaiser, E., Kominoski, J., Dhillon, B., & Martens-Habbena, W. (2023). Year-around survey and manipulation experiments reveal differential sensitivities of soil prokaryotic and fungal communities to saltwater intrusion in Florida Everglades wetlands. Science of The Total Environment, 858, 159865. https://doi.org/10.1016/j.scitotenv.2022.159865 Instead of citing this package, which is an
Inventory of soil prokaryotic and fungal microbiome (via 16S rRNA gene amplicons and ITS sequencing) from Shark River Slough and Taylor Slough, Everglades National Park (FCE LTER), Florida, USA, February 2019 - October 2020
Global sea-level rise is transforming coastal ecosystems, especially freshwater wetlands, in part due to increased saltwater exposure, leading to change in soil microbial communities and many important biogeochemical processes. Given the high spatial and temporal heterogeneity in coastal wetlands, especially in tropical or subtropical climates characterized by seasonal temperature, precipitation, and tidal fluctuations, it remains unclear which environmental factors influence the compositions of soil microbial communities in wetlands affected by varying degrees of sea-water intrusion. To address this, a two-year survey was conducted on microbial community structure in submerged surface soils from 14 wetland sites across the Florida Everglades, representing three major ecosystem types, i.e. freshwater marshes, mangrove forests, and seagrass meadows. Bulk surface soil samples of each site were collected from February 2019 to October 2020 to cover dry and wet seasons. In addition to bulk soil samples, soil cores were collected from each site in August 2020 to assess vertical gradients of microbial communities. The dataset contains amplicon sequencing data of 16S rRNA gene (both bulk soil and soil cores) and ITS gene (only the bulk soil). The 2019 to 2020 data are published in Zhao et al. 2023. A detailed list of sequence data and their accession numbers in GenBank is provided, and data collection is complete. This data package is an inventory of sequence read archive (SRA) entries available through GenBank BioProject PRJNA804243 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA804243), PRJNA804246 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA804246), and PRJNA804228 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA804228). This data package is associated with the following publication: Zhao, J., Chakrabarti, S., Chambers, R., Weisenhorn, P., Travieso, R., Stumpf, S., Standen, E., Briceno, H., Troxler, T., Gaiser, E., Kominoski, J., Dhillon, B., & Martens-H
Alpine plant seed microbiomes, germination, and plant-soil feedbacks, Niwot Ridge and Green Lakes Valley, 2018.
Seed and soil microbiomes strongly affect plant performance, and these effects can scale-up to influence plant community structure. However, seed and soil microbial community composition are variable across landscapes, and different microbial communities can differentially influence multiple plant metrics (biomass, germination rate), and community stabilizing mechanisms. We measured how microbiomes inside seeds and in soils varied among alpine plant species and communities that differed in plant species richness and density. Across 10 common alpine plant species, we found a total of 318 bacterial and 128 fungal operational taxonomic units (OTUs) associated with seeds, with fungal richness affected by plant species identity more than sampling location. However, seed microbes had only marginally significant effects on plant germination success and timing. In contrast, soil microbes associated with two different plant species had significant effects on plant biomass, and their effect depended both on the plant species and the location the soils were sampled from.
Unraveling community adaption and survival strategy of soil microbiome under vanadium stress in nationwide mining environments
<p class="Abstract"><span><span>The vanadium (V) smelters soil harbor wide ranges of microorganisms, whose survival relies on their metabolic activities under stress.</span><span> Nonetheless, the characteristics and functions of soil microbiome in V mining environments have not been recognized at a continental scale. This study investigates microbial diversity, community assembly and metabolic traits of soil microbiome across 90 V smelters in China. A decrease in alpha diversity is observed, along with community variation, which is also jointly explained by other environmental, climatic and geographic factors. Null model shows that V promotes homogeneous selection. V also mediates co-occurrence patterns, with increased positive interspecific associations under higher V concentrations (</span><span>></span><span>559.6 mg/kg)</span><span>, e.g., <em>f_Gemmatimonadaceae</em>, <em>Nocardioides</em>, <em>Micromonospora</em>, <em>Rubrobacter</em>.</span><span> In addition, 67 metagenome assembled genomes are retrieved via metagenomic analysis. The metabolic pathways of keystone taxa are disentangled to reveal their putative involvement in the V(V) reduction process. Nitrate and nitrite reductase (<em>nirK</em>, <em>narG</em>), and <em>mtrABC</em> are found to be taxonomically affiliated with <em>Micromonospora</em>. sp, <em>FEN-1250</em>. sp, <em>Nocardioides</em>. sp, etc. Additionally, reverse citric acid cycle (rTCA) serves the main carbon fixation pathway, synthetizing alternative energy for putative V reducers, highlighting a synergistic relationship between autotrophic and heterotrophic processes to support the microbial survival. Our findings comprehensively reveal the driving forces for soil community variation under V stress, suggesting the robust strategies adopted by indigenous microorganisms to alleviate V impact, which can be exploited for bioremediation application.</span></span></p>
Unraveling community adaption and survival strategy of soil microbiome under vanadium stress in nationwide mining environments
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Data from: Chemical structure predicts the effect of plant-derived low-molecular weight compounds on soil microbiome structure and pathogen suppression
<p>1. Plant-derived low molecular weight compounds play a crucial role in shaping soil microbiome functionality. While various compounds have been demonstrated to affect soil microbes, most data are case-specific and do not provide generalizable predictions on their effects. Here we show that the chemical structural affiliation of low molecular weight compounds typically secreted by plant roots – sugars, amino acids, organic acids and phenolic acids – can predictably affect microbiome diversity, composition and functioning in terms of plant disease suppression.</p> <p>2. We amended soil with single or mixtures of representative compounds, mimicking carbon deposition by plants. We then assessed how different classes of compounds, or their combinations, affected microbiome composition and the protection of tomato plants from the soil-borne Ralstonia solanacearum bacterial pathogen.</p> <p>3. We found that chemical class predicted well the changes in microbiome composition and diversity. Organic and amino acids generally decreased the microbiome diversity compared to sugars and phenolic acids. These changes were also linked to disease incidence, with amino acids and nitrogen-containing compound mixtures inducing more severe disease symptoms connected with a reduction in bacterial community diversity.</p> <p>4. Together, our results demonstrate that low molecular weight compounds can predictably steer rhizosphere microbiome functioning providing guidelines to engineer microbiomes based on root exudation patterns by specific plant cultivars or crop regimes.</p>
Data from: Soil microbiomes underlie population persistence of an endangered plant species
Microbiomes can dramatically alter individual plant performance, yet how these effects influence higher order processes is not well resolved. In particular, little is known about how microbiome effects on individual plants alter plant population dynamics, a question critical to imperiled species conservation. Here, we integrate bioassays, multidecadal demographic data, and integral projection modeling to determine how the presence of the natural soil microbiome underlies plant population dynamics. Simulations indicated that the presence of soil microbiomes boosted population growth rates (λ) of the endangered Hypericum cumulicola by 13% on average, the difference between population growth versus decline in 76% of patches. The greatest benefit (47% increase in λ) occurred in low nutrient, high elevation habitats, suggesting that the soil microbiome may help expand H. cumulicola's distribution to include these stressful habitats. Our results demonstrate that soil microbiomes can significantly affect plant population growth and persistence, and support the incorporation of soil microbiomes into conservation planning. plant population growth and persistence, and support the incorporation of soil microbiomes into conservation planning.
Soil microbiome dataset from the University of Wisconsin Arlington and Lancaster agricultural research stations and cheese maker and vegetable processor wastewater land application sites
<p>Cheese making and vegetable processing are trillion-dollar industries globally. However, they generate immense volumes of high nitrogen wastewater that must be processed safely and cost effectively. Land application systems are frequently used by rural medium and smaller processing facilities that lack ready access to wastewater resource recovery facilities. This study utilized soil microbial data to determine system differences leading to high denitrification rates observed in incubation studies in agricultural soil collected from University of Wisconsin Agricultural Research Stations (ARS), Arlington and Lancaster stations, compared to industry cheese making and vegetable processing land application water treatment facilities. It was hypothesized that decade long frequent treatment with facility wastewater would alter the microbial communities in the system soils, but this is not the case. No clear correlations were found between soil denitrification rates and biotic or abiotic system factors and the microbial communities observed in the industry systems are similar to the ARS soils under agricultural production and to literature reported denitrifying systems such as wetlands and wastewater resource recovery facilities. Knowing that land application system management does not alter the microbial biome will allow any management advances that increase denitrification efficiency in other denitrifying systems to be readily applied to industry wastewater land application facilities. </p>
Artificial humic acid diminishes the effect of drought on the soil microbiome
<p><span lang="EN-US">Humic substances have an enormous potential for regenerative agriculture to improve soil quality and plant growth. Recently developed technologies called hydrothermal humification enabled the conversion of waste into artificial humic acids, that would allow for sustainable and large-scale applications. However, not much is known about the effect of artificially produced humic acid on the soil microbiome, and its effect on drought-exposed soil. Therefore, we studied the effect of drought stress and artificial humic acid on the soil microbiota in sandy soil in a controlled experimental design. Analyses of 16S rDNA amplicon libraries by bioinformatics and statistics revealed that both, drought and artificial humic acid application, influenced bacterial community composition significantly, but only artificial humic acid affected bacterial diversity. Bacterial families like <em>Pseudomonadaceae</em>, <em>Peptostreptococcaceae</em> and <em>Moraxellaceae</em> enriched under artificial humic acid conditions, suggest an adaptation and selection of the soil bacterial microbiome. Under drought stress, artificial humic acid treatment kept bacterial diversity stable in the changed bacterial community composition. We propose that artificial humic acid application in sandy soil can improve the soil bacterial community, diminish drought stress, favor plant growth-promoting taxa, and bring enormous potential to sequestrate carbon in soil.</span></p>
Earth Microbiome Project and Global Soil Mycobiome Data Subsets
<p>These are subsets of the publicly available Earth Microbiome Project (<a href="https://earthmicrobiome.org/">https://earthmicrobiome.org/</a>, <a href="../records/890000">https://zenodo.org/records/890000</a>) [1] and Global Soil Mycobiome project datasets (<a href="https://doi.org/10.15156/BIO/2263453"><span>https://doi.org/10.15156/BIO/2263453</span></a>) [2,3], provided for benchmarking and testing purposes. These are re-released with attribution under a CC-BY-4.0 license, following the license of the original source creators. If you use this resource, please cite the original references as given below:</p> <p>1. Thompson, L. R., <em>et al.</em> (2017). A communal catalogue reveals Earth’s multiscale microbial diversity. <em>Nature</em>, 551:457-463. <a href="http://doi.org/10.1038/nature24621" target="_blank" rel="noopener noreferrer">doi:10.1038/nature24621</a>.</p> <p>2. Tedersoo, L., <em>et al.</em> The Global Soil Mycobiome consortium dataset for boosting fungal diversity research. <em>Fungal Diversity</em> <strong>111</strong>, 573–588 (2021). https://doi.org/10.1007/s13225-021-00493-7</p> <p>3. Tedersoo, L. (2021): The Global Soil Mycobiome consortium dataset for boosting fungal diversity research v2. University of Tartu. 10.15156/BIO/2263453</p>
Variation in soil microbiome impacts on spring foliar phenology and productivity (Van Nuland et al. 2021 New Phytologist)
<p>Data associated with "<em>Natural soil microbiome variation affects spring foliar phenology with consequences for plant productivity and climate-driven range shifts</em>" (Van Nuland et al. 2021 New Phytologist). Please contact corresponding author for any questions.</p>
Data for: Soil cadmium stress-mediated sexual difference in phyllosphere microbiome and associated pathogen resistance of poplars
<p class="MsoNormal"><span>Phyllosphere associated microorganisms play a crucial role in protecting plants from diseases, while their composition and diversity are strongly influenced by heavy metal contaminants. As dioecious plants exhibited sexual dimorphism in metal accumulation and tolerance between male and female individuals, in this study we used male and female full-sibs of <em>Populus deltoides</em> to investigate whether the two plant sexes will present sexual differences in phyllosphere microbiome structure and associated pathogen resistance against a leaf pathogenic fungus after soil cadmium (Cd) exposure. We found that Cd-treated male plants </span><span>grew better </span><span>and a</span><span>ccumulated more leaf Cd than females. </span><span>Cd stress reduced leaf lesion areas of both plant sexes after leaf pathogen infection, whereas male plants exhibited better resistance than females. More importantly, Cd exposure differentially altered the structure and function of the phyllosphere microbiome of male and female plants, with more abundant ecologically beneficial microbes but decreased pathogenic fungal taxa harbored in male phyllosphere. Further <em>in vitro</em> toxicity tests suggested that such sexual difference in pathogen resistance between the two plant sexes could attribute to direct Cd toxicity and indirect shifts in phyllosphere microbiome. This study provides implication for understanding the underlying mechanism of heavy metals involved in plant-pathogen interactions.</span></p>
Biotic and abiotic drivers of coalescence asymmetry between soil and manure microbiomes
<p>The dataset includes bacterial and fungal OTU tables for all soil and manure samples after 180 days incubation, bacterial and fungal OTU abundance tables, the data for variance partitioning analysis, and the phylogenetic trees for calculating MNTD.</p>
Stimulated saprotrophic fungi in arable soil extend their activities to the rhizosphere and root microbiomes of crop seedlings
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Data from: Effects of the soil microbiome on the demography of two annual prairie plants
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Unravelling changes in the Pinus radiata root and soil microbiomes as a function of aridity
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Data for: Soil cadmium stress-mediated sexual difference in phyllosphere microbiome and associated pathogen resistance of poplars
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Data from: Soil microbiomes underlie population persistence of an endangered plant species
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