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105 results for “microbial activity”
Imprint of tree species mycorrhizal association on microbial-mediated enzyme activity and stoichiometry
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Biochar and nitrogen fertilizer promote rice yield by altering soil enzyme activity and microbial community structure
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Streptomyces pathogen suppressive activity in plant communities varying in diversity:Plant host and plant diversity effects on rhizosphere microbial community composition, diversity, structure, and function.
Effects of plant host and plant community diversity on soil rhizosphere microbial community composition, diversity, structure, and function were explored in long-term experimental plots. Soil samples were collected from the rhizosphere of one of 4 target plants species (Andropogon gerardii, Schizachyrium scoparium, Lespedeza capitata, or Lupinus perennis) growing in 1, 4, 8, 16, or 32-species plots. Pathogen-suppressive activities of soil streptomycetes were determined for every sample. In addition, soil metagenomic analyses were performed targeting bacterial or streptomycete communities. Soil edaphic characteristics were determined for every sample. Analyses consider both the effects of plant host and plant community diversity on microbial community structure and function, and the relationships of diverse taxa with plant host, plant community diversity, and soil edaphic characteristics.
Soil microbial functions and enzyme activity:BAC: Biodiversity and Climate
Climate changes forecast for our region by GCM???s and shifts in biodiversity and composition each have the potential to alter ecosystem functioning; their interactive effects are unknown. The "BAC" experiment is designed to determine the direct and interactive effects of plant species numbers, plant community composition, temperature, and precipitation on 11 productivity, C and N dynamics, stability, and plant, microbe, and insect species abundances in CDR grassland ecosystems.
Temporal and spatial distribution of microbial biomass, growth and activity in intertidal marshes, open water, and South Paramore Island in the Virginia Coast Reserve 1988-1990
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Data from: Microplastics negatively affect soil fauna but stimulate microbial activity: insights from a field-based microplastic addition experiment
<p>Microplastics are recognized as an emerging contaminant worldwide. Although microplastics have been shown to strongly affect organisms in aquatic environments, less is known about whether and how microplastics can affect different taxa within a soil community, and it is unclear whether these effects can cascade through soil food webs. By conducting a microplastic manipulation experiment, i.e. adding low-density polyethylene fragments in the field, we found that microplastic addition significantly affected the composition and abundance of microarthropod and nematode communities. Contrary to soil fauna, we found only small effects of microplastics on the biomass and structure of soil microbial communities. Nevertheless, structural equation modeling revealed that the effects of microplastics strongly cascade through the soil food webs, leading to the modification of microbial functioning with further potential consequences on soil carbon and nutrient cycling. Our results highlight that taking into account the effects of microplastics at different trophic levels is important to elucidate the mechanisms underlying the ecological impacts of microplastic pollution on soil functioning.</p>
Data collection for Tsuji et al., 2020, Microbial ecology of phototrophs in Boreal Shield lakes, Chapter 3: Biogeography and activity of chlorophototrophs in the ferruginous water columns of Boreal Shield lakes (PhD thesis)
<p>This data collection includes supplementary or raw data files related to Chapter 3 of the PhD thesis of Jackson M. Tsuji, "Biogeography and activity of chlorophototrophs in the ferruginous water columns of Boreal Shield lakes" (in "Microbial ecology of phototrophs in Boreal Shield lakes"). Specifically, the following files are included:</p> <ul> <li>ASV_table_non_rarefied_counts.tsv.gz -- non-rarefied ASV table containing 16S rRNA gene amplicon data presented in this study as raw counts. Beyond the index column and sample columns, two additional columns, "Consensus.Lineage" and "Sequence" are included in the table. These columns include the taxonomic classification of the ASV (according to Silva) and the ASV sequence, respectively.</li> <li>ASV_table_non_rarefied_percent.tsv.gz -- same as above, but the data are normalized within each sample and expressed as percentages (i.e., sum to 100%).</li> <li>ASV_table_rarefied_counts.tsv.gz -- same as "ASV_table_non_rarefied_counts.tsv.gz", except that data is rarefied to 12,000 sequences per sample. Five samples were dropped due to having <12,000 sequences.</li> <li>ASV_table_rarefied_percent.tsv.gz -- same as above, but the data are normalized within each sample and expressed as percentages (i.e., sum to 100%).</li> <li>MAG_abundances_to_unassembled_reads.tsv.gz -- table like an ASV table showing the relative abundances (expressed as percentages) of metagenome-assembled genomes within metagenomes. Aside from the index column and sample columns, additional columns are included to provide the taxonomic classification of the MAGs (based on the Genome Taxonomy Database) and the CheckM statistics of the MAGs. Relative abundances of MAGs in a metagenome are calculated as the number of mapped reads to the MAGs from the given metagenome divided by the total number of unassembled metagenome reads for that metagenome (times 100%).</li> <li>MAG_abundances_to_assembled_reads.tsv.gz -- same as above, except that relative abundances are divided by the total number of unassembled metagenome reads for that metagenome that mapped to that metagenome's assembled contigs.</li> <li>core_sample_metadata.tsv -- table of core physico-chemical and geographic metadata for the samples in this study (used to build biplots presented in the chapter). Note that "nd" means "no data available", and any measurements below detection limits have been set to 0. A limited number of values were inferred from other sampling time points -- these are noted in the table for TDFe measurements, and in addition, the light attenuation coefficient for Lake 373 in Sept. 2017 was inferred from the Sept. 2016 coefficient due to no light data being available for Sept. 2017 samples.</li> <li>metadata_descriptions.tsv -- descriptions of all metadata columns in the above file.</li> </ul> <p> </p>
Spatial patterns and effects of invasive plants on soil microbial activity and diversity along river corridors - dataset
<p>environmental data, plant community data, CLPP profiles, microbial activity data</p>
Fire decreases soil enzyme activities and reorganizes microbially-mediated nutrient cycles: a meta-analysis
<p class="MsoNormal"><span>The biogeochemical signature of fire shapes the functioning of many ecosystems. Fire changes nutrient cycles not only by volatilizing plant material, but also by altering organic matter decomposition—a process regulated by soil extracellular enzyme activities (EEAs). However, our understanding of fire effects on EEAs and their feedbacks to nutrient cycles is incomplete. We conducted a meta-analysis with 301 field studies and found that fire significantly decreased EEAs by ~20-40%. Fire decreased EEAs by decreasing soil microbial biomass and organic matter substrates. Soil nitrogen-acquiring EEA decreased alongside decreasing available nitrogen, likely from fire-driven volatilization of nitrogen and decreased microbial activity. Fire decreased soil phosphorus-acquiring EEA but increased available phosphorus, likely from pyro-mineralization of organic phosphorus. These findings suggest that fire suppresses soil microbes and consumes their substrates, thereby slowing microbially-mediated nutrient cycles (especially phosphorus) via decreased EEAs. These changes can become increasingly important as fire regimes in many ecosystems continue to shift in response to global change.</span></p>
Images of the work entitled "The spatial distribution of rhizosphere microbial activities under drought: water availability is more important than root-hair controlled exudation"
<p>These images are the images of zymography, <sup>14</sup>C imaging and neutron radiography of the work entitled "The spatial distribution of rhizosphere microbial activities under drought: water availability is more important than root-hair controlled exudation". Raw data on optimal water conditions were partially overlapping with the data of Bilyera et al., 2021, Soil Biology and Biochemistry, 162, 108426.</p>
dataset of the work entitled "The spatial distribution of rhizosphere microbial activities under drought: water availability is more important than root-hair controlled exudation"
<p>This is the dataset of the enzyme kinetics, and other biochemical properties obtained from zymography, <sup>14</sup>C images and water images of the work entitled "The spatial distribution of rhizosphere microbial activities under drought: water availability is more important than root-hair controlled exudation". </p>
Effects of pH and light exposure on the survival of bacteria and their ability to biodegrade organic compounds in clouds: Implications for microbial activity in acidic cloud water
<p>Our manuscript was submitted to ACP. Upon submission, all data must be accessible by anonymous access.</p>
Litter and root traits control soil microbial composition and enzyme activities in 28 common subtropical tree species
<p><span>1. </span><span>Plant trait-based approaches are frequently used to explore the linkages between aboveground plant communities and belowground ecosystem functions. However, the role of plant leaf litter and living root traits in driving soil microbial biomass, community composition, and enzyme activities has rarely been explored.</span></p> <p><span>2. </span><span>Here, we measured the soil microbial biomass, community composition and enzyme activities related to carbon (C), nitrogen (N), and phosphorus (P) acquisition under three-year-old monocultures of 28 common subtropical tree species in China.</span></p> <p><span>3. </span><span>We found that plant leaf litter and absorptive root traits, including leaf litter C content, litter water holding capacity, and root N content, were the three best predictors for soil microbial biomass and enzyme activities. In particular, resource-exploitative tree species with higher root N contents were associated with microbial communities with lower fungi to bacteria ratios and lower C- and P-acquisition enzyme activities. Tree species with higher leaf litter water holding capacity were associated with microbial resource acquisition strategies for C and P acquisition.</span></p> <p><span>4. </span><span>Synthesis: Our findings highlighted that plant leaf litter and root traits are important for mechanistically understanding the ecological linkage between the plant community and ecosystem functions.</span></p>
Phytochemical Screening and Microbial Activity of Essential Oil from Aerial Parts of Murraya paniculata (L.) Orange Jasmine
<p>Phytochemical Screening and Microbial Activity of Essential Oil from Aerial Parts of Murraya paniculata (L.) Orange Jasmine </p>
Phytochemical Screening and Microbial Activity of Essential Oil from Aerial Parts of Murraya paniculata (L.) Orange Jasmine
<p>Phytochemical Screening and Microbial Activity of Essential Oil from <br>Aerial Parts of Murraya paniculata (L.) Orange Jasmine </p>
Unaltered soil microbial community composition, but decreased metabolic activity in a semi-arid grassland after two years of passive experimental warming
<p>Soil microbial communities regulate soil carbon feedbacks to climate warming through microbial respiration (i.e. metabolic rate). A thorough understanding of the responses of composition, biomass and metabolic rate of soil microbial community to warming is crucial to predict soil carbon stocks in a future warmer climate. Therefore, we conducted a field manipulative experiment in a semi-arid grassland on the Loess Plateau of China to evaluate the responses of the soil microbial community to increased temperature from April 2015 to December 2017. Soil temperature was 2.0 <sup>o</sup>C higher relative to the ambient when open-top chambers (OTCs) were used. Warming did not affect microbial biomass or the composition of microbial functional groups. However, warming significantly decreased microbial respiration, directly resulting from soil pH decrease driven by the co-mediation of aboveground biomass increase, inorganic nitrogen increase and moisture decrease. These findings highlight that the soil microbial community structure of semi-arid grasslands resisted the short-term warming by 2 <sup>o</sup>C, although its metabolic rate declined.</p>
Recently fixed carbon fuels microbial activity several meters below the soil surface
<p>This data file (Scheibe_2022.xlsx) contains radiocarbon data of bulk soil carbon and CO<sub>2</sub> respired in incubations from soil profiles in three climate zones (arid, mediterranean, and humid) of the Costal Cordillera of Chile down to a depth of six meters. Variable descriptions are provided in Template Info File. The data are part of a study, which investigates how soil microbial carbon cycling affects soil formation especially in the critical zone by understanding the carbon source of microbial activity in deep soil. The study was conducted within the framework of the Deep EarthShape priority program funded by the German Science Foundation (DFG-SPP 1803).</p>
Viral genomes, functional genes, and microbial genomes of 144 activated sludge samples taken from 54 WWTPs across 13 countries on a global scale
<p>The study dataset contains 85,114 viral genomes, 1,115,185 viral functional genes, and 3,823 microbial genomes obtained from 54 WWTPs across 13 countries. </p><p>If this study dataset is useful, please cite: Fan, X., Ji, M., Mu, D. <i>et al.</i> Global diversity and biogeography of DNA viral communities in activated sludge systems. <i>Microbiome</i> <strong>11</strong>, 234 (2023). https://doi.org/10.1186/s40168-023-01672-1</p>
Fig. 5 in Catecholic alkaloid sulfonates and aromatic nitro compounds from Portulaca oleracea and screening of their anti-inflammatory and anti-microbial activities
Fig. 5. Possible biosynthetic pathway for the nitro derivatives, catecholic alkaloids and their sulfonates from P. oleracea (DDC: dopa decarboxylase; RNS: reactive nitrogen species; TH: tyrosine hydroxylase).
Fig. 6 in Catecholic alkaloid sulfonates and aromatic nitro compounds from Portulaca oleracea and screening of their anti-inflammatory and anti-microbial activities
Fig. 6. Dose-dependent inhibition of nitro derivative 12 against LPS-induced NO production in RAW 264.7 macrophage cells (n = 3) (****p <0.0001, versus vehicle control, ####p <0.0001, versus LPS-treated model, 3,4-dihydroxy-benzohydroxamic acid (Didox) was used as the positive control with IC value of 70 μM).
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.