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10 results for “environmental biofilm”
Aquatic biofilm autotrohic index, carbon dioxide flux, and environmental conditions for the APEX water table experiment 2021-2023
To better understand linkages between hydrology and ecosystem carbon flux in northern aquatic ecosystems, we evaluated the relationship between plant communities, biofilm development, and carbon dioxide (CO2) exchange following long-term changes in hydrology in an Alaskan fen. We quantified seasonal variation in biofilm composition and CO2 exchange in response to lowered and raised water-table position (relative to a control) during years with varying levels of background dissolved organic carbon (DOC). We then used nutrient-diffusing substrates to evaluate cause-effect relationships between changes in plant subsidies (i.e., leachates) and biofilm composition among water-table treatments. We found that background DOC concentration determined whether plant subsidies promoted net autotrophy or heterotrophy on nutrient diffusing substrates. In conditions where background DOC was <= 40 mg L-1, plant subsidies promoted an autotrophic biofilm. Conversely, when background DOC concentration was >= 50 mg L-1, plant subsidies promoted heterotrophy. Greater light attenuation associated with elevated levels of DOC may have overwhelmed the stimulatory effect of nutrients on autotrophic microbes by constraining photosynthesis while simultaneously allowing heterotrophs to outcompete autotrophs for available nutrients. At the ecosystem level, conditions that favored an autotrophic biofilm resulted in net CO2 uptake among all water-table treatments, whereas the site was a net source of CO2 to the atmosphere in conditions that supported greater heterotrophy. Taken together, these findings show that hydrologic history interacts with changes in dominant plant functional groups to alter biofilm composition, which has consequences for ecosystem CO2 exchange.
Data supplementing the article "Aquatic biofilms as passive environmental DNA samplers: application to benthic macroinvertebrate communities in rivers" - raw MiSeq data inventories
<p>These data supplement the article “Aquatic biofilms as passive environmental DNA samplers: application to benthic macroinvertebrate communities in rivers” Sinziana F. Rivera, Valentin Vasselon, Nathalie Mary, Olivier Monnier, Fréderic Rimet & Agnès Bouchez submitted to “Molecular Ecology Resources” journal.</p> <p>The directory is composed of: “38_samples_fastq:files”: contains raw demultiplexed fastq files (R1. fastq and R2. fastq) for each of the 38 samples used in this study to produce OTUs and taxonomic inventories.</p> <p>“Samples id.xlsx”: contains the samples ID of the fastq files</p> <p>“Inventories.xlsx”: contains single and multi-habitat morphological inventories as well as molecular inventories resulting from the study</p>
Data from: Environmental switching during biofilm development in a cold seep system and functional determinants of species sorting
The functional basis for species sorting theory remains elusive, especially for microbial community assembly in deep-sea environments. Using artificial surface-based biofilm models, our recent work revealed taxonomic succession during biofilm development in a newly defined cold seep system, the Thuwal cold seeps II, which comprises a brine pool and the adjacent normal bottom water (NBW) to form a metacommunity via the potential immigration of organisms from one patch to another. Here, we designed an experiment to investigate the effects of environmental switching between the brine pool and the NBW on biofilm assembly, which could reflect environmental filtering effects during bacterial immigration to new environments. Analyses of 16S rRNA genes of 71 biofilm samples suggested that the microbial composition of biofilms established in new environments was determined by both the source community and the incubation conditions. Moreover, a comparison of 18 metagenomes provided evidence for biofilm community assembly that was based primarily on functional features rather than taxonomic identities; metal ion resistance and amino acid metabolism were the major species sorting determinants for the succession of biofilm communities. Genome binning and pathway reconstruction of two bacterial species (Marinobacter sp. and Oleispira sp.) further demonstrated metal ion resistance and amino acid metabolism as functional traits conferring the survival of habitat generalists in both the brine pool and NBW. The results of this study shed new light on microbial community assembly in special habitats and bridge a gap in species sorting theory.
Data from: Biofilm formation and toxin production provide a fitness advantage in mixed colonies of environmental yeast isolates
Open the record for dataset details and reuse information.
Data from: Environmental switching during biofilm development in a cold seep system and functional determinants of species sorting
Open the record for dataset details and reuse information.
Multipronged impact of environmental temperature on Staphylococcus aureus infection by phage Kayvirus rodi: Implications for biofilm control
GEO Series GSE255751. Staphylococcus aureus. 6 samples. Type: Expression profiling by high throughput sequencing.
Enhanced biofilm formation aids adaptation to extreme warming and environmental instability in the diatom Thalassiosira pseudonana and its associated bacteria
<p>These files contain all data necessary to create the figures published in "Enhanced biofilm formation aids adaptation to extreme warming and environmental instability in the diatom Thalassiosira pseudonana and its associated bacteria". In most cases, these are also the data that were used for analysis. Raw data and R code are available from the author upon request. Sequencing data will be available From GenBank in due course (accession numbers will be added to the zenodo file descriptor). </p> <p>1. File "20180930_biofilm_trajectories" contains the evolutionary trajectories of biofilm forming cells. The column names are as follows: 'count' for number of cells, 'size' is a unites ImageJ estimate, '%area' gives the area of the cover slip that had biofilm growth, 'date' is the date of the measurement and was used for internal purposes only, 'temp' is the selection temperature , 'nutrient' gives the nutrient status with n+ for nutrient replete and n- for lower nutrient status, 'week' for week of the experiment. Evoplas indicates whether the measurement was for the evolved samples in their selection environment ('evo', assay temperature is the same as selection temperature) or whether it was an assay for plasticity ('plas' , assay at a temperature other than the selection temperature). assay details the assay temperature. These data can be used to re-create and analyse Figure 3. (Figures 1 and 2 are conceptual figures; i.e there are no data associated)</p> <p>2. File "20180930Ability_to_form_biofilms" contains data for analysing whether a naive planktonic sample presented with a coverslip grows in a biofilm as well as a sample selected to form biofilms. Column names are the same as above, apart from the 'ability [...]' column, which is the ratio of biofilm growth of a biofilm-selected sample compared to a naive sample. Values >1 indicate that the biofilm selected samples grew larger biofilms faster than a planktonic samples subjected to the same conditions. These data are for Figure 6. </p> <p>3. File "20183009_biofilm_characterise" contains the data for Figure 4, i.e. information on cell size, chlorophyll a content, and bacterial load. The column names are as follows: trait is for either cell diameter in µm ('size'), chlorophyll a content ('chlorophyll'), or bacterial load. Selection temp is the selection temperature and nutr, the nutrient regime with full for full f/2 media and deplete for 1/3 of f/2 media. in 'sampletype' p is for planktonic cells, bf for the biofilm cells, and pbf for planktonic cells sloughed off the biofilm. Traitvalue is for the trait values. Size in µm, chlorophyll in pg per cell, and bacterial load in % of total biomass. </p>
Characterization of Biofilm Formation, Growth, and Gene Expression on Different Materials and Environmental Conditions in Microgravity (Gene expression of Pseudomonas aeruginosa biofilms)
Microorganisms' natural ability to live as organized multicellular communities – also known as biofilms – provides them with unique survival advantages. For instance, biofilms are protected against environmental stresses thanks to their extracellular matrix, which could contribute to persistent infections after treatment. Biofilms are also capable of strongly attaching to surfaces, where their metabolism byproducts could lead to surface material degradation. Furthermore, microgravity can alter biofilm behavior in unexpected ways, making the presence of biofilms in space a risk for both astronauts and spaceflight hardware. Despite the efforts to eliminate microorganism contamination from spacecrafts surfaces, it is impossible to prevent human-associated bacteria or fungus from eventually establishing biofilm surface colonization. Nevertheless, by understanding the changes that biofilms undergo in microgravity, it is possible to identify key differences and pathways that could be targeted to significantly reduce biofilm formation. The Space Biofilms project, performed at the International Space Station, contributes to such understanding by characterizing the morphology and gene expression of bacterial and fungal biofilms formed in microgravity with respect to ground controls. Pseudomonas aeruginosa was used as model organism for the bacterial morphology and transcriptomic studies, while Penicillium rubens was used for the fungal morphology study. Bacterial biofilm formation was characterized at one, two, and three days of incubation (37°C) over six different materials: stainless steel 316, passivated stainless steel 316, a lubricant impregnated surface (LIS), catheter grade silicone with and without a linear microtopography, and cellulose membrane.
Characterization of Biofilm Formation, Growth, and Gene Expression on Different Materials and Environmental Conditions in Microgravity (Morphology of Penicillium rubens biofilms)
Microorganisms' natural ability to live as organized multicellular communities – also known as biofilms – provides them with unique survival advantages. For instance, biofilms are protected against environmental stresses thanks to their extracellular matrix, which could contribute to persistent infections after treatment. Biofilms are also capable of strongly attaching to surfaces, where their metabolism byproducts could lead to surface material degradation. Furthermore, microgravity can alter biofilm behavior in unexpected ways, making the presence of biofilms in space a risk for both astronauts and spaceflight hardware. Despite the efforts to eliminate microorganism contamination from spacecrafts surfaces, it is impossible to prevent human-associated bacteria or fugus from eventually establishing biofilm surface colonization. Nevertheless, by understanding the changes that biofilms undergo in microgravity, it is possible to identify key differences and pathways that could be targeted to significantly reduce biofilm formation. The Space Biofilms project, performed at the International Space Station, contributes to such understanding by characterizing the morphology and gene expression of bacterial and fungal biofilms formed in microgravity with respect to ground controls. Pseudomonas aeruginosa was used as model organism for the bacterial morphology and transcriptomic studies, while Penicillium rubens was used for the fungal morphology study. The data presented on this study page represent the morphology of Penicillium rubens using the confocal microscopy assay.
Characterization of Biofilm Formation, Growth, and Gene Expression on Different Materials and Environmental Conditions in Microgravity (Morphology of Pseudomonas aeruginosa biofilms)
Microorganisms' natural ability to live as organized multicellular communities – also known as biofilms – provides them with unique survival advantages. For instance, biofilms are protected against environmental stresses thanks to their extracellular matrix, which could contribute to persistent infections after treatment. Biofilms are also capable of strongly attaching to surfaces, where their metabolism byproducts could lead to surface material degradation. Furthermore, microgravity can alter biofilm behavior in unexpected ways, making the presence of biofilms in space a risk for both astronauts and spaceflight hardware. Despite the efforts to eliminate microorganism contamination from spacecrafts surfaces, it is impossible to prevent human-associated bacteria or fugus from eventually establishing biofilm surface colonization. Nevertheless, by understanding the changes that biofilms undergo in microgravity, it is possible to identify key differences and pathways that could be targeted to significantly reduce biofilm formation. The Space Biofilms project, performed at the International Space Station, contributes to such understanding by characterizing the morphology and gene expression of bacterial and fungal biofilms formed in microgravity with respect to ground controls. Pseudomonas aeruginosa was used as model organism for the bacterial morphology and transcriptomic studies, while Penicillium rubens was used for the fungal morphology study. The data presented on this study page represent the morphology of Pseudomonas aeruginosa using the confocal microscopy assay.
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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.
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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.