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506 results for “cyanobacteria”
Global eutrophication and antibiotic resistance genes dataset for "Coupling mechanisms between cyanobacteria and antibiotic resistance genes in freshwater ecosystems"
This dataset compiles global records of cyanobacteria, antibiotic resistance genes (ARGs), and associated water quality parameters to support research on freshwater ecosystem dynamics. It includes 990 metagenomes, 16,648 chlorophyll-a (Chl-a) records, and over 90 documented cases of ARGs–cyanobacteria co-occurrence under comparable spatiotemporal conditions. The dataset covers the years 2000–2024 and provides both raw measurements and harmonized tables for cross-study comparisons. Data were extracted from previously published literature and public repositories, with references to source publications included. This archive is intended to facilitate reproducible analyses, enable large-scale meta-studies, and support further exploration of microbial interactions in freshwater systems.
S75 | CyanoMetDB | Comprehensive database of secondary metabolites from cyanobacteria
<p>This is the collection associated with list S75 CyanoMetDB Comprehensive database of secondary metabolites from cyanobacteria on the NORMAN Suspect List Exchange.</p> <p><a href="https://www.norman-network.com/nds/SLE/">https://www.norman-network.com/nds/SLE/</a></p> <p>CyanoMetDB is a comprehensive database of secondary metabolites from cyanobacteria manually curated from primary references described in Jones et al (2021), DOI: <a href="https://doi.org/10.1016/j.watres.2021.117017">10.1016/j.watres.2021.117017</a> (preprint DOI: <a href="https://doi.org/10.1101/2020.04.16.038703">10.1101/2020.04.16.038703</a>). This upload contains the 2024 release. Please cite Jones et al (2021) DOI: <a href="https://doi.org/10.1016/j.watres.2021.117017">10.1016/j.watres.2021.117017</a> and this record Janssen et al (2024) DOI: <a href="https://doi.org/10.5281/zenodo.13854577">10.5281/zenodo.13854577</a> when using this CyanoMetDB Version 3!</p> <p><em><strong>Contents: </strong></em></p> <p><em><strong>CyanoMetDB XLSX database (2024 release): <a href="https://zenodo.org/records/13854577/files/CyanoMetDB_Version03.xlsx?download=1">CyanoMetDB_Version03.xlsx</a></strong></em></p> <p>Additional files for workflows:</p> <p>CSV format: <a href="https://zenodo.org/records/13854577/files/CyanoMetDB_V03_2024.csv?download=1">CyanoMetDB_V03_2024.csv</a><br>MetFrag local CSV file (original database abridged and reformatted for use in MetFrag): <a href="https://zenodo.org/records/13854577/files/CyanoMetDB_V03_2024_MetFrag.csv?download=1">CyanoMetDB_V03_2024_MetFrag.csv</a><a href="https://zenodo.org/api/files/7d71e4a9-e5f2-4ca3-ac55-6467a356ab9a/CyanoMetDB_MetFrag_Feb2021.csv"> </a><br>Additional files for matching InChIKeys (rapid suspect flagging): <a href="https://zenodo.org/records/13854577/files/CyanoMetDB_V03_2024_InChIKeys.txt?download=1">CyanoMetDB_V03_2024_InChIKeys.txt</a></p> <p>Corresponding author: Elisabeth Janssen (Eawag): <a href="mailto:Elisabeth.Janssen@eawag.ch">Elisabeth.Janssen@eawag.ch</a></p>
Cyanobacteria abundance, cyanotoxin concentration, and water quality data for the upper San Francisco Estuary, California, USA: 2014-2019
The goal of these measurements was to quantify Microcystis abundance and microcystin concentration and associated water quality conditions during summer blooms in the upper San Francisco Estuary in California, USA. Blooms of harmful algae are a major ecological concern in the area because harmful algae produce toxins and other metabolites, which deteriorate water quality and negatively impact the aquatic ecosystem. Our research team collected biological, physical, and chemical data at 2-week to 4-week intervals during the summer and fall from 2014 through 2019. Data included surface measurements of Microcystis volume (area-based diameter) by microscopy (flowCAM digital imaging flow cytometry) and subsurface (1 m depth) measurements of Microcystis, Aphanizomenon and Dolichospermum cell abundance measured by quantitative PCR, cyanotoxin concentration (total microcystins, anatoxin a and saxitoxin) measured by protein phosphatase inhibition assay or enzyme linked immunosorbent assay, and a suite of water quality parameters (water temperature, dissolved oxygen, nutrient concentration, water transparency, specific conductance, turbidity, pH, and chlorophyll a concentration). Details for the field sampling and analytical methods are available in Lehman et al. (2017). We also performed shotgun metagenomic analyses to investigate biodiversity of cyanobacteria and other aquatic microorganisms and all the DNA sequencing data are publicity available (www.ncbi.nlm.nih. gov/; BioProject ID: PRJNA434758, Kurobe et al. 2018, Lehman et al. 2021). During the study, we experienced critically dry (2014 and 2015), below normal (2016 and 2018), and wet years (2017 and 2019), therefore data obtained in this study provided a unique opportunity to assess impacts of extreme conditions on the aquatic ecosystem (Kurobe et al. 2018, Lehman et al. 2020).
Green algae, cyanobacteria and diatom concentrations from the GCE-LTER Seawater Addition Long-Term Experiment (SALTEx) Project
SALTEx (Seawater Addition Long-Term Experiment) is a field experiment designed to simulate saltwater intrusion in a tidal freshwater wetland to predict how chronic (Press) and acute (Pulse) salinization will affect this and other tidal freshwater ecosystems. The SALTEx experiment was initiated in 2012 and consists of 31 field plots , each 2.5 m on a side. There are three treatments (Press, Pulse, and Fresh) and two types of controls (with and without sides), each consisting of six replicates. The Press treatment plots receive regular (4 times each week) additions of a mixture of seawater and fresh river water. Pulse plots receive the same mixture of seawater and river water during September and October, which is historically a time of low flow in the river when natural saltwater intrusion occurs. The Fresh treatment plots receive regular additions of fresh river water. Treatment water is added during low tide to facilitate its infiltration into the soil, and all plots are inundated by astronomical tides at high tide. We are measuring the abundance of benthic algae with a BenthoTorch as one of the response variables for the SALTEx project.
DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region
<p>This dataset has been prepared as part of the Interreg Alpine Space project Eco-AlpsWater (ASP569) - <em>Innovative Ecological Assessment and Water Management Strategy for the Protection of Ecosystem Services in Alpine Lakes and Rivers</em>, <a href="https://www.alpine-space.eu/projects/eco-alpswater/en/home">https://www.alpine-space.eu/projects/eco-alpswater/en/home</a></p> <p>Individual archives include 16S rRNA (cyanobacteria) and 18S rRNA (microalgae) FASTA sequences and associated blastn results obtained from the high throughput sequencing of plankton and biofilm bulk/eDNA samples collected in 2019 in 37 lakes and 22 rivers across the Alpine region. These are supporting files for the paper by Salmaso et al., 2022. DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region. Science of the Total Environment, in press.</p>
Data set used in glacier algae and filamentous cyanobacteria models
<p>This is a data set for using the glacier algae and filamentous cyanobacteria models (Onuma et al., 2022). The content is as below.</p> <p>- data: observed data (bio-volume, cell count, mineral weight, EC, pH and meteorological conditions) on the bare ice surface in Qaanaaq Ice Cap (CSV files). And, model input and output data (CSV files). About the detailed information on each file, please see the readme files.</p> <p>- python: programs for the visualization (python scripts)</p> <p>- figure: png files created by the python scripts</p> <p>The codes of the glacier algae model can be downloaded below.<br> https://github.com/YukihikoOnuma/SnowAlgaeModel<br> <br> The article regarding the models is as below.<br> https://doi.org/10.1017/jog.2022.76</p>
Optimising multispectral active fluorescence to distinguish the photosynthetic variability of cyanobacteria and algae
<p>Dataset underlying the following paper:</p> <p>Courtecuisse, E.; Marchetti, E.; Oxborough, K.; Hunter, P.D.; Spyrakos, E.; Tilstone, G.H.; Simis, S.G.H. Optimising Multispectral <br> Active Fluorescence to Distinguish the Photosynthetic Variability of Cyanobacteria and Algae. Sensors 2023, 23</p> <p>This study assesses the ability of a new active fluorometer, the LabSTAF, to diagnostically assess the physiology of freshwater cyanobacteria in a reservoir exhibiting annual blooms. Specifically, we analyse the correlation of relative cyanobacteria abundance with photosynthetic parameters derived from fluorescence light curves (FLCs) obtained using several combinations of excitation wavebands, photosystem II (PSII) excitation spectra and the emission ratio of 730 over 685 nm (Fo(730/685)) using obtained with excitation protocols with varying degrees of sensitivity to cyanobacteria and algae. FLCs captured obtained with blue excitation (B) and green–orange–red (GOR) excitation wavebands capture physiology parameters of algae and cyanobacteria, respectively. The green–orange (GO) protocol, expected to have the best diagnostic properties for cyanobacteria, did not guarantee PSII saturation. PSII excitation spectra showed distinct response from cyanobacteria and algae, depending on spectral optimisation of the light dose. Fo(730/685), obtained using a combination of GOR excitation wavebands, Fo(GOR, 730/685), showed a significant correlation with the relative abundance of cyanobacteria (linear regression, p-value < 0.01, adjusted R2 = 0.42). We recommend using, in parallel, Fo(GOR, 730/685), PSII excitation spectra (appropriately optimised for cyanobacteria versus algae), and physiological parameters derived from the FLCs obtained with GOR and B protocols to assess the physiology of cyanobacteria and to ultimately predict their growth. Higher intensity LEDs (G and O) should be considered to reach PSII saturation to further increase diagnostic sensitivity to the cyanobacteria component of the community.</p>
Number of cyanobacteria in Toolik Lake at 1 meter depth during June, July and August 1996 , Arctic LTER, summer 1996.
Number of cyanobacteria in Toolik Lake at 1 meter depth during June, July and August 1996. Samples were transported to the Dept. of Fisheries and Oceans in West Vancouver, British Columbia, Canada for analysis.
Cover of ground lichens, bryophytes, and cyanobacteria: Biodiversity II: Effects of Plant Biodiversity on Population and Ecosystem Processes
Biodiversity II (E120) is designed to determine how the number of plant species affects the dynamics of ecological processes at the population, community, and ecosystem levels. By experimentally manipulating the number of species and the kinds of species, the amount of plant growth and the change from year to year, that result can be examined. Plots are large (9m x 9m actively maintained) and well-replicated, allowing responses of plant pathogens, insect herbivores, seed predators, soil parameters, invasive plant species and other variables to also be studied. Plots were seeded in May 1994 to have 1, 2, 4, 8, or 16 species, with roughly 30 replicates of each diversity level. The species composition of each plot was chosen by random draw from a pool of 18 grassland perennials that included four warm-season (C4) grasses, four cool-season (C3) grasses, four legumes, four non-legume forbs, and two woody species. All species occur in monoculture allowing comparison of responses of each species in monoculture to combinations of these same species. The experiment was established in 1994 by the lead investigators David Tilman, Peter Reich, Johannes Knops, and David Wedin. Experiment 120 is similar to Experiment 123, but it uses larger plots to provide a large capacity for long-term subexperiments.
Effect of foot disturbance to cyanobacteria-dominated biocrusts on microbes and nitrogen in Chihuhuahan grassland and shrubland
Interactions between plants and soil microbes influence plant nutrient transformations, including nitrogen (N) fixation, nutrient mineralization, and resource exchanges through fungal networks. Physical disturbances to soils can disrupt soil microbes and associated processes that support plant and microbial productivity. In low resource drylands, biological soil crusts ("biocrusts") occupy surface soils and house key autotrophic and diazotrophic bacteria, non-vascular plants, or lichens. Interactions among biocrusts, plants, and fungal networks between them are hypothesized to drive carbon and nutrient dynamics; however, comparisons across ecosystems are needed to generalize how soil disturbances alter microbial communities and their contributions to N pools and transformations. To evaluate linkages among plants, fungi, and biocrusts, we disturbed all unvegetated surfaces with human foot trampling twice yearly in dry conditions from 2013-2018 in cyanobacteria-dominated biocrusts in Chihuahuan Desert grassland and shrubland ecosystems. Our study included microbial communities and N pools sampled at different time points in the disturbance treatments at one or both sites. We began our sampling after observations in April 2018 that the chlorophyll a content was at least double in control than disturbed plots in both ecosystems (Chung et al. 2019). Stomping occurred in May, and we collected soil and plant samples in June 2018 for N pools and soil and root fungal abundance. We collected additional soil samples in September 2018 and conducted the 15N tracer experiment to observe rates of N transfer from biocrust to plants before the fall stomp treatment in October. We collected chlorophyll a samples and soils for sequencing bacteria in September of 2019, also before the fall stomp treatment.
FIG. 1 in Marine cyanobacteria diversity and biotechnological potential in Caribbean waters
FIG. 1. — Map showing Caribbean countries were studies on cyanobacteria have been reported (gray) and those that have no reports yet (white).
Data and code from: Seasonal variation in the response to a toxin-producing cyanobacteria in Daphnia
<p>Data and code accompanying: </p> <p>Hegg, Radersma & Uller. 2022. Seasonal variation in the response to a toxin-producing cyanobacteria in Daphnia. Freshwater Biology, accepted.</p> <p><strong>Abstract</strong></p> <ol> <li>Many populations of water fleas (<em>Daphnia</em>) are exposed to algal blooms dominated by microcystin-producing cyanobacteria. However, the severity of these effects on <em>Daphnia</em> fitness remain poorly understood in natural populations. </li> <li>We investigated seasonal changes in body size, reproduction and survival of <em>Daphnia</em> <em>longispina</em> individuals from five eutrophic lakes in southern Sweden. We tested whether individuals collected before, during or following algal blooms differed in their reproduction and survival when experimentally exposed to microcystin-producing cyanobacteria. </li> <li>The concentration of microcystin in the lakes was significantly higher during summer and autumn compared to spring, but there were substantial differences between lakes. The reproductive output of individuals declined consistently over the season, and this decline was stronger for <em>Daphnia</em> collected during periods of, or lakes from, high microcystin concentration. There was little evidence that individuals adapted to the toxin over the season. </li> <li>The strong seasonal changes in body size, reproduction and survival in these <em>Daphnia</em> <em>longispina</em> appears to be partly caused by variation in the abundance of toxin-producing cyanobacteria. Populations were unable to adapt sufficiently quickly during summer and autumn to recover from the negative effects of microcystin. We therefore suggest that seasonal increases in tolerance to microcystin-producing cyanobacteria have limited effects on the eco-evolutionary dynamics between <em>Daphnia</em> and phytoplankton.</li> </ol>
Carbon Nanotube Uptake in Cyanobacteria for Near-infrared Imaging and Enhancing Bioelectricity Generation in Living Photovoltaics
<p>Dataset of the work entitled "Carbon Nanotube Uptake in Cyanobacteria for Near-infrared Imaging and Enhancing Bioelectricity Generation in Living Photovoltaics".</p>
Data from: Stochastic character mapping, Bayesian model selection, and biosynthetic pathways shed new light on the evolution of habitat preference in cyanobacteria
<p>Cyanobacteria are the only prokaryotes to have evolved oxygenic photosynthesis paving the way for complex life. Studying the evolution and ecological niche of cyanobacteria and their ancestors is crucial for understanding the intricate dynamics of biosphere evolution. These organisms frequently deal with environmental stressors such as salinity and drought, and they employ compatible solutes as a mechanism to cope with these challenges. Compatible solutes are small molecules that help maintain cellular osmotic balance in high-salinity environments, such as marine waters. Their production plays a crucial role in salt tolerance, which, in turn, influences habitat preference. Among the five known compatible solutes produced by cyanobacteria (sucrose, trehalose, glucosylglycerol, glucosylglycerate, and glycine betaine), their synthesis varies between individual strains. In this study, we work in a Bayesian stochastic mapping framework, integrating multiple sources of information about compatible solute biosynthesis in order to predict the ancestral habitat preference of Cyanobacteria. Through extensive model selection analyses and statistical tests for correlation, we identify glucosylglycerol and glucosylglycerate as the most significantly correlated with habitat preference, while trehalose exhibits the weakest correlation. Additionally, glucosylglycerol, glucosylglycerate, and glycine betaine show high loss/gain rate ratios, indicating their potential role in adaptability, while sucrose and trehalose are less likely to be lost due to their additional cellular functions. Contrary to previous findings, our analyses predict that the last common ancestor of Cyanobacteria (living at around 3180 Ma) had a 97% probability of a high salinity habitat preference and was likely able to synthesize glucosylglycerol and glucosylglycerate. Nevertheless, cyanobacteria likely colonized low-salinity environments shortly after their origin, with an 89% probability of the first cyanobacterium with low-salinity habitat preference arising prior to the Great Oxygenation Event (2460 Ma). Stochastic mapping analyses provide evidence of cyanobacteria inhabiting early marine habitats, aiding in the interpretation of the geological record. Our age estimate of ~2590 Ma for the divergence of two major cyanobacterial clades (Macro- and Microcyanobacteria) suggests that these were likely significant contributors to primary productivity in marine habitats in the lead-up to the Great Oxygenation Event, and thus played a pivotal role in triggering the sudden increase in atmospheric oxygen.</p>
FIG. 7. — A in The culture collection of cyanobacteria and microalgae at the French National Museum of Natural History: a century old but still alive and kicking! Including in memoriam: Professor Alain Couté
FIG. 7. — A, geographical distribution of cyanobacterial strains isolated around the world; B, strains isolated in the different administrative districts of France (metropolitan and overseas). Number of cyanobacterial strains in black, number of eukaryotic strains in blue. Strains isolated in France represent 58.0 % and 98.4 % of cyanobacterial and eukaryotic strains, respectively, in the collection.
FIG. 10 in The culture collection of cyanobacteria and microalgae at the French National Museum of Natural History: a century old but still alive and kicking! Including in memoriam: Professor Alain Couté
FIG. 10. — Culture of Onychonema filiforme (MNHN-ALCP-0000-086.1): A, from the 1948 catalogue of the algotheca (photo: R. Lami); B, the same culture observed in 2021 (photo: M. Jarno).
FIG. 5 in The culture collection of cyanobacteria and microalgae at the French National Museum of Natural History: a century old but still alive and kicking! Including in memoriam: Professor Alain Couté
FIG. 5. — Relative abundances of the different orders among the 1010 live strains represented in the cyanobacteria collection (left) and of the different phyla among the 345 live strains represented in the eukaryotic microalgae collection (right).
FIG. 6 in The culture collection of cyanobacteria and microalgae at the French National Museum of Natural History: a century old but still alive and kicking! Including in memoriam: Professor Alain Couté
FIG. 6. — Morphological diversity of cyanobacterial strains:A, B, Pseudochroococcus couteii (MNHN-PMC-2014-885); C, D, Planktothrix agardhii (MNHN-PMC-2002-75); E, F, Aphanizomenon gracile (MNHN-PMC-2010-627); G, H, Haloleptolyngbya elongata (MNHN-PMC-2015-895). Abbreviations: ae, aerotope; cc, cross-walls; cy, cyanophycin granules; cw, cell wall; mu, mucilage; r, reserves; s, sheath; tz, transparent zone; t, thylakoids. A, C, E, G: light microscopy; B, D, F, H: TEM micrographs. Scale bars: A, C, E, G, 10 µm; B, D, F, H, 500 nm.
FIG. 4 in The culture collection of cyanobacteria and microalgae at the French National Museum of Natural History: a century old but still alive and kicking! Including in memoriam: Professor Alain Couté
FIG. 4. — Emission spectra produced by Cool Daylight FLUO MAZDA (red) and White LEDs SLV (blue), both at a 85 μmol.m-2.s-1 (PAR) irradiance.
FIG. 1 in The culture collection of cyanobacteria and microalgae at the French National Museum of Natural History: a century old but still alive and kicking! Including in memoriam: Professor Alain Couté
FIG. 1. — From left to right: Pierre Allorge (1891-1944), Marcel Lefèvre (1897-1975) & Pierre Bourrelly (1910-1995).
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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)
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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.