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29 results for “Prochlorococcus”
Alteromonas macleodii MIT1002 growth on and uptake of Prochlorococcus-derived metabolites
This data package contains the results from a series of experiments designed to test the response of a heterotrophic, copiotrophic, gammaproteobacterium, Alteromonas macleodii strain MIT1002, to a range of metabolites released by the phytoplankton Prochlorococcus. A. macleodii MIT1002 was isolated from co-culture with Prochlorococcus, and so we hypothesized that A. macleodii MIT1002 would be able to grow on the full range of substrates tested. Instead, we found that A. macleodii MIT1002 could only grow on a narrow range of substrates, and data suggest that this substrate specificity may be related to transporter specificity. We performed two types of experiments: growth experiments and uptake experiments. Data from growth experiments are labeled with the name of the substrate being tested (e.g., “Leu,” for leucine, or “3m2ob”, for 3-methyl-2-oxobutanoic acid). For these experiments, we grew A. macleodii MIT1002 on either pyruvate (as a positive control), a selected Prochlorococcus-related substrate, or a mix of pyruvate and the metabolite. We measured growth in 96-well plates by OD600 using a plate reader which took a measurement every 0.5h for 48h. Uptake experiments are labeled with either “KHU7” (an experiment which tested A. macleodii MIT1002 growth on and uptake of 3-methyl-2-oxobutanoic acid) or “KHU8” (an experiment which tested the A macleodii MIT1002 growth on and uptake of 3-methyl-2-oxopentanoic acid -or lack thereof). For these experiments, we measured growth by flow cytometry. We measured the change in dissolved (i.e., extracellular) metabolite concentration by filtering samples, extracting organic carbon from the filtrate by solid phase extraction, and quantifying selected metabolites from the filtrate by targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS). This data package includes the peak areas for targeted metabolites generated by LC-MS/MS, the peak areas for our standard curves used for quantification, and the dissolved metabolite
Marker files for assessing Prochlorococcus genome completness
<p>Use these files with CheckM to assess Prochlorococcus genome completeness:</p> <p><em>pro-marker-checkm-refined.txt</em></p> <p>List of custom PFAM and TIGRFAM identifiers used to assess genome completeness in <em>Prochlorococcus</em> using checkM</p> <p><em>pro-marker-checkm-refined.ms</em></p> <p>CheckM marker file of custom PFAM and TIGRFAM identifiers used to assess genome completeness in <em>Prochlorococcus</em>.</p> <p><em>pro-marker-checkm-refined.hmm</em></p> <p>HMM file of custom Prochlorococcus markers for use with CheckM and hmmer3</p>
PanGEM Toolbox - Prochlorococcus pangenome
<p>Collection of all currently (1/29/2020) available genomes of Prochlorococcus, for use with the PanGEM Toolbox (https://github.com/jrcasey/PanGEM). Genomes were downloaded from NCBI and from IMG. </p>
Prochlorococcus Cell Concentrations During the BiG-RAPA Expedition (Cruise MV1015) in the Peru Current and Eastern South Pacific Subtropical Gyre Between November and December of 2010
<p>"These data include Prochlorococcus cell concentrations (total cell densities by flow cytometry and cell densities for specific ecotypes/clades determined by quantitative PCR). Samples were collected during the C-MORE Biogeochemical Gradients Role in Arranging Planktonic Assemblages (BiG-RAPA) expedition (Cruise MV1015) in the Peru Current and Eastern South Pacific Subtropical Gyre between dates 2010-11-19 and 2010-12-10 along a zonal transect from the northern coast of Chile to the island of Rapa Nui. Prochlorococcus is an important primary producer in the oligotrophic South Pacific Gyre and these data facilitate studies examining Prochlorococcus' ecology." https://www.bco-dmo.org/dataset/886299 Time is in UTC. Additional cruise information and methods can be found here: http://dmoserv3.bco-dmo.org/jg/info/BCO-DMO/C-MORE/prochlorococcus_data%7Bdir=dmoserv3.whoi.edu/jg/dir/BCO-DMO/C-MORE/,data=dmoserv3.bco-dmo.org:80/jg/serv/BCO-DMO/C-MORE/prochlorococcus_data.html0%7D?</p>
Prochlorococcus marinus digital microbe
<p>This is the digital microbe describing the model organism Prochlorococcus marinus MIT 9301. The data includes:</p> <p>- (P_MARINUS_MIT9301-contigs.db) the complete genome sequence of P. marinus MIT 9301, along with NCBI PGAP gene annotations and automatically-generated annotations from NCBI COGs, KEGG KOfam/BRITE, Pfams, and anvi'o single-copy core gene sets.</p> <p>- (P_marinus_reproducible_workflow.md) a reproducible workflow describing how the database was generated.</p>
Abundances of Heterotrophic Bacteria, Prochlorococcus, Synnechococcus, and Picoeucaryotes during the PARAGON2 cruise
<p>This dataset is part of the 2022 SCOPE-PARAGON II (PARticles And Growth in the Oceanic Nutricline) research expedition (KM2209 aboard the R/V Kilo Moana), a coordinated effort to characterize particle dynamics and remineralization in the upper 500 m of the North Pacific Subtropical Gyre (more info here: http://scope.soest.hawaii.edu/data/scope2022/scope2022.html). Cruise date: Aug 4 - Aug 12 2022; Cruise location: 17-24N, ~154W. The cruise tracked a high chlorophyll feature close to the Hawaiian Islands. Particle abundances of three separate chlorophyll containing populations were enumerated by autofluorescence using a B/D Influx flow cytometer: Prochlorococcus, Synechococcus and the pico-Eukaryotes. Heterotrophic bacteria were enumerated using the DNA stain SYBR Green I and subtracting the previously obtained Prochlorococcus concentration from the DNA positive cells. Particles were collected in situ and preserved following standard protocols for analysis in the lab (~6 months after collection). 1 micrometer polystyrene beads were added to all samples as reference. Timestamp is in UTC.</p>
MAGs generated in "Global scale phylogeography of functional traits and microdiversity in Prochlorococcus"
<p>High quality metagenomic assemblies from the manuscript "Global scale phylogeography of functional traits and microdiversity in <em>Prochlorococcus</em>". Pre-print available at: https://doi.org/10.1101/2023.01.24.525399</p>
Data from: Picoplankton carbon biomass assessments and distribution of Prochlorococcus ecotypes linked to Loop Current Eddies during summer in the southern Gulf of Mexico
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O. dioica feeding on Prochlorococcus sp.
<p>Unusually frequent spiracles ciliary reversals allow <em>Oikopleura dioica</em> fed on <em>Prochlorococcus</em> sp. to recover part of the cyanobacteria leaked from the pharyngeal filter through spiracles outside the animal’s body</p>
Spatial Distributions of Sea Surface Prochlorococcus, Synechococcus, and Picoeukaryotes
<p>The attached videos show estimated global distributions of sea surface <em>Prochlorococcus</em>, <em>Synechococcus</em>, and pico-eukaryotes cell abundances. To produce these estimates an Artificial Neural Network (ANN) is trained using more than 35 years of cell abundance observations. The training dataset is compiled using <a href="https://simonscmap.com/">Simons CMAP</a> python client (<a href="https://github.com/simonscmap/pycmap">pycmap</a>) and can be found <a href="https://doi.org/10.5281/zenodo.4108149">here</a>. Environmental variables are used as model features to predict the organism's abundances. Below is the list of employed features for each species:</p> <p> </p> <p><em>Prochlorococcus: </em><a href="https://simonscmap.com/catalog/datasets/Near_Real_Time%20SST_AVHRR_OI">Sea Surface Temperature</a> </p> <p><em>Synechococcus: </em><a href="https://simonscmap.com/catalog/datasets/Near_Real_Time%20SST_AVHRR_OI">Sea Surface Temperature</a>, <a href="https://simonscmap.com/catalog/datasets/Mercator_Pisces_Biogeochem_Climatology">Dissolved Nitrate (NO<sub>3</sub>) Concentration</a>, <a href="https://simonscmap.com/catalog/datasets/Reprocessed_8_Day_Satellite_CHL">Chlorophyll Concentration </a></p> <p>pico-eukaryotes: <a href="https://simonscmap.com/catalog/datasets/Near_Real_Time%20SST_AVHRR_OI">Sea Surface Temperature</a>, <a href="https://simonscmap.com/catalog/datasets/Mercator_Pisces_Biogeochem_Climatology">Dissolved Nitrate (NO<sub>3</sub>) Concentration</a>, <a href="https://simonscmap.com/catalog/datasets/Mercator_Pisces_Biogeochem_Climatology">Dissolved Oxygen (O<sub>2</sub>) Concentration</a>, <a href="https://simonscmap.com/catalog/datasets/SMAP_Ocean_Surface_Salinity">Sea Surface Salinity</a> </p>
Data from: Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus
Extensive genomic diversity within coexisting members of a microbial species has been revealed through selected cultured isolates and metagenomic assemblies. Yet, the cell-by-cell genomic composition of wild uncultured populations of co-occurring cells is largely unknown. In this work, we applied large-scale single-cell genomics to study populations of the globally abundant marine cyanobacterium Prochlorococcus. We show that they are composed of hundreds of subpopulations with distinct "genomic backbones," each backbone consisting of a different set of core gene alleles linked to a small distinctive set of flexible genes. These subpopulations are estimated to have diverged at least a few million years ago, suggesting ancient, stable niche partitioning. Such a large set of coexisting subpopulations may be a general feature of free-living bacterial species with huge populations in highly mixed habitats.
Supplementary data for "Novel isolates expand the physiological diversity of Prochlorococcus and illuminate its macroevolution" by Becker et. al.
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Data from: Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus
Open the record for dataset details and reuse information.
Impact of a heterotroph, Alteromonas MIT1002, on the transcriptome of Prochlorococcus NATL2A
GEO Series GSE73511. Prochlorococcus marinus str. NATL2A; Alteromonas macleodii. 42 samples. Type: Expression profiling by high throughput sequencing.
Impact of plastic leachates on marine Prochlorococcus strains
GEO Series GSE118155. Prochlorococcus marinus str. NATL2A; Prochlorococcus marinus str. MIT 9312. 18 samples. Type: Expression profiling by high throughput sequencing.
What happens to Prochlorococcus when the sun does not come up?
GEO Series GSE93197. Alteromonas macleodii; Prochlorococcus marinus str. NATL2A. 113 samples. Type: Expression profiling by high throughput sequencing.
The transcriptome landscape of Prochlorococcus MED4 and the factors for stabilizing the core genome
GEO Series GSE49517. Prochlorococcus marinus subsp. pastoris str. CCMP1986. 10 samples. Type: Expression profiling by high throughput sequencing.
Role of light in cyanophage infection of Prochlorococcus
GEO Series GSE79359. Prochlorococcus marinus subsp. pastoris str. CCMP1986; Prochlorococcus phage P-HM2. 40 samples. Type: Expression profiling by high throughput sequencing.
Emergence of metabolic coupling to the heterotroph Alteromonas promotes dark survival in Prochlorococcus
GEO Series GSE264347. Alteromonas macleodii; Prochlorococcus marinus str. NATL2A. 42 samples. Type: Expression profiling by high throughput sequencing.
Circadian and Light Perturbed Circadian Gene Expression in Prochlorococcus marinus MED4
GEO Series GSE314951. Prochlorococcus marinus. 44 samples. Type: Expression profiling by high throughput sequencing.
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