http://lod.bco-dmo.org/id/dataset/905306 eng; USA utf8 dataset Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 2023-08-01 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Transcriptomes of co-cultured marine microbes (Emiliania huxleyi, Thalassiosira pseudonana, and Synechococcus) and Ruegeria pomeroyi DSS-3 2023-08-01 publication 2023-08-01 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2023-08-21 publication https://doi.org/10.26008/1912/bco-dmo.905306.1 Mary Ann Moran University of Georgia principalInvestigator Malin Olofsson University of Georgia principalInvestigator Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. publisher Cite this dataset as: Olofsson, M., Smith, C., Moran, M. A. (2023) Transcriptomes of co-cultured marine microbes (Emiliania huxleyi, Thalassiosira pseudonana, and Synechococcus) and Ruegeria pomeroyi DSS-3. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-08-01 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.905306.1 [access date] Transcriptomes of co-cultured marine microbes and Ruegeria pomeroyi DSS-3 Dataset Description: &lt;p&gt;The CSV file available here describes the samples, methods, and fastq files for raw data available from the Joint Genome Institute (JGI) at &lt;a href=&quot;https://data.jgi.doe.gov&quot; target=&quot;_blank&quot;&gt;https://data.jgi.doe.gov&lt;/a&gt;. The data in JGI can be found under the following project ID numbers: 1290093, 1290172, 1290174, 1317772, 1317774, 1317776, 1317778, and 1334780.&lt;/p&gt; Methods and Sampling: &lt;p&gt;Laboratory studies were carried out at the University of Georgia, Athens, GA, USA. The studies took place over the following dates:&lt;br /&gt; Thalassiosira: 1-7th July 2020&lt;br /&gt; Synechococcus: 16-23rd Feb 2021&lt;br /&gt; Emiliania: 18-28th May 2021&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Emiliania huxleyi CCMP151&lt;/strong&gt;&lt;br /&gt; A laboratory study was conducted using cultures of a marine coccolithophore (&lt;em&gt;Emiliania huxleyi &lt;/em&gt;CCMP151) and heterotrophic bacterium, &lt;em&gt;Ruegeria pomeroyi&lt;/em&gt;. Coccolithophore cultures were pre-acclimated to three temperature treatments (15°, 20°, and 28° Celsius) and&amp;nbsp;grown co-cultures. The transcriptome treatments consisted of axenic coccolithophore, the coccolithophore with the bacterium, and the bacterium with the coccolithophore, and three replicates were analyzed at each sample point. Stranded RNA-Seq libraries were sequenced using an Illumina NovaSeq instrument. For co-cultures, &lt;em&gt;E. huxleyi&lt;/em&gt; and bacterial cells were separated by filtration prior to RNA extraction.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Thalassiosira pseudonana CCMP1335&lt;/strong&gt;&lt;br /&gt; A laboratory study was conducted using cultures of a marine diatom (&lt;em&gt;Thalassiosira pseudonana&lt;/em&gt; CCMP1335) and heterotrophic bacterium, &lt;em&gt;Ruegeria pomeroyi.&lt;/em&gt; Diatom cultures were pre-acclimated to three temperature treatments (14°, 20°, and 28° Celsius) and grown as co-cultures. The transcriptome treatments consisted of axenic diatom, the diatom with the bacterium, and the bacterium with the diatom, and three replicates were analyzed at each sample point. Stranded RNA-Seq libraries were sequenced using an Illumina NovaSeq instrument. For co-cultures, diatom and bacterial cells were separated by filtration prior to RNA extraction.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Synechococcus sp. WH8102&lt;/strong&gt;&lt;br /&gt; A laboratory study was conducted using cultures of a marine cyanobacterium (&lt;em&gt;Synechococcus &lt;/em&gt;sp. WH8102 and heterotrophic bacterium, &lt;em&gt;Ruegeria pomeroyi.&lt;/em&gt; &lt;em&gt;Synechococcus&lt;/em&gt; cultures were pre-acclimated to three temperature treatments (20°, 24°, and 28° Celsius) and grown as co-cultures. The transcriptome treatments consisted of axenic Synechococcus, Synechococcus with the heterotrophic bacterium, and the bacterium with the Synechococcus, and three replicates were analyzed at each sample point. Stranded RNA-Seq libraries were sequenced using an Illumina NovaSeq instrument. RNA extraction of co-cultures was carried out without prefiltration, and transcripts were separated at mapping.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1948104 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1948104 Funding provided by US Department of Energy - Joint Genome Institute (DOE-JGI) Award Number: JGI Proposal 50689 Award URL: https://dx.doi.org/10.46936/10.25585/60001361 completed Mary Ann Moran University of Georgia 706-542-6481 Department of Marine Sciences Athens GA 30602 USA mmoran@uga.edu pointOfContact Malin Olofsson University of Georgia Uppsala Sweden malin.olofsson@slu.se pointOfContact asNeeded Dataset Version: 1 Unknown Taxon JGI_Project_Name JGI_Project_ID Library_Name Sample_Name Replicate Sample_condition Filtered_Raw_Data_file Illumina NovaSeq theme None, User defined taxon project sample identification replicate treatment file_name featureType BCO-DMO Standard Parameters Automated DNA Sequencer instrument BCO-DMO Standard Instruments otherRestrictions otherRestrictions Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use. Effects of Climate Change Variables on Microbial Autotroph-Heterotroph Carbon Flux https://osprey.bco-dmo.org/project/787536 Effects of Climate Change Variables on Microbial Autotroph-Heterotroph Carbon Flux <p><em>NSF Award Abstract:</em><br /> Phytoplankton in the surface ocean are responsible for roughly half of all photosynthesis on the planet. Much of the organic material created by these photosynthetic organisms is ultimately consumed by diverse marine bacteria with differing preferences for specific types of chemical compounds. This project investigates how climate change (temperature and CO2) might alter the types and amounts of organic compounds produced by different species of marine phytoplankton and the types and amounts of compounds transferred from phytoplankton to marine bacteria. Shifts in organic compounds transferred to bacteria could alter the distribution of bacterial species in the ocean, their growth rates and efficiencies, and flows of energy through the global ocean. This project helps scientists better understand the effects of climate change on marine ecosystems. Two graduate students and a postdoctoral researcher are supported by the project, receiving interdisciplinary training in biology, chemistry, and ocean sciences. Summer research internships in the PIs' laboratories are offered to AP Biology students enrolled at Cedar Shoals High School in Athens, GA, a school that serves a diverse social and economic community.</p> <p>Much of the bacterial secondary production in the surface ocean is supported by rapid uptake of labile metabolites released from phytoplankton, either directly through excretion and diffusion or indirectly through lysis and predation. This project investigates the effects of two climate change variables (temperature and CO2) on the metabolite pools produced and released by three model phytoplankton species (a diatom, a coccolithophore, and a cyanobacterium) and assesses changes in the composition and fate of metabolites transferred to bacteria. Phytoplankton species are being grown axenically at two different temperatures and CO2 concentrations in a factorial design and endo- and exometabolite composition is determined using NMR. A suite of phytoplankton physiological characteristics is measured and evaluated in the context of metabolite composition. Experiments with heterotrophic bacteria (either model bacteria or natural bacterial communities) are being conducted to assess the effects of climate change variables on metabolite transfer from phytoplankton to marine bacteria. In the first experiment type, bacteria are co-cultured with the phytoplankton at different temperatures and CO2 concentrations, and changes in bacterial gene expression and metabolite concentrations are used to assess shifts in the composition of metabolites transferred. In the second type, bacteria are grown on phytoplankton metabolite pools produced at different temperatures and CO2 concentrations in high-throughput bioassays, and changes in bacterial traits (growth rate, carrying capacity, growth efficiency) resulting from the different climate scenarios are used to indicate changes in metabolite quality. Knowledge of how the heterotrophic processing of phytoplankton metabolites might shift in response to climate change allows better prediction of Earth's future carbon cycle.</p> <p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p> CC_Auto_Hetero_Fluxes largerWorkCitation project eng; USA oceans 2020-07-01 2021-05-28 Laboratory in Athens, GA, USA, and waters around Sapelo Island, GA, USA 0 BCO-DMO catalogue of parameters from Transcriptomes of co-cultured marine microbes (Emiliania huxleyi, Thalassiosira pseudonana, and Synechococcus) and Ruegeria pomeroyi DSS-3 Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact http://lod.bco-dmo.org/id/dataset-parameter/905368.rdf Name: Taxon Units: unitless Description: <p>name of strain</p> http://lod.bco-dmo.org/id/dataset-parameter/905369.rdf Name: JGI_Project_Name Units: unitless Description: <p>name of sequencing project at the Joint Genome Institute Data portal (<a href="https://data.jgi.doe.gov" target="_blank">https://data.jgi.doe.gov</a>)</p> http://lod.bco-dmo.org/id/dataset-parameter/905370.rdf Name: JGI_Project_ID Units: unitless Description: <p>ID number of sequencing project at the Joint Genome Institute Data portal (<a href="https://data.jgi.doe.gov" target="_blank">https://data.jgi.doe.gov</a>)</p> http://lod.bco-dmo.org/id/dataset-parameter/905371.rdf Name: Library_Name Units: unitless Description: <p>sample identifier</p> http://lod.bco-dmo.org/id/dataset-parameter/905372.rdf Name: Sample_Name Units: unitless Description: <p>sample name</p> http://lod.bco-dmo.org/id/dataset-parameter/905373.rdf Name: Replicate Units: unitless Description: <p>replicate number</p> http://lod.bco-dmo.org/id/dataset-parameter/905374.rdf Name: Sample_condition Units: unitless Description: <p>treatment conditions (temperature of acclimation in degrees C, co-culture or axenic)</p> http://lod.bco-dmo.org/id/dataset-parameter/905375.rdf Name: Filtered_Raw_Data_file Units: unitless Description: <p>name of fastq sequence file at the Joint Genome Institute Data portal (<a href="https://data.jgi.doe.gov" target="_blank">https://data.jgi.doe.gov</a>)</p> GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 21428 https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/fe86567b-e25a-4470-ac40-a48b09627a27/content download https://doi.org/10.26008/1912/bco-dmo.905306.1 download onLine dataset &lt;p&gt;Laboratory studies were carried out at the University of Georgia, Athens, GA, USA. The studies took place over the following dates:&lt;br /&gt; Thalassiosira: 1-7th July 2020&lt;br /&gt; Synechococcus: 16-23rd Feb 2021&lt;br /&gt; Emiliania: 18-28th May 2021&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Emiliania huxleyi CCMP151&lt;/strong&gt;&lt;br /&gt; A laboratory study was conducted using cultures of a marine coccolithophore (&lt;em&gt;Emiliania huxleyi &lt;/em&gt;CCMP151) and heterotrophic bacterium, &lt;em&gt;Ruegeria pomeroyi&lt;/em&gt;. Coccolithophore cultures were pre-acclimated to three temperature treatments (15°, 20°, and 28° Celsius) and&amp;nbsp;grown co-cultures. The transcriptome treatments consisted of axenic coccolithophore, the coccolithophore with the bacterium, and the bacterium with the coccolithophore, and three replicates were analyzed at each sample point. Stranded RNA-Seq libraries were sequenced using an Illumina NovaSeq instrument. For co-cultures, &lt;em&gt;E. huxleyi&lt;/em&gt; and bacterial cells were separated by filtration prior to RNA extraction.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Thalassiosira pseudonana CCMP1335&lt;/strong&gt;&lt;br /&gt; A laboratory study was conducted using cultures of a marine diatom (&lt;em&gt;Thalassiosira pseudonana&lt;/em&gt; CCMP1335) and heterotrophic bacterium, &lt;em&gt;Ruegeria pomeroyi.&lt;/em&gt; Diatom cultures were pre-acclimated to three temperature treatments (14°, 20°, and 28° Celsius) and grown as co-cultures. The transcriptome treatments consisted of axenic diatom, the diatom with the bacterium, and the bacterium with the diatom, and three replicates were analyzed at each sample point. Stranded RNA-Seq libraries were sequenced using an Illumina NovaSeq instrument. For co-cultures, diatom and bacterial cells were separated by filtration prior to RNA extraction.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Synechococcus sp. WH8102&lt;/strong&gt;&lt;br /&gt; A laboratory study was conducted using cultures of a marine cyanobacterium (&lt;em&gt;Synechococcus &lt;/em&gt;sp. WH8102 and heterotrophic bacterium, &lt;em&gt;Ruegeria pomeroyi.&lt;/em&gt; &lt;em&gt;Synechococcus&lt;/em&gt; cultures were pre-acclimated to three temperature treatments (20°, 24°, and 28° Celsius) and grown as co-cultures. The transcriptome treatments consisted of axenic Synechococcus, Synechococcus with the heterotrophic bacterium, and the bacterium with the Synechococcus, and three replicates were analyzed at each sample point. Stranded RNA-Seq libraries were sequenced using an Illumina NovaSeq instrument. RNA extraction of co-cultures was carried out without prefiltration, and transcripts were separated at mapping.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;Raw reads, mapped read counts, and quality control checks were performed at JGI and are available on the JGI Data portal.&lt;/p&gt; Specified by the Principal Investigator(s) - imported three original data files into the BCO-DMO system: Ehux.txt, Tpseudo.txt, Syn.txt. - concatenated the three files into one data file. - renamed fields to comply with BCO-DMO naming conventions. - named the final data file &quot;905306_v1_transcriptomes.csv&quot;. Specified by BCO-DMO Data Managers asNeeded 7.x-1.1 Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact Illumina NovaSeq Illumina NovaSeq PI Supplied Instrument Name: Illumina NovaSeq Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.