http://lod.bco-dmo.org/id/dataset/904246 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 2023-07-17 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) High throughput growth screening of the marine bacterium Ruegeria pomeroyi DSS-3 knockout mutants on 70 environmentally relevant marine substrates done in 2021. 2023-07-17 publication 2023-07-17 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2023-07-21 publication https://doi.org/10.26008/1912/bco-dmo.904246.1 Mary Ann Moran University of Georgia principalInvestigator Christopher R. Reisch University of Florida principalInvestigator Catalina Mejia University of Florida principalInvestigator Lidimarie Trujillo Rodriguez University of Florida 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: Schroer, W. F., Moran, M. A., Reisch, C. R., Mejia, C., Trujillo Rodriguez, L., Gray, L. G. (2023) High throughput growth screening of the marine bacterium Ruegeria pomeroyi DSS-3 knockout mutants on 70 environmentally relevant marine substrates done in 2021. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-07-17 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.904246.1 [access date] High Throughput Growth Screening Ruegeria pomeroyi Dataset Description: Methods and Sampling: &lt;p&gt;The data were generated from laboratory experiments performed at&amp;nbsp;the University of Florida,&amp;nbsp;Gainesville, Florida.&amp;nbsp;&lt;/p&gt; &lt;p&gt;Mutant cultures were pre-grown overnight in ½ YTSS medium with 50&amp;nbsp;mg ml&lt;sup&gt;-1&lt;/sup&gt;&amp;nbsp;kanamycin. Screens were performed in L1 minimal medium (Guillard and Hargraves 1993) modified to a salinity of 20 ppt and amended with ammonium (3 mM), kanamycin (50&amp;nbsp;mg ml&lt;sup&gt;-1&lt;/sup&gt;), and phosphorus as PO&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;3-&lt;/sup&gt;&amp;nbsp;at 36&amp;nbsp;mM. Overnight cultures of individual mutants (2&amp;nbsp;ml) were inoculated into 198&amp;nbsp;ml of modified L1 with a single substrate as the sole carbon source at 8 mM carbon. Plates were incubated at 25&lt;sup&gt;o&lt;/sup&gt;C with shaking, and optical density (OD&lt;sub&gt;600&lt;/sub&gt;) was read at intervals of 6-24 h until cultures entered stationary phase at ~24-72 h (SpectraMax M3, Molecular Devices, San Jose, CA). Mutants exhibiting phenotypes in the initial screen were moved to the targeted screen.&lt;/p&gt; &lt;p&gt;&amp;nbsp;&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2019589 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2019589 Funding provided by Simons Foundation (Simons) Award Number: 542391 completed Mary Ann Moran University of Georgia 706-542-6481 Department of Marine Sciences Athens GA 30602 USA mmoran@uga.edu pointOfContact Christopher R. Reisch University of Florida Dept. of Microbiology and Cell Science University of Florida Gainesville FL 32611 USA creisch@ufl.edu pointOfContact Catalina Mejia University of Florida Dept. of Microbiology and Cell Science University of Florida Gainesville FL 32611 USA catalinamejia@ufl.edu pointOfContact Lidimarie Trujillo Rodriguez University of Florida Dept. of Microbiology and Cell Science University of Florida Gainesville FL 32611 USA ltrujillo@ufl.edu pointOfContact asNeeded Dataset Version: 1 Unknown date substrate plate time well_row well_col OD SpectraMax M3 plate reader, Molecular Devices, San Jose, CA theme None, User defined date sample description incubation time or duration optical_density featureType BCO-DMO Standard Parameters plate reader 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. Center for Chemical Currencies of a Microbial Planet https://ccomp-stc.org/ Center for Chemical Currencies of a Microbial Planet Functions carried out by microscopic inhabitants of the surface ocean affect every aspect of life on our planet, regardless of distance from the coast. Ocean phytoplankton are responsible for half of the photosynthesis on Earth, the first step in a complex system that annually withdraws 50 billion metric tons of carbon from the atmosphere to sustain their growth. Of this, 25 billion metric tons participate in a rapid cycle in which biologically reactive material is released into seawater and converted back into carbon dioxide by marine bacteria within hours to days. The chemical-microbe network at the heart of this fast cycle remains poorly constrained; consequently, its primary currencies and controls remain elusive; its sensitivities to changing ocean conditions are unknown; and its responses to future climate scenarios are not predictable. The Center for Chemical Currencies of a Microbial Planet (C-CoMP) integrates research, education and knowledge transfer activities to develop a mechanistic understanding of surface ocean carbon flux within the context of a changing ocean and through increased participation in ocean sciences. C-CoMP supports science teams that merge biology, chemistry, modeling, and informatics to close long-standing knowledge gaps in the identities and dynamics of organic molecules that serve as the currencies of elemental transfer between the ocean and atmosphere. C-CoMP fosters education, outreach, and knowledge transfer activities that engage students of all ages, broaden participation in the next generation of ocean scientists, and extend novel open-science approaches into complementary academic and industrial communities. The Center framework is critical to this mission, uniquely facilitating an open exchange of experimental and computational science, methodological and conceptual challenges, and collaborations that establish integrated science and education partnerships. With expanded participation in ocean science research and ocean literacy across the US society, the next generation of ocean scientists will better reflect the diverse US population. Climate-carbon feedbacks on the marine carbon reservoir are major uncertainties for future climate projections, and the trajectory and rate of ocean changes depend directly on microbial responses to temperature increases, ocean acidification, and other perturbations driven by climate change. C-CoMP research closes an urgent knowledge gap in the mechanisms driving carbon flow between ocean and atmosphere, with global implications for predictive climate models. The Center supports interdisciplinary science teams following open and reproducible science practices to address: (1) the chemical currencies of surface ocean carbon flux; (2) the structure and regulation of the chemical-microbe network that mediates this flux; and (3) sensitivity of the network and its feedbacks on climate. C-CoMP leverages emerging tools and technologies to tackle critical challenges in these themes, in synergy with existing ocean programs and consistent with NSF’s Big Ideas. C-CoMP education and outreach activities seek to overcome barriers to ocean literacy and diversify participation in ocean research. The Center is developing (1) initiatives to expand ocean literacy in K-12 and the broader public, (2) ocean sciences undergraduate curricula and research opportunities that provide multiple entry points into research experiences, (3) post-baccalaureate programs to transition undergraduates into graduate education and careers in ocean science, and (4) interdisciplinary graduate student and postdoctoral programs that prepare the next generation of ocean scientists. The C-CoMP team includes education faculty who evaluate the impacts of education and outreach activities and export successful STEM initiatives to the education community. C-CoMP is revolutionizing the technologies for studying chemical transformations in microbial systems to build understanding of the outsized impact of microbes on elemental cycles. Open science, cross-disciplinary collaborations, community engagement, and inclusive practices foster strategic advances in critical science problems and STEM initiatives. C-CoMP science, education, and knowledge-transfer themes are efficiently addressed through a sustained network of scientists addressing critical research challenges while broadening the workforce that will tackle multi-disciplinary problems with academic, industrial and policy partners. 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. The Program's Data Management Plan (DMP) is available as a PDF document. C-CoMP largerWorkCitation program Function and Importance of Marine Bacterial Transporters of Plankton Exometabolites https://osprey.bco-dmo.org/project/884792 Function and Importance of Marine Bacterial Transporters of Plankton Exometabolites <p><strong>Project:</strong></p> <p>Observing expression of marine bacterial transporter systems with transcriptomic or proteomic tools can provide valuable information about the metabolomic environment. However, these ‘omics approaches are limited by the low rate of transporter gene annotation. Here, a barcoded, arrayed, mutant library of the marine bacterium <em>Ruegeria pomeroyi</em> DSS-3 is employed in high throughput screens to identify the target substrates of 13 transporter systems. A set of 156 isolated putative transporter mutants were screened for growth on minimal medium with 63 substrates, each as a sole carbon source. Mutants that demonstrated a growth defect on a specific substrate were selected for secondary, higher resolution, growth screening. Mutants that continued to demonstrate growth defect relative to the pooled-mutant library (pooled-BarSeq, used as an analog for wildtype) were screened for their ability to drawdown the target substate. Gene annotations were made when mutants of the given transporter demonstrated both growth and drawdown defects on the target substrate.</p> <p>In addition to the isolated mutant screens, the pooled barcoded transposon mutant library (pooled-BarSeq) was grown on minimal medium with selected substrates, each as sole carbon source, such that the relative enrichment or depletion of each mutant could demonstrate its fitness cost associated with the loss of each disrupted gene when grown on each substrate. The results of pooled-BarSeq screens had mixed consistency with the isolated mutant screens, demonstrating the value of isolated mutants for transporter annotation.</p> <p><strong>Program:</strong></p> <p>The Center for Chemical Currencies of a Microbial Planet (C-CoMP) integrates research, education and knowledge transfer activities to develop a mechanistic understanding of surface ocean carbon flux within the context of a changing ocean and through increased participation in ocean sciences. C-CoMP supports science teams that merge biology, chemistry, modeling, and informatics to close long-standing knowledge gaps in the identities and dynamics of organic molecules that serve as the currencies of elemental transfer between the ocean and atmosphere.</p> C-CoMP Marine Bacterial Transporters largerWorkCitation project eng; USA oceans 2022-07-07 2022-09-29 0 BCO-DMO catalogue of parameters from High throughput growth screening of the marine bacterium Ruegeria pomeroyi DSS-3 knockout mutants on 70 environmentally relevant marine substrates done in 2021. 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/904301.rdf Name: date Units: unitless Description: <p>date of experiment initiation in ISO Format</p> http://lod.bco-dmo.org/id/dataset-parameter/904302.rdf Name: substrate Units: unitless Description: <p>substrate screened as sole carbon source</p> http://lod.bco-dmo.org/id/dataset-parameter/904303.rdf Name: plate Units: unitless Description: <p>ID of the arrayed mutant plate used</p> http://lod.bco-dmo.org/id/dataset-parameter/904304.rdf Name: time Units: hours (hrs) Description: <p>time (hours) of sample</p> http://lod.bco-dmo.org/id/dataset-parameter/904305.rdf Name: well_row Units: unitless Description: <p>row ID of well in 96 well plate</p> http://lod.bco-dmo.org/id/dataset-parameter/904306.rdf Name: well_col Units: unitless Description: <p>column ID of well in 96 well plate</p> http://lod.bco-dmo.org/id/dataset-parameter/904307.rdf Name: OD Units: nanometer (nm) Description: <p>optical density read at 600 nm</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 8855361 https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/99d04bec-74c4-4d08-95b1-dc906bc6fa1a/content download https://doi.org/10.26008/1912/bco-dmo.904246.1 download onLine dataset &lt;p&gt;The data were generated from laboratory experiments performed at&amp;nbsp;the University of Florida,&amp;nbsp;Gainesville, Florida.&amp;nbsp;&lt;/p&gt; &lt;p&gt;Mutant cultures were pre-grown overnight in ½ YTSS medium with 50&amp;nbsp;mg ml&lt;sup&gt;-1&lt;/sup&gt;&amp;nbsp;kanamycin. Screens were performed in L1 minimal medium (Guillard and Hargraves 1993) modified to a salinity of 20 ppt and amended with ammonium (3 mM), kanamycin (50&amp;nbsp;mg ml&lt;sup&gt;-1&lt;/sup&gt;), and phosphorus as PO&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;3-&lt;/sup&gt;&amp;nbsp;at 36&amp;nbsp;mM. Overnight cultures of individual mutants (2&amp;nbsp;ml) were inoculated into 198&amp;nbsp;ml of modified L1 with a single substrate as the sole carbon source at 8 mM carbon. Plates were incubated at 25&lt;sup&gt;o&lt;/sup&gt;C with shaking, and optical density (OD&lt;sub&gt;600&lt;/sub&gt;) was read at intervals of 6-24 h until cultures entered stationary phase at ~24-72 h (SpectraMax M3, Molecular Devices, San Jose, CA). Mutants exhibiting phenotypes in the initial screen were moved to the targeted screen.&lt;/p&gt; &lt;p&gt;&amp;nbsp;&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;Minimal data processing was performed. Data were imported into Excel merged and reformatted in R version 4.2.2.&amp;nbsp;&lt;/p&gt; &lt;p&gt;A supplemental file is provided with alternate formatting, see supplemental file description for more information.&lt;/p&gt; &lt;p&gt;BCO-DMO Processing Notes:&lt;br /&gt; * Added year to date column&lt;br /&gt; * Converted date column to ISO format&lt;br /&gt; * Removed row number column&lt;/p&gt; &lt;p&gt;&amp;nbsp;&lt;/p&gt; Specified by the Principal Investigator(s) 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 SpectraMax M3 plate reader, Molecular Devices, San Jose, CA SpectraMax M3 plate reader, Molecular Devices, San Jose, CA PI Supplied Instrument Name: SpectraMax M3 plate reader, Molecular Devices, San Jose, CA Instrument Name: plate reader Instrument Short Name: Instrument Description: Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.