http://lod.bco-dmo.org/id/dataset/908475 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 2023-09-15 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Bulk dissolved organic carbon (DOC) from two microcosm incubation experiments conducted under three light treatments using water originating from West Bay of the Neuse River Estuary, North Carolina USA in 2021 and 2022 2023-09-18 publication 2023-09-18 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2023-10-10 publication https://doi.org/10.26008/1912/bco-dmo.908475.1 Scott M. Gifford University of North Carolina at Chapel Hill principalInvestigator Patricia M. Medeiros 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: Cohn, M. R., Medeiros, P. M., Gifford, S. M. (2023) Bulk dissolved organic carbon (DOC) from two microcosm incubation experiments conducted under three light treatments using water originating from West Bay of the Neuse River Estuary, North Carolina USA in 2021 and 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-09-18 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.908475.1 [access date] Dissolved Organic Carbon Dataset Description: Methods and Sampling: &lt;p&gt;Surface water samples for these experiments were collected from West Bay of the Neuse River Estuary, North Carolina USA (34°55'32.42&quot; N, 76°21'54.25&quot; W). The microcosms were 60 liters. The experiments were conducted in biological duplicates under three light treatment incubations: 12-hour light-dark cycle of photosynthetically active radiation (PAR), 12-hour light-dark cycle of UV-B radiation, or darkness. Samples were collected from the microcosms in duplicate every few days for over one month to examine how light and the resulting microbial activity altered the DOC pool over time.&lt;/p&gt; &lt;p&gt;For each 60-liter microcosm, water was sampled daily to weekly at the University of North Carolina over the month-long (September 2021) experiment or two-month-long experiment (April 2022). Water was sampled from the microcosms using a peristaltic pump (Masterflex) under gentle (75%) pressure through in-line 3-micron and 0.2-micron, 47-millimeter (mm) polycarbonate filters (Millipore Sigma) which were flushed with 250 milliliters (mL) of Milli-Q water. All tubing, filter holders and 60-mL HDPE collection bottles (Fisher Scientific) were acid-washed in 10% (v/v) HCl for six hours and triple rinsed with Milli-Q water. The collection bottles were twice rinsed with c.a. 10 mL of 0.2 micron-filtered sample water then filled to 40 mL and immediately placed in the freezer (-20&amp;nbsp;degrees Celsius). At the conclusion of the experiment (after two months), the samples were sent to the University of Georgia where they were run on a Shimadzu TOC-VCPH analyzer as in Letourneau and Medeiros (2019) which was calibrated with Consensus Reference Material as in Hansell (2005).&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Instruments and Materials:&lt;/strong&gt;&lt;br /&gt; L/S Peristaltic Pump (Masterflex EW-07557-10) and 1/4 inch Masterflex L/S Platinum-Cured Silicone Tubing: Estuarine water sampled from microcosm tank at 75% speed.&lt;/p&gt; &lt;p&gt;Millipore SX0004700 Polypropylene Swinnex Filter Holder (47 mm) used in-line with the tubing to pump sample water from the microcosm tank through a 3.0 micron and 0.2 micron polycarbonate filter (Millipore Sigma, 47 mm).&lt;/p&gt; &lt;p&gt;Hydrochloric acid (36% w/w, ThermoFisher) was diluted to 10% (v/v) with Milli-Q water for acid washing procedures.&lt;/p&gt; &lt;p&gt;60-mL HDPE dark bottle (Fisher Scientific, 029235B): 0.2 micron filtered water was collected into these acid-washed and rinsed bottles and stored at -20&amp;nbsp;degrees&amp;nbsp;Celsius until analysis.&lt;/p&gt; &lt;p&gt;Shimadzu TOC-VCPH analyzer: process samples for bulk DOC concentration, calibrated using Consensus Reference Material.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1850692 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1850692 completed Scott M. Gifford University of North Carolina at Chapel Hill 614-406-0117 4202G Murray Hall 123 South Rd Chapel Hill NC 27599 USA sgifford@email.unc.edu pointOfContact Patricia M. Medeiros University of Georgia 706-542-6744 Department of Marine Sciences Athens GA 30602-3636 USA medeiros@uga.edu pointOfContact asNeeded Dataset Version: 1 Unknown Experiment_Name Start_date Treatment Incubation_day Tank_ID DOC_uM DOC_Technical_sd Peristaltic Pump Shimadzu TOC-VCPH analyzer theme None, User defined experiment id date treatment time_elapsed tank dissolved organic Carbon featureType BCO-DMO Standard Parameters Pump Shimadzu Total Organic Carbon Analyzer TOC-VCPH 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. Bacteria as Biosensors of Carbon and Energy Flow in Marine Ecosystems: Quantitative Links Between Substrates, Transcripts, and Metabolism https://osprey.bco-dmo.org/project/753813 Bacteria as Biosensors of Carbon and Energy Flow in Marine Ecosystems: Quantitative Links Between Substrates, Transcripts, and Metabolism <p><em>NSF Award Abstract:</em><br /> The formation and flux of organic material is the foundation of ocean ecosystems, which in turn, substantially influences the global carbon cycle. As such, a fundamental goal in the ocean sciences is increasing our ability to identify marine organic matter's sources, transformations, and sinks, as well as how these components may change due to anthropogenic activities. Understanding these components is especially important in estuarine and coastal systems given these ecosystems are critical zones of organic carbon transformations. However, the dissolved organic carbon (DOC) pool in these systems consists of numerous different compounds from a multitude of sources that can turn over at vastly different rates (minutes to millennia). This makes it difficult to identify which DOC compounds support microbial growth, limiting the incorporation of microbial metabolism into predictive ecosystem models. Novel approaches are therefore needed to identify the DOC substrates driving microbial metabolism in ocean ecosystems. This project is premised on the idea that the bacterial cellular system is the ultimate chemical sensor of the organic environment and that the information recorded in the cell's active gene pool (transcripts) can be leveraged to make insights into DOC composition when the relationships between organic substrate availability, gene activity, and metabolism are known. This project identifies substrate-transcript relationships for a model marine bacterium, as well as the growth and metabolic outcomes of substrate availability. These insights are used to identify the biologically active DOC substrates in coastal environments when the model organism is added directly to coastal samples, and to interpret both historical and current environmental RNA and DNA data sets. This work provides novel insights into the substrates driving the ocean's carbon cycle and how marine bacterial cellular systems are regulated. Bioassays are developed that can be applied in many different aquatic environment settings. The project trains graduate and undergraduate students directly involved in the research and minority undergraduates will be recruited to use research modules for hands-on study of cell cultivation, bioinformatics, and microbial metabolism. High school students will be engaged through a module developed for an aquatic microbiology field trip and subsequent sample and data analysis.</p> <p>Bacterial processing of dissolved organic carbon (DOC) mediates the flux of gigatons of carbon in the ocean, yet a significant hurdle to incorporating bacterial metabolism into ocean models is the inability to quantify the DOC substrates supporting bacterial metabolism and their transformation. Metatranscriptomics (sequencing of community mRNAs) has the potential to be a sensitive method for surveying bacterioplankton responses to the DOC pool and making insights into its composition but is currently limited by insufficient knowledge as to how transcriptional patterns relate to substrate availability. This project will identify carbon substrates supporting microbial metabolism and their transformation in estuarine-coastal ecosystems by elucidating the relationships between transcript abundances and carbon substrate availability. It aims to bridge the gap between model organism and environmental -omic studies by creating quantitative inventories of transcripts in response to defined substrates, and then using these calibrated transcriptional signals to interpret environmental DOC bioassays and metatranscriptomes. The first component of the project will establish genome-wide transcript-substrate relationships in a model marine bacterium in response to individual, environmentally-relevant carbon substrates. The second component will determine the extent to which transcription and metabolism are altered when the bacterium is exposed to complex mixtures of defined and undefined substrates, revealing the potential for transcription to identify individual substrates within a complex DOC pool and how metabolic processing may shape the DOC pools labile and refractory components. Finally, these calibrated transcriptional responses will be used to identify the DOC substrates driving bacterial metabolism in an estuarine-coastal system via DOC drawdown bioassays in which the model organism is added to natural seawater samples, as well as community wide bacterioplankton responses to the extant DOC pool via metatranscriptomics.</p> Bacterial DOC Sensor largerWorkCitation project eng; USA oceans -76.365069 -76.365069 34.925672 34.925672 2021-09-02 2022-05-28 Estuaries and Coastal Ecosystems of North Carolina 0 BCO-DMO catalogue of parameters from Bulk dissolved organic carbon (DOC) from two microcosm incubation experiments conducted under three light treatments using water originating from West Bay of the Neuse River Estuary, North Carolina USA in 2021 and 2022 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/908537.rdf Name: Experiment_Name Units: unitless Description: <p>Name of incubation experiment; either &quot;Eco1&quot; or &quot;Eco2&quot;.</p> http://lod.bco-dmo.org/id/dataset-parameter/908538.rdf Name: Start_date Units: unitless Description: <p>Date the experiment was initiated. Eco1 was initiated September 2, 2021 and Eco2 was initiated April 4, 2022.</p> http://lod.bco-dmo.org/id/dataset-parameter/908539.rdf Name: Treatment Units: unitless Description: <p>Light treatment applied to incubation: &quot;L&quot; = 12 h PAR/dark; &quot;V&quot; = 12 h UV-B/dark; &quot;D&quot; = dark; and &quot;in situ&quot; = at time of collection.</p> http://lod.bco-dmo.org/id/dataset-parameter/908540.rdf Name: Incubation_day Units: days Description: <p>Days elapsed since incubation initiation</p> http://lod.bco-dmo.org/id/dataset-parameter/908541.rdf Name: Tank_ID Units: unitless Description: <p>Identifier for microcosm replicate (two tanks per light treatment)</p> http://lod.bco-dmo.org/id/dataset-parameter/908542.rdf Name: DOC_uM Units: micromoles per liter (umol L-1) Description: <p>Bulk DOC concentration</p> http://lod.bco-dmo.org/id/dataset-parameter/908543.rdf Name: DOC_Technical_sd Units: micromoles per liter (umol L-1) Description: <p>Standard deviation of the technical replication of the TOC-analyzer</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 6963 https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/6855d562-1e20-4ffc-aa39-7a1659d458e5/content download https://doi.org/10.26008/1912/bco-dmo.908475.1 download onLine dataset &lt;p&gt;Surface water samples for these experiments were collected from West Bay of the Neuse River Estuary, North Carolina USA (34°55'32.42&quot; N, 76°21'54.25&quot; W). The microcosms were 60 liters. The experiments were conducted in biological duplicates under three light treatment incubations: 12-hour light-dark cycle of photosynthetically active radiation (PAR), 12-hour light-dark cycle of UV-B radiation, or darkness. Samples were collected from the microcosms in duplicate every few days for over one month to examine how light and the resulting microbial activity altered the DOC pool over time.&lt;/p&gt; &lt;p&gt;For each 60-liter microcosm, water was sampled daily to weekly at the University of North Carolina over the month-long (September 2021) experiment or two-month-long experiment (April 2022). Water was sampled from the microcosms using a peristaltic pump (Masterflex) under gentle (75%) pressure through in-line 3-micron and 0.2-micron, 47-millimeter (mm) polycarbonate filters (Millipore Sigma) which were flushed with 250 milliliters (mL) of Milli-Q water. All tubing, filter holders and 60-mL HDPE collection bottles (Fisher Scientific) were acid-washed in 10% (v/v) HCl for six hours and triple rinsed with Milli-Q water. The collection bottles were twice rinsed with c.a. 10 mL of 0.2 micron-filtered sample water then filled to 40 mL and immediately placed in the freezer (-20&amp;nbsp;degrees Celsius). At the conclusion of the experiment (after two months), the samples were sent to the University of Georgia where they were run on a Shimadzu TOC-VCPH analyzer as in Letourneau and Medeiros (2019) which was calibrated with Consensus Reference Material as in Hansell (2005).&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Instruments and Materials:&lt;/strong&gt;&lt;br /&gt; L/S Peristaltic Pump (Masterflex EW-07557-10) and 1/4 inch Masterflex L/S Platinum-Cured Silicone Tubing: Estuarine water sampled from microcosm tank at 75% speed.&lt;/p&gt; &lt;p&gt;Millipore SX0004700 Polypropylene Swinnex Filter Holder (47 mm) used in-line with the tubing to pump sample water from the microcosm tank through a 3.0 micron and 0.2 micron polycarbonate filter (Millipore Sigma, 47 mm).&lt;/p&gt; &lt;p&gt;Hydrochloric acid (36% w/w, ThermoFisher) was diluted to 10% (v/v) with Milli-Q water for acid washing procedures.&lt;/p&gt; &lt;p&gt;60-mL HDPE dark bottle (Fisher Scientific, 029235B): 0.2 micron filtered water was collected into these acid-washed and rinsed bottles and stored at -20&amp;nbsp;degrees&amp;nbsp;Celsius until analysis.&lt;/p&gt; &lt;p&gt;Shimadzu TOC-VCPH analyzer: process samples for bulk DOC concentration, calibrated using Consensus Reference Material.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;N/A; this dataset reports raw DOC concentrations and standard deviations from technical replicates.&lt;/p&gt; Specified by the Principal Investigator(s) - Imported original file named &quot;Results_DOC_R1.xlsx&quot; into the BCO-DMO system. - Flagged '-9999' as a missing data value; missing data are blank/empty in the final CSV file. - Renamed fields to comply with BCO-DMO naming conventions. - Created the 'Start_date' column and added the dates for each experiment. - Saved the final file as &quot;908475_v1_doc.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 Peristaltic Pump Peristaltic Pump PI Supplied Instrument Name: Peristaltic Pump PI Supplied Instrument Description:L/S Peristaltic Pump (Masterflex EW-07557-10) and 1/4 inch Masterflex L/S Platinum-Cured Silicone Tubing: Estuarine water sampled from microcosm tank at 75% speed. Instrument Name: Pump Instrument Short Name: Instrument Description: A pump is a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action. Pumps can be classified into three major groups according to the method they use to move the fluid: direct lift, displacement, and gravity pumps Shimadzu TOC-VCPH analyzer Shimadzu TOC-VCPH analyzer PI Supplied Instrument Name: Shimadzu TOC-VCPH analyzer PI Supplied Instrument Description:Shimadzu TOC-VCPH analyzer: process samples for bulk DOC concentration, calibrated using Consensus Reference Material. Instrument Name: Shimadzu Total Organic Carbon Analyzer TOC-VCPH Instrument Short Name:TOC-VCPH Instrument Description: The Shimadzu Total Organic Carbon Analyzer TOC-VCPH is a PC-controlled, total organic carbon analyzer (high-sensitivity model), designed to measure total carbon (TC), inorganic carbon (IC), total organic carbon (TOC), and non-purgeable organic carbon (NPOC); an optional accessory enables the measurement of particulate organic carbon (POC) and total nitrogen (TN) as well. The instrument uses the 680 degrees Celsius combustion catalytic oxidation method to analyze aqueous samples, and optionally solid and gas samples.