http://lod.bco-dmo.org/id/dataset/944277
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
2024-11-21
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Dissolved inorganic nutrients from two microcosm incubation experiments conducted on sample water collected from West Bay of the Neuse River Estuary, North Carolina USA in 2021 and 2022
2024-12-02
publication
2024-12-02
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-12-02
publication
https://doi.org/10.26008/1912/bco-dmo.944277.1
Scott M. Gifford
University of North Carolina at Chapel Hill
principalInvestigator
Melanie R. Cohn
University of North Carolina at Chapel Hill
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: Cerda, S. K., Cohn, M. R., Gifford, S. M. (2024) Dissolved inorganic nutrients from two microcosm incubation experiments conducted on sample water collected 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 2024-12-02 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.944277.1 [access date]
Dissolved Inorganic Nutrients Dataset Description: Methods and Sampling: <p>Surface water samples for these experiments were collected from West Bay of the Neuse River Estuary, North Carolina USA (34°55'32.42" N, 76°21'54.25" W) and distributed into six microcosms. 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. 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 (um) 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-milliter (mL) HDPE collection bottles (Fisher Scientific) were acid washed in 10% (v/v) HCl for six hours and triple rinsed with Milli-Q water. &lt;0.2 um filtrate was collected from each tank for dissolved inorganic nutrient analysis and stored for one month at -20 degrees Celisus (°C). Acid-washed glassware was used for NOx and NH4 assays, and RBS phosphate-free detergent washed glassware was used for SRP assay.</p>
<p>NOx was quantified using 2% vanadium chloride in hydrochloric acid to reduce nitrate to nitrite, then using the Greiss reaction on 1 mL sample volumes following Garcia-Robledo et al. (2014). 10 standard solutions ranging from 0.1 to 10 micromolar (uM) were created in saltwater (sodium chloride in Milli-Q at in situ salinity).</p>
<p>NH4 was measured using a colorimetric alkalic nitroprusside reaction in 96-well plates as described in Bower and Holm-Hanson, 1980. 10 standard solutions of NH4 were created ranging from 0.5 to 25 uM using saltwater similarly to NOx standards. For summer samples, NOx and NH4 absorbance were measured with quartz cuvettes at 540 nanometers (nm) (NOx) and 630 nm (NH4). Spring samples were measured on a Tecan plate reader.</p>
<p>Soluble reactive phosphorus SRP was measured using a modified molybdenum blue assay from Murphy and Riley (1962). Seven standards were prepared ranging from 0.1 to 4 uM in saltwater similar to NOx and NH4. All measurements were quantified with quartz cuvettes at 885 nm.</p>
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
Melanie R. Cohn
University of North Carolina at Chapel Hill
440-840-7829
3105K Murray Hall, CB#3300
Chapel Hill
NC
27559
USA
mcohn@email.unc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Experiment
Date_Start
Incubation_Day
Treatment
Tank_ID
Replicate
NOx
NH4
SRP
Tecan Infinite 200Pro (i-control v2.0.10.0)
Genesys 10S UV-Vis Spectrophotometer (ThermoFisher)
theme
None, User defined
experiment id
date
time_elapsed
treatment
tank
replicate
nitrate plus nitrite
Ammonium
SRP
featureType
BCO-DMO Standard Parameters
plate reader
Spectrometer
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
-76.36506944
-76.36506944
34.92567222
34.92567222
2021-09-02
2022-04-04
Estuaries and Coastal Ecosystems of North Carolina
0
BCO-DMO catalogue of parameters from Dissolved inorganic nutrients from two microcosm incubation experiments conducted on sample water collected 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/944288.rdf
Name: Experiment
Units: unitless
Description: <p>Name of incubation experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/944289.rdf
Name: Date_Start
Units: unitless
Description: <p>Start date of experiment. Eco1 was initiated September 2, 2021 and Eco2 was initiated April 4, 2022.</p>
http://lod.bco-dmo.org/id/dataset-parameter/944290.rdf
Name: Incubation_Day
Units: days
Description: <p>Days elapsed since incubation initiation</p>
http://lod.bco-dmo.org/id/dataset-parameter/944291.rdf
Name: Treatment
Units: unitless
Description: <p>Light treatment applied to incubation: 12 h PAR/dark (L), 12 h UV-B/dark (V), dark (D), or in situ at time of collection (in situ)</p>
http://lod.bco-dmo.org/id/dataset-parameter/944292.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/944293.rdf
Name: Replicate
Units: unitless
Description: <p>Replicate from individual micocosm</p>
http://lod.bco-dmo.org/id/dataset-parameter/944294.rdf
Name: NOx
Units: micromolar (uM)
Description: <p>Total nitrate and nitrite concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/944295.rdf
Name: NH4
Units: micromolar (uM)
Description: <p>Ammonium concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/944296.rdf
Name: SRP
Units: micromolar (uM)
Description: <p>Soluble reactive phosphorus concentration</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
6833
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/cda628da-fe96-42be-9575-42eff5836bc7/content
download
https://doi.org/10.26008/1912/bco-dmo.944277.1
download
onLine
dataset
<p>Surface water samples for these experiments were collected from West Bay of the Neuse River Estuary, North Carolina USA (34°55'32.42" N, 76°21'54.25" W) and distributed into six microcosms. 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. 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 (um) 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-milliter (mL) HDPE collection bottles (Fisher Scientific) were acid washed in 10% (v/v) HCl for six hours and triple rinsed with Milli-Q water. &lt;0.2 um filtrate was collected from each tank for dissolved inorganic nutrient analysis and stored for one month at -20 degrees Celisus (°C). Acid-washed glassware was used for NOx and NH4 assays, and RBS phosphate-free detergent washed glassware was used for SRP assay.</p>
<p>NOx was quantified using 2% vanadium chloride in hydrochloric acid to reduce nitrate to nitrite, then using the Greiss reaction on 1 mL sample volumes following Garcia-Robledo et al. (2014). 10 standard solutions ranging from 0.1 to 10 micromolar (uM) were created in saltwater (sodium chloride in Milli-Q at in situ salinity).</p>
<p>NH4 was measured using a colorimetric alkalic nitroprusside reaction in 96-well plates as described in Bower and Holm-Hanson, 1980. 10 standard solutions of NH4 were created ranging from 0.5 to 25 uM using saltwater similarly to NOx standards. For summer samples, NOx and NH4 absorbance were measured with quartz cuvettes at 540 nanometers (nm) (NOx) and 630 nm (NH4). Spring samples were measured on a Tecan plate reader.</p>
<p>Soluble reactive phosphorus SRP was measured using a modified molybdenum blue assay from Murphy and Riley (1962). Seven standards were prepared ranging from 0.1 to 4 uM in saltwater similar to NOx and NH4. All measurements were quantified with quartz cuvettes at 885 nm.</p>
Specified by the Principal Investigator(s)
<p>For each assay, standard curves were created. The limit of detection (LOD) was calculated from this standard curve, where the LOD= 3.3 times the standard error of standard curve divided by the slope of the calibration curve.</p>
Specified by the Principal Investigator(s)
- Imported original file "Results_inorganics.xlsx" into the BCO-DMO system.
- Marked "-9999" as a missing data value (missing data are empty/blank in the final CSV file).
- Renamed fields to comply with BCO-DMO naming conventions.
- Filled in experiment start dates in Date_Start column.
- Rounded values in columns NOx, NH4, and SRP to 2 decimal places as advised by data provider.
- Saved the final file as "944277_v1_dissolved_inorganic_nutrients.csv".
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
Tecan Infinite 200Pro (i-control v2.0.10.0)
Tecan Infinite 200Pro (i-control v2.0.10.0)
PI Supplied Instrument Name: Tecan Infinite 200Pro (i-control v2.0.10.0) PI Supplied Instrument Description:used for NOx and NH4 measurements from spring samples 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.
Genesys 10S UV-Vis Spectrophotometer (ThermoFisher)
Genesys 10S UV-Vis Spectrophotometer (ThermoFisher)
PI Supplied Instrument Name: Genesys 10S UV-Vis Spectrophotometer (ThermoFisher) PI Supplied Instrument Description:used in scanning mode, fast, at 1 nm intervals to measure the absorbance of the filtrate Instrument Name: Spectrometer Instrument Short Name:Spectrometer Instrument Description: A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0460/