Contributors | Affiliation | Role |
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Thrash, J. Cameron | University of Southern California (USC) | Principal Investigator |
Rauch, Shannon | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
Sampling was conducted on R/V Pelican cruise PE23-20 in the Northern Gulf of Mexico in May 2023. All CTD casts were conducted according to standard ship operator procedure. Refer to the Cruise Plan (Supplemental File) for more information.
The data were collected using a SeaBird 911 plus system with twelve 12-liter Niskin bottles. The instruments included in the 911 plus suite are dual Temperature (SBE 3), dual Conductivity (SBE 4), and dual Oxygen (SBE 43) sensors. Additionally, the suite included an SBE 27 pH/Oxidation, Wetlabs ECO Fluorometer, and a Wetlabs CDOM sensor. Serial numbers and calibration information are stored in the Header Information included in the original .cnv files (see Supplemental Files for an example header file).
The data were processed using Seabird's SBEDataProccessing_Win32 software. The data were converted from hexadecimal to engineering units first. Using the software's Bin Averaging tool, the data were also averaged in bins of 1.0 meters. For the binned data, see the related dataset https://www.bco-dmo.org/dataset/907873. The attached Supplemental File contains the complete Seabird header from one cast (C6C_1).
- Imported the original .cnv files (20 total; one per cast) into the BCO-DMO system.
- Captured the starting latitude, starting longitude, and starting date/time from the Seabird headers as columns.
- Concatenated the separate files into one dataset.
- Converted starting latitude and longitude to decimal degrees (rounded to 5 decimal places).
- Converted starting date/time to ISO8601 format.
- Created the Cast column based on the original file name.
- Renamed fields to comply with BCO-DMO parameter naming conventions.
- Saved the final file as "908001_v1_PE23-20_Un-binned_CTD.csv".
File |
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908001_v1_PE23-20_Un-binned_CTD.csv (Comma Separated Values (.csv), 7.17 MB) MD5:f7e45755195133c275bde171a6306e90 Primary data file for dataset ID 908001, version 1. |
File |
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Cruise_Plan_May2023_f.pdf (Portable Document Format (.pdf), 2.13 MB) MD5:934bced1024c455cb2323d66e1544d34 PE23-20 Cruise Plan |
PE23-20_unbinned_CTD_header_file.txt (Plain Text, 12.48 KB) MD5:80280616519c174d6bb3968597629fcb Supplemental file for dataset ID 908001, version 1. Example of a CTD header file extracted from the original .cnv file named "CTD_C6C_1_converted.cnv" |
Parameter | Description | Units |
Cast | Cast identifier | unitless |
Lat_Start | Latitude at start of cast | degrees North |
Lon_Start | Longitude at start of cast (negative values = West) | degrees East |
ISO_DateTime_Start_UTC | Date and time (UTC) at start of cast | unitless |
altM | Altimeter | meters (m) |
avgsvCM | Average Sound Velocity (Chen-Millero) | meters per second (m/s) |
nbf | Number of bottles fired | unitless |
c0S_m | Conductivity | Siemens per meter (S/m) |
c1S_m | Conductivity, 2 | Siemens per meter (S/m) |
depSM | Depth (salt water) | meters (m) |
dz_dtM | Descent rate | meters per second (m/s) |
flECO_AFL | Fluorescence, WET Labs ECO-AFL/FL | milligrams per cubic meter (mg/m^3) |
wetCDOM | Fluorescence, WET Labs CDOM | milligrams per cubic meter (mg/m^3) |
latitude | Latitude | degrees North |
longitude | Longitude (negative values = West) | degrees East |
sbeox0Mg_L | Oxygen, SBE 43 | milligrams per liter (mg/L) |
sbeox1Mg_L | Oxygen, SBE 43, 2 | milligrams per liter (mg/L) |
ptempC | Pressure temperature | degrees Celsius |
prDM | Pressure, Digiquartz | decibars (db) |
sal00 | Salinity, Practical | PSU |
ph | pH | unitless (pH scale) |
svCM | Sound Velocity (Chen-Millero) | meters per second (m/s) |
spar | SPAR, Biospherical/Licor | micromoles photons per square meter per second (umol photons/m^2/sec) |
t090C | Temperature (ITS-90) | degrees Celsius |
t190C | Temperature, 2 (ITS-90) | degrees Celsius |
timeS | Time elapsed | seconds |
timeM | Time elapsed | minutes |
flag | Flag | unitless |
Dataset-specific Instrument Name | SeaBird 911 plus system |
Generic Instrument Name | CTD Sea-Bird SBE 911plus |
Dataset-specific Description | SeaBird 911 plus system with twelve 12-liter Niskin bottles |
Generic Instrument Description | The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics |
Dataset-specific Instrument Name | Wetlabs ECO Fluorometer |
Generic Instrument Name | Fluorometer |
Generic Instrument Description | A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. |
Dataset-specific Instrument Name | Wetlabs CDOM |
Generic Instrument Name | Fluorometer |
Generic Instrument Description | A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. |
Dataset-specific Instrument Name | 12-liter Niskin bottles |
Generic Instrument Name | Niskin bottle |
Generic Instrument Description | A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. |
Dataset-specific Instrument Name | SBE 27 pH/Oxidation |
Generic Instrument Name | Sea-Bird SBE 27 pH/O.R.P. sensor |
Generic Instrument Description | The SBE 27 pH and O.R.P. (Redox) sensor combines a pressure-balanced, glass-electrode, Ag/AgCl reference probe and platinum O.R.P. electrode to provide in-situ measurements at depths to 1200 m. The replaceable pH probe is permanently sealed and is supplied with a soaker bottle attachment that prevents the reference electrode from drying out during storage. The SBE 27 is intended for use as an add-on auxiliary sensor for profiling CTDs (SBE 9plus; SBE 19, 19plus, and 19plus V2 SeaCAT; and SBE 25 and 25plus Sealogger). |
Dataset-specific Instrument Name | dual Oxygen (SBE 43) sensors |
Generic Instrument Name | Sea-Bird SBE 43 Dissolved Oxygen Sensor |
Generic Instrument Description | The Sea-Bird SBE 43 dissolved oxygen sensor is a redesign of the Clark polarographic membrane type of dissolved oxygen sensors. more information from Sea-Bird Electronics |
Dataset-specific Instrument Name | dual Temperature (SBE 3) sensors |
Generic Instrument Name | Sea-Bird SBE-3 Temperature Sensor |
Generic Instrument Description | The SBE-3 is a slow response, frequency output temperature sensor manufactured by Sea-Bird Electronics, Inc. (Bellevue, Washington, USA). It has an initial accuracy of +/- 0.001 degrees Celsius with a stability of +/- 0.002 degrees Celsius per year and measures seawater temperature in the range of -5.0 to +35 degrees Celsius. more information from Sea-Bird Electronics |
Dataset-specific Instrument Name | dual Conductivity (SBE 4) sensors |
Generic Instrument Name | Sea-Bird SBE-4 Conductivity Sensor |
Generic Instrument Description | The Sea-Bird SBE-4 conductivity sensor is a modular, self-contained instrument that measures conductivity from 0 to 7 Siemens/meter. The sensors (Version 2; S/N 2000 and higher) have electrically isolated power circuits and optically coupled outputs to eliminate any possibility of noise and corrosion caused by ground loops. The sensing element is a cylindrical, flow-through, borosilicate glass cell with three internal platinum electrodes. Because the outer electrodes are connected together, electric fields are confined inside the cell, making the measured resistance (and instrument calibration) independent of calibration bath size or proximity to protective cages or other objects. |
Website | |
Platform | R/V Pelican |
Start Date | 2023-05-01 |
End Date | 2023-05-07 |
Description | More information is available from R2R: https://www.rvdata.us/search/cruise/PE23-20 |
NSF Award Abstract:
Decreasing marine dissolved oxygen (DO) is a widespread and growing global problem. Among the chief causes for coastal losses of DO are anthropogenic nutrient inputs that lead to seasonal hypoxia- DO concentrations below 2 mg/L. Microorganisms are the primary agents of oxygen removal, and although we have a basic mechanistic understanding of how nutrient enrichment combines with stratification to stimulate microbial metabolism and oxygen drawdown, we still do not know which microorganisms are ultimately responsible for oxygen consumption leading to, and during, coastal hypoxia in any particular region. Nor do we know the extent to which each hypoxic system arises from universal microbial mechanisms or whether there may be unique microorganisms and metabolic pathways involved in each locale. Hypoxic regions are increasing in number and size around the globe, amplifying the need to better understand the microbial processes responsible for oxygen consumption. In response, the project pursues an integrated research and education effort to study the microbial mechanisms of oxygen respiration in two coastal zones where DO depletion occurs: the northern Gulf of Mexico ?dead zone?, and the Southern California Bight. This work identifies the microorganism actively consuming oxygen in these systems, what fuels them, and whether/how those taxa respond to environmental changes. The investigators are generating microbial DO consumption rate, genetic, and taxonomic data critical to better constraining respiration models focused on water column DO depletion. In doing so, hundreds of undergraduate and students and dozens of high school STEM teachers contribute valuable data by participating in modern marine microbiological research. The project also improves integration of authentic research experiences into college and high-school classrooms in the context of a problem of global relevance.
Regions of low DO take multiple forms, from vast open ocean oxygen minimum zones (OMZs) which hover in the upper water column, to shallower coastal zones of bottom water hypoxia fueled by close proximity to fluvial inputs of human supplied nutrients. Microbial respiration is primarily responsible for the ultimate consumption of DO, and therefore understanding the microorganisms that inhabit these systems and their metabolic capabilities is critical for improving our ability to predict the timing, extent, and severity of DO depletion, and how these factors relate to environmental change. While there has been substantial research into the microbiology of OMZs, we know comparatively little about the microbial dynamics, and in particular, the microorganisms responsible for oxygen consumption, in coastal hypoxia. This integrated research and education effort is framed by the following objectives:
1. Determine the microorganisms and metabolic processes responsible for actively respiring water column DO prior to, and during, hypoxia.
2. Quantify microbial respiration rates for communities and representative water column species in both the planktonic and particle-associated fractions.
3. Integrate authentic microbiology research on a globally relevant topic into undergraduate and high school classrooms.
The work uses a combination of advanced cultivation-independent and pure culture measurements to discriminate between oxygen consumption by planktonic and particle-associated microbial fractions, as well as by communities at the surface and those in bottom waters, in two different systems of coastal DO depletion (the northern Gulf of Mexico hypoxic zone and the Southern California coastal shelf). Direct assessment of actively respiring taxa are connected with their metabolic potential, gene expression, and respiration rates. This project is determining, for the first time, the taxa actively consuming oxygen in these systems. The results also provide size fractionated respiration rates and bacterial growth efficiency (BGE) with depth across multiple sites and seasons, and importantly, also yield cell-specific respiration rates and BGE for active taxa within these systems. This data will constrain variable respiration across differing environmental conditions. The investigators are experimentally testing how alterations in environmental variables affect these respiration rates and BGEs, leading to greater predictive insight for the range of effects climate forcing will have on DO consumption. This information also facilitates comparisons between multiple marine systems to identify whether common or distinct organisms and metabolic processes are operating to remove DO.
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.
Funding Source | Award |
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NSF Division of Ocean Sciences (NSF OCE) |