Contributors | Affiliation | Role |
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Arnosti, Carol | University of North Carolina at Chapel Hill (UNC-Chapel Hill) | Principal Investigator |
Ghobrial, Sherif | University of North Carolina at Chapel Hill (UNC-Chapel Hill) | Scientist |
Mickle, Audrey | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
Water for incubation was collected via Niskin bottles mounted on a rosette, equipped with a CTD. Bulk water was collected into an acid washed 50 mL Falcon tube directly from niskin bottles.
Isotopically diluted L-[3,4,5-3H(N)]-Leucine (Revvity, NET460250UC, specific activity of 3.811 TBq/mmol) was added to 1.7ml triplicate subsamples and one TCA killed control (20 nM final concentration). Samples and killed control were incubated between 5 and 48 hours at nearly in-situ temperature or 4°C. Following incubation, live samples were killed with 100% (w/v) TCA and all samples were centrifuged (10,000 rpm at 4°C for 10 min) to pelletize cell material. The supernatant liquid was removed and 1 mL of ice cold 5% (w/v) TCA solution was added, followed by vortex mixing and centrifugation. Supernatant removal, mixing, and centrifugation were repeated using 1 mL of ice cold 80% ethanol solution. Again, the supernatant liquid was removed and each sample was left to dry in a hood overnight. After drying, 1 mL of scintillation cocktail (ScintiSafe 30% Cocktail, Fisher SX23-5) was added and left overnight so that precipitated proteins dissolve into scintillation fluid. Incorporated radioactivity was measured using a PerkinElmer Tri-Carb 2910TR LSA scintillation counter. Radioactivity was compared to 1 mL of scintillation cocktail spiked with an identical amount of isotopically diluted L-[3,4,5-3H(N)]-Leucine that was added to samples. Incorporation rate was calculated by dividing sample radioactivity by incubation time.
Data were processed using Microsoft Excel.
- Imported "20250424_BCODMO_AE2413 Bulk water_3H-Leucine_incorporation_csv.csv" into BCO-DMO system
- Removed two rows where time is NULL at submitter's request
- Converted "date" to YYYY-MM-DD format
- Created new ISO formatted datetime in UTC
- Removed string "MPa" from the "incubation_pressure" values
- Renamed fields to remove spaces and units from parameters to comply with BCO-DMO system and style requirements
- Exported file as "963407_v1_bacterial_productivity.csv"
File |
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963407_v1_bacterial_productivity.csv (Comma Separated Values (.csv), 4.61 KB) MD5:21929134d2f9af0ab5b0bb77a9ab70ea Primary data file for dataset ID 963407, version 1 |
Parameter | Description | Units |
deployment | Cruise ID | unitless |
station | Station number 24, 25, 26. | unitless |
latitude_n | Latitude of sampling site, south is negative. | Decimal degrees |
longitude_e | Longitude of sampling site, west is negative. | Decimal degrees |
ISO_DateTime_UTC | Datetime of collection in ISO format, UTC. | unitless |
date | Date of sample collection. | unitless |
time_local_est | Time of sample collection (local time), US Eastern Time (UTC-05:00) | unitless |
cast_number | Cast number (refers to cast of CTD/Niskin bottles on cruise) | unitless |
depth_description | Water column feature or oceanic zone sampled DCM (Deep Chlorophyll Maximum), OMZ (Oxygen Minimum Zone), Bathy, or Deep (bottom or near bottom). Station 26 DCM was not measured due to sampling error. | unitless |
depth_actual | Actual depth at which water was collected | m |
insitu_temp | Temperature of the samples in-situ. | degrees Celsius |
sample_type | The type of sample, whether it was incubated using water from the bulk water column, sediments, or amended | unitless |
incubation_type | The type of incubation (in epitube or excitaner vial at atmospheric pressure or in excitaner vial in pressure vessel) | unitless |
incubation_pressure | Amount of pressure applied during incubation | MPa |
incubation_temp | Temperature of 3H-Leucine incubation. | degrees Celsius |
unamended_amended | Whether the sample was amended (A) or unamended (U). | unitless |
substrate | 3H-leucine | unitless |
incubation_time | Amount of time in hours samples were incubated with 3H-leu prior to addition of TCA | hours |
DPM_Kill | Radioactivity of incorporated 3H-leucine in disintegrations per minute of killed control. | disintegrations per minute (dpm) |
DPM_rep1 | Radioactivity of incorporated 3H-leucine in disintegrations per minute of replicate 1. | disintegrations per minute (dpm) |
DPM_rep2 | Radioactivity of incorporated 3H-leucine in disintegrations per minute of replicate 2. | disintegrations per minute (dpm) |
DPM_rep3 | Radioactivity of incorporated 3H-leucine in disintegrations per minute of replicate 3. | disintegrations per minute (dpm) |
Average_incorp | Amount of incorporated 3H-leucine in picomoles per liter (average radioactivity of replicates in excess of radioactivity of killed control relative to the radioactivity of a standard amount of 3H-Leucine). | pmol L-1 |
H3_Leu | Amount of incorporated 3H-leucine in picomoles per liter per hour. | pmol L-1 h-1 |
stdev | Standard deviation in the amount of incorporated 3H-leucine in picomoles per liter per hour. | pmol L-1 h-1 |
Dataset-specific Instrument Name | CTD |
Generic Instrument Name | CTD - profiler |
Dataset-specific Description | Water for incubation was collected via Niskin bottles mounted on a rosette, equipped with a CTD. Bulk water was collected into an acid washed 50 mL Falcon tube directly from niskin bottles. |
Generic Instrument Description | The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.
This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934. |
Dataset-specific Instrument Name | PerkinElmer Tri-Carb 2910TR LSA scintillation counter |
Generic Instrument Name | Liquid Scintillation Counter |
Dataset-specific Description | Incorporated radioactivity was measured using a PerkinElmer Tri-Carb 2910TR LSA scintillation counter. |
Generic Instrument Description | Liquid scintillation counting is an analytical technique which is defined by the incorporation of the radiolabeled analyte into uniform distribution with a liquid chemical medium capable of converting the kinetic energy of nuclear emissions into light energy. Although the liquid scintillation counter is a sophisticated laboratory counting system used the quantify the activity of particulate emitting (ß and a) radioactive samples, it can also detect the auger electrons emitted from 51Cr and 125I samples.
Liquid scintillation counters are instruments assaying alpha and beta radiation by quantitative detection of visible light produced by the passage of rays or particles through a suitable scintillant incorporated into the sample. |
Dataset-specific Instrument Name | Niskin bottles |
Generic Instrument Name | Niskin bottle |
Dataset-specific Description | Water for incubation was collected via Niskin bottles mounted on a rosette, equipped with a CTD. Bulk water was collected into an acid washed 50 mL Falcon tube directly from niskin bottles. |
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. |
Website | |
Platform | R/V Atlantic Explorer |
Start Date | 2024-05-08 |
End Date | 2024-05-28 |
NSF Award Abstract:
Microbes are important players in the carbon cycle in the ocean. These organisms consume organic carbon and produce carbon dioxide in marine systems. Because the average depth of the ocean is 4000 m, microbes must work at high pressures typical of the deep ocean (>1000 m). Although high pressure is known to affect marine microbes, their carbon cycling activities have mostly been measured at surface ocean pressures. As a result, it remains unknown how closely these measurements reflect the activities of deep-sea microbes at high pressures. As a result of collaborations with scientists in Denmark and Germany, this project will be able to use special equipment to investigate the effects of high pressures on marine microbes and their carbon cycling activities. This work is necessary to quantify rates of carbon cycling and identify the microbes involved, especially in deep waters. The project will provide training for diverse undergraduate and graduate students, and a postdoc who will conduct novel research in the U.S., Denmark, and Germany, both at sea and in the lab. The scientists will also teach middle school students about the role of microbes in the carbon cycle and pressure effects on life in the ocean. The project will provide internships for high school students, focusing on first-generation students who would like to go to college. This work may aid in future efforts to identify enzymes that function well under high pressure.
Heterotrophic microbes (e.g., bacteria and archaea) are found throughout the ocean. Their biogeochemical functions help determine the rates and locations at which carbon and nutrients are regenerated, as well as the extent to which organic matter is preserved. Although research has shown that pressure profoundly affects the activities of marine microbes, most investigations of microbial communities of the deep sea are conducted at atmospheric pressure, due to the limited availability of specialized equipment. In collaboration with the Danish Center for Hadal Research at the University of Southern Denmark, this study will identify the effects of pressure on microbial communities and their extracellular enzymes of pressures characteristic of bathy- and abyssopelagic depths. At sea and in the lab, the scientific team will compare the effects of depressurization on the activities of enzymes produced by microbial communities of the deep ocean, as well as the effects of high pressure on surface-water derived enzymes and communities. Fieldwork will take place in Danish coastal waters, well as in the open North Atlantic and Pacific Oceans. Using pressurization systems and in situ incubations, this study will measure hydrolysis rates of peptides and polysaccharides, two of the major classes of marine organic matter. Project activities will also focus on developing the means to measure enzyme activities in situ in the deep ocean. In collaboration with colleagues from the Max Planck Institute for Marine Microbiology in Germany, this proect will additionally investigate whether pressure affects the selfish uptake of polysaccharides. These studies will provide new insight into understudied but key factors that help determine the fate of organic matter in the deep ocean.
This project is funded by the Biological and Chemical Oceanography Programs.
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) |