| Contributors | Affiliation | Role |
|---|---|---|
| Joye, Samantha B. | University of Georgia (UGA) | Principal Investigator |
| Hunter, Kimberley | University of Georgia (UGA) | Scientist |
| Mickle, Audrey | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
Sediment samples were collected by the HOV Alvin using PVC push cores. Upon arrival at the surface, the cores were described and cataloged prior to being sectioned into discrete 3 cm depth intervals. Methane samples were collected first. Porewater was separated from the sediment using a manually-actuated porewater press as described by Joye et al., 2004. Whole sediment subsamples for radiotracer sulfate reduction rates and anaerobic oxidation of methane rates were collected in triplicate from a parallel core and were handled, injected, incubated, and analyzed using the methods described in Joye et al., 2004.
CH4: Methane samples (3 cc whole sediment) were collected into a glass serum vial, preserved with 2 mL 2 M N₂-purged NaOH, crimp-sealed with a butyl rubber stopper and stored at room temperature until analysis. Concentrations were determined by headspace analysis using an SRI 8610 GC-FID with Agilent J&W HP-PLOT Al2O3 S Capillary Column, 50 m, 0.53 mm, 15.00 μm (Prod. No. 19095P-S25E). See Joye et al., 2004.
SO4: Water sample was filtered through a pre-rinsed 0.2 μm regenerated cellulose Target2 syringe filter (Thermo Scientific, Prod. No. F25047) into a 7 mL scintillation vial. Samples were acidified with 10 μL of concentrated HNO3 per 1 mL sample, sealed with a PTFE-lined cap, and stored at room temperature until analysis. Sample analysis was performed with a Dionex Integrion HPIC using KOH eluent supplied by a Dionex EGC 500 KOH Eluent Generator Cartridge (Prod. No. 075778), Dionex CR-ATC Continuously Regenerated Trap Column (Prod. No. 088662), Dionex ADRS 600 Dynamically Regenerated Suppressor (Prod. No. 088666), Dionex IonPac AG18 Guard Column (Prod. No. 060551), Dionex IonPac AS18 Analytical Column (Prod. No. 060549) and Dionex CRD 200 Carbonate Removal Device (Prod. No. 062983). See Weston et al., 2006.
CH4 data was processed using SRI Instruments PeakSimple software. SO4 data was processed using DIONEX Chromeleon software. Radioisotope data was processed using PerkinElmer QuantaSmart software.
This section documents curation actions performed prior to publication review with the submitter, and additional information relevant to understanding and reusing this dataset. It distinguishes changes made to the submitted (meta)data from unresolved issues and/or enhancements that improve future reuse and interoperability.
CURATION ACTIONS PERFORMED ON DATA
- Loaded AT50-22 Sediment Rates V2.xlsx (Sheet1), header row 8, units row 9 skipped, blank trailing columns dropped, missing values "", "nd", "ND"
- Renamed columns to BCO-DMO convention: Collection Date to Collection_Date, Collection Time to Collection_Time, Alvin Dive # to Alvin_Dive_number, Lat (N) to Lat, Long (W) to Long, Depth Range to Depth_Range, Mid-point Depth to Midpoint_Depth, Sulfate Reduction to Sulfate_Reduction, Anaerobic Methane Oxidation to Anaerobic_Methane_Oxidation
- Normalized Collection_Date values: slashes converted to hyphens, single-digit day zero-padded, single-digit month zero-padded, yielding consistent dd-mm-yy hyphenated format
- Converted Collection_Date from dd-mm-yy string to ISO date (%Y-%m-%d)
- Extracted non-numeric values from SO4 column into new SO4_flag column (suffix _flag), preserving metadata, isolating "BDL" (below detection limit) entries from numeric sulfate values
- Combined Collection_Date and Collection_Time into new datetime column Collection_DateTime, ISO 8601 formatted
- Reordered columns: Site, Collection_DateTime, Collection_Date, Collection_Time, Alvin_Dive_number, Lat, Long, Depth, Depth_Range, Midpoint_Depth, CH4, SO4, SO4_flag, Anaerobic_Methane_Oxidation, Sulfate_Reduction
- Output as 1000873_v1_at50_22_sediment_rates.csv
CURATION ACTIONS PERFORMED ON METADATA
- BCO-DMO's standard metadata entry and text formatting steps were performed.
- Used the provided information to add context to the abstract.
ISSUES POTENTIALLY IMPACTING REUSE
- Collection times provided do not clarify timezone.
| Parameter | Description | Units |
| Site | Site name | unitless |
| Collection_DateTime | Datetime of sample collection | unitless |
| Collection_Date | Date of sample collection | unitless |
| Collection_Time | Time of sample collection (24 hr) | unitless |
| Alvin_Dive_number | Alvin dive number | unitless |
| Lat | Latitude of sample collection, positive is North | decimal degrees |
| Long | Longitude of sample collection, negative is West | decimal degrees |
| Depth | Seafloor depth from which sample was collected | meters (m) |
| Depth_Range | The depth interval below the seafloor from which the sample was taken. OLW = Overlying water sample. | centimeters (cm) |
| Midpoint_Depth | The mid-point depth of the sediment layer from which the sample was taken. OLW = Overlying water sample. | centimeters (cm) |
| CH4 | Methane. Method detection limit = 1 µM | micromolar (µM) |
| SO4 | Sulfate. Method detection limit = 0.1 mM. See SO4_flag for Below detection limit indicator | millimolar (mM) |
| SO4_flag | Sulfate indicator: BDL = Below detection limit. Method detection limit = 0.1 mM | unitless |
| Anaerobic_Methane_Oxidation | Anaerobic oxidation of methane rate | nmol cm⁻³ d⁻¹ |
| Sulfate_Reduction | Sulfate reduction rate | nmol cm⁻³ d⁻¹ |
| Dataset-specific Instrument Name | SRI 8610 GC-FID |
| Generic Instrument Name | Gas Chromatograph |
| Dataset-specific Description | Concentrations were determined by headspace analysis using an SRI 8610 GC-FID with Agilent J&W HP-PLOT Al2O3 S Capillary Column, 50 m, 0.53 mm, 15.00 μm (Prod. No. 19095P-S25E). |
| Generic Instrument Description | Instrument separating gases, volatile substances, or substances dissolved in a volatile solvent by transporting an inert gas through a column packed with a sorbent to a detector for assay. (from SeaDataNet, BODC) |
| Dataset-specific Instrument Name | HOV Alvin |
| Generic Instrument Name | HOV Alvin |
| Dataset-specific Description | Sediment samples were collected by the HOV Alvin using PVC push cores. |
| Generic Instrument Description | Human Occupied Vehicle (HOV) Alvin is part of the National Deep Submergence Facility (NDSF). Alvin enables in-situ data collection and observation by two scientists to depths reaching 6,500 meters, during dives lasting up to ten hours.
Commissioned in 1964 as one of the world’s first deep-ocean submersibles, Alvin has remained state-of-the-art as a result of numerous overhauls and upgrades made over its lifetime. The most recent upgrades, begun in 2011 and completed in 2021, saw the installation of a new, larger personnel sphere with a more ergonomic interior; improved visibility and overlapping fields of view; longer bottoms times; new lighting and high-definition imaging systems; improved sensors, data acquisition and download speed. It also doubled the science basket payload, and improved the command-and-control system allowing greater speed, range and maneuverability.
With seven reversible thrusters, it can hover in the water, maneuver over rugged topography, or rest on the sea floor. It can collect data throughout the water column, produce a variety of maps and perform photographic surveys. Alvin also has two robotic arms that can manipulate instruments, obtain samples, and its basket can be reconfigured daily based on the needs of the upcoming dive.
Alvin's depth rating of 6,500m gives researchers in-person access to 99% of the ocean floor. Alvin is a proven and reliable platform capable of diving for up to 30 days in a row before requiring a single scheduled maintenance day. Recent collaborations with autonomous vehicles such as Sentry have proven extremely beneficial, allowing PIs to visit promising sites to collect samples and data in person within hours of their being discovered, and UNOLs driven technological advances have improved the ability for scientific outreach and collaboration via telepresence
Alvin is named for Allyn Vine, a WHOI engineer and geophysicist who helped pioneer deep submergence research and technology.
(from https://www.whoi.edu/what-we-do/explore/underwater-vehicles/hov-alvin/, accessed 2022-09-09) |
| Dataset-specific Instrument Name | VWR refrigerated incubator model 89508-420 |
| Generic Instrument Name | Incubator |
| Dataset-specific Description | Whole sediment subsamples for radiotracer sulfate reduction rates and anaerobic oxidation of methane rates were collected in triplicate from a parallel core and were handled, injected, incubated, and analyzed using the methods described in Joye et al., 2004. |
| Generic Instrument Description | A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled.
Note: we have more specific terms for shipboard incubators (https://www.bco-dmo.org/instrument/629001) and in-situ incubators (https://www.bco-dmo.org/instrument/494). |
| Dataset-specific Instrument Name | Dionex Integrion HPIC with Dionex AS-AP Autosampler |
| Generic Instrument Name | Ion Chromatograph |
| Dataset-specific Description | Sample analysis was performed with a Dionex Integrion HPIC using KOH eluent supplied by a Dionex EGC 500 KOH Eluent Generator Cartridge (Prod. No. 075778), Dionex CR-ATC Continuously Regenerated Trap Column (Prod. No. 088662), Dionex ADRS 600 Dynamically Regenerated Suppressor (Prod. No. 088666), Dionex IonPac AG18 Guard Column (Prod. No. 060551), Dionex IonPac AS18 Analytical Column (Prod. No. 060549) and Dionex CRD 200 Carbonate Removal Device (Prod. No. 062983). |
| Generic Instrument Description | Ion chromatography is a form of liquid chromatography that measures concentrations of ionic species by separating them based on their interaction with a resin. Ionic species separate differently depending on species type and size. Ion chromatographs are able to measure concentrations of major anions, such as fluoride, chloride, nitrate, nitrite, and sulfate, as well as major cations such as lithium, sodium, ammonium, potassium, calcium, and magnesium in the parts-per-billion (ppb) range. From: http://serc.carleton.edu/microbelife/research_methods/biogeochemical/ic.... |
| Dataset-specific Instrument Name | Perkin Elmer Tri-Carb 2910TR liquid scintillation counter |
| Generic Instrument Name | Liquid Scintillation Counter |
| Dataset-specific Description | Perkin Elmer Tri-Carb 2910TR liquid 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 to 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 | PVC push cores |
| Generic Instrument Name | Push Corer |
| Dataset-specific Description | Sediment samples were collected by the HOV Alvin using PVC push cores. |
| Generic Instrument Description | Capable of being performed in numerous environments, push coring is just as it sounds. Push coring is simply pushing the core barrel (often an aluminum or polycarbonate tube) into the sediment by hand. A push core is useful in that it causes very little disturbance to the more delicate upper layers of a sub-aqueous sediment.
Description obtained from: http://web.whoi.edu/coastal-group/about/how-we-work/field-methods/coring/ |
| Dataset-specific Instrument Name | manually-actuated porewater press |
| Generic Instrument Name | Sediment Porewater Sampler |
| Dataset-specific Description | Porewater was separated from the sediment using a manually-actuated porewater press as described by Joye et al. 2004. |
| Generic Instrument Description | A device that collects samples of pore water from various horizons below the seabed. |
| Website | |
| Platform | R/V Atlantis |
| Start Date | 2024-04-06 |
| End Date | 2024-04-30 |
| Description | Project: Collaborative research: Regulation and dynamics of microbial communities and biogeochemical cycling in hydrothermally-influenced habitats in the Gulf of California
Chief: Joye, Samantha |
NSF Award Abstract:
Oceanic hydrothermal ecosystems have captivated the imagination of scientists and the general public since their discovery ~40 years ago. These habitats are characterized by extremes in temperature and pH, low oxygen concentrations, and high concentrations of toxic metals. Despite this, these ecosystems support rich and abundant microbial communities that achieve high rates of biogeochemical cycling. This project supports unprecedented studies to identify the impact of chemical regimes on microbial and viral community composition, diversity, and activity in areas in the Gulf of California along a range of hydrothermalism and dissolve oxygen levels. The project provides training opportunities for undergraduate and graduate students. Results are communicated through talks and lectures, publications, and data sharing through public repositories. The work will be shared through Ocean Discovery Camp and Clubs for diverse middle school students, displays at the Georgia Museum of Art, and a collaboration with the BBC Planet Earth III – Oceans team. Through these cumulative efforts, the project will forge a strong legacy in education and in fostering ocean literacy and promoting ocean advocacy in the general public.
The Gulf of California is a system where hydrothermal fluids flow through and alter sediment prior to discharge into deep waters. In sediments, fluid flow modulates biological dynamics through changes in carbon loading and electron accepter availability. In the water column, inorganic and organic energy sources are injected into hypoxic deep waters, creating dynamic chemical niches. This project studies how gradients in geochemistry shape and modulate the microbial and viral communities that carry out key biogeochemical reactions in sediments and in the water column of Guaymas and Pescadero Basins. The research integrates data streams from biogeochemistry, genomics, and microbiology, including single-cell activity approaches, to achieve unprecedented insight into regulatory mechanisms and dynamics. The project includes experiments and observations in the laboratory and at sea during an expedition on the R/V Atlantis with the deep submergence vehicle ALVIN in 2022. Key topics for investigation include: (1) Do variations in geochemical regimes select for metabolically plastic microbial populations? (2) Do different microbes become active under specific geochemical conditions or do the same microbes adapt to changing geochemical conditions? (3) What is the role of viruses in shaping the microbial populations present in highly dynamic hydrothermal habitats?
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 |
|---|---|
| NSF Division of Ocean Sciences (NSF OCE) |