| Contributors | Affiliation | Role |
|---|---|---|
| Dick, Gregory J. | University of Michigan | Principal Investigator |
| Rauch, Shannon | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
Physical and chemical metadata (sal, Mn, O2, temp, etc.) for microbiological samples from Guyamas Basin plumes.
The following publications are associated with this data:
Anantharaman, K.A., M.B. Duhaime, J.A. Breier, K. Wendt, B.M. Toner, and G.J. Dick (2014). Sulfur oxidation genes in diverse deep-sea viruses. Science 344: 757-760. doi:10.1126/science.1252229
Li, M., B.M. Toner, B.J. Baker, J.A. Breier, C.S. Sheik, and G.J. Dick (2014). Microbial iron uptake as a mechanism for dispersing iron from deep-sea hydrothermal vents. Nature Communications 5: 3192. doi:10.1038/ncomms4192
Li, M., S. Jain, B.J. Baker, C. Taylor, and G.J. Dick (2014). Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume. Environmental Microbiology 16: 60-71. doi:10.1111/1462-2920.12182
Sheik, C.S. 2, S. Jain, and G.J. Dick (2014). Metabolic flexibility of enigmatic SAR324 revealed through metagenomics and metatranscriptomics. Environmental Microbiology 16: 304-317. doi:10.1111/1462-2920.12165
Baker, B.J., C.S. Sheik, C.A. Taylor, S. Jain, A. Bhasi, J.D. Cavalcoli, and G.J. Dick (2013). Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling. The ISME Journal 7: 1962-1973. doi:10.1038/ismej.2013.85
Dick, G.J., K. Anantharaman, B.J. Baker, M. Li, D.C. Reed, and C.S. Sheik (2013). Hydrothermal vent plume microbiology: ecological and biogeographic linkages to seafloor and water column habitats. Frontiers in Microbiology 4: 124. doi:10.3389/fmicb.2013.00124
Anantharaman, K., J.A. Breier, C.S. Sheik, and G.J. Dick (2013). Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea bacteria. Proceedings of the National Academy of Sciences 110: 330-335. doi:10.1073/pnas.1215340110
Baker, B.J., R.A. Lesniewski, and G.J. Dick. Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume (2012). The ISME Journal 6: 2269-2279. doi:10.1038/ismej.2012.64
Lesniewski, R.A., S. Jain, P.D. Schloss, K. Anantharaman,and G.J. Dick (2012). The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and chemolithotrophs. The ISME Journal 6: 2257-2268. doi:10.1038/ismej.2012.63
Hydrothermal plumes were detected by turbidity anomalies as measured by an air-calibrated transmissometer (WetLabs) on a CTD rosette (Sea-Bird). Water samples were collected in 10-L niskin bottles by CTD Rosette (Sea-Bird).
Samples were transferred from niskin bottles to acidwashed 50 mL polypropylene tubes. Samples for dissolved Mn (dMn) were filtered through 0.2 um acid-washed nucleopore polycarbonate filters within 1 h of collection. Filtrate (dMn) and unfiltered total Mn samples (tMn) were stabilized by acidification acidification with Optima grade nitric acid to a pH of <2 and stored at 4 degrees C until analysis. All shipboard manipulations were performed in a laminar flow hood with clean techniques. Mn concentrations were determined on a Thermoquest Finnigan Element 2 double focusing, single collector, magnetic sector inductively coupled plasma mass spectrometer (ICP-MS) at the SIO unified laboratory analytical facility. ICP-MS was done at low resolution following instrument and induction parameters described previously (Field et al., 1999). Samples were diluted 1:50 in 2% nitric acid in quartz-distilled (QD) water prior to analysis. A calibration curve was prepared as described previously (Rodushkin and Ruth, 1998) using matrix-matched external standards made with 2% natural seawater stripped of metals by precipitation with Optima ammonium hydroxide. Indium (1 ppb) was used as an internal standard in all standards and samples. Standard additions (Willard et al., 1965) were used to rule out a matrix effect. To confirm analytical accuracy, reference waters CASS-4 and NASS-5 (Verplank et al., 2001) were included in the analysis as samples. Our experimentally determined average Mn concentration for CASS was 56 ± 10 nM (reported to be 51 nM) and for NASS-5 it was16 ± 8 nM (reported to be 17 nM). Six samples from station 1 were collected, processed and analyzed in duplicate. The average standard deviation was 8 nM, which includes variation due to both sampling and analytical error.
BCO-DMO processing:
- modified parameter names to conform with BCO-DMO naming conventions;
- formatted date to mm/dd/yyyy; added separate month, day, and year columns;
- converted lat and lon to decimal degrees.
| File |
|---|
Guaymas_metadata.csv (Comma Separated Values (.csv), 834 bytes) MD5:dee8c0bbf3b75d76659b5d7598e86536 Primary data file for dataset ID 543286 |
| Parameter | Description | Units |
| sample | Sample identification number. | unitless |
| sample_type | Type of sample. | text |
| month | 2-digit month. | mm (01-12) |
| day | 2-digit day of month. | dd (01-31) |
| year | 4-digit year | YYYY |
| date | Date formatted as month/day/year. | mm/dd/yyyy |
| cast | Cast identification number. | unitless |
| lat | Latitude. Positive values = North. | decimal degrees |
| lon | Longitude. Negative values = West. | decimal degrees |
| depth_w | Depth of the water. | meters (m) |
| depth | Sample depth. | meters (m) |
| sal | Salinity. | parts per million (ppm) |
| Mn_tot | Total Manganese (Mn) concentration. | nanomolar (nM) |
| Mn_diss | Dissolved Manganese (Mn) concentration. | nanomolar (nM) |
| O2 | Oxygen (O2) concentration. | micromolar (um) |
| temp | Temperature. | degrees Celsius (C ) |
| filter_type | Type of filter. | text |
| filter_pore_size | Pore size of the filter. | micrometers (um) |
| Dataset-specific Instrument Name | CTD Sea-Bird |
| Generic Instrument Name | CTD Sea-Bird |
| Dataset-specific Description | Hydrothermal plumes were detected by turbidity anomalies as measured by an air-calibrated transmissometer (WetLabs) on a CTD rosette (Sea-Bird). Water samples were collected in 10-l niskin bottles by CTD Rosette (Sea-Bird). |
| Generic Instrument Description | A Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics. This instrument designation is used when specific make and model are not known or when a more specific term is not available in the BCO-DMO vocabulary. Refer to the dataset-specific metadata for more information about the specific CTD used. More information from: http://www.seabird.com/ |
| Dataset-specific Instrument Name | Thermoquest Finnigan Element 2 |
| Generic Instrument Name | Inductively Coupled Plasma Mass Spectrometer |
| Dataset-specific Description | Mn concentrations were determined on a Thermoquest Finnigan Element 2 double focusing, single collector, magnetic sector inductively coupled plasma mass spectrometer (ICP-MS) at the SIO unified laboratory analytical facility. |
| Generic Instrument Description | An ICP Mass Spec is an instrument that passes nebulized samples into an inductively-coupled gas plasma (8-10000 K) where they are atomized and ionized. Ions of specific mass-to-charge ratios are quantified in a quadrupole mass spectrometer. |
| Dataset-specific Instrument Name | Niskin bottle |
| Generic Instrument Name | Niskin bottle |
| Dataset-specific Description | Water samples were collected in 10-l niskin bottles by CTD Rosette (Sea-Bird). Samples were transferred from niskin bottles to acidwashed 50 ml polypropylene tubes. |
| 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 | Transmissometer |
| Generic Instrument Name | Transmissometer |
| Dataset-specific Description | Hydrothermal plumes were detected by turbidity anomalies as measured by an air-calibrated transmissometer (WetLabs) on a CTD rosette (Sea-Bird). |
| Generic Instrument Description | A transmissometer measures the beam attenuation coefficient of the lightsource over the instrument's path-length. This instrument designation is used when specific manufacturer, make and model are not known. |
| Website | |
| Platform | R/V New Horizon |
| Start Date | 2014-07-07 |
| End Date | 2014-07-23 |
| Description | GoCAL1 Cruise.
Guaymas Basin, Gulf of California.
San Diego, CA to San Diego, CA.
July 7 – 23, 2004.
R/V New Horizon
Chief Scientists: Fred Prahl and Brian Popp
OCE-0094329 |
| Website | |
| Platform | R/V New Horizon |
| Start Date | 2005-01-25 |
| End Date | 2005-02-09 |
| Description | GoCAL2 Cruise.
Guaymas Basin, Gulf of California.
San Diego, CA to San Diego, CA.
January 25 – February 9, 2005.
R/V New Horizon
Chief Scientists: Fred Prahl and Brian Popp
OCE-0326573 |
| Website | |
| Platform | R/V New Horizon |
| Start Date | 2005-07-23 |
| End Date | 2005-08-13 |
| Description | GoCAL3 Cruise.
Guaymas Basin, Gulf of California.
San Diego, CA to San Diego, CA.
July 23 – August 13, 2005.
R/V New Horizon
Chief Scientists: Fred Prahl and Brian Popp
OCE-0326573 |
Description from NSF award abstract:
Deep-sea hydrothermal vent plumes are globally distributed along the 60,000-km mid-ocean ridge system and are hot spots of microbial biogeochemistry in the deep oceans. These plumes play host to important interactions between microbial communities and hydrothermal inputs; hydrothermal energy sources stimulate enhanced microbial activity and productivity, and microorganisms mediate the flux of elements and energy from deep-sea hydrothermal vents into the oceans. This hydrothermal flux is a significant source of two key micronutrients, iron and manganese, for the oceans. Despite this importance, microbial communities in deep sea-hydrothermal plumes have been understudied relative to those inhabiting near-vent and subsurface environments. The overall goal of this project is to reveal the microbial community dynamics responsible for enhanced microbial activities and mediation of geochemical processes that has been observed in deep-sea hydrothermal plumes. This research project is focused on plumes in the Guaymas Basin (Gulf of California), where previous results showed dramatic enhancement of microbial activity and enzymatic manganese (II) oxidation relative to the ambient deep sea. Cutting-edge DNA sequencing technologies will be utilized to characterize the microbial diversity, metabolic potential and physiological state of plume versus background communities through metagenomics and metatranscriptomics. The specific objectives are:
(1) to utilize hundreds of thousands of rRNA gene sequences available from DNA and RNA to compare community structure and population-specific activity in plumes versus background;
(2) to reconstruct composite genomes from the most abundant deep-sea microbial populations and evaluate their metabolic capabilities and nutritional needs; and
(3) to quantitatively compare gene content and expression profiles in plume and background, with a focus on uncovering metabolic shifts towards chemolithoautotrophy.
Overall, results are expected to shed light on the nature of microbial players and processes in plumes: is plume biogeochemistry mediated by indigenous deep-sea microorganisms that have been stimulated by hydrothermal inputs, or by plume-specific groups that were entrained from near-vent environments?
| Funding Source | Award |
|---|---|
| NSF Division of Ocean Sciences (NSF OCE) | |
| Gordon and Betty Moore Foundation (GBMF) |