Physical and chemical metadata for microbiological samples from R/V New Horizon cruises GoCAL1, GoCAL2, GoCAL3 in the Guaymas Basin, Gulf of California from 2005-2014 (Guaymas plumes project)

Website: https://www.bco-dmo.org/dataset/543286
Version: 19 Dec 2014
Version Date: 2014-12-19

Project
» Linking biogeochemistry and microbial community dynamics in deep-sea hydrothermal plumes (Guaymas plumes)
ContributorsAffiliationRole
Dick, Gregory J.University of MichiganPrincipal Investigator
Rauch, ShannonWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager


Dataset Description

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


Acquisition 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).

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.


Processing Description

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.


[ table of contents | back to top ]

Parameters

ParameterDescriptionUnits
sampleSample identification number. unitless
sample_typeType of sample. text
month2-digit month. mm (01-12)
day2-digit day of month. dd (01-31)
year4-digit year YYYY
dateDate formatted as month/day/year. mm/dd/yyyy
castCast identification number. unitless
latLatitude. Positive values = North. decimal degrees
lonLongitude. Negative values = West. decimal degrees
depth_wDepth of the water. meters (m)
depthSample depth. meters (m)
salSalinity. parts per million (ppm)
Mn_totTotal Manganese (Mn) concentration. nanomolar (nM)
Mn_dissDissolved Manganese (Mn) concentration. nanomolar (nM)
O2Oxygen (O2) concentration. micromolar (um)
tempTemperature. degrees Celsius (C )
filter_typeType of filter. text
filter_pore_sizePore size of the filter. micrometers (um)


[ table of contents | back to top ]

Instruments

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
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
Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics, no specific unit identified. This instrument designation is used when specific make and model are not known. See also other SeaBird instruments listed under CTD. More information from Sea-Bird Electronics.

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.

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.


[ table of contents | back to top ]

Deployments

GoCAL1

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

GoCAL2

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

GoCAL3

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


[ table of contents | back to top ]

Project Information

Linking biogeochemistry and microbial community dynamics in deep-sea hydrothermal plumes (Guaymas plumes)


Coverage: Guaymas Basin and Carmen Basin, Gulf of California


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?



[ table of contents | back to top ]

Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)
Gordon and Betty Moore Foundation (GBMF)

[ table of contents | back to top ]