Dataset: physical and chemical data
Deployment: GoCAL1

Physical and chemical metadata for microbiological samples from Guaymas Basin plumes.

Principal Investigator:

Gregory J. Dick (University of Michigan)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

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

Current State:

Final no updates expected

Version:

19 Dec 2014

Version Date:

2014-12-19

Data URL:

https://osprey.bco-dmo.org/dataset-deployment/543293/data

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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

Methods & Sampling

Dataset 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.

Data Processing Description

Dataset 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.

More information about this dataset deployment

Funding

Award Number	Funding Source
GBMF2609	Gordon and Betty Moore Foundation
OCE-1029242	NSF Division of Ocean Sciences

Instruments

CTD Sea-Bird

Supplied Description:

Instrument Type

Generic Name: CTD Sea-Bird

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic 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.

Inductively Coupled Plasma Mass Spectrometer

Supplied Name: Thermoquest Finnigan Element 2

Supplied 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.

Instrument Type

Generic Name: Inductively Coupled Plasma Mass Spectrometer

Acronym: ICP Mass Spec

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB15/

Generic 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.

Niskin bottle

Supplied 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.

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic 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.

Transmissometer

Supplied Description:

Hydrothermal plumes were detected by turbidity anomalies as measured by an air-calibrated transmissometer (WetLabs) on a CTD rosette (Sea-Bird).

Instrument Type

Generic Name: Transmissometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/124/

Generic 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.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
sample	Sample identification number.	unitless	sample
sample_type	Type of sample.	text	sample_type
month	2-digit month.	mm (01-12)	month
day	2-digit day of month.	dd (01-31)	day
year	4-digit year	YYYY	year
date	Date formatted as month/day/year.	mm/dd/yyyy	date
cast	Cast identification number.	unitless	cast
lat	Latitude. Positive values = North.	decimal degrees	lat
lon	Longitude. Negative values = West.	decimal degrees	lon
depth_w	Depth of the water.	meters (m)	depth_w
depth	Sample depth.	meters (m)	depth
sal	Salinity.	parts per million (ppm)	sal
Mn_tot	Total Manganese (Mn) concentration.	nanomolar (nM)	Mn
Mn_diss	Dissolved Manganese (Mn) concentration.	nanomolar (nM)	Mn
O2	Oxygen (O2) concentration.	micromolar (um)	O2
temp	Temperature.	degrees Celsius (C )	temp
filter_type	Type of filter.	text	no_bcodmo_term
filter_pore_size	Pore size of the filter.	micrometers (um)	filter_size

Database

Contribute Data

Dataset: physical and chemical data
Deployment: GoCAL1

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: physical and chemical dataDeployment: GoCAL1

Dataset acquisition description

Dataset Processing Description

Dataset: physical and chemical data
Deployment: GoCAL1