Dataset: ETSP qPCR
Deployment: MV1104

Water column amoA and Nitrospina-like 16S rRNA gene abundances from qPCR in the Eastern Tropical South Pacific

View Data: For data, See Dataset Metadata Page: https://www.bco-dmo.org/dataset/826781

Principal Investigator:

Karen L. Casciotti (Stanford University)

Contact:

Alyson E. Santoro (University of California-Santa Barbara, UCSB)

BCO-DMO Data Manager:

Dana Stuart Gerlach (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Expression of Microbial Nitrification in the Stable Isotopic Systematics of Oceanic Nitrite and Nitrate (Microbial Nitrification)

Version:

Deployment Synonyms:

ETSP2011

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Description

These data appear in the following:

Figure S7 of Santoro, et al. (2020)
Table S5 of Santoro, et al. (2020)
Figure S6 in pre-print on ESSOAr (doi.org/10.1002/essoar.10503499.1)

Methods & Sampling

Dataset acquisition description

Seawater samples were obtained during the R/V Atlantis (AT15-61) and R/V Melville (MV1104) cruises in Jan-Feb 2010 and Mar-Apr 2011. Water samples were collected at discrete depths using a standard 24-bottle Niskin rosette sampler equipped with an SBE9plus conductivity-temperature-depth (CTD) sensor package (SeaBird Electronics, Bellevue, WA). Samples for nucleic acid extraction and qPCR were collected from the rosette in 2-4 L polycarbonate bottles. Cells were harvested by pressure filtration onto 25 mm diameter, 0.2 µm pore-size polyethersulfone membrane filters (Supor-200, Pall Corporation, Port Washington, NY) housed in polypropylene filter holders (Whatman SwinLok, GE Healthcare, Pittsburgh, PA) using a peristaltic pump and silicone tubing. DNA was extracted according to Santoro,et al. (2010). For DNA extraction and analysis methods followed Santoro, et al. (2010). Sample volumes of 1-4 liters were filtered depending on the biomass present at each station and depth, and the filters were flash frozen in liquid nitrogen in 2 mL gasketed bead beating tubes (Fisher Scientific).

Data Processing Description

Dataset Processing Description

Water samples were collected, filtered with peristaltic pressure onto 25 mm 0.2 µm pore size Supor filters.
DNA was extracted according to Santoro et al. 2010.
Abundance of bacterial amoA genes by quantitative PCR (qPCR) using SYBR Green chemistry followed that of Santoro et al. (2010).
Abundance of archaeal amoA genes belonging to one of two ecotypes (WCA and WCB) were quantified using TaqMan assays following protocols described in Mosier and Francis (2011).
Nitrospina-like 16S rRNA genes were quantified using the SYBR Green assay described in Mincer et al. (2007).

Data processing: Reported abundances are the mean of triplicate qPCR reactions. Gene abundances per qPCR reaction were converted to abundance per liter of seawater using the volume of seawater filtered, the DNA extraction elution volume, and the volume of extract added to each reaction. Conversion assumes 100% DNA extraction efficiency.

BCO-DMO processing:

Added a conventional header with dataset name, PI name, version date
Adjusted parameter names to comply with database requirements.
Combined year, month, day fields into one date field.
Units in parentheses removed and added to Parameter Description metadata section.
Default missing identifier of 'NaN' replaced with 'nd' ('nd' is BCO-DMO system default missing data identifier).
BDL (below detection limit) identifier maintained

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0961098	NSF Division of Ocean Sciences

Instruments

CTD Sea-Bird 9

Supplied Name: CTD Sea-Bird 9 plus

Supplied Description:

SBE9plus conductivity-temperature-depth (CTD) sensor package (SeaBird Electronics, Bellevue, WA)

Instrument Type

Generic Name: CTD Sea-Bird 9

Acronym: CTD SBE 9

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

Generic Description:

The Sea-Bird SBE 9 is a type of CTD instrument package. The SBE 9 is the Underwater Unit and is most often combined with the SBE 11 Deck Unit (for real-time readout using conductive wire) when deployed from a research vessel. The combination of the SBE 9 and SBE 11 is called a SBE 911. The SBE 9 uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 and SBE 4). The SBE 9 CTD can be configured with auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorometer, altimeter, etc.). Note that in most cases, it is more accurate to specify SBE 911 than SBE 9 since it is likely a SBE 11 deck unit was used. more information from Sea-Bird Electronics

Niskin bottle

Supplied Name: 24-bottle Niskin rosette sampler

Supplied Description:

24-bottle Niskin rosette sampler

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.

qPCR Thermal Cycler

Supplied Name: BioRad CFX96 quantitative PCR machine

Supplied Description:

BioRad CFX96 quantitative PCR machine (Bio-Rad, Inc. in Hercules, CA)

Instrument Type

Generic Name: qPCR Thermal Cycler

Acronym: qPCR

Generic Description:

An instrument for quantitative polymerase chain reaction (qPCR), also known as real-time polymerase chain reaction (Real-Time PCR).

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
ISO_Date_Local	Date of sampling in ISO format (yyyy-mm-dd), Time zone in 2010 was GMT-5, Time zone in 2011 was GMT-4	yyyy-mm-dd	date_local
Latitude	Latitude of sample collection	decimal degrees	lat
Longitude	Longitude of sample collection	decimal degrees	lon
Station	Station number	unitless	station
Cast	Cast number	unitless	cast
Depth	Depth of sample collection	meters (m)	depth
Vol_filtered	Volume of seawater filtered (in liters)	liters (L)	vol_filt
AOB_amoA	Abundance of ammonia-oxidizing betaproteobacterial ammonia monooxygenase subunit A (amoA) genes	copies per milliliter (copies/mL)	abundance
AOB_amoA_SD	Standard deviation of abundance of ammonia-oxidizing betaproteobacterial monooxygenase subunit A (amoA) genes	copies per milliliter (copies/mL)	std_dev
AOA_amoA	Abundance of ammonia-oxidizing archaeal monooxygenase subunit A (amoA) genes	copies per milliliter (copies/mL)	abundance
AOA_amoA_SD	Standard deviation of abundance of ammonia-oxidizing archaeal monooxygenase subunit A (amoA) genes	copies per milliliter (copies/mL)	std_dev
WCA_amoA	Abundance of Water Column A clade archaeal monooxygenase subunit A (amoA) genes	copies per milliliter (copies/mL)	abundance
WCA_amoA_SD	Standard deviation of abundance of Water Column A clade archaeal monooxygenase subunit A (amoA) genes	copies per milliliter (copies/mL)	std_dev
WCB_amoA	Abundance of Water Column B clade archaeal monooxygenase subunit A (amoA) genes	copies per milliliter (copies/mL)	abundance
WCB_amoA_SD	Standard deviation of abundance of Water Column Bclade archaeal monooxygenase subunit A (amoA) genes	copies per milliliter (copies/mL)	std_dev
NIT_16S	Abundance of Nitrospina-like 16S rRNA genes	copies per milliliter (copies/mL)	abundance
NIT_16S_SD	Standard deviation of abundance of Nitrospina-like 16S rRNA genes	copies per milliliter (copies/mL)	std_dev
Year	Deployment year	unitless	year
Month	Deployment month	unitless	month_local
Day	Deployment day	unitless	day_local

Database

Contribute Data

Dataset: ETSP qPCR
Deployment: MV1104

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: ETSP qPCRDeployment: MV1104

Dataset acquisition description

Dataset Processing Description

Dataset: ETSP qPCR
Deployment: MV1104