Dataset: SCCS Diazotroph Abundances
Deployment: SP1727

qPCR abundance data

View Data: For data, See Dataset Metadata Page: https://osprey.bco-dmo.org/dataset/881028

Principal Investigator:

Jonathan P. Zehr (University of California-Santa Cruz, UCSC)

Co-Principal Investigator:

Kevin R. Arrigo (Stanford University)

Contact:

Kendra Turk-Kubo (University of California-Santa Cruz, UCSC)

BCO-DMO Data Manager:

Karen Soenen (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Collaborative Research: Biogeochemical significance of the abundant, uncultivated symbiotic cyanobacteria UCYN-A (BSUCS)

Version:

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Description

These data were published in Turk-Kubo et al. (2021). Table 1, Figure 3, Table S1, Table S2

Meaning different No Data values:

UD = undetected
na = not applicable
- - = parameter not measured
DNQ = detected, not quantified
Empty cells = means that the value reported in the average nifH L-1 column is quantified.

Methods & Sampling

Dataset acquisition description

Samples were collected using standard oceanographic techniques. A CTD Rosette with 24 10L Niskin bottles was lowered to the maximum sampling depth and then brought back to the surface. Methodology described in depth in Turk-Kubo et al. (2021)

Data Processing Description

Dataset Processing Description

Samples for the measurement of nitrate plus nitrite and phosphate (PO43−) concentrations were filtered through precombusted GF/F filters and analyzed using standard techniques on a Lachat QuikChem 8000 Flow Injection Analyzer. Chl a samples from each depth were filtered onto GF/F filters, extracted in the dark at 3 °C in 90% acetone for 24 h and measured fluorometrically using a Turner Fluorometer TD-700 as described in Welschmeyer et al.

For DNA collection and extraction, seawater was filtered through SterivexTM filters using gentle peristaltic pumping and flash-frozen in liquid N2. DNA was extracted using the DNeasy Plant Kit (Qiagen, Germantown, MD) using modifications to the manufacturer’s guidelines described in detail in Moisander et al. 2007. On-column steps were automated using a QIACube (Qiagen). DNA was quantified using the Picogreen® dsDNA Quantitation kit (Molecular Probes, Eugene, OR).

Gene-based abundance estimates of UCYN-A1, UCYN-A2, Crocosphaera (UCYN-B), Trichodesmium, Richelia associated with Hemiaulus (Het-2), and gamma A (γ-24774A11) were determined using Taqman® qPCR assays. Protocols used for all aspects of qPCR analysis, including reaction conditions, the use of linearized plasmids and inhibition reactions, and calculation of unknowns follow those described in detail by Goebel et al. 2010, apart from a 64 °C annealing temperature for the UCYN-A2 assay. The LOD and LOQ for all assays ranged between 25-31 and 200-250 nifH copies l−1, respectively. Targets with nifH copies >LOD and <LOQ are detected not quantified (DNQ).

Methodology described in depth in Turk-Kubo et al. (2021).

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1559152	NSF Division of Ocean Sciences
OCE-1559165	NSF Division of Ocean Sciences

Instruments

Flow Injection Analyzer

Supplied Name: Lachat QuikChem 8000 Flow Injection Analyzer

Supplied Description:

Nutrients were measured on a Lachat QuikChem 8000 Flow Injection Analyzer.

Instrument Type

Generic Name: Flow Injection Analyzer

Acronym: FIA

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB36/

Generic Description:

An instrument that performs flow injection analysis. Flow injection analysis (FIA) is an approach to chemical analysis that is accomplished by injecting a plug of sample into a flowing carrier stream. FIA is an automated method in which a sample is injected into a continuous flow of a carrier solution that mixes with other continuously flowing solutions before reaching a detector. Precision is dramatically increased when FIA is used instead of manual injections and as a result very specific FIA systems have been developed for a wide array of analytical techniques.

Turner Designs 700 Laboratory Fluorometer

Supplied Name: Turner Fluorometer TD-700

Supplied Description:

Fluorometric analysis of Chl a was measured using a Turner Fluorometer TD-700 (Turner Designs, Inc., San Jose, CA).

Instrument Type

Generic Name: Turner Designs 700 Laboratory Fluorometer

Acronym: TD-700

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0510/

Generic Description:

The TD-700 Laboratory Fluorometer is a benchtop fluorometer designed to detect fluorescence over the UV to red range. The instrument can measure concentrations of a variety of compounds, including chlorophyll-a and fluorescent dyes, and is thus suitable for a range of applications, including chlorophyll, water quality monitoring and fluorescent tracer studies. Data can be output as concentrations or raw fluorescence measurements.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
Cruise	Cruise ID	unitless	cruise_id
Station	Station number	unitless	station
Depth	Sampling depth	meters (m)	depth
latitude	sampling latittude, south is negative	decimal degrees	lat
longitude	sampling longitude, west is negative	decimal degrees	lon
Sample_Date	sampling date	unitless	date
bottom_depth	bottom depth	meters (m)	depth_bottom
mix_layer_depth	mixed layer depth	meters (m)	depth_mixed_layer
temperature	temperature	Degrees Celcius (°C)	temp
salinity	salinity	psu	sal
oxygen	oxygen	milliliters per liter (mL L-1)	O2
fluorescence	fluoresence	milligrams per cubic meters (mg m-3)	fluor
PAR	Photosynthetically active radiation	unitless	PAR
potential_density	potential density. σθ	kilograms per cubic meters (kg m-3)	sigma_0
Nitrate	nitrate	micromoles (µM)	NO3
Phosphate	phosphate (PO43- )	micromoles (µM)	PO43-
P	P* is the amount of dissolved PO43− in the environment relative to what is expected if N and P uptake and remineralization proceed according to Redfield proportions. P* = PO43− − (NO3− + NO2−)/16	unitless	P
chla_ave	Average chlorophyll a	micrograms per liter (µg L-1)	chl_a
chla_stdev	Standard deviation chlorophyll a	micrograms per liter (µg L-1)	chl_a
UCYN_A1_ave	Average of UCYN-A1 gene expression	nitrogenase gene per liter (nifH L-1)	genetic_conc
UCYN_A1_stdev	Standard deviation of UCYN-A1 gene expression	nitrogenase gene per liter (nifH L-1)	genetic_conc
UCYN_A1_DNQ	UCYN-A1 gene expression detected, not quantified	unitless	sample_descrip
UCYN_A2_ave	Average of UCYN-A2 gene expression	nitrogenase gene per liter (nifH L-1)	genetic_conc
UCYN_A2_stdev	Standard deviation of UCYN-A2 gene expression	nitrogenase gene per liter (nifH L-1)	genetic_conc
UCYN_A2_DNQ	UCYN-A2 gene expression detected, not quantified	unitless	sample_descrip
UCYN_B_ave	Average of UCYN-B gene expression	nitrogenase gene per liter (nifH L-1)	genetic_conc
UCYN_B_stdev	Standard deviation of UCYN-B gene expression	nitrogenase gene per liter (nifH L-1)	genetic_conc
UCYN_B_DNQ	UCYN-B gene expression detected, not quantified	unitless	sample_descrip
Tricho_ave	Average of UCYN-A1 gene expression	nitrogenase gene per liter (nifH L-1)	genetic_conc
Tricho_stdev	Standard deviation of UCYN-A1 gene expression	nitrogenase gene per liter (nifH L-1)	genetic_conc
Tricho_DNQ	UCYN-A1 gene expression detected, not quantified	unitless	sample_descrip
Het_2_ave	Average of UCYN-A1 gene expression	nitrogenase gene per liter (nifH L-1)	genetic_conc
Het_2_stdev	Standard deviation of UCYN-A1 gene expression	nitrogenase gene per liter (nifH L-1)	genetic_conc
Het_2_DNQ	UCYN-A1 gene expression detected, not quantified	unitless	sample_descrip
g_24774A11_ave	Average of γ-24774A11 gene expression	nitrogenase gene per liter (nifH L-1)	genetic_conc
g_24774A11_stdev	Standard deviation of γ-24774A11 gene expression	nitrogenase gene per liter (nifH L-1)	genetic_conc
g_24774A11_DNQ	γ-24774A11 gene expression detected, not quantified	unitless	sample_descrip

Database

Contribute Data

Dataset: SCCS Diazotroph Abundances
Deployment: SP1727

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: SCCS Diazotroph AbundancesDeployment: SP1727

Dataset acquisition description

Dataset Processing Description

Dataset: SCCS Diazotroph Abundances
Deployment: SP1727