Dataset: Prochlorococcus_narB
Deployment: HOT_Prochlorococcus

Abundance of Prochlorococcus cells containing gene narB at HOT and BATS

Principal Investigator:

Sallie W. Chisholm (Massachusetts Institute of Technology, MIT-Dept CEE)

Contact:

Paul Berube (Massachusetts Institute of Technology, MIT-Dept CEE)

BCO-DMO Data Manager:

Ms Dicky Allison (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Nitrate Assimilation and the Ecology of Prochlorococcus: Features and Implications of Intraspecific Diversity in a Model Marine Phototroph (Prochloro_ecology)

Current State:

Final with updates expected

Version:

working draft of final

Deployment Synonyms:

See dataset

Version Date:

2016-03-30

Data URL:

https://www.bco-dmo.org/dataset-deployment/641501/data

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Description

Two year time series of the abundance of Prochlorococcus cells containing the nitrate reductase gene (narB) at the HOT and BATS sites in the Pacific and Atlantic Oceans. The goal was to collect long-term, high-resolution data on the temporal and spatial variability of Prochlorococcus narB genotypes belonging to the HLII and LLI clades. The abundance of Prochlorococcus cells containing narB for each of these clades was determined by quantitative PCR at 12 depths every month from October 2005 to December 2007 at two locations: BATS location (5 nautical mile radius around 31 40'N, 64 10'W) and HOT Station ALOHA (5 nautical mile radius around 22 45'N, 158 00' W). These field samples are a subset of those utilized in the "Prochlorococcus HOT/BATS" dataset (http://www.bco-dmo.org/dataset/3381).

These data are reported and described in:

Berube, P. M., Coe, A., Roggensack, S. E., & Chisholm, S. W. (2015). Temporal dynamics of Prochlorococcuscells with the potential for nitrate assimilation in the subtropical Atlantic and Pacific oceans. Limnology and Oceanography, 61(2), 482–495. doi:10.1002/lno.10226

Methods & Sampling

Dataset acquisition description

Sample processing and analyses are detailed in the publications listed below. Briefly, 100ml of seawater was collected onto 25mm dia polycarbonate filters (0.22um pore size), rinsed with Tris-buffered saline, flash frozen in liquid N2, and stored at -80C until extraction. DNA was extracted using a combination of 5min of bead beating and 15min heat lysis at 95C. Extracted DNA was used as template of quantitative PCR reactions using primers specifically designed to target the narB gene from the HLII and LLI clades of Prochlorococcus. Standard curves used for quantitation of field data were derived from DNA extracted from defined cell numbers of cultured representatives of each clade.

Data Processing Description

Dataset Processing Description

Estimated abundances that fell below the lowest value of the standard curve were set to the theoretical detection limit of 0.65 cells/mL. Samples were excluded if their melt curves contained multiple peaks or peaks different from those in the DNA standards. Samples were excluded if the coefficient of variation (standard deviation divided by the mean) was greater than 50%. The no data value "nd" refers to missing or excluded measurements.

Related files and references:

Analysis and data processing used the same field samples and methods as described in the following publication, but with different primer sets:

Malmstrom, R. R., Coe, A., Kettler, G. C., Martiny, A. C., Frias-Lopez, J., Zinser, E. R., & Chisholm, S. W. (2010). Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans. The ISME Journal, 4(10), 1252–1264. doi:10.1038/ismej.2010.60

More information about this dataset deployment

Funding

Award Number	Funding Source
DBI-0424599	NSF Division of Biological Infrastructure
GBMF495	Gordon and Betty Moore Foundation
OCE-1153588	NSF Division of Ocean Sciences

Instruments

Flow Cytometer

Supplied Name: influx flow cytometer

Supplied Description:

from Becton Dickinson, Franklin Lakes, NJ, USA

Instrument Type

Generic Name: Flow Cytometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/

Generic Description:

Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
gene	nitrate reductase gene (narB) in one of two clades (HLII and LLI)	text	no_bcodmo_term
site	Location of the measurement at one of two sites located at the HOT and BATS sites	text	site
lat	Latitude; north is positive	decimal degrees	lat
lon	Longitude; east is positive	decimal degrees	lon
cruiseid	The cruise identification	numeric	cruiseid
year	Year the measurement was taken in YYYY format	unitless	year
month	Month the measurement was taken	mm	month_gmt
day	Day the measurement was taken	dd	day
date	Date the sample was taken	mm/dd/yy	date
yrday_gmt	The year day the sample was taken with 1 meaning January 1	decimal number	yrday_gmt
abundance	Abundance of HLII or LLI clade Prochlorococcus cells containing the narB gene	cells/milliliter	abundance
temp	Temperature at the sample location	degrees centigrade	temp
sal	Salinity measured at the sample location	PSS-78	sal
depth	Depth at which the sample was taken	meters	depth
sigma_0	Potential density	kilograms/cubic meter	sigma_0
standard_deviation	Standard deviation of the abundance measurements	cells/milliliter	std_dev

Database

Contribute Data

Dataset: Prochlorococcus_narB
Deployment: HOT_Prochlorococcus

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Prochlorococcus_narBDeployment: HOT_Prochlorococcus

Dataset acquisition description

Dataset Processing Description

Dataset: Prochlorococcus_narB
Deployment: HOT_Prochlorococcus