Dataset: Prochlorococcus HOT/BATS

Name: Five year time-series of Prochlorococcus ecotype abundance at HOT and BATS sites from 2002-2008 (C-MORE project, Prochlorococcus project)
Published: 2014-11-26
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:31.6667 E:-64.1667 S:22.75 W:-158

Project:

Center for Microbial Oceanography: Research and Education (C-MORE)

The Ecology of Prochlorococcus: Toward a Model System for Microbial Oceanography (Prochlorococcus )

Lead Principal Investigator:

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

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

Principal Investigator:

Sallie W. Chisholm

Co-Principal Investigator:

Daniele Veneziano (Massachusetts Institute of Technology, MIT)

Scientist:

Dr Rex Malmstrom (Massachusetts Institute of Technology, MIT)

BCO-DMO Data Manager:

Robert C. Groman (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version Date:

2014-11-26

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Five year time-series of Prochlorococcus ecotype abundance at HOT and BATS sites from 2002-2008 (C-MORE project, Prochlorococcus project)

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Description

The goal was to collect long-term, high-resolution data on the temporal and spatial variability of Prochlorococcus ecotypes in the Pacific and Atlantic Oceans. The abundance of five Prochlorococcus ecotypes was determined by quantitative PCR at 12 depths every month for 5 years at two locations:

BATS location (5 nautical mile radius around 31 40'N, 64 10'W)
HOT Station ALOHA (5 nautical mile radius around 22 45'N, 158 00' W)

Methods & Sampling

Sample processing and analyses are detailed in the publication 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 different Prochlorococcus ecotypes. Standard curves used for quantitation of field data were derived from DNA extracted from cultured representatives belonging to each ecotype.

Malmstrom, RR, A Coe, GC Kettler, AC Martiny, J Frias-Lopez, ER Zinser, and SW Chisholm. 2010. Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans. The ISME Journal. 4(10): 1252-1264

Data 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. Missing data points were determined by linear interpolation when abundance estimates were available for the depths immediately above and below the missing value.

In November 2014, the online data were updated to correct relatively minor errors from HOT cruises 187 and 188. The "no data" value in the original data (-9999) was replaced with the "nd" string.

Data Files

File
hot_bats_2014.csv (Comma Separated Values (.csv), 750.67 KB) MD5:3447a8d3c816d659e27e8666793855a2 Primary data file for dataset ID 3381

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-0425602

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
BATS_Prochlorococcus	See dataset	2002-11-13	Bermuda Atlantic Time Series Vessel	Sallie W. Chisholm (Chief Scientist)	data info
HOT_Prochlorococcus	See dataset	2002-11-13	Hawaii Ocean Time-series Vessel	Sallie W. Chisholm (Chief Scientist) Sallie W. Chisholm (Lead Principal Investigator) Daniele Veneziano (Co-Principal Investigator)	data info

Instruments

None available yet

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
ecotype	A group of organisms, normally a subdivision of a species, that is adapted to a specific environment		no_bcodmo_term
site	Location of the measurement, in this case one of two sites located at the HOT and BATS sites.		site
lat	Latitude, north is positive	decimal degrees	lat
lon	Longitude, east is positive	decimal degrees	lon
year	Year the measurement was taken		year
month	Month the measurement was taken		month_gmt
day	Day the measurement was taken		day_gmt
abundance	Number of bacteria counted	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 measurement	cells/milliliter	no_bcodmo_term
date	Date the sample was taken, in the form of mm/dd/yy		date
yrday_gmt	The year day the sample was taken, with 1 meaning January 1.		yrday_gmt
cruiseid	The cruise identification		cruiseid

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Database

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Dataset: Prochlorococcus HOT/BATS