Dataset: WS1209 strains
Deployment: WS1209

Microbial culture collection, strain IDs, locations and depth from cruise WB1209

Principal Investigator:

Paul Jensen (University of California-San Diego, UCSD-SIO)

Co-Principal Investigator:

Gregory Rouse (University of California-San Diego, UCSD-SIO)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

The Chemical Ecology of Marine Sediment Bacteria (CEMSB)

Current State:

Final no updates expected

Version:

2016-01-19

Version Date:

2016-01-19

Data URL:

https://osprey.bco-dmo.org/dataset-deployment/632986/data

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Description

This dataset includes microbial Salinispora strains and co-occurring bacteria found in samples from WS1209, their associated collection information, and links to GenBank accession pages. The collections were made from sediments off of Yucatan in the Mexican Caribbean Sea. Bacteria were cultured from marine sediments and identified based on 16S sequence analysis.

Coordinates (this study) or year of isolation are given for each strain, as well as sample depth if known. BC stands for Banco Chinchorro, which divided into North (N), Middle (M), and South (S) locations.
The following are also flagged in the data:
* Genome sequence available.
+ Strains used in secondary assays to determine the temporal onset of antagonism.

Related Reference:

Patin,NV; Duncan,KR; Dorrestein,PC; Jensen,PR. (2012) Competitive strategies differentiate closely related species of marine actinobacteria. ISME J 10:478-490. doi:10.1038/ismej.2015.128

Methods & Sampling

Dataset acquisition description

Methodolody (pdf)

Data Processing Description

Dataset Processing Description

BCO-DMO Processing:

- added conventional header with dataset name, PI name, version date
- renamed parameters to BCO-DMO standard
- added hyperlinks to GenBank accessions
- changed '<1' to 'lt_1'
- split collection year and location into 2 columns, adding 'nd' in empty cells
- replaced empty cells with 'nd' (no data)
- replaced blanks with underscores

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1235142	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Thermal Cycler

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Thermal Cycler

Generic Description:

A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
sample	sample identification	unitless	sample
species_strain	species and strain	unitless	species
GenBank_accession	GenBank accession number	unitless	accession_number
BLAST_pcent	BLAST result	percent	no_bcodmo_term
seq_avail_flag	genome sequence available	unitless	flag
study_2_flag	flag denoting strains used in secondary assays to determine the temporal onset of antagonism	unitless	flag
site	collection site	unitless	site
lat	latitude; north is positive	decimal degrees	lat
lon	lonitude; east is positive	decimal degrees	lon
year	year of Isolation	yyyy	year
depth	collection depth	meters	depth

Database

Contribute Data

Dataset: WS1209 strains
Deployment: WS1209

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: WS1209 strainsDeployment: WS1209

Dataset acquisition description

Dataset Processing Description

Dataset: WS1209 strains
Deployment: WS1209