Dataset: Microbial isolates
Deployment: Milos_vents_2012

Microbial isolates from sediment samples collected at Paleochori Bay, Milos island, Greece

Principal Investigator:

Costantino Vetriani (Rutgers University, Rutgers IMCS)

BCO-DMO Data Manager:

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

Project:

Autotrophic carbon fixation at a shallow-water hydrothermal system: Constraining microbial activity, isotopic and geochemical regimes (Hydrothermal Autotrophic Carbon Fixation)

Current State:

Final with updates expected

Version Date:

2016-06-28

Data URL:

https://www.bco-dmo.org/dataset-deployment/650215/data

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Description

This dataset includes microbial isolates and links to repositories at GenBank and Leibniz-Institut DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH).

Related Datasets:
GenBank accessions
Sample log

Methods & Sampling

Dataset acquisition description

Samples were collected at the shallow-water hydrothermal vent sites at Paleochori Bay, Milos Island, Greece. Sequence data (bacterial ssrRNA) was obtained using the Ion Torrent platform from total RNA extracted from thirty-two sediment and microbial biofilm samples characterized along a transect. Sequence data are currently being generated and analyzed, they will be deposited in GenBank prior to publication and will be made available to the scientific community.

Data Processing Description

Dataset Processing Description

BCO-DMO Processing:

- added conventional header with dataset name, PI name, version date, reference information
- renamed parameters to BCO-DMO standard
- created links to GenBank and DSMZ accession pages

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1124141	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name:

Supplied Description:

Ion Torrent platform

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.

Push Corer

Supplied Name:

Supplied Description:

push cores were collected by SCUBA divers

Instrument Type

Generic Name: Push Corer

Generic Description:

Capable of being performed in numerous environments, push coring is just as it sounds. Push coring is simply pushing the core barrel (often an aluminum or polycarbonate tube) into the sediment by hand. A push core is useful in that it causes very little disturbance to the more delicate upper layers of a sub-aqueous sediment.

Description obtained from: http://web.whoi.edu/coastal-group/about/how-we-work/field-methods/coring/

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
species	species	unitless	species
sample_origin	sample origin	unitless	sample_descrip
DSMZ_accession	Leibniz-Institut DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH) accession number	unitless	accession_number
GenBank_acc	NCBI GenBank accession number for the 16S rRNA gene	unitless	accession_number
reference_paper	reference	unitless	reference_paper

Database

Contribute Data

Dataset: Microbial isolates
Deployment: Milos_vents_2012

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Microbial isolatesDeployment: Milos_vents_2012

Dataset acquisition description

Dataset Processing Description

Dataset: Microbial isolates
Deployment: Milos_vents_2012