Dataset: kinetoplastid SSU rRNA seq.
Deployment: OC454-02

Microbial metatranscriptomics: upper and lower halocline water column

Principal Investigator:

Virginia P. Edgcomb (Woods Hole Oceanographic Institution, WHOI)

Co-Principal Investigator:

Joan M. Bernhard (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

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

Project:

Pickled Protists or Community Uniquely Adapted to Hypersalinity? (Pickled Protists)

Current State:

Final no updates expected

Version:

2015-03-19

Version Date:

2015-03-19

Data URL:

https://www.bco-dmo.org/dataset-deployment/554067/data

Expand/Collapse All

Description

Cloned SSU rRNA sequences of kinetoplastids detected in Discovery, Urania and Kryos Basin haloclines and brines.

Related Reference:

Edgcomb, V.P., W. Orsi, H.-W. Breiner, A. Stock, S. Filker, M.M. Yakimov, and T. Stoeck. 2011, Novel kinetoplastids associated with hypersaline anoxic lakes in the Eastern Mediterranean deep-sea. Deep-Sea Research I 58(10):1040-1048.

Methods & Sampling

Dataset acquisition description

The position of the halocline was determined during the R/V Oceanus cruise using a SBE9 CTD (Sea-Bird Electronics, USA) equipped with an SBE43 oxygen sensor (Sea-Bird Electronics, USA). Samples were collected from the halocline and brine of Discovery basin using a rosette equipped with Niskin bottles (12 L) on R/V Oceanus.

RNA was extracted as described in detail previously (Alexander et al., 2009) using bead beating of filters in an extraction buffer and E-Matrix tubes (QBiogene, MP Biomedicals, USA), followed by the RNA/DNA Allprep kit (Qiagen, Hildesheim, Germany) according to the manufacturer's instructions. Total RNA was transcribed into cDNA using the Two-Step Omniscript Reverse Transcription kit (Qiagen) according to the manufacturer's instructions. Subsequently, the small subunit ribosomal RNA gene (18S rRNA) was amplified using the kinetoplastid-specific primers 14F (5′-CTGCCAGTAGTCATATATGCTTGTTTCAAGGA-3′) and 2026R (5′-GATCCTCTGCAGGTTCACCTACAGCT-3′) (von der Heyden et al., 2004).

Data Processing Description

Dataset Processing Description

PCR products were cloned and Sanger sequenced (bidirectionally)

BCO-DMO Processing:
original file: EdgcombKinetoplastid.xlsx
- added conventional header with dataset name, PI name, version date
- renamed parameters to BCO-DMO standard
- converted lat/lon to decimal degrees from degrees-decimal minutes
- added cruise id's
- added html links to GenBank Popset

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0849578	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name: Sequencer

Supplied Description:

Roche 454 FLX Titanium 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.

Niskin bottle

Supplied Description:

12L Niskin bottles mounted on a General Oceanics rosette sampler equipped with a SBE- 911plus conductivity-temperature-depth (CTD) sensor (Sea- Bird Electronics)

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic Description:

A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.

Submersible Incubation Device-In Situ Microbial Sampler

Supplied Name: MS_SID

Supplied Description:

Microbial Sampler - In Situ Incubation Device (MS-SID)

Instrument Type

Generic Name: Submersible Incubation Device-In Situ Microbial Sampler

Acronym: SID-ISMS

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/82/

Generic Description:

The Submersible Incubation Device-In Situ Microbial Sampler (SID-ISMS) system was developed for the 2011 NSF funded DHAB Metazoans Mediterranean Brine research project and first used on cruise AT18-14. The system includes several integrated components including: a 2 liter incubation chamber; fixation filters and water sample bottles; a High Range CTD (Neil Brown Ocean Sensors, Inc., USA) equipped with two turbidity sensors (Wet Labs ECOView); an Aanderra 2808F oxygen optode; an SDSL-data link; and a sonardyne beacon, a pinger and a 24 volt deep-sea battery. The sensors and sampling devices are mounted on a frame that is attached to the hydro-wire. Lowering rate and recovery speed are controlled by a winch mounted on the surface vessel.

Thermal Cycler

Supplied Name: PCR

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
cruise_id	cruise identification	unitless	cruise_id
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
sample_location	sampling location	unitless	site_descrip
sample_descrip	description of sample	unitless	sample_descrip
depth	depth	meters	depth
sal	total salinity	unitless	sal
O2	dissolved oxygen	ml/L	O2
cond	conductivity	S/m	cond
accession_number	GenBank accession number	unitless	accession_number
url	link to GenBank accession data	unitless	no_bcodmo_term

Database

Contribute Data

Dataset: kinetoplastid SSU rRNA seq.
Deployment: OC454-02

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: kinetoplastid SSU rRNA seq.Deployment: OC454-02

Dataset acquisition description

Dataset Processing Description

Dataset: kinetoplastid SSU rRNA seq.
Deployment: OC454-02