Dataset: PRS bacteria identification
Deployment: FK141215

Culture-independent identification of bacteria present in the pressure-retaining seawater (PRS) sampler deployed during Leggo drop 1

Principal Investigator:

Douglas Bartlett (University of California-San Diego Scripps, UCSD-SIO)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Patterns of Microbial Community Structure Within and Between Hadal Environments (Mariana Perspectives)

Current State:

Final no updates expected

Version:

13 March 2017

Version Date:

2017-03-13

Data URL:

https://www.bco-dmo.org/dataset-deployment/684367/data

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Description

Culture-independent identification of bacteria present in the pressure-retaining seawater (PRS) sampler deployed during Leggo drop 1.

Methods & Sampling

Dataset acquisition description

This data set is associated with PI Douglas Bartlett (NSF OCE-1536776) and Schmidt Ocean Institute R/V Falkor cruise FK141215. The cruise occurred December 15-21, 2014 in the Challenger Deep within the territorial waters of the Federated States of Micronesia. During this cruise the Leggo lander was deployed multiple times and drops 1 and 3 recovered seawater samples that were analyzed. Additional details can be found at: https://schmidtocean.org/cruise/expanding-mariana-trench-perspectives/ and https://scripps.ucsd.edu/labs/dbartlett/contact/challenger-deep-cruise-2014/

Leggo Lander Drop 1:
Time (in Guam) deployed/recovered: December 16, 9:00/19:26.
Position at deployment: 11° 21.9836 N 142° 25.9533 E, middle section of the Challenger Deep.
Greatest depth of dive: approximately ~10,900 m.
In situ temperature on seafloor: 2.6°C.
Notes: This drop recovered seawater samples from about a meter off the seafloor. This included a 3 L Niskin bottle of seawater and ~ 150 mls of seawater collected in a pressure-retaining seawater sampler. The PRS sampler held more than 81% of the in situ pressure.

PRS data:
The culture independent identification of the bacteria present in the pressure-retaining seawater (PRS) sampler deployed during Leggo drop 1. This involved cell sorting, multiple displacement amplification, and 16S rRNA gene PCR and sequencing. More complete details are described in:

Leon-Zayas, R., Novotny, M., Podell, S., Shepard, C. M., Berkenpas, E., Nikolenko, S., Pevzner, P., Lasken, R. S. and Bartlett, D. H. 2015. Single cells within the Puerto Rico Trench suggest hadal adaptation of microbial lineages. Appl. Environ. Microbiol. 81: 8265-8276. doi:10.1128/AEM.01659-15

Colony Identification:
Data from the identification of bacteria cultured from the Leggo drop 1 and 3 Niskin bottles are available as a supplemental file (.txt). These identifications were performed using standard methods associated with PCR amplification of the 16S rRNA gene followed by dideoxy sequencing at Retrogen Inc.

Data Processing Description

Dataset Processing Description

The only processing of the data is that the 16S rRNA gene sequences has been examined using BLAST: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

BCO-DMO Processing:
-modified parameter names to conform with BCO-DMO naming conventions;
-replaced spaces with underscores;
-replaced '-' with 'nd' (no data);
-added dates, times, locations from metadata form.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1536776	NSF Division of Ocean Sciences

Instruments

Flow Cytometer

Supplied Name:

Supplied Description:

Cells were sorted using a flow cytometer

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)

Leggo Lander

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Leggo Lander

Generic Description:

The "Leggo Lander" is a lander system that primarily relies on syntactic foam for buoyancy and uses iridium GPS, radio signal, strobe light and flag for surface recovery, and acoustics for underwater monitoring and instrument control. The lander has a timer with 5 control settings for various operations. It routinely measures pressure (depth) throughout its dive and temperature on the seafloor. The lander payloads include a pressure-retaining seawater sampler plus 2 liter Niskin bottle, and a camera/battery/light system that also includes a 30 liter Niskin bottle and a sea cucumber trap. With the camera payload it travels down or up the water column at about 39 meters per minute (~ 4.5 hours for a descent to the Challenger Deep at ~10,920 m).

(Description obtained from the R/V Falkor FK141215 post-cruise report (PDF))

Niskin bottle

Supplied Description:

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.

Thermal Cycler

Supplied Name:

Supplied Description:

Multiple displacement amplification and 16S rRNA gene PCR and sequencing were performed

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
SILVA_classification	SILVA classification	unitless	taxon
partial_16S_seq	Partial 16S rRNA gene sequence	unitless	sequence

Database

Contribute Data

Dataset: PRS bacteria identification
Deployment: FK141215

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: PRS bacteria identificationDeployment: FK141215

Dataset acquisition description

Dataset Processing Description

Dataset: PRS bacteria identification
Deployment: FK141215