Dataset: Chemosynthetic biofilm diversity

Name: Samples sequenced from chemosynthetic biofilm communities in deep-sea hydrothermal vents collected on the R/V Atlantis AT26-10 in the East Pacific Rise, Pacific Ocean from 2013 - 2014 (Microbial Communities at Deep-Sea Vents project)
Published: 2015-02-10
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:9.84667 E:-104.29114 S:9.83798 W:-104.29321

Project:

An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents (Microbial Communities at Deep-Sea Vents)

Program:

Dimensions of Biodiversity (Dimensions of Biodiversity)

Center for Dark Energy Biosphere Investigations (C-DEBI)

Principal Investigator:

Costantino Vetriani (Rutgers University, Rutgers IMCS)

Data Manager:

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

BCO-DMO Data Manager:

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

Version:

2015-02-10

Version Date:

2015-02-10

Validated:

Yes

Current State:

Final no updates expected

Samples sequenced from chemosynthetic biofilm communities in deep-sea hydrothermal vents collected on the R/V Atlantis AT26-10 in the East Pacific Rise, Pacific Ocean from 2013 - 2014 (Microbial Communities at Deep-Sea Vents project)

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Description

This dataset is a sample log of sequenced samples collected by ROV/Jason in the East Pacific Rise, Pacific Ocean. The taxonomic composition of the active microbial community present in biofilm and fluid samples was investigated by sequencing 16S rRNA transcripts.

Methods & Sampling

Samples were collected at several sites along the East Pacific Rise hydrothermal vent zone. They included ROV/Jason deployments J2-758, J2-759, J2-760, J2-761, J2-762.

About 1 GB of raw sequence data (bacterial ssrRNA) was obtained using the Ion Torrent platform from total RNA extracted from sixteen microbial biofilm samples characterized by different temperature, redox and biological regimes. Samples included background references. Sequence data are currently being analyzed and will be deposited in GenBank prior to publication and will be made available to the scientific community. [2015-02-04]

The use of rRNA transcripts instead of DNA will allow us to identify the fraction of the population actively transcribing in situ. Sixteen microbial biofilm samples characterized by different temperature, redox and biological regimes were used. These samples included biofilm formed on experimental colonizers deployed at selected vents to obtain early stage biofilm. A comparison of early stage and established biofilms will help to understand how the community changes in relation to biofilm age and geochemical regimes.

Data Processing Description

We have optimized a RNA extraction protocol from biofilm biomass using the RNeasy kit (Qiagen). Following extraction and DNase treatment, we generated cDNA using random primers (SuperScript III First-Strand kit). cDNA from biolfilm and fluid samples was used to amplify the 16S rRNA gene with tagged primers and subjected to sequencing. Obtained sequences are currently being analyzed using the QIIME pipeline. The reads are being dereplicated, denoised, screened for chimeric sequences and taxonomically classified using the RDP and GreenGenes databases. Multivariate ordination techniques will be used to discriminate among samples with similar community structures.

Data Files

File
AT26-10_samples.csv (Comma Separated Values (.csv), 2.53 KB) MD5:d459044b425e22288c6c1fa6d0bbba85 Primary data file for dataset ID 549138

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1136451

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
AT26-10		2013-12-29	R/V Atlantis	Stefan M. Sievert (Chief Scientist)	data info

Instruments

Automated DNA Sequencer

Supplied Name: Automated Sequencer

Supplied Description:

Ion Torrent next-generation sequencing 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.

McLane Pump

Supplied Description:

Large Volume Pump (LVP): McLane WTS 6-1-142LV

Instrument Type

Generic Name: McLane Pump

Generic Description:

McLane pumps sample large volumes of seawater at depth. They are attached to a wire and lowered to different depths in the ocean. As the water is pumped through the filter, particles suspended in the ocean are collected on the filters. The pumps are then retrieved and the contents of the filters are analyzed in a lab.

ROV Jason

Supplied Description:

Instrument Type

Generic Name: ROV Jason

Generic Description:

The Remotely Operated Vehicle (ROV) Jason is operated by the Deep Submergence Laboratory (DSL) at Woods Hole Oceanographic Institution (WHOI). WHOI engineers and scientists designed and built the ROV Jason to give scientists access to the seafloor that didn't require them leaving the deck of the ship. Jason is a two-body ROV system. A 10-kilometer (6-mile) fiber-optic cable delivers electrical power and commands from the ship through Medea and down to Jason, which then returns data and live video imagery. Medea serves as a shock absorber, buffering Jason from the movements of the ship, while providing lighting and a bird’s eye view of the ROV during seafloor operations. During each dive (deployment of the ROV), Jason pilots and scientists work from a control room on the ship to monitor Jason’s instruments and video while maneuvering the vehicle and optionally performing a variety of sampling activities. Jason is equipped with sonar imagers, water samplers, video and still cameras, and lighting gear. Jason’s manipulator arms collect samples of rock, sediment, or marine life and place them in the vehicle’s basket or on "elevator" platforms that float heavier loads to the surface. More information is available from the operator site at URL.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
sample_num	sample number	unitless	sample
cruise_id	cruise identification	unitless	cruise_id
dive	Alvin or Jason dive number	unitless	dive_id
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
date	date of collection	yyyy-mm-dd	date
habitat	habitat at collection site	unitless	site_descrip
site	name of collection site	unitless	site
sample	sample identification	unitless	sample
sample_description	sample description	unitless	sample_descrip
collection_method	how sample was collected	unitless	sampling_method
nucleic_acid	type of nucleic acid measured	unitless	no_bcodmo_term
nucleic_acid_conc	total concentration of the nucleic acid	ng/uL	no_bcodmo_term
cDNA	concentration of cDNA	ng/uL	no_bcodmo_term

Status message

Database

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Dataset: Chemosynthetic biofilm diversity