Dataset: 16S rRNA Sequences

Name: 16S rRNA sequence data from venting fluids and microbial mats; collected on R/V Atlantis cruise AT18-08 at the Axial Seamount, Juan de Fuca Ridge in 2011
Published: 2016-01-27
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:45.946 E:-129.982 S:45.928 W:-129.985

Project:

Function, activity, and adaptation of microbial communities in geochemically diverse subseafloor habitats (AXIAL)

Principal Investigator:

Julie Huber (Marine Biological Laboratory, MBL)

BCO-DMO Data Manager:

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

Version:

27 Jan 2016

Version Date:

2016-01-27

Validated:

Yes

Current State:

Final no updates expected

16S rRNA sequence data from venting fluids and microbial mats; collected on R/V Atlantis cruise AT18-08 at the Axial Seamount, Juan de Fuca Ridge in 2011

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Description

16S rRNA sequence data from venting fluids and microbial mats at Axial Seamount, 2011. Samples collected on the AT18-08 cruise.

Methods & Sampling

Diffuse fluids were collected from newly discovered snowblower vents at Axial Seamount in late July 2011 with the ROV Jason II using the hydrothermal fluid and particle sampler (Butterfield et al., 2004). White and orange flocculent materials were collected on the subsequent University Of Washington Visions' 11 cruise, in support of the Regional Scale Nodes component of the Ocean Observatories Initiative in August 2011. White flocculent material was collected from the orifice of the Subway snowblower vent on dives R1467 (White Floc 1) and R1472 (White Floc 2) and orange flocculent material was collected on the seafloor distal to Marker 33 during dive R1472 where it coated freshly deposited basalt. All of the fluid and floc samples analyzed in this study are from a small area in the south rift zone at the southeastern edge of Axial Caldera, with the exception of background seawater which was collected outside of the caldera.

Total genomic DNA was extracted from Sterivex filters as previously described (Sogin et al., 2006) with the minor modifications described by Akerman et al. (2013). Total genomic DNA was extracted from 20 to 30mg of wet flocculent material using a MoBio UltraClean® Soil DNA Isolation Kit. The V6 region of 16S rRNA genes were amplified in triplicate for each sample with previously reported primers designed for archaea and bacteria (Huber et al., 2007) that were modified to include indices and barcodes compatible with the Illumina HiSeq1000 platform rather than 454 Life Sciences Adapters (Eren et al., 2013). Triplicate PCR amplifications were pooled for each sample, cleaned with a Qiagen MinElute kit, and quanitified by PicoGreen assay on a Turner Biosystems spectrophotometer. Fifty nanograms of each cleaned amplicon library was then size selected with a 2% agarose PippinPrep cassette to produce a narrow range of fragment sizes from 200 to 300 bp for sequencing and cleaned again to remove agarose. All of the amplicon libraries included in this study were sequenced in the same run and on the same paired end lane, along with 60 other libraries. Equimolar amounts of pooled amplicon libraries and a metagenomic library were run in the same lane to avoid known difficulties of sequencing low complexity amplicon libraries with Illumina (Caporaso et al., 2012).

Related references:
Meyer, J.L., Akerman, N.H., Proskurowski, G. and J.A. Huber. 2013. Microbiological characterization of post-eruption "snowblower" vents at Axial Seamount, Juan de Fuca Ridge. Frontiers in Microbiology. 4:153. doi:10.3389/fmicb.2013.00153

Data Processing Description

Paired Illumina sequencing reads were quality filtered to remove any reads containing ambiguous nucleotides and only pairs with perfectly overlapping reads were used for further analysis. Quality-filtered reads are publicly available through the VAMPS database, http://vamps.mbl.edu,under the project name JAH_AXV_Bv6 and JAH_AXV_Av6, where orange floc is listed as "eruption mat", white floc 1 is listed as "snow_R1467", and white floc 2 is listed as "snow_R1472". Sequences were clustered at 97% similarity with a minimum word length of 30, using usearch (Edgar, 2010). Taxonomy was assigned by global alignment for sequence taxonomy (GAST; Huse et al., 2008) with the SILVA 111 database (Quast et al., 2012). Operational taxonomic units (OTUs) were then analyzed with Qiime 1.5 (Caporaso et al., 2010). Even sequencing depth per sample was established by multiple rarefactions to roughly 75% of the smallest sequencing depth, using a total of 195,000 bacterial reads and 145,000 archaeal reads per sample. To compare bacterial communities in snowblower fluids and flocculent samples to background seawater by dendrogram, we retrieved bacterial V6 454 reads from background seawater collected outside the Axial Caldera from the VAMPS database under the project name KCK_SMT_Bv6, fluid sample FS501. To compensate for the fewer number of reads in the background seawater sample, a second set of multiple rarefactions was performed with 7112 reads per sample. Distance matrices were calculated for 10 rarefactions using the Morisita-Horn index (Horn, 1966) and the resulting tree topographies were clustered using UPGMA to create a final jackknifed tree.

BCO-DMO Processing:
- modified parameter names to conform with BCO-DMO naming conventions;
- removed "m" (meters) in depth column;
- changed format of date to YYYYmmdd;
- replaced commas with semi-colons;
- Added cruise_id field.

Data Files

File
Snowblower_16SrRNA.csv (Comma Separated Values (.csv), 2.24 KB) MD5:ec70c3f6dd3b9e8f4c816cb19056787a Primary data file for dataset ID 636566

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-0929167

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
AT18-08	NeMO 2011	2011-07-19	R/V Atlantis	William Chadwick (Chief Scientist)	data info

Instruments

ROV Jason

Supplied Name:

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.

Spectrophotometer

Supplied Name: Turner Biosystems spectrophotometer

Supplied Description:

Instrument Type

Generic Name: Spectrophotometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/

Generic Description:

An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples.

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

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

Supplied Name	Supplied description	Supplied Units	Standard Name
cruise_id	Cruise identifier.	dimensionless	cruise_id
organism	Organism.	dimensionless	taxon
env_biome	Biome.	dimensionless	site_descrip
env_feature	Environmental feature.	dimensionless	site_descrip
geo_loc_name	Geographic location name.	dimensionless	site_descrip
sample_name	Sample name.	dimensionless	sample
vent_name	Vent name.	dimensionless	site
sample_title	Sample title.	dimensionless	sample
collection_date	Year, month, and day of sample collection.	YYYYmmdd	date
depth	Depth of sample collection.	meters (m)	depth
env_material	Environmental material.	dimensionless	site_descrip
lat	Latitude of sample collection.	decimal degrees	lat
lon	Longitude of sample collection.	decimal degrees	lon
bioproject_accession	NCBI BioProject accession number.	dimensionless	accession_number
bioproject_link	Hyperlink to NCBI BioProject.	dimensionless	accession_number
biosample_number	NCBI BioSample number.	dimensionless	accession_number
biosample_link	Hyperlink to NCBI BioSample.	dimensionless	accession_number

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Database

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Dataset: 16S rRNA Sequences