URLhttps://www.bco-dmo.org/dataset/654298
Download URLhttps://www.bco-dmo.org/dataset/654298/data/download
Media Typetext/tab-separated-values
CreatedAugust 18, 2016
ModifiedSeptember 2, 2016
StateFinal no updates expected
Brief DescriptionBacterial 16S rRNA sequences from hydrothermal plume particles

Acquisition Description

The investigators deployed sediment traps adjacent to two active hydrothermal vents at 9°50'N on the East Pacific Rise (EPR) to assess the variability in bacterial community structure associated with plume particles on the timescale of weeks to months, to determine whether an endemic population of plume microbes exists, and to establish ecological relationships between bacterial populations and vent chemistry. Automated rRNA intergenic spacer analysis (ARISA) indicated that there are separate communities at the two different vents and temporal community variations between each vent. Correlation analysis between chemistry and microbiology indicated that shifts in the coarse particulate (>1 mm) Fe ⁄ (Fe+Mn+Al), Cu, V, Ca, Al, 232Th, and Ti as well as fine-grained particulate (<1 mm) Fe ⁄ (Fe+Mn+Al), Fe, Ca, and Co are reflected in shifts in microbial populations. 16S rRNA clone libraries from each trap at three time points revealed a high percentage of Epsilonproteobacteria clones and hyperthermophilic Aquificae. There is a shift toward the end of the experiment to more Gammaproteobacteria and Alphaproteobacteria, many of whom likely participate in Fe and S cycling. The particle-attached plume environment is genetically distinct from the surrounding seawater. While work to date in hydrothermal environments has focused on determining the microbial communities on hydrothermal chimneys and the basaltic lavas that form the surrounding seafloor, little comparable data exist on the plume environment that physically and chemically connects them. By employing sediment traps for a time-series approach to sampling, the investigators show that bacterial community composition on plume particles changes on timescales much shorter than previously known.

Processing Description

Chimera were checked with Bellerophon.

Instruments

Instance Description

Applied Biosystems Automated DNA Sequencer

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.

Details
Instance Description (Thermo-Electron Element 2)

Inductively Coupled Plasma Mass Spectrometer (ICP Mass Spec) - Thermo-Electron Element 2

An ICP Mass Spec is an instrument that passes nebulized samples into an inductively-coupled gas plasma (8-10000 K) where they are atomized and ionized. Ions of specific mass-to-charge ratios are quantified in a quadrupole mass spectrometer.

Parameters

cruise_id [cruise_id]
Details
cruise_id
Cruie identifier
cruise designation; name
location [site]
Details
location
Sampling location
Sampling site identification.
lat [latitude]
Details
lat
Latitude of sampling

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

lon [longitude]
Details
lon
Longitude of sampling

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes

depth [depth]
Details
depth
Depth at which sample was collected

Observation/sample depth below the sea surface. Units often reported as: meters, feet.


When used in a JGOFS/GLOBEC dataset the depth is a best estimate; usually but not always calculated from pressure; calculated either from CTD pressure using Fofonoff and Millard (1982; UNESCO Tech Paper #44) algorithm adjusted for 1980 equation of state for seawater (EOS80) or simply equivalent to nominal depth as recorded during sampling if CTD pressure was unavailable.

description [sample_descrip]
Details
description
Description of the sequence
text description of sample collected
accession_num [accession number]
Details
accession_num
NCBI accession number
Database identifier assigned by repository and linked to GenBank or other repository.
accession_link [accession number]
Details
accession_link
Link to NCBI for the accession number
Database identifier assigned by repository and linked to GenBank or other repository.
popset_id [accession number]
Details
popset_id
NCBI PopSet ID number
Database identifier assigned by repository and linked to GenBank or other repository.
popset_link [accession number]
Details
popset_link
Link to NCBI for the PopSet ID
Database identifier assigned by repository and linked to GenBank or other repository.

Dataset Maintainers

NameAffiliationContact
Jason B. SylvanTexas A&M University (TAMU)
Katrina J. EdwardsUniversity of Southern California (USC)
Christopher R. GermanWoods Hole Oceanographic Institution (WHOI)
Olivier RouxelUniversite de Brest
Benjamin C. PyensonArizona State University (ASU)
Shannon RauchWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project TitleEPR 9 North Plume Particles
AcronymRESET06
URLhttps://www.bco-dmo.org/project/654288
CreatedAugust 18, 2016
ModifiedAugust 24, 2016
Project Description

The investigators deployed sediment traps adjacent to two active hydrothermal vents at 9°50'N on the East Pacific Rise (EPR) to assess the variability in bacterial community structure associated with plume particles on the timescale of weeks to months, to determine whether an endemic population of plume microbes exists, and to establish ecological relationships between bacterial populations and vent chemistry. Automated rRNA intergenic spacer analysis (ARISA) indicated that there are separate communities at the two different vents and temporal community variations between each vent. Correlation analysis between chemistry and microbiology indicated that shifts in the coarse particulate (>1 mm) Fe ⁄ (Fe+Mn+Al), Cu, V, Ca, Al, 232Th, and Ti as well as fine-grained particulate (<1 mm) Fe ⁄ (Fe+Mn+Al), Fe, Ca, and Co are reflected in shifts in microbial populations. 16S rRNA clone libraries from each trap at three time points revealed a high percentage of Epsilonproteobacteria clones and hyperthermophilic Aquificae. There is a shift toward the end of the experiment to more Gammaproteobacteria and Alphaproteobacteria, many of whom likely participate in Fe and S cycling. The particle-attached plume environment is genetically distinct from the surrounding seawater. While work to date in hydrothermal environments has focused on determining the microbial communities on hydrothermal chimneys and the basaltic lavas that form the surrounding seafloor, little comparable data exist on the plume environment that physically and chemically connects them. By employing sediment traps for a time-series approach to sampling, the investigators show that bacterial community composition on plume particles changes on timescales much shorter than previously known.

Project Maintainers
NameAffiliationRoleContact
Jason B. SylvanTexas A&M University (TAMU)Principal Investigator
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