URLhttps://www.bco-dmo.org/dataset/658175
Download URLhttps://www.bco-dmo.org/dataset/658175/data/download
Media Typetext/tab-separated-values
CreatedSeptember 1, 2016
ModifiedSeptember 2, 2016
StateFinal no updates expected
Brief DescriptionBacterial 16S rRNA sequences from seafloor rocks (silicates and sulfides)

Acquisition Description

Samples were taken from the following locations and depths:
Kilo Moana (~2600 m water depth),
ABE (~2100 m water depth),
Tui Malila (~1875 m water depth), and
Mariner (~1900 m water depth) hydrothermal vent fields

The East Lau Spreading Center (ELSC) and Valu Fa Ridge (VFR) comprise a ridge segment in the southwest Pacific Ocean where rapid transitions in the underlying mantle chemistry manifest themselves as gradients in seafloor rock geochemistry. The investigators studied the geology and microbial diversity of three silicate rock samples and three inactive sulfide chimney samples collected, from north to south, at the vent fields Kilo Moana, ABE, Tui Malila, and Mariner. This is the first study of microbial populations on basaltic andesite, which was sampled at Mariner vent field. Silicate rock geochemistry exhibits clear latitudinal trends that are mirrored by changes in bacterial community composition. Alphaproteobacteria, Epsilonproteobacteria, and Bacteroidetes are most common on a silicate collected from Kilo Moana and their proportions decrease linearly on silicates collected further south. Conversely, a silicate from Mariner vent field hosts high proportions of a unique lineage of Chloroflexi unrelated (<90% sequence similarity) to previously recovered environmental clones or isolates, which decrease at ABE and are absent at Kilo Moana. The exteriors of inactive sulfide structures are dominated by lineages of sulfur oxidizing Alphaproteobacteria, Gammaproteobacteria, and Epsilonproteobacteria, while the interior of one chimney is dominated by putative sulfur-reducing Deltaproteobacteria. A comparison of bacterial communities on inactive sulfides from this and previous studies reveals the presence of a clade of uncultured Bacteroidetes exclusive to sulfidic environments, and a high degree of heterogeneity in bacterial community composition from one sulfide structure to another. In light of the heterogeneous nature of bacterial communities observed here and in previous studies of both active and inactive hydrothermal sulfide structures, the presence of numerous niches may be detected on these structures in the future by finer scale sampling and analysis.

Processing Description

Chimera were checked with Bellerophon.

Instruments

Automated DNA Sequencer [Automated DNA Sequencer]
Details
Instance Description (Automated DNA Sequencer)

Applied Biosystems 

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.

Inductively Coupled Plasma Optical Emission Spectrophotometer [Inductively Coupled Plasma Optical Emission Spectrometer]
Details
Instance Description (Inductively Coupled Plasma Optical Emission Spectrophotometer)

Thermo Scientific iCAP 6500

Also referred to as an Inductively coupled plasma atomic emission spectroscope (ICP-AES). These instruments pass nebulised samples into an inductively-coupled gas plasma (8-10000 K) where they are atomised and excited. The de-excitation optical emissions at characteristic wavelengths are spectroscopically analysed. It is often used in the detection of trace metals.

Inductively Coupled Plasma mass spectrometer [Inductively Coupled Plasma Mass Spectrometer]
Details
Instance Description (Inductively Coupled Plasma mass spectrometer)

Thermo Scientific XSERIES 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.
X-Ray Diffractometer [X-ray diffractometer]
Details
Instance Description (X-Ray Diffractometer)

Siemens D-500

Instruments that identify crystalline solids by measuring the characteristic spaces between layers of atoms or molecules in a crystal.

Parameters

cruise_id [cruise_id]
Details
cruise_id
Cruie identifier
cruise designation; name
description [sample_descrip]
Details
description
Description of the sequence
text description of sample collected
sample [sample]
Details
sample
Sample name

unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

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.

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)
Shannon RauchWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project TitleLau Basin low temperature geomicrobiology
AcronymLau Basin Geomicrobio
URLhttps://www.bco-dmo.org/project/655679
CreatedAugust 24, 2016
ModifiedAugust 24, 2016
Project Description

The East Lau Spreading Center (ELSC) and Valu Fa Ridge (VFR) comprise a ridge segment in the southwest Pacific Ocean where rapid transitions in the underlying mantle chemistry manifest themselves as gradients in seafloor rock geochemistry. The investigators studied the geology and microbial diversity of three silicate rock samples and three inactive sulfide chimney samples collected, from north to south, at the vent fields Kilo Moana, ABE, Tui Malila, and Mariner. This is the first study of microbial populations on basaltic andesite, which was sampled at Mariner vent field. Silicate rock geochemistry exhibits clear latitudinal trends that are mirrored by changes in bacterial community composition. Alphaproteobacteria, Epsilonproteobacteria, and Bacteroidetes are most common on a silicate collected from Kilo Moana and their proportions decrease linearly on silicates collected further south. Conversely, a silicate from Mariner vent field hosts high proportions of a unique lineage of Chloroflexi unrelated (<90% sequence similarity) to previously recovered environmental clones or isolates, which decrease at ABE and are absent at Kilo Moana. The exteriors of inactive sulfide structures are dominated by lineages of sulfur oxidizing Alphaproteobacteria, Gammaproteobacteria, and Epsilonproteobacteria, while the interior of one chimney is dominated by putative sulfur-reducing Deltaproteobacteria. A comparison of bacterial communities on inactive sulfides from this and previous studies reveals the presence of a clade of uncultured Bacteroidetes exclusive to sulfidic environments, and a high degree of heterogeneity in bacterial community composition from one sulfide structure to another. In light of the heterogeneous nature of bacterial communities observed here and in previous studies of both active and inactive hydrothermal sulfide structures, the presence of numerous niches may be detected on these structures in the future by finer scale sampling and analysis.

Note: This project was supported by NSF award OCE-0732369 as add-on work to the original proposal. The proposal abstract is available from NSF.

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