URLhttps://www.bco-dmo.org/dataset/654352
Download URLhttps://www.bco-dmo.org/dataset/654352/data/download
Media Typetext/tab-separated-values
CreatedAugust 18, 2016
ModifiedSeptember 2, 2016
StateFinal no updates expected
Brief DescriptionBacterial 16S rRNA sequences from inactive sulfide chimneys

Acquisition Description

Hydrothermal chimneys are a globally dispersed habitat on the seafloor associated with mid-ocean ridge (MOR) spreading centers. Active, hot, venting sulfide structures from MORs have been examined for microbial diversity and ecology since their discovery in the mid-1970s, and recent work has also begun to explore the microbiology of inactive sulfides—structures that persist for decades to millennia and form moderate to massive deposits at and below the seafloor.

The investigators studied bacterial diversity on inactive hydrothermal sulfide chimney samples from 9°N on the East Pacific Rise to learn their bacterial community composition, potential ecological roles, and succession from active venting to inactive chimneys. The investigators used tag pyrosequencing of the V6 region of the 16S rRNA and full-length 16S rRNA sequencing on inactive hydrothermal sulfide chimney samples from 9°N on the East Pacific Rise to learn their bacterial composition, metabolic potential, and succession from venting to nonventing (inactive) regimes. Many bacteria on inactive sulfide chimneys are closely related to lineages involved in sulfur, nitrogen, iron, and methane cycling, and two common groups found on active chimneys are nearly absent from inactive vents, where they were replaced by groups likely involved in the elemental cycling mentioned above. Alpha-, beta-, delta-, and gammaproteobacteria and members of the phylum Bacteroidetes dominate all inactive sulfides. Greater than 26% of the V6 tags obtained are closely related to lineages involved in sulfur, nitrogen, iron, and methane cycling. Epsilonproteobacteria represent <4% of the V6 tags recovered from inactive sulfides and 15% of the full-length clones, despite their high abundance in active chimneys. Members of the phylum Aquificae, which arecommon in active vents, were absent from both the V6 tags and full-length 16S rRNA data sets. In both analyses, the proportions of alphaproteobacteria, betaproteobacteria, and members of the phylum Bacteroidetes were greater than those found on active hydrothermal sulfides. These shifts in bacterial population structure on inactive chimneys reveal ecological succession following cessation of venting and also imply a potential shift in microbial activity and metabolic guilds on hydrothermal sulfides, the dominant biome that results from seafloor venting.

Processing Description

Full-length 16S rRNA sequences were chimera checked with Bellerophon. For V6 16S rRN sequences obtained through 454 sequencing, sequences <50 bp were eliminated, as were sequences that contained any mismatches to the PCR primers or that contained one or more undetermined nucleotides (N’s).

In addition to NCBI, data have been deposited in the Marine Biological Laboratory's (MBL) VAMPS system (https://vamps.mbl.edu/): Dataset KCK_SBF_Bv6, samples 4053_M2_D3_DF, 4053_M3_O_DF03, 4053_M3_O_DF4wt, 4057_M2_DF04, 4059_M3_O_DF02, 4059_M4_I_DF02, 4059_M4_O_DF02 and 4059_M4_sph

Instruments

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

Automated DNA Sequencer, Applied Biosystems and Roche 454 GS20 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.

Parameters

cruise_id [cruise_id]
Details
cruise_id
Cruie identifier
cruise designation; name
location [site]
Details
location
Sampling location
Sampling site identification.
lat_end [lat_end]
Details
lat_end
Ending latitude of range of sampling

latitude at end time of measurement; in decimal degrees (negative denotes South)

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)
Brandy M. TonerUniversity of Minnesota, Twin Cities (UMTC)
Katrina J. EdwardsUniversity of Southern California (USC)
Shannon RauchWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project TitleRidge2000 Integrated Studies at 9degN East Pacific Rise: Establishing a Role for Fe and S Microbial Metabolism in Ocean Crust Weathering
AcronymBacwards
URLhttps://www.bco-dmo.org/project/654280
CreatedAugust 18, 2016
ModifiedSeptember 2, 2016
Project Description

Hydrothermal chimneys are a globally dispersed habitat on the seafloor associated with mid-ocean ridge (MOR) spreading centers. Active, hot, venting sulfide structures from MORs have been examined for microbial diversity and ecology since their discovery in the mid-1970s, and recent work has also begun to explore the microbiology of inactive sulfides—structures that persist for decades to millennia and form moderate to massive deposits at and below the seafloor. The investigators studied bacterial diversity on inactive hydrothermal sulfide chimney samples from 9°N on the East Pacific Rise to learn their bacterial community composition, potential ecological roles, and succession from active venting to inactive chimneys. The investigators used tag pyrosequencing of the V6 region of the 16S rRNA and full-length 16S rRNA sequencing on inactive hydrothermal sulfide chimney samples from 9°N on the East Pacific Rise to learn their bacterial composition, metabolic potential, and succession from venting to nonventing (inactive) regimes. Many bacteria on inactive sulfide chimneys are closely related to lineages involved in sulfur, nitrogen, iron, and methane cycling, and two common groups found on active chimneys are nearly absent from inactive vents, where they were replaced by groups likely involved in the elemental cycling mentioned above. Alpha-, beta-, delta-, and gammaproteobacteria and members of the phylum Bacteroidetes dominate all inactive sulfides. Greater than 26% of the V6 tags obtained are closely related to lineages involved in sulfur, nitrogen, iron, and methane cycling. Epsilonproteobacteria represent <4% of the V6 tags recovered from inactive sulfides and 15% of the full-length clones, despite their high abundance in active chimneys. Members of the phylum Aquificae, which arecommon in active vents, were absent from both the V6 tags and full-length 16S rRNA data sets. In both analyses, the proportions of alphaproteobacteria, betaproteobacteria, and members of the phylum Bacteroidetes were greater than those found on active hydrothermal sulfides. These shifts in bacterial population structure on inactive chimneys reveal ecological succession following cessation of venting and also imply a potential shift in microbial activity and metabolic guilds on hydrothermal sulfides, the dominant biome that results from seafloor venting.

Note: This project was supported by NSF award OCE-0241791 as add-on work to the original proposal. The proposal abstract is available from NSF.

Project Maintainers
NameAffiliationRoleContact
Katrina J. EdwardsUniversity of Southern California (USC)Principal Investigator
Wolfgang BachUniversity of BremenCo-Principal Investigator
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