URLhttps://www.bco-dmo.org/dataset/626263
Download URLhttps://www.bco-dmo.org/dataset/626263/data/download
Media Typetext/tab-separated-values
CreatedNovember 10, 2015
ModifiedAugust 19, 2016
StateFinal no updates expected
Brief DescriptionAccession numbers for raw sequence reads; samples collected on cruise KNOX02RR.

Acquisition Description

All methodology can be located in the reference:
Tully and Heidelberg 2013. Microbial communities associated with ferromanganese nodules and the surrounding sediments. Frontiers in Microbiology. 4(161). doi:10.3389/fmicb.2013.00161

In summary (refer to publication above for complete description of methodology):
Sediment and FeMn nodules were collected during Expedition Knox-02RR (December 2006–January 2007 aboard the R/V Roger Revelle). Extraction of DNA from nodules proceeded using a modified phenol-chloroform extraction method. Due to low yield using the described phenol-chloroform method, extraction of DNA from sediment samples was performed using the MoBio PowerLyzer PowerSoil DNA kit following the manufacturer's protocol. All samples with >0.1 ng/uL final DNA concentration were cleaned and concentrated and samples were resuspended in 20 uL of sterile, DNase-free H2O. Samples were amplified using PCR, targeting the V4 region of the 16S rRNA gene. All amplifications were performed using the FastStart High Fidelity PCR System (Roche). Initial PCR products were pooled and the PCR product (~550 bp) was gel excised using the Qiagen Gel Extraction Kit (Qiagen) following the manufacturer's protocol. Excised DNA products were amplified in duplicate to generate sufficient material for pyrosequencing. PCR products were pooled and cleaned using the AMPure Bead XP (Agencourt) kit, following the manufacturer's protocol. Samples were quantified using PicoGreen and visualized using Agilent Bioanalyzer using the High Sensitivity (Agilent) chip.

Processing Description

Data processing can be located in the reference:
Tully and Heidelberg 2013. Microbial communities associated with ferromanganese nodules and the surrounding sediments. Frontiers in Microbiology. 4(161). doi:10.3389/fmicb.2013.00161

Instruments

Qubit 1.0 [Fluorometer]
Details
Instance Description (Qubit 1.0)

Samples were then quantified using the Qubit 1.0 fluorometer and the Qubit dsDNA HS Assay Kit (Life Technologies).

A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.

Details
Instance Description (PCR)

Samples were amplified using PCR, targeting the V4 region of the 16S rRNA gene. All amplifications were performed using the FastStart High Fidelity PCR System (Roche).

General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). 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.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

Parameters

cruise_id [cruise_id]
Details
cruise_id
Cruise identification number.
cruise designation; name
bioproject_ID [unknown]
Details
bioproject_ID
NCBI BioProject ID number.
association with a community-wide standard parameter is not yet defined
SRA_ID [unknown]
Details
SRA_ID
NCBI SRA ID number.
association with a community-wide standard parameter is not yet defined
strategy [unknown]
Details
strategy

16S rRNA hypervariable gene amplification.

association with a community-wide standard parameter is not yet defined
source [unknown]
Details
source

Various samples collected via multicore instrument.

association with a community-wide standard parameter is not yet defined
selection [unknown]
Details
selection

Available aseptic samples.

association with a community-wide standard parameter is not yet defined
primer [unknown]
Details
primer

Primer used. FU515-GTGY CAGCMGCCGCGGTA & RU1048-CGRCRCCATGYANCWC

association with a community-wide standard parameter is not yet defined
bioproject_URL [unknown]
Details
bioproject_URL
Hyperlink to NCBI BioProject.
association with a community-wide standard parameter is not yet defined
SRA_URL [unknown]
Details
SRA_URL
Hyperlink to NCBI SRA.
association with a community-wide standard parameter is not yet defined
accession_ID [unknown]
Details
accession_ID
NCBI accession number.
association with a community-wide standard parameter is not yet defined
accession_URL [unknown]
Details
accession_URL
Hyperlink to NCBI accession.
association with a community-wide standard parameter is not yet defined
sample_name [unknown]
Details
sample_name

Sample identifer.

association with a community-wide standard parameter is not yet defined
sample_name2 [unknown]
Details
sample_name2

Sample identifer.

association with a community-wide standard parameter is not yet defined
sample_description [unknown]
Details
sample_description

Description of the sample: Surface sediments and ferromanganese nodules.

association with a community-wide standard parameter is not yet defined
sample_location [unknown]
Details
sample_location

Location of sampling: South Pacific Ocean, central gyre.

association with a community-wide standard parameter is not yet defined
lat [latitude]
Details
lat
Latitude of sample collection.

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

lon [longitude]
Details
lon
Longitude of sample collection.

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

sample_depth [unknown]
Details
sample_depth
Depth at which sample was collected.
association with a community-wide standard parameter is not yet defined
method [unknown]
Details
method

DNA extraction method; via phenol:chloroform method

association with a community-wide standard parameter is not yet defined
barcode [unknown]
Details
barcode

DNA barcode.

association with a community-wide standard parameter is not yet defined

Dataset Maintainers

NameAffiliationContact
John F. HeidelbergUniversity of Southern California (USC-WIES)
Benjamin J. TullyUniversity of Southern California (USC)
Benjamin J. TullyUniversity of Southern California (USC)
Shannon RauchWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project TitleDeep phylogenetic and metagenomic analysis of microbial diversity associated with ferromanganese nodules collected from the South Pacific Gyre
AcronymMicrobial Diversity SPG
URLhttps://www.bco-dmo.org/project/626257
CreatedNovember 10, 2015
ModifiedNovember 10, 2015
Project Description

Project description obtained from C-DEBI:
The importance of microbial mediation in the biogeochemical cycles of the ocean is well documented. A major source of marine metallic minerals exists as ferromanganese (polymetallic) nodules in the deep ocean (4,000-5,000 m deep). Composed predominantly of iron, manganese, copper, nickel, and zinc, these nodules play a key role in governing the biogeochemical availability of many of these metals in the global ocean. While it is assumed that microorganisms mediate some of the processes that form nodules, it is poorly constrained as to which organisms mediate these processes or how these processes in turn may support microbial metabolisms. We propose using fingerprinting and sequencing methods to examine the microbial community diversity of organism associated with ferromanganese nodule collected from the South Pacific Gyre. Further, because many of the microbial organisms present in the deep-sea are novel and uncultivated, we plan to perform metagenomic analysis to link phylogenetic identity with physiology, with the goal of generating (near-)complete environmental genomes. The proposed research will be the first attempt to determine how the microbiology of deep oceanic nodules shape and are shaped by the environment.

This project was funded by a C-DEBI Graduate Student Fellowship.

Project Maintainers
NameAffiliationRoleContact
John F. HeidelbergUniversity of Southern California (USC-WIES)Principal Investigator
Benjamin J. TullyUniversity of Southern California (USC)Contact
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