Dataset: South China Sea 16S

Name: 16S gene sequencing of microbial communities in South China Sea sediments from January to March 2014
Published: 2018-10-15
License: https://creativecommons.org/licenses/by/4.0/
Keywords: oceans

Cite This Dataset

Spatial Extent: N:18.3514 E:117 S:12.919 W:115.0472

Temporal Extent: 2014-01-30 - 2014-03-07

Project:

Edginess in the subsurface: Microbial diversity of deep subseafloor ecotones (Edginess in the subsurface)

Program:

Center for Dark Energy Biosphere Investigations (C-DEBI)

Principal Investigator:

Frederick Colwell (Oregon State University, OSU)

Co-Principal Investigator:

Andrew Thurber (Oregon State University, OSU)

BCO-DMO Data Manager:

Mathew Biddle (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2018-10-15

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Data URL:

https://www.bco-dmo.org/dataset/748024/data

16S gene sequencing of microbial communities in South China Sea sediments from January to March 2014

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Description

Three locations in the SCS were cored during IODP Expedition 349 at sites U1431 (15° 22.5379’ N, 117° 00.0022’ E, 4240 meters below sea level (mbsl)), U1432 (18° 21.0831’ N, 116° 23.4504’ E, 3829 mbsl), and U1433 (12° 55.1380’ N, 115° 02.8345’ E, 4379 mbsl). Cores were split lengthwise onboard to reveal geological interfaces and the exposed sediment was aseptically scraped away prior to sampling. Samples were collected only from the center of the cores, avoiding the outside edges of the cores that may have contacted the core barrel. Samples were stored at -80°C until analysis. Down-core measurements of sediment methane concentrations, alkalinity, and pore water sulfate, ammonium, and phosphate were made onboard. Sediment ages were calculated based on paleomagnetic analysis and nanofossil characterization for each site.

All samples described in this study were collected using an advanced piston core, a tool that minimizes core disturbance. In order to check whether contamination occurred, and consistent with other deep microbiology coring studies, we compared microbial communities present in fluids that drained from the core barrel (possibly from seawater intrusion during core retrieval) to those present in the center of the cores, a so-called fluid community tracer (FCT) approach. Samples of the drilling fluid from core U1433 were collected immediately when cores were brought onto the deck and were frozen at -80°C until analysis. To compare microbial communities in the drilling fluids to those in the cores, DNA from 10 FCT samples (235-790 mbsf) and a whole-round sample (13.5 mbsf) was extracted using a FastDNA Spin Kit for Soil (MP Biomedical, OH, USA). Pyrosequencing of the archaeal 16S rRNA gene of the FCT samples and the whole-round sample was conducted with a Roche 454 GS FLX+ Titanium platform (Roche 454 Life Sciences, CT, USA) at the Majorbio Bio-Pharm Technology Co., Ltd. (Shanghai, China). Primers used for amplification were Arch_344F (5′-ACGGGGCGCAGCAGGCGCGA-3′) and Arch_915R (5′-GTGCTCCCCCGCCAATTCCT-3′).

Additional award numbers:

Consortium for Ocean Leadership; award number: IUSSP410
C-DEBI; subaward number: 59209190
DCO/DLC; subaward number: 53587

Data are publicly accessible at NCBI under accession number PRJNA362622.

Acquisition Description

DNA was extracted from 0.25 g of wet sediment using a MoBio PowerSoil DNA Isolation Kit. Extracted DNA was amplified in technical triplicate 25 uL reactions using universal 16S rRNA gene primers 515-fwd and 806-rev with Illumina sequencing adapters and barcodes. Triplicate PCR products were pooled, visualized on an agarose gel, and cleaned using a MoBio UltraClean PCR Clean-Up Kit. PCR products were quantified using a Qubit fluorometer and pooled prior to sequencing. Paired-end 250-bp sequencing was performed on an Illumina MiSeq at Oregon State University’s Center for Genome Research and Biocomputing. A sediment-free extraction was amplified and sequenced alongside sediment samples.

Processing Description

Sequences were processed using mothur (v 1.38.0; (38)). Reads were clustered at 97% and classified against the SILVA database (v. 119). Singleton OTUs were removed prior to analysis. OTUs that were present in greater than 1% relative abundance in the negative (sediment-free) control and classified as common human or kit contaminants (39) were removed from the dataset. To confirm their identity, phylogenetic trees were generated for all OTUs classified as ANME and for the 8 most abundant OTUs classified to known sulfate-reducing bacteria lineages with Fasttree (v. 2.1.10; 40)) using the Jukes-Cantor model (Supp. Figs. 1 and 2).

BCO-DMO Processing Notes:

translated the "collection_date" fromat from DD-Mon-YY (7-Mar-14) to YYYY-MM-DD (2014-03-14).
added conventional header with dataset name, PI name, version date
modified parameter names to conform with BCO-DMO naming conventions
removed hemisphere declarations in the latitude and longitude fields.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-0939564

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
IODP-349	IODP Expedition 349	2014-01-26	R/V JOIDES Resolution	Chun-Feng Li (Chief Scientist)	data info

Instruments

Advanced Piston Corer

(more info)

Short Name: APC

Generic Description

The JOIDES Resolution's Advanced Piston Corer (APC) is used in soft ooze and sediments. The APC is a hydraulically actuated piston corer designed to recover relatively undisturbed samples from very soft to firm sediments.

More information is available from IODP (PDF).

PI supplied instrument name: advanced piston core

Dataset-specific description

All samples described in this study were collected using an advanced piston core, a tool that minimizes core disturbance.

Automated DNA Sequencer

(more info)

Short Name: Automated Sequencer

Generic Description

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.

PI supplied instrument name: Illumina MiSeq

Dataset-specific description

Paired-end 250-bp sequencing was performed on an Illumina MiSeq at Oregon State University’s Center for Genome Research and Biocomputing.

Fluorometer

(more info)

Short Name: Fluorometer

Community Standard Description

Generic Description

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.

PI supplied instrument name: Qubit fluorometer

Dataset-specific description

PCR products were quantified using a Qubit fluorometer and pooled prior to sequencing.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
Sample_Name	sample name	unitless	sample
collection_date	date the sediment was collected	unitless	date
depth	depth where samples were taken below sea floor.	meters (m)	depth_core
lat	Latitude in decimal degrees north	decimal degrees	lat
lon	Longitude in decimal degrees east	decimal degrees	lon
sedimentology	description of sediment type	unitless	sample_descrip
elev	water depth at the sampling site	meters (m)	depth

Database

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Dataset: South China Sea 16S