Download URLhttps://www.bco-dmo.org/dataset/748024/data/download
Media Type text/tab-separated-values
Created October 15, 2018
Modified October 15, 2018
State Final no updates expected
Brief Description

16S gene sequencing of microbial communities from South China Sea sediments

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. 


Illumina MiSeq [Automated DNA Sequencer]
Instance Description (Illumina MiSeq)

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

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.

Qubit fluorometer [Fluorometer]
Instance Description (Qubit fluorometer)

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

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.

advanced piston core [Advanced Piston Corer]
Instance Description (advanced piston core)

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

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).


Sample_Name [sample]

sample name

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

collection_date [date]
date the sediment was collected

date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)

depth [depth_core]

depth where samples were taken below sea floor.

depth in core; mid-point of interval sampled
lat [latitude]

Latitude in decimal degrees north

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

lon [longitude]

Longitude in decimal degrees east

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

sedimentology [sample_descrip]
description of sediment type
text description of sample collected
elev [depth]

water depth at the sampling site

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.

Dataset Maintainers

Frederick S. ColwellOregon State University (OSU)
Andrew R. ThurberOregon State University (OSU)
Mathew BiddleOregon State University (OSU)
Woods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project Title Edginess in the subsurface: Microbial diversity of deep subseafloor ecotones
Acronym Edginess in the subsurface
Created September 5, 2018
Modified September 5, 2018
Project Description

Project summary:

For subseafloor microorganisms, defined geological and chemical gradients affect population sizes and community structure. We examined how distinct sediment types influence microbial diversity and community composition and the factors that drive deep-subsurface microbial community structure (e.g., depth, interstitial water chemistry, sample location). During IODP Expedition 349 (South China Sea Tectonics), either coupled ash/clay or turbidite/clay boundaries were sampled, DNA extracted, and the 16S rRNA gene analyzed on an Illumina MiSeq platform. Microbial communities in sediments were distinct from communities in drilling fluid, indicating that drilling-based contamination was unlikely. Illumina sequencing of the 16S rRNA gene yielded 5,453 OTUs (97% identity) representing 44 bacterial phyla and 3 archaeal phyla. Members of the Atribacteria dominated all microbial communities among all sites. Sulfate-reducing bacteria were relatively rare within sulfate-replete sediments in all cores. Ordination of the microbial communities using weighted UniFrac distances revealed significant differences in communities both between sites and between the sulfate reduction zone and methanogenic zone at two of the sites. The number of observed taxa followed an exponential decline with sediment age only in the sulfate reduction zone. Species evenness increased linearly with sediment age regardless of geochemical zonation in the sediment column. Our investigation helps to characterize the factors that drive microbial community structure of the subseafloor and highlights the need to focus on habitat heterogeneity at a scale pertinent to bacteria and archaea in studies of microbial ecology.

This project is funded with:
Center for Dark Energy Biosphere Investigations (C-DEBI); subaward number: 59209190
Deep Carbon Observatory (DCO) /Deep Life Community (DLC); subaward number: 53587
Consortium for Ocean Leadership; award number: IUSSP410

Data Project Maintainers
Frederick S. ColwellOregon State University (OSU)Principal Investigator
Andrew R. ThurberOregon State University (OSU)Co-Principal Investigator