Dataset: Microbial 16S rRNA gene amplicon SRA numbers

Name: Sequence read accession (SRA) numbers for bacterial and archaeal 16S rRNA gene amplicons from the DeepCCZ and Abyssline programs
Published: 2023-10-25
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.861683.1

Spatial Extent: N:19.4724 E:-116.4598 S:4.8879 W:-153.7464

Temporal Extent: 2013-10-08 - 2018-06-13

Project:

DeepCCZ (DeepCCZ)

Principal Investigator:

Matthew J. Church (University of Montana)

Co-Principal Investigator:

Jeffrey C. Drazen (University of Hawaii at Manoa, SOEST)

Craig R. Smith (University of Hawaii at Manoa, SOEST)

Scientist:

Emma Wear (University of Montana)

Contact:

Emma Wear

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2023-10-25

Restricted:

Validated:

Current State:

Final no updates expected

Sequence read accession (SRA) numbers for bacterial and archaeal 16S rRNA gene amplicons from the DeepCCZ and Abyssline programs

Abstract:

This dataset includes sequence read accession (SRA) numbers for bacterial and archaeal 16S rRNA gene amplicons from the DeepCCZ and Abyssline programs.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2023-10-25	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.861683.1	2024-06-13

Description

This sample set includes 16S rRNA gene amplicon sequences from both samples newly collected on the DeepCCZ cruise in the western Clarion-Clipperton Zone and re-sequenced, archival samples from the Abyssline01 and Abyssline02 cruises in the northeastern Clarion-Clipperton Zone.

Methods & Sampling

On the DeepCCZ cruise, benthic samples (sediments and nodules) were collected using the ROV Lu'ukai, using push corers and the ROV's manipulator arm. On the Abyssline cruises, benthic samples were collected with box corers and megacorers. On both cruises, water samples were collected with Niskin bottles mounted on a sampling rosette.

Sediment samples were sectioned into depth horizons and stored frozen at -80 degrees Celsius (C). Nodules were rinsed with 0.2-µm-filtered seawater and frozen whole at -80C. On DeepCCZ, seawater was sequentially collected on 3 µm and 0.2 µm pore-size filters; on the Abyssline cruises, seawater was collected on 0.2 micrometer (µm) pore-size filters. Filters were stored frozen at -80C.

Genomic DNA was extracted from seawater filters using a DNeasy Plant Mini Kit (Qiagen) with modifications as described in Shulse et al. (2017; doi: 10.1002/mbo3.428). Genomic DNA was extracted from subsamples of sediments and nodules using the FastDNA Spin Kit for Soil, modified as described in Shulse et al. (2017). gDNA was concentrated using the Zymo Clean & Concentrator-5 kit.

The V4-V5 region of the 16S rRNA gene was amplified using primers 515F-Y and 926R as recommended by Parada et al. (2016; doi: 10.1111/1462-2920.13023), with a multiplexing index on the forward primer following the design of the Earth Microbiome Project (https://earthmicrobiome.org/protocols-and-standards/16s/). Triplicate amplifications were combined and cleaned with an ENZA Cycle Pure Kit (Omega Bio-Tek) and then pooled at approximately equimolar proportions into two libraries. Libraries were sequenced at the University of Montana on an Illumina MiSeq using paired-end 250 v2 chemistry. Samples were demultiplexed by the sequencing facility.

Problem Report:
On DeepCCZ, sediments were not collected from the seamount in APEI 1 due to ROV constraints.

Data Processing Description

Data Processing:
Demultiplexing was conducted by the sequencing facility.

BCO-DMO Processing

- Imported original file named "DeepCCZ_DNA_metadata_for_BCODMO_v2.xlsx" into the BCO-DMO system.
- Changed date format to YYYY-MM-DD.
- Converted longitude from positive degrees west to negative degrees east.
- Replaced mu symbol with u.
- Saved the final file as "861683_v1_sra.csv".

Data Files

File
861683_v1_sra.csv (Comma Separated Values (.csv), 151.32 KB) MD5:816205c2eaed6b6e1fd3c92853c66793 Primary data file for dataset ID 861683, version 1.

More Information about this dataset

Funding Sources

Funding Source	Award Number
Gordon and Betty Moore Foundation	GBMF5596
National Oceanic and Atmospheric Administration	NA17OAR0110209

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
KM1808	DeepCCZ	2018-05-14	R/V Kilo Moana	Craig R. Smith (Chief Scientist)	data info
MV1313	ABYSSLINE01	2013-10-03	R/V Melville	Craig R. Smith (Chief Scientist)	data info
TN319	ABYSSLINE02	2015-02-13	R/V Thomas G. Thompson	Craig R. Smith (Chief Scientist)	data info

Instruments

Box Corer

Supplied Name: box corers

Supplied Description:

Instrument Type

Generic Name: Box Corer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/51/

Generic Description:

General description of a box corer:

A box corer is a marine geological tool that recovers undisturbed soft surface sediments. It is designed for minimum disturbance of the sediment surface by bow wave effects. Traditionally, it consists of a weighted stem fitted to a square sampling box. The corer is lowered vertically until it impacts with the seabed. At this point the instrument is triggered by a trip as the main coring stem passes through its frame. While pulling the corer out of the sediment a spade swings underneath the sample to prevent loss. When hauled back on board, the spade is under the box. (definition from the SeaVox Device Catalog)

Box corers are one of the simplest and most commonly used types of sediment corers. The stainless steel sampling box can contain a surface sediment block as large as 50cm x 50cm x 75cm with negligible disturbance. Once the sediment is recovered onboard, the sediment box can be detached from the frame and taken to a laboratory for subsampling and further analysis. The core sample size is controlled by the speed at which the corer is lowered into the ocean bottom. When the bottom is firm, a higher speed is required to obtain a complete sample. A depth pinger or other depth indicator is generally used to determine when the box is completely filled with sediment. Once the core box is filled with sediment, the sample is secured by moving the spade-closing lever arm to lower the cutting edge of the spade into the sediment, until the spade completely covers the bottom of the sediment box. (definition from Woods Hole Oceanographic Institution).

Multi Corer

Supplied Name: megacorers

Supplied Description:

Instrument Type

Generic Name: Multi Corer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/51/

Generic Description:

The Multi Corer is a benthic coring device used to collect multiple, simultaneous, undisturbed sediment/water samples from the seafloor. Multiple coring tubes with varying sampling capacity depending on tube dimensions are mounted in a frame designed to sample the deep ocean seafloor. For more information, see Barnett et al. (1984) in Oceanologica Acta, 7, pp. 399-408.

Niskin bottle

Supplied Description:

Water samples were collected with Niskin bottles mounted on a sampling rosette.

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic Description:

A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.

Push Corer

Supplied Name: push corers

Supplied Description:

Instrument Type

Generic Name: Push Corer

Generic Description:

Capable of being performed in numerous environments, push coring is just as it sounds. Push coring is simply pushing the core barrel (often an aluminum or polycarbonate tube) into the sediment by hand. A push core is useful in that it causes very little disturbance to the more delicate upper layers of a sub-aqueous sediment.

Description obtained from: http://web.whoi.edu/coastal-group/about/how-we-work/field-methods/coring/

Remotely Operated Vehicle

Supplied Name: ROV Lu'ukai

Supplied Description:

See: https://www.soest.hawaii.edu/UMC/cms/Luukai.php

SOEST took delivery of the ROV Lu'ukai in 2013. It is a two-part, "top hat" system, consisting of the vehicle itself, performing science operations on the seabed or in the water column, and a Tether Management System (TMS) which hovers above the working vehicle and relays power and data to and from the support ship on the surface. The two components are launched, recovered and transported to the ocean floor as a stacked unit. Upon arrival at the work site, the ROV vehicle is "undocked" from the TMS and piloted to the seabed to commence a mission. Upon completion of the mission, the vehicle is docked to the TMS and the "stack" is then recovered to deck.

Instrument Type

Generic Name: Remotely Operated Vehicle

Acronym: ROV

Generic Description:

Remotely operated underwater vehicles (ROVs) are unoccupied, highly maneuverable underwater robots operated by a person aboard a surface vessel. They are linked to the ship by a group of cables that carry electrical signals back and forth between the operator and the vehicle. Most are equipped with at least a video camera and lights. Additional equipment is commonly added to expand the vehicle’s capabilities. These may include a still camera, a manipulator or cutting arm, water samplers, and instruments that measure water clarity, light penetration, and temperature.

Thermal Cycler

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Thermal Cycler

Generic Description:

A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. 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. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.

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

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
bioproject_accession	NCBI SRA BioProject accession number	unitless	accession_number
sample_name	sample name	unitless	sample
SRA_run_ID	NCBI SRA run ID	unitless	SRA_run
design_description	basic description of how sequences were generated	unitless	sampling_method
Cruise	name of cruise on which sample was collected	unitless	cruise_id
Isolation_Source	physical substrate from which DNA was sequenced	unitless	sample_descrip
latitude	latitude, in degrees north	decimal degrees North	lat
longitude	longitude (negative values = West)	decimal degrees East	lon
CCZ_region	administrative region where sample was collected, following the terminology of the International Seabed Authority	unitless	region
benthic_structure	bathymetric feature where sample was collected	unitless	site_descrip
bottom_depth	total depth of water column where sample was collected	m	depth_bottom
sample_depth	depth where sample was collected (seawater samples: depth in water column in m; sediment and nodule samples: depth (range) in sediments where collected)	m or cm or descriptive	depth
date_collected	date sample was collected from the field (UTC); format: YYYY-MM-DD Format: %Y-%m-%d	unitless	date
filter_size_range	size range of filter cut-offs on which DNA was collected (water column samples only)	um	filter_size
sample_size	amount of sample collected from the environment (seawater samples: volume filtered in L; sediment: volume frozen in mL)	L or mL or descriptive	volume
sample_size_extracted	volume or mass of sample from which DNA was extracted (large nodules were extracted multiple times and resulting gDNA was combined with weighting by extraction mass)	L or g	volume

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Dataset: Microbial 16S rRNA gene amplicon SRA numbers