Sequence read accession (SRA) numbers for bacterial and archaeal 16S rRNA gene amplicons from the DeepCCZ and Abyssline programs from 2013-10-08 to 2018-06-13 (NCEI Accession 0294392)

This dataset contains physical data collected on R/V Kilo Moana, R/V Melville, and R/V Thomas G. Thompson during cruises KM1808, MV1313, and TN319 from 2013-10-08 to 2018-06-13. These data include depth and depth_bottom. The instruments used to collect these data include Box Corer, Multi Corer, Niskin bottle, Push Corer, Remotely Operated Vehicle, and Thermal Cycler. These data were collected by Craig R. Smith and Jeffrey C. Drazen of University of Hawaii at Manoa and Emma Wear and Matthew J. Church of University of Montana as part of the "DeepCCZ (DeepCCZ)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2024-06-13.

The following is the text of the dataset description provided by BCO-DMO:

Microbial 16S rRNA gene amplicon SRA numbers

Dataset 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 and 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; https://doi.org/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; https://doi.org/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.