Dataset: Accession numbers for metagenome-assembled genomes (MAGs) from samples collected in 2018 on R/V Thompson cruise TN350 at the Upper and Lower Cones, Upper Caldera Wall and NW Caldera, Brothers Volcano

Final no updates expectedDOI: 10.26008/1912/bco-dmo.868323.1Version 1 (2022-01-19)Dataset Type:Cruise Results

Principal Investigator: Anna-Louise Reysenbach (Portland State University)

Co-Principal Investigator: Susan Humphris (Woods Hole Oceanographic Institution)

BCO-DMO Data Manager: Shannon Rauch (Woods Hole Oceanographic Institution)


Project: Collaborative Research: Hydrothermal and Microbiological Investigations of the Active Brothers Volcano in the Kermadec Arc (Brothers Volcano Microbiology)


Abstract

Accession numbers for metagenome-assembled genomes (MAGs) from the Upper and Lower Cones, Upper Caldera Wall and NW Caldera, Brothers Volcano. Published in Reysenbach & St. John et al., 2020. Sequence data is available in NCBI Genbank under BioProject accession PRJNA546572.

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Water samples and hydrothermal vent deposits were collected as described in Reysenbach & St. John et al., 2020. Samples were collected with remotely operated vehicle ROV Jason. Water samples were obtained using major water samplers. Hydrothermal deposits were placed in sealed bioboxes in the ROV sampling basket to restrict flushing of samples by surrounding seawater during the ascent. Once shipboard, 1L of water samples were filtered through a 0.2-μm Sterivex filter (Merck). For the hydrothermal deposits, the outer few millimeters (up to approximately 5 mm) was subsampled for DNA extraction. These exterior samples were homogenized and stored in cryovials at -80 degrees C for subsequent DNA extraction. For the water samples, the DNA was extracted from the sterivex filters as previously described by R. E. Anderson et al. (2017). The DNA was extracted from the homogenized hydrothermal depot samples using the DNeasy PowerSoil kit (Qiagen) All purified environmental DNA was stored at -80 degrees C. After DNA extraction and library preparation, metagenomes were sequenced using the Illumina HiSeq 3000.


Related Datasets

IsRelatedTo

Dataset: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA546572
Portland State University. hydrothermal vent metagenome, Brothers Volcano 16S rRNA gene amplicon sequencing and metagenome-assembled genomes (MAGs) sequencing and assembly. 2020/11. In: BioProject [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; 2011-. Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA546572. NCBI:BioProject: PRJNA546572.

Related Publications

Results

Reysenbach, A.-L., St. John, E., Meneghin, J., Flores, G. E., Podar, M., Dombrowski, N., … Bach, W. (2020). Complex subsurface hydrothermal fluid mixing at a submarine arc volcano supports distinct and highly diverse microbial communities. Proceedings of the National Academy of Sciences, 117(51), 32627–32638. doi:10.1073/pnas.2019021117
Methods

Anderson, R. E., Reveillaud, J., Reddington, E., Delmont, T. O., Eren, A. M., McDermott, J. M., Seewald, J. S., & Huber, J. A. (2017). Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents. Nature communications, 8(1), 1114. https://doi.org/10.1038/s41467-017-01228-6
Software

A. Ultsch, F. Mörchen. (2005). "ESOM-Maps: Tools for clustering, visualization, and classification with Emergent SOM" (Technical Report, Dept. of Mathematics and Computer Science, University of Marburg, Marburg, Germany).
Software

Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114–2120. doi:10.1093/bioinformatics/btu170
Software

Kang, D. D., Froula, J., Egan, R., & Wang, Z. (2015). MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ, 3, e1165. doi:10.7717/peerj.1165