Dataset: GenBank accession numbers for microbial 16S rRNA sequences collected at the East Pacific Rise by DSV/Alvin during R/V Atlantis research cruises (Jan. 2004 - June 2006) (Microbial Communities at Deep-Sea Vents project)

Final no updates expectedVersion (2017-04-20)Dataset Type:Cruise Results

Principal Investigator: Stefan M. Sievert (Woods Hole Oceanographic Institution)

BCO-DMO Data Manager: Nancy Copley (Woods Hole Oceanographic Institution)

Program: Dimensions of Biodiversity (Dimensions of Biodiversity)

Program: Center for Dark Energy Biosphere Investigations (C-DEBI)

Project: An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents (Microbial Communities at Deep-Sea Vents)

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Bacterial diversity and successional patterns during biofilm formation on freshly exposed basalt surfaces at diffuse-flow deep-sea vents.

This dataset is the microbial community composition based on 16 rRNA gene analysis of biofilms on basalt collected during research cruises AT11-07, AT11-10, AT11-20 and AT15-06 at the 9ºN deep-sea hydrothermal vent field on the East Pacific Rise, Pacific Ocean between Jan. 2004 and June 2006. The dataset contains links to full-length 16S rRNA sequence data deposited at NCBI GenBank with accession numbers KT257735- KT257859. The 16S rRNA tag data were assigned GenBank SRA Bioproject number PRJNA288972.

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Methods
Ashelford, K. E., Chuzhanova, N. A., Fry, J. C., Jones, A. J., & Weightman, A. J. (2006). New Screening Software Shows that Most Recent Large 16S rRNA Gene Clone Libraries Contain Chimeras. Applied and Environmental Microbiology, 72(9), 5734–5741. doi:10.1128/aem.00556-06
Methods
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., … Knight, R. (2010). QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7(5), 335–336. doi:10.1038/nmeth.f.303
Methods
Huber, T., Faulkner, G., & Hugenholtz, P. (2004). Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics, 20(14), 2317–2319. doi:10.1093/bioinformatics/bth226
Methods
Lozupone, C., Lladser, M. E., Knights, D., Stombaugh, J., & Knight, R. (2010). UniFrac: an effective distance metric for microbial community comparison. The ISME Journal, 5(2), 169–172. doi:10.1038/ismej.2010.133
Methods
Polz, M. F., & Cavanaugh, C. M. (1998). Bias in Template-to-Product Ratios in Multitemplate PCR. Applied and Environmental Microbiology, 64(10), 3724–3730.

Sievert, S. M. (2017) GenBank accession numbers for microbial 16S rRNA sequences collected at the East Pacific Rise by DSV/Alvin during R/V Atlantis research cruises (Jan. 2004 - June 2006) (Microbial Communities at Deep-Sea Vents project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version ) Version Date 2017-04-20 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/687844 [access date]

Terms of Use

This dataset is licensed under Creative Commons Attribution 4.0.


If you wish to use this dataset, it is highly recommended that you contact the original principal investigators (PI). Should the relevant PI be unavailable, please contact BCO-DMO (info@bco-dmo.org) for additional guidance. For general guidance please see the BCO-DMO Terms of Use document.

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Funded by the U.S. National Science Foundation