U.S. Department of EnergyOffice of Scientific and Technical Information
Narrative for Bioproject PRJNA623111
Abstract
This Narrative is part of a collection used in publications focused on the microbial ecology of fjord sediment in the high Arctic, Svalbard. This paper took a genome-centric approach to uncover novel metabolic capabilities of the Acidobacteriota clade. Metagenomic data was coupled with amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes, and transcripts (available under NCBI-Genbank Bioproject PRJNA623111), and gene expression analyses of tetrathionate-amended microcosms. This Narrative contains the metagenomic assemblies that were constructed within KBase for reproducibility. These include: stnF metagenome assembly stnAB metagenome assembly stnAC metagenome assembly These metagenome assemblies served as the launching point for an additional publication focused on a different clade of bacteria (Buongiorno et al., 2020). Link to that Narrative landing page here. Please cite: Flieder, Mathias, Joy Buongiorno, Craig W. Herbold, Bela Hausmann, Thomas Rattei, Karen G. Lloyd, Alexander Loy, and Kenneth Wasmund. "Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling." The ISME Journal (2021): 1-22.
- Authors:
-
- Division of Natural Sciences, Maryville College, Maryville, TN, USA; Department of Microbiology, University of Tennessee, Knoxville, TN, USA
- Publication Date:
- Research Org.:
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
- Keywords:
- acidobacteriota, MAGs, metagenome-assembled genomes, amplicon sequencing, 16SDefulfobacterota, marine sediment, Candidatus
- OSTI Identifier:
- 1817654
- DOI:
- https://doi.org/10.25982/97146.7/1817654
Citation Formats
Buongiorno, Joy. Narrative for Bioproject PRJNA623111. United States: N. p., 2021.
Web. doi:10.25982/97146.7/1817654.
Buongiorno, Joy. Narrative for Bioproject PRJNA623111. United States. doi:https://doi.org/10.25982/97146.7/1817654
Buongiorno, Joy. 2021.
"Narrative for Bioproject PRJNA623111". United States. doi:https://doi.org/10.25982/97146.7/1817654. https://www.osti.gov/servlets/purl/1817654. Pub date:Sat Aug 21 00:00:00 EDT 2021
@article{osti_1817654,
title = {Narrative for Bioproject PRJNA623111},
author = {Buongiorno, Joy},
abstractNote = {This Narrative is part of a collection used in publications focused on the microbial ecology of fjord sediment in the high Arctic, Svalbard. This paper took a genome-centric approach to uncover novel metabolic capabilities of the Acidobacteriota clade. Metagenomic data was coupled with amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes, and transcripts (available under NCBI-Genbank Bioproject PRJNA623111), and gene expression analyses of tetrathionate-amended microcosms. This Narrative contains the metagenomic assemblies that were constructed within KBase for reproducibility. These include: stnF metagenome assembly stnAB metagenome assembly stnAC metagenome assembly These metagenome assemblies served as the launching point for an additional publication focused on a different clade of bacteria (Buongiorno et al., 2020). Link to that Narrative landing page here. Please cite: Flieder, Mathias, Joy Buongiorno, Craig W. Herbold, Bela Hausmann, Thomas Rattei, Karen G. Lloyd, Alexander Loy, and Kenneth Wasmund. "Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling." The ISME Journal (2021): 1-22.},
doi = {10.25982/97146.7/1817654},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Sat Aug 21 00:00:00 EDT 2021},
month = {Sat Aug 21 00:00:00 EDT 2021}
}
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
journal, January 2015
- Li, Dinghua; Liu, Chi-Man; Luo, Ruibang
- Bioinformatics, Vol. 31, Issue 10
Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment
journal, August 2020
- Buongiorno, Joy; Sipes, Katie; Wasmund, Kenneth
- PLOS ONE, Vol. 15, Issue 8
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
journal, April 2012
- Peng, Y.; Leung, H. C. M.; Yiu, S. M.
- Bioinformatics, Vol. 28, Issue 11
The life sulfuric: microbial ecology of sulfur cycling in marine sediments: Microbial sulfur cycling in marine sediments
journal, May 2017
- Wasmund, Kenneth; Mußmann, Marc; Loy, Alexander
- Environmental Microbiology Reports, Vol. 9, Issue 4
The Biogeochemical Sulfur Cycle of Marine Sediments
journal, April 2019
- Jørgensen, Bo Barker; Findlay, Alyssa J.; Pellerin, André
- Frontiers in Microbiology, Vol. 10
Trimmomatic: a flexible trimmer for Illumina sequence data
journal, April 2014
- Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern
- Bioinformatics, Vol. 30, Issue 15
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm
journal, August 2014
- Wu, Yu-Wei; Tang, Yung-Hsu; Tringe, Susannah G.
- Microbiome, Vol. 2, Issue 1
metaSPAdes: a new versatile metagenomic assembler
journal, March 2017
- Nurk, Sergey; Meleshko, Dmitry; Korobeynikov, Anton
- Genome Research, Vol. 27, Issue 5
Fast gapped-read alignment with Bowtie 2
journal, March 2012
- Langmead, Ben; Salzberg, Steven L.
- Nature Methods, Vol. 9, Issue 4
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
journal, May 2015
- Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.
- Genome Research, Vol. 25, Issue 7
Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases
journal, October 2014
- Müller, Albert Leopold; Kjeldsen, Kasper Urup; Rattei, Thomas
- The ISME Journal, Vol. 9, Issue 5
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
journal, October 2015
- Wu, Yu-Wei; Simmons, Blake A.; Singer, Steven W.
- Bioinformatics, Vol. 32, Issue 4
Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions
journal, November 2011
- Angel, Roey; Claus, Peter; Conrad, Ralf
- The ISME Journal, Vol. 6, Issue 4
Oxygen in the Sea Bottom Measured with a Microelectrode
journal, March 1980
- Revsbech, N. P.; Jorgensen, B. B.; Blackburn, T. H.
- Science, Vol. 207, Issue 4437
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
journal, January 2009
- Langmead, Ben; Trapnell, Cole; Pop, Mihai
- Genome Biology, Vol. 10, Issue 3