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Title: Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions

Abstract

This Narrative is part of a collection used in a single publication. The paper took a metagnomic and metatranscriptomic approach to examine a bioreactor's response to the presence of sulfate, which reduces the production of methane, a valuable product, while producing hydrogen sulfide, a corrosive contaminant. This Narrative collection has been created to highlight the types of analyses done for this publication. They are as follows (in order): SJ1 Metagenomes: a metagenomic analysis of sample SJ1, the initial bioreactor. SJ1 Metatranscriptomes: QC-filtered raw RNA reads were aligned to individual MAGs and assembled into transcripts. Metagenome-discovered food webs in a long-term methanogenic bioreactor and rapid switch to sulfate reducing conditions (this Narrative): the public Narrative referenced in the paper, which contains several key MAGs.

Authors:
ORCiD logo ; ORCiD logo
  1. Cornell Univ., Ithaca, NY (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Oak Ridge Associated Univ., Oak Ridge, TN (United States)
Publication Date:
DOE Contract Number:  
AC02–05CH11231
Product Type:
Dataset
Research Org.:
Cornell Univ., Ithaca, NY (United States); Department of Energy Systems Biology Knowledgebase; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Subject:
59 BASIC BIOLOGICAL SCIENCES
Keywords:
metagenomics, metatranscriptomics, bioinformatics
OSTI Identifier:
1637903
DOI:
https://doi.org/10.25982/51077.6/1637903

Citation Formats

St. James, Andrew, and Crockett, Zachary. Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions. United States: N. p., 2020. Web. doi:10.25982/51077.6/1637903.
St. James, Andrew, & Crockett, Zachary. Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions. United States. doi:https://doi.org/10.25982/51077.6/1637903
St. James, Andrew, and Crockett, Zachary. 2020. "Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions". United States. doi:https://doi.org/10.25982/51077.6/1637903. https://www.osti.gov/servlets/purl/1637903. Pub date:Thu Jul 09 00:00:00 EDT 2020
@article{osti_1637903,
title = {Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions},
author = {St. James, Andrew and Crockett, Zachary},
abstractNote = {This Narrative is part of a collection used in a single publication. The paper took a metagnomic and metatranscriptomic approach to examine a bioreactor's response to the presence of sulfate, which reduces the production of methane, a valuable product, while producing hydrogen sulfide, a corrosive contaminant. This Narrative collection has been created to highlight the types of analyses done for this publication. They are as follows (in order): SJ1 Metagenomes: a metagenomic analysis of sample SJ1, the initial bioreactor. SJ1 Metatranscriptomes: QC-filtered raw RNA reads were aligned to individual MAGs and assembled into transcripts. Metagenome-discovered food webs in a long-term methanogenic bioreactor and rapid switch to sulfate reducing conditions (this Narrative): the public Narrative referenced in the paper, which contains several key MAGs.},
doi = {10.25982/51077.6/1637903},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2020},
month = {7}
}

Works referenced in this record:

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journal, November 2012


Comparison of Butyric Acid, Ethanol, Lactic Acid, and Propionic Acid as Hydrogen Donors for the Reductive Dechlorination of Tetrachloroethene
journal, March 1997


TopHat: discovering splice junctions with RNA-Seq
journal, March 2009


Efficiently gap-filling reaction networks
journal, June 2014


A Genomic Perspective on Protein Families
journal, October 1997


CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
journal, May 2015


High-throughput generation, optimization and analysis of genome-scale metabolic models
journal, August 2010


Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014


CDD/SPARCLE: functional classification of proteins via subfamily domain architectures
journal, November 2016


Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997


metaSPAdes: a new versatile metagenomic assembler
journal, March 2017


Molecular Biomarker-Based Biokinetic Modeling of a PCE-Dechlorinating and Methanogenic Mixed Culture
journal, March 2013


The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
journal, November 2013


Energy Recovery from Wastewater Treatment Plants in the United States: A Case Study of the Energy-Water Nexus
journal, April 2010


The ecology and biotechnology of sulphate-reducing bacteria
journal, May 2008


BLAST+: architecture and applications
journal, January 2009


TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
journal, January 2013


Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
journal, January 2009


Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM
journal, July 2013


Accelerated Profile HMM Searches
journal, October 2011


Fast gapped-read alignment with Bowtie 2
journal, March 2012


The Pfam protein families database: towards a more sustainable future
journal, December 2015


KBase: The United States Department of Energy Systems Biology Knowledgebase
journal, July 2018


The RAST Server: Rapid Annotations using Subsystems Technology
journal, January 2008


Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
journal, March 2012


SMART: recent updates, new developments and status in 2015
journal, October 2014


TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
journal, January 2007


20 years of the SMART protein domain annotation resource
journal, October 2017


MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
journal, October 2015


FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010


    Works referencing / citing this record:

    metaSPAdes: a new versatile metagenomic assembler
    journal, March 2017


    MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
    journal, October 2015


    Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    journal, March 2012


    SMART: recent updates, new developments and status in 2015
    journal, October 2014


    The Pfam protein families database: towards a more sustainable future
    journal, December 2015


    TopHat: discovering splice junctions with RNA-Seq
    journal, March 2009


    High-throughput generation, optimization and analysis of genome-scale metabolic models
    journal, August 2010


    Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
    journal, December 2014


    BLAST+: architecture and applications
    journal, January 2009


    Molecular Biomarker-Based Biokinetic Modeling of a PCE-Dechlorinating and Methanogenic Mixed Culture
    journal, March 2013


    TIGRFAMs and Genome Properties in 2013
    journal, November 2012


    Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    journal, January 2009


    The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
    journal, November 2013


    Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM
    journal, July 2013


    Accelerated Profile HMM Searches
    journal, October 2011


    The ecology and biotechnology of sulphate-reducing bacteria
    journal, May 2008


    TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    journal, January 2013


    CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
    journal, May 2015


    CDD/SPARCLE: functional classification of proteins via subfamily domain architectures
    journal, November 2016


    A Genomic Perspective on Protein Families
    journal, October 1997


    Energy Recovery from Wastewater Treatment Plants in the United States: A Case Study of the Energy-Water Nexus
    journal, April 2010


    Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    journal, September 1997


    Efficiently gap-filling reaction networks
    journal, June 2014


    KBase: The United States Department of Energy Systems Biology Knowledgebase
    journal, July 2018


    Comparison of Butyric Acid, Ethanol, Lactic Acid, and Propionic Acid as Hydrogen Donors for the Reductive Dechlorination of Tetrachloroethene
    journal, March 1997


    The RAST Server: Rapid Annotations using Subsystems Technology
    journal, January 2008


    Fast gapped-read alignment with Bowtie 2
    journal, March 2012


    FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
    journal, March 2010


    TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
    journal, January 2007


    20 years of the SMART protein domain annotation resource
    journal, October 2017