Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants

Stolze, Yvonne; Bremges, Andreas; Maus, Irena; Pühler, Alfred; Sczyrba, Alexander; Schlüter, Andreas

doi:10.1111/1751-7915.12982

Title: Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants

Abstract

Summary Biogas production is performed anaerobically by complex microbial communities with key species driving the process. Hence, analyses of their in situ activities are crucial to understand the process. In a previous study, metagenome sequencing and subsequent genome binning for different production‐scale biogas plants ( BGP s) resulted in four genome bins of special interest, assigned to the phyla Thermotogae , Fusobacteria , Spirochaetes and Cloacimonetes , respectively, that were genetically analysed. In this study, metatranscriptome sequencing of the same BGP samples was conducted, enabling in situ transcriptional activity determination of these genome bins. For this, mapping of metatranscriptome reads on genome bin sequences was performed providing transcripts per million ( TPM ) values for each gene. This approach revealed an active sugar‐based metabolism of the Thermotogae and Spirochaetes bins and an active amino acid‐based metabolism of the Fusobacteria and Cloacimonetes bins. The data also hint at syntrophic associations of the four corresponding species with methanogenic Archaea .

Authors:

Stolze, Yvonne ^[1]; Bremges, Andreas ^[2]; Maus, Irena ^[1]; Pühler, Alfred ^[1]; Sczyrba, Alexander ^[2];

^[1]

Center for Biotechnology ‐ CeBiTec Bielefeld University Universitätsstraße 27 33615 Bielefeld Germany
Center for Biotechnology ‐ CeBiTec Bielefeld University Universitätsstraße 27 33615 Bielefeld Germany, Faculty of Technology Bielefeld University Universitätsstraße 25 33615 Bielefeld Germany

Publication Date:: Mon Dec 04 00:00:00 EST 2017

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1411252

Alternate Identifier(s):: OSTI ID: 1411255; OSTI ID: 1625856

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Published Article

Journal Name:: Microbial Biotechnology (Online)

Additional Journal Information:: Journal Name: Microbial Biotechnology (Online) Journal Volume: 11 Journal Issue: 4; Journal ID: ISSN 1751-7915

Publisher:: Wiley-Blackwell

Country of Publication:: United Kingdom

Language:: English

Subject:: Biotechnology & Applied Microbiology; Microbiology

Citation Formats


                    Stolze, Yvonne, Bremges, Andreas, Maus, Irena, Pühler, Alfred, Sczyrba, Alexander, and Schlüter, Andreas. Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants.  United Kingdom: N. p., 2017. 
Web.  doi:10.1111/1751-7915.12982.

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                    Stolze, Yvonne, Bremges, Andreas, Maus, Irena, Pühler, Alfred, Sczyrba, Alexander, & Schlüter, Andreas. Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants.  United Kingdom.  https://doi.org/10.1111/1751-7915.12982

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                    Stolze, Yvonne, Bremges, Andreas, Maus, Irena, Pühler, Alfred, Sczyrba, Alexander, and Schlüter, Andreas. Mon .  
"Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants".  United Kingdom.  https://doi.org/10.1111/1751-7915.12982.

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@article{osti_1411252,

  title        = {Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants},

  author       = {Stolze, Yvonne and Bremges, Andreas and Maus, Irena and Pühler, Alfred and Sczyrba, Alexander and Schlüter, Andreas},

  abstractNote = {Summary Biogas production is performed anaerobically by complex microbial communities with key species driving the process. Hence, analyses of their in situ activities are crucial to understand the process. In a previous study, metagenome sequencing and subsequent genome binning for different production‐scale biogas plants ( BGP s) resulted in four genome bins of special interest, assigned to the phyla Thermotogae , Fusobacteria , Spirochaetes and Cloacimonetes , respectively, that were genetically analysed. In this study, metatranscriptome sequencing of the same BGP samples was conducted, enabling in situ transcriptional activity determination of these genome bins. For this, mapping of metatranscriptome reads on genome bin sequences was performed providing transcripts per million ( TPM ) values for each gene. This approach revealed an active sugar‐based metabolism of the Thermotogae and Spirochaetes bins and an active amino acid‐based metabolism of the Fusobacteria and Cloacimonetes bins. The data also hint at syntrophic associations of the four corresponding species with methanogenic Archaea .},

  doi          = {10.1111/1751-7915.12982},

  journal      = {Microbial Biotechnology (Online)},

  number       = 4,

  volume       = 11,

  place        = {United Kingdom},

  year         = {Mon Dec 04 00:00:00 EST 2017},

  month        = {Mon Dec 04 00:00:00 EST 2017}

}

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Title: Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants

Abstract

Citation Formats

Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy journal, February 2016

A genomic view on syntrophic versus non-syntrophic lifestyle in anaerobic fatty acid degrading communities journal, December 2014

The Ferredoxin:NAD + Oxidoreductase (Rnf) from the Acetogen Acetobacterium woodii Requires Na + and Is Reversibly Coupled to the Membrane Potential journal, September 2013

Cellular adhesiveness and cellulolytic capacity in Anaerolineae revealed by omics-based genome interpretation journal, May 2016

Bacterial chemoreceptors and chemoeffectors journal, November 2014

Hydrogen production by hyperthermophilic and extremely thermophilic bacteria and archaea: mechanisms for reductant disposal journal, July 2010

Syntrophic Growth of Desulfovibrio alaskensis Requires Genes for H 2 and Formate Metabolism as Well as Those for Flagellum and Biofilm Formation journal, January 2015

Recovering complete and draft population genomes from metagenome datasets journal, March 2016

Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants journal, July 2016

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion: Genome-centric resolution through deep metagenomics journal, July 2016

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software journal, October 2017

Deeper insight into the structure of the anaerobic digestion microbial community; the biogas microbiome database is expanded with 157 new genomes journal, September 2016

A novel archaeal species belonging to Methanoculleus genus identified via de-novo assembly and metagenomic binning process in biogas reactors journal, August 2017

Genomic Insights into Syntrophy: The Paradigm for Anaerobic Metabolic Cooperation journal, October 2012

Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant journal, July 2015

Classification of metagenomic sequences: methods and challenges journal, September 2012

Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing journal, April 2012

Biogas production: current state and perspectives journal, September 2009

Trends in Global Greenhouse Gas Emissions from 1990 to 2010 journal, April 2016

Complete genome sequence of the strain Defluviitoga tunisiensis L3, isolated from a thermophilic, production-scale biogas plant journal, June 2015

Solid-state anaerobic digestion of lignocellulosic biomass: Recent progress and perspectives journal, April 2016

Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms journal, January 2013

Biogas Production from Protein-Rich Biomass: Fed-Batch Anaerobic Fermentation of Casein and of Pig Blood and Associated Changes in Microbial Community Composition journal, October 2013

Quantitative approaches to the study of bistability in the lac operon of Escherichia coli journal, April 2008

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The Thermotoga maritima Phenotype Is Impacted by Syntrophic Interaction with Methanococcus jannaschii in Hyperthermophilic Coculture journal, January 2006

Biofuels from food processing wastes journal, April 2016

Diversity of the resident microbiota in a thermophilic municipal biogas plant journal, September 2008

Fuelling the future: microbial engineering for the production of sustainable biofuels journal, March 2016

dbCAN: a web resource for automated carbohydrate-active enzyme annotation journal, May 2012

Review on research achievements of biogas from anaerobic digestion journal, May 2015

Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates journal, August 2016

Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions journal, January 2015

Bacterial chemotaxis: information processing, thermodynamics, and behavior journal, April 2016

Thermotoga lettingae sp. nov., a novel thermophilic, methanol-degrading bacterium isolated from a thermophilic anaerobic reactor journal, July 2002

Near-optimal probabilistic RNA-seq quantification journal, April 2016

Syntrophy in anaerobic global carbon cycles journal, December 2009

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An introduction to the analysis of shotgun metagenomic data journal, June 2014

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journal, February 2016

A genomic view on syntrophic versus non-syntrophic lifestyle in anaerobic fatty acid degrading communities
journal, December 2014

The Ferredoxin:NAD ⁺ Oxidoreductase (Rnf) from the Acetogen Acetobacterium woodii Requires Na ⁺ and Is Reversibly Coupled to the Membrane Potential
journal, September 2013

Cellular adhesiveness and cellulolytic capacity in Anaerolineae revealed by omics-based genome interpretation
journal, May 2016

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journal, November 2014

Hydrogen production by hyperthermophilic and extremely thermophilic bacteria and archaea: mechanisms for reductant disposal
journal, July 2010

Syntrophic Growth of Desulfovibrio alaskensis Requires Genes for H ₂ and Formate Metabolism as Well as Those for Flagellum and Biofilm Formation
journal, January 2015

Recovering complete and draft population genomes from metagenome datasets
journal, March 2016

Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants
journal, July 2016

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion: Genome-centric resolution through deep metagenomics
journal, July 2016

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
journal, October 2017

Deeper insight into the structure of the anaerobic digestion microbial community; the biogas microbiome database is expanded with 157 new genomes
journal, September 2016

A novel archaeal species belonging to Methanoculleus genus identified via de-novo assembly and metagenomic binning process in biogas reactors
journal, August 2017

Genomic Insights into Syntrophy: The Paradigm for Anaerobic Metabolic Cooperation
journal, October 2012

Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant
journal, July 2015

Classification of metagenomic sequences: methods and challenges
journal, September 2012

Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing
journal, April 2012

Biogas production: current state and perspectives
journal, September 2009

Trends in Global Greenhouse Gas Emissions from 1990 to 2010
journal, April 2016

Complete genome sequence of the strain Defluviitoga tunisiensis L3, isolated from a thermophilic, production-scale biogas plant
journal, June 2015

Solid-state anaerobic digestion of lignocellulosic biomass: Recent progress and perspectives
journal, April 2016

Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms
journal, January 2013

Biogas Production from Protein-Rich Biomass: Fed-Batch Anaerobic Fermentation of Casein and of Pig Blood and Associated Changes in Microbial Community Composition
journal, October 2013

Quantitative approaches to the study of bistability in the lac operon of Escherichia coli
journal, April 2008

Bacterial Na+-translocating ferredoxin:NAD+ oxidoreductase
journal, October 2010

The Thermotoga maritima Phenotype Is Impacted by Syntrophic Interaction with Methanococcus jannaschii in Hyperthermophilic Coculture
journal, January 2006

Biofuels from food processing wastes
journal, April 2016

Diversity of the resident microbiota in a thermophilic municipal biogas plant
journal, September 2008

Fuelling the future: microbial engineering for the production of sustainable biofuels
journal, March 2016

dbCAN: a web resource for automated carbohydrate-active enzyme annotation
journal, May 2012

Review on research achievements of biogas from anaerobic digestion
journal, May 2015

Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates
journal, August 2016

Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions
journal, January 2015

Bacterial chemotaxis: information processing, thermodynamics, and behavior
journal, April 2016

Thermotoga lettingae sp. nov., a novel thermophilic, methanol-degrading bacterium isolated from a thermophilic anaerobic reactor
journal, July 2002

Near-optimal probabilistic RNA-seq quantification
journal, April 2016

Syntrophy in anaerobic global carbon cycles
journal, December 2009

Metagenomics and CAZyme Discovery
book, January 2017

Chemotaxis Control of Transient Cell Aggregation
journal, July 2015

An introduction to the analysis of shotgun metagenomic data
journal, June 2014

Local Gene Regulation Details a Recognition Code within the LacI Transcriptional Factor Family
journal, November 2010

Degradation efficiency of agricultural biogas plants – A full-scale study
journal, February 2015