Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants
Abstract
Biofuel production from conversion of biomass is indispensable in the portfolio of renewable energies. Complex microbial communities are involved in the anaerobic digestion process of plant material, agricultural residual products and food wastes. Analysis of the genetic potential and microbiology of communities degrading biomass to biofuels is considered to be the key to develop process optimisation strategies. Hence, due to the still incomplete taxonomic and functional characterisation of corresponding communities, new and unknown species are of special interest. Three mesophilic and one thermophilic production-scale biogas plants (BGPs) were taxonomically profiled using high-throughput 16S rRNA gene amplicon sequencing. All BGPs shared a core microbiome with the thermophilic BGP featuring the lowest diversity. However, the phyla Cloacimonetes and Spirochaetes were unique to BGPs 2 and 3, Fusobacteria were only found in BGP3 and members of the phylum Thermotogae were present only in the thermophilic BGP4. Taxonomic analyses revealed that these distinctive taxa mostly represent so far unknown species. The only exception is the dominant Thermotogae OTU featuring 16S rRNA gene sequence identity to Defluviitoga tunisiensis L3, a sequenced and characterised strain. To further investigate the genetic potential of the biogas communities, corresponding metagenomes were sequenced in a deepness of 347.5 Gbp inmore »
- Authors:
-
- Bielefeld Univ. (Germany)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1626973
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Biotechnology for Biofuels
- Additional Journal Information:
- Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 1754-6834
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES; Biotechnology & Applied Microbiology; Energy & Fuels
Citation Formats
Stolze, Yvonne, Bremges, Andreas, Rumming, Madis, Henke, Christian, Maus, Irena, Pühler, Alfred, Sczyrba, Alexander, and Schlüter, Andreas. Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants. United States: N. p., 2016.
Web. doi:10.1186/s13068-016-0565-3.
Stolze, Yvonne, Bremges, Andreas, Rumming, Madis, Henke, Christian, Maus, Irena, Pühler, Alfred, Sczyrba, Alexander, & Schlüter, Andreas. Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants. United States. https://doi.org/10.1186/s13068-016-0565-3
Stolze, Yvonne, Bremges, Andreas, Rumming, Madis, Henke, Christian, Maus, Irena, Pühler, Alfred, Sczyrba, Alexander, and Schlüter, Andreas. Tue .
"Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants". United States. https://doi.org/10.1186/s13068-016-0565-3. https://www.osti.gov/servlets/purl/1626973.
@article{osti_1626973,
title = {Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants},
author = {Stolze, Yvonne and Bremges, Andreas and Rumming, Madis and Henke, Christian and Maus, Irena and Pühler, Alfred and Sczyrba, Alexander and Schlüter, Andreas},
abstractNote = {Biofuel production from conversion of biomass is indispensable in the portfolio of renewable energies. Complex microbial communities are involved in the anaerobic digestion process of plant material, agricultural residual products and food wastes. Analysis of the genetic potential and microbiology of communities degrading biomass to biofuels is considered to be the key to develop process optimisation strategies. Hence, due to the still incomplete taxonomic and functional characterisation of corresponding communities, new and unknown species are of special interest. Three mesophilic and one thermophilic production-scale biogas plants (BGPs) were taxonomically profiled using high-throughput 16S rRNA gene amplicon sequencing. All BGPs shared a core microbiome with the thermophilic BGP featuring the lowest diversity. However, the phyla Cloacimonetes and Spirochaetes were unique to BGPs 2 and 3, Fusobacteria were only found in BGP3 and members of the phylum Thermotogae were present only in the thermophilic BGP4. Taxonomic analyses revealed that these distinctive taxa mostly represent so far unknown species. The only exception is the dominant Thermotogae OTU featuring 16S rRNA gene sequence identity to Defluviitoga tunisiensis L3, a sequenced and characterised strain. To further investigate the genetic potential of the biogas communities, corresponding metagenomes were sequenced in a deepness of 347.5 Gbp in total. A combined assembly comprised 80.3 % of all reads and resulted in the prediction of 1.59 million genes on assembled contigs. Genome binning yielded genome bins comprising the prevalent distinctive phyla Cloacimonetes, Spirochaetes, Fusobacteria and Thermotogae. Comparative genome analyses between the most dominant Thermotogae bin and the very closely related Defluviitoga tunisiensis L3 genome originating from the same BGP revealed high genetic similarity. This finding confirmed applicability and reliability of the binning approach. The four highly covered genome bins of the other three distinct phyla showed low or very low genetic similarities to their closest phylogenetic relatives, and therefore indicated their novelty. In this study, the 16S rRNA gene sequencing approach and a combined metagenome assembly and binning approach were used for the first time on different production-scale biogas plants and revealed insights into the genetic potential and functional role of so far unknown species.},
doi = {10.1186/s13068-016-0565-3},
journal = {Biotechnology for Biofuels},
number = 1,
volume = 9,
place = {United States},
year = {2016},
month = {7}
}
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Figures / Tables:
Table 1: Physico-chemical characteristics and fed substrates of the four different biogas plants analysed in this study and optimal ranges of some of the parameters
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Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors
journal, June 2018
- Maus, Irena; Rumming, Madis; Bergmann, Ingo
- Biotechnology for Biofuels, Vol. 11, Issue 1
Genetic repertoires of anaerobic microbiomes driving generation of biogas
journal, September 2018
- Grohmann, Anja; Vainshtein, Yevhen; Euchner, Ellen
- Biotechnology for Biofuels, Vol. 11, Issue 1
Intermittent fasting for microbes: how discontinuous feeding increases functional stability in anaerobic digestion
journal, October 2018
- Bonk, Fabian; Popp, Denny; Weinrich, Sören
- Biotechnology for Biofuels, Vol. 11, Issue 1
Sulfide level in municipal sludge digesters affects microbial community response to long-chain fatty acid loads
journal, November 2019
- Shakeri Yekta, Sepehr; Liu, Tong; Axelsson Bjerg, Mette
- Biotechnology for Biofuels, Vol. 12, Issue 1
New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters
journal, February 2020
- Campanaro, Stefano; Treu, Laura; Rodriguez-R, Luis M.
- Biotechnology for Biofuels, Vol. 13, Issue 1
Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics
journal, March 2020
- Maus, Irena; Klocke, Michael; Derenkó, Jaqueline
- Environmental Microbiome, Vol. 15, Issue 1
Characterization of Core Microbiomes and Functional Profiles of Mesophilic Anaerobic Digesters Fed With Chlorella vulgaris Green Microalgae and Maize Silage
journal, October 2019
- Wirth, Roland; Böjti, Tamás; Lakatos, Gergely
- Frontiers in Energy Research, Vol. 7
Genome Analyses and Genome-Centered Metatranscriptomics of Methanothermobacter wolfeii Strain SIV6, Isolated from a Thermophilic Production-Scale Biogas Fermenter
journal, December 2019
- Hassa, Julia; Wibberg, Daniel; Maus, Irena
- Microorganisms, Vol. 8, Issue 1
Bioinformatics for NGS-based metagenomics and the application to biogas research
journal, November 2017
- Jünemann, Sebastian; Kleinbölting, Nils; Jaenicke, Sebastian
- Journal of Biotechnology, Vol. 261
Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies
journal, January 2018
- Campanaro, Stefano; Treu, Laura; Kougias, Panagiotis G.
- Scientific Reports, Vol. 8, Issue 1
Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates
journal, August 2016
- Maus, Irena; Koeck, Daniela E.; Cibis, Katharina G.
- Biotechnology for Biofuels, Vol. 9, Issue 1
Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting
journal, April 2017
- Lemos, Leandro N.; Pereira, Roberta V.; Quaggio, Ronaldo B.
- Frontiers in Microbiology, Vol. 8
Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants
journal, April 2019
- Heyer, R.; Schallert, K.; Siewert, C.
- Microbiome, Vol. 7, Issue 1
CAMISIM: simulating metagenomes and microbial communities
journal, February 2019
- Fritz, Adrian; Hofmann, Peter; Majda, Stephan
- Microbiome, Vol. 7, Issue 1
New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters
text, January 2020
- Campanaro, Stefano; Treu, Laura; Rodriguez-R, Luis M.
- BioMed Central
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