Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics
The current focus on renewable energy in global policy highlights the importance of methane production from biomass through anaerobic digestion (AD). To improve biomass digestion while ensuring overall process stability, microbiome-based management strategies become more important. In this study, me...
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-09-01
|
| Series: | Microorganisms |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2607/11/10/2412 |
| _version_ | 1827720332398559232 |
|---|---|
| author | Julia Hassa Tom Jonas Tubbesing Irena Maus Robert Heyer Dirk Benndorf Mathias Effenberger Christian Henke Benedikt Osterholz Michael Beckstette Alfred Pühler Alexander Sczyrba Andreas Schlüter |
| author_facet | Julia Hassa Tom Jonas Tubbesing Irena Maus Robert Heyer Dirk Benndorf Mathias Effenberger Christian Henke Benedikt Osterholz Michael Beckstette Alfred Pühler Alexander Sczyrba Andreas Schlüter |
| author_sort | Julia Hassa |
| collection | DOAJ |
| description | The current focus on renewable energy in global policy highlights the importance of methane production from biomass through anaerobic digestion (AD). To improve biomass digestion while ensuring overall process stability, microbiome-based management strategies become more important. In this study, metagenomes and metaproteomes were used for metagenomically assembled genome (MAG)-centric analyses to investigate a full-scale biogas plant consisting of three differentially operated digesters. Microbial communities were analyzed regarding their taxonomic composition, functional potential, as well as functions expressed on the proteome level. Different abundances of genes and enzymes related to the biogas process could be mostly attributed to different process parameters. Individual MAGs exhibiting different abundances in the digesters were studied in detail, and their roles in the hydrolysis, acidogenesis and acetogenesis steps of anaerobic digestion could be assigned. <i>Methanoculleus thermohydrogenotrophicum</i> was an active hydrogenotrophic methanogen in all three digesters, whereas <i>Methanothermobacter wolfeii</i> was more prevalent at higher process temperatures. Further analysis focused on MAGs, which were abundant in all digesters, indicating their potential to ensure biogas process stability. The most prevalent MAG belonged to the class <i>Limnochordia</i>; this MAG was ubiquitous in all three digesters and exhibited activity in numerous pathways related to different steps of AD. |
| first_indexed | 2024-03-10T21:02:49Z |
| format | Article |
| id | doaj.art-a4568e6f85b746c186fe9b8f922be0f7 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T21:02:49Z |
| publishDate | 2023-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-a4568e6f85b746c186fe9b8f922be0f72023-11-19T17:26:21ZengMDPI AGMicroorganisms2076-26072023-09-011110241210.3390/microorganisms11102412Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and MetaproteomicsJulia Hassa0Tom Jonas Tubbesing1Irena Maus2Robert Heyer3Dirk Benndorf4Mathias Effenberger5Christian Henke6Benedikt Osterholz7Michael Beckstette8Alfred Pühler9Alexander Sczyrba10Andreas Schlüter11Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, GermanyComputational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, GermanyGenome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, GermanyMultidimensional Omics Data Analyses Group, Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Bunsen-Kirchhoff-Straße 11, Dortmund 44139, GermanyBiosciences and Process Engineering, Anhalt University of Applied Sciences, Bernburger Straße 55, Postfach 1458, 06366 Köthen, GermanyBavarian State Research Center for Agriculture, Institute for Agricultural Engineering and Animal Husbandry, Vöttinger Straße 36, 85354 Freising, GermanyComputational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, GermanyComputational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, GermanyComputational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, GermanyGenome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, GermanyComputational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, GermanyGenome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, GermanyThe current focus on renewable energy in global policy highlights the importance of methane production from biomass through anaerobic digestion (AD). To improve biomass digestion while ensuring overall process stability, microbiome-based management strategies become more important. In this study, metagenomes and metaproteomes were used for metagenomically assembled genome (MAG)-centric analyses to investigate a full-scale biogas plant consisting of three differentially operated digesters. Microbial communities were analyzed regarding their taxonomic composition, functional potential, as well as functions expressed on the proteome level. Different abundances of genes and enzymes related to the biogas process could be mostly attributed to different process parameters. Individual MAGs exhibiting different abundances in the digesters were studied in detail, and their roles in the hydrolysis, acidogenesis and acetogenesis steps of anaerobic digestion could be assigned. <i>Methanoculleus thermohydrogenotrophicum</i> was an active hydrogenotrophic methanogen in all three digesters, whereas <i>Methanothermobacter wolfeii</i> was more prevalent at higher process temperatures. Further analysis focused on MAGs, which were abundant in all digesters, indicating their potential to ensure biogas process stability. The most prevalent MAG belonged to the class <i>Limnochordia</i>; this MAG was ubiquitous in all three digesters and exhibited activity in numerous pathways related to different steps of AD.https://www.mdpi.com/2076-2607/11/10/2412biogas microbiomebiogas process chainanaerobic digestionmetagenomic binningmetagenome analysesmetaproteome analyses |
| spellingShingle | Julia Hassa Tom Jonas Tubbesing Irena Maus Robert Heyer Dirk Benndorf Mathias Effenberger Christian Henke Benedikt Osterholz Michael Beckstette Alfred Pühler Alexander Sczyrba Andreas Schlüter Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics Microorganisms biogas microbiome biogas process chain anaerobic digestion metagenomic binning metagenome analyses metaproteome analyses |
| title | Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics |
| title_full | Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics |
| title_fullStr | Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics |
| title_full_unstemmed | Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics |
| title_short | Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics |
| title_sort | uncovering microbiome adaptations in a full scale biogas plant insights from mag centric metagenomics and metaproteomics |
| topic | biogas microbiome biogas process chain anaerobic digestion metagenomic binning metagenome analyses metaproteome analyses |
| url | https://www.mdpi.com/2076-2607/11/10/2412 |
| work_keys_str_mv | AT juliahassa uncoveringmicrobiomeadaptationsinafullscalebiogasplantinsightsfrommagcentricmetagenomicsandmetaproteomics AT tomjonastubbesing uncoveringmicrobiomeadaptationsinafullscalebiogasplantinsightsfrommagcentricmetagenomicsandmetaproteomics AT irenamaus uncoveringmicrobiomeadaptationsinafullscalebiogasplantinsightsfrommagcentricmetagenomicsandmetaproteomics AT robertheyer uncoveringmicrobiomeadaptationsinafullscalebiogasplantinsightsfrommagcentricmetagenomicsandmetaproteomics AT dirkbenndorf uncoveringmicrobiomeadaptationsinafullscalebiogasplantinsightsfrommagcentricmetagenomicsandmetaproteomics AT mathiaseffenberger uncoveringmicrobiomeadaptationsinafullscalebiogasplantinsightsfrommagcentricmetagenomicsandmetaproteomics AT christianhenke uncoveringmicrobiomeadaptationsinafullscalebiogasplantinsightsfrommagcentricmetagenomicsandmetaproteomics AT benediktosterholz uncoveringmicrobiomeadaptationsinafullscalebiogasplantinsightsfrommagcentricmetagenomicsandmetaproteomics AT michaelbeckstette uncoveringmicrobiomeadaptationsinafullscalebiogasplantinsightsfrommagcentricmetagenomicsandmetaproteomics AT alfredpuhler uncoveringmicrobiomeadaptationsinafullscalebiogasplantinsightsfrommagcentricmetagenomicsandmetaproteomics AT alexandersczyrba uncoveringmicrobiomeadaptationsinafullscalebiogasplantinsightsfrommagcentricmetagenomicsandmetaproteomics AT andreasschluter uncoveringmicrobiomeadaptationsinafullscalebiogasplantinsightsfrommagcentricmetagenomicsandmetaproteomics |