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Hassa J, Tubbesing TJ, Maus I, Heyer R, Benndorf D, Effenberger M, Henke C, Osterholz B, Beckstette M, Pühler A, Sczyrba A, Schlüter A. Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics. Microorganisms 2023; 11:2412. [PMID: 37894070 PMCID: PMC10608942 DOI: 10.3390/microorganisms11102412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
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. Methanoculleus thermohydrogenotrophicum was an active hydrogenotrophic methanogen in all three digesters, whereas Methanothermobacter wolfeii 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 Limnochordia; this MAG was ubiquitous in all three digesters and exhibited activity in numerous pathways related to different steps of AD.
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Affiliation(s)
- Julia Hassa
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
| | - Tom Jonas Tubbesing
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Irena Maus
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
| | - Robert Heyer
- Multidimensional Omics Data Analyses Group, Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Bunsen-Kirchhoff-Straße 11, Dortmund 44139, Germany
- Multidimensional Omics Data Analyses Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Dirk Benndorf
- Biosciences and Process Engineering, Anhalt University of Applied Sciences, Bernburger Straße 55, Postfach 1458, 06366 Köthen, Germany
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Mathias Effenberger
- Bavarian State Research Center for Agriculture, Institute for Agricultural Engineering and Animal Husbandry, Vöttinger Straße 36, 85354 Freising, Germany
| | - Christian Henke
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Benedikt Osterholz
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Michael Beckstette
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Alfred Pühler
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
| | - Alexander Sczyrba
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Andreas Schlüter
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
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Shang Z, Wang R, Zhang X, Tu Y, Sheng C, Yuan H, Wen L, Li Y, Zhang J, Wang X, Yang G, Feng Y, Ren G. Differential effects of petroleum-based and bio-based microplastics on anaerobic digestion: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162674. [PMID: 36894074 DOI: 10.1016/j.scitotenv.2023.162674] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
The number of plastics is increasing owing to the rapid development of the plastics industry. Microplastics (MPs) are formed during the use of both petroleum-based plastics and newly developed bio-based plastics. These MPs are inevitably released into the environment and are enriched in wastewater treatment plant sludge. Anaerobic digestion is a popular sludge stabilization method for wastewater treatment plants. Understanding the potential impacts of different MPs on anaerobic digestion is critical. This paper provides a comprehensive review of the mechanisms of petroleum-based MPs and bio-based MPs in anaerobic digestion methane production and compares their potential effects on biochemical pathways, key enzyme activities, and microbial communities. Finally, it identifies problems that must be solved in the future, proposes the focus of future research, and predicts the future development direction of the plastics industry.
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Affiliation(s)
- Zezhou Shang
- College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Rui Wang
- College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Xiyi Zhang
- College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Yongle Tu
- College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China
| | - Chenjing Sheng
- College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Huan Yuan
- College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Lei Wen
- College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Yulu Li
- College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Jing Zhang
- College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Xiaojiao Wang
- College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China.
| | - Gaihe Yang
- College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Yongzhong Feng
- College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Guangxin Ren
- College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
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Köller N, Hahnke S, Zverlov V, Wibberg D, Klingl A, Busche T, Klocke M, Pühler A, Schlüter A, Liebl W, Maus I. Anaeropeptidivorans aminofermentans gen. nov., sp. nov., a mesophilic proteolytic salt-tolerant bacterium isolated from a laboratory-scale biogas fermenter, and emended description of Clostridium colinum. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748496 DOI: 10.1099/ijsem.0.005668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
An anaerobic bacterial strain, designated strain M3/9T, was isolated from a laboratory-scale biogas fermenter fed with maize silage supplemented with 5 % wheat straw. Cells were straight, non-motile rods, which stained Gram-negative. Optimal growth occurred between 30 and 40°C, at pH 7.5-8.5, and up to 3.9 % (w/v) NaCl was tolerated. When grown on peptone from casein and soymeal, strain M3/9T produced mainly acetic acid, ethanol, and isobutyric acid. The major cellular fatty acids of the novel strain were C16 : 0 and C16 : 0 DMA. The genome of strain M3/9T is 3757 330 bp in size with a G+C content of 38.45 mol%. Phylogenetic analysis allocated strain M3/9T within the family Lachnospiraceae with Clostridium colinum DSM 6011T and Anaerotignum lactatifermentans DSM 14214T being the most closely related species sharing 57.86 and 56.99% average amino acid identity and 16S rRNA gene sequence similarities of 91.58 and 91.26 %, respectively. Based on physiological, chemotaxonomic and genetic data, we propose the description of a novel species and genus Anaeropeptidivorans aminofermentans gen. nov., sp. nov., represented by the type strain M3/9T (=DSM 100058T=LMG 29527T). In addition, an emended description of Clostridium colinum is provided.
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Affiliation(s)
- Nora Köller
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Sarah Hahnke
- Department of Human Medicine, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Vladimir Zverlov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.,Institute for Bio- and Geosciences (IBG-5), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Andreas Klingl
- Plant Development, Department Biology I - Botany, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Tobias Busche
- Medical Faculty OWL & Centrum für Biotechnologie (CeBiTec), Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Michael Klocke
- Institute of Agricultural and Urban Ecological Projects affiliated to Berlin Humboldt University (IASP), Philippstraße 13, 10115 Berlin, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.,Institute for Bio- and Geosciences (IBG-5), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
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Biogas Production and Microbial Communities of Mesophilic and Thermophilic Anaerobic Co-Digestion of Animal Manures and Food Wastes in Costa Rica. ENERGIES 2022. [DOI: 10.3390/en15093252] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Biomass generated from agricultural operations in Costa Rica represents an untapped renewable resource for bioenergy generation. This study investigated the effects of two temperatures and three mixture ratios of manures and food wastes on biogas production and microbial community structure. Increasing the amount of fruit and restaurant wastes in the feed mixture significantly enhanced the productivity of the systems (16% increase in the mesophilic systems and 41% in the thermophilic). The methane content of biogas was also favored at higher temperatures. Beta diversity analysis, based on high-throughput sequencing of 16S rRNA gene, showed that microbial communities of the thermophilic digestions were more similar to each other than the mesophilic digestions. Species richness of the thermophilic digestions was significantly greater than the corresponding mesophilic digestions (F = 40.08, p = 0.003). The mesophilic digesters were dominated by Firmicutes and Bacteroidetes while in thermophilic digesters, the phyla Firmicutes and Chloroflexi accounted for up to 90% of all sequences. Methanosarcina represented the key methanogen and was more abundant in thermophilic digestions. These results demonstrate that increasing digestion temperature and adding food wastes can alleviate the negative impact of low C:N ratios on anaerobic digestion.
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Villalobos Solis MI, Chirania P, Hettich RL. In silico evaluation of a targeted metaproteomics strategy for broad screening of cellulolytic enzyme capacities in anaerobic microbiome bioreactors. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:32. [PMID: 35303956 PMCID: PMC8933973 DOI: 10.1186/s13068-022-02125-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/22/2022] [Indexed: 01/01/2023]
Abstract
BACKGROUND Microbial-driven solubilization of lignocellulosic material is a natural mechanism that is exploited in anaerobic digesters (ADs) to produce biogas and other valuable bioproducts. Glycoside hydrolases (GHs) are the main enzymes that bacterial and archaeal populations use to break down complex polysaccharides in these reactors. Methodologies for rapidly screening the physical presence and types of GHs can provide information about their functional activities as well as the taxonomical diversity within AD systems but are largely unavailable. Targeted proteomic methods could potentially be used to provide snapshots of the GHs expressed by microbial consortia in ADs, giving valuable insights into the functional lignocellulolytic degradation diversity of a community. Such observations would be essential to evaluate the hydrolytic performance of a reactor or potential issues with it. RESULTS As a proof of concept, we performed an in silico selection and evaluation of groups of tryptic peptides from five important GH families derived from a dataset of 1401 metagenome-assembled genomes (MAGs) in anaerobic digesters. Following empirical rules of peptide-based targeted proteomics, we selected groups of shared peptides among proteins within a GH family while at the same time being unique compared to all other background proteins. In particular, we were able to identify a tractable unique set of peptides that were sufficient to monitor the range of GH families. While a few thousand peptides would be needed for comprehensive characterization of the main GH families, we found that at least 50% of the proteins in these families (such as the key families) could be tracked with only 200 peptides. The unique peptides selected for groups of GHs were found to be sufficient for distinguishing enzyme specificity or microbial taxonomy. These in silico results demonstrate the presence of specific unique GH peptides even in a highly diverse and complex microbiome and reveal the potential for development of targeted metaproteomic approaches in ADs or lignocellulolytic microbiomes. Such an approach could be valuable for estimating molecular-level enzymatic capabilities and responses of microbial communities to different substrates or conditions, which is a critical need in either building or utilizing constructed communities or defined cultures for bio-production. CONCLUSIONS This in silico study demonstrates the peptide selection strategy for quantifying relevant groups of GH proteins in a complex anaerobic microbiome and encourages the development of targeted metaproteomic approaches in fermenters. The results revealed that targeted metaproteomics could be a feasible approach for the screening of cellulolytic enzyme capacities for a range of anaerobic microbiome fermenters and thus could assist in bioreactor evaluation and optimization.
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Affiliation(s)
| | - Payal Chirania
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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Singh A, Moestedt J, Berg A, Schnürer A. Microbiological Surveillance of Biogas Plants: Targeting Acetogenic Community. Front Microbiol 2021; 12:700256. [PMID: 34484143 PMCID: PMC8415747 DOI: 10.3389/fmicb.2021.700256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/21/2021] [Indexed: 11/15/2022] Open
Abstract
Acetogens play a very important role in anaerobic digestion and are essential in ensuring process stability. Despite this, targeted studies of the acetogenic community in biogas processes remain limited. Some efforts have been made to identify and understand this community, but the lack of a reliable molecular analysis strategy makes the detection of acetogenic bacteria tedious. Recent studies suggest that screening of bacterial genetic material for formyltetrahydrofolate synthetase (FTHFS), a key marker enzyme in the Wood-Ljungdahl pathway, can give a strong indication of the presence of putative acetogens in biogas environments. In this study, we applied an acetogen-targeted analyses strategy developed previously by our research group for microbiological surveillance of commercial biogas plants. The surveillance comprised high-throughput sequencing of FTHFS gene amplicons and unsupervised data analysis with the AcetoScan pipeline. The results showed differences in the acetogenic community structure related to feed substrate and operating parameters. They also indicated that our surveillance method can be helpful in the detection of community changes before observed changes in physico-chemical profiles, and that frequent high-throughput surveillance can assist in management towards stable process operation, thus improving the economic viability of biogas plants. To our knowledge, this is the first study to apply a high-throughput microbiological surveillance approach to visualise the potential acetogenic population in commercial biogas digesters.
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Affiliation(s)
- Abhijeet Singh
- Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Moestedt
- Tekniska Verken i Linköping AB, Department R&D, Linköping, Sweden
| | | | - Anna Schnürer
- Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Detman A, Bucha M, Treu L, Chojnacka A, Pleśniak Ł, Salamon A, Łupikasza E, Gromadka R, Gawor J, Gromadka A, Drzewicki W, Jakubiak M, Janiga M, Matyasik I, Błaszczyk MK, Jędrysek MO, Campanaro S, Sikora A. Evaluation of acidogenesis products' effect on biogas production performed with metagenomics and isotopic approaches. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:125. [PMID: 34051845 PMCID: PMC8164749 DOI: 10.1186/s13068-021-01968-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/06/2021] [Indexed: 06/09/2023]
Abstract
BACKGROUND During the acetogenic step of anaerobic digestion, the products of acidogenesis are oxidized to substrates for methanogenesis: hydrogen, carbon dioxide and acetate. Acetogenesis and methanogenesis are highly interconnected processes due to the syntrophic associations between acetogenic bacteria and hydrogenotrophic methanogens, allowing the whole process to become thermodynamically favorable. The aim of this study is to determine the influence of the dominant acidic products on the metabolic pathways of methane formation and to find a core microbiome and substrate-specific species in a mixed biogas-producing system. RESULTS Four methane-producing microbial communities were fed with artificial media having one dominant component, respectively, lactate, butyrate, propionate and acetate, for 896 days in 3.5-L Up-flow Anaerobic Sludge Blanket (UASB) bioreactors. All the microbial communities showed moderately different methane production and utilization of the substrates. Analyses of stable carbon isotope composition of the fermentation gas and the substrates showed differences in average values of δ13C(CH4) and δ13C(CO2) revealing that acetate and lactate strongly favored the acetotrophic pathway, while butyrate and propionate favored the hydrogenotrophic pathway of methane formation. Genome-centric metagenomic analysis recovered 234 Metagenome Assembled Genomes (MAGs), including 31 archaeal and 203 bacterial species, mostly unknown and uncultivable. MAGs accounted for 54%-67% of the entire microbial community (depending on the bioreactor) and evidenced that the microbiome is extremely complex in terms of the number of species. The core microbiome was composed of Methanothrix soehngenii (the most abundant), Methanoculleus sp., unknown Bacteroidales and Spirochaetaceae. Relative abundance analysis of all the samples revealed microbes having substrate preferences. Substrate-specific species were mostly unknown and not predominant in the microbial communities. CONCLUSIONS In this experimental system, the dominant fermentation products subjected to methanogenesis moderately modified the final effect of bioreactor performance. At the molecular level, a different contribution of acetotrophic and hydrogenotrophic pathways for methane production, a very high level of new species recovered, and a moderate variability in microbial composition depending on substrate availability were evidenced. Propionate was not a factor ceasing methane production. All these findings are relevant because lactate, acetate, propionate and butyrate are the universal products of acidogenesis, regardless of feedstock.
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Affiliation(s)
- Anna Detman
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Michał Bucha
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
- Faculty of Earth Sciences, University of Silesia in Katowice, Sosnowiec, Poland
| | - Laura Treu
- Department of Biology, University of Padova, Padova, Italy
| | - Aleksandra Chojnacka
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw, University of Life Sciences, Warsaw, Poland
| | - Łukasz Pleśniak
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
- Institute of Geological Sciences, University of Wroclaw, Wrocław, Poland
| | | | - Ewa Łupikasza
- Faculty of Earth Sciences, University of Silesia in Katowice, Sosnowiec, Poland
| | - Robert Gromadka
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Jan Gawor
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | | | - Wojciech Drzewicki
- Institute of Geological Sciences, University of Wroclaw, Wrocław, Poland
| | - Marta Jakubiak
- Institute of Geological Sciences, University of Wroclaw, Wrocław, Poland
| | - Marek Janiga
- Oil and Gas Institute, National Research Institute, Cracow, Poland
| | - Irena Matyasik
- Oil and Gas Institute, National Research Institute, Cracow, Poland
| | - Mieczysław K Błaszczyk
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw, University of Life Sciences, Warsaw, Poland
| | | | | | - Anna Sikora
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland.
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Ma S, Jiang F, Huang Y, Zhang Y, Wang S, Fan H, Liu B, Li Q, Yin L, Wang H, Liu H, Ren Y, Li S, Cheng L, Fan W, Deng Y. A microbial gene catalog of anaerobic digestion from full-scale biogas plants. Gigascience 2021; 10:giaa164. [PMID: 33506264 PMCID: PMC7842101 DOI: 10.1093/gigascience/giaa164] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/10/2020] [Accepted: 12/18/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Biogas production with anaerobic digestion (AD) is one of the most promising solutions for both renewable energy production and resolving the environmental problem caused by the worldwide increase in organic waste. However, the complex structure of the microbiome in AD is poorly understood. FINDINGS In this study, we constructed a microbial gene catalog of AD (22,840,185 genes) based on 1,817 Gb metagenomic data derived from digestate samples of 56 full-scale biogas plants fed with diverse feedstocks. Among the gene catalog, 73.63% and 2.32% of genes were taxonomically annotated to Bacteria and Archaea, respectively, and 57.07% of genes were functionally annotated with KEGG orthologous groups. Our results confirmed the existence of core microbiome in AD and showed that the type of feedstock (cattle, chicken, and pig manure) has a great influence on carbohydrate hydrolysis and methanogenesis. In addition, 2,426 metagenome-assembled genomes were recovered from all digestate samples, and all genomes were estimated to be ≥80% complete with ≤10% contamination. CONCLUSIONS This study deepens our understanding of the microbial composition and function in the AD process and also provides a huge number of reference genome and gene resources for analysis of anaerobic microbiota.
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Affiliation(s)
- Shichun Ma
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
| | - Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120,China
| | - Yan Huang
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
| | - Yan Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Sen Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Hui Fan
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
| | - Bo Liu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Qiang Li
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
| | - Lijuan Yin
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Hengchao Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Hangwei Liu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Yuwei Ren
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Shuqu Li
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Lei Cheng
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
| | - Wei Fan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Yu Deng
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
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Rettenmaier R, Schneider M, Munk B, Lebuhn M, Jünemann S, Sczyrba A, Maus I, Zverlov V, Liebl W. Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellum. Microorganisms 2020; 8:E915. [PMID: 32560349 PMCID: PMC7355431 DOI: 10.3390/microorganisms8060915] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/06/2020] [Accepted: 06/11/2020] [Indexed: 01/02/2023] Open
Abstract
Bacterial hydrolysis of polysaccharides is an important step for the production of sustainable energy, for example during the conversion of plant biomass to methane-rich biogas. Previously, Hungateiclostridium thermocellum was identified as cellulolytic key player in thermophilic biogas microbiomes with a great frequency as an accompanying organism. The aim of this study was to physiologically characterize a recently isolated co-culture of H. thermocellum and the saccharolytic bacterium Defluviitalea raffinosedens from a laboratory-scale biogas fermenter. The characterization focused on cellulose breakdown by applying the measurement of cellulose hydrolysis, production of metabolites, and the activity of secreted enzymes. Substrate degradation and the production of volatile metabolites was considerably enhanced when both organisms acted synergistically. The metabolic properties of H. thermocellum have been studied well in the past. To predict the role of D. raffinosedens in this bacterial duet, the genome of D. raffinosedens was sequenced for the first time. Concomitantly, to deduce the prevalence of D. raffinosedens in anaerobic digestion, taxonomic composition and transcriptional activity of different biogas microbiomes were analyzed in detail. Defluviitalea was abundant and metabolically active in reactor operating at highly efficient process conditions, supporting the importance of this organism for the hydrolysis of the raw substrate.
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Affiliation(s)
- Regina Rettenmaier
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (M.S.); (W.L.)
| | - Martina Schneider
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (M.S.); (W.L.)
| | - Bernhard Munk
- Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany; (B.M.); (M.L.)
| | - Michael Lebuhn
- Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany; (B.M.); (M.L.)
| | - Sebastian Jünemann
- Center for Biotechnology (CeBiTec), Universitätsstr. 27, 33615 Bielefeld, Germany;
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany;
| | - Alexander Sczyrba
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany;
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Universitätsstr. 27, 33615 Bielefeld, Germany;
| | - Vladimir Zverlov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (M.S.); (W.L.)
- Institute of Molecular Genetics, RAS, Kurchatov Sq. 2, 123182 Moscow, Russia
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (M.S.); (W.L.)
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Genome Analyses and Genome-Centered Metatranscriptomics of Methanothermobacter wolfeii Strain SIV6, Isolated from a Thermophilic Production-Scale Biogas Fermenter. Microorganisms 2019; 8:microorganisms8010013. [PMID: 31861790 PMCID: PMC7022856 DOI: 10.3390/microorganisms8010013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/13/2019] [Accepted: 12/16/2019] [Indexed: 12/18/2022] Open
Abstract
In the thermophilic biogas-producing microbial community, the genus Methanothermobacter was previously described to be frequently abundant. The aim of this study was to establish and analyze the genome sequence of the archaeal strain Methanothermobacter wolfeii SIV6 originating from a thermophilic industrial-scale biogas fermenter and compare it to related reference genomes. The circular chromosome has a size of 1,686,891 bases, featuring a GC content of 48.89%. Comparative analyses considering three completely sequenced Methanothermobacter strains revealed a core genome of 1494 coding sequences and 16 strain specific genes for M. wolfeii SIV6, which include glycosyltransferases and CRISPR/cas associated genes. Moreover, M. wolfeii SIV6 harbors all genes for the hydrogenotrophic methanogenesis pathway and genome-centered metatranscriptomics indicates the high metabolic activity of this strain, with 25.18% of all transcripts per million (TPM) belong to the hydrogenotrophic methanogenesis pathway and 18.02% of these TPM exclusively belonging to the mcr operon. This operon encodes the different subunits of the enzyme methyl-coenzyme M reductase (EC: 2.8.4.1), which catalyzes the final and rate-limiting step during methanogenesis. Finally, fragment recruitment of metagenomic reads from the thermophilic biogas fermenter on the SIV6 genome showed that the strain is abundant (1.2%) within the indigenous microbial community. Detailed analysis of the archaeal isolate M. wolfeii SIV6 indicates its role and function within the microbial community of the thermophilic biogas fermenter, towards a better understanding of the biogas production process and a microbial-based management of this complex process.
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11
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Levi Mortera S, Soggiu A, Vernocchi P, Del Chierico F, Piras C, Carsetti R, Marzano V, Britti D, Urbani A, Roncada P, Putignani L. Metaproteomic investigation to assess gut microbiota shaping in newborn mice: A combined taxonomic, functional and quantitative approach. J Proteomics 2019; 203:103378. [PMID: 31102759 DOI: 10.1016/j.jprot.2019.103378] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/23/2019] [Accepted: 05/13/2019] [Indexed: 12/16/2022]
Abstract
Breastfeeding is nowadays known to be one of the most critical factors contributing to the development of an efficient immune system. In the last decade, a consistent number of pieces of evidence demonstrated the relationship between a healthy organism and its gut microbiota. However, this link is still not fully understood and requires further investigation. We recently adopted a murine model to describe the impact of either maternal milk or parental genetic background, on the composition of the gut microbial population in the first weeks of life. A metaproteomic approach to such complex environments is a big challenge that requires a strong effort in both data production and analysis, including the set-up of dedicated multitasking bioinformatics pipelines. Herein we present an LC-MS/MS based investigation to monitor mouse gut microbiota in the early life, aiming at characterizing its functions and metabolic activities together with a taxonomic description in terms of operational taxonomic units. We provided a quantitative evaluation of bacterial metaproteins, taking into account differential expression results in relation to the functional and taxonomic classification, particularly with proteins from orthologues groups. This allowed the reduction of the bias arising from the presence of a high number of shared peptides, and proteins, among different bacterial species. We also focused on host mucosal proteome and its modulation, according to different microbiota composition. SIGNIFICANCE: This paper would represent a reference work for investigations on gut microbiota in early life, from both a microbiological and a functional proteomic point of view. We focused on the shaping of the mouse gut microbiota in dependence on the feeding modality, defining a reliable taxonomic description, highlighting some functional characteristics of the microbial community, and performing a first quantitative evaluation by data independent analysis in metaproteomics.
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Affiliation(s)
| | - Alessio Soggiu
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - Pamela Vernocchi
- Human Microbiome Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Cristian Piras
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - Rita Carsetti
- B cell Pathophysiology Unit, Immunology Research Area and Unit of Diagnostic Immunology, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Valeria Marzano
- Human Microbiome Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Domenico Britti
- C.I.S. - Interdepartmental Services Centre of Veterinary for Human and Animal Health, University of Catanzaro "Magna Græcia", Catanzaro, Italy.; Department of Health Sciences, University of Catanzaro "Magna Græcia", Catanzaro, Italy
| | - Andrea Urbani
- Catholic University of Sacred Heart, Rome, Italy; Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Paola Roncada
- Department of Health Sciences, University of Catanzaro "Magna Græcia", Catanzaro, Italy
| | - Lorenza Putignani
- Parasitology Unit and Human Microbiome Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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12
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Hassa J, Maus I, Off S, Pühler A, Scherer P, Klocke M, Schlüter A. Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants. Appl Microbiol Biotechnol 2018; 102:5045-5063. [PMID: 29713790 PMCID: PMC5959977 DOI: 10.1007/s00253-018-8976-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 12/15/2022]
Abstract
The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.
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Affiliation(s)
- Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Sandra Off
- Dept. Biotechnologie, Hochschule für angewandte Wissenschaften (HAW) Hamburg Ulmenliet 20, 21033, Hamburg, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Paul Scherer
- Dept. Biotechnologie, Hochschule für angewandte Wissenschaften (HAW) Hamburg Ulmenliet 20, 21033, Hamburg, Germany
| | - Michael Klocke
- Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469, Potsdam, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany.
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13
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Hassa J, Maus I, Off S, Pühler A, Scherer P, Klocke M, Schlüter A. Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants. Appl Microbiol Biotechnol 2018. [PMID: 29713790 DOI: 10.1007/s00253-018-8976-7)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.
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Affiliation(s)
- Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Sandra Off
- Dept. Biotechnologie, Hochschule für angewandte Wissenschaften (HAW) Hamburg Ulmenliet 20, 21033, Hamburg, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Paul Scherer
- Dept. Biotechnologie, Hochschule für angewandte Wissenschaften (HAW) Hamburg Ulmenliet 20, 21033, Hamburg, Germany
| | - Michael Klocke
- Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469, Potsdam, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany.
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14
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Maus I, Rumming M, Bergmann I, Heeg K, Pohl M, Nettmann E, Jaenicke S, Blom J, Pühler A, Schlüter A, Sczyrba A, Klocke M. Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:167. [PMID: 29951113 PMCID: PMC6010159 DOI: 10.1186/s13068-018-1162-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/01/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND Previous studies on the Miscellaneous Crenarchaeota Group, recently assigned to the novel archaeal phylum Bathyarchaeota, reported on the dominance of these Archaea within the anaerobic carbohydrate cycle performed by the deep marine biosphere. For the first time, members of this phylum were identified also in mesophilic and thermophilic biogas-forming biofilms and characterized in detail. RESULTS Metagenome shotgun libraries of biofilm microbiomes were sequenced using the Illumina MiSeq system. Taxonomic classification revealed that between 0.1 and 2% of all classified sequences were assigned to Bathyarchaeota. Individual metagenome assemblies followed by genome binning resulted in the reconstruction of five metagenome-assembled genomes (MAGs) of Bathyarchaeota. MAGs were estimated to be 65-92% complete, ranging in their genome sizes from 1.1 to 2.0 Mb. Phylogenetic classification based on core gene sets confirmed their placement within the phylum Bathyarchaeota clustering as a separate group diverging from most of the recently known Bathyarchaeota clusters. The genetic repertoire of these MAGs indicated an energy metabolism based on carbohydrate and amino acid fermentation featuring the potential for extracellular hydrolysis of cellulose, cellobiose as well as proteins. In addition, corresponding transporter systems were identified. Furthermore, genes encoding enzymes for the utilization of carbon monoxide and/or carbon dioxide via the Wood-Ljungdahl pathway were detected. CONCLUSIONS For the members of Bathyarchaeota detected in the biofilm microbiomes, a hydrolytic lifestyle is proposed. This is the first study indicating that Bathyarchaeota members contribute presumably to hydrolysis and subsequent fermentation of organic substrates within biotechnological biogas production processes.
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Affiliation(s)
- Irena Maus
- Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Madis Rumming
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
- Computational Metagenomics, Faculty of Technology, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Ingo Bergmann
- Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Kathrin Heeg
- Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Marcel Pohl
- Biochemical Conversion Department, Deutsches Biomasseforschungszentrum gemeinnützige GmbH, Torgauer Straße 116, 04347 Leipzig, Germany
| | - Edith Nettmann
- Urban Water Management and Environmental Engineering, Faculty of Civil and Environmental Engineering, Ruhr University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Sebastian Jaenicke
- Dept. Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Jochen Blom
- Dept. Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
- Computational Metagenomics, Faculty of Technology, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Michael Klocke
- Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
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15
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Bomble YJ, Lin CY, Amore A, Wei H, Holwerda EK, Ciesielski PN, Donohoe BS, Decker SR, Lynd LR, Himmel ME. Lignocellulose deconstruction in the biosphere. Curr Opin Chem Biol 2017; 41:61-70. [DOI: 10.1016/j.cbpa.2017.10.013] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 12/18/2022]
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16
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Jünemann S, Kleinbölting N, Jaenicke S, Henke C, Hassa J, Nelkner J, Stolze Y, Albaum SP, Schlüter A, Goesmann A, Sczyrba A, Stoye J. Bioinformatics for NGS-based metagenomics and the application to biogas research. J Biotechnol 2017; 261:10-23. [PMID: 28823476 DOI: 10.1016/j.jbiotec.2017.08.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 12/19/2022]
Abstract
Metagenomics has proven to be one of the most important research fields for microbial ecology during the last decade. Starting from 16S rRNA marker gene analysis for the characterization of community compositions to whole metagenome shotgun sequencing which additionally allows for functional analysis, metagenomics has been applied in a wide spectrum of research areas. The cost reduction paired with the increase in the amount of data due to the advent of next-generation sequencing led to a rapidly growing demand for bioinformatic software in metagenomics. By now, a large number of tools that can be used to analyze metagenomic datasets has been developed. The Bielefeld-Gießen center for microbial bioinformatics as part of the German Network for Bioinformatics Infrastructure bundles and imparts expert knowledge in the analysis of metagenomic datasets, especially in research on microbial communities involved in anaerobic digestion residing in biogas reactors. In this review, we give an overview of the field of metagenomics, introduce into important bioinformatic tools and possible workflows, accompanied by application examples of biogas surveys successfully conducted at the Center for Biotechnology of Bielefeld University.
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Affiliation(s)
- Sebastian Jünemann
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany; Faculty of Technology, Bielefeld University, Bielefeld, Germany.
| | - Nils Kleinbölting
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Sebastian Jaenicke
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany; Bioinformatics and Systems Biology, Justus-Liebig-Universität, Gießen, Germany
| | - Christian Henke
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Johanna Nelkner
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Yvonne Stolze
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Stefan P Albaum
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-Universität, Gießen, Germany
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany; Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Jens Stoye
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany; Faculty of Technology, Bielefeld University, Bielefeld, Germany
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17
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Maus I, Bremges A, Stolze Y, Hahnke S, Cibis KG, Koeck DE, Kim YS, Kreubel J, Hassa J, Wibberg D, Weimann A, Off S, Stantscheff R, Zverlov VV, Schwarz WH, König H, Liebl W, Scherer P, McHardy AC, Sczyrba A, Klocke M, Pühler A, Schlüter A. Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:264. [PMID: 29158776 PMCID: PMC5684752 DOI: 10.1186/s13068-017-0947-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 11/01/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND To elucidate biogas microbial communities and processes, the application of high-throughput DNA analysis approaches is becoming increasingly important. Unfortunately, generated data can only partialy be interpreted rudimentary since databases lack reference sequences. RESULTS Novel cellulolytic, hydrolytic, and acidogenic/acetogenic Bacteria as well as methanogenic Archaea originating from different anaerobic digestion communities were analyzed on the genomic level to assess their role in biomass decomposition and biogas production. Some of the analyzed bacterial strains were recently described as new species and even genera, namely Herbinix hemicellulosilytica T3/55T, Herbinix luporum SD1DT, Clostridium bornimense M2/40T, Proteiniphilum saccharofermentans M3/6T, Fermentimonas caenicola ING2-E5BT, and Petrimonas mucosa ING2-E5AT. High-throughput genome sequencing of 22 anaerobic digestion isolates enabled functional genome interpretation, metabolic reconstruction, and prediction of microbial traits regarding their abilities to utilize complex bio-polymers and to perform specific fermentation pathways. To determine the prevalence of the isolates included in this study in different biogas systems, corresponding metagenome fragment mappings were done. Methanoculleus bourgensis was found to be abundant in three mesophilic biogas plants studied and slightly less abundant in a thermophilic biogas plant, whereas Defluviitoga tunisiensis was only prominent in the thermophilic system. Moreover, several of the analyzed species were clearly detectable in the mesophilic biogas plants, but appeared to be only moderately abundant. Among the species for which genome sequence information was publicly available prior to this study, only the species Amphibacillus xylanus, Clostridium clariflavum, and Lactobacillus acidophilus are of importance for the biogas microbiomes analyzed, but did not reach the level of abundance as determined for M. bourgensis and D. tunisiensis. CONCLUSIONS Isolation of key anaerobic digestion microorganisms and their functional interpretation was achieved by application of elaborated cultivation techniques and subsequent genome analyses. New isolates and their genome information extend the repository covering anaerobic digestion community members.
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Affiliation(s)
- Irena Maus
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Andreas Bremges
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
- Faculty of Technology, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Brunswick, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunscheig, Inhoffenstraße 7, 38124 Brunswick, Germany
| | - Yvonne Stolze
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Sarah Hahnke
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Katharina G. Cibis
- Johannes Gutenberg-University, Institute of Microbiology and Wine Research, Johann-Joachim Becherweg 15, 55128 Mainz, Germany
| | - Daniela E. Koeck
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Yong S. Kim
- Faculty Life Sciences/Research Center ‘Biomass Utilization Hamburg’, University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany
| | - Jana Kreubel
- Johannes Gutenberg-University, Institute of Microbiology and Wine Research, Johann-Joachim Becherweg 15, 55128 Mainz, Germany
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Aaron Weimann
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Brunswick, Germany
| | - Sandra Off
- Faculty Life Sciences/Research Center ‘Biomass Utilization Hamburg’, University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany
| | - Robbin Stantscheff
- Johannes Gutenberg-University, Institute of Microbiology and Wine Research, Johann-Joachim Becherweg 15, 55128 Mainz, Germany
- Institut für Forensische Genetik GmbH, Im Derdel 8, 48168 Münster, Germany
| | - Vladimir V. Zverlov
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
- Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, Moscow, 123182 Russia
| | - Wolfgang H. Schwarz
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Helmut König
- Johannes Gutenberg-University, Institute of Microbiology and Wine Research, Johann-Joachim Becherweg 15, 55128 Mainz, Germany
| | - Wolfgang Liebl
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Paul Scherer
- Faculty Life Sciences/Research Center ‘Biomass Utilization Hamburg’, University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany
| | - Alice C. McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Brunswick, Germany
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
- Faculty of Technology, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Michael Klocke
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
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