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Singh A, Müller B, Schnürer A. Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP. Sci Rep 2021; 11:13298. [PMID: 34168213 PMCID: PMC8225771 DOI: 10.1038/s41598-021-92658-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/14/2021] [Indexed: 02/06/2023] Open
Abstract
Acetogens play a key role in anaerobic degradation of organic material and in maintaining biogas process efficiency. Profiling this community and its temporal changes can help evaluate process stability and function, especially under disturbance/stress conditions, and avoid complete process failure. The formyltetrahydrofolate synthetase (FTHFS) gene can be used as a marker for acetogenic community profiling in diverse environments. In this study, we developed a new high-throughput FTHFS gene sequencing method for acetogenic community profiling and compared it with conventional terminal restriction fragment length polymorphism of the FTHFS gene, 16S rRNA gene-based profiling of the whole bacterial community, and indirect analysis via 16S rRNA profiling of the FTHFS gene-harbouring community. Analyses and method comparisons were made using samples from two laboratory-scale biogas processes, one operated under stable control and one exposed to controlled overloading disturbance. Comparative analysis revealed satisfactory detection of the bacterial community and its changes for all methods, but with some differences in resolution and taxonomic identification. FTHFS gene sequencing was found to be the most suitable and reliable method to study acetogenic communities. These results pave the way for community profiling in various biogas processes and in other environments where the dynamics of acetogenic bacteria have not been well studied.
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Affiliation(s)
- Abhijeet Singh
- grid.6341.00000 0000 8578 2742Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Almas Allé 5, Box 7025, 750 07 Uppsala, Sweden
| | - Bettina Müller
- grid.6341.00000 0000 8578 2742Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Almas Allé 5, Box 7025, 750 07 Uppsala, Sweden
| | - Anna Schnürer
- grid.6341.00000 0000 8578 2742Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Almas Allé 5, Box 7025, 750 07 Uppsala, Sweden
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Liu T, Schnürer A, Björkmalm J, Willquist K, Kreuger E. Diversity and Abundance of Microbial Communities in UASB Reactors during Methane Production from Hydrolyzed Wheat Straw and Lucerne. Microorganisms 2020; 8:E1394. [PMID: 32932830 PMCID: PMC7565072 DOI: 10.3390/microorganisms8091394] [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: 07/12/2020] [Revised: 09/04/2020] [Accepted: 09/09/2020] [Indexed: 01/04/2023] Open
Abstract
The use of straw for biofuel production is encouraged by the European Union. A previous study showed the feasibility of producing biomethane in upflow anaerobic sludge blanket (UASB) reactors using hydrolyzed, steam-pretreated wheat straw, before and after dark fermentation with Caldicellulosiruptor saccharolyticus, and lucerne. This study provides information on overall microbial community development in those UASB processes and changes related to acidification. The bacterial and archaeal community in granular samples was analyzed using high-throughput amplicon sequencing. Anaerobic digestion model no. 1 (ADM1) was used to predict the abundance of microbial functional groups. The sequencing results showed decreased richness and diversity in the microbial community, and decreased relative abundance of bacteria in relation to archaea, after process acidification. Canonical correspondence analysis showed significant negative correlations between the concentration of organic acids and three phyla, and positive correlations with seven phyla. Organic loading rate and total COD fed also showed significant correlations with microbial community structure, which changed over time. ADM1 predicted a decrease in acetate degraders after a decrease to pH ≤ 6.5. Acidification had a sustained effect on the microbial community and process performance.
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Affiliation(s)
- Tong Liu
- Department of Molecular Science, Swedish University of Agricultural Science, Uppsala BioCenter, 750 07 Uppsala, Sweden;
| | - Anna Schnürer
- Department of Molecular Science, Swedish University of Agricultural Science, Uppsala BioCenter, 750 07 Uppsala, Sweden;
| | - Johanna Björkmalm
- RISE, Forskningsbyn Ideon Scheelevägen 27, 223 70 Lund, Sweden; (J.B.); (K.W.)
| | - Karin Willquist
- RISE, Forskningsbyn Ideon Scheelevägen 27, 223 70 Lund, Sweden; (J.B.); (K.W.)
| | - Emma Kreuger
- Division of Biotechnology, Department of Chemistry, Lund University, P.O. Box 118, 221 00 Lund, Sweden
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Westerholm M, Müller B, Singh A, Karlsson Lindsjö O, Schnürer A. Detection of novel syntrophic acetate-oxidizing bacteria from biogas processes by continuous acetate enrichment approaches. Microb Biotechnol 2017; 11:680-693. [PMID: 29239113 PMCID: PMC6011928 DOI: 10.1111/1751-7915.13035] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/11/2017] [Accepted: 11/12/2017] [Indexed: 11/27/2022] Open
Abstract
To enrich syntrophic acetate‐oxidizing bacteria (SAOB), duplicate chemostats were inoculated with sludge from syntrophic acetate oxidation (SAO)‐dominated systems and continuously supplied with acetate (0.4 or 7.5 g l−1) at high‐ammonia levels. The chemostats were operated under mesophilic (37°C) or thermophilic (52°C) temperature for about six hydraulic retention times (HRT 28 days) and were sampled over time. Irrespective of temperature, a methane content of 64–69% and effluent acetate level of 0.4–1.0 g l−1 were recorded in chemostats fed high acetate. Low methane production in the low‐acetate chemostats indicated that the substrate supply was below the threshold for methanization of acetate via SAO. Novel representatives within the family Clostridiales and genus Syntrophaceticus (class Clostridia) were identified to represent putative SAOB candidates in mesophilic and thermophilic conditions respectively. Known SAOB persisted at low relative abundance in all chemostats. The hydrogenotrophic methanogens Methanoculleus bourgensis (mesophilic) and Methanothermobacter thermautotrophicus (thermophilic) dominated archaeal communities in the high‐acetate chemostats. In line with the restricted methane production in the low‐acetate chemostats, methanogens persisted at considerably lower abundance in these chemostats. These findings strongly indicate involvement in SAO and tolerance to high ammonia levels of the species identified here, and have implications for understanding community function in stressed anaerobic processes.
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Affiliation(s)
- Maria Westerholm
- Uppsala BioCenter, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7025, SE-750 07, Uppsala, Sweden
| | - Bettina Müller
- Uppsala BioCenter, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7025, SE-750 07, Uppsala, Sweden
| | - Abhijeet Singh
- Uppsala BioCenter, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7025, SE-750 07, Uppsala, Sweden
| | - Oskar Karlsson Lindsjö
- Uppsala BioCenter, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7025, SE-750 07, Uppsala, Sweden
| | - Anna Schnürer
- Uppsala BioCenter, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7025, SE-750 07, Uppsala, Sweden
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BEAP profiles as rapid test system for status analysis and early detection of process incidents in biogas plants. J Ind Microbiol Biotechnol 2017; 44:465-476. [PMID: 28064390 DOI: 10.1007/s10295-016-1894-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/22/2016] [Indexed: 11/26/2022]
Abstract
A method was developed to quantify the performance of microorganisms involved in different digestion levels in biogas plants. The test system was based on the addition of butyrate (BCON), ethanol (ECON), acetate (ACON) or propionate (PCON) to biogas sludge samples and the subsequent analysis of CH4 formation in comparison to control samples. The combination of the four values was referred to as BEAP profile. Determination of BEAP profiles enabled rapid testing of a biogas plant's metabolic state within 24 h and an accurate mapping of all degradation levels in a lab-scale experimental setup. Furthermore, it was possible to distinguish between specific BEAP profiles for standard biogas plants and for biogas reactors with process incidents (beginning of NH4+-N inhibition, start of acidification, insufficient hydrolysis and potential mycotoxin effects). Finally, BEAP profiles also functioned as a warning system for the early prediction of critical NH4+-N concentrations leading to a drop of CH4 formation.
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Koch K, Huber B, Bajón Fernández Y, Drewes JE. Methane from CO₂: Influence of different CO₂ concentrations in the flush gas on the methane production in BMP tests. WASTE MANAGEMENT (NEW YORK, N.Y.) 2016; 49:36-39. [PMID: 26818184 DOI: 10.1016/j.wasman.2016.01.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 01/17/2016] [Accepted: 01/17/2016] [Indexed: 06/05/2023]
Abstract
The influence of carbon dioxide (CO2) in the headspace gas on the specific methane (CH4) production of blank samples with just inoculum during Biochemical Methane Potential (BMP) tests was studied. The headspace of the bottles had been flushed with 15 different ratios of CO2 and N2 prior to incubation, while they were treated otherwise identically. The results revealed that the CH4 yield increased linearly with higher ratio of CO2 in the flush gas reaching a 30% higher yield at pure CO2 relative to pure N2 headspace conditions. However, a slightly distinct lag is noticeable during the initial phase of the degradation process at high ratios of CO2, hypothesizing a reversible disturbance of the biocenosis. Further experiments and analyses need to be performed to elucidate the underlying mechanisms.
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Affiliation(s)
- Konrad Koch
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 8, D-85748 Garching, Germany.
| | - Bettina Huber
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 8, D-85748 Garching, Germany; Bavarian State Research Center for Agriculture, Central Department for Quality Assurance and Analytics, Lange Point 6, D-85354 Freising, Germany
| | - Yadira Bajón Fernández
- Cranfield Water Science Institute, School of Energy, Environment and Agrifood, Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK
| | - Jörg E Drewes
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 8, D-85748 Garching, Germany
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Lebuhn M, Derenkó J, Rademacher A, Helbig S, Munk B, Pechtl A, Stolze Y, Prowe S, Schwarz WH, Schlüter A, Liebl W, Klocke M. DNA and RNA Extraction and Quantitative Real-Time PCR-Based Assays for Biogas Biocenoses in an Interlaboratory Comparison. Bioengineering (Basel) 2016; 3:bioengineering3010007. [PMID: 28952569 PMCID: PMC5597165 DOI: 10.3390/bioengineering3010007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/24/2015] [Indexed: 01/17/2023] Open
Abstract
Five institutional partners participated in an interlaboratory comparison of nucleic acid extraction, RNA preservation and quantitative Real-Time PCR (qPCR) based assays for biogas biocenoses derived from different grass silage digesting laboratory and pilot scale fermenters. A kit format DNA extraction system based on physical and chemical lysis with excellent extraction efficiency yielded highly reproducible results among the partners and clearly outperformed a traditional CTAB/chloroform/isoamylalcohol based method. Analytical purpose, sample texture, consistency and upstream pretreatment steps determine the modifications that should be applied to achieve maximum efficiency in the trade-off between extract purity and nucleic acid recovery rate. RNA extraction was much more variable, and the destination of the extract determines the method to be used. RNA stabilization with quaternary ammonium salts was an as satisfactory approach as flash freezing in liquid N2. Due to co-eluted impurities, spectrophotometry proved to be of limited value for nucleic acid qualification and quantification in extracts obtained with the kit, and picoGreen® based quantification was more trustworthy. Absorbance at 230 nm can be extremely high in the presence of certain chaotropic guanidine salts, but guanidinium isothiocyanate does not affect (q)PCR. Absolute quantification by qPCR requires application of a reliable internal standard for which correct PCR efficiency and Y-intercept values are important and must be reported.
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Affiliation(s)
- Michael Lebuhn
- Bavarian State Research Center for Agriculture, Department for Quality Assurance and Analytics, Lange Point 6, 85354 Freising, Germany.
| | - Jaqueline Derenkó
- Leibniz Institute for Agricultural Engineering Potsdam-Bornim, Department Bioengineering, Max-Eyth-Allee 100, 14469 Potsdam, Germany.
| | - Antje Rademacher
- Leibniz Institute for Agricultural Engineering Potsdam-Bornim, Department Bioengineering, Max-Eyth-Allee 100, 14469 Potsdam, Germany.
| | - Susanne Helbig
- Beuth University of Applied Sciences, Department of Life Sciences and Technology, Luxemburger Strasse 10, 13353 Berlin, Germany.
| | - Bernhard Munk
- Bavarian State Research Center for Agriculture, Department for Quality Assurance and Analytics, Lange Point 6, 85354 Freising, Germany.
| | - Alexander Pechtl
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, D-85354 Freising-Weihenstephan, Germany.
| | - Yvonne Stolze
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Bielefeld, Germany.
| | - Steffen Prowe
- Beuth University of Applied Sciences, Department of Life Sciences and Technology, Luxemburger Strasse 10, 13353 Berlin, Germany.
| | - Wolfgang H Schwarz
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, D-85354 Freising-Weihenstephan, Germany.
| | - Andreas Schlüter
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Bielefeld, Germany.
| | - Wolfgang Liebl
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, D-85354 Freising-Weihenstephan, Germany.
| | - Michael Klocke
- Leibniz Institute for Agricultural Engineering Potsdam-Bornim, Department Bioengineering, Max-Eyth-Allee 100, 14469 Potsdam, Germany.
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