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Wunderer M, Markt R, Lackner N, Wagner AO. The glutamyl tail length of the cofactor F 420 in the methanogenic Archaea Methanosarcina thermophila and Methanoculleus thermophilus. Sci Total Environ 2022; 809:151112. [PMID: 34688753 DOI: 10.1016/j.scitotenv.2021.151112] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/01/2021] [Accepted: 10/17/2021] [Indexed: 06/13/2023]
Abstract
The cofactor F420 is synthesized by many different organisms and as a redox cofactor, it plays a crucial role in the redox reactions of catabolic and biosynthetic metabolic pathways. It consists of a deazaflavin structure, which is linked via lactate to an oligoglutamate chain, that can vary in length. In the present study, the methanogenic Archaea Methanosarcina thermophila and Methanoculleus thermophilus were cultivated on different carbon sources and their coenzyme F420 composition has been assayed by reversed-phase ion-pair high-performance liquid chromatography with fluorometric detection regarding both, overall cofactor F420 production and distribution of F420 glutamyl tail length. In Methanosarcina thermophila cultivated on methanol, acetate, and a mixture of acetate and methanol, the most abundant cofactors were F420-5 and F420-4, whereby the last digit refers to the number of expressed glutamyl rests. By contrast, in the obligate CO2 reducing Methanoculleus thermophilus the most abundant cofactors were F420-3 and F420-4. In Methanosarcina thermophila, the relative proportions of the expressed F420 tail length changed during batch growth on all three carbon sources. Over time F420-3 and F420-4 decreased while F420-5 and F420-6 increased in their relative proportion in comparison to total F420 content. In contrast, in Methanoculleus thermophilus the relative abundance of the different F420 cofactors remained stable. It was also possible to differentiate the two methanogenic Archaea based on the glutamyl tail length of the cofactor F420. The cofactor F420-5 in concentrations >2% could only be assigned to Methanosarcina thermophila. In all four variants a trend for a positive correlation between the DNA concentration and the total concentration of the cofactor could be shown. Except for the variant Methanosarcinathermophila with acetate as sole carbon source the same could be shown between the concentration of the mcrA gene copy number and the total concentration of the cofactor.
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Affiliation(s)
- Mathias Wunderer
- Universität Innsbruck, Department of Microbiology, Technikerstraße 25d, 6020 Innsbruck, Austria.
| | - Rudolf Markt
- Universität Innsbruck, Department of Microbiology, Technikerstraße 25d, 6020 Innsbruck, Austria
| | - Nina Lackner
- Universität Innsbruck, Department of Microbiology, Technikerstraße 25d, 6020 Innsbruck, Austria
| | - Andreas O Wagner
- Universität Innsbruck, Department of Microbiology, Technikerstraße 25d, 6020 Innsbruck, Austria
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Markt R, Endler L, Amman F, Schedl A, Penz T, Büchel-Marxer M, Grünbacher D, Mayr M, Peer E, Pedrazzini M, Rauch W, Wagner AO, Allerberger F, Bergthaler A, Insam H. Detection and abundance of SARS-CoV-2 in wastewater in Liechtenstein, and the estimation of prevalence and impact of the B.1.1.7 variant. J Water Health 2022; 20:114-125. [PMID: 35100159 DOI: 10.2166/wh.2021.180] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The new coronavirus 2 (SARS-CoV-2) is known to be also shed through feces, which makes wastewater-based surveillance possible, independent of symptomatic cases and unbiased by any testing strategies and frequencies. We investigated the entire population of the Principality of Liechtenstein with samples from the wastewater treatment plant Bendern (serving all 39,000 inhabitants). Twenty-four-hour composite samples were taken once or twice a week over a period of 6 months from September 2020 to March 2021. Viral RNA was concentrated using the PEG centrifugation method followed by reverse transcription quantitative PCR. The aim of this research was to assess the suitability of SARS-CoV-2 fragments to relate the viral wastewater signal to the incidences and assess the impact of the emerging B.1.1.7. variant. The viral load in the wastewater peaked at almost 9 × 108 viral fragments per person equivalent (PE) and day on October 25, and showed a second peak on December 22 reaching a viral load of approximately 2 × 108 PE-1d-1. Individual testing showed a lag of 4 days and a distinct underestimation of cases at the first peak when testing frequency was low. The wastewater signal showed an immediate response to the implementation of non-pharmaceutical interventions. The new virus variant B.1.1.7. was first detected in wastewater on December 23, while it was first observed with individual testing on January 13, 2021. Further, our data indicate that the emergence of new virus variant may change the wastewater signal, probably due to different shedding patterns, which should be considered in future models.
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Affiliation(s)
- R Markt
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria E-mail:
| | - L Endler
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, Vienna 1090, Austria
| | - F Amman
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, Vienna 1090, Austria
| | - A Schedl
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, Vienna 1090, Austria
| | - T Penz
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, Vienna 1090, Austria
| | - M Büchel-Marxer
- Ministry of Social Affairs and Culture, Peter-Kaiser-Platz 1, Vaduz 9490, Principality of Liechtenstein
| | - D Grünbacher
- Unit of Environmental Engineering, Department of Infrastructure, Universität Innsbruck, Technikerstraße 13, Innsbruck 6020, Austria
| | - M Mayr
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria E-mail:
| | - E Peer
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria E-mail:
| | - M Pedrazzini
- Ministry of Social Affairs and Culture, Peter-Kaiser-Platz 1, Vaduz 9490, Principality of Liechtenstein
| | - W Rauch
- Unit of Environmental Engineering, Department of Infrastructure, Universität Innsbruck, Technikerstraße 13, Innsbruck 6020, Austria
| | - A O Wagner
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria E-mail:
| | - F Allerberger
- Austrian Agency for Health and Food Safety (AGES), Vienna 1220, Austria
| | - A Bergthaler
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, Vienna 1090, Austria
| | - H Insam
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria E-mail:
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3
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Markt R, Mayr M, Peer E, Wagner AO, Lackner N, Insam H. Detection and Stability of SARS-CoV-2 Fragments in Wastewater: Impact of Storage Temperature. Pathogens 2021; 10:1215. [PMID: 34578246 PMCID: PMC8471725 DOI: 10.3390/pathogens10091215] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/02/2022] Open
Abstract
SARS-CoV-2 wastewater epidemiology suffers from uncertainties concerning sample storage. We show the effect of the storage of wastewater on the detectable SARS-CoV-2 load. Storage at 4 °C for up to 9 days had no significant effect, while storage at -20 °C led to a significant reduction in gene copy numbers.
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Affiliation(s)
- Rudolf Markt
- Department of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria; (M.M.); (E.P.); (A.O.W.); (N.L.); (H.I.)
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4
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Markt R, Mayr M, Peer E, Wagner AO, Lackner N, Insam H. Detection and Stability of SARS-CoV-2 Fragments in Wastewater: Impact of Storage Temperature. Pathogens 2021; 10. [PMID: 34578246 DOI: 10.1101/2021.02.22.21250768] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 05/21/2023] Open
Abstract
SARS-CoV-2 wastewater epidemiology suffers from uncertainties concerning sample storage. We show the effect of the storage of wastewater on the detectable SARS-CoV-2 load. Storage at 4 °C for up to 9 days had no significant effect, while storage at -20 °C led to a significant reduction in gene copy numbers.
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Affiliation(s)
- Rudolf Markt
- Department of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Markus Mayr
- Department of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Evelyn Peer
- Department of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Andreas O Wagner
- Department of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Nina Lackner
- Department of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Heribert Insam
- Department of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
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Margesin R, Volgger G, Wagner AO, Zhang D, Poyntner C. Biodegradation of lignin monomers and bioconversion of ferulic acid to vanillic acid by Paraburkholderia aromaticivorans AR20-38 isolated from Alpine forest soil. Appl Microbiol Biotechnol 2021; 105:2967-2977. [PMID: 33687503 PMCID: PMC8007519 DOI: 10.1007/s00253-021-11215-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/10/2021] [Accepted: 02/28/2021] [Indexed: 11/24/2022]
Abstract
Abstract Lignin bio-valorization is an emerging field of applied biotechnology and has not yet been studied at low temperatures. Paraburkholderia aromaticivorans AR20-38 was examined for its potential to degrade six selected lignin monomers (syringic acid, p-coumaric acid, 4-hydroxybenzoic acid, ferulic acid, vanillic acid, benzoic acid) from different upper funneling aromatic pathways. The strain degraded four of these compounds at 10°C, 20°C, and 30°C; syringic acid and vanillic acid were not utilized as sole carbon source. The degradation of 5 mM and 10 mM ferulic acid was accompanied by the stable accumulation of high amounts of the value-added product vanillic acid (85–89% molar yield; 760 and 1540 mg l−1, respectively) over the whole temperature range tested. The presence of essential genes required for reactions in the upper funneling pathways was confirmed in the genome. This is the first report on biodegradation of lignin monomers and the stable vanillic acid production at low and moderate temperatures by P. aromaticivorans. Key points • Paraburkholderia aromaticivorans AR20-38 successfully degrades four lignin monomers. • Successful degradation study at low (10°C) and moderate temperatures (20–30°C). • Biotechnological value: high yield of vanillic acid produced from ferulic acid.
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Affiliation(s)
- Rosa Margesin
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
| | - Georg Volgger
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Andreas O Wagner
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Dechao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Caroline Poyntner
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
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Mutschlechner M, Lackner N, Markt R, Salvenmoser W, Dunlap CA, Wagner AO. Proposal of Thermoactinomyces mirandus sp. nov., a filamentous, anaerobic bacterium isolated from a biogas plant. Antonie Van Leeuwenhoek 2020; 114:45-54. [PMID: 33215328 PMCID: PMC7840651 DOI: 10.1007/s10482-020-01497-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/04/2020] [Indexed: 11/24/2022]
Abstract
We isolated a filamentous, thermophilic, and first anaerobic representative of the genus Thermoactinomyces, designated strain AMNI-1T, from a biogas plant in Tyrol, Austria and report the results of a phenotypic, genetic, and phylogenetic investigation. Strain AMNI-1T was observed to form a white branching mycelium that aggregates into pellets when grown in liquid medium. Cells could primarily utilize lactose, glucose, and mannose as carbon and energy sources, with acetate accelerating and yeast extract being mandatory for growth. The optimum growth temperature and pH turned out to be 55 °C and pH 7.0, respectively, with an optimum NaCl concentration of 0–2% (w/v). 16S rRNA gene sequence comparison indicated that the genetic relatedness between strain AMNI-1T and Thermoactinomyces intermedius, Thermoactinomyces khenchelensis, and Thermoactinomyces vulgaris was less than 97%. The G + C content of the genomic DNA was 44.7 mol%. The data obtained suggest that the isolate represents a novel and first anaerobic species of the genus Thermoactinomyces, for which the name Thermoactinomyces mirandus is proposed. The type strain is AMNI-1T (= DSM 110094T = LMG 31503T). The description of the genus Thermoactinomyces is emended accordingly.
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Affiliation(s)
- Mira Mutschlechner
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020, Innsbruck, Austria.
| | - Nina Lackner
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020, Innsbruck, Austria
| | - Rudolf Markt
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020, Innsbruck, Austria
| | - Willi Salvenmoser
- Department of Zoology, Universität Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria
| | - Christopher A Dunlap
- Crop Bioprotection Research Unit, Agricultural Research Service, US Department of Agriculture, National Center for Agricultural Utilization Research, Peoria, IL, 61604, USA
| | - Andreas O Wagner
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020, Innsbruck, Austria
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Lackner N, Wagner AO, Illmer P. Effect of sulfate addition on carbon flow and microbial community composition during thermophilic digestion of cellulose. Appl Microbiol Biotechnol 2020; 104:4605-4615. [PMID: 32219464 PMCID: PMC7190589 DOI: 10.1007/s00253-020-10546-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 01/20/2020] [Accepted: 03/15/2020] [Indexed: 01/04/2023]
Abstract
Substrates with high sulfate levels pose problems for biogas production as they allow sulfate reducing bacteria to compete with syntrophic and methanogenic members of the community. In addition, the end product of sulfate reduction, hydrogen sulfide, is toxic and corrosive. Here we show how sulfate addition affects physiological processes in a thermophilic methanogenic system by analyzing the carbon flow and the microbial community with quantitative PCR and amplicon sequencing of the 16s rRNA gene. A sulfate addition of 0.5 to 3 g/L caused a decline in methane production by 73-92%, while higher sulfate concentrations had no additional inhibitory effect. Generally, sulfate addition induced a shift in the composition of the microbial community towards a higher dominance of Firmicutes and decreasing abundances of Bacteroidetes and Euryarchaeota. The abundance of methanogens (e.g., Methanoculleus and Methanosarcina) was reduced, while sulfate reducing bacteria (especially Candidatus Desulforudis and Desulfotomaculum) increased significantly in presence of sulfate. The sulfate addition had a significant impact on the carbon flow within the system, shifting the end product from methane and carbon dioxide to acetate and carbon dioxide. Interestingly, methane production quickly resumed, when sulfate was no longer present in the system. Despite the strong impact of sulfate addition on the carbon flow and the microbial community structure during thermophilic biogas production, short-term process disturbances caused by unexpected introduction of sulfate may be overcome due to the high resilience of the engaged microorganisms.
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Affiliation(s)
- Nina Lackner
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020, Innsbruck, Austria.
| | - Andreas O Wagner
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020, Innsbruck, Austria
| | - Paul Illmer
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020, Innsbruck, Austria
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Lackner N, Wagner AO, Markt R, Illmer P. pH and Phosphate Induced Shifts in Carbon Flow and Microbial Community during Thermophilic Anaerobic Digestion. Microorganisms 2020; 8:E286. [PMID: 32093251 PMCID: PMC7074938 DOI: 10.3390/microorganisms8020286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 01/11/2023] Open
Abstract
pH is a central environmental factor influencing CH4 production from organic substrates, as every member of the complex microbial community has specific pH requirements. Here, we show how varying pH conditions (5.0-8.5, phosphate buffered) and the application of a phosphate buffer per se induce shifts in the microbial community composition and the carbon flow during nine weeks of thermophilic batch digestion. Beside monitoring the methane production as well as volatile fatty acid concentrations, amplicon sequencing of the 16S rRNA gene was conducted. The presence of 100 mM phosphate resulted in reduced CH4 production during the initial phase of the incubation, which was characterized by a shift in the dominant methanogenic genera from a mixed Methanosarcina and Methanoculleus to a pure Methanoculleus system. In buffered samples, acetate strongly accumulated in the beginning of the batch digestion and subsequently served as a substrate for methanogens. Methanogenesis was permanently inhibited at pH values ≤5.5, with the maximum CH4 production occurring at pH 7.5. Adaptations of the microbial community to the pH variations included shifts in the archaeal and bacterial composition, as less competitive organisms with a broad pH range were able to occupy metabolic niches at unfavorable pH conditions.
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Affiliation(s)
- Nina Lackner
- Department of Microbiology, Universität Innsbruck, 6020 Innsbruck, Austria; (A.O.W.); (R.M.); (P.I.)
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Wagner AO, Markt R, Mutschlechner M, Lackner N, Prem EM, Praeg N, Illmer P. Medium Preparation for the Cultivation of Microorganisms under Strictly Anaerobic/Anoxic Conditions. J Vis Exp 2019:10.3791/60155. [PMID: 31475968 PMCID: PMC6796894 DOI: 10.3791/60155] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In contrast to aerobic organisms, strictly anaerobic microorganisms require the absence of oxygen and usually a low redox potential to initiate growth. As oxygen is ubiquitous in air, retaining O2-free conditions during all steps of cultivation is challenging but a prerequisite for anaerobic culturing. The protocol presented here demonstrates the successful cultivation of an anaerobic mixed culture derived from a biogas plant using a simple and inexpensive method. A precise description of the entire anoxic culturing process is given including media preparation, filling of cultivation flasks, supplementation with redox indicator and reducing agents to provide low redox potentials as well as exchanging the headspace to keep media free from oxygen. Furthermore, a detailed overview of aseptically inoculating gas tight serum flasks (by using sterile syringes and needles) and suitable incubation conditions is provided. The present protocol further deals with gas and liquid sampling for subsequent analyses regarding gas composition and volatile fatty acid concentrations using gas chromatography (GC) and high performance liquid chromatography (HPLC), respectively, and the calculation of biogas and methane yield considering the ideal gas law.
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Affiliation(s)
| | - Rudolf Markt
- Department of Microbiology, Universität Innsbruck
| | | | - Nina Lackner
- Department of Microbiology, Universität Innsbruck
| | - Eva M Prem
- Department of Microbiology, Universität Innsbruck
| | - Nadine Praeg
- Department of Microbiology, Universität Innsbruck
| | - Paul Illmer
- Department of Microbiology, Universität Innsbruck
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Wagner AO, Markt R, Puempel T, Illmer P, Insam H, Ebner C. Sample preparation, preservation, and storage for volatile fatty acid quantification in biogas plants. Eng Life Sci 2016; 17:132-139. [PMID: 32624760 DOI: 10.1002/elsc.201600095] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 06/24/2016] [Accepted: 07/12/2016] [Indexed: 11/10/2022] Open
Abstract
Volatile fatty acids (VFA) represent short-chain fatty acids consisting of six or fewer carbon atoms that can be distilled at atmospheric pressure. In anaerobic digestion processes VFAs are of central importance for maintaining stable reactor performance and biogas production, are used as indicators for arising problems and are important process monitoring parameters. In the present study, sludge derived form a full-scale anaerobic digester of a wastewater treatment plant was spiked with formate, acetate, propionate, and butyrate in order to evaluate various commonly used techniques for VFA extraction, preservation, and storage. It was shown that VFA extraction after centrifugation warranted the highest recovery rates for spiked VFAs. Moreover, experiments clearly indicated the importance of a fast sample handling, including the necessity of immediate cooling of the samples. Chemical sample preservation within a narrow time frame or deep freezing emerged as an alternative to instant VFA extraction. Short-time storage of extracted VFA samples at + 4°C is an option for up to 7 days, for longer periods storage at -20°C was found to be applicable.
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Affiliation(s)
- Andreas O Wagner
- Institute of Microbiology University of Innsbruck Innsbruck Austria
| | - Rudolf Markt
- Institute of Microbiology University of Innsbruck Innsbruck Austria.,alpS GmbH Innsbruck Austria
| | - Thomas Puempel
- Institute of Microbiology University of Innsbruck Innsbruck Austria
| | - Paul Illmer
- Institute of Microbiology University of Innsbruck Innsbruck Austria
| | - Heribert Insam
- Institute of Microbiology University of Innsbruck Innsbruck Austria
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Reitschuler C, Spötl C, Hofmann K, Wagner AO, Illmer P. Archaeal Distribution in Moonmilk Deposits from Alpine Caves and Their Ecophysiological Potential. Microb Ecol 2016; 71:686-699. [PMID: 26790864 DOI: 10.1007/s00248-015-0727-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 12/27/2015] [Indexed: 06/05/2023]
Abstract
(Alpine) caves are, in general, windows into the Earth's subsurface. Frequently occurring structures in caves such as moonmilk (secondary calcite deposits) offer the opportunity to study intraterrestrial microbial communities, adapted to oligotrophic and cold conditions. This is an important research field regarding the dimensions of subsurface systems and cold regions on Earth. On a methodological level, moonmilk deposits from 11 caves in the Austrian Alps were collected aseptically and investigated using a molecular (qPCR and DGGE sequencing-based) methodology in order to study the occurrence, abundance, and diversity of the prevailing native Archaea community. Furthermore, these Archaea were enriched in complex media and studied regarding their physiology, with a media selection targeting different physiological requirements, e.g. methanogenesis and ammonia oxidation. The investigation of the environmental samples showed that all moonmilk deposits were characterized by the presence of the same few habitat-specific archaeal species, showing high abundances and constituting about 50 % of the total microbial communities. The largest fraction of these Archaea was ammonia-oxidizing Thaumarchaeota, while another abundant group was very distantly related to extremophilic Euryarchaeota (Moonmilk Archaea). The archaeal community showed a depth- and oxygen-dependent stratification. Archaea were much more abundant (around 80 %), compared to bacteria, in the actively forming surface part of moonmilk deposits, decreasing to about 5 % down to the bedrock. Via extensive cultivation efforts, it was possible to enrich the enigmatic Moonmilk Archaea and also AOA significantly above the level of bacteria. The most expedient prerequisites for cultivating Moonmilk Archaea were a cold temperature, oligotrophic conditions, short incubation times, a moonmilk surface inoculum, the application of erythromycin, and anaerobic (microaerophilic) conditions. On a physiological level, it seems that methanogenesis is of marginal importance, while ammonia oxidation and a still undiscovered metabolic pathway are vital elements in the (archaeal) moonmilk biome.
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Affiliation(s)
- Christoph Reitschuler
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria.
| | - Christoph Spötl
- Institute of Geology, University of Innsbruck, Innrain 52, A-6020, Innsbruck, Austria
| | - Katrin Hofmann
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria
| | - Andreas O Wagner
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria
| | - Paul Illmer
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria
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12
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Hofmann K, Pauli H, Praeg N, Wagner AO, Illmer P. Methane-cycling microorganisms in soils of a high-alpine altitudinal gradient. FEMS Microbiol Ecol 2016; 92:fiw009. [PMID: 26790465 DOI: 10.1093/femsec/fiw009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2016] [Indexed: 11/13/2022] Open
Abstract
Methanogens and methanotrophs play unique roles as producers and consumers of the greenhouse gas methane (CH4) in soils, respectively. Here, we aimed to reveal whether and to which extent methane-cyclers occur in high-alpine soils, and to assess their spatial distribution along an altitudinal gradient (2700-3500 m) in the Austrian Alps at sites located within the alpine (2700-2900 m), the alpine-nival (3000-3100 m) and the nival belts (3200-3500 m). Methanococcales and Methanocella spp. were most abundant among all quantified methanogenic guilds, whereas Methanosarcinales were not detected in the studied soil. The detected methanogens seem to be capable of persisting despite a highly oxic low-temperature environment. Methanogenic and methanotrophic activities and abundances of methanotrophs, Methanococcales and Methanocella spp. declined with altitude. Methanogenic and methanotrophic abundances were best explained by mean annual soil temperature and dissolved organic carbon, respectively. Alpine belt soils harbored significantly more methane-cyclers than those of the nival belt, indicating some influence of plant cover. Our results show that methanogens are capable of persisting in high-alpine cold soils and might help to understand future changes of these environments caused by climate warming.
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Affiliation(s)
- Katrin Hofmann
- Institute of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Harald Pauli
- Institute for Interdisciplinary Mountain Research, Austrian Academy of Sciences and Center for Global Change and Sustainability, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Nadine Praeg
- Institute of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Andreas O Wagner
- Institute of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Paul Illmer
- Institute of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
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Wagner AO, Praeg N, Reitschuler C, Illmer P. Effect of DNA extraction procedure, repeated extraction and ethidium monoazide (EMA)/propidium monoazide (PMA) treatment on overall DNA yield and impact on microbial fingerprints for bacteria, fungi and archaea in a reference soil. Appl Soil Ecol 2015; 93:56-64. [PMID: 26339125 PMCID: PMC4461152 DOI: 10.1016/j.apsoil.2015.04.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 04/01/2015] [Accepted: 04/04/2015] [Indexed: 05/21/2023]
Abstract
Different DNA extraction protocols were evaluated on a reference soil. A wide difference was found in the total extractable DNA as derived from different extraction protocols. Concerning the DNA yield phenol-chloroform-isomyl alcohol extraction resulted in high DNA yield but also in a remarkable co-extraction of contaminants making PCR from undiluted DNA extracts impossible. By comparison of two different extraction kits, the Macherey&Nagel SoilExtract II kit resulted in the highest DNA yields when buffer SL1 and the enhancer solution were applied. The enhancer solution not only significantly increased the DNA yield but also the amount of co-extracted contaminates, whereas additional disintegration strategies did not. Although a three times repeated DNA extraction increased the total amount of extracted DNA, microbial fingerprints were merely affected. However, with the 5th extraction this changed. A reduction of total DGGE band numbers was observed for archaea and fungi, whereas for bacteria the diversity increased. The application of ethidium monoazide (EMA) or propidium monoazide (PMA) treatment aiming on the selective removal of soil DNA derived from cells lacking cell wall integrity resulted in a significant reduction of total extracted DNA, however, the hypothesized effect on microbial fingerprints failed to appear indicating the need for further investigations.
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Affiliation(s)
- Andreas O. Wagner
- Corresponding author. Tel.: +43 512 507 51342; fax: +43 512 507 51398.
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Walter A, Franke-Whittle IH, Wagner AO, Insam H. Methane yields and methanogenic community changes during co-fermentation of cattle slurry with empty fruit bunches of oil palm. Bioresour Technol 2015; 175:619-23. [PMID: 25453442 DOI: 10.1016/j.biortech.2014.10.085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/16/2014] [Accepted: 10/17/2014] [Indexed: 05/28/2023]
Abstract
The biomethane potential and structural changes of the methanogenic community in a solid-state anaerobic digestion process co-digesting cattle slurry and empty fruit bunches were investigated under mesophilic (37°C) and thermophilic (55°C) conditions. Phylogenetic microarrays revealed the presence of two hydrogenotrophic genera (Methanoculleus and Methanobrevibacter) and one acetoclastic genus (Methanosarcina). Methanosarcina numbers were found to increase in both mesophilic and thermophilic treatments of empty fruit bunches. Methanobrevibacter, which dominated in the cattle slurry, remained constant during anaerobic digestion (AD) at 37°C and decreased in numbers during digestion at 55°C. Numbers of Methanoculleus remained constant at 37°C and increased during the thermophilic digestion. Physicochemical data revealed non-critical concentrations for important monitoring parameters such as total ammonia nitrogen, free ammonia nitrogen and volatile fatty acids in all treatments after AD. The biomethane potential of empty fruit bunches was higher under thermophilic conditions than under mesophilic conditions.
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Affiliation(s)
- Andreas Walter
- Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria; Hochschule Hamm-Lippstadt, Biotechnologie, Marker Allee 76-78, 59063 Hamm, Germany
| | - Ingrid H Franke-Whittle
- Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria
| | - Andreas O Wagner
- Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria
| | - Heribert Insam
- Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria
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Lins P, Schwarzenauer T, Reitschuler C, Wagner AO, Illmer P. Methanogenic potential of formate in thermophilic anaerobic digestion. Waste Manag Res 2012; 30:1031-40. [PMID: 22588113 DOI: 10.1177/0734242x12445655] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In the present study the methanogenic potential of formate (HCOO(-)) during thermophilic anaerobic digestion was investigated. After appropriate conditions for methanogenesis (HCOO(-) and inoculum concentration, pH and duration of incubation) were assessed, an experiment with initial 31 replicates was run. Diluted fermenter sludge was used as inoculum, and process parameters including the pH, quality and quantity of the produced biogas and the concentrations of volatile fatty acids and HCO(3) (-) were determined. Remarkably, after 5 days of incubation the highest CH(4) production was calculated for a HCOO(-) concentration of 200 mmol L(-1), a concentration, however, which might not occur in situ. During the phase of high CH(4) production HCOO(-) was degraded with a rate of 1.5 mmol L(-1) h(-1), and distinct changes of Gibbs free energy for several reactions were observed. Based on denaturing high-performance liquid chromatography, denaturing gradient gel electrophoresis, and additional subsequent sequencing approaches the hydrogenotrophic Methanothermobacter wolfeii was the dominant methanogen responsible for CH(4) production. Further confirmation was achieved due to the detection of autofluorescing rods with a size of up to ~3 µm, which were often arranged in pairs and chains. It was shown that even high concentrations of HCOO(-) are readily degraded, which might lead to an underestimation of both, the concentration and thus, the importance of HCOO(-) in anaerobic digestion.
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Affiliation(s)
- Philipp Lins
- University of Innsbruck, Institute of Microbiology, Innsbruck, Austria.
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Wagner AO, Hofmann K, Prem E, Illmer P. Methanogenic activities in alpine soils. Folia Microbiol (Praha) 2012; 57:371-3. [DOI: 10.1007/s12223-012-0145-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 01/04/2012] [Indexed: 10/28/2022]
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Wagner AO, Malin C, Lins P, Illmer P. Effects of various fatty acid amendments on a microbial digester community in batch culture. Waste Manag 2011; 31:431-7. [PMID: 21071199 DOI: 10.1016/j.wasman.2010.10.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 10/22/2010] [Accepted: 10/22/2010] [Indexed: 05/24/2023]
Abstract
Since biogas production is becoming increasingly important the understanding of anaerobic digestion processes is fundamental. However, large-scale digesters often lack online sensor equipment to monitor key parameters. Furthermore the possibility to selectively change fermenting parameter settings in order to investigate methane output or microbial changes is limited. In the present study we examined the possibility to investigate the microbial community of a large scale (750,000 L) digester within a laboratory small-scale approach. We studied the short-term response of the downscaled communities on various fatty acids and its effects on gas production and compared it with data from the original digester sludge. Even high loads of formic acid led to distinct methane formation, whereas high concentrations of other acids (acetic, butyric, propionic acid) caused a marked inhibition of methanogenesis coupled with an increase in hydrogen concentration. Molecular microbial techniques (DGGE/quantitative real-time-PCR) were used to monitor the microbial community changes which were related to data from GC and HPLC analysis. DGGE band patterns showed that the same microorganisms which were already dominant in the original digester re-established again in the lab-scale experiment. Very few microorganisms dominated the whole fermenting process and species diversity was not easily influenced by moderate varying fatty acid amendments--Methanoculleus thermophilus being the most abundant species throughout the variants. MCR-copy number determined via quantitative real-time-PCR--turned out to be a reliable parameter for quantification of methanogens, even in a very complex matrix like fermenter sludge. Generally the downscaled batch approach was shown to be appropriate to investigate microbial communities from large-scale digesters.
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Affiliation(s)
- Andreas O Wagner
- University of Innsbruck, Institute of Microbiology, Technikerstr. 25, A-6020 Innsbruck, Austria.
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Illmer P, Schwarzenauer T, Malin C, Wagner AO, Miller LM, Gstraunthaler G. Process parameters within a 750,000 litre anaerobic digester during a year of disturbed fermenter performance. Waste Manag 2009; 29:1838-43. [PMID: 19282166 DOI: 10.1016/j.wasman.2009.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Revised: 01/29/2009] [Accepted: 02/01/2009] [Indexed: 05/08/2023]
Abstract
A 750,000litre fermenter was studied throughout one entire year by investigating the concentrations of volatile fatty acids (acetic, butyric, i-butyric, propionic, valeric and i-valeric acids), pH, concentrations of total C, N, S and NH(4)(+)-N, amounts of chemical and biological oxygen demand, and abundance of acetogenic microorganisms. Additionally several process parameters such as temperature, retention time, dry weight and input of substrate and liquids, and the concentrations and amounts of CH(4), H(2), CO(2) and H(2)S within the biogas were monitored continuously. Various volatile fatty acids and the ratio of acetic to propionic acid were shown to allow a rough indication on the fermentation but were not sufficiently precise to describe the fermenter performance. Nutrient compounds and special fractions, such as easily extractable carbohydrates or the concentration of total fats were more strongly correlated to the gas production of the fermenter. Results of an MPN-method for the determination of acetogenic microorganisms point to an important role of these microorganisms during the phase of restoration of the fermenter performance.
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Affiliation(s)
- P Illmer
- University of Innsbruck, Institute of Microbiology, Technikerstr. 25, A-6020 Innsbruck, Austria.
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Mayrhofer S, Mikoviny T, Waldhuber S, Wagner AO, Innerebner G, Franke-Whittle IH, Märk TD, Hansel A, Insam H. Microbial community related to volatile organic compound (VOC) emission in household biowaste. Environ Microbiol 2006; 8:1960-74. [PMID: 17014495 DOI: 10.1111/j.1462-2920.2006.01076.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Malodorous emissions and potentially pathogenic microorganisms which develop during domestic organic waste collection are not only a nuisance but may also pose health risks. The aim of the present study was to determine whether the presence of specific microorganisms in biowastes is directly related to the composition of the emitted volatile organic compounds (VOCs). The succession of microbial communities during 16 days of storage in organic waste collection bins was studied by denaturing gradient gel electrophoresis (DGGE) of amplified 16S ribosomal DNA in parallel with a classical cultivation and isolation approach. Approximately 60 different bacterial species and 20 different fungal species were isolated. Additionally, some bacterial species were identified through sequencing of excised DGGE bands. Proton transfer reaction mass spectrometry (PTR-MS) was used to detect VOCs over the sampling periods, and co-inertia analyses of VOC concentrations with DGGE band intensities were conducted. Positive correlations, indicating production of the respective VOC or enhancement of microbial growth, and negative correlations, indicating the use of, or microbial inhibition by the respective compound, were found for the different VOCs. Measurement of the VOC emission pattern from a pure culture of Lactococcus lactis confirmed the positive correlations for the protonated masses 89 (tentatively identified as butyric acid), 63 (tentatively identified as dimethylsulfide), 69 (likely isoprene) and 73 (likely butanone).
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Affiliation(s)
- Sabine Mayrhofer
- Institut für Mikrobiologie, Universität Innsbruck, Innsbruck, Austria.
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