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Effect of Alkaline and Mechanical Pretreatment of Wheat Straw on Enrichment Cultures from Pachnoda marginata Larva Gut. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9010060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In order to partially mimic the efficient lignocellulose pretreatment process performed naturally in the gut system of Pachnoda marginata larvae, two wheat straw pretreatments were evaluated: a mechanical pretreatment via cutting the straw into two different sizes and an alkaline pretreatment with calcium hydroxide. After pretreatment, gut enrichment cultures on wheat straw at alkaline pH were inoculated and kept at mesophilic conditions over 45 days. The methanogenic community was composed mainly of the Methanomicrobiaceae and Methanosarcinaceae families. The combined pretreatment, size reduction and alkaline pretreatment, was the best condition for methane production. The positive effect of the straw pretreatment was higher in the midgut cultures, increasing the methane production by 192%, while for hindgut cultures the methane production increased only by 149% when compared to non-pretreated straw. Scanning electron microscopy (SEM) showed that the alkaline pretreatment modified the surface of the wheat straw fibers, which promoted biofilm formation and microbial growth. The enrichment cultures derived from larva gut microbiome were able to degrade larger 1 mm alkaline treated and smaller 250 µm but non-pretreated straw at the same efficiency. The combination of mechanical and alkaline pretreatments resulted in increased, yet not superimposed, methane yield.
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2
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Dalby FR, Nikolausz M, Hansen MJ, Feilberg A. Effects of combined tannic acid/fluoride on sulfur transformations and methanogenic pathways in swine manure. PLoS One 2021; 16:e0257759. [PMID: 34555107 PMCID: PMC8459979 DOI: 10.1371/journal.pone.0257759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 09/10/2021] [Indexed: 01/04/2023] Open
Abstract
Livestock manure emits reduced sulfur compounds and methane, which affect nature and the climate. These gases are efficiently mitigated by addition of a tannic acid-sodium fluoride combination inhibitor (TA-NaF), and to some extent by acidification. In this paper, TA-NaF treatment was performed on swine manure to study the treatment influence on methanogenic pathways and sulfur transformation pathways in various laboratory experiments. Stable carbon isotope labeling revealed that both untreated and TA-NaF treated swine manures were dominated by hydrogenotrophic methanogenesis. However, in supplementary experiments in wastewater sludge, TA-NaF clearly inhibited acetoclastic methanogenesis, whereas acidification inhibited hydrogenotrophic methanogenesis. In swine manure, TA-NaF inhibited s-amino acid catabolism to a larger extent than sulfate reduction. Conversely, acidification reduced sulfate reduction activity more than s-amino acid degradation. TA-NaF treatment had no significant effect on methanogenic community structure, which was surprising considering clear effects on isotope ratios of methane and carbon dioxide. Halophile sulfate reducers adapted well to TA-NaF treatment, but the community change also depended on temperature. The combined experimental work resulted in a proposed inhibition scheme for sulfur transformations and methanogenic pathways as affected by TA-NaF and acidification in swine manure and in other inocula.
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Affiliation(s)
- Frederik Rask Dalby
- Department of Engineering, Air Quality Engineering, Aarhus University, Aarhus N, Denmark
| | - Marcell Nikolausz
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Michael Jørgen Hansen
- Department of Engineering, Air Quality Engineering, Aarhus University, Aarhus N, Denmark
| | - Anders Feilberg
- Department of Engineering, Air Quality Engineering, Aarhus University, Aarhus N, Denmark
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3
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Impact of Surface Properties of Porous SiOC‐Based Materials on the Performance of
Geobacter
Biofilm Anodes. ChemElectroChem 2021. [DOI: 10.1002/celc.202001568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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4
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Quejigo JR, Korth B, Kuchenbuch A, Harnisch F. Redox Potential Heterogeneity in Fixed-Bed Electrodes Leads to Microbial Stratification and Inhomogeneous Performance. CHEMSUSCHEM 2021; 14:1155-1165. [PMID: 33387375 PMCID: PMC7986606 DOI: 10.1002/cssc.202002611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/28/2020] [Indexed: 06/12/2023]
Abstract
Bed electrodes provide high electrode area-to-volume ratios represent a promising configuration for transferring bioelectrochemical systems close to industrial applications. Nevertheless, the intrinsic electrical resistance leads to poor polarization behavior. Therefore, the distribution of Geobacter spp. and their electrochemical performance within exemplary fixed-bed electrodes are investigated. A minimally invasive sampling system allows characterization of granules from different spatial locations of bed electrodes. Cyclic voltammetry of single granules (n=63) demonstrates that the major share of electroactivity (134.3 mA L-1 ) is achieved by approximately 10 % of the bed volume, specifically that being close to the current collector. Nevertheless, analysis of the microbial community reveals that Geobacter spp. dominated all sampled granules. These findings clearly demonstrate the need for engineered bed electrodes to improve electron exchange between microorganisms and granules.
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Affiliation(s)
- Jose Rodrigo Quejigo
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research GmbH – UFZPermoser Str. 1504318LeipzigGermany
| | - Benjamin Korth
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research GmbH – UFZPermoser Str. 1504318LeipzigGermany
| | - Anne Kuchenbuch
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research GmbH – UFZPermoser Str. 1504318LeipzigGermany
| | - Falk Harnisch
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research GmbH – UFZPermoser Str. 1504318LeipzigGermany
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5
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Korth B, Kuchenbuch A, Harnisch F. Availability of Hydrogen Shapes the Microbial Abundance in Biofilm Anodes based on
Geobacter
Enrichment. ChemElectroChem 2020. [DOI: 10.1002/celc.202000731] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Benjamin Korth
- Department of Environmental Microbiology Helmholtz Centre for Environmental Research GmbH – UFZ Permoser Str. 15 04318 Leipzig Germany
| | - Anne Kuchenbuch
- Department of Environmental Microbiology Helmholtz Centre for Environmental Research GmbH – UFZ Permoser Str. 15 04318 Leipzig Germany
| | - Falk Harnisch
- Department of Environmental Microbiology Helmholtz Centre for Environmental Research GmbH – UFZ Permoser Str. 15 04318 Leipzig Germany
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6
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De Vrieze J. The next frontier of the anaerobic digestion microbiome: From ecology to process control. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2020; 3:100032. [PMID: 36159602 PMCID: PMC9488066 DOI: 10.1016/j.ese.2020.100032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/29/2020] [Accepted: 05/05/2020] [Indexed: 05/11/2023]
Abstract
The anaerobic digestion process has been one of the key processes for renewable energy recovery from organic waste streams for over a century. The anaerobic digestion microbiome is, through the continuous development of novel techniques, evolving from a black box to a well-defined consortium, but we are not there yet. In this perspective, I provide my view on the current status and challenges of the anaerobic digestion microbiome, as well as the opportunities and solutions to exploit it. I consider identification and fingerprinting of the anaerobic digestion microbiome as complementary tools to monitor the anaerobic digestion microbiome. However, data availability, method-inherent biases and correct taxa identification hamper the accuracy and reproducibility of anaerobic digestion microbiome characterization. Standardisation of microbiome research in anaerobic digestion and other engineered systems will be essential in the coming decades, for which I proposed some targeted solutions. These will bring anaerobic digestion from a single-purpose energy-recovery technology to a versatile process for integrated resource recovery. It is my opinion that the exploitation of the microbiome will be a driver of innovation, and that it has a key role to play in the bio-based economy of the decades to come.
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Kumar G, Mathimani T, Sivaramakrishnan R, Shanmugam S, Bhatia SK, Pugazhendhi A. Application of molecular techniques in biohydrogen production as a clean fuel. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 722:137795. [PMID: 32208247 DOI: 10.1016/j.scitotenv.2020.137795] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/06/2020] [Accepted: 03/06/2020] [Indexed: 06/10/2023]
Abstract
Considering the future energy demand and pollution to the environment, biohydrogen, a biofuel, produced from biological sources have garnered increased attention. The present review emphasis the various techniques and methods employed to enumerate the microbial community and enhancement of hydrogen production by dark fermentation. Notably, molecular techniques such as terminal restriction fragment length polymorphism (T-RFLP), quantitative real-time PCR (q-PCR), fluorescent in-situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), ribosomal intergenic spacer analysis (RISA), and next generation sequencing (NGS) have been extensively discussed on identifying the microbial population in hydrogen production. Further, challenges and merits of the molecular techniques have been elaborated.
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Affiliation(s)
- Gopalakrishnan Kumar
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea; Department of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Thangavel Mathimani
- Department of Energy and Environment, National Institute of Technology, Tiruchirappalli - 620015, Tamil Nadu, India
| | - Ramachandran Sivaramakrishnan
- Laboratory of Cyanobacterial Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sabarathinam Shanmugam
- Key Laboratory of Low-grade Energy Utilization Technologies and Systems, Chongqing University, Ministry of Education, Chongqing 400044 China; Institute of Engineering Thermophysics, Chongqing University, Chongqing 400044, China
| | - Shashi Kant Bhatia
- Department of Biological Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Arivalagan Pugazhendhi
- Innovative Green Product Synthesis and Renewable Environment Development Research Group, Faculty of Environment and Labour Safety, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
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8
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Bonk F, Popp D, Weinrich S, Sträuber H, Becker D, Kleinsteuber S, Harms H, Centler F. Determination of Microbial Maintenance in Acetogenesis and Methanogenesis by Experimental and Modeling Techniques. Front Microbiol 2019; 10:166. [PMID: 30800108 PMCID: PMC6375858 DOI: 10.3389/fmicb.2019.00166] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 01/22/2019] [Indexed: 11/21/2022] Open
Abstract
For biogas-producing continuous stirred tank reactors, an increase in dilution rate increases the methane production rate as long as substrate input can be converted fully. However, higher dilution rates necessitate higher specific microbial growth rates, which are assumed to have a strong impact on the apparent microbial biomass yield due to cellular maintenance. To test this, we operated two reactors at 37°C in parallel at dilution rates of 0.18 and 0.07 days-1 (hydraulic retention times of 5.5 and 14 days, doubling times of 3.9 and 9.9 days in steady state) with identical inoculum and a mixture of volatile fatty acids as sole carbon sources. We evaluated the performance of the Anaerobic Digestion Model No. 1 (ADM1), a thermodynamic black box approach (TBA), and dynamic flux balance analysis (dFBA), to describe the experimental observations. All models overestimated the impact of dilution rate on the apparent microbial biomass yield when using default parameter values. Based on our analysis, a maintenance coefficient value below 0.2 kJ per carbon mole of microbial biomass per hour should be used for the TBA, corresponding to 0.12 mmol ATP per gram dry weight per hour for dFBA, which strongly deviates from the value of 9.8 kJ Cmol h-1 that has been suggested to apply to all anaerobic microorganisms at 37°C. We hypothesized that a decrease in dilution rate might select taxa with minimized maintenance expenditure. However, no major differences in the dominating taxa between the reactors were observed based on amplicon sequencing of 16S rRNA genes and terminal restriction fragment length polymorphism analysis of mcrA genes. Surprisingly, Methanosaeta dominated over Methanosarcina even at a dilution rate of 0.18 days-1, which contradicts previous model expectations. Furthermore, only 23-49% of the bacterial reads could be assigned to known syntrophic fatty acid oxidizers, indicating that unknown members of this functional group remain to be discovered. In conclusion, microbial maintenance was found to be much lower for acetogenesis and methanogenesis than previously assumed, likely due to the exceptionally low growth rates in anaerobic digestion. This finding might also be relevant for other microbial systems operating at similarly low growth rates.
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Affiliation(s)
- Fabian Bonk
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Denny Popp
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Sören Weinrich
- Biochemical Conversion Department, DBFZ-Deutsches Biomasseforschungszentrum gGmbH, Leipzig, Germany
| | - Heike Sträuber
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Daniela Becker
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
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9
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Improved Methanogenic Communities for Biogas Production. BIOFUEL AND BIOREFINERY TECHNOLOGIES 2019. [DOI: 10.1007/978-3-030-10516-7_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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10
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Bonk F, Popp D, Weinrich S, Sträuber H, Kleinsteuber S, Harms H, Centler F. Ammonia Inhibition of Anaerobic Volatile Fatty Acid Degrading Microbial Communities. Front Microbiol 2018; 9:2921. [PMID: 30555446 PMCID: PMC6284035 DOI: 10.3389/fmicb.2018.02921] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/14/2018] [Indexed: 11/16/2022] Open
Abstract
Ammonia inhibition is an important reason for reactor failures and economic losses in anaerobic digestion. Its impact on acetic acid degradation is well-studied, while its effect on propionic and butyric acid degradation has received little attention and is consequently not considered in the Anaerobic Digestion Model No. 1 (ADM1). To compare ammonia inhibition of the degradation of these three volatile fatty acids (VFAs), we fed a mixture of them as sole carbon source to three continuous stirred tank reactors (CSTRs) and increased ammonium bicarbonate concentrations in the influent from 52 to 277 mM. The use of this synthetic substrate allowed for the determination of degradation efficiencies for the individual acids. While butyric acid degradation was hardly affected by the increase of ammonia concentration, propionic acid degradation turned out to be even more inhibited than acetic acid degradation with degradation efficiencies dropping to 31 and 65% for propionic and acetic acid, respectively. The inhibited reactors acclimatized and approximated pre-disturbance degradation efficiencies toward the end of the experiment, which was accompanied by strong microbial community shifts, as observed by amplicon sequencing of 16S rRNA genes and terminal restriction fragment length polymorphism (T-RFLP) of mcrA genes. The acetoclastic methanogen Methanosaeta was completely replaced by Methanosarcina. The propionic acid degrading genus Syntrophobacter was replaced by yet unknown propionic acid degraders. The butyric acid degrading genus Syntrophomonas and hydrogenotrophic Methanomicrobiaceae were hardly affected. We hypothesized that the ammonia sensitivity of the initially dominating taxa Methanosaeta and Syntrophobacter led to a stronger inhibition of the acetic and propionic acid degradation compared to butyric acid degradation and hydrogenotrophic methanogenesis, which were facilitated by the ammonia tolerant taxa Syntrophomonas and Methanomicrobiaceae. We implemented this hypothesis into a multi-taxa extension of ADM1, which was able to simulate the dynamics of both microbial community composition and VFA concentration in the experiment. It is thus plausible that the effect of ammonia on VFA degradation strongly depends on the ammonia sensitivity of the dominating taxa, for syntrophic propionate degraders as much as for acetoclastic methanogens.
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Affiliation(s)
- Fabian Bonk
- Department of Environmental Microbiology, UFZ–Helmholtz Center for Environmental Research, Leipzig, Germany
| | - Denny Popp
- Department of Environmental Microbiology, UFZ–Helmholtz Center for Environmental Research, Leipzig, Germany
| | - Sören Weinrich
- Biochemical Conversion Department, DBFZ-Deutsches Biomasseforschungszentrum gGmbH, Leipzig, Germany
| | - Heike Sträuber
- Department of Environmental Microbiology, UFZ–Helmholtz Center for Environmental Research, Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, UFZ–Helmholtz Center for Environmental Research, Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, UFZ–Helmholtz Center for Environmental Research, Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, UFZ–Helmholtz Center for Environmental Research, Leipzig, Germany
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11
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Lv Z, Leite AF, Harms H, Glaser K, Liebetrau J, Kleinsteuber S, Nikolausz M. Microbial community shifts in biogas reactors upon complete or partial ammonia inhibition. Appl Microbiol Biotechnol 2018; 103:519-533. [DOI: 10.1007/s00253-018-9444-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/17/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
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12
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Bonk F, Popp D, Weinrich S, Sträuber H, Kleinsteuber S, Harms H, Centler F. Intermittent fasting for microbes: how discontinuous feeding increases functional stability in anaerobic digestion. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:274. [PMID: 30323859 PMCID: PMC6173896 DOI: 10.1186/s13068-018-1279-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/29/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND Demand-driven biogas production could play an important role for future sustainable energy supply. However, feeding a biogas reactor according to energy demand may lead to organic overloading and, thus, to process failures. To minimize this risk, digesters need to be actively steered towards containing more robust microbial communities. This study focuses on acetogenesis and methanogenesis as crucial process steps for avoiding acidification. We fed lab-scale anaerobic digesters with volatile fatty acids under various feeding regimes and disturbances. The resulting microbial communities were analyzed on DNA and RNA level by terminal restriction fragment length polymorphism of the mcrA gene, 16S rRNA gene amplicon sequencing, and a [2-13C]-acetate assay. A modified Anaerobic Digestion Model 1 (ADM1) that distinguishes between the acetoclastic methanogens Methanosaeta and Methanosarcina was developed and fitted using experimental abiotic and biotic process parameters. RESULTS Discontinuous feeding led to more functional resilience than continuous feeding, without loss in process efficiency. This was attributed to a different microbial community composition. Methanosaeta dominated the continuously fed reactors, while its competitor Methanosarcina was washed out. With discontinuous feeding, however, the fluctuating acetic acid concentrations provided niches to grow and co-exist for both organisms as shown by transcription analysis of the mcrA gene. Our model confirmed the higher functional resilience due to the higher abundance of Methanosarcina based on its higher substrate uptake rate and higher resistance to low pH values. Finally, we applied our model to maize silage as a more complex and practically relevant substrate and showed that our model is likely transferable to the complete AD process. CONCLUSIONS The composition of the microbial community determined the AD functional resilience against organic overloading in our experiments. In particular, communities with higher share of Methanosarcina showed higher process stability. The share of these microorganisms can be purposefully increased by discontinuous feeding. A model was developed that enables derivation of the necessary feeding regime for a more robust community with higher share of Methanosarcina.
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Affiliation(s)
- Fabian Bonk
- Department of Environmental Microbiology, UFZ–Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig, Germany
| | - Denny Popp
- Department of Environmental Microbiology, UFZ–Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig, Germany
| | - Sören Weinrich
- Biochemical Conversion Department, DBFZ Deutsches Biomasseforschungszentrum Gemeinnützige GmbH, Torgauer Str. 116, 04347 Leipzig, Germany
| | - Heike Sträuber
- Department of Environmental Microbiology, UFZ–Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, UFZ–Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, UFZ–Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, UFZ–Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig, Germany
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13
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Ozbayram EG, Kleinsteuber S, Nikolausz M, Ince B, Ince O. Bioaugmentation of anaerobic digesters treating lignocellulosic feedstock by enriched microbial consortia. Eng Life Sci 2018; 18:440-446. [PMID: 32624925 DOI: 10.1002/elsc.201700199] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/16/2018] [Accepted: 04/05/2018] [Indexed: 11/07/2022] Open
Abstract
Three different bioaugmentation cultures enriched from natural and engineered cellulolytic environments (cow and goat rumen, a biogas reactor digesting sorghum biomass) were compared for their enhancement potential on the anaerobic digestion of wheat straw. Methane yields were determined in batch tests using the Automatic Methane Potential Test System operated for 30 days under mesophilic conditions. All cultures had positive effects on substrate degradation, and higher methane yields were observed in the bioaugmented reactors compared to control reactors set up with standard inoculum. However, the level of enhancement differed according to the type of the enrichment culture. Methane yield in batch reactors augmented with 2% cow rumen derived enrichment culture was increased by only 6%. In contrast, reactors amended with 2% goat rumen derived enrichment culture or with the bioaugmentation culture obtained from the biogas reactor digesting sorghum biomass produced 27 and 20% more methane, respectively. The highest methane yield was recorded in reactors amended with 6% goat rumen derived enrichment culture, which represented an increase by 36%. The microbial communities were quite similar at the end of the batch tests independently of the bioaugmentation sources, indicating that the introduced microbial communities of the enrichment cultures did not dominate the reactors.
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Affiliation(s)
- Emine Gozde Ozbayram
- Department of Environmental Engineering Faculty of Civil Engineering Istanbul Technical University Istanbul Turkey
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology Helmholtz Centre for Environmental Research - UFZ Leipzig Germany
| | - Marcell Nikolausz
- Department of Environmental Microbiology Helmholtz Centre for Environmental Research - UFZ Leipzig Germany
| | - Bahar Ince
- Institute of Environmental Sciences Boğaziçi University Istanbul Turkey
| | - Orhan Ince
- Department of Environmental Engineering Faculty of Civil Engineering Istanbul Technical University Istanbul Turkey
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14
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Enrichment of lignocellulose-degrading microbial communities from natural and engineered methanogenic environments. Appl Microbiol Biotechnol 2017; 102:1035-1043. [DOI: 10.1007/s00253-017-8632-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/02/2017] [Accepted: 11/05/2017] [Indexed: 01/05/2023]
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15
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Lambrecht J, Cichocki N, Hübschmann T, Koch C, Harms H, Müller S. Flow cytometric quantification, sorting and sequencing of methanogenic archaea based on F 420 autofluorescence. Microb Cell Fact 2017; 16:180. [PMID: 29084543 PMCID: PMC5663091 DOI: 10.1186/s12934-017-0793-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/24/2017] [Indexed: 02/08/2023] Open
Abstract
Background The widely established production of CH4 from renewable biomass in industrial scale anaerobic reactors may play a major role in the future energy supply. It relies on methanogenic archaea as key organisms which represent the bottleneck in the process. The quantitative analysis of these organisms can help to maximize process performance, uncover disturbances before failure, and may ultimately lead to community-based process control schemes. Existing qPCR and fluorescence microscopy-based methods are very attractive but can be cost-intensive and laborious. Results In this study we present an autofluorescence-based, flow cytometric method for the fast low-cost quantification of methanogenic archaea in complex microbial communities and crude substrates. The method was applied to a methanogenic enrichment culture (MEC) and digester samples (DS). The methanogenic archaea were quantified using the distinct fluorescence of their cofactor F420 in a range from 3.7 × 108 (± 3.3 × 106) cells mL−1 and 1.8 x 109 (± 1.1 × 108) cells mL−1. We evaluated different fixation methods and tested the sample stability. Stable abundance and fluorescence intensity were recorded up to 26 days during aerobic storage in PBS at 6 °C. The discrimination of the whole microbial community from the ubiquitous particle noise was facilitated by SYBR Green I staining and enabled calculation of relative abundances of methanogenic archaea of up to 9.64 ± 0.23% in the MEC and up to 4.43 ± 0.74% in the DS. The metaprofiling of the mcrA gene reinforced the results. Conclusions The presented method allows for fast and reliable quantification of methanogenic archaea in microbial communities under authentic digester conditions and can thus be useful for process monitoring and control in biogas digesters. Electronic supplementary material The online version of this article (10.1186/s12934-017-0793-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johannes Lambrecht
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Nicolas Cichocki
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Thomas Hübschmann
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Christin Koch
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Susann Müller
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany.
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16
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Ozbayram EG, Kleinsteuber S, Nikolausz M, Ince B, Ince O. Effect of bioaugmentation by cellulolytic bacteria enriched from sheep rumen on methane production from wheat straw. Anaerobe 2017; 46:122-130. [PMID: 28323135 DOI: 10.1016/j.anaerobe.2017.03.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 03/14/2017] [Accepted: 03/15/2017] [Indexed: 12/15/2022]
Abstract
The aim of this study was to determine the potential of bioaugmentation with cellulolytic rumen microbiota to enhance the anaerobic digestion of lignocellulosic feedstock. An anaerobic cellulolytic culture was enriched from sheep rumen fluid using wheat straw as substrate under mesophilic conditions. To investigate the effects of bioaugmentation on methane production from straw, the enrichment culture was added to batch reactors in proportions of 2% (Set-1) and 4% (Set-2) of the microbial cell number of the standard inoculum slurry. The methane production in the bioaugmented reactors was higher than in the control reactors. After 30 days of batch incubation, the average methane yield was 154 mLN CH4 gVS-1 in the control reactors. Addition of 2% enrichment culture did not enhance methane production, whereas in Set-2 the methane yield was increased by 27%. The bacterial communities were examined by 454 amplicon sequencing of 16S rRNA genes, while terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of mcrA genes was applied to analyze the methanogenic communities. The results highlighted that relative abundances of Ruminococcaceae and Lachnospiraceae increased during the enrichment. However, Cloacamonaceae, which were abundant in the standard inoculum, dominated the bacterial communities of all batch reactors. T-RFLP profiles revealed that Methanobacteriales were predominant in the rumen fluid, whereas the enrichment culture was dominated by Methanosarcinales. In the batch rectors, the most abundant methanogens were affiliated to Methanobacteriales and Methanomicrobiales. Our results suggest that bioaugmentation with sheep rumen enrichment cultures can enhance the performance of digesters treating lignocellulosic feedstock.
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Affiliation(s)
- E Gozde Ozbayram
- Department of Environmental Engineering, Faculty of Civil Engineering, Istanbul Technical University, Maslak, Istanbul, Turkey.
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
| | - Marcell Nikolausz
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
| | - Bahar Ince
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul, Turkey.
| | - Orhan Ince
- Department of Environmental Engineering, Faculty of Civil Engineering, Istanbul Technical University, Maslak, Istanbul, Turkey.
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17
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Lucas R, Groeneveld J, Harms H, Johst K, Frank K, Kleinsteuber S. A critical evaluation of ecological indices for the comparative analysis of microbial communities based on molecular datasets. FEMS Microbiol Ecol 2016; 93:fiw209. [PMID: 27798064 DOI: 10.1093/femsec/fiw209] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2016] [Indexed: 01/15/2023] Open
Abstract
In times of global change and intensified resource exploitation, advanced knowledge of ecophysiological processes in natural and engineered systems driven by complex microbial communities is crucial for both safeguarding environmental processes and optimising rational control of biotechnological processes. To gain such knowledge, high-throughput molecular techniques are routinely employed to investigate microbial community composition and dynamics within a wide range of natural or engineered environments. However, for molecular dataset analyses no consensus about a generally applicable alpha diversity concept and no appropriate benchmarking of corresponding statistical indices exist yet. To overcome this, we listed criteria for the appropriateness of an index for such analyses and systematically scrutinised commonly employed ecological indices describing diversity, evenness and richness based on artificial and real molecular datasets. We identified appropriate indices warranting interstudy comparability and intuitive interpretability. The unified diversity concept based on 'effective numbers of types' provides the mathematical framework for describing community composition. Additionally, the Bray-Curtis dissimilarity as a beta-diversity index was found to reflect compositional changes. The employed statistical procedure is presented comprising commented R-scripts and example datasets for user-friendly trial application.
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Affiliation(s)
- Rico Lucas
- UFZ-Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstr. 15, 04318 Leipzig, Germany
| | - Jürgen Groeneveld
- UFZ-Helmholtz Centre for Environmental Research, Department of Ecological Modelling, Permoserstr. 15, 04318 Leipzig, Germany.,Institute of Forest Growth and Computer Science, Technische Universität Dresden, PO 1117, 01735 Tharandt, Germany
| | - Hauke Harms
- UFZ-Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstr. 15, 04318 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Karin Johst
- UFZ-Helmholtz Centre for Environmental Research, Department of Ecological Modelling, Permoserstr. 15, 04318 Leipzig, Germany
| | - Karin Frank
- UFZ-Helmholtz Centre for Environmental Research, Department of Ecological Modelling, Permoserstr. 15, 04318 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Sabine Kleinsteuber
- UFZ-Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstr. 15, 04318 Leipzig, Germany
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18
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Leite AF, Janke L, Harms H, Richnow HH, Nikolausz M. Lessons learned from the microbial ecology resulting from different inoculation strategies for biogas production from waste products of the bioethanol/sugar industry. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:144. [PMID: 27429647 PMCID: PMC4947286 DOI: 10.1186/s13068-016-0548-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/08/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND During strategic planning of a biogas plant, the local availability of resources for start-up and operation should be taken into consideration for a cost-efficient process. Because most bioethanol/sugar industries in Brazil are located in remote areas, the use of fresh cattle manure from local farms could be a solution for the inoculation of the biogas process. This study investigated the diversity and dynamics of bacterial and archaeal communities and the performance of biogas reactors inoculated with manure and a mixed inoculum from different biogas reactors as for a controlled start-up until steady state. RESULTS Laboratory-scale biogas reactors were fed semi-continuously with sugarcane filter cake alone (mono-digestion) or together with bagasse (co-digestion). At the initial start-up, the reactors inoculated with the mixed inoculum displayed a less diverse taxonomic composition, but with higher presence of significant abundances compared to reactors inoculated with manure. However, in the final steady state, the communities of the differently inoculated reactors were very similarly characterized by predominance of the methanogenic genera Methanosarcina and Methanobacterium, the bacterial families Bacteroidaceae, Prevotellaceae and Porphyromonadaceae (phylum Bacteroidetes) and Synergistaceae (phylum Synergistetes). In the mono-digestion reactors, the methanogenic communities varied greater than in the co-digestion reactors independently of the inoculation strategy. CONCLUSION The microbial communities involved in the biogas production from waste products of the Brazilian bioethanol/sugar industry were relatively similar and stable at the reactor's steady phase independently of the inoculum source (manure or mixed inoculum). Therefore, the locally available manure can be used as inoculum for start-up of the biogas process, since it also contains the microbial resources needed. The strong fluctuation of methanogenic communities in mono-digestion reactors indicates higher risk of process instability than in co-digestion reactors.
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Affiliation(s)
- Athaydes Francisco Leite
- />Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Leandro Janke
- />Department of Biochemical Conversion, Deutsches Biomasseforschungszentrum gemeinnützige GmbH, Torgauerstrasse 116, 04347 Leipzig, Germany
| | - Hauke Harms
- />Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Hans-Hermann Richnow
- />Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Marcell Nikolausz
- />Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
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19
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Popp D, Harms H, Sträuber H. The alkaloid gramine in the anaerobic digestion process-inhibition and adaptation of the methanogenic community. Appl Microbiol Biotechnol 2016; 100:7311-22. [PMID: 27138201 DOI: 10.1007/s00253-016-7571-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/12/2016] [Accepted: 04/18/2016] [Indexed: 01/04/2023]
Abstract
As many plant secondary metabolites have antimicrobial activity, microorganisms of the anaerobic digestion process might be affected when plant material rich in these compounds is digested. Hitherto, the effects of plant secondary metabolites on the anaerobic digestion process are poorly investigated. In this study, the alkaloid gramine, a constituent of reed canary grass, was added daily to a continuous co-digestion of grass silage and cow manure. A transient decrease of the methane yield by 17 % and a subsequent recovery was observed, but no effect on other process parameters. When gramine was infrequently spiked in higher amounts, the observed inhibitory effect was even more pronounced including a 53 % decrease of the methane yield and an increase of acetic acid concentrations up to 96 mM. However, the process recovered and the process parameters were finally at initial values (methane yield around 255 LN CH4 per gram volatile solids of substrate and acetic acid concentration lower than 2 mM). The bacterial communities of the reactors remained stable upon gramine addition. In contrast, the methanogenic community changed from a well-balanced mixture of five phylotypes towards a strong dominance of Methanosarcina (more than two thirds of the methanogenic community) while Methanosaeta disappeared. Batch inhibition assays revealed that acetic acid was only converted to methane via acetoclastic methanogenesis which was more strongly affected by gramine than hydrogenotrophic methanogenesis and acetogenesis. Hence, when acetoclastic methanogenesis is the dominant pathway, a shift of the methanogenic community is necessary to digest gramine-rich plant material.
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Affiliation(s)
- Denny Popp
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318, Leipzig, Germany.
| | - Hauke Harms
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318, Leipzig, Germany
| | - Heike Sträuber
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318, Leipzig, Germany
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