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Sun L, Liu T, Müller B, Schnürer A. The microbial community structure in industrial biogas plants influences the degradation rate of straw and cellulose in batch tests. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:128. [PMID: 27330562 PMCID: PMC4912747 DOI: 10.1186/s13068-016-0543-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 06/02/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Materials rich in lignocellulose, such as straw, are abundant, cheap and highly interesting for biogas production. However, the complex structure of lignocellulose is difficult for microbial cellulolytic enzymes to access, limiting degradation. The rate of degradation depends on the activity of members of the microbial community, but the knowledge of this community in the biogas process is rather limited. This study, therefore, investigated the degradation rate of cellulose and straw in batch cultivation test initiated with inoculums from four co-digestion biogas plants (CD) and six wastewater treatment plants (WWTP). The results were correlated to the bacterial community by 454-pyrosequencing targeting 16S rRNA gene and by T-RFLP analysis targeting genes of glycoside hydrolase families 5 (cel5) and 48 (cel48), combined with construction of clone libraries. RESULTS UniFrac principal coordinate analysis of 16S rRNA gene amplicons revealed a clustering of WWTPs, while the CDs were more separated from each other. Bacteroidetes and Firmicutes dominated the community with a comparably higher abundance of the latter in the processes operating at high ammonia levels. Sequences obtained from the cel5 and cel 48 clone libraries were also mainly related to the phyla Firmicutes and Bacteroidetes and here ammonia was a parameter with a strong impact on the cel5 community. The results from the batch cultivation showed similar degradation pattern for eight of the biogas plants, while two characterised by high ammonia level and low bacterial diversity, showed a clear lower degradation rate. Interestingly, two T-RFs from the cel5 community were positively correlated to high degradation rates of both straw and cellulose. One of the respective partial cel5 sequences shared 100 % identity to Clostridium cellulolyticum. CONCLUSION The degradation rate of cellulose and straw varied in the batch tests dependent on the origin of the inoculum and was negatively correlated with the ammonia level. The cellulose-degrading community, targeted by analysis of the glycoside hydrolase families 5 (cel5) and 48 (cel48), showed a dominance of bacteria belonging the Firmicutes and Bacteriodetes, and a positive correlation was found between the cellulose degradation rate of wheat straw with the level of C. cellulolyticum.
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Affiliation(s)
- Li Sun
- />Department of Microbiology, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, 750 07 Uppsala, Sweden
| | - Tong Liu
- />Department of Microbiology, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, 750 07 Uppsala, Sweden
| | - Bettina Müller
- />Department of Microbiology, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, 750 07 Uppsala, Sweden
| | - Anna Schnürer
- />Department of Microbiology, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, 750 07 Uppsala, Sweden
- />Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Science, 1432 Ås, Norway
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Jiménez J, Theuerl S, Bergmann I, Klocke M, Guerra G, Romero-Romero O. Prokaryote community dynamics in anaerobic co-digestion of swine manure, rice straw and industrial clay residuals. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2016; 74:824-835. [PMID: 27533857 DOI: 10.2166/wst.2016.170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The aim of this study was to analyze the effect of the addition of rice straw and clay residuals on the prokaryote methane-producing community structure in a semi-continuously stirred tank reactor fed with swine manure. Molecular techniques, including terminal restriction fragment length polymorphism and a comparative nucleotide sequence analyses of the prokaryotic 16S rRNA genes, were performed. The results showed a positive effect of clay addition on methane yield during the co-digestion of swine manure and rice straw. At the digestion of swine manure, the bacterial phylum Firmicutes and the archaeal family Methanosarcinaceae, particularly Methanosarcina species, were predominant. During the co-digestion of swine manure and rice straw the microbial community changed, and with the addition of clay residual, the phylum Bacteroidetes predominated. The new nutritional conditions resulted in a shift in the archaeal family Methanosarcinaceae community as acetoclastic Methanosaeta species became dominant.
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Affiliation(s)
- Janet Jiménez
- Universidad de Sancti Spíritus, Ave. de los Mártires, No. 360, Sancti Spíritus, Sancti Spíritus CP 60100, Cuba E-mail:
| | - Susanne Theuerl
- Department Bioengineering, Leibniz Institute for Agricultural Engineering Potsdam-Bornim (ATB), Max-Eyth-Allee 100, Potsdam D-14469, Germany
| | - Ingo Bergmann
- Department Bioengineering, Leibniz Institute for Agricultural Engineering Potsdam-Bornim (ATB), Max-Eyth-Allee 100, Potsdam D-14469, Germany
| | - Michael Klocke
- Department Bioengineering, Leibniz Institute for Agricultural Engineering Potsdam-Bornim (ATB), Max-Eyth-Allee 100, Potsdam D-14469, Germany
| | - Gilda Guerra
- Facultad de Biología. Universidad de La Habana, Calle 25 e/ I y J, Vedado, La Habana CP. 10400, Cuba
| | - Osvaldo Romero-Romero
- Universidad de Sancti Spíritus, Ave. de los Mártires, No. 360, Sancti Spíritus, Sancti Spíritus CP 60100, Cuba E-mail:
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Szuhaj M, Ács N, Tengölics R, Bodor A, Rákhely G, Kovács KL, Bagi Z. Conversion of H2 and CO2 to CH4 and acetate in fed-batch biogas reactors by mixed biogas community: a novel route for the power-to-gas concept. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:102. [PMID: 27168764 PMCID: PMC4862154 DOI: 10.1186/s13068-016-0515-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 04/25/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND Applications of the power-to-gas principle for the handling of surplus renewable electricity have been proposed. The feasibility of using hydrogenotrophic methanogens as CH4 generating catalysts has been demonstrated. Laboratory and scale-up experiments have corroborated the benefits of the CO2 mitigation via biotechnological conversion of H2 and CO2 to CH4. A major bottleneck in the process is the gas-liquid mass transfer of H2. RESULTS Fed-batch reactor configuration was tested at mesophilic temperature in laboratory experiments in order to improve the contact time and H2 mass transfer between the gas and liquid phases. Effluent from an industrial biogas facility served as biocatalyst. The bicarbonate content of the effluent was depleted after some time, but the addition of stoichiometric CO2 sustained H2 conversion for an extended period of time and prevented a pH shift. The microbial community generated biogas from the added α-cellulose substrate with concomitant H2 conversion, but the organic substrate did not facilitate H2 consumption. Fed-batch operational mode allowed a fourfold increase in volumetric H2 load and a 6.5-fold augmentation of the CH4 formation rate relative to the CSTR reactor configuration. Acetate was the major by-product of the reaction. CONCLUSIONS Fed-batch reactors significantly improve the efficiency of the biological power-to-gas process. Besides their storage function, biogas fermentation effluent reservoirs can serve as large-scale bio CH4 reactors. On the basis of this recognition, a novel concept is proposed, which merges biogas technology with other means of renewable electricity production for improved efficiency and sustainability.
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Affiliation(s)
- Márk Szuhaj
- />Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726 Hungary
| | - Norbert Ács
- />Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726 Hungary
| | - Roland Tengölics
- />Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, 6726 Hungary
| | - Attila Bodor
- />Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726 Hungary
| | - Gábor Rákhely
- />Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726 Hungary
- />Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, 6726 Hungary
| | - Kornél L. Kovács
- />Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726 Hungary
- />Department of Oral Biology and Experimental Dental Research, University of Szeged, Tisza L. krt. 64, Szeged, 6720 Hungary
- />Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, 6726 Hungary
| | - Zoltán Bagi
- />Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726 Hungary
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Nolla-Ardèvol V, Peces M, Strous M, Tegetmeyer HE. Metagenome from a Spirulina digesting biogas reactor: analysis via binning of contigs and classification of short reads. BMC Microbiol 2015; 15:277. [PMID: 26680455 PMCID: PMC4683858 DOI: 10.1186/s12866-015-0615-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 12/14/2015] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Anaerobic digestion is a biological process in which a consortium of microorganisms transforms a complex substrate into methane and carbon dioxide. A good understanding of the interactions between the populations that form this consortium can contribute to a successful anaerobic digestion of the substrate. In this study we combine the analysis of the biogas production in a laboratory anaerobic digester fed with the microalgae Spirulina, a protein rich substrate, with the analysis of the metagenome of the consortium responsible for digestion, obtained by high-throughput DNA sequencing. The obtained metagenome was also compared with a metagenome from a full scale biogas plant fed with cellulose rich material. RESULTS The optimal organic loading rate for the anaerobic digestion of Spirulina was determined to be 4.0 g Spirulina L(-1) day(-1) with a specific biogas production of 350 mL biogas g Spirulina (-1) with a methane content of 68 %. Firmicutes dominated the microbial consortium at 38 % abundance followed by Bacteroidetes, Chloroflexi and Thermotogae. Euryarchaeota represented 3.5 % of the total abundance. The most abundant organism (14.9 %) was related to Tissierella, a bacterium known to use proteinaceous substrates for growth. Methanomicrobiales and Methanosarcinales dominated the archaeal community. Compared to the full scale cellulose-fed digesters, Pfam domains related to protein degradation were more frequently detected and Pfam domains related to cellulose degradation were less frequent in our sample. CONCLUSIONS The results presented in this study suggest that Spirulina is a suitable substrate for the production of biogas. The proteinaceous substrate appeared to have a selective impact on the bacterial community that performed anaerobic digestion. A direct influence of the substrate on the selection of specific methanogenic populations was not observed.
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Affiliation(s)
- Vimac Nolla-Ardèvol
- Institute for Genome Research and Systems Biology, Center for Biotechnology, Office G2-152, Bielefeld University, Universitätsstraße 27, Bielefeld, D-33615, Germany.
| | - Miriam Peces
- Department of Chemical Engineering, University of Barcelona, C/ Martí i Franquès, 1, 6th floor, Barcelona, 08028, Spain.
- Centre for Solid Waste Bioprocessing, Schools of Civil and Chemical Engineering, University of Queensland, Brisbane, 4072, QLD, Australia.
| | - Marc Strous
- Institute for Genome Research and Systems Biology, Center for Biotechnology, Office G2-152, Bielefeld University, Universitätsstraße 27, Bielefeld, D-33615, Germany.
- Department of Geoscience, University of Calgary, 2500 University Drive NW, T2N 1 N4, Calgary, AB, Canada.
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, D-28359, Germany.
| | - Halina E Tegetmeyer
- Institute for Genome Research and Systems Biology, Center for Biotechnology, Office G2-152, Bielefeld University, Universitätsstraße 27, Bielefeld, D-33615, Germany.
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, D-28359, Germany.
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Ju F, Zhang T. Experimental Design and Bioinformatics Analysis for the Application of Metagenomics in Environmental Sciences and Biotechnology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:12628-40. [PMID: 26451629 DOI: 10.1021/acs.est.5b03719] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Recent advances in DNA sequencing technologies have prompted the widespread application of metagenomics for the investigation of novel bioresources (e.g., industrial enzymes and bioactive molecules) and unknown biohazards (e.g., pathogens and antibiotic resistance genes) in natural and engineered microbial systems across multiple disciplines. This review discusses the rigorous experimental design and sample preparation in the context of applying metagenomics in environmental sciences and biotechnology. Moreover, this review summarizes the principles, methodologies, and state-of-the-art bioinformatics procedures, tools and database resources for metagenomics applications and discusses two popular strategies (analysis of unassembled reads versus assembled contigs/draft genomes) for quantitative or qualitative insights of microbial community structure and functions. Overall, this review aims to facilitate more extensive application of metagenomics in the investigation of uncultured microorganisms, novel enzymes, microbe-environment interactions, and biohazards in biotechnological applications where microbial communities are engineered for bioenergy production, wastewater treatment, and bioremediation.
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Affiliation(s)
- Feng Ju
- Environmental Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong , Hong Kong SRA, China
| | - Tong Zhang
- Environmental Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong , Hong Kong SRA, China
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56
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Ziganshina EE, Belostotskiy DE, Ilinskaya ON, Boulygina EA, Grigoryeva TV, Ziganshin AM. Effect of the Organic Loading Rate Increase and the Presence of Zeolite on Microbial Community Composition and Process Stability During Anaerobic Digestion of Chicken Wastes. MICROBIAL ECOLOGY 2015; 70:948-60. [PMID: 26045158 DOI: 10.1007/s00248-015-0635-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/22/2015] [Indexed: 05/24/2023]
Abstract
This study investigates the effect of the organic loading rate (OLR) increase from 1.0 to 3.5 g VS L(-1) day(-1) at constant hydraulic retention time (HRT) of 35 days on anaerobic reactors' performance and microbial diversity during mesophilic anaerobic digestion of ammonium-rich chicken wastes in the absence/presence of zeolite. The effects of anaerobic process parameters on microbial community structure and dynamics were evaluated using a 16S ribosomal RNA gene-based pyrosequencing approach. Maximum 12 % of the total ammonia nitrogen (TAN) was efficiently removed by zeolite in the fixed zeolite reactor (day 87). In addition, volatile fatty acids (VFA) in the fixed zeolite reactor accumulated in lower concentrations at high OLR of 3.2-3.5 g VS L(-1) day(-1). Microbial communities in the fixed zeolite reactor and reactor without zeolite were dominated by various members of Bacteroidales and Methanobacterium sp. at moderate TAN and VFA levels. The increase of the OLR accompanied by TAN and VFA accumulation and increase in pH led to the predominance of representatives of the family Erysipelotrichaceae and genera Clostridium and Methanosarcina. Methanosarcina sp. reached relative abundances of 94 and 57 % in the fixed zeolite reactor and reactor without zeolite at the end of the experimental period, respectively. In addition, the diminution of Synergistaceae and Crenarchaeota and increase in the abundance of Acholeplasmataceae in parallel with the increase of TAN, VFA, and pH values were observed.
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Affiliation(s)
- Elvira E Ziganshina
- Department of Microbiology, Kazan (Volga Region) Federal University, Kazan, 420008, The Republic of Tatarstan, Russia
| | - Dmitry E Belostotskiy
- Department of Technologies, A. E. Arbuzov Institute of Organic and Physical Chemistry, Russian Academy of Sciences, Kazan, 420088, The Republic of Tatarstan, Russia
| | - Olga N Ilinskaya
- Department of Microbiology, Kazan (Volga Region) Federal University, Kazan, 420008, The Republic of Tatarstan, Russia
| | - Eugenia A Boulygina
- Laboratory of Omics Technologies, Kazan (Volga Region) Federal University, Kazan, 420008, The Republic of Tatarstan, Russia
| | - Tatiana V Grigoryeva
- Laboratory of Omics Technologies, Kazan (Volga Region) Federal University, Kazan, 420008, The Republic of Tatarstan, Russia
| | - Ayrat M Ziganshin
- Department of Microbiology, Kazan (Volga Region) Federal University, Kazan, 420008, The Republic of Tatarstan, Russia.
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57
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Metagenome approaches revealed a biological prospect for improvement on mesophilic cellulose degradation. Appl Microbiol Biotechnol 2015; 99:10871-9. [DOI: 10.1007/s00253-015-6945-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 08/11/2015] [Accepted: 08/18/2015] [Indexed: 10/23/2022]
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58
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Differences in biomass degradation between newly isolated environmental strains of Clostridium thermocellum and heterogeneity in the size of the cellulosomal scaffoldin. Syst Appl Microbiol 2015; 38:424-32. [DOI: 10.1016/j.syapm.2015.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 06/05/2015] [Accepted: 06/05/2015] [Indexed: 11/21/2022]
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59
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Tomazetto G, Hahnke S, Koeck DE, Wibberg D, Maus I, Pühler A, Klocke M, Schlüter A. Complete genome analysis of Clostridium bornimense strain M2/40(T): A new acidogenic Clostridium species isolated from a mesophilic two-phase laboratory-scale biogas reactor. J Biotechnol 2015; 232:38-49. [PMID: 26256097 DOI: 10.1016/j.jbiotec.2015.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 07/23/2015] [Accepted: 08/04/2015] [Indexed: 12/17/2022]
Abstract
Taxonomic and functional profiling based on metagenome analyses frequently revealed that members of the class Clostridia dominate biogas reactor communities and perform different essential metabolic pathways in the biogas fermentation process. Clostridium bornimense strain M2/40(T) was recently isolated from a mesophilic two-phase lab-scale biogas reactor continuously fed with maize silage and wheat straw. The genome of the strain was completely sequenced and manually annotated to reconstruct its metabolic potential regarding carbohydrate active enzyme production and fermentation of organic compounds for consolidated biofuel production from biomass. The C. bornimense M2/40(T) genome consists of a chromosome (2,917,864bp in size) containing 2613 protein coding sequences, and a 699,161bp chromid (secondary replicon) harboring 680 coding sequences. Both replicons feature very similar GC-contents of approximately 29%. The complex genome comprises three prophage regions, two CRISPR-cas systems and a putative cellulosomal gene cluster that is located on the second replicon (chromid) of the strain. The overexpressed glycosyl hydrolases (GH) CelK (GH9) and CelA (GH48) encoded in the cellulosomal gene cluster were shown to be active on the substrates xylan and xyloglucan whereas XghA (GH74) is highly active on xyloglucan. Reconstruction of fermentation pathways from genome sequence data revealed that strain M2/40(T) encodes all enzymes for hydrogen, acetate, formate, lactate, butyrate, and ethanol production, leading to the classification of the isolate as acidogenic bacterium. Phylogenetic analyses uncovered that the closest characterized relative of C. bornimense is C. cellulovorans. Comparative analyses of the C. bornimense and C. cellulovorans genomes revealed considerable rearrangements within their chromosomes suggesting that both species evolved separately for a relatively long period of time and adapted to specific tasks within microbial consortia responsible for anaerobic digestion.
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Affiliation(s)
- Geizecler Tomazetto
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Sarah Hahnke
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering Potsdam-Bornim (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Daniela E Koeck
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Michael Klocke
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering Potsdam-Bornim (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany.
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Sun L, Pope PB, Eijsink VGH, Schnürer A. Characterization of microbial community structure during continuous anaerobic digestion of straw and cow manure. Microb Biotechnol 2015; 8:815-27. [PMID: 26152665 PMCID: PMC4554469 DOI: 10.1111/1751-7915.12298] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 05/13/2015] [Indexed: 01/22/2023] Open
Abstract
Responses of bacterial and archaeal communities to the addition of straw during anaerobic digestion of manure at different temperatures (37°C, 44°C and 52°C) were investigated using five laboratory-scale semi-continuous stirred tank reactors. The results revealed that including straw as co-substrate decreased the species richness for bacteria, whereas increasing the operating temperature decreased the species richness for both archaea and bacteria, and also the evenness of the bacteria. Taxonomic classifications of the archaeal community showed that Methanobrevibacter dominated in the manure samples, while Methanosarcina dominated in all digesters regardless of substrate. Increase of the operating temperature to 52°C led to increased relative abundance of Methanoculleus and Methanobacterium. Among the bacteria, the phyla Firmicutes and Bacteroidetes dominated within all samples. Compared with manure itself, digestion of manure resulted in a higher abundance of an uncultured class WWE1 and lower abundance of Bacilli. Adding straw to the digesters increased the level of Bacteroidia, while increasing the operating temperature decreased the level of this class and instead increased the relative abundance of an uncultured genus affiliated to order MBA08 (Clostridia). A considerable fraction of bacterial sequences could not be allocated to genus level, indicating that novel phylotypes are resident in these communities.
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Affiliation(s)
- Li Sun
- Department of Microbiology, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, SE-750 07, Uppsala, Sweden
| | - Phillip B Pope
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Vincent G H Eijsink
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Anna Schnürer
- Department of Microbiology, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, SE-750 07, Uppsala, Sweden.,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
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Wirth R, Lakatos G, Böjti T, Maróti G, Bagi Z, Kis M, Kovács A, Ács N, Rákhely G, Kovács KL. Metagenome changes in the mesophilic biogas-producing community during fermentation of the green alga Scenedesmus obliquus. J Biotechnol 2015; 215:52-61. [PMID: 26087313 DOI: 10.1016/j.jbiotec.2015.06.396] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 06/08/2015] [Accepted: 06/12/2015] [Indexed: 01/02/2023]
Abstract
A microalgal biomass offers a potential alternative to the maize silage commonly used in biogas technology. In this study, photoautotrophically grown Scenedesmus obliquus was used as biogas substrate. This microalga has a low C/N ratio of 8.5 relative to the optimum 20-30. A significant increase in the ammonium ion content was not observed. The methane content of the biogas generated from Sc. obliquus proved to be higher than that from maize silage, but the specific biogas yield was lower. Semi-continuous steady biogas production lasted for 2 months. Because of the thick cell wall of Sc. obliquus, the biomass-degrading microorganisms require additional time to digest its biomass. The methane concentration in the biogas was also high, in co-digestion (i.e., 52-56%) as in alga-fed anaerobic digestion (i.e., 55-62%). These results may be related to the relative predominance of the order Clostridiales in co-digestion and to the more balanced C/N ratio of the mixed algal-maize biomass. Predominance of the order Methanosarcinales was observed in the domain Archaea, which supported the diversity of metabolic pathways in the process.
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Affiliation(s)
- Roland Wirth
- Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - Gergely Lakatos
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
| | - Tamás Böjti
- Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - Gergely Maróti
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
| | - Zoltán Bagi
- Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - Mihály Kis
- Institute of Plant Biology, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
| | - Attila Kovács
- Phytoplankton and Macrophyte Research Team, Balaton Limnological Institute, Klebersberg Kuno 3, H-8237 Tihany, Hungary.
| | - Norbert Ács
- Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
| | - Kornél L Kovács
- Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary; Department of Oral Biology and Experimental Dental Research, University of Szeged, Tisza L. krt. 64, H-6720 Szeged, Hungary.
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Wei Y, Zhou H, Zhang J, Zhang L, Geng A, Liu F, Zhao G, Wang S, Zhou Z, Yan X. Insight into Dominant Cellulolytic Bacteria from Two Biogas Digesters and Their Glycoside Hydrolase Genes. PLoS One 2015; 10:e0129921. [PMID: 26070087 PMCID: PMC4466528 DOI: 10.1371/journal.pone.0129921] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 05/13/2015] [Indexed: 12/30/2022] Open
Abstract
Diverse cellulolytic bacteria are essential for maintaining high lignocellulose degradation ability in biogas digesters. However, little was known about functional genes and gene clusters of dominant cellulolytic bacteria in biogas digesters. This is the foundation to understand lignocellulose degradation mechanisms of biogas digesters and apply these gene resource for optimizing biofuel production. A combination of metagenomic and 16S rRNA gene clone library methods was used to investigate the dominant cellulolytic bacteria and their glycoside hydrolase (GH) genes in two biogas digesters. The 16S rRNA gene analysis revealed that the dominant cellulolytic bacteria were strains closely related to Clostridium straminisolvens and an uncultured cellulolytic bacterium designated BG-1. To recover GH genes from cellulolytic bacteria in general, and BG-1 in particular, a refined assembly approach developed in this study was used to assemble GH genes from metagenomic reads; 163 GH-containing contigs ≥ 1 kb in length were obtained. Six recovered GH5 genes that were expressed in E. coli demonstrated multiple lignocellulase activities and one had high mannanase activity (1255 U/mg). Eleven fosmid clones harboring the recovered GH-containing contigs were sequenced and assembled into 10 fosmid contigs. The composition of GH genes in the 163 assembled metagenomic contigs and 10 fosmid contigs indicated that diverse GHs and lignocellulose degradation mechanisms were present in the biogas digesters. In particular, a small portion of BG-1 genome information was recovered by PhyloPythiaS analysis. The lignocellulase gene clusters in BG-1 suggested that it might use a possible novel lignocellulose degradation mechanism to efficiently degrade lignocellulose. Dominant cellulolytic bacteria of biogas digester possess diverse GH genes, not only in sequences but also in their functions, which may be applied for production of biofuel in the future.
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Affiliation(s)
- Yongjun Wei
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Haokui Zhou
- Department of Microbiology, the Chinese University of Hong Kong, the Prince of Wales Hospital, Hong Kong, China
| | - Jun Zhang
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lei Zhang
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Alei Geng
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fanghua Liu
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guoping Zhao
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Microbiology, the Chinese University of Hong Kong, the Prince of Wales Hospital, Hong Kong, China
- Shanghai-MOST Key Laboratory for Health and Disease Genomics, Chinese National Human Genome Center, Shanghai, China
| | - Shengyue Wang
- Shanghai-MOST Key Laboratory for Health and Disease Genomics, Chinese National Human Genome Center, Shanghai, China
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (XY); (ZZ)
| | - Xing Yan
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (XY); (ZZ)
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Resource recovery from wastewater: application of meta-omics to phosphorus and carbon management. Curr Opin Biotechnol 2015; 33:260-7. [DOI: 10.1016/j.copbio.2015.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 12/20/2014] [Accepted: 03/05/2015] [Indexed: 01/21/2023]
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64
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Čater M, Fanedl L, Malovrh Š, Marinšek Logar R. Biogas production from brewery spent grain enhanced by bioaugmentation with hydrolytic anaerobic bacteria. BIORESOURCE TECHNOLOGY 2015; 186:261-269. [PMID: 25836034 DOI: 10.1016/j.biortech.2015.03.029] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Revised: 03/04/2015] [Accepted: 03/05/2015] [Indexed: 05/19/2023]
Abstract
Lignocellulosic substrates are widely available but not easily applied in biogas production due to their poor anaerobic degradation. The effect of bioaugmentation by anaerobic hydrolytic bacteria on biogas production was determined by the biochemical methane potential assay. Microbial biomass from full scale upflow anaerobic sludge blanket reactor treating brewery wastewater was a source of active microorganisms and brewery spent grain a model lignocellulosic substrate. Ruminococcus flavefaciens 007C, Pseudobutyrivibrio xylanivorans Mz5(T), Fibrobacter succinogenes S85 and Clostridium cellulovorans as pure and mixed cultures were used to enhance the lignocellulose degradation and elevate the biogas production. P. xylanivorans Mz5(T) was the most successful in elevating methane production (+17.8%), followed by the coculture of P. xylanivorans Mz5(T) and F. succinogenes S85 (+6.9%) and the coculture of C. cellulovorans and F. succinogenes S85 (+4.9%). Changes in microbial community structure were detected by fingerprinting techniques.
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Affiliation(s)
- Maša Čater
- Division of Microbiology and Microbial Biotechnology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230 Domžale, Slovenia
| | - Lijana Fanedl
- Division of Microbiology and Microbial Biotechnology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230 Domžale, Slovenia
| | - Špela Malovrh
- Division of Animal Breeding Sciences, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230 Domžale, Slovenia
| | - Romana Marinšek Logar
- Division of Microbiology and Microbial Biotechnology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230 Domžale, Slovenia.
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Community shifts in a well-operating agricultural biogas plant: how process variations are handled by the microbiome. Appl Microbiol Biotechnol 2015; 99:7791-803. [PMID: 25998656 DOI: 10.1007/s00253-015-6627-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 04/15/2015] [Accepted: 04/19/2015] [Indexed: 02/03/2023]
Abstract
This study provides a comprehensive, long-term microbiological study of a continuously operated, mesophilic, agricultural biogas plant fed with whole-crop silages of maize and rye, cattle manure and cattle slurry. The microbial community structure was accessed by high-throughput 16S rRNA gene amplicon sequencing. For the characterisation of the microbial dynamics, the community profiling method terminal restriction fragment length polymorphism (TRFLP) in combination with a cloning-sequencing approach as well as a LC-MS/MS approach for protein identification were applied. Our results revealed that the anaerobic digestion is a highly sensitive process: small variations in the process performance induce fluctuations in the microbial community composition and activity. In this context, it could be proven that certain microbial species were better adapted to changing process condition such as temperature (interspecies competition) and that there is a physiological compensation between different microorganisms so that the reactor efficiency was not adversely affected despite of structural and functional changes within the microbial community.
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66
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De Vrieze J, Saunders AM, He Y, Fang J, Nielsen PH, Verstraete W, Boon N. Ammonia and temperature determine potential clustering in the anaerobic digestion microbiome. WATER RESEARCH 2015; 75:312-23. [PMID: 25819618 DOI: 10.1016/j.watres.2015.02.025] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 02/13/2015] [Accepted: 02/15/2015] [Indexed: 05/07/2023]
Abstract
Anaerobic digestion is regarded as a key environmental technology in the present and future bio-based economy. The microbial community completing the anaerobic digestion process is considered complex, and several attempts already have been carried out to determine the key microbial populations. However, the key differences in the anaerobic digestion microbiomes, and the environmental/process parameters that drive these differences, remain poorly understood. In this research, we hypothesized that differences in operational parameters lead to a particular composition and organization of microbial communities in full-scale installations. A total of 38 samples were collected from 29 different full-scale anaerobic digestion installations, showing constant biogas production in function of time. Microbial community analysis was carried out by means of amplicon sequencing and real-time PCR. The bacterial community in all samples was dominated by representatives of the Firmicutes, Bacteroidetes and Proteobacteria, covering 86.1 ± 10.7% of the total bacterial community. Acetoclastic methanogenesis was dominated by Methanosaetaceae, yet, only the hydrogenotrophic Methanobacteriales correlated with biogas production, confirming their importance in high-rate anaerobic digestion systems. In-depth analysis of operational and environmental parameters and bacterial community structure indicated the presence of three potential clusters in anaerobic digestion. These clusters were determined by total ammonia concentration, free ammonia concentration and temperature, and characterized by an increased relative abundance of Bacteroidales, Clostridiales and Lactobacillales, respectively. None of the methanogenic populations, however, could be significantly attributed to any of the three clusters. Nonetheless, further experimental research will be required to validate the existence of these different clusters, and to which extent the presence of these clusters relates to stable or sub-optimal anaerobic digestion.
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Affiliation(s)
- Jo De Vrieze
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Aaron Marc Saunders
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngårdsholmsvej 49, 9000 Aalborg, Denmark
| | - Ying He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing Fang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Per Halkjaer Nielsen
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngårdsholmsvej 49, 9000 Aalborg, Denmark
| | - Willy Verstraete
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
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Stöveken J, Singh R, Kolkenbrock S, Zakrzewski M, Wibberg D, Eikmeyer F, Pühler A, Schlüter A, Moerschbacher B. Successful heterologous expression of a novel chitinase identified by sequence analyses of the metagenome from a chitin-enriched soil sample. J Biotechnol 2015; 201:60-8. [DOI: 10.1016/j.jbiotec.2014.09.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 08/29/2014] [Accepted: 09/09/2014] [Indexed: 12/20/2022]
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Wirth R, Lakatos G, Maróti G, Bagi Z, Minárovics J, Nagy K, Kondorosi É, Rákhely G, Kovács KL. Exploitation of algal-bacterial associations in a two-stage biohydrogen and biogas generation process. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:59. [PMID: 25873997 PMCID: PMC4395902 DOI: 10.1186/s13068-015-0243-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 03/20/2015] [Indexed: 05/12/2023]
Abstract
BACKGROUND The growing concern regarding the use of agricultural land for the production of biomass for food/feed or energy is dictating the search for alternative biomass sources. Photosynthetic microorganisms grown on marginal or deserted land present a promising alternative to the cultivation of energy plants and thereby may dampen the 'food or fuel' dispute. Microalgae offer diverse utilization routes. RESULTS A two-stage energetic utilization, using a natural mixed population of algae (Chlamydomonas sp. and Scenedesmus sp.) and mutualistic bacteria (primarily Rhizobium sp.), was tested for coupled biohydrogen and biogas production. The microalgal-bacterial biomass generated hydrogen without sulfur deprivation. Algal hydrogen production in the mixed population started earlier but lasted for a shorter period relative to the benchmark approach. The residual biomass after hydrogen production was used for biogas generation and was compared with the biogas production from maize silage. The gas evolved from the microbial biomass was enriched in methane, but the specific gas production was lower than that of maize silage. Sustainable biogas production from the microbial biomass proceeded without noticeable difficulties in continuously stirred fed-batch laboratory-size reactors for an extended period of time. Co-fermentation of the microbial biomass and maize silage improved the biogas production: The metagenomic results indicated that pronounced changes took place in the domain Bacteria, primarily due to the introduction of a considerable bacterial biomass into the system with the substrate; this effect was partially compensated in the case of co-fermentation. The bacteria living in syntrophy with the algae apparently persisted in the anaerobic reactor and predominated in the bacterial population. The Archaea community remained virtually unaffected by the changes in the substrate biomass composition. CONCLUSION Through elimination of cost- and labor-demanding sulfur deprivation, sustainable biohydrogen production can be carried out by using microalgae and their mutualistic bacterial partners. The beneficial effect of the mutualistic mixed bacteria in O2 quenching is that the spent algal-bacterial biomass can be further exploited for biogas production. Anaerobic fermentation of the microbial biomass depends on the composition of the biogas-producing microbial community. Co-fermentation of the mixed microbial biomass with maize silage improved the biogas productivity.
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Affiliation(s)
- Roland Wirth
- />Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Gergely Lakatos
- />Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary
| | - Gergely Maróti
- />Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary
| | - Zoltán Bagi
- />Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - János Minárovics
- />Department of Oral Biology and Experimental Dental Research, University of Szeged, Tisza L. krt. 64, 6720 Szeged, Hungary
| | - Katalin Nagy
- />Department of Oral Biology and Experimental Dental Research, University of Szeged, Tisza L. krt. 64, 6720 Szeged, Hungary
| | - Éva Kondorosi
- />Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary
| | - Gábor Rákhely
- />Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- />Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary
| | - Kornél L Kovács
- />Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- />Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary
- />Department of Oral Biology and Experimental Dental Research, University of Szeged, Tisza L. krt. 64, 6720 Szeged, Hungary
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Neuhaus J, Schrödl W, Shehata AA, Krüger M. Detection of Clostridium botulinum in liquid manure and biogas plant wastes. Folia Microbiol (Praha) 2015; 60:451-6. [PMID: 25753763 DOI: 10.1007/s12223-015-0381-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 02/19/2015] [Indexed: 11/28/2022]
Abstract
Biogas plants have been considered as a source for possible amplification and distribution of pathogenic bacteria capable of causing severe infections in humans and animals. Manure and biogas wastes could be sources for spore-forming bacteria such as Clostridium botulinum. In the present study, 24 liquid manure and 84 biogas waste samples from dairies where the majority of the cows suffered from chronic botulism were investigated for the presence of botulinum neurotoxins (BoNT) and C. botulinum spores. The prevalence of BoNT/A, B, C, D, and E in biogas wastes was 16.6, 8.3, 10.7, 7.1, and 10.8 %, respectively, while in manure, the prevalence was 0.0, 0.0, 0.0, 8.3, and 4.1 %, respectively. After enrichment of samples in reinforced cultural medium, they were tested for C. botulinum BoNT/A, B, C, D, and E using ELISA (indirect C. botulinum detection). The prevalence of C. botulinum type A, B, C, D, and E samples in biogas wastes was 20.2, 15.5, 19, 10.7, and 34.8 %, respectively, while the prevalence in liquid manure was 0.0, 0.0, 0.0, 8.3, and 12.5 %, respectively. In conclusion, the occurrence of BoNT and C. botulinum spores in biogas waste of diseased animals indicates an increased and underestimated hygienic risk. Application of digestates from biogas fermentations as fertilizers could lead to an accumulation of long lifespan spores in the environment and could be a possible health hazard.
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Affiliation(s)
- Jürgen Neuhaus
- Institute of Bacteriology and Mycology, Faculty of Veterinary Medicine, Leipzig University, An den Tierkliniken 29, 04103, Leipzig, Germany
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Stolze Y, Zakrzewski M, Maus I, Eikmeyer F, Jaenicke S, Rottmann N, Siebner C, Pühler A, Schlüter A. Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:14. [PMID: 25688290 PMCID: PMC4329661 DOI: 10.1186/s13068-014-0193-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/22/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Decomposition of biomass for biogas production can be practiced under wet and dry fermentation conditions. In contrast to the dry fermentation technology, wet fermentation is characterized by a high liquid content and a relatively low total solid content. In this study, the composition and functional potential of a biogas-producing microbial community in an agricultural biogas reactor operating under wet fermentation conditions was analyzed by a metagenomic approach applying 454-pyrosequencing. The obtained metagenomic dataset and corresponding 16S rRNA gene amplicon sequences were compared to the previously sequenced comparable metagenome from a dry fermentation process, meeting explicitly identical boundary conditions regarding sample and community DNA preparation, sequencing technology, processing of sequence reads and data analyses by bioinformatics tools. RESULTS High-throughput metagenome sequencing of community DNA from the wet fermentation process applying the pyrosequencing approach resulted in 1,532,780 reads, with an average read length of 397 bp, accounting for approximately 594 million bases of sequence information in total. Taxonomic comparison of the communities from wet and dry fermentation revealed similar microbial profiles with Bacteria being the predominant superkingdom, while the superkingdom Archaea was less abundant. In both biogas plants, the bacterial phyla Firmicutes, Bacteroidetes, Spirochaetes and Proteobacteria were identified with descending frequencies. Within the archaeal superkingdom, the phylum Euryarchaeota was most abundant with the dominant class Methanomicrobia. Functional profiles of the communities revealed that environmental gene tags representing methanogenesis enzymes were present in both biogas plants in comparable frequencies. 16S rRNA gene amplicon high-throughput sequencing disclosed differences in the sub-communities comprising methanogenic Archaea between both processes. Fragment recruitments of metagenomic reads to the reference genome of the archaeon Methanoculleus bourgensis MS2(T) revealed that dominant methanogens within the dry fermentation process were highly related to the reference. CONCLUSIONS Although process parameters, substrates and technology differ between the wet and dry biogas fermentations analyzed in this study, community profiles are very similar at least at higher taxonomic ranks, illustrating that core community taxa perform key functions in biomass decomposition and methane synthesis. Regarding methanogenesis, Archaea highly related to the type strain M. bourgensis MS2(T) dominate the dry fermentation process, suggesting the adaptation of members belonging to this species to specific fermentation process parameters.
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Affiliation(s)
- Yvonne Stolze
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Martha Zakrzewski
- />QIMR Berghofer Medical Research Institute Herston, 300 Herston Road, Brisbane, QLD 4006 Australia
| | - Irena Maus
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Felix Eikmeyer
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Sebastian Jaenicke
- />Bioinformatics Resource Facility, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Nils Rottmann
- />NORTH-TEC Maschinenbau GmbH, Oldenhörn 1, 25821 Bredstedt, Germany
| | - Clemens Siebner
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Alfred Pühler
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Andreas Schlüter
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
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Singh KM, Patel AK, Shah RK, Reddy B, Joshi CG. Potential functional gene diversity involved in methanogenesis and methanogenic community structure in Indian buffalo (Bubalus bubalis) rumen. J Appl Genet 2015; 56:411-26. [PMID: 25663664 DOI: 10.1007/s13353-015-0270-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/26/2014] [Accepted: 01/06/2015] [Indexed: 11/26/2022]
Abstract
Understanding the methanogen community structure and methanogenesis from Bubalus bubalis in India may be beneficial to methane mitigation. Our current understanding of the microbial processes leading to methane production is incomplete, and further advancement in the knowledge of methanogenesis pathways would provide means to manipulate its emission in the future. In the present study, we evaluated the methanogenic community structure in the rumen as well as their potential genes involved in methanogenesis. The taxonomic and metabolic profiles of methanogens were assessed by shotgun sequencing of rumen metagenome by Ion Torrent semiconductor sequencing. The buffalo rumen contained representative genera of all the families of methanogens. Members of Methanobacteriaceae were found to be dominant, followed by Methanosarcinaceae, Methanococcaceae, Methanocorpusculaceae, and Thermococcaceae. A total of 60 methanogenic genera were detected in buffalo rumen. Methanogens related to the genera Methanobrevibacter, Methanosarcina, Methanococcus, Methanocorpusculum, Methanothermobacter, and Methanosphaera were predominant, representing >70 % of total archaeal sequences. The metagenomic dataset indicated the presence of genes involved in the methanogenesis and acetogenesis pathways, and the main functional genes were those of key enzymes in the methanogenesis. Sequences related to CoB--CoM heterodisulfide reductase, methyl coenzyme M reductase, f420-dependent methylenetetrahydromethanopterin reductase, and formylmethanofuran dehydrogenase were predominant in rumen. In addition, methenyltetrahydrofolate cyclohydrolase, methylenetetrahydrofolate dehydrogenase, 5,10-methylenetetrahydrofolate reductase, and acetyl-coenzyme A synthetase were also recovered.
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Affiliation(s)
- Krishna M Singh
- Department of Animal Biotechnology, Anand Agricultural University, Anand, India,
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Analysis of microbial community structure and composition in leachates from a young landfill by 454 pyrosequencing. Appl Microbiol Biotechnol 2015; 99:5657-68. [DOI: 10.1007/s00253-015-6409-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 01/13/2015] [Accepted: 01/15/2015] [Indexed: 10/24/2022]
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73
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Kovács E, Wirth R, Maróti G, Bagi Z, Nagy K, Minárovits J, Rákhely G, Kovács KL. Augmented biogas production from protein-rich substrates and associated metagenomic changes. BIORESOURCE TECHNOLOGY 2015; 178:254-261. [PMID: 25316194 DOI: 10.1016/j.biortech.2014.08.111] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/24/2014] [Accepted: 08/25/2014] [Indexed: 05/07/2023]
Abstract
This study demonstrates that appropriate adaptation of the microbial community to protein-rich biomass can lead to sustainable biogas production. The process of acclimation to these unusual mono-substrates was controlled by the protease activity of the microbial community. Meat extract (C/N=3.32) and kitchen waste (C/N=12.43) were used as biogas substrates. Metagenome analysis highlighted several mesophilic strains that displayed a preference for protein degradation. Bacillus coagulans, Bacillus subtilis and Pseudomonas fluorescens were chosen for detailed investigation. Pure cultures were added to biogas reactors fed solely with protein-rich substrates. The bioaugmentation resulted in a 50% increase in CH4 production even without any acclimation. The survival and biological activity of the added bacteria were followed in fed-batch fermenters by qPCR. Stable biogas production was observed for an extended period of time in laboratory CSTR reactors fed with biomass of low C/N.
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Affiliation(s)
- Etelka Kovács
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Közép fasor 52, Hungary; Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, H-6726 Szeged, Temesvári krt. 52, Hungary.
| | - Roland Wirth
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Közép fasor 52, Hungary.
| | - Gergely Maróti
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, H-6726 Szeged, Temesvári krt. 52, Hungary.
| | - Zoltán Bagi
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Közép fasor 52, Hungary.
| | - Katalin Nagy
- Department of Oral Biology and Experimental Dental Research, University of Szeged, H-6720 Szeged, Tisza L. krt. 64, Hungary.
| | - János Minárovits
- Department of Oral Biology and Experimental Dental Research, University of Szeged, H-6720 Szeged, Tisza L. krt. 64, Hungary.
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Közép fasor 52, Hungary; Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, H-6726 Szeged, Temesvári krt. 52, Hungary.
| | - Kornél L Kovács
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Közép fasor 52, Hungary; Department of Oral Biology and Experimental Dental Research, University of Szeged, H-6720 Szeged, Tisza L. krt. 64, Hungary; Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, H-6726 Szeged, Temesvári krt. 52, Hungary.
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Fröschle B, Heiermann M, Lebuhn M, Messelhäusser U, Plöchl M. Hygiene and Sanitation in Biogas Plants. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 151:63-99. [PMID: 26337844 DOI: 10.1007/978-3-319-21993-6_3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The increasing number of agricultural biogas plants and higher amounts of digestate spread on agricultural land arouse a considerable interest in the hygiene situation of digested products. This chapter reviews the current knowledge on sanitation during anaerobic digestion and the hygienic status of digestate concerning a multitude of pathogens potentially compromising the health of humans, animals and plants. Physical, chemical and biological parameters influencing the efficiency of sanitation in anaerobic digestion are considered. The degree of germ reduction depends particularly on the resistance of the pathogen of concern, the processing conditions, the feedstock composition and the diligence of the operation management. Most scientific studies facing sanitation in biogas plants have provided data ascertaining reduction of pathogens by the biogas process. Some pathogens, however, are able to persist virtually unaffected due to the ability to build resistant permanent forms. As compared to the feedstock, the sanitary status of the digestate is thus improved or in the worst case, the sanitary quality remains almost unchanged. According to this, the spreading of digestate on agricultural area in accordance to current rules and best practice recommendations is considered to impose no additional risk for the health of humans, animals and plants.
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Affiliation(s)
- Bianca Fröschle
- Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Lange Point 6, 85354, Freising, Germany,
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75
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Desta AF, Assefa F, Leta S, Stomeo F, Wamalwa M, Njahira M, Appolinaire D. Microbial community structure and diversity in an integrated system of anaerobic-aerobic reactors and a constructed wetland for the treatment of tannery wastewater in Modjo, Ethiopia. PLoS One 2014; 9:e115576. [PMID: 25541981 PMCID: PMC4277355 DOI: 10.1371/journal.pone.0115576] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 11/29/2014] [Indexed: 11/18/2022] Open
Abstract
A culture-independent approach was used to elucidate the microbial diversity and structure in the anaerobic-aerobic reactors integrated with a constructed wetland for the treatment of tannery wastewater in Modjo town, Ethiopia. The system has been running with removal efficiencies ranging from 94%-96% for COD, 91%-100% for SO4(2-) and S(2-), 92%-94% for BOD, 56%-82% for total Nitrogen and 2%-90% for NH3-N. 16S rRNA gene clone libraries were constructed and microbial community assemblies were determined by analysis of a total of 801 unique clone sequences from all the sites. Operational Taxonomic Unit (OTU)--based analysis of the sequences revealed highly diverse communities in each of the reactors and the constructed wetland. A total of 32 phylotypes were identified with the dominant members affiliated to Clostridia (33%), Betaproteobacteria (10%), Bacteroidia (10%), Deltaproteobacteria (9%) and Gammaproteobacteria (6%). Sequences affiliated to the class Clostridia were the most abundant across all sites. The 801 sequences were assigned to 255 OTUs, of which 3 OTUs were shared among the clone libraries from all sites. The shared OTUs comprised 80 sequences belonging to Clostridiales Family XIII Incertae Sedis, Bacteroidetes and unclassified bacterial group. Significantly different communities were harbored by the anaerobic, aerobic and rhizosphere sites of the constructed wetland. Numerous representative genera of the dominant bacterial classes obtained from the different sample sites of the integrated system have been implicated in the removal of various carbon- containing pollutants of natural and synthetic origins. To our knowledge, this is the first report of microbial community structure in tannery wastewater treatment plant from Ethiopia.
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Affiliation(s)
- Adey Feleke Desta
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Fassil Assefa
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Seyoum Leta
- Centre for Environmental Science, College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Francesca Stomeo
- Biosciences eastern and central Africa- International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Mark Wamalwa
- Biosciences eastern and central Africa- International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Moses Njahira
- Biosciences eastern and central Africa- International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Djikeng Appolinaire
- Biosciences eastern and central Africa- International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
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76
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First draft genome sequence of the amylolytic Bacillus thermoamylovorans wild-type strain 1A1 isolated from a thermophilic biogas plant. J Biotechnol 2014; 192 Pt A:154-5. [DOI: 10.1016/j.jbiotec.2014.09.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 09/19/2014] [Indexed: 01/27/2023]
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77
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Maus I, Wibberg D, Stantscheff R, Stolze Y, Blom J, Eikmeyer FG, Fracowiak J, König H, Pühler A, Schlüter A. Insights into the annotated genome sequence of Methanoculleus bourgensis MS2(T), related to dominant methanogens in biogas-producing plants. J Biotechnol 2014; 201:43-53. [PMID: 25455016 DOI: 10.1016/j.jbiotec.2014.11.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/18/2014] [Accepted: 11/21/2014] [Indexed: 01/13/2023]
Abstract
The final step of the biogas production process, the methanogenesis, is frequently dominated by members of the genus Methanoculleus. In particular, the species Methanoculleus bourgensis was identified to play a role in different biogas reactor systems. The genome of the type strain M. bourgensis MS2(T), originally isolated from a sewage sludge digestor, was completely sequenced to analyze putative adaptive genome features conferring competitiveness within biogas reactor environments to the strain. Sequencing and assembly of the M. bourgensis MS2(T) genome yielded a chromosome with a size of 2,789,773 bp. Comparative analysis of M. bourgensis MS2(T) and Methanoculleus marisnigri JR1 revealed significant similarities. The absence of genes for a putative ammonium uptake system may indicate that M. bourgensis MS2(T) is adapted to environments rich in ammonium/ammonia. Specific genes featuring predicted functions in the context of osmolyte production were detected in the genome of M. bourgensis MS2(T). Mapping of metagenome sequences derived from a production-scale biogas plant revealed that M. bourgensis MS2(T) almost completely comprises the genetic information of dominant methanogens present in the biogas reactor analyzed. Hence, availability of the M. bourgensis MS2(T) genome sequence may be valuable regarding further research addressing the performance of Methanoculleus species in agricultural biogas plants.
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Affiliation(s)
- Irena Maus
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Daniel Wibberg
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Robbin Stantscheff
- Institute of Microbiology and Wine Research, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Yvonne Stolze
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jochen Blom
- Department of Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Gießen, Germany
| | | | - Jochen Fracowiak
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Helmut König
- Institute of Microbiology and Wine Research, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Alfred Pühler
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
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78
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Tomazetto G, Wibberg D, Schlüter A, Oliveira VM. New FeFe-hydrogenase genes identified in a metagenomic fosmid library from a municipal wastewater treatment plant as revealed by high-throughput sequencing. Res Microbiol 2014; 166:9-19. [PMID: 25446611 DOI: 10.1016/j.resmic.2014.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 10/08/2014] [Accepted: 11/04/2014] [Indexed: 12/18/2022]
Abstract
A fosmid metagenomic library was constructed with total community DNA obtained from a municipal wastewater treatment plant (MWWTP), with the aim of identifying new FeFe-hydrogenase genes encoding the enzymes most important for hydrogen metabolism. The dataset generated by pyrosequencing of a fosmid library was mined to identify environmental gene tags (EGTs) assigned to FeFe-hydrogenase. The majority of EGTs representing FeFe-hydrogenase genes were affiliated with the class Clostridia, suggesting that this group is the main hydrogen producer in the MWWTP analyzed. Based on assembled sequences, three FeFe-hydrogenase genes were predicted based on detection of the L2 motif (MPCxxKxxE) in the encoded gene product, confirming true FeFe-hydrogenase sequences. These sequences were used to design specific primers to detect fosmids encoding FeFe-hydrogenase genes predicted from the dataset. Three identified fosmids were completely sequenced. The cloned genomic fragments within these fosmids are closely related to members of the Spirochaetaceae, Bacteroidales and Firmicutes, and their FeFe-hydrogenase sequences are characterized by the structure type M3, which is common to clostridial enzymes. FeFe-hydrogenase sequences found in this study represent hitherto undetected sequences, indicating the high genetic diversity regarding these enzymes in MWWTP. Results suggest that MWWTP have to be considered as reservoirs for new FeFe-hydrogenase genes.
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Affiliation(s)
- Geizecler Tomazetto
- Division of Microbial Resources, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, CP 6171, CEP 13081-970 Campinas, SP, Brazil.
| | - Daniel Wibberg
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Andreas Schlüter
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Valéria M Oliveira
- Division of Microbial Resources, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, CP 6171, CEP 13081-970 Campinas, SP, Brazil.
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79
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Solli L, Håvelsrud OE, Horn SJ, Rike AG. A metagenomic study of the microbial communities in four parallel biogas reactors. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:146. [PMID: 25328537 PMCID: PMC4200192 DOI: 10.1186/s13068-014-0146-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/22/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND Biogas is a renewable energy carrier which is used for heat and power production or, in the form of purified methane, as a vehicle fuel. The formation of methane from organic materials is carried out by a mixed microbial community under anaerobic conditions. However, details about the microbes involved and their function are limited. In this study we compare the metagenomes of four parallel biogas reactors digesting a protein-rich substrate, relate microbiology to biogas performance, and observe differences in these reactors' microbial communities compared to the original inoculum culture. RESULTS The biogas process performance during the startup phase of four parallel continuous stirred tank reactors (designated R1, R2, R3, and R4) co-digesting fish waste and cow manure was studied. The microbial composition of the inoculum (day 0) and the four reactors at day 59 was studied and compared using 454 FLX Titanium pyrosequencing. In the inoculum and the reactor samples, the Bacteria Clostridium and Syntrophomonas were highly abundant, and the dominating methanogen was the hydrogenotrophic Methanoculleus. Syntrophic prokaryotes frequently found in biogas reactors with high concentrations of ammonium and volatile fatty acids were detected in all samples. The species Candidatus Cloacimonas acidaminovorans of the candidate phylum Cloacimonetes (WWE1) increased in all reactors and was the dominating bacterium at day 59. In particular, this bacterium showed a very high abundance in R1, which distinguished this reactor significantly from the other reactors in terms of microbial composition. Methane production and the reactor slurry characteristics were monitored in the digestion period. Generally all four reactors operated stably and showed rather similar characteristics. The average methane production in the reactors varied between 0.278 and 0.296 L gVS(-1), with the lowest production in R1. CONCLUSIONS This study showed that four parallel reactors co-digesting manure and fish waste silage operated stably during a startup phase. Several important Archaea and Bacteria degrading the protein-rich substrate were identified. In particular, microorganisms involved in syntrophic methane production seemed to be important. The detailed characterization of the microbial communities presented in this work may be useful for the operation of biogas plants degrading substrates with high concentrations of proteins.
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Affiliation(s)
- Linn Solli
- />Bioforsk, Norwegian Institute for Agricultural and Environmental Research, Frederik A. Dahls vei 20, 1432 Ås ᅟ, Norway
| | - Othilde Elise Håvelsrud
- />Department of Microbiology, Oslo University Hospital, P.O. Box 4950, Nydalen, 0424 Oslo, Norway
| | - Svein Jarle Horn
- />Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, N-1432, Ås ᅟ, Norway
| | - Anne Gunn Rike
- />Norwegian Geotechnical Institute, Sognsveien 72, P.O. Box 3930, Ullevål Stadion, N-0806 Oslo, Norway
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80
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Riemenschneider C, Zerr W, Vater N, Brunn H, Mohring SAI, Hamscher G. Analysis and behavior of colistin during anaerobic fermentation. BIORESOURCE TECHNOLOGY 2014; 170:303-309. [PMID: 25151074 DOI: 10.1016/j.biortech.2014.07.100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 06/18/2014] [Accepted: 07/24/2014] [Indexed: 05/23/2023]
Abstract
A new analytical method for the determination of colistin in fermenter samples was developed followed by a study on the behavior of this substance during anaerobic fermentation. Analysis of colistin A and B was carried out by liquid chromatography-tandem mass spectrometry. Separation of the analytes was performed on a Security Guard column (4×3mm). Fourteen fermentation tests in batch as well as in continuous reactors were carried out. After 44days of anaerobic digestion of cattle manure, initially spiked with 500mg/kg of colistin sulfate, a considerable decrease of the colistin concentration to less than 1mg/kg could be observed. Furthermore, the daily production of biogas and methane was measured. A correlation between gas production and colistin concentration could not be determined. However, an increase of 10% of the cumulative methane production was observed in those fermenters spiked with an initial bolus of 500mg/kg colistin.
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Affiliation(s)
- C Riemenschneider
- Landesbetrieb Hessisches Landeslabor (LHL), Standort Kassel, Druseltalstraße 67, 34131 Kassel, Germany; Justus Liebig University Giessen, Institute of Food Chemistry and Food Biotechnology, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - W Zerr
- LHL, Standort Bad Hersfeld, Schloss Eichhof, 36251 Bad Hersfeld, Germany
| | - N Vater
- Landesbetrieb Hessisches Landeslabor (LHL), Standort Kassel, Druseltalstraße 67, 34131 Kassel, Germany
| | - H Brunn
- LHL, Standort Giessen, Schubertstraße 60, 35392 Giessen, Germany
| | - S A I Mohring
- Justus Liebig University Giessen, Institute of Food Chemistry and Food Biotechnology, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - G Hamscher
- Justus Liebig University Giessen, Institute of Food Chemistry and Food Biotechnology, Heinrich-Buff-Ring 58, 35392 Giessen, Germany.
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81
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Kohrs F, Heyer R, Magnussen A, Benndorf D, Muth T, Behne A, Rapp E, Kausmann R, Heiermann M, Klocke M, Reichl U. Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants. Anaerobe 2014; 29:59-67. [DOI: 10.1016/j.anaerobe.2013.11.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 11/22/2013] [Accepted: 11/25/2013] [Indexed: 12/20/2022]
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82
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Complete genome sequence of the cellulolytic thermophile Ruminoclostridium cellulosi wild-type strain DG5 isolated from a thermophilic biogas plant. J Biotechnol 2014; 188:136-7. [DOI: 10.1016/j.jbiotec.2014.08.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 08/21/2014] [Indexed: 12/26/2022]
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83
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Hahnke S, Striesow J, Elvert M, Mollar XP, Klocke M. Clostridium bornimense sp. nov., isolated from a mesophilic, two-phase, laboratory-scale biogas reactor. Int J Syst Evol Microbiol 2014; 64:2792-2797. [DOI: 10.1099/ijs.0.059691-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel anaerobic, mesophilic, hydrogen-producing bacterium, designated strain M2/40T, was isolated from a mesophilic, two-phase, laboratory-scale biogas reactor fed continuously with maize silage supplemented with 5 % wheat straw. 16S rRNA gene sequence comparison revealed an affiliation to the genus
Clostridium
sensu stricto (cluster I of the clostridia), with
Clostridium cellulovorans
as the closest characterized species, showing 93.8 % sequence similarity to the type strain. Cells of strain M2/40T were rods to elongated filamentous rods that showed variable Gram staining. Optimal growth occurred at 35 °C and at pH 7. Grown on glucose, the main fermentation products were H2, CO2, formate, lactate and propionate. The DNA G+C content was 29.6 mol%. The major fatty acids (>10 %) were C16 : 0, summed feature 10 (C18 : 1ω11c/ω9t/ω6t and/or unknown ECL 17.834) and C18 : 1ω11c dimethylacetal. Based on phenotypic, chemotaxonomic and phylogenetic differences, strain M2/40T represents a novel species within the genus
Clostridium
, for which we propose the name Clostridium bornimense sp. nov. The type strain is M2/40T ( = DSM 25664T = CECT 8097T).
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Affiliation(s)
- Sarah Hahnke
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering Potsdam-Bornim (ATB), D-14469 Potsdam, Germany
| | - Jutta Striesow
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering Potsdam-Bornim (ATB), D-14469 Potsdam, Germany
| | - Marcus Elvert
- Organic Geochemistry Group, MARUM–Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, D-28359 Bremen, Germany
| | - Xavier Prieto Mollar
- Organic Geochemistry Group, MARUM–Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, D-28359 Bremen, Germany
| | - Michael Klocke
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering Potsdam-Bornim (ATB), D-14469 Potsdam, Germany
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84
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Tukacs-Hájos A, Pap B, Maróti G, Szendefy J, Szabó P, Rétfalvi T. Monitoring of thermophilic adaptation of mesophilic anaerobe fermentation of sugar beet pressed pulp. BIORESOURCE TECHNOLOGY 2014; 166:288-94. [PMID: 24926601 DOI: 10.1016/j.biortech.2014.05.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/16/2014] [Accepted: 05/17/2014] [Indexed: 05/06/2023]
Abstract
Anaerobe fermentation of sugar beet pressed pulp was investigated in pilot-scale digesters. Thermophilic adaptation of mesophilic culture was monitored using chemical analysis and metagenomic characterization of the sludge. Temperature adaptation was achieved by increasing the temperature gradually (2 °C day(-1)) and by greatly decreasing the OLR. During stable run, the OLR was increased gradually to 11.29 kg VS m(-3)d(-1) and biogas yield was 5% higher in the thermophilic reactor. VFA levels increased in the thermophilic reactor with increased OLR (acetic acid 646 mg L(-1), propionic acid 596 mg L(-1)), then VFA decreased and the operation was manageable beside the relative high tVFA (1300-2000 mg L(-1)). The effect of thermophilic adaptation on the microbial communities was studied using a sequencing-based metagenomic approach. Connections between physico-chemical parameters and populations of bacteria and methanogen archaea were revealed.
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Affiliation(s)
| | - Bernadett Pap
- Seqomics Biotechnology Ltd., H-6782 Mórahalom, Vállalkozók útja 7., Hungary
| | - Gergely Maróti
- Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, H-6726 Szeged, Temesvári krt. 62., Hungary
| | - Judit Szendefy
- Biogáz Fejlesztő Ltd., H-7400 Kaposvár, Pécsi út 8-10., Hungary
| | - Piroska Szabó
- Institute of Chemistry, Faculty for Forestry, University of West Hungary, H-9400 Sopron, Bajcsy-Zs. u. 4., Hungary
| | - Tamás Rétfalvi
- Institute of Chemistry, Faculty for Forestry, University of West Hungary, H-9400 Sopron, Bajcsy-Zs. u. 4., Hungary.
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85
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Hahnke S, Wibberg D, Tomazetto G, Pühler A, Klocke M, Schlüter A. Whole genome sequence of Clostridium bornimense strain M2/40 isolated from a lab-scale mesophilic two-phase biogas reactor digesting maize silage and wheat straw. J Biotechnol 2014; 184:199-200. [DOI: 10.1016/j.jbiotec.2014.05.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/27/2014] [Indexed: 10/25/2022]
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86
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Neuhaus J, Shehata AA, Krüger M. Detection of pathogenic clostridia in biogas plant wastes. Folia Microbiol (Praha) 2014; 60:15-9. [DOI: 10.1007/s12223-014-0334-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 06/24/2014] [Indexed: 11/29/2022]
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87
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Fotidis IA, Wang H, Fiedel NR, Luo G, Karakashev DB, Angelidaki I. Bioaugmentation as a solution to increase methane production from an ammonia-rich substrate. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:7669-76. [PMID: 24873631 DOI: 10.1021/es5017075] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Ammonia-rich substrates inhibit the anaerobic digestion (AD) process and constitute the main reason for low energy recovery in full-scale reactors. It is estimated that many full-scale AD reactors are operating in ammonia induced "inhibited steady-state" with significant losses of the potential biogas production yield. To date there are not any reliable methods to alleviate the ammonia toxicity effect or to efficiently digest ammonia-rich waste. In the current study, bioaugmentation as a possible method to alleviate ammonia toxicity effect in a mesophilic continuously stirred-tank reactor (CSTR) operating under "inhibited steady state" was tested. A fast growing hydrogenotrophic methanogen (i.e., Methanoculleus bourgensis MS2(T)) was bioaugmented in the CSTR reactor at high ammonia levels (5 g NH4(+)-N L(-1)). A second CSTR reactor was used as control with no bioaugmentation. The results derived from this study clearly demonstrated a 31.3% increase in methane production yield in the CSTR reactor, at steady-state, after bioaugmentation. Additionally, high-throughput 16S rRNA gene sequencing analysis showed a 5-fold increase in relative abundance of Methanoculleus spp. after bioaugmentation. On the contrary to all methods used today to alleviate ammonia toxicity effect, the tested bioaugmentation process performed without interrupting the continuous operation of the reactor and without replacing the ammonia-rich feedstock.
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Affiliation(s)
- Ioannis A Fotidis
- Department of Environmental Engineering, Technical University of Denmark , Building 113, DK-2800 Kgs. Lyngby, Denmark
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88
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Ziganshina EE, Bagmanova AR, Khilyas IV, Ziganshin AM. Assessment of a biogas-generating microbial community in a pilot-scale anaerobic reactor. J Biosci Bioeng 2014; 117:730-6. [DOI: 10.1016/j.jbiosc.2013.11.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/25/2013] [Accepted: 11/18/2013] [Indexed: 10/25/2022]
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89
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Koeck DE, Zverlov VV, Liebl W, Schwarz WH. Comparative genotyping of Clostridium thermocellum strains isolated from biogas plants: genetic markers and characterization of cellulolytic potential. Syst Appl Microbiol 2014; 37:311-9. [PMID: 24951450 DOI: 10.1016/j.syapm.2014.05.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 10/25/2022]
Abstract
Clostridium thermocellum is among the most prevalent of known anaerobic cellulolytic bacteria. In this study, genetic and phenotypic variations among C. thermocellum strains isolated from different biogas plants were determined and different genotyping methods were evaluated on these isolates. At least two C. thermocellum strains were isolated independently from each of nine different biogas plants via enrichment on cellulose. Various DNA-based genotyping methods such as ribotyping, RAPD (Random Amplified Polymorphic DNA) and VNTR (Variable Number of Tandem Repeats) were applied to these isolates. One novel approach - the amplification of unknown target sequences between copies of a previously discovered Random Inserted Mobile Element (RIME) - was also tested. The genotyping method with the highest discriminatory power was found to be the amplification of the sequences between the insertion elements, where isolates from each biogas plant yielded a different band pattern. Cellulolytic potentials, optimal growth conditions and substrate spectra of all isolates were characterized to help identify phenotypic variations. Irrespective of the genotyping method used, the isolates from each individual biogas plant always exhibited identical patterns. This is suggestive of a single C. thermocellum strain exhibiting dominance in each biogas plant. The genotypic groups reflect the results of the physiological characterization of the isolates like substrate diversity and cellulase activity. Conversely, strains isolated across a range of biogas plants differed in their genotyping results and physiological properties. Both strains isolated from one biogas plant had the best specific cellulose-degrading properties and might therefore achieve superior substrate utilization yields in biogas fermenters.
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Affiliation(s)
- Daniela E Koeck
- Department of Microbiology, TechnischeUniversitätMünchen, Emil-Ramann-Str. 4, D-85350 Freising-Weihenstephan, Germany
| | - Vladimir V Zverlov
- Department of Microbiology, TechnischeUniversitätMünchen, Emil-Ramann-Str. 4, D-85350 Freising-Weihenstephan, Germany; Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, 123182 Moscow, Russia
| | - Wolfgang Liebl
- Department of Microbiology, TechnischeUniversitätMünchen, Emil-Ramann-Str. 4, D-85350 Freising-Weihenstephan, Germany
| | - Wolfgang H Schwarz
- Department of Microbiology, TechnischeUniversitätMünchen, Emil-Ramann-Str. 4, D-85350 Freising-Weihenstephan, Germany.
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90
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Yu H, Wang Q, Wang Z, Sahinkaya E, Li Y, Ma J, Wu Z. Start-up of an anaerobic dynamic membrane digester for waste activated sludge digestion: temporal variations in microbial communities. PLoS One 2014; 9:e93710. [PMID: 24695488 PMCID: PMC3973557 DOI: 10.1371/journal.pone.0093710] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/05/2014] [Indexed: 11/18/2022] Open
Abstract
An anaerobic dynamic membrane digester (ADMD) was developed to digest waste sludge, and pyrosequencing was used to analyze the variations of the bacterial and archaeal communities during the start-up. Results showed that bacterial community richness decreased and then increased over time, while bacterial diversity remained almost the same during the start-up. Proteobacteria and Bacteroidetes were the major phyla. At the class level, Betaproteobacteria was the most abundant at the end of start-up, followed by Sphingobacteria. In the archaeal community, richness and diversity peaked at the end of the start-up stage. Principle component and cluster analyses demonstrated that archaeal consortia experienced a distinct shift and became stable after day 38. Methanomicrobiales and Methanosarcinales were the two predominant orders. Further investigations indicated that Methanolinea and Methanosaeta were responsible for methane production in the ADMD system. Hydrogenotrophic pathways might prevail over acetoclastic means for methanogenesis during the start-up, supported by specific methanogenic activity tests.
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Affiliation(s)
- Hongguang Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, PR China
| | - Qiaoying Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, PR China
- * E-mail: (QYW); (ZWW)
| | - Zhiwei Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, PR China
- * E-mail: (QYW); (ZWW)
| | - Erkan Sahinkaya
- Istanbul Medeniyet University, Bioengineering Department, Kadıköy, Istanbul, Turkey
| | - Yongli Li
- Laboratory of Polymères, Biopolymères and Surfaces, UMR 6270, University of Rouen-CNRS-INSA, Boulevard Maurice de Broglie, Mont-Saint-Aignan, France
| | - Jinxing Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, PR China
| | - Zhichao Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, PR China
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91
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Tuan NN, Chang YC, Yu CP, Huang SL. Multiple approaches to characterize the microbial community in a thermophilic anaerobic digester running on swine manure: a case study. Microbiol Res 2014; 169:717-24. [PMID: 24629524 DOI: 10.1016/j.micres.2014.02.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 02/07/2014] [Accepted: 02/10/2014] [Indexed: 11/25/2022]
Abstract
In this study, the first survey of microbial community in thermophilic anaerobic digester using swine manure as sole feedstock was performed by multiple approaches including denaturing gradient gel electrophoresis (DGGE), clone library and pyrosequencing techniques. The integrated analysis of 21 DGGE bands, 126 clones and 8506 pyrosequencing read sequences revealed that Clostridia from the phylum Firmicutes account for the most dominant Bacteria. In addition, our analysis also identified additional taxa that were missed by the previous researches, including members of the bacterial phyla Synergistetes, Planctomycetes, Armatimonadetes, Chloroflexi and Nitrospira which might also play a role in thermophilic anaerobic digester. Most archaeal 16S rRNA sequences could be assigned to the order Methanobacteriales instead of Methanomicrobiales comparing to previous studies. In addition, this study reported that the member of Methanothermobacter genus was firstly found in thermophilic anaerobic digester.
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Affiliation(s)
- Nguyen Ngoc Tuan
- Department of Life Sciences, National Central University, No. 300 Jhongda Rd., Jhongli City 32001, Taiwan
| | - Yi-Chia Chang
- Department of Life Sciences, National Central University, No. 300 Jhongda Rd., Jhongli City 32001, Taiwan
| | - Chang-Ping Yu
- Institute of Urban Environment, Chinese Academy of Science, Xiamen 361021, China
| | - Shir-Ly Huang
- Department of Life Sciences, National Central University, No. 300 Jhongda Rd., Jhongli City 32001, Taiwan; Center for Biotechnology and Biomedical Engineering, National Central University, No. 300 Jhongda Rd., Jhongli City 32001, Taiwan.
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92
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Dai X, Luo F, Yi J, He Q, Dong B. Biodegradation of polyacrylamide by anaerobic digestion under mesophilic condition and its performance in actual dewatered sludge system. BIORESOURCE TECHNOLOGY 2014; 153:55-61. [PMID: 24345566 DOI: 10.1016/j.biortech.2013.11.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/31/2013] [Accepted: 11/07/2013] [Indexed: 06/03/2023]
Abstract
Polyacrylamide (PAM) used in sludge dewatering widely exists in high-solid anaerobic digestion. Degradation of polyacrylamide accompanied with accumulation of its toxic monomer is important to disposition of biogas residues. The potential of anaerobic digestion activity in microbial utilization of PAM was investigated in this study. The results indicated that the utilization rate of PAM (as nitrogen source) was influenced by accumulation of ammonia, while cumulative removal of amide group was accorded with zeroth order reaction in actual dewatered system. The adjoining amide group can combined into ether group after biodegradation. PAM can be broken down in different position of its carbon chain backbone. In actual sludge system, the hydrolytic PAM was liable to combined tyrosine-rich protein to form colloid complex, and then consumed as carbon source to form monomer when easily degradable organics were exhausted. The accumulation of acrylamide was leveled off ultimately, accompanied with the yield of methane.
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Affiliation(s)
- Xiaohu Dai
- National Engineering Research Center for Urban Pollution Control, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - Fan Luo
- National Engineering Research Center for Urban Pollution Control, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - Jing Yi
- National Engineering Research Center for Urban Pollution Control, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - Qunbiao He
- National Engineering Research Center for Urban Pollution Control, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - Bin Dong
- National Engineering Research Center for Urban Pollution Control, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China.
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93
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Town JR, Links MG, Fonstad TA, Dumonceaux TJ. Molecular characterization of anaerobic digester microbial communities identifies microorganisms that correlate to reactor performance. BIORESOURCE TECHNOLOGY 2014; 151:249-57. [PMID: 24246480 DOI: 10.1016/j.biortech.2013.10.070] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/10/2013] [Accepted: 10/15/2013] [Indexed: 05/13/2023]
Abstract
A time-course analysis was conducted of thermophilic anaerobic digestion of dairy manure and wheat distillery thin stillage. Sequencing of chaperonin targets provided a phylogenetic survey of both bacteria and archaea in the digestate, along with an appraisal of the diversity of the reactor microbiome. A total of 1129 bacterial operational taxonomic units (OTU) were detected in the reactors, with OTU related to Clostridium becoming numerically dominant by day 7, and Acetivibrio-related OTU by day 35. Archaeal communities were less diverse, with 19 OTU detected representing both acetoclastic and hydrogenotrophic methanogens. Regardless of input material, the same organisms came to dominate the reactors, reflecting strong selective pressures present in the digesters. Principal coordinate analysis of the microbial communities showed that the bacterial communities clustered based on factors other than input material. Bacterial and archaeal OTU were identified with significant correlations to performance parameters, suggesting important roles in the methane production pathway.
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Affiliation(s)
- Jennifer R Town
- Agriculture and Agri-Food Canada, 107 Science Pl., Saskatoon, SK S7N 0X2, Canada; Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Dr., Saskatoon, SK S7N 5B4, Canada
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94
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Kovács E, Wirth R, Maróti G, Bagi Z, Rákhely G, Kovács KL. Biogas production from protein-rich biomass: fed-batch anaerobic fermentation of casein and of pig blood and associated changes in microbial community composition. PLoS One 2013; 8:e77265. [PMID: 24146974 PMCID: PMC3797734 DOI: 10.1371/journal.pone.0077265] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 08/30/2013] [Indexed: 11/23/2022] Open
Abstract
It is generally accepted as a fact in the biogas technology that protein-rich biomass substrates should be avoided due to inevitable process inhibition. Substrate compositions with a low C/N ratio are considered difficult to handle and may lead to process failure, though protein-rich industrial waste products have outstanding biogas generation potential. This common belief has been challenged by using protein-rich substrates, i.e. casein and precipitated pig blood protein in laboratory scale continuously stirred mesophilic fed-batch biogas fermenters. Both substrates proved suitable for sustained biogas production (0.447 L CH4/g protein oDM, i.e. organic total solids) in high yield without any additives, following a period of adaptation of the microbial community. The apparent key limiting factors in the anaerobic degradation of these proteinaceous materials were the accumulation of ammonia and hydrogen sulfide. Changes in time in the composition of the microbiological community were determined by next-generation sequencing-based metagenomic analyses. Characteristic rearrangements of the biogas-producing community upon protein feeding and specific differences due to the individual protein substrates were recognized. The results clearly demonstrate that sustained biogas production is readily achievable, provided the system is well-characterized, understood and controlled. Biogas yields (0.45 L CH4/g oDM) significantly exceeding those of the commonly used agricultural substrates (0.25-0.28 L CH4/g oDM) were routinely obtained. The results amply reveal that these high-energy-content waste products can be converted to biogas, a renewable energy carrier with flexible uses that can replace fossil natural gas in its applications. Process control, with appropriate acclimation of the microbial community to the unusual substrate, is necessary. Metagenomic analysis of the microbial community by next-generation sequencing allows a precise determination of the alterations in the community composition in the course of the process.
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Affiliation(s)
- Etelka Kovács
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Roland Wirth
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gergely Maróti
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Zoltán Bagi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary
- Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Kornél L. Kovács
- Department of Biotechnology, University of Szeged, Szeged, Hungary
- Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
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95
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Stark L, Giersch T, Wünschiers R. Efficiency of RNA extraction from selected bacteria in the context of biogas production and metatranscriptomics. Anaerobe 2013; 29:85-90. [PMID: 24096086 DOI: 10.1016/j.anaerobe.2013.09.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 09/05/2013] [Accepted: 09/10/2013] [Indexed: 10/26/2022]
Abstract
Understanding the microbial population in anaerobic digestion is an essential task to increase efficient substrate use and process stability. The metabolic state, represented e.g. by the transcriptome, of a fermenting system can help to find markers for monitoring industrial biogas production to prevent failures or to model the whole process. Advances in next-generation sequencing make transcriptomes accessible for large-scale analyses. In order to analyze the metatranscriptome of a mixed-species sample, isolation of high-quality RNA is the first step. However, different extraction methods may yield different efficiencies in different species. Especially in mixed-species environmental samples, unbiased isolation of transcripts is important for meaningful conclusions. We applied five different RNA-extraction protocols to nine taxonomic diverse bacterial species. Chosen methods are based on various lysis and extraction principles. We found that the extraction efficiency of different methods depends strongly on the target organism. RNA isolation of gram-positive bacteria was characterized by low yield whilst from gram-negative species higher concentrations can be obtained. Transferring our results to mixed-species investigations, such as metatranscriptomics with biofilms or biogas plants, leads to the conclusion that particular microorganisms might be over- or underrepresented depending on the method applied. Special care must be taken when using such metatranscriptomics data for, e.g. process modeling.
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Affiliation(s)
- Lucy Stark
- Faculty of Mathematics, Natural Sciences and Computer Sciences, University of Applied Sciences Mittweida, Technikumplatz 17, 09648 Mittweida, Germany.
| | - Tina Giersch
- Faculty of Mathematics, Natural Sciences and Computer Sciences, University of Applied Sciences Mittweida, Technikumplatz 17, 09648 Mittweida, Germany
| | - Röbbe Wünschiers
- Faculty of Mathematics, Natural Sciences and Computer Sciences, University of Applied Sciences Mittweida, Technikumplatz 17, 09648 Mittweida, Germany
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96
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Lyu C, Chen C, Ge F, Liu D, Zhao S, Chen D. A preliminary metagenomic study of puer tea during pile fermentation. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2013; 93:3165-3174. [PMID: 23553377 DOI: 10.1002/jsfa.6149] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Revised: 02/20/2013] [Accepted: 04/01/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND Up to now, there has been no report on the taxonomic and functional analysis of the microbial community in fermenting puer tea by pyrosequencing. In this study, metagenomic pyrosequencing was first used in fermenting puer tea to delineate a relatively comprehensive overview of the microbial taxonomy while also preliminarily characterising the functional ontologies of microbial genes present in puer tea pile fermentation. RESULTS A total of 251 738 pyrosequencing reads (9197 contigs and 145 402 singletons) were generated by pyrosequencing. Taxonomic analysis revealed three dominant bacterial phyla, Actinobacteria (30.08%), Proteobacteria (24.47%) and Firmicutes (20.23%), and one dominant eukaryotic phylum, Ascomycota (15.21%) [corrected]. A total of 58 664 hits were categorised into 28 functional subsystems based on the SEED database. Moreover, two categories, 'metabolism of terpenoids and polyketides' and 'biosynthesis of other secondary metabolites', were selectively analysed and 69 enzyme genes were presented in 16 pathways. CONCLUSION The dominant microbes of puer tea fermentation were bacteria in the present study, and yeasts rather than moulds accounted for the overwhelming majority of Eukaryota. The analysis of functional genes and metabolic pathways will be helpful for further study of the mechanism of puer tea fermentation at molecular level.
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Affiliation(s)
- Changyong Lyu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
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97
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Bareither CA, Wolfe GL, McMahon KD, Benson CH. Microbial diversity and dynamics during methane production from municipal solid waste. WASTE MANAGEMENT (NEW YORK, N.Y.) 2013; 33:1982-1992. [PMID: 23318155 DOI: 10.1016/j.wasman.2012.12.013] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/13/2012] [Accepted: 12/14/2012] [Indexed: 06/01/2023]
Abstract
The objectives of this study were to characterize development of bacterial and archaeal populations during biodegradation of municipal solid waste (MSW) and to link specific methanogens to methane generation. Experiments were conducted in three 0.61-m-diameter by 0.90-m-tall laboratory reactors to simulate MSW bioreactor landfills. Pyrosequencing of 16S rRNA genes was used to characterize microbial communities in both leachate and solid waste. Microbial assemblages in effluent leachate were similar between reactors during peak methane generation. Specific groups within the Bacteroidetes and Thermatogae phyla were present in all samples and were particularly abundant during peak methane generation. Microbial communities were not similar in leachate and solid fractions assayed at the end of reactor operation; solid waste contained a more abundant bacterial community of cellulose-degrading organisms (e.g., Firmicutes). Specific methanogen populations were assessed using quantitative polymerase chain reaction. Methanomicrobiales, Methanosarcinaceae, and Methanobacteriales were the predominant methanogens in all reactors, with Methanomicrobiales consistently the most abundant. Methanogen growth phases coincided with accelerated methane production, and cumulative methane yield increased with increasing total methanogen abundance. The difference in methanogen populations and corresponding methane yield is attributed to different initial cellulose and hemicellulose contents of the MSW. Higher initial cellulose and hemicellulose contents supported growth of larger methanogen populations that resulted in higher methane yield.
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Affiliation(s)
- Christopher A Bareither
- Civil & Environmental Engineering, Colorado State University, Ft. Collins, CO 80532, USA; Geological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
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98
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Draft genome sequence of the cellulolytic Clostridium thermocellum wild-type strain BC1 playing a role in cellulosic biomass degradation. J Biotechnol 2013; 168:62-3. [PMID: 23968723 DOI: 10.1016/j.jbiotec.2013.08.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 08/09/2013] [Indexed: 01/14/2023]
Abstract
The bacterium Clostridium thermocellum BC1, a thermophilic, anaerobic bacterium of the family Clostridiaceae, was isolated from a compost treatment site in Germany. It is able to grow efficiently on cellulose and cellodextrins. The draft genome sequence of C. thermocellum BC1 has been established and provides the genetic basis for application of this microorganism in thermophilic degradation of cellulosic biomass.
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99
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Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity. ISME JOURNAL 2013; 8:88-102. [PMID: 23949661 DOI: 10.1038/ismej.2013.120] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 05/30/2013] [Accepted: 06/07/2013] [Indexed: 11/08/2022]
Abstract
Cellulose is the most abundant biopolymer on Earth. Optimising energy recovery from this renewable but recalcitrant material is a key issue. The metaproteome expressed by thermophilic communities during cellulose anaerobic digestion was investigated in microcosms. By multiplying the analytical replicates (65 protein fractions analysed by MS/MS) and relying solely on public protein databases, more than 500 non-redundant protein functions were identified. The taxonomic community structure as inferred from the metaproteomic data set was in good overall agreement with 16S rRNA gene tag pyrosequencing and fluorescent in situ hybridisation analyses. Numerous functions related to cellulose and hemicellulose hydrolysis and fermentation catalysed by bacteria related to Caldicellulosiruptor spp. and Clostridium thermocellum were retrieved, indicating their key role in the cellulose-degradation process and also suggesting their complementary action. Despite the abundance of acetate as a major fermentation product, key methanogenesis enzymes from the acetoclastic pathway were not detected. In contrast, enzymes from the hydrogenotrophic pathway affiliated to Methanothermobacter were almost exclusively identified for methanogenesis, suggesting a syntrophic acetate oxidation process coupled to hydrogenotrophic methanogenesis. Isotopic analyses confirmed the high dominance of the hydrogenotrophic methanogenesis. Very surprising was the identification of an abundant proteolytic activity from Coprothermobacter proteolyticus strains, probably acting as scavenger and/or predator performing proteolysis and fermentation. Metaproteomics thus appeared as an efficient tool to unravel and characterise metabolic networks as well as ecological interactions during methanisation bioprocesses. More generally, metaproteomics provides direct functional insights at a limited cost, and its attractiveness should increase in the future as sequence databases are growing exponentially.
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100
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Eikmeyer FG, Köfinger P, Poschenel A, Jünemann S, Zakrzewski M, Heinl S, Mayrhuber E, Grabherr R, Pühler A, Schwab H, Schlüter A. Metagenome analyses reveal the influence of the inoculant Lactobacillus buchneri CD034 on the microbial community involved in grass ensiling. J Biotechnol 2013; 167:334-43. [PMID: 23880441 DOI: 10.1016/j.jbiotec.2013.07.021] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/10/2013] [Accepted: 07/10/2013] [Indexed: 10/26/2022]
Abstract
Silage is green fodder conserved by lactic acid fermentation performed by epiphytic lactic acid bacteria under anaerobic conditions. To improve the ensiling process and the quality of the resulting silage, starter cultures are added to the fresh forage. A detailed analysis of the microbial community playing a role in grass ensiling has been carried out by high throughput sequencing technologies. Moreover, the influence of the inoculant Lactobacillus buchneri CD034 on the microbial community composition was studied. For this purpose, grass was ensiled untreated or inoculated with L. buchneri CD034. The fresh forage as well as silages after 14 and 58 days of fermentation were characterized physico-chemically. Characteristic silage conditions such as increased titers of lactic acid bacteria and higher concentrations of acetic acid were observed in the inoculated silage in comparison to the untreated samples. Taxonomic community profiles deduced from 16S rDNA amplicon sequences indicated that the relative abundance of Lactococci diminished in the course of fermentations and that the proportion of bacteria belonging to the phyla Proteobacteria and Bacteroidetes increased during the fermentation of untreated silage. In the inoculated silage, members of these phyla were repressed due to an increased abundance of Lactobacilli. In addition, metagenome analyses of silage samples confirmed taxonomic profiles based on 16S rDNA amplicons. Moreover, Lactobacillus plantarum, Lactobacillus brevis and Lactococcus lactis were found to be dominant species within silages as analyzed by means of fragment recruitments of metagenomic sequence reads on complete reference genome sequences. Fragment recruitments also provided clear evidence for the competitiveness of the inoculant strain L. buchneri CD034 during the fermentation of the inoculated silage. The inoculation strain was able to outcompete other community members and also affected physico-chemical characteristics of the silage.
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Affiliation(s)
- Felix G Eikmeyer
- Institute for Genome Research and Systems Biology, Center for Biotechnology, Bielefeld University, D-33594 Bielefeld, Germany
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