Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing

Kroeber M, Bekel T, Diaz NN, Goesmann A, Jaenicke S, Krause L, Miller D, Runte KJ, Viehoever P, Pühler A, Schlueter A (2009)
JOURNAL OF BIOTECHNOLOGY 142(1): 38-49.

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The phylogenetic structure of the microbial community residing in a fermentation sample from a production-scale biogas plant fed with maize silage. green rye and liquid manure was analysed by an integrated approach using clone library sequences and metagenome sequence data obtained by 454-pyrosequencing. Sequencing of 109 clones from a bacterial and an archaeal 165-rDNA amplicon library revealed that the obtained nucleotide sequences are similar but not identical to 165-rDNA database sequences derived from different anaerobic environments including digestors and bioreactors. Most of the bacterial 165-rDNA sequences could be assigned to the phylum Firmicutes with the most abundant class Clostridia and to the class Bacteroidetes, whereas most archaeal 165-rDNA sequences cluster close to the methanogen Methanoculleus bourgensis. Further sequences of the archaeal library most probably represent so far non-characterised species within the genus Methanoculleus. A similar result derived from phylogenetic analysis of mcrA clone sequences. The mcrA gene product encodes the a-subunit of methyl-coenzyme-M reductase involved in the final step of methanogenesis. BLASTn analysis applying stringent settings resulted in assignment of 165-rDNA metagenome sequence reads to 62 165-rDNA amplicon sequences thus enabling frequency of abundance estimations for 165-rDNA clone library sequences. Ribosomal Database Project (RDP) Classifier processing of metagenome 165-rDNA reads revealed abundance of the phyla Firmicutes, Bacteroidetes and Euryarchaeota and the orders Clostridiales, Bacteroidales and Methanomicrobiales. Moreover, a large fraction of 165-rDNA metagenome reads could not be assigned to lower taxonomic ranks, demonstrating that numerous microorganisms in the analysed fermentation sample of the biogas plant are still unclassified or unknown. (C) 2009 Elsevier B.V. All rights reserved.
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Kroeber M, Bekel T, Diaz NN, et al. Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. JOURNAL OF BIOTECHNOLOGY. 2009;142(1):38-49.
Kroeber, M., Bekel, T., Diaz, N. N., Goesmann, A., Jaenicke, S., Krause, L., Miller, D., et al. (2009). Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. JOURNAL OF BIOTECHNOLOGY, 142(1), 38-49. doi:10.1016/j.jbiotec.2009.02.010
Kroeber, M., Bekel, T., Diaz, N. N., Goesmann, A., Jaenicke, S., Krause, L., Miller, D., Runte, K. J., Viehoever, P., Pühler, A., et al. (2009). Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. JOURNAL OF BIOTECHNOLOGY 142, 38-49.
Kroeber, M., et al., 2009. Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. JOURNAL OF BIOTECHNOLOGY, 142(1), p 38-49.
M. Kroeber, et al., “Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing”, JOURNAL OF BIOTECHNOLOGY, vol. 142, 2009, pp. 38-49.
Kroeber, M., Bekel, T., Diaz, N.N., Goesmann, A., Jaenicke, S., Krause, L., Miller, D., Runte, K.J., Viehoever, P., Pühler, A., Schlueter, A.: Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. JOURNAL OF BIOTECHNOLOGY. 142, 38-49 (2009).
Kroeber, Magdalena, Bekel, Thomas, Diaz, Naryttza N., Goesmann, Alexander, Jaenicke, Sebastian, Krause, Lutz, Miller, Dimitri, Runte, Kai J., Viehoever, Prisca, Pühler, Alfred, and Schlueter, Andreas. “Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing”. JOURNAL OF BIOTECHNOLOGY 142.1 (2009): 38-49.
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Data provided by Europe PubMed Central.

Microbiome dynamics and adaptation of expression signatures during methane production failure and process recovery.
Grohmann A, Fehrmann S, Vainshtein Y, Haag NL, Wiese F, Stevens P, Naegele HJ, Oechsner H, Hartsch T, Sohn K, Grumaz C., Bioresour. Technol. 247(), 2018
PMID: 28954247
The dynamic changes and interactional networks of prokaryotic community between co-digestion and mono-digestions of corn stalk and pig manure.
Wang M, Zhang X, Zhou J, Yuan Y, Dai Y, Li D, Li Z, Liu X, Yan Z., Bioresour. Technol. 225(), 2017
PMID: 27875765
Comparative Analysis of Methanogenic Communities in Different Laboratory-Scale Anaerobic Digesters.
Ziganshin AM, Ziganshina EE, Kleinsteuber S, Nikolausz M., Archaea 2016(), 2016
PMID: 28074084
Herbinix luporum sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor.
Koeck DE, Hahnke S, Zverlov VV., Int. J. Syst. Evol. Microbiol. 66(10), 2016
PMID: 27453473
Efficiency and biotechnological aspects of biogas production from microalgal substrates.
Klassen V, Blifernez-Klassen O, Wobbe L, Schluter A, Kruse O, Mussgnug JH., J. Biotechnol. 234(), 2016
PMID: 27449486
An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant.
Ortseifen V, Stolze Y, Maus I, Sczyrba A, Bremges A, Albaum SP, Jaenicke S, Fracowiak J, Puhler A, Schluter A., J. Biotechnol. 231(), 2016
PMID: 27312700
Degradation of oxytetracycline and its impacts on biogas-producing microbial community structure.
Coban H, Ertekin E, Ince O, Turker G, Akyol C, Ince B., Bioprocess Biosyst Eng 39(7), 2016
PMID: 26974525
Spatiotemporal dynamics of bacterial and archaeal communities in household biogas digesters from tropical and subtropical regions of Yunnan Province, China.
Tian G, Li Q, Dong M, Wu Y, Yang B, Zhang L, Li Y, Yin F, Zhao X, Wang Y, Xiao W, Cui X, Zhang W., Environ Sci Pollut Res Int 23(11), 2016
PMID: 26916266
Microbial community structural analysis of an expanded granular sludge bed (EGSB) reactor for beet sugar industrial wastewater (BSIW) treatment.
Ambuchi JJ, Liu J, Wang H, Shan L, Zhou X, Mohammed MO, Feng Y., Appl. Microbiol. Biotechnol. 100(10), 2016
PMID: 26795960
Hydrolysis of synthetic polyesters by Clostridium botulinum esterases.
Perz V, Baumschlager A, Bleymaier K, Zitzenbacher S, Hromic A, Steinkellner G, Pairitsch A, Lyskowski A, Gruber K, Sinkel C, Kuper U, Ribitsch D, Guebitz GM., Biotechnol. Bioeng. 113(5), 2016
PMID: 26524601
Metagenome from a Spirulina digesting biogas reactor: analysis via binning of contigs and classification of short reads.
Nolla-Ardevol V, Peces M, Strous M, Tegetmeyer HE., BMC Microbiol. 15(), 2015
PMID: 26680455
Clostridium cluster I and their pathogenic members in a full-scale operating biogas plant.
Dohrmann AB, Walz M, Lowen A, Tebbe CC., Appl. Microbiol. Biotechnol. 99(8), 2015
PMID: 25472441
Application of Anaerobic Digestion Model No. 1 to describe the syntrophic acetate oxidation of poultry litter in thermophilic anaerobic digestion.
Rivera-Salvador V, Lopez-Cruz IL, Espinosa-Solares T, Aranda-Barradas JS, Huber DH, Sharma D, Toledo JU., Bioresour. Technol. 167(), 2014
PMID: 25011081
Monitoring of thermophilic adaptation of mesophilic anaerobe fermentation of sugar beet pressed pulp.
Tukacs-Hajos A, Pap B, Maroti G, Szendefy J, Szabo P, Retfalvi T., Bioresour. Technol. 166(), 2014
PMID: 24926601
Improved picoliter-sized micro-reactors for high-throughput biological analysis.
Han W, Yuan L, Wei Q, Li Y, Ren L, Zhou X, Yu J, Yu Y., Sci China Life Sci 56(12), 2013
PMID: 24302294
DGGE analysis of buffalo manure eubacteria for hydrogen production: effect of pH, temperature and pretreatments.
Carillo P, Carotenuto C, Di Cristofaro F, Kafantaris I, Lubritto C, Minale M, Morrone B, Papa S, Woodrow P., Mol. Biol. Rep. 39(12), 2012
PMID: 23014994
Cultivation-independent methods applied to the microbial prospection of oil and gas in soil from a sedimentary basin in Brazil.
Miqueletto PB, Andreote FD, Dias AC, Ferreira JC, Dos Santos Neto EV, de Oliveira VM., AMB Express 1(), 2011
PMID: 22018208

50 References

Data provided by Europe PubMed Central.

The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill.
Luton PE, Wayne JM, Sharp RJ, Riley PW., Microbiology (Reading, Engl.) 148(Pt 11), 2002
PMID: 12427943
Effect of bowel preparation and colonoscopy on post-procedure intestinal microbiota composition.
Mai V, Greenwald B, Morris JG Jr, Raufman JP, Stine OC., Gut 55(12), 2006
PMID: 17124165
A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.
Manichanh C, Chapple CE, Frangeul L, Gloux K, Guigo R, Dore J., Nucleic Acids Res. 36(16), 2008
PMID: 18682527
Methanogenic population structure in a variety of anaerobic bioreactors.
McHugh S, Carton M, Mahony T, O'Flaherty V., FEMS Microbiol. Lett. 219(2), 2003
PMID: 12620635
Anaerobic bacterial degradation for the effective utilization of biomass
Ohmiya, Biotechnol. Bioprocess. Eng. 10(), 2005
"Candidatus Cloacamonas acidaminovorans": genome sequence reconstruction provides a first glimpse of a new bacterial division.
Pelletier E, Kreimeyer A, Bocs S, Rouy Z, Gyapay G, Chouari R, Riviere D, Ganesan A, Daegelen P, Sghir A, Cohen GN, Medigue C, Weissenbach J, Le Paslier D., J. Bacteriol. 190(7), 2008
PMID: 18245282
Investigation of methanogen population structure in biogas reactor by molecular characterization of methyl-coenzyme M reductase A (mcrA) genes
Rastogi, Bioresour. Technol. (), 2007
Microbial population in the biomass adhering to supporting material in a packed-bed reactor degrading organic solid waste.
Sasaki K, Haruta S, Ueno Y, Ishii M, Igarashi Y., Appl. Microbiol. Biotechnol. 75(4), 2007
PMID: 17334757
IncP-1-beta plasmid pGNB1 isolated from a bacterial community from a wastewater treatment plant mediates decolorization of triphenylmethane dyes.
Schluter A, Krahn I, Kollin F, Bonemann G, Stiens M, Szczepanowski R, Schneiker S, Puhler A., Appl. Environ. Microbiol. 73(20), 2007
PMID: 17675426
The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology.
Schluter A, Bekel T, Diaz NN, Dondrup M, Eichenlaub R, Gartemann KH, Krahn I, Krause L, Kromeke H, Kruse O, Mussgnug JH, Neuweger H, Niehaus K, Puhler A, Runte KJ, Szczepanowski R, Tauch A, Tilker A, Viehover P, Goesmann A., J. Biotechnol. 136(1-2), 2008
PMID: 18597880
Microbial community of a mesophilic propionate-degrading methanogenic consortium in chemostat cultivation analyzed based on 16S rRNA and acetate kinase genes.
Shigematsu T, Era S, Mizuno Y, Ninomiya K, Kamegawa Y, Morimura S, Kida K., Appl. Microbiol. Biotechnol. 72(2), 2006
PMID: 16496142
Molecular characterization of microbial communities in fault-bordered aquifers in the Miocene formation of northernmost Japan
Shimizu, Geobiology 4(), 2006
Isolation and characterization of a new Clostridium sp. that performs effective cellulosic waste digestion in a thermophilic methanogenic bioreactor.
Shiratori H, Ikeno H, Ayame S, Kataoka N, Miya A, Hosono K, Beppu T, Ueda K., Appl. Environ. Microbiol. 72(5), 2006
PMID: 16672520
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.
Wang Q, Garrity GM, Tiedje JM, Cole JR., Appl. Environ. Microbiol. 73(16), 2007
PMID: 17586664
Production and energetic use of biogas from energy crops and wastes in Germany.
Weiland P., Appl. Biochem. Biotechnol. 109(1-3), 2003
PMID: 12794299
Diversity of the resident microbiota in a thermophilic municipal biogas plant.
Weiss A, Jerome V, Freitag R, Mayer HK., Appl. Microbiol. Biotechnol. 81(1), 2008
PMID: 18820906
Metagenomics: read length matters.
Wommack KE, Bhavsar J, Ravel J., Appl. Environ. Microbiol. 74(5), 2008
PMID: 18192407
Enhancement of biogas production from solid substrates using different techniques--a review.
Yadvika , Santosh , Sreekrishnan TR, Kohli S, Rana V., Bioresour. Technol. 95(1), 2004
PMID: 15207286

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