Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing

Zakrzewski M, Goesmann A, Jaenicke S, Jünemann S, Eikmeyer FG, Szczepanowski R, Al-Soud WA, Sørensen S, Pühler A, Schlüter A (2012)
Journal of Biotechnology 158(4): 248-258.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
DOI
Autor*in
Zakrzewski, MarthaUniBi; Goesmann, AlexanderUniBi ; Jaenicke, SebastianUniBi; Jünemann, SebastianUniBi; Eikmeyer, Felix GregorUniBi ; Szczepanowski, RafaelUniBi; Al-Soud, Waleed Abu; Sørensen, Søren; Pühler, AlfredUniBi ; Schlüter, AndreasUniBi
Einrichtung
Centrum für Biotechnologie > Arbeitsgruppe A. Pühler
Technische Fakultät > Computational Genomics
Centrum für Biotechnologie > Graduate Center > Graduate Cluster Industrial Biotechnology
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Abstract / Bemerkung
Structural composition and gene content of a biogas-producing microbial community from a production-scale biogas plant fed with renewable primary products was recently analyzed by means of a metagenome sequencing approach. To determine the transcriptionally active part of the same biogas community and to identify key transcripts for the biogas production process, the metatranscriptome of the microorganisms was sequenced for the first time. The metatranscriptome sequence dataset generated on the Genome Sequencer FLX platform is represented by 484,920 sequence reads. Taxonomic profiling of the active part of the community by classification of 16S ribosomal sequence tags revealed that members of the Euryarchaeota and Firmicutes account for the dominant phyla. Only smaller fractions of the 16S ribosomal sequence tags were assigned to the phyla Bacteroidetes, Actinobacteria and Synergistetes. Among the mRNA-derived sequence tags from the metatranscriptome dataset, transcripts encoding enzymes involved in substrate hydrolysis, acidogenesis, acetate formation and methanogenesis could be identified. Transcripts for enzymes functioning in methanogenesis are among the most abundant mRNA tags indicating that the corresponding pathway is very active in the methanogenic sub-community. As a frame of reference for evaluation of metatranscriptome sequence data, the 16S rDNA-based taxonomic profile of the community was analyzed by means of high-throughput 16S rDNA amplicon sequencing. Processing of the obtained amplicon reads resulted in 18,598 high-quality 16S rDNA sequences covering the V3-V4 hypervariable region of the 16S rRNA gene. Comparison of the taxonomic profiles deduced from 16S rDNA amplicon sequences and the metatranscriptome dataset indicates a high transcriptional activity of archaeal species. Overall, it was shown that the most abundant species dominating the community also contributed the majority of the transcripts. In the future, key transcripts for the biogas production process will provide valuable markers for evaluation of the performance of biogas-producing microbial communities with the objective to optimize the biotechnology of this process.
Erscheinungsjahr
2012
Zeitschriftentitel
Journal of Biotechnology
Band
158
Ausgabe
4
Seite(n)
248-258
ISSN
0168-1656
Page URI
https://pub.uni-bielefeld.de/record/2484618

Zitieren

Zakrzewski M, Goesmann A, Jaenicke S, et al. Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. Journal of Biotechnology. 2012;158(4):248-258.
Zakrzewski, M., Goesmann, A., Jaenicke, S., Jünemann, S., Eikmeyer, F. G., Szczepanowski, R., Al-Soud, W. A., et al. (2012). Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. Journal of Biotechnology, 158(4), 248-258. doi:10.1016/j.jbiotec.2012.01.020
Zakrzewski, Martha, Goesmann, Alexander, Jaenicke, Sebastian, Jünemann, Sebastian, Eikmeyer, Felix Gregor, Szczepanowski, Rafael, Al-Soud, Waleed Abu, Sørensen, Søren, Pühler, Alfred, and Schlüter, Andreas. 2012. “Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing”. Journal of Biotechnology 158 (4): 248-258.
Zakrzewski, M., Goesmann, A., Jaenicke, S., Jünemann, S., Eikmeyer, F. G., Szczepanowski, R., Al-Soud, W. A., Sørensen, S., Pühler, A., and Schlüter, A. (2012). Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. Journal of Biotechnology 158, 248-258.
Zakrzewski, M., et al., 2012. Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. Journal of Biotechnology, 158(4), p 248-258.
M. Zakrzewski, et al., “Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing”, Journal of Biotechnology, vol. 158, 2012, pp. 248-258.
Zakrzewski, M., Goesmann, A., Jaenicke, S., Jünemann, S., Eikmeyer, F.G., Szczepanowski, R., Al-Soud, W.A., Sørensen, S., Pühler, A., Schlüter, A.: Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. Journal of Biotechnology. 158, 248-258 (2012).
Zakrzewski, Martha, Goesmann, Alexander, Jaenicke, Sebastian, Jünemann, Sebastian, Eikmeyer, Felix Gregor, Szczepanowski, Rafael, Al-Soud, Waleed Abu, Sørensen, Søren, Pühler, Alfred, and Schlüter, Andreas. “Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing”. Journal of Biotechnology 158.4 (2012): 248-258.

68 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Long-term investigation of microbial community composition and transcription patterns in a biogas plant undergoing ammonia crisis.
Fischer MA, Güllert S, Refai S, Künzel S, Deppenmeier U, Streit WR, Schmitz RA., Microb Biotechnol 12(2), 2019
PMID: 30381904
Shift in Bacterial Community Structure Drives Different Atrazine-Degrading Efficiencies.
Liu X, Chen K, Chuang S, Xu X, Jiang J., Front Microbiol 10(), 2019
PMID: 30761118
Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants.
Heyer R, Schallert K, Siewert C, Kohrs F, Greve J, Maus I, Klang J, Klocke M, Heiermann M, Hoffmann M, Püttker S, Calusinska M, Zoun R, Saake G, Benndorf D, Reichl U., Microbiome 7(1), 2019
PMID: 31029164
Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep.
Cui G, Li J, Gao Z, Wang Y., PeerJ 7(), 2019
PMID: 31149407
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
Anaerobic digestion of spent mushroom substrate under thermophilic conditions: performance and microbial community analysis.
Xiao Z, Lin M, Fan J, Chen Y, Zhao C, Liu B., Appl Microbiol Biotechnol 102(1), 2018
PMID: 29079864
Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants.
Stolze Y, Bremges A, Maus I, Pühler A, Sczyrba A, Schlüter A., Microb Biotechnol 11(4), 2018
PMID: 29205917
Detection of novel syntrophic acetate-oxidizing bacteria from biogas processes by continuous acetate enrichment approaches.
Westerholm M, Müller B, Singh A, Karlsson Lindsjö O, Schnürer A., Microb Biotechnol 11(4), 2018
PMID: 29239113
Association of Tongue Bacterial Flora and Subtypes of Liver-Fire Hyperactivity Syndrome in Hypertensive Patients.
Luo JW, Lin CH, Zhu YB, Zheng XY, Wu YX, Chen WW, Yang X., Evid Based Complement Alternat Med 2018(), 2018
PMID: 29541146
Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies.
Campanaro S, Treu L, Kougias PG, Zhu X, Angelidaki I., Sci Rep 8(1), 2018
PMID: 29386622
The application of rumen simulation technique (RUSITEC) for studying dynamics of the bacterial community and metabolome in rumen fluid and the effects of a challenge with Clostridium perfringens.
Wetzels SU, Eger M, Burmester M, Kreienbrock L, Abdulmawjood A, Pinior B, Wagner M, Breves G, Mann E., PLoS One 13(2), 2018
PMID: 29415046
Thermophilic Alkaline Fermentation Followed by Mesophilic Anaerobic Digestion for Efficient Hydrogen and Methane Production from Waste-Activated Sludge: Dynamics of Bacterial Pathogens as Revealed by the Combination of Metagenomic and Quantitative PCR Analyses.
Wan J, Jing Y, Rao Y, Zhang S, Luo G., Appl Environ Microbiol 84(6), 2018
PMID: 29330191
Targeting Bacteria and Methanogens To Understand the Role of Residual Slurry as an Inoculant in Stored Liquid Dairy Manure.
Habtewold J, Gordon R, Sokolov V, VanderZaag A, Wagner-Riddle C, Dunfield K., Appl Environ Microbiol 84(7), 2018
PMID: 29374043
Microbial rRNA gene expression and co-occurrence profiles associate with biokinetics and elemental composition in full-scale anaerobic digesters.
Ziels RM, Svensson BH, Sundberg C, Larsson M, Karlsson A, Yekta SS., Microb Biotechnol 11(4), 2018
PMID: 29633555
Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion.
Jia Y, Ng SK, Lu H, Cai M, Lee PKH., Biotechnol Biofuels 11(), 2018
PMID: 29713376
A comparative study of eubacterial communities by PCR-DGGE fingerprints in anoxic and aerobic biotrickling filters used for biogas desulfurization.
Valle A, Fernández M, Ramírez M, Rovira R, Gabriel D, Cantero D., Bioprocess Biosyst Eng 41(8), 2018
PMID: 29704053
Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants.
Hassa J, Maus I, Off S, Pühler A, Scherer P, Klocke M, Schlüter A., Appl Microbiol Biotechnol 102(12), 2018
PMID: 29713790
Genetic repertoires of anaerobic microbiomes driving generation of biogas.
Grohmann A, Vainshtein Y, Euchner E, Grumaz C, Bryniok D, Rabus R, Sohn K., Biotechnol Biofuels 11(), 2018
PMID: 30250507
Epimural bacterial community structure in the rumen of Holstein cows with different responses to a long-term subacute ruminal acidosis diet challenge.
Wetzels SU, Mann E, Pourazad P, Qumar M, Pinior B, Metzler-Zebeli BU, Wagner M, Schmitz-Esser S, Zebeli Q., J Dairy Sci 100(3), 2017
PMID: 28041738
Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes.
Maus I, Bremges A, Stolze Y, Hahnke S, Cibis KG, Koeck DE, Kim YS, Kreubel J, Hassa J, Wibberg D, Weimann A, Off S, Stantscheff R, Zverlov VV, Schwarz WH, König H, Liebl W, Scherer P, McHardy AC, Sczyrba A, Klocke M, Pühler A, Schlüter A., Biotechnol Biofuels 10(), 2017
PMID: 29158776
Description of Proteiniphilum saccharofermentans sp. nov., Petrimonas mucosa sp. nov. and Fermentimonas caenicola gen. nov., sp. nov., isolated from mesophilic laboratory-scale biogas reactors, and emended description of the genus Proteiniphilum.
Hahnke S, Langer T, Koeck DE, Klocke M., Int J Syst Evol Microbiol 66(3), 2016
PMID: 26782749
Microbial communities from 20 different hydrogen-producing reactors studied by 454 pyrosequencing.
Etchebehere C, Castelló E, Wenzel J, del Pilar Anzola-Rojas M, Borzacconi L, Buitrón G, Cabrol L, Carminato VM, Carrillo-Reyes J, Cisneros-Pérez C, Fuentes L, Moreno-Andrade I, Razo-Flores E, Filippi GR, Tapia-Venegas E, Toledo-Alarcón J, Zaiat M., Appl Microbiol Biotechnol 100(7), 2016
PMID: 26825820
Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy.
Campanaro S, Treu L, Kougias PG, De Francisci D, Valle G, Angelidaki I., Biotechnol Biofuels 9(), 2016
PMID: 26839589
Changes in rhizosphere bacterial gene expression following glyphosate treatment.
Newman MM, Lorenz N, Hoilett N, Lee NR, Dick RP, Liles MR, Ramsier C, Kloepper JW., Sci Total Environ 553(), 2016
PMID: 26901800
Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis.
Luo G, Fotidis IA, Angelidaki I., Biotechnol Biofuels 9(), 2016
PMID: 26941838
Epimural Indicator Phylotypes of Transiently-Induced Subacute Ruminal Acidosis in Dairy Cattle.
Wetzels SU, Mann E, Metzler-Zebeli BU, Pourazad P, Qumar M, Klevenhusen F, Pinior B, Wagner M, Zebeli Q, Schmitz-Esser S., Front Microbiol 7(), 2016
PMID: 26973642
Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies.
Güllert S, Fischer MA, Turaev D, Noebauer B, Ilmberger N, Wemheuer B, Alawi M, Rattei T, Daniel R, Schmitz RA, Grundhoff A, Streit WR., Biotechnol Biofuels 9(), 2016
PMID: 27279900
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, Pühler A, Schlüter A., J Biotechnol 231(), 2016
PMID: 27312700
Mesophilic and thermophilic alkaline fermentation of waste activated sludge for hydrogen production: Focusing on homoacetogenesis.
Wan J, Jing Y, Zhang S, Angelidaki I, Luo G., Water Res 102(), 2016
PMID: 27420808
Efficiency and biotechnological aspects of biogas production from microalgal substrates.
Klassen V, Blifernez-Klassen O, Wobbe L, Schlüter A, Kruse O, Mussgnug JH., J Biotechnol 234(), 2016
PMID: 27449486
Perspectives for microbial community composition in anaerobic digestion: from abundance and activity to connectivity.
De Vrieze J, Verstraete W., Environ Microbiol 18(9), 2016
PMID: 27376701
Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type.
Heyer R, Benndorf D, Kohrs F, De Vrieze J, Boon N, Hoffmann M, Rapp E, Schlüter A, Sczyrba A, Reichl U., Biotechnol Biofuels 9(), 2016
PMID: 27462366
Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants.
Stolze Y, Bremges A, Rumming M, Henke C, Maus I, Pühler A, Sczyrba A, Schlüter A., Biotechnol Biofuels 9(), 2016
PMID: 27462367
Process parameters and changes in the microbial community patterns during the first 240 days of an agricultural energy crop digester.
Weithmann N, Weig AR, Freitag R., AMB Express 6(1), 2016
PMID: 27485518
Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates.
Maus I, Koeck DE, Cibis KG, Hahnke S, Kim YS, Langer T, Kreubel J, Erhard M, Bremges A, Off S, Stolze Y, Jaenicke S, Goesmann A, Sczyrba A, Scherer P, König H, Schwarz WH, Zverlov VV, Zverlov VV, Liebl W, Pühler A, Schlüter A, Klocke M., Biotechnol Biofuels 9(), 2016
PMID: 27525040
Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion.
De Vrieze J, Regueiro L, Props R, Vilchez-Vargas R, Jáuregui R, Pieper DH, Lema JM, Carballa M., Biotechnol Biofuels 9(), 2016
PMID: 27843490
Age-Related Differences in the Luminal and Mucosa-Associated Gut Microbiome of Broiler Chickens and Shifts Associated with Campylobacter jejuni Infection.
Awad WA, Mann E, Dzieciol M, Hess C, Schmitz-Esser S, Wagner M, Hess M., Front Cell Infect Microbiol 6(), 2016
PMID: 27921008
Complete genome sequence of the novel Porphyromonadaceae bacterium strain ING2-E5B isolated from a mesophilic lab-scale biogas reactor.
Hahnke S, Maus I, Wibberg D, Tomazetto G, Pühler A, Klocke M, Schlüter A., J Biotechnol 193(), 2015
PMID: 25444871
Insights into the annotated genome sequence of Methanoculleus bourgensis MS2(T), related to dominant methanogens in biogas-producing plants.
Maus I, Wibberg D, Stantscheff R, Stolze Y, Blom J, Eikmeyer FG, Fracowiak J, König H, Pühler A, Schlüter A., J Biotechnol 201(), 2015
PMID: 25455016
Transcriptomics in the tropics: Total RNA-based profiling of Costa Rican bromeliad-associated communities.
Goffredi SK, Jang GE, Haroon MF., Comput Struct Biotechnol J 13(), 2015
PMID: 25755850
Investigation of methanogenic community structures in rural biogas digesters from different climatic regions in Yunnan, southwest China.
Dong M, Wu Y, Li Q, Tian G, Yang B, Li Y, Zhang L, Wang Y, Xiao W, Yin F, Zhao X, Zhang W, Cui X., Curr Microbiol 70(5), 2015
PMID: 25575901
Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions.
Stolze Y, Zakrzewski M, Maus I, Eikmeyer F, Jaenicke S, Rottmann N, Siebner C, Pühler A, Schlüter A., Biotechnol Biofuels 8(), 2015
PMID: 25688290
Biogas production from brewery spent grain enhanced by bioaugmentation with hydrolytic anaerobic bacteria.
Čater M, Fanedl L, Malovrh Š, Marinšek Logar R., Bioresour Technol 186(), 2015
PMID: 25836034
Resource recovery from wastewater: application of meta-omics to phosphorus and carbon management.
Sales CM, Lee PK., Curr Opin Biotechnol 33(), 2015
PMID: 25827118
Metaproteomics of complex microbial communities in biogas plants.
Heyer R, Kohrs F, Reichl U, Benndorf D., Microb Biotechnol 8(5), 2015
PMID: 25874383
Community shifts in a well-operating agricultural biogas plant: how process variations are handled by the microbiome.
Theuerl S, Kohrs F, Benndorf D, Maus I, Wibberg D, Schlüter A, Kausmann R, Heiermann M, Rapp E, Reichl U, Pühler A, Klocke M., Appl Microbiol Biotechnol 99(18), 2015
PMID: 25998656
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.
Ziganshina EE, Belostotskiy DE, Ilinskaya ON, Boulygina EA, Grigoryeva TV, Ziganshin AM., Microb Ecol 70(4), 2015
PMID: 26045158
Classes of organic molecules targeted by a methanogenic microbial consortium grown on sedimentary rocks of various maturities.
Meslé M, Dromart G, Haeseler F, Oger PM., Front Microbiol 6(), 2015
PMID: 26136731
Characterization of microbial community structure during continuous anaerobic digestion of straw and cow manure.
Sun L, Pope PB, Eijsink VG, Schnürer A., Microb Biotechnol 8(5), 2015
PMID: 26152665
Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant.
Bremges A, Maus I, Belmann P, Eikmeyer F, Winkler A, Albersmeier A, Pühler A, Schlüter A, Sczyrba A., Gigascience 4(), 2015
PMID: 26229594
Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity.
Lü F, Bize A, Guillot A, Monnet V, Madigou C, Chapleur O, Mazéas L, He P, Bouchez T., ISME J 8(1), 2014
PMID: 23949661
Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques.
Vanwonterghem I, Jensen PD, Ho DP, Batstone DJ, Tyson GW., Curr Opin Biotechnol 27(), 2014
PMID: 24863897
Microbiomes in bioenergy production: from analysis to management.
Koch C, Müller S, Harms H, Harnisch F., Curr Opin Biotechnol 27(), 2014
PMID: 24863898
Dynamics in the microbial cytome-single cell analytics in natural systems.
Koch C, Harms H, Müller S., Curr Opin Biotechnol 27(), 2014
PMID: 24525083
Multiple approaches to characterize the microbial community in a thermophilic anaerobic digester running on swine manure: a case study.
Tuan NN, Chang YC, Yu CP, Huang SL., Microbiol Res 169(9-10), 2014
PMID: 24629524
Straw- and slurry-associated prokaryotic communities differ during co-fermentation of straw and swine manure.
Li J, Rui J, Pei Z, Sun X, Zhang S, Yan Z, Wang Y, Liu X, Zheng T, Li X., Appl Microbiol Biotechnol 98(10), 2014
PMID: 24633443
Isolation and differentiation of methanogenic Archaea from mesophilic corn-fed on-farm biogas plants with special emphasis on the genus Methanobacterium.
Stantscheff R, Kuever J, Rabenstein A, Seyfarth K, Dröge S, König H., Appl Microbiol Biotechnol 98(12), 2014
PMID: 24639207
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.
Hahnke S, Wibberg D, Tomazetto G, Pühler A, Klocke M, Schlüter A., J Biotechnol 184(), 2014
PMID: 24905146
A metagenomic study of the microbial communities in four parallel biogas reactors.
Solli L, Håvelsrud OE, Horn SJ, Rike AG., Biotechnol Biofuels 7(1), 2014
PMID: 25328537
Thermophilic microbial cellulose decomposition and methanogenesis pathways recharacterized by metatranscriptomic and metagenomic analysis.
Xia Y, Wang Y, Fang HH, Jin T, Zhong H, Zhang T., Sci Rep 4(), 2014
PMID: 25330991
Biostimulation to identify microbial communities involved in methane generation in shallow, kerogen-rich shales.
Meslé M, Périot C, Dromart G, Oger P., J Appl Microbiol 114(1), 2013
PMID: 22979955
Evaluation of stable isotope fingerprinting techniques for the assessment of the predominant methanogenic pathways in anaerobic digesters.
Nikolausz M, Walter RF, Sträuber H, Liebetrau J, Schmidt T, Kleinsteuber S, Bratfisch F, Günther U, Richnow HH., Appl Microbiol Biotechnol 97(5), 2013
PMID: 23299457
Towards a metagenomic understanding on enhanced biomethane production from waste activated sludge after pH 10 pretreatment.
Wong MT, Zhang D, Li J, Hui RK, Tun HM, Brar MS, Park TJ, Chen Y, Leung FC., Biotechnol Biofuels 6(1), 2013
PMID: 23506434
Metagenome analyses reveal the influence of the inoculant Lactobacillus buchneri CD034 on the microbial community involved in grass ensiling.
Eikmeyer FG, Köfinger P, Poschenel A, Jünemann S, Zakrzewski M, Heinl S, Mayrhuber E, Grabherr R, Pühler A, Schwab H, Schlüter A., J Biotechnol 167(3), 2013
PMID: 23880441
Draft genome sequence of the cellulolytic Clostridium thermocellum wild-type strain BC1 playing a role in cellulosic biomass degradation.
Koeck DE, Wibberg D, Koellmeier T, Blom J, Jaenicke S, Winkler A, Albersmeier A, Zverlov VV, Zverlov VV, Pühler A, Schwarz WH, Schlüter A., J Biotechnol 168(1), 2013
PMID: 23968723
Operational aspects, pH transition and microbial shifts of a H2S desulfurizing biotrickling filter with random packing material.
Montebello AM, Bezerra T, Rovira R, Rago L, Lafuente J, Gamisans X, Campoy S, Baeza M, Gabriel D., Chemosphere 93(11), 2013
PMID: 24041568
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.
McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, Knight R, Caporaso JG., Gigascience 1(1), 2012
PMID: 23587224
Complete genome sequence of the hydrogenotrophic, methanogenic archaeon Methanoculleus bourgensis strain MS2(T), Isolated from a sewage sludge digester.
Maus I, Wibberg D, Stantscheff R, Eikmeyer FG, Seffner A, Boelter J, Szczepanowski R, Blom J, Jaenicke S, König H, Pühler A, Schlüter A., J Bacteriol 194(19), 2012
PMID: 22965103

69 References

Daten bereitgestellt von Europe PubMed Central.

Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
Thermotoga lettingae sp. nov., a novel thermophilic, methanol-degrading bacterium isolated from a thermophilic anaerobic reactor.
Balk M, Weijma J, Stams AJ., Int. J. Syst. Evol. Microbiol. 52(Pt 4), 2002
PMID: 12148651
PyNAST: a flexible tool for aligning sequences to a template alignment
Caporaso, Bioinformatics 26(), 2009
QIIME allows analysis of high-throughput community sequencing data.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R., Nat. Methods 7(5), 2010
PMID: 20383131
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R., Proc. Natl. Acad. Sci. U.S.A. 108 Suppl 1(), 2010
PMID: 20534432
16S rDNA characterisation of bacterial and archaeal communities during start-up of anaerobic thermophilic digestion of cattle manure.
Chachkhiani M, Dabert P, Abzianidze T, Partskhaladze G, Tsiklauri L, Dudauri T, Godon JJ., Bioresour. Technol. 93(3), 2004
PMID: 15062816
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM., Nucleic Acids Res. 37(Database issue), 2008
PMID: 19004872
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL., Appl. Environ. Microbiol. 72(7), 2006
PMID: 16820507

Durbin, 1998
Profile hidden Markov models.
Eddy SR., Bioinformatics 14(9), 1998
PMID: 9918945
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Edgar RC., Nucleic Acids Res. 32(5), 2004
PMID: 15034147
Search and clustering orders of magnitude faster than BLAST.
Edgar RC., Bioinformatics 26(19), 2010
PMID: 20709691
The Pfam protein families database.
Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A., Nucleic Acids Res. 36(Database issue), 2007
PMID: 18039703
WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads.
Gerlach W, Junemann S, Tille F, Goesmann A, Stoye J., BMC Bioinformatics 10(), 2009
PMID: 20021646
Metatranscriptomic approach to analyze the functional human gut microbiota.
Gosalbes MJ, Durban A, Pignatelli M, Abellan JJ, Jimenez-Hernandez N, Perez-Cobas AE, Latorre A, Moya A., PLoS ONE 6(3), 2011
PMID: 21408168
Rfam: annotating non-coding RNAs in complete genomes.
Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A., Nucleic Acids Res. 33(Database issue), 2005
PMID: 15608160
The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme.
Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S., Cell 35(3 Pt 2), 1983
PMID: 6197186
Operation of the CO dehydrogenase/acetyl coenzyme A pathway in both acetate oxidation and acetate formation by the syntrophically acetate-oxidizing bacterium Thermacetogenium phaeum.
Hattori S, Galushko AS, Kamagata Y, Schink B., J. Bacteriol. 187(10), 2005
PMID: 15866934
Thermacetogenium phaeum gen. nov., sp. nov., a strictly anaerobic, thermophilic, syntrophic acetate-oxidizing bacterium.
Hattori S, Kamagata Y, Hanada S, Shoun H., Int. J. Syst. Evol. Microbiol. 50 Pt 4(), 2000
PMID: 10939667
Validation of two ribosomal RNA removal methods for microbial metatranscriptomics.
He S, Wurtzel O, Singh K, Froula JL, Yilmaz S, Tringe SG, Wang Z, Chen F, Lindquist EA, Sorek R, Hugenholtz P., Nat. Methods 7(10), 2010
PMID: 20852648
Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing.
Huse SM, Dethlefsen L, Huber JA, Mark Welch D, Welch DM, Relman DA, Sogin ML., PLoS Genet. 4(11), 2008
PMID: 19023400
Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing.
Jaenicke S, Ander C, Bekel T, Bisdorf R, Droge M, Gartemann KH, Junemann S, Kaiser O, Krause L, Tille F, Zakrzewski M, Puhler A, Schluter A, Goesmann A., PLoS ONE 6(1), 2011
PMID: 21297863
Analysis of the metagenome from a biogas-producing microbial community by means of bioinformatics methods
Jaenicke, 2011
Detection of methanogenic Archaea in peat: comparison of PCR primers targeting the mcrA gene.
Juottonen H, Galand PE, Yrjala K., Res. Microbiol. 157(10), 2006
PMID: 17070673
Biology of trans-translation.
Keiler KC., Annu. Rev. Microbiol. 62(), 2008
PMID: 18557701
Estimating the growth rate of slowly growing marine bacteria from RNA content.
Kemp PF, Lee S, Laroche J., Appl. Environ. Microbiol. 59(8), 1993
PMID: 16349018
Microbial community analysis of a biogas-producing completely stirred tank reactor fed continuously with fodder beet silage as mono-substrate.
Klocke M, Mahnert P, Mundt K, Souidi K, Linke B., Syst. Appl. Microbiol. 30(2), 2006
PMID: 16697135
The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota.
Kosaka T, Kato S, Shimoyama T, Ishii S, Abe T, Watanabe K., Genome Res. 18(3), 2008
PMID: 18218977
Anaerobic digestion of renewable biomass: thermophilic temperature governs methanogen population dynamics.
Krakat N, Westphal A, Schmidt S, Scherer P., Appl. Environ. Microbiol. 76(6), 2010
PMID: 20097828
Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor.
Krause L, Diaz NN, Edwards RA, Gartemann KH, Kromeke H, Neuweger H, Puhler A, Runte KJ, Schluter A, Stoye J, Szczepanowski R, Tauch A, Goesmann A., J. Biotechnol. 136(1-2), 2008
PMID: 18611419
Phylogenetic classification of short environmental DNA fragments.
Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J., Nucleic Acids Res. 36(7), 2008
PMID: 18285365
Isolation and Characterization of a Thermophilic Bacterium Which Oxidizes Acetate in Syntrophic Association with a Methanogen and Which Grows Acetogenically on H(2)-CO(2).
Lee MJ, Zinder SH., Appl. Environ. Microbiol. 54(1), 1988
PMID: 16347518
The structure of the bacterial and archaeal community in a biogas digester as revealed by denaturing gradient gel electrophoresis and 16S rDNA sequencing analysis.
Liu FH, Wang SB, Zhang JS, Zhang J, Yan X, Zhou HK, Zhao GP, Zhou ZH., J. Appl. Microbiol. 106(3), 2009
PMID: 19187154
ARB: a software environment for sequence data.
Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar , Buchner A, Lai T, Steppi S, Jobb G, Forster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, Konig A, Liss T, Lussmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH., Nucleic Acids Res. 32(4), 2004
PMID: 14985472
Molecular analyses of methyl-coenzyme M reductase alpha-subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage.
Lueders T, Chin KJ, Conrad R, Friedrich M., Environ. Microbiol. 3(3), 2001
PMID: 11321536
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
Syntrophomonas wolfei gen. nov. sp. nov., an Anaerobic, Syntrophic, Fatty Acid-Oxidizing Bacterium.
McInerney MJ, Bryant MP, Hespell RB, Costerton JW., Appl. Environ. Microbiol. 41(4), 1981
PMID: 16345745
Syntrophy in anaerobic global carbon cycles.
McInerney MJ, Sieber JR, Gunsalus RP., Curr. Opin. Biotechnol. 20(6), 2009
PMID: 19897353
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.
Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19900971
Polyphasic analyses of methanogenic archaeal communities in agricultural biogas plants.
Nettmann E, Bergmann I, Pramschufer S, Mundt K, Plogsties V, Herrmann C, Klocke M., Appl. Environ. Microbiol. 76(8), 2010
PMID: 20154117
Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum.
Nolling J, Breton G, Omelchenko MV, Makarova KS, Zeng Q, Gibson R, Lee HM, Dubois J, Qiu D, Hitti J, Wolf YI, Tatusov RL, Sabathe F, Doucette-Stamm L, Soucaille P, Daly MJ, Bennett GN, Koonin EV, Smith DR., J. Bacteriol. 183(16), 2001
PMID: 11466286
KEGG: Kyoto Encyclopedia of Genes and Genomes.
Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M., Nucleic Acids Res. 27(1), 1999
PMID: 9847135
The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum).
Pierce E, Xie G, Barabote RD, Saunders E, Han CS, Detter JC, Richardson P, Brettin TS, Das A, Ljungdahl LG, Ragsdale SW., Environ. Microbiol. 10(10), 2008
PMID: 18631365
Characterization of an anaerobic population digesting a model substrate for maize in the presence of trace metals.
Pobeheim H, Munk B, Muller H, Berg G, Guebitz GM., Chemosphere 80(8), 2010
PMID: 20615524
Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre.
Poretsky RS, Hewson I, Sun S, Allen AE, Zehr JP, Moran MA., Environ. Microbiol. 11(6), 2009
PMID: 19207571
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB.
Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO., Nucleic Acids Res. 35(21), 2007
PMID: 17947321
Identification of a large noncoding RNA in extremophilic eubacteria.
Puerta-Fernandez E, Barrick JE, Roth A, Breaker RR., Proc. Natl. Acad. Sci. U.S.A. 103(51), 2006
PMID: 17164334
Enzymology of the Wood–Ljungdahl pathway of acetogenesis
Ragsdale, Ann. N.Y. Acad. Sci. 1125(), 2008
Acetogenesis and the Wood–Ljungdahl pathway of CO2 fixation
Ragsdale, Bba-Proteins Proteom 1784(), 2008
Investigation of methanogen population structure in biogas reactor by molecular characterization of methyl-coenzyme M reductase A (mcrA) genes.
Rastogi G, Ranade DR, Yeole TY, Patole MS, Shouche YS., Bioresour. Technol. 99(13), 2007
PMID: 18155901
Characterization of 10S RNA: a new stable rna molecule from Escherichia coli.
Ray BK, Apirion D., Mol. Gen. Genet. 174(1), 1979
PMID: 384159
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
Clostridium ultunense sp. nov., a mesophilic bacterium oxidizing acetate in syntrophic association with a hydrogenotrophic methanogenic bacterium.
Schnurer A, Schink B, Svensson BH., Int. J. Syst. Bacteriol. 46(4), 1996
PMID: 8863449
Enzyme activities in and energetics of acetate metabolism by the mesophilic syntrophically acetate-oxidizing anaerobe Clostridium ultunense
Schnürer, FEMS Microbiol. Lett. 154(), 1997
Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column.
Shi Y, Tyson GW, DeLong EF., Nature 459(7244), 2009
PMID: 19444216
Structure and function of enzymes involved in the methanogenic pathway utilizing carbon dioxide and molecular hydrogen.
Shima S, Warkentin E, Thauer RK, Ermler U., J. Biosci. Bioeng. 93(6), 2002
PMID: 16233244
Microbial diversity in the deep sea and the underexplored "rare biosphere".
Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, Arrieta JM, Herndl GJ., Proc. Natl. Acad. Sci. U.S.A. 103(32), 2006
PMID: 16880384
Evaluation of molecular methods used for establishing the interactions and functions of microorganisms in anaerobic bioreactors.
Talbot G, Topp E, Palin MF, Masse DI., Water Res. 42(3), 2007
PMID: 17719078
The COG database: new developments in phylogenetic classification of proteins from complete genomes.
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV., Nucleic Acids Res. 29(1), 2001
PMID: 11125040
Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome.
Urich T, Lanzen A, Qi J, Huson DH, Schleper C, Schuster SC., PLoS ONE 3(6), 2008
PMID: 18575584
The regulation of ribosomal RNA synthesis and bacterial cell growth.
Wagner R., Arch. Microbiol. 161(2), 1994
PMID: 7511368
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
Syntrophaceticus schinkii gen. nov., sp. nov., an anaerobic, syntrophic acetate-oxidizing bacterium isolated from a mesophilic anaerobic filter.
Westerholm M, Roos S, Schnurer A., FEMS Microbiol. Lett. 309(1), 2010
PMID: 20546311
Tepidanaerobacter acetatoxydans sp. nov., an anaerobic, syntrophic acetate-oxidizing bacterium isolated from two ammonium-enriched mesophilic methanogenic processes.
Westerholm M, Roos S, Schnurer A., Syst. Appl. Microbiol. 34(4), 2011
PMID: 21498020
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
Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction.
Yu Y, Lee C, Kim J, Hwang S., Biotechnol. Bioeng. 89(6), 2005
PMID: 15696537
Isolation of RNA from bacterial samples of the human gastrointestinal tract.
Zoetendal EG, Booijink CC, Klaassens ES, Heilig HG, Kleerebezem M, Smidt H, de Vos WM., Nat Protoc 1(2), 2006
PMID: 17406329
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 22342600
PubMed | Europe PMC

Suchen in

Google Scholar