Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes

Maus, Irena; Bremges, Andreas; Stolze, Yvonne; Hahnke, Sarah; Cibis, Katharina G.; Koeck, Daniela E.; Kim, Yong S.; Kreubel, Jana; Hassa, Julia; Wibberg, Daniel; Weimann, Aaron; Off, Sandra; Stantscheff, Robbin; Zverlov, Vladimir V.; Schwarz, Wolfgang H.; König, Helmut; Liebl, Wolfgang; Scherer, Paul; McHardy, Alice C.; Sczyrba, Alexander; Klocke, Michael; Pühler, Alfred; Schlüter, Andreas

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, et al. (2017)
Biotechnology for Biofuels 10(1): 264.

Zeitschriftenaufsatz | Veröffentlicht | Englisch

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https://biotechnologyforbiofuels.biomedcentral.com/articles/10.1186/s13068-017-0[...]

DOI

https://doi.org/10.1186/s13068-017-0947-1

URN

urn:nbn:de:0070-pub-29155164

Autor*in

Maus, Irena^UniBi; Bremges, Andreas^UniBi ; Stolze, Yvonne^UniBi; Hahnke, Sarah; Cibis, Katharina G.; Koeck, Daniela E.; Kim, Yong S.; Kreubel, Jana; Hassa, Julia^UniBi ; Wibberg, Daniel^UniBi; Weimann, Aaron; Off, Sandra
Alle

Einrichtung

Centrum für Biotechnologie > Arbeitsgruppe A. Sczyrba
Technische Fakultät > Computational Metagenomics

Abstract / Bemerkung

Background To elucidate biogas microbial communities and processes, the application of high-throughput DNA analysis approaches is becoming increasingly important. Unfortunately, generated data can only partialy be interpreted rudimentary since databases lack reference sequences. Results Novel cellulolytic, hydrolytic, and acidogenic/acetogenic Bacteria as well as methanogenic Archaea originating from different anaerobic digestion communities were analyzed on the genomic level to assess their role in biomass decomposition and biogas production. Some of the analyzed bacterial strains were recently described as new species and even genera, namely Herbinix hemicellulosilytica T3/55T, Herbinix luporum SD1DT, Clostridium bornimense M2/40T, Proteiniphilum saccharofermentans M3/6T, Fermentimonas caenicola ING2-E5BT, and Petrimonas mucosa ING2-E5AT. High-throughput genome sequencing of 22 anaerobic digestion isolates enabled functional genome interpretation, metabolic reconstruction, and prediction of microbial traits regarding their abilities to utilize complex bio-polymers and to perform specific fermentation pathways. To determine the prevalence of the isolates included in this study in different biogas systems, corresponding metagenome fragment mappings were done. Methanoculleus bourgensis was found to be abundant in three mesophilic biogas plants studied and slightly less abundant in a thermophilic biogas plant, whereas Defluviitoga tunisiensis was only prominent in the thermophilic system. Moreover, several of the analyzed species were clearly detectable in the mesophilic biogas plants, but appeared to be only moderately abundant. Among the species for which genome sequence information was publicly available prior to this study, only the species Amphibacillus xylanus, Clostridium clariflavum, and Lactobacillus acidophilus are of importance for the biogas microbiomes analyzed, but did not reach the level of abundance as determined for M. bourgensis and D. tunisiensis. Conclusions Isolation of key anaerobic digestion microorganisms and their functional interpretation was achieved by application of elaborated cultivation techniques and subsequent genome analyses. New isolates and their genome information extend the repository covering anaerobic digestion community members.

Stichworte

Anaerobic digestion Biomethanation Genome sequencing Fragment recruitment Defluviitoga tunisiensis Methanoculleus bourgensis

Erscheinungsjahr

2017

Zeitschriftentitel

Biotechnology for Biofuels

Band

Ausgabe

Art.-Nr.

264

ISSN

1754-6834

Page URI

https://pub.uni-bielefeld.de/record/2915516

Zitieren

Maus I, Bremges A, Stolze Y, et al. Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes. Biotechnology for Biofuels. 2017;10(1): 264.

Maus, I., Bremges, A., Stolze, Y., Hahnke, S., Cibis, K. G., Koeck, D. E., Kim, Y. S., et al. (2017). Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes. Biotechnology for Biofuels, 10(1), 264. doi:10.1186/s13068-017-0947-1

Maus, Irena, Bremges, Andreas, Stolze, Yvonne, Hahnke, Sarah, Cibis, Katharina G., Koeck, Daniela E., Kim, Yong S., et al. 2017. “Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes”. Biotechnology for Biofuels 10 (1): 264.

Maus, I., Bremges, A., Stolze, Y., Hahnke, S., Cibis, K. G., Koeck, D. E., Kim, Y. S., Kreubel, J., Hassa, J., Wibberg, D., et al. (2017). Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes. Biotechnology for Biofuels 10:264.

Maus, I., et al., 2017. Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes. Biotechnology for Biofuels, 10(1): 264.

I. Maus, et al., “Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes”, Biotechnology for Biofuels, vol. 10, 2017, : 264.

Maus, I., Bremges, A., Stolze, Y., Hahnke, S., Cibis, K.G., Koeck, D.E., Kim, Y.S., Kreubel, J., Hassa, J., Wibberg, D., Weimann, A., Off, S., Stantscheff, R., Zverlov, V.V., Schwarz, W.H., König, H., Liebl, W., Scherer, P., McHardy, A.C., Sczyrba, A., Klocke, M., Pühler, A., Schlüter, A.: Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes. Biotechnology for Biofuels. 10, : 264 (2017).

Maus, Irena, Bremges, Andreas, Stolze, Yvonne, Hahnke, Sarah, Cibis, Katharina G., Koeck, Daniela E., Kim, Yong S., Kreubel, Jana, Hassa, Julia, Wibberg, Daniel, Weimann, Aaron, Off, Sandra, Stantscheff, Robbin, Zverlov, Vladimir V., Schwarz, Wolfgang H., König, Helmut, Liebl, Wolfgang, Scherer, Paul, McHardy, Alice C., Sczyrba, Alexander, Klocke, Michael, Pühler, Alfred, and Schlüter, Andreas. “Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes”. Biotechnology for Biofuels 10.1 (2017): 264.

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Manzoor S, Schnürer A, Bongcam-Rudloff E, Müller B., 2016

Amphibacillus xylanus hen. Nov., sp. nov., a facultatively anaerobic sporeforming xylan-digesting bacterium which lacks cytochrome, quinone, and catalase
Nimura Y, Koh E, Yanadiga F, Suzuki KI, Komagata K, Kozaki M., 1990

Clostridium clariflavum sp. nov. and Clostridium caenicola sp. nov., moderately thermophilic, cellulose-/cellobiose-digesting bacteria isolated from methanogenic sludge.
Shiratori H, Sasaya K, Ohiwa H, Ikeno H, Ayame S, Kataoka N, Miya A, Beppu T, Ueda K., Int. J. Syst. Evol. Microbiol. 59(Pt 7), 2009
PMID: 19542130

Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis.
Holden MT, Hauser H, Sanders M, Ngo TH, Cherevach I, Cronin A, Goodhead I, Mungall K, Quail MA, Price C, Rabbinowitsch E, Sharp S, Croucher NJ, Chieu TB, Mai NT, Diep TS, Chinh NT, Kehoe M, Leigh JA, Ward PN, Dowson CG, Whatmore AM, Chanter N, Iversen P, Gottschalk M, Slater JD, Smith HE, Spratt BG, Xu J, Ye C, Bentley S, Barrell BG, Schultsz C, Maskell DJ, Parkhill J., PLoS ONE 4(7), 2009
PMID: 19603075

Complete genome sequence of Herbinix luporum SD1D, a new cellulose degrading bacterium isolated from a thermophilic biogas reactor
Koeck DE, Maus I, Wibberg D, Winkler A, Zverlov VV, Liebl W., 2016

First draft genome sequence of the amylolytic Bacillus thermoamylovorans wild-type strain 1A1 isolated from a thermophilic biogas plant.
Koeck DE, Wibberg D, Maus I, Winkler A, Albersmeier A, Zverlov VV, Puhler A, Schwarz WH, Liebl W, Schluter A., J. Biotechnol. 192 Pt A(), 2014
PMID: 25270021

Complete genome sequence of the methanogenic neotype strain Methanobacterium formicicum MF(T.).
Maus I, Stantscheff R, Wibberg D, Stolze Y, Winkler A, Puhler A, Konig H, Schluter A., J. Biotechnol. 192 Pt A(), 2014
PMID: 25270020

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, Konig H, Puhler A, Schluter A., J. Biotechnol. 201(), 2014
PMID: 25455016

Methanoculleus palmolei sp. nov., an irregularly coccoid methanogen from an anaerobic digester treating wastewater of a palm oil plant in north-Sumatra, Indonesia.
Zellner G, Messner P, Winter J, Stackebrandt E., Int. J. Syst. Bacteriol. 48 Pt 4(), 1998
PMID: 9828413

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