Complete genome sequence of Peptoniphilus sp. strain ING2-D1G isolated from a mesophilic lab-scale completely stirred tank reactor utilizing maize silage in co-digestion with pig and cattle manure for biomethanation

Journal of Biotechnology

Volumn 192, Issue Part A, 2014, Pages 59-61

  Tomazetto, Geizecler ^a   Hahnke, Sarah ^b   Maus, Irena ^a   Wibberg, Daniel ^a   Pühler, Alfred ^a   Schlüter, Andreas ^a   Klocke, Michael ^b  

^a BIELEFELD UNIVERSITY   (Germany)

^b LEIBNIZ INSTITUTE FOR AGRICULTURAL ENGINEERING AND BIOECONOMY ATB   (Germany)

Author keywords

Anaerobic digestion; Biomass degradation; Biomethanation; Clostridiales; Protein degradation

Indexed keywords

BACTERIA; FERTILIZERS; GENES; GENETIC ENGINEERING; MANURES; PROTEINS; PROTEOLYSIS; TANKS (CONTAINERS); VOLATILE FATTY ACIDS;

ANAEROBIC BACTERIUM; BIO-METHANATION; BIOMASS DEGRADATIONS; CLOSTRIDIALES; COMPLETE GENOMES; COMPLETELY STIRRED TANK REACTORS; PROTEIN DEGRADATION; WHOLE GENOME SEQUENCES;

ANAEROBIC DIGESTION;

ACETIC ACID; BIOGAS; BUTYRIC ACID; LACTIC ACID; BACTERIAL RNA; BIOFUEL; MANURE; METHANE; RNA 16S;

ANAEROBIC DIGESTION; ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENOME; BACTERIAL METABOLISM; BACTERIAL STRAIN; BACTERIUM ISOLATE; BACTERIUM ISOLATION; BIODEGRADATION; CATTLE; CHROMOSOME SIZE; FERMENTATION; GENE SEQUENCE; GENETIC CODE; MAIZE; MANURE; NONHUMAN; NUCLEOTIDE SEQUENCE; PEPTONIPHILUS; PROTEIN DEGRADATION; SILAGE; STIRRED REACTOR; SWINE; ANIMAL; BACTERIUM; BIOREACTOR; BIOSYNTHESIS; BOVINE; GENETICS; METABOLISM; MOLECULAR GENETICS; PIG;

ANIMALS; BACTERIA; BASE SEQUENCE; BIOFUELS; BIOREACTORS; CATTLE; GENOME, BACTERIAL; MANURE; METHANE; MOLECULAR SEQUENCE DATA; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SWINE; ZEA MAYS;

EID: 84910020424     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2014.09.011     Document Type: Article

References (35)

1. Angelidaki I., Karakashev D., Batstone D.J., Plugge C.M., Stams A.J. Biomethanation and its potential. Methods Enzymol. 2011, 494:327-351.
2. Cao G.L., Zhao L., Wang A.J., Wang Z.Y., Ren N.Q. Single-step bioconversion of lignocellulose to hydrogen using novel moderately thermophilic bacteria. Biotechnol. Biofuel. 2014, 7:82.
3. Cho E., Park S.N., Kim H.K., Kim D.S., Jung J., Baek J.H., Lim Y.K., Jo E., Choi M.H., Chang Y.H., Shin Y., Paek J., Shin J.H., Kim J., Choi S.H., Park H.S., Kim H., Kook J.K. Draft genome sequence of the novel Peptoniphilus sp. strain ChDC B134, isolated from a human periapical abscess lesion. Genome Announc. 2014, 1(5):e00822-e913.
4. Citron D.M., Tyrrell K.L., Goldstein E.J. Peptoniphilus coxii sp. nov. and Peptoniphilus tyrrelliae sp. nov. isolated from human clinical infections. Anaerobe 2012, 18:244-248.
5. Cosentino S., Voldby L.M., Møller .A.F., Lund O. PathogenFinder - distinguishing friend from foe using bacterial whole genome sequence data. PLoS ONE 2013, 8(10):e77302.
6. Dassa B., Borovok I., Lamed R., Henrissat B., Coutinho P., Hemme C.L., Huang Y., Zhou J., Bayer E.A. Genome-wide analysis of Acetivibrio cellulolyticus provides a blueprint of an elaborate cellulosome system. Genomics 2012, 13:1-13.
7. Dowd S.E., Wolcott R.D., Sun Y., McKeehan T., Smith E., Rhoads D. Polymicrobial nature of chronic diabetic foot ulcer biofilm infections determined using bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP). PLoS ONE 2008, 3:e3326.
8. Feinberg L., Foden J., Barret T., Davenport K.W., Bruce D., Detter C., Tapia R., Han C., Lapidus A., Lucas S., Cheng J.F., Pitluck S., Woyke T., Ivanova N., Mikhailova N., Land M., Hauser L., Argyros D.A., Goodwin L., Hogsett D., Caiazza N. Complete genome sequence of the cellulolytic thermophile Clostridium thermocellum DSM1313. J. Biotechnol. 2011, 193:2906-2907.
9. 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.
10. Hanreich A., Schimpf U., Zakrzewski M., Schlüter A., Benndorf D., Heyer R., Rapp E., Pühler A., Reichl U., Klocke M. Metagenome and metaproteome analyses of microbial communities in mesophilic biogas-producing anaerobic batch fermentations indicate concerted plant carbohydrate degradation. Syst. Appl. Microbiol. 2013, 36:330-338.
11. Jousimies-Somer H.R., Summanen P., Ditron D.M., Baron E.J., Wexler H.M., Finegold S.M. Wadsworth-KTL Anaerobic Bacteriology Manual 2002, Star Publishing, Belmont. sixth ed.
12. Jung M.Y., Cho J.H., Sin Y., Paek J., Park I.S., Kim J.S., Kim W., Ma J.Y., Park S.J., Chang Y.H. Peptoniphilus rhinitidis sp. nov., isolated from specimens of chronic rhinosinusitis. Anaerobe 2014, pii: S1075-9964(14)00091-2.
13. Klocke M., Mähnert P., Mundt K., Souidi K., Linke B. Microbial community analysis of a biogas-producing completely stirred tank reactor fed continuously with fodder beet silage as mono-substrate. Syst. Appl. Microbiol. 2007, 30:139-151.
14. Koeck D.E., Wibberg D., Koellmeier T., Blom J., Jaenicke S., Winkler A., Albersmeier A., Zverlov V.V., Pühler A., Schwarz W.H., Schlüter A. Draft genome sequence of the cellulolytic Clostridium thermocellum wild-type strain BC1 playing a role in cellulosic biomass degradation. J. Biotechnol. 2013, 168:62-63.
15. Koeck D.E., Wibberg D., Maus I., Winkler A., Albersmeier A., Zverlov V.V., Liebl W., Pühler A., Schwarz W.H., Schlüter A. Complete genome sequence of the cellulolytic thermophile Ruminoclostridium cellulosi wild-type strain DG5 isolated from a thermophilic biogas plant. J. Biotechnol. 2014, 188:136-137.
16. Kröber M., Bekel T., Diaz N.N., Goesmann A., Jaenicke S., Krause L., Miller D., Runte K.J., Viehöver P., Pühler A., Schlüter A. Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. J. Biotechnol. 2009, 142:38-49.
17. Küberl A., Schneider J., Thallinger G.G., Anderl I., Wibberg D., Hajek T., Jaenicke S., Brinkrolf K., Goesmann A., Szczepanowski R., Pühler A., Schwab H., Glieder A., Pichler H. High-quality genome sequence of Pichia pastoris CBS7435. J. Biotechnol. 2011, 154:312-320.
18. Lebuhn M., Hanreich A., Klocke M., Schlüter A., Bauer C., Pérez C.C. Towards molecular biomarkers for biogas production from lignocellulose-rich substrates. Anaerobe 2014, 29:10-21.
19. Maus I., Wibberg D., Stantscheff R., Cibis K., Eikmeyer F.G., Köning H., Pühler A., Schlüter A. Complete genome sequence of the hydrogenotrophic archeon Methanobacterium sp Mb1 isolated from a production-scale biogas plant. J. Biotechnol. 2013, 168:734-736.
20. T, isolated from a sewage sludge digester. J. Bacteriol. 2012, 194:5487-5488.
21. Meyer F., Goesmann A., McHardy A.C., Bartels D., Bekel T., Clausen J., Jalinowski J., Link B., Rupp O., Giegerich R., Pühler A. GenDB - an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 2003, 31:2187-2195.
22. Miller M.E.B., Antonopoulos D.A., Rincon M.T., et al. Diversity and strain specificity of plant cell wall degrading enzymes revealed by draft genome of Ruminococcus flavefaciens FD-1. PLoS ONE 2009, 4:e6650.
23. Mishra A.K., Hugon P., Robert C., Raoult D., Fournier P.E. Non-contiguous-finished genome sequence and description of Peptoniphilus grossensis sp. nov. Stand Genomic Sci. 2012, 7:320-330.
24. Mishra A.K., Hugon P., Lagier J.C., Nguyen T.T., Robert C., Couderc C., Raoult D., Fournier P.-E. Non-contiguous-finished genome sequence and description of Peptoniphilus obesi sp. nov. Stand Genomic Sci. 2013, 7:357-369.
25. Mishra A.K., Lagier J.C., Nguyen T.-T., Raoult D., Fournier P.E. Non contiguous-finished genome sequence and description of Peptoniphilus senegalensis. sp. nov. Stand Genomic Sci. 2013, 7:370-381.
26. Mishra A.K., Lagier J.C., Robert C., Raoult D., Fournier P.E. Non-contiguous-finished genome sequence and description of Peptoniphilus timonensis sp. nov. Stand Genomic Sci. 2012, 7:1-11.
27. Nettmann E., Bergmann I., Pramschüfer S., Mundt K., Plogsties V., Herrmann C., Klocke M. Polyphasic analyses of methanogenic archaeal communities in agricultural biogas plants. Appl. Environ. Microbiol. 2010, 76:2540-2548. (erratum 77: 394).
28. Rademacher A., Nolte C., Schönberg M., Klocke M. Temperature increases from 55 to 75°C in a two-phase biogas reactor result in fundamental alterations within the bacterial and archaeal community structure. Appl. Microbiol. Biotechnol. 2012, 96:565-576.
29. Rademacher A., Zakrzewski M., Schlüter A., Schönberg M., Szczepanowski R., Goesmann A., Pühler A., Klocke M. Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing. FEMS Microbiol. Ecol. 2012, 79:785-799.
30. Schlüter A., Bekel T., Diaz N.N., Dondrup M., Eichenlaub R., Gartemann K.H., Krahn I., Krause L., Krömeke H., Kruse O., Mussgnug J.H., Neuweger H., Niehaus K., Pühler A., Runte K., Szczepanowski R., Tauch A., Tilker A., Viehöver P., Goesmann A. The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology. J. Biotechnol. 2008, 136:77-90.
31. St-Pierre B., Wright A.D. Comparative metagenomic analysis of bacterial populations in three full-scale mesophilic anaerobic manure digesters. Appl. Microbiol. Biotechnol. 2014, 98:2709-2717.
32. Sundberg C., Al-Soud W.A., Larsson M., Alm E., Yekta S.S., Svensson B.H., Sørensen S.J., Karlsson A. 454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters. FEMS Microbiol. Ecol. 2013, 85:612-626.
33. Walter G., Vernier M., Pinelli P.O., Million M., Coulange M., Seng P., Stein A. Bone and joint infections due to anaerobic bacteria: an analysis of 61 cases and review of the literature. Eur. J. Clin. Microbiol. Infect. Dis. 2014, 33:1355-1364.
34. Wibberg D., Blom J., Jaenicke S., Kollin F., Rupp O., Scherf B., Schneiker-Bekel S., Sczcepanowski R., Goesman A., Setubal J.C., Schmitt R., Pühler A., Schlüter A. Complete sequencing of Agrobacterium sp H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plamid. J. Biotechnol. 2011, 155:50-62.
35. Yi Z., Su X., Revindran V., Mackie R.I., Cann I. Molecular and biochemical analyses of CbCel9a/Cel48A, a highly secreted multi-modular cellulase by Caldicellulosiruptor bescii during growth on crystalline cellulose. PloS ONE 2013, 8:e84172.