Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants

Anaerobe

Volumn 29, Issue , 2014, Pages 59-67

  Kohrs, F ^a   Heyer, R ^a   Magnussen, A ^a   Benndorf, D ^a   Muth, T ^b   Behne, A ^a   Rapp, E ^b   Kausmann, R ^c   Heiermann, M ^c   Klocke, M ^c   Reichl, U ^a,b  

^a OTTO VON GUERICKE UNIVERSITY   (Germany)

^b MAX PLANCK INSTITUTE FOR DYNAMICS OF COMPLEX TECHNICAL SYSTEMS   (Germany)

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

Author keywords

Anaerobic digestion; Community profiling; Fractionation; GeLC MS MS; KEGG pathway analysis; Liquid isoelectric focusing; Metaproteomics

Indexed keywords

BIOGAS; METAPROTEOME; MICROBIAL PROTEIN; PEPTIDE; PROTEIN; PROTEOME; UNCLASSIFIED DRUG; ARCHAEAL PROTEIN; BACTERIAL PROTEIN; BIOFUEL; FUNGAL PROTEIN; METHANE; WASTE;

ARTICLE; BIOGAS PLANT; CONTROLLED STUDY; ENERGY RESOURCE; FRACTIONATION; HYDROLYSIS; ISOELECTRIC FOCUSING; LIQUID CHROMATOGRAPHY; METHANOGENESIS; METHANOMICROBIALES; METHANOSARCINALES; MICROBIAL COMMUNITY; MOLECULAR WEIGHT; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; SAMPLE; TANDEM MASS SPECTROMETRY; BIOREACTOR; BIOSYNTHESIS; CHEMISTRY; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; METAGENOME; MICROBIAL CONSORTIUM; PHYSIOLOGY; PLANT; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROCEDURES; PROTEIN DEGRADATION; TEMPERATURE; WASTE;

METHANOMICROBIALES; METHANOSARCINALES;

ARCHAEAL PROTEINS; BACTERIAL PROTEINS; BIOFUELS; BIOREACTORS; ELECTROPHORESIS, POLYACRYLAMIDE GEL; FUNGAL PROTEINS; ISOELECTRIC FOCUSING; METAGENOME; METHANE; METHANOMICROBIALES; METHANOSARCINALES; MICROBIAL CONSORTIA; PLANTS; PROTEOLYSIS; PROTEOME; TANDEM MASS SPECTROMETRY; TEMPERATURE; WASTE PRODUCTS;

EID: 84902369705     PISSN: 10759964     EISSN: 10958274     Source Type: Journal    
DOI: 10.1016/j.anaerobe.2013.11.009     Document Type: Article

References (46)

1. Ward A.J., Hobbs P.J., Holliman P.J., Jones D.L., et al. Optimisation of the anaerobic digestion of agricultural resources. Bioresour Technol 2008, 99(17):7928-7940.
2. Weiland P. Biogas production: current state and perspectives. Appl Microbiol Biotechnol 2010, 85(4):849-860.
3. Wirth R., Kovacs E., Maroti G., Bagi Z., Rakhely G., Kovacs L.L., et al. Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing. Biotechnol Biofuels 2012, 5(1):41.
4. Thauer R.K. Biochemistry of methanogenesis: a tribute to Marjory Stephenson. 1998 Marjory Stephenson Prize Lecture. Microbiology 1998, 144(9):2377-2406.
5. Klocke M., Nettmann E., Bergmann I., Mundt K., Souidi K., Mumme J., et al. Characterization of the methanogenic archaea within two-phase biogas reactor systems operated with plant biomass. Syst Appl Microbiol 2008, 31(3):190-205.
6. Nelson M.C., Morrison M., Yu Z.T. Ameta-analysis of the microbial diversity observed in anaerobic digesters. Bioresour Technol 2011, 102(4):3730-3739.
7. Schluter A., Bekel T., Diaz N.N., Dondrup M., Eichenlaub R., Gartemann K.H., et al. The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology. JBiotechnol 2008, 136(1-2):77-90.
8. Hofman-Bang J., Zheng D., Westermann P., Ahring B.K., Raskin L., et al. Molecular ecology of anaerobic reactor systems. Adv Biochem Eng Biotechnol 2003, 81:151-203.
9. Ram R.J., VerBerkmoes N.C., Thelen M.P., Tyson G.W., Baker B.J., Blake R.C., et al. Community proteomics of a natural microbial biofilm. Science 2005, 308(5730):1915-1920.
10. Schneider T., Keiblinger K.M., Schmid E., Sterflinger-Gleixner K., Ellersdorfer G., Roschitzki B., et al. Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions. ISME J 2012, 6(9):1749-1762.
11. Benndorf D., Balcke G.U., Harms H., von Bergen M., et al. Functional metaproteome analysis of protein extracts from contaminated soil and groundwater. ISME J 2007, 1(3):224-234.
12. Kuhn R., Benndorf D., Rapp E., Reichl U., Palese L.L., Pollice A., et al. Metaproteome analysis of sewage sludge from membrane bioreactors. Proteomics 2011, 11(13):2738-2744.
13. Siggins A., Gunnigle E., Abram F. Exploring mixed microbial community functioning: recent advances in metaproteomics. FEMS Microbiol Ecol 2012, 80(2):265-280.
14. Heyer R., Kohrs F., Benndorf D., Rapp E., Kausmann R., Heiermann M., et al. Metaproteome analysis of the microbial communities in agricultural biogas plants. New Biotechnol 2013, 30(6):614-622.
15. Hanreich A., Schimpf U., Zakrzewski M., Schluter A., Benndorf D., Heyer R., et al. Metagenome and metaproteome analyses of microbial communities in mesophilic biogas-producing anaerobic batch fermentations indicate concerted plant carbohydrate degradation. Syst Appl Microbiol 2013, 36(5):330-338.
16. Hanreich A., Heyer R., Benndorf D., Rapp E., Pioch M., Reichl U., et al. Metaproteome analysis to determine the metabolically active part of a thermophilic microbial community producing biogas from agricultural biomass. Can J Microbiol 2012, 58(7):917-922.
17. Abram F., Gunnigle E., O'Flaherty V. Optimisation of protein extraction and 2-DE for metaproteomics of microbial communities from anaerobic wastewater treatment biofilms. Electrophoresis 2009, 30(23):4149-4151.
18. Abram F., Enright A.M., O'Reilly J., Botting C.H., Collins G., O'Flaherty V., et al. Ametaproteomic approach gives functional insights into anaerobic digestion. JAppl Microbiol 2011, 110(6):1550-1560.
19. Muth T., Benndorf D., Reichl U., Rapp E., Martens L., et al. Searching for a needle in a stack of needles: challenges in metaproteomics data analysis. Mol Biosyst 2013, 9(4):578-585.
20. Stone M.D., Odland R.M., McGowan T., Onsongo G., Tang C., Rhodus N.L., et al. Novel in situ collection of tumor interstitial fluid from a head and neck squamous carcinoma reveals a unique proteome with diagnostic potential. Clin Proteomics 2010, 6(3):75-82.
21. Wilm M., Shevchenko A., Houthaeve T., Breit S., Schweigerer L., Fotsis T., et al. Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 1996, 379(6564):466-469.
22. Rieger C., Weiland P. Prozessstörungen frühzeitig erkennen. Biogas J 2006, 4(6):18-20.
23. Schweikl H., Klein U., Schindlbeck M., Wieczorek H., et al. Avacuolar-type ATPase, partially purified from potassium transporting plasma membranes of tobacco hornworm midgut. JBiol Chem 1989, 264(19):11136-11142.
24. Laemmli U.K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 1970, 227(5259):680-685.
25. Hörth P., Miller C.A., Preckel T., Wenz C., et al. Efficient fractionation and improved protein identification by peptide OFFGEL electrophoresis. Mol Cell Proteomics 2006, 5(10):1968-1974.
26. Perkins D.N., Pappin D.J., Creasy D.M., Cottrell J.S., et al. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20(18):3551-3567.
27. Consortium U. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 2012, 40(D1):D71-D75.
28. Helsens K., Martens L., Vandekerckhove J., Gevaert K., et al. MascotDatfile: an open-source library to fully parse and analyse MASCOT MS/MS search results. Proteomics 2007, 7(3):364-366.
29. Acland A., Agarwala R., Barrett T., Beck J., Benson D.A., Bollin C., et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2013, 41(D1):D8-D20.
30. Kanehisa M., Goto S., Sato Y., Furumichi M., Tanabe M., et al. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 2012, 40(D1):D109-D114.
31. Piehowski P.D., Petyuk V.A., Orton D.J., Xie F., Moore R.J., Ramirez-Restrepo M., et al. Sources of technical variability in quantitative LC-MS proteomics: human brain tissue sample analysis. JProteome Res 2013, 12(5):2128-2137.
32. Kiraga J., Mackiewicz P., Mackiewicz D., Kowalczuk M., Biecek P., Polak N., et al. The relationships between the isoelectric point and length of proteins, taxonomy and ecology of organisms. BMC Genomics 2007, 8.
33. Holcapek M., Jirasko R., Lisa M. Recent developments in liquid chromatography-mass spectrometry and related techniques. JChromatogr A 2012, 1259:3-15.
34. Davis M.T., Beierle J., Bures E.T., McGinley M.D., Mort J., Robinson J.H., et al. Automated LC-LC-MS-MS platform using binary ion-exchange and gradient reversed-phase chromatography for improved proteomic analyses. JChromatogr B 2001, 752(2):281-291.
35. Krause L., Diaz N.N., Edwards R.A., Gartemann K.H., Kromeke H., Neuweger H., et al. Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor. JBiotechnol 2008, 136(1-2):91-101.
36. Pender S., Toomey M., Carton M., Eardly D., Patching J.W., Colleran E., et al. Long-term effects of operating temperature and sulphate addition on the methanogenic community structure of anaerobic hybrid reactors. Water Res 2004, 38(3):619-630.
37. Krakat N., Westphal A., Schmidt S., Scherer P., et al. Anaerobic digestion of renewable biomass: thermophilic temperature governs methanogen population dynamics. Appl Environ Microbiol 2010, 76(6):1842-1850.
38. McHugh S., Carton M., Mahony T., O'Flaherty V., et al. Methanogenic population structure in a variety of anaerobic bioreactors. FEMS Microbiol Lett 2003, 219(2):297-304.
39. Bourque J.S., Guiot S.R., Tartakovsky B. Methane production in an UASB reactor operated under periodic mesophilic-thermophilic conditions. Biotechnol Bioeng 2008, 100(6):1115-1121.
40. Leven L., Eriksson A.R., Schnurer A. Effect of process temperature on bacterial and archaeal communities in two methanogenic bioreactors treating organic household waste. FEMS Microbiol Ecol 2007, 59(3):683-693.
41. Nettmann E., Bergmann I., Pramschufer S., Mundt K., Plogsties V., Herrmann C., et al. Polyphasic analyses of methanogenic archaeal communities in agricultural biogas plants. Appl Environ Microbiol 2010, 76(8):2540-2548.
42. Ritari J., Koskinen K., Hultman J., Kurola J.M., Kymalainen M., Romantschuk M., et al. Molecular analysis of meso- and thermophilic microbiota associated with anaerobic biowaste degradation. BMC Microbiol 2012, 12:121.
43. Davidson A.L., Chen J. ATP-binding cassette transporters in bacteria. Annu Rev Biochem 2004, 73:241-268.
44. Kletzin A., Adams M.W. Molecular and phylogenetic characterization of pyruvate and 2-ketoisovalerate ferredoxin oxidoreductases from Pyrococcus furiosus and pyruvate ferredoxin oxidoreductase from Thermotoga maritima. JBacteriol 1996, 178(1):248-257.
45. Lovell C.R., Przybyla A., Ljungdahl L.G. Primary structure of the thermostable formyltetrahydrofolate synthetase from Clostridium thermoaceticum. Biochemistry 1990, 29(24):5687-5694.
46. Kendall M.M., Boone D.R. The order methanosarcinales. Prokaryotes: a handbook on the biology of bacteria 2006, vol. 3:244-256. 3rd ed.