Ecology and biotechnological potential of the thermophilic fermentative Coprothermobacter spp.

FEMS Microbiology Ecology

Volumn 91, Issue 5, 2015, Pages

  Gagliano, M C ^a   Braguglia, C M ^a   Petruccioli, M ^b   Rossetti, S ^a  

^a WATER RESEARCH INSTITUTE   (Italy)

^b UNIVERSITY OF TUSCIA   (Italy)

Author keywords

Coprothermobacter; Protein fermentation; Proteolytic thermophiles; Syntrophy

Indexed keywords

ANOXIC CONDITIONS; BIOTECHNOLOGY; CATALYSIS; ENZYME ACTIVITY; FEEDING; FERMENTATION; INOCULATION; INSTRUMENTATION; METABOLISM; MICROBIAL COMMUNITY; MICROBIAL ECOLOGY; PHYLOGENY; PROTEIN; THERMOPHILIC BACTERIUM;

BACTERIA (MICROORGANISMS); COPROTHERMOBACTER; DICTYOGLOMI; FIRMICUTES; THERMOTOGA;

PEPTIDE HYDROLASE; RNA 16S;

BACTERIAL GENOME; BIOREACTOR; BIOTECHNOLOGY; CLASSIFICATION; ECOLOGY; FERMENTATION; GENETICS; METABOLISM; MICROBIOLOGY; PHYLOGENY; PHYSIOLOGY; PROTEIN DEGRADATION; TEMPERATURE; THERMOANAEROBACTER;

BIOREACTORS; BIOTECHNOLOGY; ECOLOGY; FERMENTATION; GENOME, BACTERIAL; PEPTIDE HYDROLASES; PHYLOGENY; PROTEOLYSIS; RNA, RIBOSOMAL, 16S; TEMPERATURE; THERMOANAEROBACTER;

EID: 84954216151     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1093/femsec/fiv018     Document Type: Short Survey

References (87)

1. Alexiev A, Coil DA, Badger JH, et al. Complete genome sequence of Coprothermobacter proteolyticus DSM 5265. Genome Announc 2014;2:1-2.
2. Antranikian G, Klingeberg M. United states patent no. 5, 346, 820, 1994.
3. Beiko RG. Telling the whole story in a 10,000-genome world. Biol Direct 2011;6:34.
4. Cai H, Gu J, Wang Y. Protease complement of the thermophilic bacterium Coprothermobacter proteolyticus. In Arabina HR, Tran Q-N (eds). Proceeding of the International Conference on Bioinformatics and Computational Biology BIOCOMP'11. Las Vegas, Nevada: ISBN 2011 pp. 18-21.
5. Cheon J, Hidaka T, Mori S, et al. Applicability of random cloning method to analyze microbial community in full-scale anaerobic digesters. J Biosci Bioeng 2008;106:134-40.
6. Cheon J, Hong F, Hidaka T, et al. Microbial population dynamics in a thermophilic methane digester fed with garbage. Water Sci Technol 2007;55:175-82.
7. do Nascimento WCA, Martins MLL. Production and properties of an extracellular protease from thermophilic Bacillus sp. Braz J Microbiol 2004;35:91-6.
8. Elleuche S, Schroder C, Sahm K, et al. Extremozymes - biocatalysts with unique properties from extremophilic microorganisms. Curr Microbiol 2014;29:116-23.
9. Etchebehere C, Muxí L. Thiosulfate reduction and alanine production in glucose fermentation by members of the genus Coprothermobacter. Antonie Van Leeuwenhoek 2000;77:321-7.
10. Etchebehere C, Pavan ME, Zorzópulos J, et al. Coprothermobacter platensis sp. nov., a new anaerobic proteolytic thermophilic bacterium isolated from an anaerobic mesophilic sludge. Int J Syst Bacteriol 1998; 48:1297-304.
11. Fu Q, Kobayashi H, Kawaguchi H, et al. A thermophilic gramnegative nitrate-reducing bacterium, Calditerrivibrio nitroreducens, exhibiting electricity generation capability. Environ Sci Technol 2013a;47:12583-90.
12. Fu Q, Kobayashi H, Kawaguchi H, et al. Electrochemical and phylogenetic analyses of current-generating microorganisms in a thermophilic microbial fuel cell. J Biosci Bioeng 2013b;115:268-71.
13. Fu Q, Kobayashi H, Kuramochi Y, et al. Bioelectrochemical analyses of a thermophilic biocathode catalyzing sustainable hydrogen production. Int J Hydrogen Energ 2013c;38:15638-45.
14. Gagliano MC, Braguglia CM, Gallipoli A, et al. Microbial diversity in innovative mesophilic/thermophilic temperaturephased anaerobic digestion of sludge. Environ Sci Pollut R 2014, DOI:10.1007/s11356-014-3061-y.
15. Gagliano MC, Braguglia CM, Gianico A, et al. Thermophilic anaerobic digestion of thermal pretreated sludge: Role of microbial community structure and correlation with process performances. Water Res 2015;68:498-509.
16. Gagliano MC, Braguglia CM, Rossetti S. In situ identification of the synthrophic protein fermentative Coprothermobacter spp. involved in the thermophilic anaerobic digestion process. FEMS Microbiol Lett 2014;358:55-63.
17. Ge H, Batstone DJ, Jensen PD. Effect of temperature increase from 55°C to 70°C on anaerobic digestion: methanogenic activity and microbial community. In: Di Salvo B (ed). AWA Biosolids and Source Management National Conference: Program and Abstracts. AWA Biosolids and Source Management National Conference, St Leonards, NSW, Australia: Australian Water Association 2012, p. 51.
18. Guo X, Wang C, Sun F, et al. A comparison of microbial characteristics between the thermophilic and mesophilic anaerobic digesters exposed to elevated food waste loadings. Bioresource Technol 2014;152:420-8.
19. Ha PT, Lee TK, Rittmann BE, et al. Treatment of alcohol distillery wastewater using a Bacteroidetes-dominant thermophilic microbial fuel cell. Environ Sci Technol 2012;46:3022-30.
20. Hatamoto M, Imachi H, Ohashi A, et al. Identification and cultivation of anaerobic, syntrophic long-chain fatty acid-degrading microbes from mesophilic and thermophilic methanogenic sludges. Appl Environ Microb 2007;73:1332-40.
21. Hatamoto M, Imachi H, Yashiro Y, et al. Detection of active butyrate-degrading microorganisms in methanogenic sludges by RNA-based stable isotope probing. Appl Environ Microb 2008;74:3610-4.
22. Ho DP. A high-rate high temperature anaerobic digestion system for sludge treatment. PhD, The University of Queensland, Australia - School of Chemical Engineering, Advanced Water Management Centre, 2014.
23. Ho DP, Jensen PD, Batstone DJ. Effects of temperature and hydraulic retention time on acetotrophic pathways and performance in high-rate sludge digestion. Environ Sci Technol 2014;48:6468-76.
24. Holland PM, Abramson RD, Watson R, et al. Detection of specific polymerase chain reaction product by utilizing the 5|-3| exonuclease activity of Thermus aquaticus DNA polymerase. P Natl Acad Sci USA 1991;88:7276-7280.
25. Hori T, Haruta S, Ueno Y, et al. Dynamic transition of a methanogenic population in response to the concentration of volatile fatty acids in a thermophilic anaerobic digester. Appl Environ Microb 2006;72:1623-30.
26. Hussain A, Guiot SR, Mehta P, et al. Electricity generation from carbon monoxide and syngas in a microbial fuel cell. Appl Microbiol Biot 2011;90:827-36.
27. Jong BC, Kim BH, Chang IS, et al. Enrichment, performance, and microbial diversity of a thermophilic mediatorless microbial fuel cell. Environ Sci Technol 2006;40:6449-54.
28. Kanno M, et al. Isolation of butanol- and isobutanol-tolerant bacteria and physiological characterization of their butanol tolerance. Appl Environ Microb 2013;79:6998-7005.
29. Kato S, Kosaka T, Watanabe K. Comparative transcriptome analysis of responses of Methanothermobacter thermautotrophicus to different environmental stimuli. Environ Microbiol 2008;10:893-905.
30. Kawagoshi Y, Hino N, Fujimoto A, et al. Effect of inoculum conditioning on hydrogen fermentation and pH effect on bacterial community relevant to hydrogen production. J Biosci Bioeng 2005;100:524-30.
31. Kersters I, Houwen F, Verstraete W. Thermophilic, anaerobic degradation of gelatin by Thermobacteroides proteolyticus. Biotechnol Lett 1993;15:931-6.
32. Kersters I, Maestrojuan GM, Torck U, et al. Isolation of Coprothermobacter proteolyticus from an anaerobic digest and further characterization of the species. Syst Appl Microbiol 1994;17:289-95.
33. Klingeberg M, Hashwa F, Antranikian G. Properties of extremely thermostable proteases from anaerobic hyperthermophilic bacteria. Appl Microbiol Biot 1991;34:715-9.
34. Kobayashi T, Li YY, Harada H. Analysis of microbial community structure and diversity in the thermophilic anaerobic digestion of waste activated sludge. Water Sci Technol 2008;57:1199-205.
35. Kobayashi T, Li YY, Harada H, et al. Upgrading of the anaerobic digestion of waste activated sludge by combining temperature-phased anaerobic digestion and intermediate ozonation. Water Sci Technol 2009;59:185-93.
36. Köllmeier T, Analyse spezialisierter Bakterien gemeinschaften und deren cellulolytische Hauptvertreter für die Hydrolyse in thermophilen Biogasanlagen. München: Thesis, Technischen Universität. 2013, Avalaible at Deutsche National Bibliotek: http://d-nb.info/1050025660/34 (24 March 2015, date last accessed).
37. Krakat N, Westphal A, Satke K, et al. The microcosm of a biogas fermenter: comparison of moderate hyperthermophilic (60°C) with thermophilic (55°C) conditions. Eng Life Sci 2010;10:520-7.
38. Kunisawa T. Evaluation of the phylogenetic position of the sulfate-reducing bacterium Thermodesulfovibrio yellowstonii (phylum Nitrospirae) by means of gene order data from completely sequenced genomes. Int J Syst Evol Micr 2010;60:1090-102.
39. Lan G, Li Z, Zou C, et al. Enrichment and diversity analysis of the thermophilic microbes in a high temperature petroleum reservoir. Afr J Microbiol Res 2011;5:1850-7.
40. Lee M, Hidaka T, Tsuno H. Two-phased hyperthermophilic anaerobic co-digestion of waste activated sludge with kitchen garbage. J Biosci Bioeng 2009;108:408-13.
41. Lienen T, Kleyböcker A, Verstraete W, et al. Moderate temperature increase leads to disintegration of floating sludge and lower abundance of the filamentous bacterium Microthrix parvicella in anaerobic digesters. Water Res 2014;65: 203-12.
42. LüF, Bize A, Guillot A, et al. Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity. ISME J 2014a;8:88-102.
43. LüF, Li T, Wang T, et al. Improvement of sludge digestate biodegradability by thermophilic bioaugmentation. Appl Microbiol Biot 2014b;98:969-77.
44. Luo G,Wang W, Angelidaki I. Anaerobic digestion for simultaneous sewage sludge treatment and CO biomethanation: process performance and microbial ecology. Environ Sci Technol 2013;47:10685-93.
45. Majeed T, Tabassum R, Orts WJ, et al. Expression and characterization of Coprothermobacter proteolyticus alkaline serine protease. Sci World J 2013;2013:1-6.
46. Mbadinga SM, Li K-P, Zhou L, et al. Analysis of alkane-dependent methanogenic community derived fromproduction water of a high-temperature petroleum reservoir. Appl Microbiol Biot 2012;96:531-42.
47. Menes RJ, Fernández A, Mux L. Physiological and molecular characterisation of an anaerobic thermophilic oleatedegrading enrichment culture. Anaerobe 2001;7:17-24.
48. Motte J-C, Trably E, Hamelin J, et al. Total solid content drives hydrogen production throughmicrobial selection during thermophilic fermentation. Bioresource Technol 2014;166: 610-5.
49. Nakamura K, Terada T, Sekiguchi Y, et al. Application of pseudomurein endoisopeptidase to fluorescence in situ hybridization of methanogens within the family Methanobacteriaceae. Appl Environ Microb 2006;72:6907-13.
50. Nazina TN, Shestakova NM, Grigor'yan AA, et al. Phylogenetic diversity and activity of anaerobic microorganisms of hightemperature horizons of the Dagang oil field (P. R. China). Microbiology 2006;75:55-65.
51. NishidaH, Beppu T, Ueda K. Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and Thermotogae. Genomics 2011;98:370-5.
52. NissiläME,Tähti HP, Rintala JA, et al. Effects of heat treatment on hydrogen production potential and microbial community of thermophilic compost enrichment cultures. Bioresour Technol 2011;102:4501-6.
53. Ollivier BM, Mah RA, Ferguson TJ, et al. Emendation of the genus Thermobacteroides: Thermobacteroides proteolyticus sp. nov., a proteolytic acetogen from a methanogenic enrichment. Int J Syst Bacteriol 1985;35:425-8.
54. Ollivier B, Patel BK, Garcia JL. Anaerobes from extreme environments. In: Seckbach J (ed). Journey to Diverse Microbial Worlds. Dordrecht: Kluwer Academic Publishers, 2000, 75-90.
55. Palatsi J, Vinãs M, Guivernau M, et al. Anaerobic digestion of slaughterhouse waste: main process limitations and microbial community interactions. Bioresource Technol 2011;102:2219-27.
56. Pervin HM, Dennis PG, Lim HJ, et al. Drivers of microbial community composition in mesophilic and thermophilic temperature-phased anaerobic digestion pre-treatment reactors. Water Res 2013;47:7098-108.
57. Rainey FA, Stackebrandt E. Transfer of the type species of the genus Thermobacteroides to the genus Thermoanaerobacter as Thermoanaerobacter acetoethylicus (Ben-Bassat and Zeikus 1981) comb. nov., description of Coprothemobacter gen. nov., and reclassification of Themobacteroides proteolyticus. Int J Syst Bacteriol 1993;43:857-9.
58. Ritari J, Koskinen K, Hultman J, et al. Molecular analysis of meso- and thermophilic microbiota associated with anaerobic biowaste degradation. BMC Microbiol 2012;12:121.
59. Riviére D, Desvignes V, Pelletier E, et al. Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge. ISME J 2009;3:700-14.
60. Saitou N, Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406-25.
61. Sarti A, Pozzi E, Chinalia Fa, et al. Microbial processes and bacterial populations associated to anaerobic treatment of sulfate-rich wastewater. Process Biochem 2010;45: 164-70.
62. Sasaki K, Haruta S, Tatara M, et al. Microbial community in methanogenic packed-bed reactor successfully operating at short hydraulic retention time. J Biosci Bioeng 2006;101: 271-3.
63. Sasaki K, Haruta S, Ueno Y, et al. Microbial population in the biomass adhering to supporting material in a packed-bed reactor degrading organic solid waste. Appl Microbiol Biot 2007;75:941-52.
64. Sasaki K, Morita M, Sasaki D, et al. Syntrophic degradation of proteinaceous materials by the thermophilic strains Coprothermobacter proteolyticus and Methanothermobacter thermautotrophicus. J Biosci Bioeng 2011;112:469-72.
65. Sasaki D, Morita M, Sasaki K, et al. Acceleration of cellulose degradation and shift of product via methanogenic coculture of a cellulolytic bacterium with a hydrogenotrophic methanogen. J Biosci Bioeng 2012;114:435-9.
66. Sasaki D, Sasaki K, Watanabe A, et al. Operation of a cylindrical bioelectrochemical reactor containing carbon fiber fabric for efficient methane fermentation from thickened sewage sludge. Bioresource Technol 2013;129:366-73.
67. Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. P Natl Acad Sci USA 2004;101:11030-5.
68. Tamura K, Stecher G, Peterson D, et al. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013;30:2725-9.
69. Tandishabo K, Iga Y, Tamaki H, et al. Characterization of a novel Coprothermobacter sp. strain IT3 isolated from an anaerobic digester-hydrogen production and peptidase profiles at higher temperature. J Env Conserv Eng 2012a;41: 753-61.
70. Tandishabo K, Nakamura K, Umetsu K, et al. Distribution and role of Coprothermobacter spp. in anaerobic digesters. J Biosci Bioeng 2012b;114:518-20.
71. Tandishabo K, Takahashi A, Nakamura K, et al. Characterization of the rhodanese enzyme in Coprothermobacter strains. ISETS07 2007;07:1202-3.
72. Tang Y-Q, Ji P, Hayashi J, et al. Characteristic microbial community of a dry thermophilic methanogenic digester: its longterm stability and change with feeding. Appl Microbiol Biot 2011;91:1447-61.
73. Tang Y-Q, Matsui T, Morimura S, et al. Effect of temperature on microbial community of a glucose-degrading methanogenic consortium under hyperthermophilic chemostat cultivation. J Biosci Bioeng 2008;106:180-7.
74. Tang Y, Shigematsu Ikbal T, et al. The effects of micro-aeration on the phylogenetic diversity of microorganisms in a thermophilic anaerobicmunicipal solid-waste digester.Water Res 2004;38:2537-50.
75. Tatara M, Makiuchi T, Ueno Y, et al. Methanogenesis from acetate and propionate by thermophilic down-flow anaerobic packed-bed reactor. Bioresource Technol 2008;99:4786-95.
76. Tezel U, Tandukar M, Hajaya MG, et al. Transition of municipal sludge anaerobic digestion from mesophilic to thermophilic and long-term performance evaluation. Bioresource Technol 2014;170:385-94.
77. Tian Z, Zhang Y, Li Y, et al. Rapid establishment of thermophilic anaerobic microbial community during the one-step startup of thermophilic anaerobic digestion from a mesophilic digester. Water Res 2015;69:9-19.
78. Toplak A, Wu B, Fusetti F, et al. Proteolysin, a novel highly thermostable and cosolvent-compatible protease from the thermophilic bacterium Coprothermobacter proteolyticus. Appl Environ Microb 2013;79:5625-32.
79. Ueno Y, Tatara M. Microbial population in a thermophilic packed-bed reactor for methanogenesis from volatile fatty acids. Enzyme Microb Tech 2008;43:302-308.
80. Wagner AO, Lins P, Malin C, et al. Impact of protein-, lipid- and cellulose-containing complex substrates on biogas production and microbial communities in batch experiments. Sci Total Environ 2013;458-460:256-66.
81. Whidden C, Zeh N, Beiko RG. Supertrees based on the subtree prune-and-regraft distance. Syst Biol 2014;63: 566-81.
82. Wrighton KC, Agbo P,Warnecke F, et al. A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells. ISME J 2008;2:1146-56.
83. Yabu H, Sakai C, Fujiwara T, et al. Thermophilic two-stage dry anaerobic digestion of model garbage with ammonia stripping. J Biosci Bioeng 2011;111:312-9.
84. Yamada C, Kato S, Ueno Y, et al. Inhibitory effects of ferrihydrite on a thermophilic methanogenic community. Microbes Environ 2014;29:227-30.
85. Yutin N, Puigbó P, Koonin E, et al. Phylogenomics of prokaryotic ribosomal proteins. PLoS One 2012; 7:e36972.
86. Zamanzadeh M, Parker WJ, Verastegui Y, et al. Biokinetics and bacterial communities of propionate oxidizing bacteria in phased anaerobic sludge digestion systems. Water Res 2013;47:1558-69.
87. Zhang H, Banaszak JE, Parameswaran P, et al. Focused-Pulsed sludge pre-treatment increases the bacterial diversity and relative abundance of acetoclastic methanogens in a fullscale anaerobic digester. Water Res 2009;43:4517-26.