Biodiversity characterization of cellulolytic bacteria present on native Chaco soil by comparison of ribosomal RNA genes

Research in Microbiology

Volumn 163, Issue 3, 2012, Pages 221-232

  Talia, Paola ^a   Sede, Silvana M ^b   Campos, Eleonora ^a   Rorig, Marcela ^a   Principi, Dario ^a   Tosto, Daniela ^a   Hopp, H Esteban ^a,c   Grasso, Daniel ^a   Cataldi, Angel ^a  

^a INSTITUTO NACIONAL DE TECNOLOGÍA AGROPECUARIA INTA   (Argentina)

^b INSTITUTO DE BOTÁNICA DARWINION   (Argentina)

^c UNIVERSIDAD DE BUENOS AIRES   (Argentina)

Author keywords

16S rRNA; Biodiversity; Cellulose; Native forest soil

Indexed keywords

CELLULOSE; RIBOSOME RNA;

ARTICLE; BIODIVERSITY; BREVUNDIMONAS; CAULOBACTER; COMPARATIVE STUDY; GENE EXPRESSION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLUM; PRIORITY JOURNAL; PROTEOBACTERIA; SEQUENCE ANALYSIS; SOIL ANALYSIS; TAXONOMY; VARIOVORAX;

BACTERIA; BIODIVERSITY; CELLULOSE; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY;

ACHROMOBACTER; ACIDOBACTERIA; ACIDOTHERMUS; ACIDOVORAX; ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BREVUNDIMONAS; CAULOBACTER; DELFTIA; DEVOSIA; MICROMONOSPORA; PAENIBACILLUS; PROTEOBACTERIA; PSEUDOMONAS; SPHINGOMONAS; STENOTROPHOMONAS; STREPTOMYCES; VARIOVORAX; XANTHOMONAS;

EID: 84859446073     PISSN: 09232508     EISSN: 17697123     Source Type: Journal    
DOI: 10.1016/j.resmic.2011.12.001     Document Type: Article

References (88)

1. Allegrucci N., Cabello M.N., Arambarri A.M. Diversity of saprotrophic anamorphic ascomycetes from native forests in Argentina: an updated review. Darwiniana 2009, 47:108-124.
2. Barr B.K., Hsieh Y.L., Ganem B., Wilson D.B. Identification of two functionally different classes of exocellulases. Biochemistry 1996, 35:586-592.
3. Bond P.L., Hugenholtz P., Keller J., Blackall L.L. Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Appl. Environ. Microbiol. 1995, 61:1910-1916.
4. Carrillo L., Benitez Ahrendts M.R., Maldonado M.J. Alkali thermophilic actinomycetes in a subtropical area of Jujuy, Argentina. Rev. Argentina Microbiol. 2009, 41:112-116.
5. Cermeno P., Falkowski P.G. Controls on diatom biogeography in the ocean. Science 2009, 325:1539-1541.
6. Chaiyaso T., Kuntiya A., Techapun C., Leksawasdi N., Seesuriyachan P., Hanmoungjai P. Optimization of cellulase-free xylanase production by thermophilic Streptomyces thermovulgaris TISTR1948 through Plackett-Burman and response surface methodological approaches. Biosci. Biotechnol. Biochem. 2011, 75:531-537.
7. Cole J.R., Chai B., Marsh T.L., Farris R.J., Wang Q., Kulam S.A., Chandra S., McGarrell D.M., Schmidt T.M., Garrity G.M., Tiedje J.M. The ribosomal database project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 2003, 31:442-443.
8. Chu H., Fierer N., Lauber C.L., Caporaso J.G., Knight R., Grogan P. Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environ. Microbiol. 2010, 12:2998-3006.
9. Dehority B.A., Tirabasso P.A., Grifo A.P. Most-probable-number procedures for enumerating ruminal bacteria, including the simultaneous estimation of total and cellulolytic numbers in one medium. Appl. Environ. Microbiol. 1989, 55:2789-2792.
10. Donofrio R.S., Bestervelt L.L., Saha R., Bagley S.T. Selective enumeration strategies for Brevundimonas diminuta from drinking water. J. Ind. Microbiol. Biotechnol. 2010, 37:407-417.
11. Dunbar J., Takala S., Barns S.M., Davis J.A., Kuske C.R. Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl. Environ. Microbiol. 1999, 65:1662-1669.
12. Fazi S., Amalfitano S., Piccini C., Zoppini A., Puddu A., Pernthaler J. Colonization of overlaying water by bacteria from dry river sediments. Environ. Microbiol. 2008, 10:2760-2772.
13. Flemming C.A., Lee H., Trevors J.T. Bioluminescent most-probable-number method to enumerate lux-marked Pseudomonas aeruginosa UG2Lr in soil. Appl. Environ. Microbiol. 1994, 60:3458-3461.
14. Fritz I., Strömpl C., Nikitin D.I., Lysenko A.M., Abraham W.R. Brevundimonas mediterranea sp. nov., a non-stalked species from the Mediterranean Sea. Int. J. Syst. Evol. Microbiol. 2005, 55:479-486.
15. Fukuda A., Hagiwara H., Ishimura T., Kouduka M., Ioka S., Amano Y., Tsunogai U., Suzuki Y., Mizuno T. Geomicrobiological properties of ultra-deep granitic groundwater from the Mizunami Underground Research Laboratory (MIU), central Japan. Microb. Ecol. 2010, 60:214-225.
16. Germida J.J. Growth of indigenous Rhizobium leguminosarum and Rhizobium meliloti in soils amended with organic nutrients. Appl. Environ. Microbiol. 1988, 54:257-263.
17. Gjermansen M., Nilsson M., Yang L., Tolker-Nielsen T. Characterization of starvation-induced dispersion in Pseudomonas putida biofilms: genetic elements and molecular mechanisms. Mol. Microbiol. 2010, 75:815-826.
18. Granhall U., Welsh A., Throbäck I.N., Hjort K., Hansson M., Hallin S. Bacterial community diversity in paper mills processing recycled paper. J. Ind. Microbiol. Biotechnol. 2010, 37:1061-1069.
19. Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 2010, 59:307-321.
20. Guo R., Ding M., Zhang S.L., Xu G.J., Zhao F.K. Molecular cloning and characterization of two novel cellulase genes from the mollusk Ampullaria crossean. J. Comp. Physiol. 2008, 178:209-215.
21. Haichar F.e.Z., Wafa A., Christen R., Heulin T., Marol C., Marais M.-F., Mougel C., Ranjard L., Balesdent J., Berge O. Identification of cellulolytic bacteria in soil by stable isotope probing. Environ. Microbiol. 2007, 9:625-634.
22. Haldane J.B.S. An exact test for randomness of mating. J. Genet. 1954, 52:631-635.
23. Hankin L., Anagostakis S.L. Solid media containing carboxymethylcellulose to detect cellulase activity of microorganisms. J. Gen. Microbiol. 1977, 98:109-115.
24. Head I.M., Saunders J.R., Pickup R.W. Microbial evolution, diversity, and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microbiol. Ecol. 1998, 35:1-21.
25. Higashi S., Abe M.l Scanning electron microscopy of Rhizobium trifolii infection sites on root hairs of white clover. Appl. Environ. Microbiol. 1980, 40:1094-1099.
26. Horner-Devine M.C., Carney K.M., Bohannan B.J.M. An ecological perspective on bacterial biodiversity. Proc. R. Soc. Lond. B 2004, 271:113-122.
27. Hosoi-Tanabe S., Zhang H., Zhu D., Nagata S., Ban S., Imura S. Comprehensive analysis of an Antarctic bacterial community with the adaptability of growth at higher temperatures than those in Antarctica. Biocontrol Sci. 2010, 15:57-62.
28. Hubbell D.H., Morales V.M., Umali-Garcia M. Pectolytic enzymes in Rhizobium. Appl. Environ. Microbiol. 1978, 35:210-213.
29. Hugenholtz P., Goebel B.M., Pace N.R. Impact of culture independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 1998, 180:4765-4774.
30. Izquierdo J.A., Sizova M.V., Lynd L.R. Diversity of bacteria and glycosyl hydrolase family 48 genes in cellulolytic consortia enriched from thermophilic biocompost. Appl. Environ. Microbiol. 2010, 76:3545-3553.
31. Jing H., Cockburn D., Zhang Q., Clarke A.J. Production and purification of the isolated family 2a carbohydrate-binding module from Cellulomonas fimi. Protein Expr. Purif. 2009, 64:63-68.
32. Juárez-Jiménez B., Manzanera M., Rodelas B., Martínez-Toledo M.V., Gonzalez-López J., Crognale S., Pesciaroli C., Fenice M. Metabolic characterization of a strain (BM90) of Delftia tsuruhatensis showing highly diversified capacity to degrade low molecular weight phenols. Biodegradation 2010, 21:475-489.
33. Kang M.S., Im W.T., Jung H.M., Kim M.K., Goodfellow M., Kim K.K., Yang H.C., An D.S., Lee S.T. Cellulomonas composti sp. nov., a cellulolytic bacterium isolated from cattle farm compost. Int. J. Syst. Evol. Microbiol. 2007, 57:1256-1260.
34. Kato S., Haruta S., Cui Z.J., Ishii M., Igarashi Y. Stable coexistence of five bacterial strains as a cellulose-degrading community. Appl. Environ. Microbiol. 2005, 71:7099-7106.
35. Katoh K., Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 2008, 9:286-298.
36. Kim J.-S., Sparovek G., Longo R.M., De Melo W.J., Crowley D. Bacterial diversity of terra preta and pristine forest soil from the Western Amazon. Soil Biol. Biochem. 2007, 39:684-690.
37. Kim S.J., Lee C.M., Han B.R., Kim M.Y., Yeo Y.S., Yoon S.H., Koo B.S., Jun H.K. Characterization of a gene encoding cellulase from uncultured soil bacteria. FEMS Microbiol. Lett. 2008, 282:44-51.
38. Kurakake M., Ide N., Komaki T. Biological pretreatment with two bacterial strains for enzymatic hydrolysis of office paper. Curr. Microbiol. 2007, 54:424-428.
39. Lednická D., Mergaert J., Cnockaert M.C., Swings J. Isolation and identification of cellulolytic bacteria involved in the degradation of natural cellulosic fibres. Syst. Appl. Microbiol. 2000, 23:292-299.
40. Linger J.G., Adney W.S., Darzins A. Heterologous expression and extracellular secretion of cellulolytic enzymes by Zymomonas mobilis. Appl. Environ. Microbiol. 2010, 76:6360-6369.
41. Lozupone C., Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 2005, 71:8228-8235.
42. Lynd L.R., Weimer P.J., Van Zyl W.H., Pretorius I.S. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol. Mol. Biol. Rev. 2002, 66:506-577.
43. Maki M., Leung K.T., Qin W. The prospects of cellulase-producing bacteria for the bioconversion of lignocellulosic biomass. Int. J. Biol. Sci. 2009, 5:500-516.
44. Männistö M.K., Häggblom M.M. Characterization of psychrotolerant heterotrophic bacteria from Finnish Lapland. Syst. Appl. Microbiol. 2006, 29:229-243.
45. Marques A.R., Coutinho P.M., Videira P., Fialho A.M., Sá-Correia I. Sphingomonas paucimobilis beta-glucosidase Bgl1: a member of a new bacterial subfamily in glycoside hydrolase family 1. Biochem. J. 2003, 370:793-804.
46. Masai E., Katayama Y., Fukuda M. Genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds. Biosci. Biotechnol. Biochem. 2007, 71:1-15.
47. Mateos P.F., Jimenez-Zurdo J.I., Chen J., Squartini A.S., Haack S.K., Martinez-Molina E. Cell associated pectinolytic and cellulolytic enzymes in Rhizobium leguminosarum biovar trifolii. Appl. Environ. Microbiol. 1992, 58:1816-1822.
48. McCaig A.E., Glover L.A., Prosser J.I. Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl. Environ. Microbiol. 1999, 65:1721-1730.
49. Mehnaz S., Baig D.N., Lazarovits G. Genetic and phenotypic diversity of plant growth promoting rhizobacteria isolated from sugarcane plants growing in Pakistan. Microbiol. Biotechnol. 2010, 20:1614-1623.
50. Mohagheghi A., Grohmann K., Himmel M., Leighton L., Updegraff D.M. Isolation and characterization of Acidothermus cellulolyticus gen. nov., sp. nov., a new genus of thermophilic, acidophilic, cellulolytic bacteria. Int. J. Syst. Bacteriol. 1986, 36:435-443.
51. Moyer C.L., Tiedje J.M., Dobbs F.C., Karl D.M. A computer simulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature. Appl. Environ. Microbiol. 1996, 62:2501-2507.
52. Nierman W.C., Feldblyum T.V., Laub M.T., Paulsen I.T., Nelson K.E., Eisen J., Heidelberg J.F., Alley M.R.K., Ohta N., Maddocki J.R., Potocka I., Nelson W.C., Newton A., Stephens C., et al. Complete genome sequence of Caulobacter crescentus. PNAS 2001, 98:4136-4141.
53. Nikolova P.V., Creagh A.L., Duff S.J., Haynes C.A. Thermostability and irreversible activity loss of exoglucanase/xylanase Cex from Cellulomonas fimi. Biochemistry 1997, 36:1381-1388.
54. Pérez-Avalos O., Sánchez-Herrera L.M., Salgado L.M., Ponce-Noyola T. A bifunctional endoglucanase/endoxylanase from Cellulomonas flavigena with potential use in industrial processes at different pH. Curr. Microbiol. 2008, 57:39-44.
55. Pittl E., Innerebner G., Wanek W., Insam H. Microbial communities of arboreal and ground soils in the Esquinas rainforest, Costa Rica. Plant Soil 2010, 329:65-74.
56. Ponce-Noyola T., de la Torre M. Regulation of cellulases and xylanases from a derepressed mutant of Cellulomonas flavigena growing on sugar-cane bagasse in continuous culture. Bioresour. Technol. 2001, 78:285-291.
57. Popowska M., Miernik A., Rzeczycka M., Łopaciuk A. The impact of environmental contamination with antibiotics on levels of resistance in soil bacteria. Environ. Qual. 2010, 39:1679-1687.
58. Principi P., Villa F., Sorlini C., Cappitelli F. Molecular studies of microbial community structure on stained pages of Leonardo da Vinci's Atlantic Codex. Microb. Ecol. 2011, 61:214-222.
59. Quince C., Lanzen A., Curtis T.P., Davenport R.J., Hall N., Head I.M., Read L.F., Sloan W.T. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Meth. 2009, 6:639-641.
60. Rättö M., Suihko M.L., Siika-aho M. Polysaccharide-producing bacteria isolated from paper machine slime deposits. J. Ind. Microbiol. Biotechnol. 2005, 32:109-114.
61. Reese E.T., Siu R.G.H., Levinson H.S. The biological degradation of soluble cellulose derivatives and its relationship to the mechanism of cellulose hydrolysis. J. Bacteriol. 1950, 59:485-497.
62. Rehman F.U., Aslam M., Tariq M.I., Shaheen A., Sami A.J., Naveed N.H., Batool A.I. Isolation of cellulolytic activities from Tribolium castaneum (red flour beetle). African J. Biotechnol. 2009, 8:6710-6715.
63. Roesch L.F.W., Fulthorpe R.R., Riva A., Casella G., Hadwin A.K.M., Kent A.D., Daroub S.H., Camargo F.A.O., Farmerie W.G., Triplett E.W. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 2007, 1:283-290.
64. Russek E., Colwell R.R. Computation of most probable numbers. Appl. Environ. Microbiol. 1983, 45:1646-1650.
65. Sait M., Hugenholtz P., Janssen P.H. Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ. Microbiol. 2002, 4:654-666.
66. Sánchez-Herrera L.M., Ramos-Valdivia A.C., de la Torre M., Salgado L.M., Ponce-Noyola T. Differential expression of cellulases and xylanases by Cellulomonas flavigena grown on different carbon sources. Appl. Microbiol. Biotechnol. 2007, 77:589-595.
67. Saratale G.D., Saratale R.G., Lo Y.C., Chang J.S. Multicomponent cellulase production by Cellulomonas biazotea NCIM-2550 and its applications for cellulosic biohydrogen production. Biotechnol. Prog. 2010, 26:406-416.
68. Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.A., Oakley B.B., Parks D.H., Robinson C.J., Sahl J.W., Stres B., Thallinger G.G., Van Horn D.J., Weber C.F. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 2009, 75:7537-7541.
69. Schloss P.D., Handelsman J. Status of the microbial census. Microbiol. Mol. Biol. Rev. 2004, 68:686-691.
70. Segers P., Vancanneyt M., Pot B., Torck U., Hoste B., Dewettinck D., Falsen E., Kersters K., De Vos P. Classification of Pseudomonas diminuta Leifson and Hugh 1954 and Pseudomonas vesicularis Busing, Doll, and Freytag 1953 in Brevundimonas gen. nov. as Brevundimonas diminuta comb. nov. and Brevundimonas vesicularis comb. nov., respectively. Int. J. Syst. Bacteriol. 1994, 44:499-510.
71. Semêdo L.T., Gomes R.C., Bon E.P., Soares R.M., Linhares L.F., Coelho R.R. Endocellulase and exocellulase activities of two Streptomyces strains isolated from a forest soil. Appl. Biochem. Biotechnol. 2000, 84:267-276.
72. Shen H., Gilkes N.R., Kilburn D.G., Miller R.C.J., Warren R.A. Cellobiohydrolase B, a second exo-cellobiohydrolase from the cellulolytic bacterium Cellulomonas fimi. Biochem. J. 1995, 311:67-74.
73. Shivaji S., Reddy G.S., Aduri R.P., Kutty R., Ravenschlag K. Bacterial diversity of a soil sample from Schirmacher Oasis, Antarctica. Cell. Mol. Biol. 2004, 50:525-536.
74. Smant G., Stokkermans J.P., Yan Y., De Boer J.M., Baum T.J., Wang X., Hussey R.S., Gommers F.J., Henrissat B., Davis E.L., Helder J., Schots A., Bakker J. Endogenous cellulases in animals: isolation of β-1,4-endoglucanase genes from two species of plant-parasitic cyst nematodes. Proc. Natl. Acad. Sci. 1998, 95:4906-4911.
75. Stackebrandt E., Goebel B.M. A place for DNA-DNA reassociation and 16S rRNA sequence-analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 1994, 44:846-849.
76. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol. Biol. Evol. 2011, 28:2731-2739.
77. Thomas P., Kumari S., Swarna G.K., Gowda T.K. Papaya shoot tip associated endophytic bacteria isolated from in vitro cultures and host-endophyte interaction in vitro and in vivo. Can. J. Microbiol. 2007, 53:380-390.
78. Ude S., Arnold D.L., Moon C.D., Timms-Wilson T., Spiers A.J. Biofilm formation and cellulose expression among diverse environmental Pseudomonas isolates. Environ. Microbiol. 2006, 11:1997-2011.
79. Wang W.D., Song Y.B., Wang Y.J., Gao Y.M., Jing R.Y., Cui Z.J. Biodiversity of mesophilic microbial community BYND-8 capability of lignocellulose degradation and its effect on biogas production. Huan Jing Ke Xue 2011, 32:253-258.
80. Watanabe H., Tokuda G. Cellulolytic systems in insects. Annu. Rev. Entomol. 2010, 55:609-632.
81. Watanabe H., Noda H., Tokuda G., Lo N. A cellulase gene of termite origin. Nature 1998, 394:330-331.
82. Weisburg W.G., Barns S.M., Pelletier D.A., Lane D.J. 16S Ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 1991, 173:697-703.
83. Wood T.M., McCrae S.I., Bhat K.M. The mechanism of fungal cellulase action. Synergism between enzyme components of Penicillium pinophilum cellulase in solubilizing hydrogen bond-ordered cellulose. Biochem. J. 1989, 260:37-43.
84. Yan Z.C., Wang B., Li Y.Z., Gong X., Zhang H.Q., Gao P.J. Morphologies and phylogenetic classification of cellulolytic Myxobacteria. Syst. Appl. Microbiol. 2003, 26:104-109.
85. Yang H., Wu H., Wang X., Cui Z., Li Y. Selection and characteristics of a switchgrass-colonizing microbial community to produce extracellular cellulases and xylanases. Bioresour. Technol. 2011, 102:3546-3550.
86. Yeasmin S., Kim C.H., Park H.J., Sheikh M.I., Lee J.Y., Kim J.W., Back K.K., Kim S.H. Cell surface display of cellulase activity-free xylanase enzyme on Saccharomyces cerevisiae EBY100. Appl. Biochem. Biotechnol. 2011, 164:299-304.
87. Yin L.J., Huang P.S., Lin H.H. Isolation of cellulase-producing bacteria and characterization of the cellulase from the isolated bacterium Cellulomonas sp. YJ5. J. Agric. Food Chem. 2010, 58:9833-9837.
88. Yoon J.H., Kang S.J., Lee J.S., Oh H.W., Oh T.K. Brevundimonas lenta sp. nov., isolated from soil. Int. J. Syst. Evol. Microbiol. 2007, 57:2236-2240.