Diversity and activity of cellulose-decomposing bacteria, isolated from a sandy and a loamy soil after long-term manure application

Microbial Ecology

Volumn 55, Issue 3, 2008, Pages 512-522

  Ulrich, Andreas ^a   Klimke, Gabriele ^a   Wirth, Stephan ^a  

^a LEIBNIZ CENTRE FOR AGRICULTURAL LANDSCAPE RESEARCH ZALF   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; CELLULOSE; FERTILIZER; RIBOSOME DNA; RNA 16S;

ARTICLE; BACTERIUM; BIODIVERSITY; BIOMASS; CLASSIFICATION; GENETICS; ISOLATION AND PURIFICATION; MANURE; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SOIL;

BACTERIA; BIODIVERSITY; BIOMASS; CELLULOSE; DNA, BACTERIAL; DNA, RIBOSOMAL; FERTILIZERS; MANURE; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, RIBOSOMAL, 16S; SOIL; SOIL MICROBIOLOGY;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA; GAMMAPROTEOBACTERIA; STREPTOMYCES;

EID: 41049092553     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-007-9296-0     Document Type: Article

References (48)

1. Akasaka H, Izawa T, Ueki K, Ueki A (2003) Phylogeny of numerically abundant culturable anaerobic bacteria associated with degradation of rice plant residue in Japanese paddy field soil. FEMS Microbiol Ecol 43:149-161
2. Berg B, Laskowski R (2006) Litter decomposition: a guide to carbon and nutrient turnover. Adv Ecol Res Vol. 38. Elsevier, Amsterdam
3. Bergquist PL, Gibbs MD, Morris DD, Te'o VS, Saul DJ, Moran HW (1999) Molecular diversity of thermophilic cellulolytic and hemicellulolytic bacteria. FEMS Microbiol Ecol 28:99-110
4. Blackwood CB, Marsh T, Kim SH, Paul EA (2003) Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities. Appl Environ Microbiol 69:926-932
5. Chun J, Goodfellow M (1995) A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 45:240-245
6. Crawford DL (1998) Biodegradation of agricultural and urban wastes. In: Goodfellow M, Williams ST, Mordarski M (eds) Actinomycetes in biotechnology. Academic, London, pp 433-439
7. Dilly O, Bartsch S, Rosenbrock P, Buscot F, Munch JC (2001) Shifts in physiological capabilities of the microbiota during the decomposition of leaf litter in a black alder (Alnus glutinosa (Gaertn.) L.) forest. Soil Biol Biochem 33:921-930
8. DIN-ISO 13536 (1997) Bestimmung der potentiellen Kationenaustauschkapazität und Basensättigung. Beuth, Berlin Wien Zürich
9. Dunbar J, Ticknor LO, Kuske CR (2001) Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities. Appl Environ Microbiol 67:190-197
10. Dunger W, Fiedler HJ (1997) Methoden der Bodenbiologie. Gustav Fischer Verlag Jena, Stuttgart, Lübeck, Ulm
11. Ellmer F, Köhn W (2004) Versuchsführer 2004. Institut für Pflanzenbauwissenschaften, Landwirtschaftlich-Gärtnerische Fakultät, Humboldt-Universität zu Berlin
12. Eriksson KEL, Blanchette RA, Ander P (1990) Microbial and enzymatic degradation of wood and wood components, Ch. 2.6. Cellulose degradation by bacteria, Springer Series in Wood Science (Timell TE, ed.). Springer, Berlin
13. Esham EC, Ye W, Morgan MA (2000) Identification and characterization of humic substances-degrading bacterial isolates from an estuarine environment. FEMS Microbiol Ecol 34:103-111
14. Felsenstein J (1993) PHYLIP (Phylogeny Inference Package) version 3.6a2. Distributed by the author. Department of Genetics, University of Washington, Seattle
15. Garbeva P, van Veen JA, van Elsas JD (2004) Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness. Annu Rev Phytopathol 42:243-270
16. Gilkes NR, Henrissat B, Kilburn DG, Miller RC Jr, Warren RAJ (1991) Domains in microbial β-1,4-glycanases: sequence conservation, function, and enzyme families. Microbiol Rev 55:303-315
17. Girvan MS, Bullimore J, Pretty JN, Osborn AM, Ball AS (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol 69:1800-1809
18. Halliwell G (1965) Hydrolysis of fibrous cotton and reprecipitated cellulose by cellulolytic enzymes from soil micro-organisms. Biochem J 96:270-281
19. Hartmann M, Fliessbach A, Oberholzer HR, Widmer F (2006) Ranking the magnitude of crop and farming systems on soil microbial biomass and genetic structure of bacterial communities. FEMS Microbiol Ecol 57:378-388
20. Hendricks CW, Doyle JD, Hugley B (1995) A new solid medium for enumerating cellulose-utilizing bacteria in soil. Appl Environ Microbiol 61:2016-2019
21. Hiroki M (1993) Effect of arsenic pollution on soil microbial population. Soil Sci Plant Nutr 2:227-235
22. Hiroki M, Watanabe MM (1996) Microbial community and rate of cellulose decomposition in peat soils in a mire. Soil Sci Plant Nutr 42:893-903
23. Körschens M, Pfefferkorn A (1998) Der Statische Düngungsversuch und andere Feldversuche. UFZ-Umweltforschungszentrum Leipzig-Halle GmbH
24. Larue R, Yu ZT, Parisi VA, Egan AR, Morrison M (2005) Novel microbial diversity adherent to plant biomass in the herbivore gastrointestinal tract, as revealed by ribosomal intergenic spacer analysis and rrs gene sequencing. Environ Microbiol 7:530-543
25. Lednicka D, Mergaert J, Cnockaert MC, Swings J (2000) Isolation and identification of cellulolytic bacteria involved in the degradation of natural cellulosic fibres. Syst Appl Microbiol 23:292-299
26. Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS (2002) Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 66:506-577
27. Marschner P, Kandeler E, Marschner B (2003) Structure and function of the soil microbial community in a long-term fertilizer experiment. Soil Biol Biochem 35:453-461
28. Meiwes KJ, König N, Khanna PK, Prenzel J, Ulrich B (1984) Chemische Untersuchungsverfahren für Mineralboden, Auflagehumus und Wurzeln zur Charakterisierung und Bewertung der Versauerung in Waldböden, Berichte des Forschungszentrums Waldökosysteme, Vol. 7, Universität Göttingen
29. Meyers PR, Bourn WR, Steyn LM, van Helden PD, Beyers AD, Brown GD (1998) Novel method for rapid measurement of growth of Mycobacteria in detergent-free media. J Clin Microbiol 36:2752-2754
30. Munzel U, Hothorn LA (2001) A unified approach to simultaneous rank test procedures in the unbalanced one-way layout. Biomet J 43:553-569
31. O'Donnell AG, Seasman M, Macrae A, Waite I, Davies JT (2001) Plants and fertilisers as drivers of change in microbial community structure and function in soils. Plant Soil 232:135-145
32. Pourcher AM, Sutra L, Hébé I, Moguedet G, Bollet C, Simoneau P, Gardan L (2001) Enumeration and characterization of cellulolytic bacteria from refuse of a landfill. FEMS Microbiol Ecol 34:229-241
33. Rabinovich ML, Melnik MS, Bolobova AV (2002) Microbial cellulases. Appl Biochem Microbiol 38:305-321
34. Rogers JA, Hsu JC (2001) Multiple comparisons of biodiversity. Biomet J 43:617-625
35. Ruijssenaars HJ, Hartmans S (2001) Plate screening methods for the detection of polysaccharase-producing microorganisms. Appl Microbiol Biotechnol 55:143-149
36. Smalla K, Oros-Sichler M, Milling A, Heuer H, Baumgarte S, Becker R, Neuber G, Kropf S, Ulrich A, Tebbe CC (2007) Bacterial diversity of soils assessed by DGGE, T-RFLP and SSCP fingerprints of PCR-amplified 16S rRNA gene fragments: do the different methods provide similar results? J Microbiol Methods 69:470-479
37. Teather RM, Wood PJ (1982) Use of Congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from bovine rumen. Appl Environ Microbiol 43:777-780
38. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The Clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882
39. Toyota K, Kuninaga S (2006) Comparison of soil microbial community between soils amended with or without farmyard manure. Appl Soil Ecol 33:39-48
40. Ulrich A, Becker R (2006) Soil parent material is a key determinant of the bacterial community structure in arable soils. FEMS Microbiol Ecol 56:430-443
41. Ulrich A, Wirth S (1999) Phylogenetic diversity and population densities of culturable cellulolytic soil bacteria across an agricultural encatchment. Microb Ecol 37:238-247
42. Wachinger G, Bronnenmeier K, Staudenberger WL, Schrempf H (1989) Identification of mycelium-associated cellulase from Streptomyces reticuli. Appl Environ Microbiol 55:2653-2657
43. Ward JH (1963) Hierarchical grouping to optimize an objective function. J Am Stat Ass 58:236
44. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697-703
45. Widmer F, Rasche F, Hartmann M, Fliessbach A (2006) Community structures and substrate utilization of bacteria in soils from organic and conventional farming systems of the DOK long-term field experiment. Appl Soil Ecol 33:294-307
46. Wirth S, Ulrich A (2002) Cellulose-degrading potentials and phylogenetic classification of carboxymethyl-cellulose decomposing bacteria isolated from soil. Syst Appl Microbiol 25:584-591
47. Wirth SJ, Wolf GA (1992) Micro-plate, colourimetric assay for endo-acting cellulase, xylanase, chitinase, 1,3-ß-glucanase and amylase extracted from forest soil horizons. Soil Biol Biochem 24:511-519
48. Wood TM, Garcia-Campayo V (1990) Enzymology of cellulose degradation. Biodegradation 1:147-161