Bacterial Diversity in Agricultural Soils during Litter Decomposition

Applied and Environmental Microbiology

Volumn 70, Issue 1, 2004, Pages 468-474

  Dilly, Oliver ^a,c,e   Bloem, Jaap ^d   Vos, An ^d   Munch, Jean Charles ^b  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b INSTITUTE OF EPIDEMIOLOGY   (Germany)

^c UNIVERSITY OF KIEL   (Germany)

^d WAGENINGEN UNIVERSITY   (Netherlands)

^e UNIVERSITY OF HAMBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CROPS; DECOMPOSITION; DNA; ELECTROPHORESIS; GENES; RNA; SOILS; VEGETATION;

BACTERIAL DIVERSITY; GENES CODING;

BACTERIA;

BACTERIAL DNA; DNA; NYLON; RIBOSOME RNA;

AGRICULTURE; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; BACTERIAL GROWTH; CLIMATE; CONTROLLED STUDY; CROP PRODUCTION; DECOMPOSITION; DEGRADATION; DENATURING GRADIENT GEL ELECTROPHORESIS; GENE AMPLIFICATION; GENETIC VARIABILITY; GRASSLAND; LITTER DECOMPOSITION; MICROORGANISM; NONHUMAN; RYE; SOIL MICROFLORA; SOIL POLLUTION; STRAIN DIFFERENCE; VEGETATION; WHEAT;

AGRICULTURE; BACTERIA; BIODEGRADATION, ENVIRONMENTAL; DNA, BACTERIAL; DNA, RIBOSOMAL; ECOSYSTEM; ELECTROPHORESIS; LOLIUM; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SOIL; SOIL MICROBIOLOGY; TRITICUM;

BACTERIA (MICROORGANISMS); SECALE CEREALE; TRITICUM AESTIVUM;

EID: 0347760409     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.70.1.468-474.2004     Document Type: Article

References (34)

1. Atlas, R. M., and R. Bartha. 1998. Microbial ecology: fundamentals and applications. Addison-Wesley Publishing Company, Reading, Pa.
2. Beare, M. 1997. Fungal and bacterial pathways of organic matter decomposition and nitrogen mineralization in arable soils, p. 37-70. In L. Brussard and R. Ferrera-Cerrato (ed.), Soil ecology in sustainable agricultural systems. CRC Lewis Publishers, Boca Raton, Fla.
3. Bengtsson, J. 2002. Disturbance and resilience in soil animal communities. Eur. J. Soil Biol. 38:119-125.
4. Bloem, J., and A. M. Breure. 2003. Microbial indicators, p. 259-282. In B. A. Markert, A. M. Breure, and H. G. Zechmeister (ed.), Bioindicators/biomonitors - principles, assessment, concepts. Elsevier, Amsterdam, The Netherlands.
5. Bloem, J., M. Veninga, and J. Shepherd. 1995. Fully automatic determination of soil bacterium numbers, cell volumes, and frequencies of dividing cells by confocal laser scanning microscopy and image analysis. Appl. Environ. Microbiol. 61:926-936.
6. Dilly, O., and J.-C. Munch. 1996. Microbial biomass content, basal respiration and enzyme activities during the course of decomposition of leaf litter in a black alder (Alnus glutinosa (L) Gaertn.) forest. Soil Biol. Biochem. 28:1073-1081.
7. Dilly, O., S. Bartsch, P. Rosenbrock, F. Buscot, and J.-C. Munch. 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. Duineveld, B. M., G. A. Kowalchuk, A. Keijzer, J. D. van Elsas, and J. A. van Veen. 2001. Analysis of bacterial communities in the rhizosphere of chrysanthemum via denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA as well as DNA fragments coding for 16S rRNA. Appl. Environ. Microbiol. 67:172-178.
9. Ekschmitt, K., A. Klein, B. Pieper, and V. Wolters. 2001. Biodiversity and functioning of ecological communities - why is diversity important in some cases and unimportant in others? J. Plant Nutr. Soil Sci. 164:239-246.
10. Giller, K. E., and G. Gadisch. 1997. Driven by nature: a sense of arrival or departure, p. 393-399. In G. Cadisch and K. E. Giller (ed.), Driven by nature. Plant litter quality and decomposition. CAB International, Wallingford, United Kingdom.
11. Griffiths, B. S., K. Ritz, R. D. Bardgett, R. Cook, S. Christensen, F. Ekelund, S. Sørensen, E. Bååth, J. Bloem, P. de Ruiter, J. Dolfing, and B. Nicolardot. 2000. Ecosystem response of pasture soil communities to fumigation-induced microbial diversity reductions: an examination of the biodiversity-ecosystem function relationship. Oikos 90:279-294.
12. Griffiths, B. S., K. Ritz, R. Wheatly, H. L. Kuan, B. Boag, S. Christensen, F. Ekelund, S. J. Sorensen, S. Muller, and J. Bloem. 2001. An examination of the biodiversity-ecosystem function relationship in arable soil microbial communities. Soil Biol. Biochem. 33:1713-1722.
13. Heal, O. W., J. M. Anderson, and M. J. Swift. 1997. Plant litter quality and decomposition: an historical overview, p. 3-10. In G. Cadisch and K. E. Giller (ed,), Driven by nature. Plant litter quality and decomposition. CAB International, Wallingford, United Kingdom.
14. Hughes, J. R., J. J. Hellmann, T. H. Ricketts, and B. J. M. Bohannan. 2001. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67:4399-4406.
15. Kim-Jong, S., M. Sakai, A. Hosoda, T. Matsuguchi, and J. S. Kim. 1999. Application of DGGE analysis to the study of bacterial community structure in plant roots and in nonrhizosphere soil. Soil Sci. Plant Nutr. 45:493-497.
16. Laverman, A. M., A. G. C. L. Speksnijder, M. Braster, G. A. Kowalchuk, H. A. Verhoef, H. W. van Verseveld, and H. W. van Verseveld. 2001. Spatio-temporal stability of an ammonia-oxidizing community in a nitrogen-saturated forest soil. Microb. Ecol. 42:35-45.
17. McCaig, A. E., L. Glover, and J. I. Posser. 1999. Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grassland pastures. Appl. Environ. Microbiol. 65:1721-1730,
18. Michel, P. H., and J. Bloem. 1993. Conversion factors for estimation of cell production rates of soil bacteria from thymidine and leucine incorporation. Soil Biol. Biochem. 25:943-950.
19. Muyzer, G. 1999. DGGE/TGGE: a method for identifying genes from natural ecosystems. Curr. Opin. Microbiol. 2:317-322.
20. Muyzer, G., E. C. de Waal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified gene coding for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
21. Neely, C. L., M. H. Beare, W. L. Hargrove, and D. C. Coleman. 1991. Relationships between fungal and bacterial substrate-induced respiration, biomass and plant residue decomposition. Soil Biol. Biochem. 23:947-954.
22. Nübel, U., F. Garcia-Pichel, M. Kühl, and G. Muyzer. 1999. Quantifying microbial diversity: morphotypes, 16S rRNA genes, and carotinoids of oxygenic phototrophs in microbial mats. Appl. Environ. Microbiol. 65:422-430.
23. Odum, E. P. 1969. The strategy of ecosystem development. Science 164:262-270.
24. Odum, H. T. 1956. Efficiencies, size of organisms, and community structure. Ecology 37:592-597.
25. Pielou, E. C. 1983. Population and community ecology. Principles and methods. Gordon and Breach Science Publishers, New York, N.Y.
26. Putman, R. J. 1994. Community ecology. Chapman & Hall, London, United Kingdom.
27. Rosenbrock, P., F. Buscot, and J.-C. Munch. 1995. Fungal succession and changes in the fungal degradation potential during the early stages of litter decomposition in black alder forest (Alnus glutinosa (Gaertn.) L.). Eur. J. Soil Biol. 31:1-11.
28. Sessitsch, A., A. Weilharter, M. H. Gerzabek, H. Kirschmann, and E. Kandeler. 2001. Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment. Appl. Environ. Microbiol. 67:4215-4224.
29. Slater, J. H. and D Lovatt. 1984. Biodegradation and the significance of microbial communities, p. 439-485. In D. T. Gibson (ed.), Microbial degradation of organic compounds. Marcel Dekker, Inc., New York, N.Y.
30. Thirup, L., Johansen, A., and A. Winding. 2003. Microbial succession in the rhizosphere of live and decomposing barley roots as affected by the antagonistic strain Pseudomonas fluorescens DR54-BN14 or the fungicide Imazalil. FEMS Microbiol. Ecol. 43:383-392.
31. Watson, R.-J., and B. Blackwell. 2000. Purification and characterization of a common soil component which inhibits the polymerase chain reaction Can. J. Microbiol. 46:633-642.
32. Westergaard, K., A. K. Müller, S. Christensen, J. Bloem, and S. J. Sorensen. 2001. Effects of tylosin as a disturbance on the soil microbial community. Soil Biol. Biochem. 33:2061-2071.
33. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271.
34. Zvyagintsev, D. G. 1994. Vertical distribution of microbial communities in soils, p. 29-37. In K. Ritz, J. Dighton, and K. E. Giller (ed.), Beyond the biomass. Blackwell Scientific Publications, Oxford, United Kingdom.