Microbial Population Structures in Soil Particle Size Fractions of a Long-Term Fertilizer Field Experiment

Applied and Environmental Microbiology

Volumn 67, Issue 9, 2001, Pages 4215-4224

  Sessitsch, Angela ^a   Weilharter, Alexandra ^a   Gerzabek, Martin H ^a   Kirchmann, Holger ^b   Kandeler, Ellen ^c  

^a ARC SEIBERSDORF RESEARCH GMBH   (Austria)

^b SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^c UNIVERSITY OF HOHENHEIM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; FERTILIZER;

ARTICLE; BACTERIUM; CLASSIFICATION; DNA SEQUENCE; ECOSYSTEM; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR CLONING; MOLECULAR GENETICS; PARTICLE SIZE; PHYLOGENY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RNA GENE; SOIL; UTILIZATION REVIEW;

BACTERIA; CLONING, MOLECULAR; DNA, BACTERIAL; ECOSYSTEM; FERTILIZERS; GENES, RRNA; MOLECULAR SEQUENCE DATA; PARTICLE SIZE; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; SEQUENCE ANALYSIS, DNA; SOIL; SOIL MICROBIOLOGY;

EID: 0035462376     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.67.9.4215-4224.2001     Document Type: Article

References (59)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment tool. J. Mol. Biol. 215:403-410.
2. Amann, R. I., W. Ludwig, and K.-H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
3. 14C-labelled glucose and legume material in soils: properties influencing the accumulation of organic residue C and microbial biomass C. Soil Biol. Biochem. 24:455-466.
4. Borneman, J., P. W. Skroch, K. M. O'Sullivan, J. A. Palus, N. G. Rumjanek, J. L. Jansen, J. Nienhuis, and E. W. Triplett. 1996. Molecular microbial diversity of an agricultural soil in Wisconsin. Appl. Environ. Microbiol. 62:1935-1943.
5. Brussaard, L., L. A. Bouwman, M. Geurs, J. Hassink, and K. B. Zwart. 1990. Biomass composition and temporal dynamics of soil organisms of a silt loam soil under conventional and integrated management. Neth. J. Agric. Sci. 38:283-302.
6. Christensen, B. T. 1992. Physical fractionation of soil and organic matter in primary particle size and density separates. Adv. Soil Sci. 20:1-90.
7. Clement, B. G., L. E. Kehl, K. L. DeBord, and C. L. Kitts. 1998. Terminal restriction fragment patterns (TRFPs), a rapid, PCR-based method for the comparison of complex bacterial communities. J. Microbiol. Methods 31: 135-142.
8. Cole, S. T., and I. S. Girons. 1994. Bacterial genomics. FEMS Microbiol. Rev. 14:139-160.
9. Corpet, F. 1988. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16:10881-10890.
10. Dunbar, J., S. Takala, S. M. Barns, J. A. Davis, and C. R. Kuske. 1999. Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl. Environ. Microbiol. 65:1662-1669.
11. Dunbar, J., L. O. Ticknor, and C. R. Kuske. 2000. Assessment of microbial diversity in four Southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis. Appl. Environ. Microbiol. 66:2443-2950.
12. Dunbar, J., L. O. Ticknor, and C. R. Kuske. 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.
13. Elliot, E. T., R. V. Anderson, D. C. Coleman, and C. V. Cole. 1980. Habitable pore space and microbial trophic interactions. Oikos 35:327-335.
14. Felske, A., A. Wolterink, R. van Lis, and A. D. L. Akkermans. 1998. Phylogeny of the main bacterial 16S rRNA sequences in Drentse A grassland soils (The Netherlands). Appl. Environ. Microbiol. 64:871-879.
15. Foster, R. C. 1988. Microenvironments of soil microorganisms. Biol. Fertil. Soils 6:189-203.
16. Fredrickson, J. K., D. L. Balkwill, G. R. Drake, M. F. Romine, D. B. Ringelberg, and D. C. White. 1995. Aromatic-degrading Sphingomonas isolates from the deep subsurface. Appl. Environ Microbiol. 61:1917-1922.
17. Gelsomino, A., A. C. Keijzer-Wolters, G. Cacco, and J. D. van Elsas. 1999. Assessment of bacterial community structure in soil by polymerase chain reaction and denaturing gradient gel electrophoresis. J. Microbiol. Methods 38:1-15.
18. Gerzabek, M. H., H. Kirchmann, and F. Pichlmayer. 1995. Response of soil aggregate stability to manure amendments in a long-term experiment in Ultuna, Sweden. Z. Pflanzenernsaehr. Bodenkd. 158:257-260.
19. Gerzabek, M. H., F. Pichlmayer, H. Kirchmann, and G. Haberhauer. 1997. The response of soil organic matter to manure amendments in a long-term experiment in Ultuna, Sweden. Eur. J. Soil Sci. 48:273-282.
20. 15N natural abundance to different amendments in a long-term experiment at Ultuna, Sweden. Agronomic Agric. Environ. 19:457-466.
21. Gerzabek, M. H., G. Haberhauer, E. Kandeler, A. Sessitsch, and H. Kirchmann. Response of organic matter pools and enzyme activities in particle size fractions to organic amendments in a long-term field experiment. In Proceedings of the Third Symposium ISMOM, Naples-Capri, Italy, in press.
22. Hassink, J., L. A. Bouman, K. B. Zwart, J. Bloem, and L. Brussaard. 1993. Relationships between soil texture, physical protection of organic matter, soil biota, and C and N mineralization in grassland soils. Geoderma 57:105-128.
23. Hassink, J., L. A. Bouwman, K. B. Zwart, and L. Brussaard. 1993. Relationships between habitable pore space, soil biota and mineralization rates in grassland soils. Soil Biol. Biochem. 25:47-55.
24. Hattori, T. 1988. Soil aggregates as habitats of microorganisms. Rep. Inst. Agric. Res. Tohuku Univ. 37:23-36.
25. Hedlund, B. P., J. J. Gosink, and J. T. Staley. 1996. Phylogeny of Prosthecobactor, the fusiform caulobacters: members of a recently discovered division of the Bacteria. Int. J. Syst. Bacteriol. 46:960-966.
26. Heynen, C. E., J. D. van Elsas, P. J. Kuikman, and J. A. van Veen. 1988. Dynamics of Rhizobium leguminosarum biovar trifolii introduced into soil: the effect of bentonite clay on predation by protozoa. Soil Biol. Biochem. 20:483-488.
27. Jocteur Monrozier, L., J. N. Ladd, A. W. Fitzpatrick, R. C. Foster, and M. Raupach. 1991. Components and microbial biomass content of size fractions in soils of contrasting aggregation. Geoderma 49:37-62.
28. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules, p. 21-132. In H. H. Munro (ed.), Mammalian protein metabolism. Academic Press, New York, N. Y.
29. Jürgens K., J. Pernthaler, S. Schalla, and R. Amann. 1999. Morphological and compositional changes in a planktonic bacterial community in response to enhanced protozoan grazing. Appl. Environ. Microbiol. 65:1241-1250.
30. Kanazawa, S., and Z. Filip. 1986. Distribution of microorganisms, total hiomass, and enzyme activities in different particles of brown soil. Microb. Ecol. 12:205-215.
31. Kandeler, E., M. Stemmer, and E.-M. Klimanek. 1999. Response of soil microbial biomass, urease and xylanase within particle-size fractions to long-term soil management. Soil Biol. Biochem. 31:261-273.
32. Kandeler, E., D. Tscherko, K. D. Bruce, M. Stemmer, P. J. Hobbs, R. D. Bardgett, and W. Amelung. 2000. Structure and function of the soil microbial community in microhabitats of a heavy metal polluted soil. Soil Biol. Biochem. 32:390-400.
33. Kim, E., P. J. Aversano, M. F. Romine, R. P. Schneider, and G. J. Zylstra. 1996. Homology between genes for aromatic hydrocarbon degradation in surface and deep-subsurface Sphingomonas strains. Appl. Environ. Microbiol. 62:1467-1470.
34. Kirchmann, H., J. Persson, and K. Carlgren. 1994. The Ultuna long-term soil organic matter experiment, 1956-1991. Reports and dissertation 17. Department of Soil Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
35. Kirchmann, H., F. Pichlmayer, and M. H. Gerzabek. 1996. Sulfur balances and sulfur-34 abundance in a long-term fertilizer experiment. Soil Sci. Soc. Am. J. 60:174-178.
36. Kirchmann, H., and M. H. Gerzabek. 1999. Relationship between soil organic matter and micropores in a long-term experiment at Ultuna, Sweden. J. Plant Nutr. Soil Sci. 162:493-198.
37. Ladd, J. N., R. C. Foster, P. Nannipieri, and J. M. Oades. 1996. Soil structure and biological activity. Soil Biochem. 9:23-78.
38. Liu, W.-T., T. L. Marsh, H. Cheng, and L. J. Forney. 1997. Characterization of microbial diversity by determining terminal restriction length polymorphisms of genes encoding 16S rDNA. Appl. Environ. Microbiol. 63:4516-4522.
39. Ludwig, W., S. H. Bauer, M. Bauer, I. Held, G. Kirchhof, R. Schulze, I. Huber, S. Spring, A. Hartmann, and K. H. Schleifer, 1997. Detection and in situ identification of representatives of a widely distributed new bacterial phylum. FEMS Microbiol. Lett. 153:181-190.
40. Lünsdorf, H., R. W. Erb, W.-R. Abraham, and K. N. Timmis. 2000 "Clay hutches": a novel interaction between bacteria and clay minerals. Environ. Microbiol. 2:161-168.
41. Maidak, B. L., G. J. Olsen, N. Larsen, R. Overbeek, M. J. McCaughey, and C. R. Woese. 1997. The RDP (Ribosomal Database Project). Nucleic Acids Res. 25:109-111.
42. Marsh, T. L., P. Saxman, J. Cole, and J. Tiedje. 2000. Terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis. Appl. Environ. Microbiol. 66:3616-3620.
43. Nei, M., and W.-H. Li. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76:5269-5273.
44. Nüsslein, K., and J. M. Tiedje. 1998. Characterization of the dominant and rare members of a young Hawaiian soil bacterial community with small-subunit ribosomal DNA amplified from DNA fractionated on the basis of its guanine and cytosine composition. Appl. Environ. Microbiol. 64:1283-1289.
45. Nüsslein, K., and J. M. Tiedje. 1999. Soil bacterial community shift correlated with change from forest to pasture vegetation in a tropical soil. Appl. Environ. Microbiol. 65:3622-3626.
46. Oades, J. M. 1984. Soil organic matter and structural stability: mechanisms and implications for management. Plant Soil 76:319-337.
47. Osborn, A. M., E. R. B. Moore, and K. N. Timmis. 2000. An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ. Microbiol. 2:39-50.
48. Postma, J., and J. A. van Veen. 1990. Habitable pore space and survival of Rhizobium leguminosarum biovar trifolii introduced into soil. Microb. Ecol. 19:149-161.
49. Ramírez-Saad, H. C., A. Sessitsch, W. M. de Vos, and A. D. L. Akkermans. 2000. Bacterial community changes and enrichment of Burkholderia-like bacteria induced by chlorinated benzoates in a peat-forest soil-microcosm. Syst. Appl. Microbiol. 23:591-598.
50. Scala, D. J., and L. J. Kerkhof. 2000. Horizontal heterogeneity of denitrifying bacterial communities in marine sediments by terminal restriction fragment length polymorphism analysis. Appl. Environ. Microbiol. 66:1980-1986.
51. Stemmer, M., M. H. Gerzabek, and E. Kandeler. 1998. Organic matter and enzyme activity in particle size fractions of soils obtained after low-energy sonication. Soil Biol. Biochem. 30:9-17.
52. Stemmer, M., M. H. Gerzabek, and E. Kandeler. 1999. Invertase and xylanase activity of bulk soil and particle-size fractions during maize straw decomposition. Soil Biol. Biochem. 31:9-18.
53. Suzuki, M. T., and S. J. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625-630.
54. Tisdall, J. M., and J. M. Oades. 1982. Organic matter and water stable aggregates in soils. J. Soil Sci. 33:141-163.
55. Torsvik, V., J. Goksøyr, and F. L. Daae. 1990. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56:782-787.
56. van de Peer, V., and R. de Wachter. 1994. TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl. Biosci. 10:569-570.
57. van Elsas, J. D., and K. Smalla. 1995. Extraction of microbial community DNA from soils, p.1-11. In F. J. de Bruijn, J. D. van Elsas, and A. D. L. Akkermans (ed.), Molecular microbial ecology manual. Kluwer Academic Publishers, Dordrecht, The Netherlands.
58. van Gestel, M., R. Merckx, and K. Vlassek. 1996. Spatial distribution of microbial biomass in microaggregates of a silty-loam soil and the relation with the resistance of microorganisms to soil drying. Soil Biol. Biochem. 28:503-510.
59. Weisburg, W. G., S. M. Barns, D. A. Pelletier, and D. J. Lane. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173:697-703.