Community Composition and Functioning of Denitrifying Bacteria from Adjacent Meadow and Forest Soils

Applied and Environmental Microbiology

Volumn 69, Issue 10, 2003, Pages 5974-5982

  Rich, J J ^a   Heichen, R S ^a   Bottomley, P J ^a   Cromack Jr , K ^a   Myrold, D D ^a  

^a OREGON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; DENITRIFICATION; GENES; SOILS;

DOMINANT GENOTYPES;

MICROBIOLOGY;

NITROUS OXIDE REDUCTASE;

ARTICLE; DENITRIFICATION; ENZYME ACTIVITY; FOREST; GENE FUNCTION; GENE SEQUENCE; GENOTYPE; GRAM NEGATIVE BACTERIUM; GRASS; MOLECULAR CLONING; MULTIVARIATE ANALYSIS; NITRIFICATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RHIZOBIACEAE; SEQUENCE ANALYSIS; SOIL ANALYSIS; UNITED STATES; VEGETATION;

ALTITUDE; ECOSYSTEM; MOLECULAR SEQUENCE DATA; NITRATES; OREGON; OXIDOREDUCTASES; PHYLOGENY; POACEAE; POLYMERASE CHAIN REACTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RHIZOBIACEAE; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; TREES;

ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); NEGIBACTERIA; RHIZOBIACEAE; RHIZOBIALES;

EID: 0142040877     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.69.10.5974-5982.2003     Document Type: Article

References (48)

1. 2O release and on the community structure of ammonia oxidizers and denitrifiers. Appl. Environ. Microbiol. 68:5685-5692.
2. Bohlen, P. J., P. M. Groffman, C. T. Driscoll, T. J. Fahey, and T. G. Siccama. 2001. Plant-soil-microbial interactions in a northern hardwood forest. Ecology 82:965-978.
3. Braker, G., H. L. Ayala-del-Rio, A. H. Devol, A. Fesefeldt, and J. M. Tiedje. 2001. Community structure of denitrifiers, Bacteria, and Archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes. Appl. Environ. Microbiol. 67:1893-1901.
4. Braker, G., J. Zhou, L. Wu, A. H. Devol, and J. M. Tiedje. 2000. Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in Pacific Northwest marine sediment communities. Appl. Environ. Microbiol. 66:2096-2104.
5. Davidson, E. A., S. C. Hart, and M. K. Firestone. 1992. Internal cycling of nitrate in soils of a mature coniferous forest. Ecology 73:1148-1156.
6. Dayhoff, M. O., R. M. Schwartz, and B. C. Orcutt. 1979. A model of evolutionary change in proteins, p. 345-352. In M. O. Dayhoff (ed.), Atlas of protein sequence and structure, vol. 5. National Biomedical Research Foundation, Washington, D.C.
7. Dufrêne, M., and P. Legendre. 1997. Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecol. Monogr. 61:53-73.
8. Friedrich, M. W. 2002. Phylogenetic analysis reveals multiple lateral transfers of adenosine-5′-phosphate reductase genes among sulfate-reducing microorganisms. J. Bacteriol. 184:278-289.
9. Goris, J., P. De Vos, T. Coenye, B. Hoste, D. Janssens, H. Brim, L. Diels, M. Mergeay, K. Kersters, and P. Vandamme. 2001. Classification of metal-resistant bacteria from industrial biotopes of Ralstonia campinensis sp. nov., Ralstonia metallidurans sp. nov. and Ralstonia basilensis Steinle et al. 1998 emend. Int. J. Syst. Evol. Microbiol. 51:1773-1782.
10. Griffiths, R. P., P. S. Homann, and R. Riley. 1998. Denitrification enzyme activity of Douglas-fir and red alder forest soils of the Pacific Northwest. Soil Biol. Biochem. 30:1147-1157.
11. 1 nitrite reductase) in Pseudomonas stutzeri during the transition from aerobic respiration to denitrification: evidence for a denitrification-specific nitrate- and nitrite-responsive regulatory system. J. Bacteriol. 181:161-166.
12. Hunt, H. W., E. R. Ingham, D. C. Coleman, E. T. Elliott, and C. P. P. Reid. 1988. Nitrogen limitation of production and decomposition in prairie, mountain meadow, and pine forest. Ecology 69:1009-1016.
13. Hyman, M. R., and D. J. Arp. 1987. Quantification and removal of some contaminating gases from acetylene used to study gas-utilizing enzymes and microorganisms. Appl. Environ. Microbiol. 53:298-303.
14. Ingham, E. R., D. C. Coleman, and J. C. Moore. 1989. An analysis of food-web structure and function in a shortgrass prairie, a mountain meadow, and a lodgepole pine forest. Biol. Fertil. Soils 8:29-37.
15. Jones, D. T., W. R. Taylor, and J. M. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. Bioinformatics 8:275-282.
16. Kitagawa, W., S. Takami, K. Miyauchi, E. Masai, Y. Kamagata, J. M. Tiedje, and M. Fukuda. 2002. Novel 2,4-dichlorophenoxyacetic acid degradation genes from oligotrophic Bradyrhizobium sp. strain HW13 isolated from a pristine environment. J. Bacteriol. 184:509-518.
17. Kleikemper, J., M. H. Schroth, W. V. Sigler, M. Schmucki, S. M. Bernasconi, and J. Zeyer. 2002. Activity and diversity of sulfate-reducing bacteria in a petroleum hydrocarbon-contaminated aquifer. Appl. Environ. Microbiol. 68:1516-1523.
18. Kowalchuk, G. A., D. S. Buma, W. de Boer, P. G. L. Klinkhamer, and J. A. van Veen. 2002. Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms. Antonie Leeuwenhoek 81:509-520.
19. Kruskal, J. B. 1964. Non-metric multidimensional scaling: a numerical method. Psychometrika 29:115-129.
20. Lueders, T., and M. W. Friedrich. 2002. Effects of amendment with ferrihydrite and gypsum on the structure and activity of methanogenic populations in rice field soil. Appl. Environ. Microbiol. 68:2484-2494.
21. Magee, T. K., and J. A. Antos. 1992. Tree invasion into a mountain-top meadow in the Oregon Coast Range, USA. J. Veg. Sci. 3:485-494.
22. Maidak, B. L., J. R. Cole, T. G. Lilburn, C. T. J. Parker, P. R. Saxman, R. J. Farris, G. M. Garrity, G. J. Olsen, T. M. Schmidt, and J. M. Tiedje. 2001. The RDP-11 (Ribosomal Database Project). Nucleic Acids Res. 29:173-174.
23. McCune, B., and J. B. Grace. 2002. Analysis of ecological communities. MjM Software, Gleneden Beach, Oregon.
24. Mielke, P. W., Jr. 1984. Meteorological applications of permutation techniques based on distance functions, p. 813-830. In P. R. Krishnaiah and P. K. Sen (ed.), Handbook of statistics. Elsevier Science Publishers, New York, N.Y.
25. Miller, E. A., and C. B. Halpern. 1998. Effects of environment and grazing disturbance on tree establishment in meadows of the central Cascade Range, Oregon, USA. J. Veg. Sci. 9:265-282.
26. Mintie, A. T., R. S. Heichen, K. J. Cromack, Jr., D. D. Myrold, and P. J. Bottomley. 2003. Ammonia-oxidizing bacteria along meadow-to-forest transects in the Oregon Cascade Mountains. Appl. Environ. Microbiol. 69:3129-3136.
27. Myrold, D. D. 1988. Denitrification in ryegrass and winter wheat cropping systems of Western Oregon. Soil Sci. Soc. Am. J. 52:412-416.
28. Ollinger, S. V., M. L. Smith, M. E. Martin, R. A. Hallett, C. L. Goodale, and J. D. Aber. 2002. Regional variation in foliar chemistry and N cycling among forests of diverse history and composition. Ecology 83:339-355.
29. Parke, D., and L. N. Ornston. 1986. Enzymes of the β-ketoadipate pathway are inducible in Rhizobium and Agrobacterium spp. and constitutive in Bradyrhizobium spp. J. Bacteriol. 165:288-292.
30. Parsons, L. L., R. E. Murray, and M. S. Smith. 1991. Soil denitrification dynamics: spatial and temporal variations of enzyme activity, populations, and nitrogen gas loss. Soil Sci. Soc. Am. J. 55:90-95.
31. Paulsen, I. T., et al. 2002. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc. Natl. Acad. Sci. USA 99:13148-13153.
32. Philippot, L., S. Piutti, F. Martin-Laurent, S. Hallet, and J. C. Germon. 2002. Molecular analysis of the nitrate-reducing community from unplanted and maize-planted soils. Appl. Environ. Microbiol. 68:6121-6128.
33. Priemé, A., G. Braker, and J. M. Tiedje. 2002. Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils. Appl. Environ. Microbiol. 68:1893-1900.
34. Ramakrishnan, B., T. Leuders, P. F. Dunfield, R. Conrad, and M. W. Friedrich. 2001. Archeal community structure in rice soils from different geographical regions before and after initiation of methane production. FEMS Microbiol. Ecol. 37:175-186.
35. Rich, J. J. 2003. Ph.D. thesis. Oregon State University, Corvallis.
36. Rösch, C., A. Mergel, and H. Bothe. 2002. Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil. Appl. Environ. Microbiol. 68:3818-3829.
37. Sabaty, M., C. Schwintner, S. Cahors, P. Richaud, and A. Verméglio. 1999. Nitrite and nitrous oxide reductase regulation by nitrogen oxides in Rhodobacter sphaeroides f. sp. denitrificans IL106. J. Bacteriol. 181:6028-6032.
38. Saito, A., H. Mitsui, R. Hattori, K. Minamisawa, and T. Hattori. 1998. Slow-growing and oligotrophic soil bacteria phylogenetically close to Bradyrhizobium japonicum. FEMS Microbiol. Ecol. 25:277-286.
39. Scala, D. J., and L. J. Kerkhof. 1999. Diversity of nitrous oxide reductase (nosZ) genes in continental shelf sediments. Appl. Environ. Microbiol. 65:1681-1687.
40. 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.
41. Scala, D. J., and L. J. Kerkhof. 1998. Nitrous oxide reductase (nosZ) gene-specific PCR primers for detection of denitrifiers and three nosZ genes from marine sediments. FEMS Microbiol. Lett. 162:61-68.
42. Schmidt, H. A., K. Strimmer, M. Vingron, and A. von Haeseler. 2002. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.
43. Sullivan, J. T., B. D. Eardly, P. van Berkum, and C. W. Ronson. 1996. Four unnamed species of nonsymbiotic rhizobia isolated from the rhizosphere of Lotus corniculatus. Appl. Environ. Microbiol. 62:2818-2825.
44. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The Clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24:4876-4882.
45. Tiedje, J. M. 1994. Denitrifiers, p. 245-265. In R. W. Weaver, J. S. Angle, and P. J. Bottomley (ed.), Methods of soil analysis, part 2 - microbiological and biochemical properties. Soil Science Society of America, Inc., Madison, Wis.
46. Tiedje, J. M. 1988. Ecology of denitrification and dissimilatory nitrate reduction to ammonium, p. 170-244. In A. J. B. Zehnder (ed.), Biology of anaerobic microorganisms. John Wiley and Sons, New York, N.Y.
47. Vermes, J.-F., and D. D. Myrold. 1992. Denitrification in forest soils of Oregon. Can. J. For. Res. 22:504-512.
48. Zumft, W. G. 1999. The denitrifying prokaryotes. In M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer, and E. Stackebrandt (ed.), The prokaryotes: an evolving electronic resource for the microbiological community, 3rd ed., release 3.0. [Online.] Springer-Verlag, New York, N.Y. http://141.150.157.117:8080/prokPUB/index.htm.