Changes in nitrification and bacterial community structure upon cross-inoculation of Scots pine forest soils with different initial nitrification rates

Soil Biology and Biochemistry

Volumn 41, Issue 2, 2009, Pages 243-250

  Nugroho, Rully A ^a   Röling, Wilfred F M ^a   van Straalen, Nico M ^a   Verhoef, Herman A ^a  

^a VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

Bacterial communities; Bioaugmentation; Cross inoculation; Net nitrification; Scots pine

Indexed keywords

ACIDS; BACTERIOLOGY; COLLOIDS; DENITRIFICATION; ELECTROPHORESIS; GELATION; NITRIFICATION; OXIDATION;

BACTERIAL COMMUNITIES; BIOAUGMENTATION; CROSS-INOCULATION; NET NITRIFICATION; SCOTS PINE;

SOILS;

AMMONIA; BACTERIUM; BIOREMEDIATION; COMMUNITY STRUCTURE; CONIFEROUS FOREST; ELECTROKINESIS; FOREST SOIL; GAMMA RAY RADIATION; GEL; INOCULATION; NITRIFICATION; RNA; SOIL REMEDIATION;

BACTERIA (MICROORGANISMS); PINUS SYLVESTRIS;

EID: 58149510309     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.soilbio.2008.10.020     Document Type: Article

References (36)

1. Balser T.C., and Firestone M.K. Linking microbial community composition and soil processes in a California annual grassland and mixed-conifer forest. Biogeochemistry 73 (2005) 395-415
2. Bäckman J.S.K., Hermansson A., Tebbe C.C., and Lindgren P.-E. Liming induced growth of a diverse flora of ammonia-oxidising bacteria in acid spruce forest soil as determined by SSCP and DGGE. Soil Biology & Biochemistry 35 (2003) 1337-1347
3. Bell T., Newman J.A., Silverman B.W., Turner S.L., and Lilley A.K. The contribution of species richness and composition to bacterial services. Nature 436 (2005) 1157-1160
4. Bottomley P.J., Taylor A.E., Boyle S.A., McMahon S.K., Rich J.J., Cromack Jr. K., and Myrold D.D. Responses of nitrification and ammonia-oxidizing bacteria to reciprocal transfers of soil between adjacent coniferous forest and meadow vegetation in the Cascade Mountains of Oregon. Microbial Ecology 48 (2004) 500-508
5. Booth M.S., Stark J.M., and Rastetter E. Controls on nitrogen cycling in terrestrial ecosystems: a synthetic analysis of literature data. Ecological Monographs 75 (2005) 139-157
6. Compton J.E., Watrud L.S., Porteous L.A., and DeGrood S. Response of soil microbial biomass and community composition to chronic nitrogen additions at Harvard forest. Forest Ecology and Management 196 (2004) 143-158
7. de Boer W., Gunnewiek P.J.A.K., and Parkinson D. Variability of N mineralization and nitrification in a simple, simulated microbial forest soil community. Soil Biology & Biochemistry 28 (1996) 203-211
8. de Boer W., and Kester R.A. Variability of nitrification potentials in patches of undergrowth vegetation in primary Scots pine stands. Forest Ecology and Management 86 (1996) 97-103
9. Griffiths B.S., Kuan H.L., Ritz K., Glover L.A., McCaig A.E., and Fenwick C. The relationship between microbial community structure and functional stability, tested experimentally in an upland pasture soil. Microbial Ecology 47 (2004) 104-113
10. Griffiths B.S., Ritz K., Bardgett R.D., Cook R., Ekelund F., Sørensen S.J., Bååth E., Bloem J., de Ruiter P.C., Dolfing J., and Nicolardot B. Ecosystem response of pasture soil communities to fumigation-induced microbial diversity reductions: an examination of the biodiversity-ecosystem function relationship. Oikos 90 (2000) 279-294
11. Hammer Ø., Harper D.A.T., and Ryan P.D. PAST: paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4 1 (2001) 9
12. Jones H.E., West H.M., Chamberlain P.M., Parekh N.R., Beresford N.A., and Crout N.M.J. Effects of gamma irradiation on Holcus lanatus (Yorkshire fog grass) and associated soil microorganisms. Journal of Environmental Radioactivity 74 (2004) 57-71
13. Laverman A.M., Braster M., Röling W.F.M., and van Verseveld H.W. Bacterial community structure and metabolic profiles in a forest soil exhibiting spatially variable net nitrate production. Soil Biology & Biochemistry 37 (2005) 1581-1588
14. Laverman A.M., Speksnijder A.G.C.L., Braster M., Kowalchuk G.A., Verhoef H.A., and van Verseveld H.W. Spatiotemporal stability on an ammonia-oxidizing community in a nitrogen-saturated forest soil. Microbial Ecology 42 (2001) 35-45
15. Laverman A.M., Zoomer H.R., van Verseveld H.W., and Verhoef H.A. Temporal and spatial variation of nitrogen transformations in a coniferous forest soil. Soil Biology & Biochemistry 32 (2000) 1661-1670
16. Leininger S., Urich T., Schloter M., Schwark L., Qi J., Nicol G.W., Prosser J.I., Schuster S.C., and Schleper C. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442 (2006) 806-809
17. Marschner P., and Rumberger A. Rapid changes in the rhizosphere bacterial community structure during re-colonization of sterilized soil. Biology and Fertility of Soils 40 (2004) 1-6
18. McLaren A.D. Radiation as a technique in soil biology and biochemistry. Soil Biology & Biochemistry 1 (1969) 63-73
19. McNamara N.P., Black H.I.J., Beresford N.A., and Parekh N.R. Effects of acute gamma irradiation on chemical, physical and biological properties of soils. Applied Soil Ecology 24 (2003) 117-132
20. Meier E.A., Thorburn P.J., and Probert M.E. Occurrence and simulation of nitrification in two contrasting sugarcane soils from the Australian wet tropics. Australian Journal of Soil Research 44 (2006) 1-9
21. Muyzer G., de Waal E.C., and Uitterlinden A.G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology 59 (1993) 695-700
22. Nugroho R.A., Röling W.F.M., Laverman A.M., and Verhoef H.A. Presence of Nitrosospira cluster 2 bacteria corresponds to N transformation rates in nine acid Scots pine forest soils. FEMS Microbiology Ecology 53 (2005) 472-481
23. Nugroho R.A., Röling W.F.M., Laverman A.M., and Verhoef H.A. Low nitrification rates in acid Scots pine forest soils are due to pH-related factors. Microbial Ecology 53 (2007) 89-97
24. Persson T., and Wirén A. Nitrogen mineralization and potential nitrification at different depths in acid forest soil. Plant and Soil 168/169 (1995) 55-65
25. Röling W.F.M., van Breukelen B.M., Braster M., Lin B., and van Verseveld H.W. Relationships between microbial community structure and hydrochemistry in a landfill leachate-polluted aquifer. Applied and Environmental Microbiology 67 (2001) 4619-4629
26. Shaw R.G., and Mitchell-Olds T. ANOVA for unbalanced data: an overview. Ecology 74 (1993) 1638-1645
27. Thompson J.P. Soil sterilization methods to show VA-mycorrhizae aid P and Zn nutrition of wheat in vertisols. Soil Biology & Biochemistry 22 (1990) 229-240
28. Tolli J., and King G.M. Diversity and structure of bacterial chemolithotrophic communities in pine forest and agroecosystem soils. Applied and Environmental Microbiology 71 (2005) 8411-8418
29. Treusch A.H., Leininger S., Kletzin A., Schuster S.C., Klenk H.-P., and Schleper C. Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environmental Microbiology 7 (2005) 1985-1995
30. Valentine D.L. Adaptations to energy stress dictate the ecology and evolution of the Archaea. Nature Reviews Microbiology 5 (2007) 316-323
31. van Niel E.W.J., Arts P.A.M., Wesselink B.J., Robertson L.A., and Kuenen J.G. Competition between heterotrophic and autotrophic nitrifiers for ammonia in chemostat cultures. FEMS Microbiology Ecology 102 (1993) 109-118
32. van Verseveld H.W., and Röling W.F.M. Cluster analysis and statistical comparison of molecular community profile data. In: Kowalchuk G.A., de Bruijn F.J., Head J.M., Akkermans A.D.L., and van Elsas J.D. (Eds). Molecular Microbial Ecology Manual. second ed. vol. 1.7.4 (2004) 1-24
33. Verhagen F.J.M., Duyts H., and Laanbroek H.J. Competition for ammonium between nitrifying and heterotrophic bacteria in continuously percolated soil columns. Applied and Environmental Microbiology 58 (1992) 3303-3311
34. Verhagen F.J.M., and Laanbroek H.J. Competition for ammonium between nitrifying and heterotrophic bacteria in dual energy-limited chemostats. Applied and Environmental Microbiology 57 (1991) 3255-3263
35. Verhagen F.J.M., Laanbroek H.J., and Woldendorp J.W. Competition for ammonium between plant roots and nitrifying and heterotrophic bacteria and the effects of protozoan grazing. Plant and Soil 170 (1995) 241-250
36. Wheatley R.E., Caul S., Crabb D., Daniell T.J., Griffiths B.S., and Ritz K. Microbial population dynamics related to temporal variations in nitrification in three arable fields. European Journal of Soil Science 54 (2003) 707-714