Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems

Ecology

Volumn 91, Issue 12, 2010, Pages 3463-3470

  Ramirez, Kelly S ^a   Lauber, Christian L ^a   Knight, Rob ^a,b   Bradford, Mark A ^c   Fierer, Noah ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^c Yale School of the Environment   (United States)

Author keywords

16S rRNA genes; Microbial ecology; N fertilization; Nitrogen; Pyrosequencing; Soil bacteria; Soil bacterial diversity; Soil microbiology

Indexed keywords

BACTERIAL RNA; FERTILIZER; NITROGEN; RNA 16S;

AMMONIA; BACTERIUM; ECOSYSTEM FUNCTION; EXPERIMENTAL STUDY; FERTILIZER APPLICATION; GRASSLAND; HUMAN ACTIVITY; NITRATE; NITROGEN; NUTRIENT AVAILABILITY; PH; PHYSIOLOGICAL RESPONSE; PLANT COMMUNITY; RNA; SOIL CARBON; SOIL MICROORGANISM; SPECIES DIVERSITY; SPECIES RICHNESS;

ARTICLE; BACTERIUM; ECOSYSTEM; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; PHYLOGENY; UNITED STATES;

BACTERIA; ECOSYSTEM; FERTILIZERS; MICHIGAN; MINNESOTA; NITROGEN; PHYLOGENY; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY;

CEDAR CREEK [KENTUCKY]; KENTUCKY; UNITED STATES;

BACTERIA (MICROORGANISMS);

EID: 78650358038     PISSN: 00129658     EISSN: None     Source Type: Journal    
DOI: 10.1890/10-0426.1     Document Type: Article

References (39)

1. Bowman, W. D., T. A. Theodose, J. C. Schardt, and R. T. Conant. 1993. Constraints of nutrient availability on primary production in two alpine tundra communities. Ecology 74: 2085-2097.
2. Clark, C. M., S. E. Hobbie, R. Venterea, and D. Tilman. 2009. Long-lasting effects on nitrogen cycling 12 years after treatments cease despite minimal long-term nitrogen retention. Global Change Biology 15:1755-1766.
3. Costello, E. K., C. L. Lauber, M. Hamady, N. Fierer, J. I. Gordon, and R. Knight. 2009. Bacterial community variation in human body habitats across space and time. Science 326: 1694-1697.
4. Crum, J. R., and H. P. Collins. 1995. KBS soils. (http://lter.kbs. Msu.edu/about/site-description/soils.php)
5. Faith, D. P. 1992. Conservation evaluation and phylogenetic diversity. Biological Conservation 61:1-10.
6. Fierer, N., M. A. Bradford, and R. B. Jackson. 2007. Toward an ecological classification of soil bacteria. Ecology 88:1354-1364.
7. Fierer, N., and R. B. Jackson. 2006. The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences USA 103:626-631.
8. Fierer, N., J. P. Schimel, and P. A. Holden. 2003. Variations in microbial community composition through two soil depth profiles. Soil Biology and Biochemistry 35:167-176.
9. Fierer, N., M. S. Strickland, D. Liptzin, M. A. Bradford, and C. C. Cleveland. 2009. Global patterns in belowground communities. Ecology Letters 12:1238-1249.
10. Galloway, J. N., et al. 2004. Nitrogen cycles: past, present, and future. Biogeochemistry 70:153-226.
11. Gilliam, F. S. 2006. Response of the herbaceous layer of forest ecosystems to excess nitrogen deposition. Journal of Ecology 94:1176-1191.
12. Gough, L., C. W. Osenberg, K. L. Gross, and S. L. Collins. 2000. Fertilization effects on species density and primary productivity in herbaceous plant communities. Oikos 89: 428-439. (Pubitemid 30343053)
13. Gu, L., W. M. Post, and A. W King. 2004. Fast labile carbon turnover obscures sensitivity of heterotrophic respiration from soil to temperature: a model analysis. Global Biogeochemical Cycles 18:GB1022.
14. Hallin, S., C. M. Jones, M. Schloter, and L. Philippot. 2009. Relationship between N-cycling communities and ecosystem functioning in a 50-year-old fertilization experiment. ISME Journal 3:597-605.
15. Hamady, M., and R. Knight. 2009. Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Research 7:1141-1152.
16. Hamady, M., J. J. Walker, K. Harris, N. J. Gold, and R. Knight. 2008. Error-correcting barcoded primers allow hundreds of samples to be pyrosequenced in multiplex. Nature Methods 5:235-237.
17. Hartman, W. H., C. J. Richardson, R. Vilgalys, and G. L. Bruland. 2008. Environmental and anthropogenic controls over bacterial communities in wetland soils. Proceedings of the National Academy of Sciences USA 105:17842-17847.
18. Hill, T. C., K. A. Walsh, J. A. Harris, and B. F. Moffett. 2003. Using ecological diversity measures with bacterial communities. FEMS Microbiology Ecology 43:1-11.
19. Jones, R. T., M. S. Robeson, C. L. Lauber, M. Hamady, R. Knight, and N. Fierer. 2009. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME Journal 3:442-453.
20. Lauber, C. L., M. Hamady, R. Knight, and N. Fierer. 2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Applied Environmental Microbiology 75:5111-5120.
21. LeBauer, D. S., and K. K. Treseder. 2008. Nitrogen limitation of net primary productivity in terrestrial ecosystems is globally distributed. Ecology 89:371-379.
22. Lozupone, C. A., and R. Knight. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology 71:8228-8235.
23. Lozupone, C. A., and R. Knight. 2008. Species divergence and the measurement of microbial diversity. FEMS Microbiology Reviews 32:557-578.
24. Nemergut, D. R., A. R. Townsend, S. R. Sattin, K. R. Freeman, N. Fierer, J. C. Neff, W. D. Bowman, C. W. Schadt, M. N. Weintraub, and S. K. Schmidt. 2008. The effects of chronic nitrogen fertilization on alpine tundra soil microbial communities: implications for carbon and nitrogen cycling. Environmental Microbiology 11:3093-3105.
25. Padmanabhan, P., S. Padmanabhan, C. DeRito, A. Gray, D. Gannon, J. R. Snape, C. S. Tsai, W. Park, C. Jeon, and E. L. Madsen. 2003. Respiration of 13C-labeled substrates added to soil in the field and subsequent 16S rRNA gene analysis of 13C-labeled soil DNA. Applied and Environmental Microbiology 69:1614-1622.
26. Prosser, J. I., and G. W. Nicol. 2008. Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environmental Microbiology 10:2931-2941.
27. R Development Core Team. 2008. R version 2.8.1. R Foundation for Statistical Computing, Vienna, Austria. (www.r-project.org)
28. Ramette, A. 2007. Multivariate analyses in microbial ecology. FEMS Microbiology Ecology 62:142.
29. Reeder, J., and R. Knight. 2009. The "rare biosphere": a reality check. Nature Methods 6:636-637.
30. Sinsabaugh, R. L., M. E. Gallo, C. Lauber, M. P. Waldrop, and D. R. Zak. 2005. Extracellular enzyme activities and soil organic matter dynamics for northern hardwood forests receiving simulated nitrogen deposition. Biogeochemistry 75: 201-215.
31. Stevens, M. H. H., and W. P. Carson. 2002. Resource quantity, not resource heterogeneity, maintains plant diversity. Ecology Letters 5:420-426.
32. Suding, N. S., S. L. Collins, L. Gough, C. Clark, E. A. Cleland, K. L. Gross, D. G. Milchunas, and S. Pennings. 2005. Functional- and abundance-based mechanisms explain diversity loss due to N fertilization. Proceedings of the National Academy of Sciences USA 102:4387-4392.
33. Tilman, D. 1984. Plant dominance along an experimental nutrient gradient. Ecology 65:1445-1453.
34. Tilman, D. 1987. Secondary succession and the pattern of plant dominance along experimental nitrogen gradients. Ecological Monographs 57:189-214.
35. Treseder, K. K. 2008. Nitrogen additions and microbial biomass: a meta-analysis of ecosystem studies. Ecology Letters 11:1111-1120.
36. Vitousek, P. M., S. Hättenschwiler, L. Olander, and S. Allison. 2002. Nitrogen and nature. Ambio 31:97-101.
37. Vitousek, P. M., and R. W. Howarth. 1991. Nitrogen limitation on land and in the sea: How can it occur? Biogeochemistry 13:87-115.
38. Waldrop, M. P., D. R. Zak, and R. L. Sinsabaugh. 2004. Microbial community response to nitrogen deposition in northern forest ecosystems. Soil Biology and Biochemistry 36:1443-1451.
39. Zeglin, L., M. Sturova, R. L. Sinsabaugh, and S. L. Coolins. 2007. Microbial responses to nitrogen addition in three contrasting grassland ecosystems. Oecologia 154:349-359.