Long-Term Nitrogen Amendment Alters the Diversity and Assemblage of Soil Bacterial Communities in Tallgrass Prairie

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Coolon, Joseph D ^a,b   Jones, Kenneth L ^a,c   Todd, Timothy C ^a   Blair, John M ^a   Herman, Michael A ^a  

^a KANSAS STATE UNIVERSITY   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

^c UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NITROGEN; RIBOSOME RNA; RNA 16S;

ACIDOBACTERIA; ARTICLE; BACTERIUM DETECTION; BACTEROIDETES; COMMUNITY STRUCTURE; CONTROLLED STUDY; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; PHYLOGENY; PHYLUM; PRAIRIE; PROTEOBACTERIA; SOIL MICROFLORA; SPECIES DOMINANCE; SPECIES RICHNESS; VERRUCOMICROBIA;

BACTERIA; BIOTA; FOOD; NITROGEN; PHOSPHORUS; POACEAE; RNA, RIBOSOMAL, 16S; SOIL; SOIL MICROBIOLOGY;

ACIDOBACTERIA; ACTINOBACTERIA; BACTERIA (MICROORGANISMS); FIRMICUTES; GAMMAPROTEOBACTERIA; NITROSPIRA; PROTEOBACTERIA; VERRUCOMICROBIA;

EID: 84879533388     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0067884     Document Type: Article

References (62)

1. Falkowski PG, Fenchel T, Delong EF, (2008) The microbial engines that drive Earth's biogeochemical cycles. Science 320: 1034-1039.
2. Bowen JL, Ward BB, Morrison HG, Hobbie JE, Valiela I, et al. (2011) Microbial community composition in sediments resists perturbation by nutrient enrichment. ISME 5: 1540-1548.
3. Baath E, Frostegard A, Pennanen T, Fritze H, (1995) Microbial community structure and pH response in relation to soil organic-matter quality in wood-ash fertilized, clear-cut or burned coniferous forest soils. Soil Biology & Biochemistry 27: 229-240.
4. Pietikainen J, Fritze H, (1995) Clear-cutting and prescribed burning in coniferous forest- Comparison of effects on soil fungal and total microbial biomass, respiration activity and nitrification. Soil Biology & Biochemistry 27: 101-109.
5. Allison VJ, Miller RM, Jastrow JD, Matamala R, Zak DR, (2005) Changes in soil microbial community structure in a tallgrass prairie chronosequence. Journal of the Soil Science Society of America 69: 1412-1421.
6. Jangid K, Williams MA, Franzluebbers AJ, Sanderlin JS, Reeves JH, et al. (2008) Relative impacts of land-use, management intensity and fertilization upon soil microbial community structure in agricultural systems. Soil Biology & Biochemistry 40: 2843-2853.
7. Vazquez FJ, Acea MJ, Carballas T, (1993) Soil microbial populations after wildfire. Fems Microbiology Ecology 13: 93-103.
8. Bittman S, Forge TA, Kowalenko CG, (2005) Responses of the bacterial and fungal biomass in a grassland soil to multi-year applications of dairy manure slurry and fertilizer. Soil Biology & Biochemistry 37: 613-623.
9. Marschner P, Kandeler E, Marschner B, (2003) Structure and function of the soil microbial community in a long-term fertilizer experiment. Soil Biology & Biochemistry 35: 453-461.
10. Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, et al. (2012) Comparative metagenomic, phylogenetic, and physiological analyses of soil microbial communities across nitrogen gradients. ISME 6: 1007-1017.
11. Nemergut DR, Townsend AR, Sattin SR, Freeman K, Fierer N, et al. (2008) The effects of chronic nitrogen fertilization on alpine tundra soil microbial communities: implications for carbon and nitrogen cycling. Environmental Microbiology 10: 3093-3105.
12. Ramirez KS, Craine JM, Fierer N, (2012) Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes. Global Change Biology 18: 1918-1927.
13. Allison SD, Martiny JBH, (2008) Resistance, resilience, and redundancy in microbial communities. Proc Nat Acad Sci 105: 11512-11519.
14. Samson F, Knopf F, (1994) Prairie conservation in North America. BioScience 44: 418-421.
15. Groffman PM, Rice CW, Tiedje JM, (1993) Denitrification in a tallgrass prairie landscape. Ecology 74: 855-862.
16. Sotomayor D, Rice CW, (1996) Denitrification in soil profiles beneath grassland and cultivated soils. Journal of the Soil Science Society of America 60: 1822-1828.
17. Jangid K, Williams MA, Franzluebbers AJ, Blair JM, Coleman DC, et al. (2009) Development of soil microbial communities during tallgrass prairie restoration. Soil Biol Biochem 42: 302-312.
18. Dell CJ, Williams MA, Rice CW, (2005) Partitioning of nitrogen over five growing seasons in tallgrass prairie. Ecology 86: 1280-1287.
19. Williams MA, Rice CW, (2007) Seven years of enhanced water availability influences the physiological, structural, and functional attributes of a soil microbial community. Applied Soil Ecology 35: 535-545.
20. Acosta-Martinez V, Dowd S, Allen SV, (2008) Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biology & Biochemistry 40: 2762-2770.
21. Roesch LFW, Fulthorpe RR, Riva A, Casella G, Hadwin AKM, et al. (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. Isme Journal 1: 283-290.
22. Ramirez KS, Lauber CL, Knight R, Bradford MA, Fierer N, (2010) Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems. Ecology 91: 3463-3470.
23. Collins SL, Calabrese LB, (2012) Effects of fire, grazing and topographic variation on vegetation structure in tallgrass prairie. Journal of Vegetation Science 23: 563-575.
24. Knapp AK, Seastedt TR, (1986) Detritus accumulation limits productivity of tallgrass prairie. BioScience 36: 662-668.
25. Blair JM, (1997) Fire, N availability, and plant response in grasslands: A test of the transient maxima hypothesis. Ecology 78: 2359-2368.
26. Kitchen DJ, Blair JM, Callaham Jr MA, (2009) Annual fire and mowing alter biomass, depth distribution, and C and N content of roots and soil in tallgrass prairie. Palnt and soil 323: 235-247.
27. Briggs JM, Knapp AK, (1995) Interannual Variability In Primary Production In Tallgrass Prairie- Climate, Soil-Moisture, Topographic Position, And Fire As Determinants Of Aboveground Biomass. American Journal of Botany 82: 1024-1030.
28. Turner CL, Blair JM, Schartz RJ, Neel JC, (1997) Soil N and plant responses to fire, topography, and supplemental N in tallgrass prairie. Ecology 78: 1832-1843.
29. Clark CM, Cleland EE, Collins SL, Fargione JE, Gough L, et al. (2007) Environmental and plant community determinants of species loss following nitrogen enrichment. Ecology Letters 10: 596-607.
30. Suding KN, Collins SL, Gough L, Clark C, Cleland EE, et al. (2005) Functional and abundance based mechanisms explain diversity loss due to nitrogen fertilization. Proc Natl Acad Sci USA 102: 4387-4392.
31. Clark CM, Tilman D, (2008) Loss of plant species after chronic low-level nitrogen deposition to prairie grasslands. Nature 451: 712-715.
32. Watanabe K, Kodama Y, Harayama S, (2001) Design and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting. Journal of Microbiological Methods 44: 253-262.
33. Vasileiadis S, Puglisi E, Arena M, Cappa F, Cocconcelli PS, et al. (2012) Soil Bacterial Diversity Screening Using Single 16S rRNA Gene V Regions Coupled with Multi-Million Read Generating Sequencing Technologies. PLoS One 7: e42671.
34. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
35. Coolon JD, Jones KL, Narayanan S, Wisely S, (2010) Microbial ecological response of the intestinal flora of Peromyscus maniculatus and P. leucopus to heavy metal contamination. Molecular Ecology 19: 67-80.
36. Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM, (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biology 8: R143.
37. Huang XQ, Madan A, (1999) CAP3: A DNA sequence assembly program. Genome Research 9: 868-877.
38. Fisher RA, Corbet AS, Williams CB, (1943) The relationship between the number of species and the number of individuals in a random sample of an animal population. Journal of Animal Ecology 12: 42-58.
39. Storey JD, Tibshirani R, (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100: 9440-9445.
40. Wang Q, Garrity GM, Tiedje JM, Cole JR, (2007) Naive Baysian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Appl Environ Microbiol 73: 5261-5267.
41. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-D145.
42. Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, et al. (2007) The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res 35: D169-D172.
43. Hamady M, Lozupone C, Knight R, (2010) Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME Journal 4: 17-27.
44. Lozupone C, Hamady M, Knight R, (2006) UniFrac- An online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinfofmatics 7: 1-14.
45. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792-1797.
46. Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, et al. (2010) Examining the global distribution of dominant archaeal populations in soil. ISME 5: 908-917.
47. Hamady M, Knight R, (2009) Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res 19: 1141-1152.
48. Konstantinidis KT, Tiedje JM, (2007) Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Current Opinion in Microbiology 10: 504-509.
49. Leininger S, Urich T, Schloter M, Schwark L, Qi J, et al. (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442: 806-809.
50. Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, et al. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedings of the National Academy of Sciences of the United States of America 103: 12115-12120.
51. Trosvik P, Skanseng B, Jakobsen KS, Stenseth NC, Naes T, et al. (2007) Multivariate analysis of complex DNA sequence electropherograms for high-throughput quantitative analysis of mixed microbial populations. Applied and Environmental Microbiology 73: 4975-4983.
52. Miller SR, Strong AL, Jones KL, Ungerer MC, (2009) Bar-Coded Pyrosequencing Reveals Shared Bacterial Community Properties along the Temperature Gradients of Two Alkaline Hot Springs in Yellowstone National Park. Applied And Environmental Microbiology 75: 4565-4572.
53. Jumpponen A, Jones KL, (2009) Massively parallel 454-sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytologist 184: 279-282.
54. Jumpponen A, Jones KL, Mattox J, Yaege C, (2009) Massively parallel 454-sequencing of fungal communities in Quercus spp. ectomycorrhizas indicates seasonal dynamics in urban and rural sites. Molecular Ecology 19: 41-53.
55. Jumpponen A, Jones KL, (2010) Seasonally dynamic fungal communities in the Quercus macrocarpa phyllosphere differ between urban and nonurban environments. New Phytologist 186: 496-513.
56. Jumpponen A, Jones KL, Blair JM, (2010) Vertical distribution of fungal communities in tallgrass prairie soil. 102: 1027-1041.
57. Youssef N, Sheik CS, Krumholz LR, Najar FZ, Roe BA, et al. (2009) Comparison of Species Richness Estimates Obtained Using Nearly Complete Fragments and Simulated Pyrosequencing-Generated Fragments in 16S rRNA Gene-Based Environmental Surveys. Appl Environ Microbiol 75: 5227-5236.
58. Garcia FO, Rice CW, (1994) Microbial Biomass Dynamics in Tallgrass Prairie. Soil Science Society of America Journal 58: 816-823.
59. Fierer N, Jackson RB, (2006) The diversity and biogeography of soil bacterial communities. PNAS 103: 626-631.
60. Campbell BJ, Paulson SW, Hanson TE, Mack MC, Schuur EAG, (2010) The effect of nutrient deposition on bacterial communities in Arctic tundra soil. Environmental Microbiology 12: 1872-1854.
61. Nacke H, Thurmer A, Wollherr A, C W, Hodac L, et al. (2011) Pyrosequencing-Based Assessment of Bacterial Community Structure Along Different Management Types in German Forest and Grassland Soils. PLoS One 6: e17000.
62. Evans SE, Wallenstein MD, (2011) Soil microbial community response to drying and rewetting stress: does historical precipitation regime matter? Biogeochemistry 109: 101-116.