Soil Functional Operating Range Linked to Microbial Biodiversity and Community Composition Using Denitrifiers as Model Guild

PLoS ONE

Volumn 7, Issue 12, 2012, Pages

  Hallin, Sara ^a   Welsh, Allana ^a   Stenström, John ^a   Hallet, Stephanie ^b   Enwall, Karin ^a   Bru, David ^b   Philippot, Laurent ^b  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^b UNIV BOURGOGNE FRANCHE COMTÉ   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMMUNITY STRUCTURE; CONTROLLED STUDY; DENITRIFICATION; DENITRIFYER; ENVIRONMENTAL EXPOSURE; GENOTYPE; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NITROGEN CYCLING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SALT TOLERANCE; SOIL ANALYSIS; SOIL FERTILIZATION; SOIL ORGANISM; SPECIES COMPOSITION; TEMPERATURE SENSITIVITY; UNINDEXED SEQUENCE;

BACTERIA; BIODIVERSITY; ECOSYSTEM; ENVIRONMENT; GENOTYPE; METAGENOME; MODELS, THEORETICAL; PHYLOGENY; SALTS; SOIL; SOIL MICROBIOLOGY; SWEDEN; TEMPERATURE;

BACTERIA (MICROORGANISMS);

EID: 84871404209     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0051962     Document Type: Article

References (50)

1. Hooper DU, Chapin III FS, Ewel JJ, Hector A, Inchausti P, et al. (2005) Effects of biodiversity on ecosystem functioning: a consensus of current knowledge. Ecol Monograph 75: 3-35.
2. van der Heijden MGA, Bardgett RD, van Straalen NM, (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11: 296-310.
3. O'Mullan GDO, Ward BB, (2005) Relationship of temporal and spatial variabilities of ammonia-oxidizing bacteria to nitrification rates in Monterey bay, California. Appl Environ Microb 71: 697-705.
4. Ptacnik R, Solimini AG, Andersen T, Tamminen T, Brettum P, et al. (2088) Diversity predicts stability and resource use efficiency in natural phytoplankton communities. Proc Natl Acad Sci USA 105: 5134-5138.
5. Griffiths BS, Ritz K, Bardgett RD, Cook R, Christensen S, et al. (2000) Ecosystem response of pasture soil communities to fumigation-induced microbial diversity reductions: an examination of the biodiversity-ecosystem function relationship. Oikos 90: 279-294.
6. Hol WHG, De Boer W, Termorshuizen AJ, Meyer KM, Schneider JHM, et al. (2010) Reduction of rare soil microbes modifies plant-herbivore interactions. Ecol Lett 13: 292-301.
7. Wertz S, Degrange V, Prosser JI, Poly F, Commeaux C, et al. (2006) Maintenance of soil functioning following erosion of microbial diversity. Environ Microbiol 8: 2162-2169.
8. Maherali H, Klironomos JN, (2007) Influence of phylogeny on fungal community assembly and ecosystem functioning. Science 316: 1746-1748.
9. Wittebolle L, Marzorati M, Clement L, Balloi A, Daffonchio D, et al. (2009) Initial community evenness favours functionality under selective stress. Nature 458: 623-626.
10. Loreau M, Hector A, (2001) Partitioning selection and complementarity in biodiversity experiments. Nature 412: 72-76.
11. Tilman D, (1999) The ecological consequences of changes in biodiversity: a search for general principles. Ecology 80: 1455-1474.
12. Yachi S, Loreau M, (1999) Biodiversity and ecosystem productivity in a fluctuating environment: The insurance hypothesis. Proc Natl Acad Sci USA 96: 1463-1468.
13. Pfisterer AB, Joshi J, Schmid B, Fischer M, (2004) Rapid decay of diversity-productivity relationships after invasion of experimental plant communities. Basic Appl Ecol 5: 5-14.
14. Hallin S, Jones CM, Schloter M, Philippot L, (2009) Relationship between N-cycling communities and ecosystem functioning in a 50-year-old fertilization experiment. ISME J 3: 597-605.
15. Philippot L, Hallin S, (2005) Finding the missing link between diversity and activity using denitrifying bacteria as a model functional community. Curr Opin Microbiol 8: 234-239.
16. Pell M, Stenberg B, Stenström J, Torstensson L, (1996) Potential denitrification activity assay in soil- with or without chloramphenicol? Soil Biol Biochem 28: 393-398.
17. Gabel RA, Schultz B, (1973) Solubility of nitrous-oxide in water, 20-80°C. Anesthesiology 38: 75-81.
18. Orcutt FS, (1937) Nitrogen metabolism of soybeans in relation to the symbiotic nitrogen fixation process. Soil Sci Plant Nutr 44: 203-215.
19. Tuomi M, Vanhala P, Karhu K, Fritze H, Liski J, (2008) Heterotrophic soil respiration- comparison of different models describing its temperature dependence. Ecol Model 211: 182-190.
20. Jones CM, Stres B, Rosenquist M, Hallin S, (2008) Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification. Molec Biol Evol 25: 1955-1966.
21. Dandie CE, Burton DL, Zebarth BJ, Trevors JT, Goyer C, (2007) Analysis of denitrification genes and comparison of nosZ, cnorB and 16S rDNA from culturable denitrifying bacteria in potato cropping systems. Syst Appl Microbiol 30: 128-138.
22. Lamb EG, Han S, Lanoil BD, Henry GHR, Brummell ME, et al. (2011) A High Arctic soil ecosystem resists long-term environmental manipulations. Global Change Biol 17: 3187-3194.
23. Mao Y, Yannarell AC, Mackie RI, (2011) Changes in N-Transforming Archaea and Bacteria in soil during the establishment of bioenergy crops. PLoS ONE 6: e24750.
24. Rösch C, Mergel A, Bothe H, (2002) Biodiversity of denitrifying and dinitrogen-fixing bacteria in an Acid forest soil. Appl Environ Microbiol 68: 3818-3829.
25. Petric I, Philippot L, Abbate C, Bispo A, Chesnot T, et al. (2011) Inter-laboratory evaluation of the ISO standard 11063 "Soil quality- Method to directly extract DNA from soil samples". J Microbiol Meth 84: 454-460.
26. Mounier E, Hallet S, Chèneby D, Benizri E, Gruet Y, et al. (2004) Influence of maize mucilage on the diversity and activity of the denitrifying community. Environ Microbiol 6: 301-312.
27. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: Open-Source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
28. Excoffier L, Smouse PE, Quattro JM, (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491.
29. Stamatakis A, (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinfomatics 22: btl446.
30. Letunic I, Bork P, (2011) Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucl Acids Res39: W475-W478.
31. Faith DP, (1992) Conservation evaluation and phylogenetic diversity. Biol Conserv 61: 1-10.
32. Webb CO, Ackerly DD, McPeek MA, Donoghue MJ, (2002) Phylogenies and community ecology. Annu Rev Ecol Syst 33: 475-505.
33. Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, et al. (2010) Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26: 1463-1464.
34. Hamady M, Lozupone C, Knight R, (2009) Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 4: 17-27.
35. Cavender-Bares J, Kozak KH, Fine PVA, Kembel SW, (2009) The merging of community ecology and phylogenetic biology. Ecol Lett 12: 603-715.
36. Smith MD, Knapp AK, (2003) Dominant species maintain ecosystem function with non-random species loss. Ecol Lett 6: 509-517.
37. Buckley DH, Schmidt TM, (2001) The structure of microbial communities in soil and the lasting impact of cultivation. Microb Ecol 42: 11-21.
38. Philippot L, Hallin S, Schloter M, (2007) Ecology of denitrifying prokaryotes in agricultural soil. Adv Agron 96: 249-305.
39. Craig MacLean R, Dickson A, Bell G, (2005) Resource competition and adaptive radiation in a microbial microcosm. EcolLett 8: 38-46.
40. Gu L, Post WM, King AW, (2004) Fast labile carbon turnover obscures sensitivity of heteroptrophic respiration from soil to temperature: a model analysis. Global Biogeochem Cycl 18: 1022.
41. Fierer N, Bradford MA, Jackson RB, (2007) Toward an ecological classification of soil bacteria. Ecology 88: 1354-1364.
42. Wawrik B, Kerkhof L, Kukor J, Zylstra G, (2005) Effect of different carbon sources on community composition of bacterial enrichments from soil. Appl Environ Microbiol 71: 6776-6783.
43. Tilman D, (1987) Secondary succession and the pattern of plant dominance along experimental nitrogen gradients. Ecol Monograph 57: 189-214.
44. Wilson SD, Tilman D, (2002) Quadratic variation in old-field species richness along gradients of disturbance and nitrogen. Ecology 83: 492-504.
45. 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.
46. Horner-Devine MC, Bohannan BJM, (2006) Phylogenetic clustering and overdispersion in bacterial communities. Ecology 87: 100-108.
47. Cadotte MW, Cardinale BJ, Oakley BW, (2008) Evolutionary history and the effect of biodiversity on plant productivity. Proc Natl Acad Sci USA 105: 17012-17017.
48. Jousset A, Schmid B, Scheu S, Eisenhauer N, (2011) Genotypic richness and dissimilarity opposingly affect ecosystem functioning. Ecol Lett 14: 537-545.
49. Oren A, (2011) Thermodynamic limits to microbial life at high salt concentrations. Environ Microbiol 13: 1908-1923.
50. Ives AR, Carpenter SR, (2007) Stability and diversity of ecosystems. Science 317: 58-62.