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Zhalnina K, de Quadros PD, Gano KA, et al. Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments. Front Microbiol. 2013;4:104doi: 10.3389/fmicb.2013.00104.
Zhalnina, K., de Quadros, P. D., Gano, K. A., Davis-Richardson, A., Fagen, J. R., Brown, C. T., Giongo, A., Drew, J. C., Sayavedra-Soto, L. A., Arp, D. J., Camargo, F. A., Daroub, S. H., Clark, I. M., McGrath, S. P., Hirsch, P. R., & Triplett, E. W. (2013). Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments. Frontiers in microbiology, 4104. https://doi.org/10.3389/fmicb.2013.00104
Zhalnina, Kateryna, et al. "Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments." Frontiers in microbiology vol. 4 (2013): 104. doi: https://doi.org/10.3389/fmicb.2013.00104
Zhalnina K, de Quadros PD, Gano KA, Davis-Richardson A, Fagen JR, Brown CT, Giongo A, Drew JC, Sayavedra-Soto LA, Arp DJ, Camargo FA, Daroub SH, Clark IM, McGrath SP, Hirsch PR, Triplett EW. Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments. Front Microbiol. 2013 May 01;4:104. doi: 10.3389/fmicb.2013.00104. eCollection 2013. PMID: 23641242; PMCID: PMC3640186.
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Front Microbiol. 2013 May 01;4:104. doi: 10.3389/fmicb.2013.00104. eCollection 2013.

Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments.

Frontiers in microbiology

Kateryna Zhalnina, Patricia D de Quadros, Kelsey A Gano, Austin Davis-Richardson, Jennie R Fagen, Christopher T Brown, Adriana Giongo, Jennifer C Drew, Luis A Sayavedra-Soto, Dan J Arp, Flavio A O Camargo, Samira H Daroub, Ian M Clark, Steve P McGrath, Penny R Hirsch, Eric W Triplett

Affiliations

  1. Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA.

PMID: 23641242 PMCID: PMC3640186 DOI: 10.3389/fmicb.2013.00104

Abstract

Agricultural land management, such as fertilization, liming, and tillage affects soil properties, including pH, organic matter content, nitrification rates, and the microbial community. Three different study sites were used to identify microorganisms that correlate with agricultural land use and to determine which factors regulate the relative abundance of the microbial signatures of the agricultural land-use. The three sites included in this study are the Broadbalk Experiment at Rothamsted Research, UK, the Everglades Agricultural Area, Florida, USA, and the Kellogg Biological Station, Michigan, USA. The effects of agricultural management on the abundance and diversity of bacteria and archaea were determined using high throughput, barcoded 16S rRNA sequencing. In addition, the relative abundance of these organisms was correlated with soil features. Two groups of microorganisms involved in nitrogen cycle were highly correlated with land use at all three sites. The ammonia oxidizing-archaea, dominated by Ca. Nitrososphaera, were positively correlated with agriculture while a ubiquitous group of soil bacteria closely related to the diazotrophic symbiont, Bradyrhizobium, was negatively correlated with agricultural management. Analysis of successional plots showed that the abundance of ammonia oxidizing-archaea declined and the abundance of bradyrhizobia increased with time away from agriculture. This observation suggests that the effect of agriculture on the relative abundance of these genera is reversible. Soil pH and NH3 concentrations were positively correlated with archaeal abundance but negatively correlated with the abundance of Bradyrhizobium. The high correlations of Ca. Nitrososphaera and Bradyrhizobium abundances with agricultural management at three long-term experiments with different edaphoclimatic conditions allowed us to suggest these two genera as signature microorganisms for agricultural land use.

Keywords: Bradyrhizobium; Ca. Nitrososphaera; agricultural land use; ammonia-oxidizing archaea; diazotrophs; soil properties

References

  1. Environ Microbiol. 2007 Sep;9(9):2364-74 - PubMed
  2. Ecology. 2010 Dec;91(12):3463-70; discussion 3503-14 - PubMed
  3. Appl Environ Microbiol. 2007 May;73(10):3196-204 - PubMed
  4. ISME J. 2011 Jul;5(7):1226-36 - PubMed
  5. J Chromatogr A. 2010 Jun 25;1217(26):4454-62 - PubMed
  6. ISME J. 2012 May;6(5):1032-45 - PubMed
  7. Environ Microbiol. 2008 Nov;10(11):2966-78 - PubMed
  8. Nucleic Acids Res. 2009 Jan;37(Database issue):D141-5 - PubMed
  9. Nat Methods. 2010 May;7(5):335-6 - PubMed
  10. ISME J. 2007 Aug;1(4):283-90 - PubMed
  11. Environ Microbiol. 2008 Jun;10(6):1601-11 - PubMed
  12. Appl Environ Microbiol. 2005 May;71(5):2695-704 - PubMed
  13. FEMS Microbiol Ecol. 2010 Dec;74(3):566-74 - PubMed
  14. Biochem Biophys Res Commun. 1979 Feb 28;86(4):968-75 - PubMed
  15. Microb Ecol. 2008 Oct;56(3):525-37 - PubMed
  16. Appl Environ Microbiol. 2011 Feb;77(4):1315-24 - PubMed
  17. Nature. 2006 Aug 17;442(7104):806-9 - PubMed
  18. J Bacteriol. 1976 Jul;127(1):149-53 - PubMed
  19. FEMS Microbiol Ecol. 2009 Oct;70(1):99-108 - PubMed
  20. Environ Microbiol. 2005 Dec;7(12):1985-95 - PubMed
  21. Proc Natl Acad Sci U S A. 2010 Oct 5;107(40):17240-5 - PubMed
  22. New Phytol. 2011 Mar;189(4):1040-1050 - PubMed
  23. Res Microbiol. 2012 Jun;163(5):349-56 - PubMed
  24. ISME J. 2010 Jul;4(7):852-61 - PubMed
  25. Philos Trans R Soc Lond B Biol Sci. 2008 Feb 27;363(1492):685-701 - PubMed
  26. Proc Natl Acad Sci U S A. 2006 Jan 17;103(3):626-31 - PubMed
  27. ISME J. 2011 Mar;5(3):532-42 - PubMed
  28. J Bacteriol. 1974 Oct;120(1):556-8 - PubMed
  29. Can J Microbiol. 1979 Mar;25(3):352-61 - PubMed
  30. Microb Ecol. 2001 Jul;42(1):11-21 - PubMed
  31. Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21206-11 - PubMed
  32. Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):4170-5 - PubMed
  33. Appl Environ Microbiol. 2001 Feb;67(2):972-6 - PubMed
  34. Microb Ecol. 2010 May;59(4):734-43 - PubMed
  35. Nature. 2009 Nov 26;462(7272):514-7 - PubMed
  36. Oecologia. 1993 Dec;96(4):451-456 - PubMed
  37. ISME J. 2011 May;5(5):908-17 - PubMed
  38. Environ Microbiol. 2009 Feb;11(2):446-56 - PubMed
  39. Philos Trans R Soc Lond B Biol Sci. 2012 May 5;367(1593):1235-44 - PubMed
  40. Open Microbiol J. 2012;6:29-33 - PubMed
  41. Front Microbiol. 2012 Mar 02;3:77 - PubMed
  42. Environ Microbiol. 2012 Feb;14(2):525-39 - PubMed
  43. J Nutr. 2000 May;130(5):1081-4 - PubMed
  44. Arch Microbiol. 2002 Oct;178(4):250-5 - PubMed
  45. ISME J. 2012 May;6(5):1007-17 - PubMed
  46. Genome Res. 2003 Sep;13(9):2164-70 - PubMed
  47. Nature. 2005 Sep 22;437(7058):543-6 - PubMed
  48. FEMS Microbiol Ecol. 2009 Nov;70(2):52-61 - PubMed
  49. ISME J. 2011 Jul;5(7):1213-25 - PubMed
  50. Arch Microbiol. 1976 May 3;108(1):45-54 - PubMed
  51. Environ Microbiol. 2012 Jun;14(6):1528-43 - PubMed

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