Display options
Cite
Ridl J, Kolar M, Strejcek M, et al. Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil. Front Microbiol. 2016;7:995doi: 10.3389/fmicb.2016.00995.
Ridl, J., Kolar, M., Strejcek, M., Strnad, H., Stursa, P., Paces, J., Macek, T., & Uhlik, O. (2016). Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil. Frontiers in microbiology, 7995. https://doi.org/10.3389/fmicb.2016.00995
Ridl, Jakub, et al. "Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil." Frontiers in microbiology vol. 7 (2016): 995. doi: https://doi.org/10.3389/fmicb.2016.00995
Ridl J, Kolar M, Strejcek M, Strnad H, Stursa P, Paces J, Macek T, Uhlik O. Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil. Front Microbiol. 2016 Jun 24;7:995. doi: 10.3389/fmicb.2016.00995. eCollection 2016. PMID: 27446035; PMCID: PMC4919359.
Copy Download .nbib Format: NLM
Share it on

Front Microbiol. 2016 Jun 24;7:995. doi: 10.3389/fmicb.2016.00995. eCollection 2016.

Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil.

Frontiers in microbiology

Jakub Ridl, Michal Kolar, Michal Strejcek, Hynek Strnad, Petr Stursa, Jan Paces, Tomas Macek, Ondrej Uhlik

Affiliations

  1. Department of Genomics and Bioinformatics, Institute of Molecular Genetics, The Czech Academy of Sciences, PragueCzech Republic; Department of Philosophy and History of Science, Faculty of Science, Charles University in Prague, PragueCzech Republic.
  2. Department of Genomics and Bioinformatics, Institute of Molecular Genetics, The Czech Academy of Sciences, Prague Czech Republic.
  3. Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Prague Czech Republic.

PMID: 27446035 PMCID: PMC4919359 DOI: 10.3389/fmicb.2016.00995

Abstract

Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco) and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq. We observed that the presence of any of the selected plants rather than fertilization shaped the microbial community structure, and the microbial populations of the root zone of each plant significantly differed from one another and/or from the bulk soil, whereas the effect of the fertilizer proved to be insignificant. When we compared microbial diversity in root zones versus bulk soil, we observed an increase in the relative abundance of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria or Bacteroidetes, taxa which are commonly considered copiotrophic. Our results thus align with the theory that fast-growing, copiotrophic, microorganisms which are adapted to ephemeral carbon inputs are enriched in the vegetated soil. Microbial functional potential indicated that some genetic determinants associated with signal transduction mechanisms, defense mechanisms or amino acid transport and metabolism differed significantly among treatments. Genetic determinants of these categories tend to be overrepresented in copiotrophic organisms. The results of our study further elucidate plant-microbe relationships in a contaminated environment with possible implications for the phyto/rhizoremediation of contaminated areas.

Keywords: contaminated soil; fertilization; functional potential; microbial community structure; plants

References

  1. Nat Methods. 2009 Sep;6(9):639-41 - PubMed
  2. Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):10967-72 - PubMed
  3. Arch Microbiol. 1998 Jan;169(1):61-70 - PubMed
  4. Sci Total Environ. 2015 Nov 15;533:177-86 - PubMed
  5. Appl Environ Microbiol. 1997 May;63(5):1933-8 - PubMed
  6. Nat Rev Microbiol. 2013 Nov;11(11):789-99 - PubMed
  7. Mol Ecol. 2015 Jan;24(1):136-50 - PubMed
  8. ISME J. 2007 Jun;1(2):134-48 - PubMed
  9. BMC Bioinformatics. 2011 Jan 28;12:38 - PubMed
  10. Chemosphere. 2005 Jan;58(4):529-33 - PubMed
  11. Appl Microbiol Biotechnol. 2013 Oct;97(20):9245-56 - PubMed
  12. BMC Bioinformatics. 2003 Sep 11;4:41 - PubMed
  13. Appl Environ Microbiol. 2001 Oct;67(10):4742-51 - PubMed
  14. ISME J. 2014 Oct;8(10):2131-42 - PubMed
  15. Appl Microbiol Biotechnol. 2012 Sep;95(6):1589-603 - PubMed
  16. Environ Sci Technol. 2002 Apr 1;36(7):1579-83 - PubMed
  17. N Biotechnol. 2012 Nov 15;30(1):15-22 - PubMed
  18. FEMS Microbiol Ecol. 2005 Apr 1;52(2):207-17 - PubMed
  19. Sci Rep. 2016 Feb 26;6:22145 - PubMed
  20. PLoS One. 2012;7(7):e40653 - PubMed
  21. Appl Environ Microbiol. 2009 Oct;75(20):6471-7 - PubMed
  22. Chemosphere. 2000 Jan;40(1):11-4 - PubMed
  23. Biotechnol Adv. 2000 Mar;18(1):23-34 - PubMed
  24. BMC Bioinformatics. 2008 Sep 19;9:386 - PubMed
  25. Nucleic Acids Res. 2009 Jan;37(Database issue):D141-5 - PubMed
  26. FEMS Microbiol Ecol. 2010 Jun;72(3):313-27 - PubMed
  27. PLoS Comput Biol. 2014 Apr 03;10(4):e1003531 - PubMed
  28. Appl Environ Microbiol. 2012 May;78(10):3560-70 - PubMed
  29. Int J Phytoremediation. 2007 Jan-Feb;9(1):71-8 - PubMed
  30. Stand Genomic Sci. 2015 Nov 14;10:101 - PubMed
  31. Environ Toxicol Chem. 2003 Sep;22(9):1998-2004 - PubMed
  32. PLoS One. 2013 Dec 13;8(12):e82443 - PubMed
  33. Microb Ecol. 2012 Apr;63(3):509-21 - PubMed
  34. Pac Symp Biocomput. 2011;:165-76 - PubMed
  35. Environ Sci Technol. 2007 Jun 15;41(12 ):4382-8 - PubMed
  36. Environ Sci Pollut Res Int. 2005;12(1):34-48 - PubMed
  37. ISME J. 2008 Sep;2(9):968-81 - PubMed
  38. Appl Environ Microbiol. 2009 Dec;75(23):7537-41 - PubMed
  39. Ecology. 2007 Jun;88(6):1354-64 - PubMed
  40. Proc Natl Acad Sci U S A. 2006 Oct 17;103(42):15280-7 - PubMed
  41. Appl Environ Microbiol. 2006 Apr;72(4):2331-42 - PubMed
  42. Antonie Van Leeuwenhoek. 2002 Aug;81(1-4):509-20 - PubMed
  43. Environ Sci Technol. 2008 Aug 1;42(15):5746-51 - PubMed
  44. Ecol Lett. 2015 Jan;18(1):85-95 - PubMed
  45. Sci Rep. 2013;3:1968 - PubMed
  46. Nucleic Acids Res. 2000 Jan 1;28(1):33-6 - PubMed
  47. Front Microbiol. 2016 Jun 02;7:837 - PubMed
  48. Proc Natl Acad Sci U S A. 2009 Sep 15;106(37):15527-33 - PubMed
  49. FEMS Microbiol Ecol. 2009 Apr;68(1):1-13 - PubMed
  50. PLoS One. 2015 May 13;10(5):e0126033 - PubMed
  51. Genome Biol. 2014;15(12):550 - PubMed

Publication Types