Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms

Juan Ignacio Rangel-Castro, Kenneth Stuart Killham, N Ostle, Graeme William Nicol, Ian C Anderson, C M Scrimgeour, P Ineson, Andrew Alexander Meharg, James Ivor Prosser

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136 Citations (Scopus)


Rhizosphere microorganisms play an important role in soil carbon flow, through turnover of root exudates, but there is little information on which organisms are actively involved or on the influence of environmental conditions on active communities. In this study, a (CO2)-C-13 pulse labelling field experiment was performed in an upland grassland soil, followed by RNA-stable isotope probing (SIP) analysis, to determine the effect of liming on the structure of the rhizosphere microbial community metabolizing root exudates. The lower limit of detection for SIP was determined in soil samples inoculated with a range of concentrations of C-13-labelled Pseudomonas fluorescens and was found to lie between 10(5) and 10(6) cells per gram of soil. The technique was capable of detecting microbial communities actively assimilating root exudates derived from recent photo-assimilate in the field. Denaturing gradient gel electrophoresis (DGGE) profiles of bacteria, archaea and fungi derived from fractions obtained from caesium trifluoroacetate (CsTFA) density gradient ultracentrifugation indicated that active communities in limed soils were more complex than those in unlimed soils and were more active in utilization of recently exuded C-13 compounds. In limed soils, the majority of the community detected by standard RNA-DGGE analysis appeared to be utilizing root exudates. In unlimed soils, DGGE profiles from C-12 and C-13 RNA fractions differed, suggesting that a proportion of the active community was utilizing other sources of organic carbon. These differences may reflect differences in the amount of root exudation under the different conditions.

Original languageEnglish
Pages (from-to)828-838
Number of pages11
JournalEnvironmental Microbiology
Issue number6
Early online date7 Mar 2005
Publication statusPublished - Jun 2005


  • gradient gel-electrophoresis
  • rhizosphere carbon-flow
  • bacterial community structure
  • 16S ribosomal-RNA
  • microbial community
  • upland grassland
  • lolium-perenne
  • DNA
  • diversity
  • turnover


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