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

Research output: Contribution to journalArticle

122 Citations (Scopus)

Abstract

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
Volume7
Issue number6
Early online date7 Mar 2005
DOIs
Publication statusPublished - Jun 2005

Fingerprint

root exudates
soil microorganism
liming
Exudates and Transudates
soil microorganisms
Isotopes
stable isotopes
stable isotope
Soil
denaturing gradient gel electrophoresis
Denaturing Gradient Gel Electrophoresis
RNA
soil
electrokinesis
gel
Rhizosphere
microbial communities
rhizosphere
microbial community
upland soils

Keywords

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

Cite this

Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms. / Rangel-Castro, Juan Ignacio; Killham, Kenneth Stuart; Ostle, N ; Nicol, Graeme William; Anderson, Ian C; Scrimgeour, C M ; Ineson, P ; Meharg, Andrew Alexander; Prosser, James Ivor.

In: Environmental Microbiology, Vol. 7, No. 6, 06.2005, p. 828-838.

Research output: Contribution to journalArticle

Rangel-Castro, JI, Killham, KS, Ostle, N, Nicol, GW, Anderson, IC, Scrimgeour, CM, Ineson, P, Meharg, AA & Prosser, JI 2005, 'Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms' Environmental Microbiology, vol. 7, no. 6, pp. 828-838. https://doi.org/10.1111/j.1462-2920.2005.00756.x
Rangel-Castro, Juan Ignacio ; Killham, Kenneth Stuart ; Ostle, N ; Nicol, Graeme William ; Anderson, Ian C ; Scrimgeour, C M ; Ineson, P ; Meharg, Andrew Alexander ; Prosser, James Ivor. / Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms. In: Environmental Microbiology. 2005 ; Vol. 7, No. 6. pp. 828-838.
@article{59ca2dab1c7b4b1aa76d9e1cff66f33c,
title = "Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms",
abstract = "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.",
keywords = "gradient gel-electrophoresis, rhizosphere carbon-flow, bacterial community structure, 16S ribosomal-RNA, microbial community, upland grassland, lolium-perenne, DNA, diversity, turnover",
author = "Rangel-Castro, {Juan Ignacio} and Killham, {Kenneth Stuart} and N Ostle and Nicol, {Graeme William} and Anderson, {Ian C} and Scrimgeour, {C M} and P Ineson and Meharg, {Andrew Alexander} and Prosser, {James Ivor}",
year = "2005",
month = "6",
doi = "10.1111/j.1462-2920.2005.00756.x",
language = "English",
volume = "7",
pages = "828--838",
journal = "Environmental Microbiology",
issn = "1462-2912",
publisher = "BLACKWELL PUBLISHING LTD",
number = "6",

}

TY - JOUR

T1 - Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms

AU - Rangel-Castro, Juan Ignacio

AU - Killham, Kenneth Stuart

AU - Ostle, N

AU - Nicol, Graeme William

AU - Anderson, Ian C

AU - Scrimgeour, C M

AU - Ineson, P

AU - Meharg, Andrew Alexander

AU - Prosser, James Ivor

PY - 2005/6

Y1 - 2005/6

N2 - 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.

AB - 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.

KW - gradient gel-electrophoresis

KW - rhizosphere carbon-flow

KW - bacterial community structure

KW - 16S ribosomal-RNA

KW - microbial community

KW - upland grassland

KW - lolium-perenne

KW - DNA

KW - diversity

KW - turnover

U2 - 10.1111/j.1462-2920.2005.00756.x

DO - 10.1111/j.1462-2920.2005.00756.x

M3 - Article

VL - 7

SP - 828

EP - 838

JO - Environmental Microbiology

JF - Environmental Microbiology

SN - 1462-2912

IS - 6

ER -