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 13CO2 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 13C-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 13C 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 12C and 13C 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.
authors.affiliation: School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK.
authors.forename: J Ignacio
authors.initials: JI
authors.lastname: Rangel-Castro
authors.forename: Ken
authors.initials: K
authors.lastname: Killham
authors.forename: Nick
authors.initials: N
authors.lastname: Ostle
authors.forename: Graeme W
authors.initials: GW
authors.lastname: Nicol
authors.forename: Ian C
authors.initials: IC
authors.lastname: Anderson
authors.forename: Charlie M
authors.initials: CM
authors.lastname: Scrimgeour
authors.forename: Phil
authors.initials: P
authors.lastname: Ineson
authors.forename: Andy
authors.initials: A
authors.lastname: Meharg
authors.forename: Jim I
authors.initials: JI
authors.lastname: Prosser
mesh_terms: D001419:Bacteria / Q000187:drug effects* / Q000235:genetics / Q000378:metabolism; D017610:Calcium Compounds / Q000494:pharmacology*; D002245:Carbon Dioxide / Q000378:metabolism*; D002247:Carbon Isotopes; D004591:Electrophoresis, Polyacrylamide Gel; D005122:Exudates and Transudates / Q000187:drug effects* / Q000382:microbiology; D005658:Fungi / Q000187:drug effects* / Q000235:genetics / Q000378:metabolism; D010087:Oxides / Q000494:pharmacology*; D018517:Plant Roots / Q000382:microbiology; D012988:Soil Microbiology
chemical_list: D017610:Calcium Compounds; D002247:Carbon Isotopes; D010087:Oxides; D002245:Carbon Dioxide; C016538:lime