The rhizosphere is active and dynamic in which newly generated carbon, derived from root exudates, and ancient carbon, in soil organic matter (SOM), are available for microbial growth. Stable isotope probing (SIP) was used to determine bacterial communities assimilating each carbon source in the rhizosphere of four plant species. Wheat, maize, rape and barrel clover (Medicago truncatula) were grown separately in the same soil under ¹³CO₂ (99% of atom ¹³C) and DNA extracted from rhizosphere soil was fractionated by isopycnic centrifugation. Bacteria-assimilating root exudates were characterized by denaturing gradient gel electrophoresis (DGGE) analysis of ¹³C-DNA and root DNA, whereas those assimilating SOM were identified from ¹²C-DNA. Plant species root exudates significantly shaped rhizosphere bacterial community structure. Bacteria related to Sphingobacteriales and Myxococcus assimilated root exudates in colonizing roots of all four plants, whwereas bacteria related to Sphingomonadales utilized both carbon sources, and were identified in light, heavy and root compartment DNA. Sphingomonadales were specific to monocotyledons, whereas bacteria related to Enterobacter and Rhizobiales colonized all compartments of all four plants, used both fresh and ancient carbon and were considered as generalists. There was also evidence for an indirect important impact of root exudates, through stimulation of SOM assimilation by a diverse bacterial community.

A specificity of Brassicaceous plants is the production of sulphur secondary metabolites called glucosinolates that can be hydrolysed into glucose and biocidal products. Among them, isothiocyanates are toxic to a wide range of microorganisms and particularly soil-borne pathogens. The aim of this study was to investigate the role of glucosinolates and their breakdown products as a factor of selection on rhizosphere microbial community associated with living Brassicaceae. We used a DNA-stable isotope probing approach to focus on the active microbial populations involved in root exudates degradation in rhizosphere. A transgenic Arabidopsis thaliana line producing an exogenous glucosinolate and the associated wild-type plant associated were grown under an enriched ¹³CO₂ atmosphere in natural soil. DNA from the rhizospheric soil was separated by density gradient centrifugation. Bacterial (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Acidobacteria), Archaea and fungal community structures were analysed by DGGE fingerprints of amplified 16S and 18S rRNA gene sequences. Specific populations were characterized by sequencing DGGE fragments. Roots of the transgenic plant line presented an altered profile of glucosinolates and other minor additional modifications. These modifications significantly influenced microbial community on roots and active populations in the rhizosphere. Alphaproteobacteria, particularly Rhizobiaceae, and fungal communities were mainly impacted by these Brassicaceous metabolites, in both structure and composition. Our results showed that even a minor modification in plant root could have important repercussions for soil microbial communities.

Summary: This work is the first report on the use of DNA‐, RNA‐SIP approaches to elucidate the dynamics and the diversity of bacterial populations actively assimilating C derived from plant residues labelled at more than 90% ¹³ C. Wheat‐residues, were incorporated and incubated into soil microcosms for 28 days. At the end of the incubation time, no more than 55% of the total CO ₂ released was ¹³ C‐labelled, suggesting the occurrence of an important priming effect process. After 7 days, more than 30% of the whole DNA extracted were labelled, allowing an efficient separation of labelled from unlabelled DNA using density gradient centrifugation. The genetic structure of bacterial community, assessed by Automated Ribosomal Intergenic Spacer Analysis technique, was deduced from the ¹³ C‐ and ¹² C‐fractions of control and enriched conditions, over the time course of the experiment. Dynamics showed that wheat residues directly induced a rapid and durable stimulation of fresh organic matter (FOM) degrading populations ( ¹³ C), while specific soil organic matter (SOM) degrading populations ( ¹² C) seemed to be indirectly stimulated only at the early time point (t7d). After 14 days of incubations, 16S rRNA clone libraries were elaborated on ¹² C‐ and ¹³ C‐RNA extracted from enriched microcosms, as well as ¹² C‐RNA extracted from control condition. Stimulation of the β‐ and γ‐subgroups of proteobacteria, where numerous populations were previously described as r‐strategists or copiotrophic organisms, was recorded in the ¹³ C‐fraction. In the mean time, several phyla like Actinobacteria, Cyanobacteria, Candidate, Gemmatimonadetes and Planctomycetes were only present in ¹² C fractions. Surprisingly, several sequences affiliated to species characterized as oligotrophic organisms were retrieved in both types of fraction. Trophic relationships between soil bacteria involved in FOM and SOM degradation were discussed on the basis of different hypotheses of Fontaine and colleagues (2003) concerning the mechanisms of the priming effect induction.

Plants adopt a variety of life history strategies to succeed in the Earth's diverse environments. Using functional traits which are defined as “morphological, biochemical, physiological, or phonological” characteristics measurable at the individual level, plants are classified according to their species’ adaptative strategies, more than their taxonomy, from fast growing plant species to slower‐growing conservative species. These different strategies probably influence the input and output of carbon (C)‐resources, from the assimilation of carbon by photosynthesis to its release in the rhizosphere soil via root exudation. However, while root exudation was known to mediate plant‐microbe interactions in the rhizosphere, it was not used as functional trait until recently. Here, we assess whether root exudate levels are useful plant functional traits in the classification of plant nutrient‐use strategies and classical trait syndromes? For this purpose, we conducted an experiment with six grass species representing along a gradient of plant resource‐use strategies, from conservative species, characterized by low biomass nitrogen (N) concentrations and a long lifespans, to exploitative species, characterized by high rates of photosynthesis and rapid rates of N acquisition. Leaf and root traits were measured for each grass and root exudate rate for each planted soil sample. Classical trait syndromes in plant ecology were found for leaf and root traits, with negative relationships observed between specific leaf area and leaf dry matter content or between specific root length and root dry matter content. However, a new root trait syndrome was also found with root exudation levels correlating with plant resource‐use strategy patterns, specifically, between root exudation rate and root dry matter content. We therefore propose root exudation rate can be used as a key functional trait in plant ecology studies and plant strategy classification.