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 13 CO 2 (99% of atom 13 C) 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 13 C-DNA and root DNA, whereas those assimilating SOM were identified from 12 C-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 collection of 75 strains of Pectobacterium chrysanthemi (including all biovars and pathovars) and the type strains of Brenneria paradisiaca (CFBP 4178T) and Pectobacterium cypripedii (CFBP 3613T) were studied by DNA–DNA hybridization, numerical taxonomy of 121 phenotypic characteristics, serology and 16S rRNA gene-based phylogenetic analyses. From analysis of 16S rRNA gene sequences, it was deduced that P. chrysanthemi strains and B. paradisiaca CFBP 4178T formed a clade distinct from the genera Pectobacterium and Brenneria; therefore, it is proposed to transfer all the strains to a novel genus, Dickeya gen. nov. By DNA–DNA hybridization, the strains of P. chrysanthemi were distributed among six genomic species: genomospecies 1 harbouring 16 strains of biovar 3 and four strains of biovar 8, genomospecies 2 harbouring 16 strains of biovar 3, genomospecies 3 harbouring two strains of biovar 6 and five strains of biovar 5, genomospecies 4 harbouring five strains of biovar 2, genomospecies 5 harbouring six strains of biovar 1, four strains of biovar 7 and five strains of biovar 9 and genomospecies 6 harbouring five strains of biovar 4 and B. paradisiaca CFBP 4178T. Two strains of biovar 3 remained unclustered. Biochemical criteria, deduced from a numerical taxonomic study of phenotypic characteristics, and serological reactions allowed discrimination of the strains belonging to the six genomic species. Thus, it is proposed that the strains clustered in these six genomic species be assigned to the species Dickeya zeae sp. nov. (type strain CFBP 2052T=NCPPB 2538T), Dickeya dadantii sp. nov. (type strain CFBP 1269T=NCPPB 898T), Dickeya chrysanthemi comb. nov. (subdivided into two biovars, bv. chrysanthemi and bv. parthenii), Dickeya dieffenbachiae sp. nov. (type strain CFBP 2051T=NCPPB 2976T), Dickeya dianthicola sp. nov. (type strain CFBP 1200T=NCPPB 453T) and Dickeya paradisiaca comb. nov., respectively.

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Iron-based nanoparticles have been proposed for an increasing number of biomedical or environmental applications although in vitro toxicity has been observed. The aim of this study was to understand the relationship between the redox state of iron-based nanoparticles and their cytotoxicity toward a Gram-negative bacterium, Escherichia coli. While chemically stable nanoparticles (gammaFe2O3) have no apparent cytotoxicity, nanoparticles containing ferrous and, particularly, zerovalent iron are cytotoxic. The cytotoxic effects appear to be associated principally with an oxidative stress as demonstrated using a mutant strain of E. coli completely devoid of superoxide dismutase activity. This stress can result from the generation of reactive oxygen species with the interplay of oxygen with reduced iron species (Fe(II) and/or Fe(0)) or from the disturbance of the electronic and/or ionic transport chains due to the strong affinity of the nanoparticles for the cell membrane.

To better understand adaptation to harsh conditions encountered in hot arid deserts, we report the first complete genome sequence and proteome analysis of a bacterium, Deinococcus deserti VCD115, isolated from Sahara surface sand. Its genome consists of a 2.8-Mb chromosome and three large plasmids of 324 kb, 314 kb, and 396 kb. Accurate primary genome annotation of its 3,455 genes was guided by extensive proteome shotgun analysis. From the large corpus of MS/MS spectra recorded, 1,348 proteins were uncovered and semiquantified by spectral counting. Among the highly detected proteins are several orphans and Deinococcus-specific proteins of unknown function. The alliance of proteomics and genomics high-throughput techniques allowed identification of 15 unpredicted genes and, surprisingly, reversal of incorrectly predicted orientation of 11 genes. Reversal of orientation of two Deinococcus-specific radiation-induced genes, ddrC and ddrH, and identification in D. deserti of supplementary genes involved in manganese import extend our knowledge of the radiotolerance toolbox of Deinococcaceae. Additional genes involved in nutrient import and in DNA repair (i.e., two extra recA, three translesion DNA polymerases, a photolyase) were also identified and found to be expressed under standard growth conditions, and, for these DNA repair genes, after exposure of the cells to UV. The supplementary nutrient import and DNA repair genes are likely important for survival and adaptation of D. deserti to its nutrient-poor, dry, and UV-exposed extreme environment.

Root-adhering soil (RAS) forms the immediate environment where plants take up water and nutrients for their growth. We report the effect of an exopolysaccharide (EPS)-producing rhizobacterium (strain YAS34) on the physical properties of sunflower (Helianthus annuus L.) RAS, associated with plant growth promotion, under both water stress and normal water supply conditions. Strain YAS34 was isolated as a major EPSproducing bacterium from the rhizoplane of sunflowers grown in a French dystric cambisol. Strain YAS34 was assigned to the Rhizobium genus by 16S ribosomal DNA gene sequencing. Inoculation of sunflower seeds and soil with strain YAS34 caused a significant increase in RAS per root dry mass (dm) (up to 100%) and a significant increase in soil macropore volume (12 to 60 m in diameter). The effect of inoculation on sunflower shoot dm (up to ؉50%) and root dm (up to ؉70%) was significant under both normal and water stress conditions. Inoculation with strain YAS34 modified soil structure around the root system, counteracting the negative effect of water deficit on growth. Using [15 N]nitrate, we showed that inoculation made the use of fertilizer more effective by increasing nitrogen uptake by sunflower plantlets.Soil structure has a strong impact on a range of processes influencing crop yield. The basic units of soil structure, named aggregates, comprise solid material and pores. These aggregates determine the mechanical and physical properties of soil such as retention and movement of water, aeration, and temperature (16). Aggregate formation is an important factor controlling germination and root growth (17).Several studies have shown that formation of stable aggregates strongly depends on both the nature and the content of organic matter (10,12,14,18,29). Unstable aggregates generally have a lower content of organic matter than do stable ones (24). Plant roots contribute to soil organic material, and thereby to soil aggregate stability, directly through the root material itself (36) and indirectly through stimulation of microbial activity in the rhizosphere (4). It is generally believed that microbial action on soil aggregation is due to the production of exopolysaccharides (EPS) (25). This is supported by experimental observations demonstrating that the amendment of soil with microbial EPS results in an increased soil aggregation (14, 26).The influence of microbes on aggregate stability has largely been studied in bulk soil (15,25,34). Relatively little attention has been paid to the influence of microorganisms, particularly EPS-producing rhizobacteria, on the aggregation of root-adhering soil (RAS) (3,36). Understanding the effects of microorganisms on RAS aggregation is important because RAS forms the immediate environment where plants take up water and nutrients for their growth. Factors liable to change the physical properties of RAS can be expected to modify absorption of water and minerals by plants. In previous work, we found that inoculation of wheat with Paenibacillus polymyxa (selected for its nit...

The phylogenetic diversity of prokaryotic communities exposed to arid conditions in the hot desert of Tataouine (south Tunisia) was estimated with a combination of a culture and - molecular-based analysis. Thirty-one isolates, representative of each dominant morphotypes, were affiliated to Actinobacteria, Firmicutes, Proteobacteria and the CFB group while none related to Archaea. Analysis of 16S rRNA gene libraries revealed the presence of species related to Bacteria and Archaea. Sequences related to Archaea were all affiliated to the non-thermophilic Crenarchaeota subgroup. Bacterial sequences were dominated by Proteobacteria, Actinobacteria and Acidobacteria; a few sequences were distributed among eight others phyla, including Thermus/Deinococcus relatives. A correlation between tolerance to desiccation and to radiation has been demonstrated for the radiotolerant bacteria Deinococcus radiodurans. Because bacteria living in the hot desert of Tataouine are one way or another tolerant to desiccation, we investigate whether they could also be tolerant to radiation. Exposition of soil samples to intense gamma radiation yields Bacillus, Thermus/Deinococcus and alpha-Proteobacteria relatives. Four of these strains correspond to radiotolerant species as revealed by evaluation of the resistance levels of the individual cultures. A detailed analysis of the resistance levels for two Thermus/Deinococcus and two alpha-Proteobacteria relatives revealed that they correspond to new radiotolerant species.

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 13 CO 2 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.