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.

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F-54501 Vandewre-les-Nancy, and URA CNRS 1977, Ecologie Microbienne, USBSE,The taxonomic position of nitrogen-fixing strains that were isolated from rhizosphere macerates of rice cultivated in the Binh Thanh region of Vietnam was determined by using polyphasic taxonomy. We determined the phylogenetic relationships of these organisms by performing DNA-rRNA hybridization experiments with a labeled rRNA probe from the type strain of Burkholderia cepacia, and we found that they belong to a single rRNA complex. Other members of this rRNA complex were also studied, and the N,-fixing strains were found to be closely related to B. cepacia. In addition, all members of the rRNA complex containing B. cepacia were studied by performing auxanographic and DNA-DNA hybridization experiments. Phenotypically and genotypically, the N,-fixing isolates constitute a single cluster together with two strains of clinical origin. These organisms constitute a new Burkholderia species, for which the name Burkholderia vietnamiensis is proposed; the type strain of this species is TVV75 (= LMG 10929). All members of this species can fix nitrogen. On the basis of our polyphasic taxonomy results and previously published data we concluded that the genus Burkholderia should be restricted to the following species: B. cepacia (the type species), Burkholderia mallei, Burkholderia pseudomallei, B. vietnamiensis, Burkholderia gladioli, Burkholderia caryophylli, Burkholderia plantarii, Burkholderia glumue, Burkholderia vandii, BurkhoMeria cocovenenans comb. nov., and Burkholderia andropogonis comb. nov. On the basis of genotypic and phenotypic results [Alcaligenes] eutrophus, [BurkhoZderia] solanacearum, and[Burkholderia] pickettii belong to two other clusters whose internal structures must be studied further.On the basis of the results of extensive phenotypic studies and DNA-rRNA and DNA-DNA hybridization experiments performed by Palleroni, Stanier, and their collaborators, the genus Pseudomonas was divided into five groups (24, 43, 46, 56). Additional phylogenetic data have shown that these groups are only very remotely related and that each of them contains species belonging to other genera (21-23, 70, 71). In addition to the former pseudomonads that have been shown to belong to the genus Xanthomonas and to a smaller group related to Pseudomonas diminuta and Pseudomonas vesicularis (21-23,43) classified in the recently described genus Brevundirnonas (52), three large groups of pseudomonads can be considered. Pseudomonas rRNA group I (43) is part of rRNA superfamily I1 (18) or the gamma subclass of the Proteobacteria (S), where it constitutes a separate rRNA complex (18,21,22,68); this group represents the authentic pseudomonads which are grouped with Pseudomonas aeruginosa, the type species (43). Although the internal relationships within this group have not been determined yet, it is evident that the genus Pseudomonas must be limited to this group and that all other Pseudomonas species have been generically misnamed as determined by phylogenetic da...

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 large collection of bacterial strains, immunotrapped from soil and from the wheat rhizoplane, was subjected to polyphasic taxonomy by examining various pheno-and genotypic parameters. Strains were grouped on (inter) repetitive extragenic palindromic DNA (REP) PCR profiles at the intraspecies level. Pheno-and genotypic characters were assessed for representatives from 13 different REP groups. Strains of nine REP groups constituting two physiological BIOLOG clusters fell in the coherent DNA-DNA reassociation group of Ochrobactrum anthropi. Strains of two REP groups constituting a separate BIOLOG cluster fell in the coherent DNA-DNA reassociation group of Ochrobactrum intermedium. Additional phenotypic characters differentiating O. anthropi and O. intermedium were found. REP group K strains constituted a different BIOLOG cluster, a separate DNA-DNA reassociation group and a distinct phylogenetic lineage in 16S rDNA homology analysis, indicating that REP group K strains represent a new species. Diagnostic phenotypic characters were found. Closest relatives were Ochrobactrum species. The name Ochrobactrum grignonense sp. nov. is proposed (type strain OgA9a T l LMG 18954 T l DSM 13338 T ). REP group J strains again constituted a different BIOLOG cluster, a separate DNA-DNA reassociation group and showed, as a biological particularity, a strict preference for the rhizoplane as habitat. Diagnostic phenotypic characters were found. This indicated that REP group J strains represent a further new species, although phylogenetic analyses using 16S rDNA homology were not able to separate the cluster of REP group J sequences significantly from 16S rDNA sequences of Ochrobactrum anthropi. The name Ochrobactrum tritici sp. nov. is proposed (type strain SCII24 T l LMG 18957 T l DSM 13340 T ).

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