Wild Wheat Rhizosphere-Associated Plant Growth-Promoting Bacteria Exudates: Effect on Root Development in Modern Wheat and Composition.

Diazotrophic bacteria isolated from the rhizosphere of a wild wheat ancestor, grown from its refuge area in the Fertile Crescent, were found to be efficient Plant Growth-Promoting Rhizobacteria (PGPR), upon interaction with an elite wheat cultivar. In nitrogen-starved plants, they increased the amount of nitrogen in the seed crop (per plant) by about twofold. A bacterial growth medium was developed to investigate the effects of bacterial exudates on root development in the elite cultivar, and to analyze the exo-metabolomes and exo-proteomes. Altered root development was observed, with distinct responses depending on the strain, for instance, with respect to root hair development. A first conclusion from these results is that the ability of wheat to establish effective beneficial interactions with PGPRs does not appear to have undergone systematic deep reprogramming during domestication. Exo-metabolome analysis revealed a complex set of secondary metabolites, including nutrient ion chelators, cyclopeptides that could act as phytohormone mimetics, and quorum sensing molecules having inter-kingdom signaling properties. The exo-proteome-comprised strain-specific enzymes, and structural proteins belonging to outer-membrane vesicles, are likely to sequester metabolites in their lumen. Thus, the methodological processes we have developed to collect and analyze bacterial exudates have revealed that PGPRs constitutively exude a highly complex set of metabolites; this is likely to allow numerous mechanisms to simultaneously contribute to plant growth promotion, and thereby to also broaden the spectra of plant genotypes (species and accessions/cultivars) with which beneficial interactions can occur.

Impact of Wheat/Faba Bean Mixed Cropping or Rotation Systems on Soil Microbial Functionalities.

Cropping systems based on carefully designed species mixtures reveal many potential advantages in terms of enhancing crop productivity, reducing pest and diseases, and enhancing ecological services. Associating cereals and legume production either through intercropping or rotations might be a relevant strategy of producing both type of culture, while benefiting from combined nitrogen fixed by the legume through its symbiotic association with nitrogen-fixing bacteria, and from a better use of P and water through mycorrhizal associations. These practices also participate to the diversification of agricultural productions, enabling to secure the regularity of income returns across the seasonal and climatic uncertainties. In this context, we designed a field experiment aiming to estimate the 2 years impact of these practices on wheat yield and on soil microbial activities as estimated through Substrate Induced Respiration method and mycorrhizal soil infectivity (MSI) measurement. It is expected that understanding soil microbial functionalities in response to these agricultural practices might allows to target the best type of combination, in regard to crop productivity. We found that the tested cropping systems largely impacted soil microbial functionalities and MSI. Intercropping gave better results in terms of crop productivity than the rotation practice after two cropping seasons. Benefits resulting from intercrop should be highly linked with changes recorded on soil microbial functionalities.

Impact of the energy crop Jatropha curcas L. on the composition of rhizobial populations nodulating cowpea (Vigna unguiculata L.) and acacia (Acacia seyal L.).

Jatropha curcas, a Euphorbiaceae species that produces many toxicants, is increasingly planted as an agrofuel plant in Senegal. The purpose of this study was to determine whether soil priming induced by J. curcas monoculture could alter the rhizobial populations that nodulate cowpea and acacia, two locally widespread legumes. Soil samples were transferred into a greenhouse from three fields previously cultivated with Jatropha for 1, 2, and 15 years, and the two trap legumes were grown in them. Control soil samples were also taken from adjacent Jatropha-fallow plots. Both legumes tended to develop fewer but larger nodules when grown in Jatropha soils. Nearly all the nifH sequences amplified from nodule DNA were affiliated to the Bradyrhizobium genus. Only sequences from Acacia seyal nodules grown in the most recent Jatropha plantation were related to the Mesorhizobium genus, which was much a more conventional finding on A. seyal than the unexpected Bradyrhizobium genus. Apart from this particular case, only minor differences were found in the respective compositions of Jatropha soil versus control soil rhizobial populations. Lastly, the structure of these rhizobial populations was systematically imbalanced owing to the overwhelming dominance of a very small number of nifH genotypes, some of which were identical across soil types or even sites. Despite these weak and sparse effects on rhizobial diversity, future investigations should focus on the characterization of the nitrogen-fixing abilities of the predominant rhizobial strains.

[Native plant resources to optimize the performances of forest rehabilitation in Mediterranean and tropical environment: some examples of nursing plant species that improve the soil mycorrhizal potential]. / Des ressources végétales endémiques pour optimiser durablement les opérations de réhabilitation du couvert forestier en milieu méditerranéen et tropical : exemple des plantes facilitatrices vectrices de propagation des champignons mycorhiziens.

The overexploitation of natural resources, resulting in an increased need for arable lands by local populations, causes a serious dysfunction in the soil's biological functioning (mineral deficiency, salt stress, etc.). This dysfunction, worsened by the climatic conditions (drought), requires the implementation of ecological engineering strategies allowing the rehabilitation of degraded areas through the restoration of essential ecological services. The first symptoms of weathering processes of soil quality in tropical and Mediterranean environments result in an alteration of the plant cover structure with, in particular, the pauperization of plant species diversity and abundance. This degradation is accompanied by a weakening of soils and an increase of the impact of erosion on the surface layer resulting in reduced fertility of soils in terms of their physicochemical characteristics as well as their biological ones (e.g., soil microbes). Among the microbial components particularly sensitive to erosion, symbiotic microorganisms (rhizobia, Frankia, mycorrhizal fungi) are known to be key components in the main terrestrial biogeochemical cycles (C, N and P). Many studies have shown the importance of the management of these symbiotic microorganisms in rehabilitation and revegetation strategies of degraded environments, but also in improving the productivity of agrosystems. In particular, the selection of symbionts and their inoculation into the soil were strongly encouraged in recent decades. These inoculants were selected not only for their impact on the plant, but also for their ability to persist in the soil at the expense of the residual native microflora. The performance of this technique was thus evaluated on the plant cover, but its impact on soil microbial characteristics was totally ignored. The role of microbial diversity on productivity and stability (resistance, resilience, etc.) of eco- and agrosystems has been identified relatively recently and has led to a questioning of the conceptual bases of controlled inoculation in sustainable land management. It has been suggested that the environmental characteristics of the area to rehabilitate should be taken into account, and more particularly its degradation level in relation to the threshold of ecological resilience. This consideration should lead to the optimization of the cultural practices to either (i) restore the original properties of an ecosystem in case of slightly degraded environments or (ii) transform an ecosystem in case of highly degraded soils (e.g., mine soils). In this chapter, we discuss, through various examples of experiments conducted in tropical and Mediterranean areas, the performance of different strategies to manage the microbial potential in soils (inoculation of exotic vs. native species, inoculation or controlled management potential microbial stratum via aboveground vegetation, etc.) based on the level of environmental degradation.

Effects of Azospirillum brasilense with genetically modified auxin biosynthesis gene ipdC upon the diversity of the indigenous microbiota of the wheat rhizosphere.

The phytostimulatory properties of Azospirillum inoculants, which entail production of the phytohormone indole-3-acetic acid (IAA), can be enhanced by genetic means. However, it is not known whether this could affect their interactions with indigenous soil microbes. Here, wheat seeds were inoculated with the wild-type strain Azospirillum brasilense Sp245 or one of three genetically modified (GM) derivatives and grown for one month. The GM derivatives contained a plasmid vector harboring the indole-3-pyruvate/phenylpyruvate decarboxylase gene ipdC (IAA production) controlled either by the constitutive promoter PnptII or the root exudate-responsive promoter PsbpA, or by an empty vector (GM control). All inoculants displayed equal rhizosphere population densities. Only inoculation with either ipdC construct increased shoot biomass compared with the non-inoculated control. At one month after inoculation, automated ribosomal intergenic spacer analysis (ARISA) revealed that the effect of the PsbpA construct on bacterial community structure differed from that of the GM control, which was confirmed by 16S rDNA-based denaturing gradient gel electrophoresis (DGGE). The fungal community was sensitive to inoculation with the PsbpA construct and especially the GM control, based on ARISA data. Overall, fungal and bacterial communities displayed distinct responses to inoculation of GM A. brasilense phytostimulators, whose effects could differ from those of the wild-type.

Quantification of denitrifying bacteria in soils by nirK gene targeted real-time PCR.

Denitrification, the reduction of nitrate to nitrous oxide or dinitrogen, is the major biological mechanism by which fixed nitrogen returns to the atmosphere from soil and water. Microorganisms capable of denitrification are widely distributed in the environment but little is known about their abundance since quantification is performed using fastidious and time-consuming MPN-based approaches. We used real-time PCR to quantify the denitrifying nitrite reductase gene (nirK), a key enzyme of the denitrifying pathway catalyzing the reduction of soluble nitrogen oxide to gaseous form. The real-time PCR assay was linear over 7 orders of magnitude and sensitive down to 10(2) copies by assay. Real-time PCR analysis of different soil samples showed nirK densities of 9.7x10(4) to 3.9x10(6) copies per gram of soil. Soil real-time PCR products were cloned and sequenced. Analysis of 56 clone sequences revealed that all cloned real-time PCR products exhibited high similarities to previously described nirK. However, phylogenetic analysis showed that most of environmental sequences are not related to nirK from cultivated denitrifiers.

Symbiotic microorganisms, a key for ecological success and protection of plants.

Plant-associated microbial diversity encompasses symbionts, protecting their host against various aggressions. Mycorrhizal and rhizospheric microorganisms buffer effects of soil toxic compounds and soil-borne pathogens. Endophytic bacteria and fungi, some of which are vertically inherited through seeds, take part in plant protection by acting directly on aggressive factors (mainly pathogens and herbivores) or by enhancing plant responses. Plant protective microbial symbionts determine the ecological success of plants; they drastically modify plant communities and related trophic webs. This review suggests approaches to improve the inventory of diversity and functions of in situ plant-associated microorganisms.