The rhizosphere supports the development and activity of a huge and diversified microbial community, including microorganisms capable to promote plant growth. Among the latter, plant growth-promoting rhizobacteria (PGPR) colonize roots of monocots and dicots, and enhance plant growth by direct and indirect mechanisms. Modification of root system architecture by PGPR implicates the production of phytohormones and other signals that lead, mostly, to enhanced lateral root branching and development of root hairs. PGPR also modify root functioning, improve plant nutrition and influence the physiology of the whole plant. Recent results provided first clues as to how PGPR signals could trigger these plant responses. Whether local and/or systemic, the plant molecular pathways involved remain often unknown. From an ecological point of view, it emerged that PGPR form coherent functional groups, whose rhizosphere ecology is influenced by a myriad of abiotic and biotic factors in natural and agricultural soils, and these factors can in turn modulate PGPR effects on roots. In this paper, we address novel knowledge and gaps on PGPR modes of action and signals, and highlight recent progress on the links between plant morphological and physiological effects induced by PGPR. We also show the importance of taking into account the size, diversity, and gene expression patterns of PGPR assemblages in the rhizosphere to better understand their impact on plant growth and functioning. Integrating mechanistic and ecological knowledge on PGPR populations in soil will be a prerequisite to develop novel management strategies for sustainable agriculture.

Research on legume nodule metabolism has contributed greatly to our knowledge of primary carbon and nitrogen metabolism in plants in general, and in symbiotic nitrogen fixation in particular. However, most previous studies focused on one or a few genes/enzymes involved in selected metabolic pathways in many different legume species. We utilized the tools of transcriptomics and metabolomics to obtain an unprecedented overview of the metabolic differentiation that results from nodule development in the model legume, Lotus japonicus. Using an array of more than 5000 nodule cDNA clones, representing 2500 different genes, we identified approximately 860 genes that were more highly expressed in nodules than in roots. One-third of these are involved in metabolism and transport, and over 100 encode proteins that are likely to be involved in signalling, or regulation of gene expression at the transcriptional or post-transcriptional level. Several metabolic pathways appeared to be co-ordinately upregulated in nodules, including glycolysis, CO(2) fixation, amino acid biosynthesis, and purine, haem, and redox metabolism. Insight into the physiological conditions that prevail within nodules was obtained from specific sets of induced genes. In addition to the expected signs of hypoxia, numerous indications were obtained that nodule cells also experience P-limitation and osmotic stress. Several potential regulators of these stress responses were identified. Metabolite profiling by gas chromatography coupled to mass spectrometry revealed a distinct metabolic phenotype for nodules that reflected the global changes in metabolism inferred from transcriptome analysis.

Hemoglobins are ubiquitous in nature and among the best-characterized proteins. Genetics has revealed crucial roles for human hemoglobins, but similar data are lacking for plants. Plants contain symbiotic and nonsymbiotic hemoglobins; the former are thought to be important for symbiotic nitrogen fixation (SNF). In legumes, SNF occurs in specialized organs, called nodules, which contain millions of nitrogen-fixing rhizobia, called bacteroids. The induction of nodule-specific plant genes, including those encoding symbiotic leghemoglobins (Lb), accompanies nodule development. Leghemoglobins accumulate to millimolar concentrations in the cytoplasm of infected plant cells prior to nitrogen fixation and are thought to buffer free oxygen in the nanomolar range, avoiding inactivation of oxygen-labile nitrogenase while maintaining high oxygen flux for respiration. Although widely accepted, this hypothesis has never been tested in planta. Using RNAi, we abolished symbiotic leghemoglobin synthesis in nodules of the model legume Lotus japonicus. This caused an increase in nodule free oxygen, a decrease in the ATP/ADP ratio, loss of bacterial nitrogenase protein, and absence of SNF. However, LbRNAi plants grew normally when fertilized with mineral nitrogen. These data indicate roles for leghemoglobins in oxygen transport and buffering and prove for the first time that plant hemoglobins are crucial for symbiotic nitrogen fixation.

Symbiotic nitrogen fixation (SNF) in legume root nodules requires differentiation and integration of both plant and bacterial metabolism. Classical approaches of biochemistry, molecular biology, and genetics have revealed many aspects of primary metabolism in legume nodules that underpin SNF. Functional genomics approaches, especially transcriptomics and proteomics, are beginning to provide a more holistic picture of the metabolic potential of nodules in model legumes like Medicago truncatula and Lotus japonicus. To extend these approaches, we have established protocols for nonbiased measurement and analysis of hundreds of metabolites from L. japonicus, using gas chromatography coupled with mass spectrometry. Following creation of mass spectral tag libraries, which represent both known and unknown metabolites, we measured and compared relative metabolite levels in nodules, roots, leaves, and flowers of symbiotic plants. Principal component analysis of the data revealed distinct metabolic phenotypes for the different organs and led to the identification of marker metabolites for each. Metabolites that were enriched in nodules included: octadecanoic acid, asparagine, glutamate, homoserine, cysteine, putrescine, mannitol, threonic acid, gluconic acid, glyceric acid-3-P, and glycerol-3-P. Hierarchical cluster analysis enabled discrimination of 10 groups of metabolites, based on distribution patterns in diverse Lotus organs. The resources and tools described here, together with ongoing efforts in the areas of genome sequencing, and transcriptome and proteome analysis of L. japonicus and Mesorhizobium loti, should lead to a better understanding of nodule metabolism that underpins SNF.The legume family comprises approximately 700 genera with more than 18,000 species, which occupy niches in almost every environment on earth (Polhill et al., 1981;Doyle and Luckow, 2003). A key to the success of this family was the evolution of mutualistic symbioses with bacteria of the family Rhizobiaceae, which enabled early legumes to utilize atmospheric N 2 as a source of nitrogen, especially when colonizing soils lacking mineral or organic nitrogen. Today, symbiotic nitrogen fixation (SNF) by rhizobia in legumes takes place in specialized plant organs called nodules. Nodules develop from cortical cells of the root or stem after contact with rhizobia in the soil (Brewin, 1991). Mature, nitrogen-fixing nodules consist of several layers of uninfected plant cells surrounding a central zone of infected and noninfected plants cells. Infected plant cells typically contain thousands of differentiated, nitrogen-fixing rhizobia, called bacteroids, which are separated from the cytoplasm, either individually or in small groups, by a unique plant membrane called the peribacteroid or symbiosome membrane (SM; Roth et al., 1988;Udvardi and Day, 1997). Microaerobic conditions within legume nodules result from restricted oxygen influx across the outer cell layers of nodules, binding and transport of oxygen by leghemoglobin in the cytoplasm of plant ce...

Legume plants have an exceptional capacity for association with microorganisms, ranging from largely nonspecific to very specific interactions. Legume-rhizobial symbiosis results in major developmental and metabolic changes for both the microorganism and host, while providing the plant with fixed nitrogen. A complex signal exchange leads to the selective rhizobial colonization of plant cells within nodules, new organs that develop on the roots of host plants. Although the nodulation mechanism is highly specific, it involves the same subset of plant phytohormones, namely auxin, cytokinin, and ethylene, which are required for root development. In addition, nodulation triggered by the rhizobia affects the development of the host root system, indicating that the microorganism can alter host developmental pathways. Nodulation by rhizobia is a prime example of how microorganisms and plants have coevolved and exemplifies how microbial colonization may affect plant developmental pathways.

Symbiotic nitrogen fixation (SNF) by intracellular rhizobia within legume root nodules requires the exchange of nutrients between host plant cells and their resident bacteria. Little is known at the molecular level about plant transporters that mediate such exchanges. Several mutants of the model legume Lotus japonicus have been identified that develop nodules with metabolic defects that cannot fix nitrogen efficiently and exhibit retarded growth under symbiotic conditions. Mapbased cloning of defective genes in two such mutants, sst1-1 and sst1-2 (for symbiotic sulfate transporter), revealed two alleles of the same gene. The gene is expressed in a nodule-specific manner and encodes a protein homologous with eukaryotic sulfate transporters. Full-length cDNA of the gene complemented a yeast mutant defective in sulfate transport. Hence, the gene was named Sst1. The sst1-1 and sst1-2 mutants exhibited normal growth and development under nonsymbiotic growth conditions, a result consistent with the nodule-specific expression of Sst1. Data from a previous proteomic study indicate that SST1 is located on the symbiosome membrane in Lotus nodules. Together, these results suggest that SST1 transports sulfate from the plant cell cytoplasm to the intracellular rhizobia, where the nutrient is essential for protein and cofactor synthesis, including nitrogenase biosynthesis. This work shows the importance of plant sulfate transport in SNF and the specialization of a eukaryotic transporter gene for this purpose.

SummaryDisruption of the TRH1 potassium transporter impairs root hair development in Arabidopsis, and also affects root gravitropic behaviour. Rescue of these morphological defects by exogenous auxin indicates a link between TRH1 activity and auxin transport. In agreement with this hypothesis, the rate of auxin translocation from shoots to roots and efflux of ] was also affected by trh1 mutation. We conclude that the TRH1 carrier is an important part of auxin transport system in Arabidopsis roots.

Both root architecture and plant N nutrition are altered by inoculation with the plant growth-promoting rhizobacteria (PGPR) Phyllobacterium strain STM196. It is known that NO3- and N metabolites can act as regulatory signals on root development and N transporters. In this study, we investigate the possible interrelated effects on root development and N transport. We show that the inhibition of Arabidopsis lateral root growth by high external NO3- is overridden by Phyllobacterium inoculation. However, the leaf NO3- pool remained unchanged in inoculated plants. By contrast, the Gln root pool was reduced in inoculated plants. Unexpectedly, NO3- influx and the expression levels of AtNRT1.1 and AtNRT2.1 genes coding for root NO3- transporters were also decreased after 8 days of Phyllobacterium inoculation. Although the mechanisms by which PGPR exert their positive effects remain unknown, our data show that they can optimize plant development independently from N supply, thus alleviating the regulatory mechanisms that operate in axenic conditions. In addition, we found that Phyllobacterium sp. elicited a very strong induction of AtNRT2.5 and AtNRT2.6, both genes preferentially expressed in the shoots whose functions are unknown.