Numerous species of soil bacteria which flourish in the rhizosphere of plants, but which may grow in, on, or around plant tissues, stimulate plant growth by a plethora of mechanisms. These bacteria are collectively known as PGPR (plant growth promoting rhizobacteria). The search for PGPR and investigation of their modes of action are increasing at a rapid pace as efforts are made to exploit them commercially as biofertilizers. After an initial clarification of the term biofertilizers and the nature of associations between PGPR and plants (i.e., endophytic versus rhizospheric), this review focuses on the known, the putative, and the speculative modes-of-action of PGPR. These modes of action include fixing N2, increasing the availability of nutrients in the rhizosphere, positively influencing root growth and morphology, and promoting other beneficial plant–microbe symbioses. The combination of these modes of actions in PGPR is also addressed, as well as the challenges facing the more widespread utilization of PGPR as biofertilizers.

Plant growth promoting rhizobacteria as biofertilizers

Plants host distinct bacterial communities on and inside various plant organs, of which those associated with roots and the leaf surface are best characterized. The phylogenetic composition of these communities is defined by relatively few bacterial phyla, including Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. A synthesis of available data suggests a two-step selection process by which the bacterial microbiota of roots is differentiated from the surrounding soil biome. Rhizodeposition appears to fuel an initial substrate-driven community shift in the rhizosphere, which converges with host genotype–dependent finetuning of microbiota profiles in the selection of root endophyte assemblages. Substrate-driven selection also underlies the establishment of phyllosphere communities but takes place solely at the immediate leaf surface. Both the leaf and root microbiota contain bacteria that provide indirect pathogen protection, but root microbiota members appear to serve additional host functions through the acquisition of nutrients from soil for plant growth. Thus, the plant microbiota emerges as a fundamental trait that includes mutualism enabled through diverse biochemical mechanisms, as revealed by studies on plant growth–promoting and plant health–promoting bacteria.

Structure and functions of the bacterial microbiota of plants

Plant growth-promoting rhizobacteria (PGPR) are the rhizosphere bacteria that can enhance plant growth by a wide variety of mechanisms like phosphate solubilization, siderophore production, biological nitrogen fixation, rhizosphere engineering, production of 1-Aminocyclopropane-1-carboxylate deaminase (ACC), quorum sensing (QS) signal interference and inhibition of biofilm formation, phytohormone production, exhibiting antifungal activity, production of volatile organic compounds (VOCs), induction of systemic resistance, promoting beneficial plant-microbe symbioses, interference with pathogen toxin production etc. The potentiality of PGPR in agriculture is steadily increased as it offers an attractive way to replace the use of chemical fertilizers, pesticides and other supplements. Growth promoting substances are likely to be produced in large quantities by these rhizosphere microorganisms that influence indirectly on the overall morphology of the plants. Recent progress in our understanding on the diversity of PGPR in the rhizosphere along with their colonization ability and mechanism of action should facilitate their application as a reliable component in the management of sustainable agricultural system. The progress to date in using the rhizosphere bacteria in a variety of applications related to agricultural improvement along with their mechanism of action with special reference to plant growth-promoting traits are summarized and discussed in this review.

Plant growth-promoting rhizobacteria (PGPR): emergence in agriculture

Diverse bacterial species possess the ability to produce the auxin phytohormone indole-3-acetic acid (IAA). Different biosynthesis pathways have been identified and redundancy for IAA biosynthesis is widespread among plant-associated bacteria. Interactions between IAA-producing bacteria and plants lead to diverse outcomes on the plant side, varying from pathogenesis to phytostimulation. Reviewing the role of bacterial IAA in different microorganism–plant interactions highlights the fact that bacteria use this phytohormone to interact with plants as part of their colonization strategy, including phytostimulation and circumvention of basal plant defense mechanisms. Moreover, several recent reports indicate that IAA can also be a signaling molecule in bacteria and therefore can have a direct effect on bacterial physiology. This review discusses past and recent data, and emerging views on IAA, a well-known phytohormone, as a microbial metabolic and signaling molecule.

Indole-3-acetic acid in microbial and microorganism-plant signaling.

The rhizosphere is a complex environment where roots interact with physical, chemical and biological properties of soil. Structural and functional characteristics of roots contribute to rhizosphere processes and both have significant influence on the capacity of roots to acquire nutrients. Roots also interact extensively with soil microorganisms which further impact on plant nutrition either directly, by influencing nutrient availability and uptake, or indirectly through plant (root) growth promotion. In this paper, features of the rhizosphere that are important for nutrient acquisition from soil are reviewed, with specific emphasis on the characteristics of roots that influence the availability and uptake of phosphorus and nitrogen. The interaction of roots with soil microorganisms, in particular with mycorrhizal fungi and non-symbiotic plant growth promoting rhizobacteria, is also considered in relation to nutrient availability and through the mechanisms that are associated with plant growth promotion.

Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms

Auxin production by Azospirillum is believed to play a major role in the observed plant growth promoting effect. By using different genetically modified strains, the contribution of auxin biosynthesis by A. brasilense in altering root morphology was evaluated in a plate assay. Inoculation with the wild type strains A. brasilense Sp245 and Sp7 resulted in a strong decrease in root length and increase in root hair formation. This effect was abolished when inoculating with an ipdC mutant of A. brasilense. The ipdC gene encodes a key enzyme in the IPyA pathway of IAA synthesis by A. brasilense. On the other hand, the observed auxin effect was further enhanced by adding tryptophan, a precursor of IAA, to the plates and could be mimicked by replacing the Azospirillum cells by a particular concentration of IAA. Furthermore, particular mutants (rpoN, scrp) and transconjugants (extra copy of ipdC) of A. brasilense were tested in the plate assay. Together, these results confirm the important role of IAA produced by Azospirillum in altering root morphology and illustrate the power of combining genetic tools and bioassays to elucidate the mechanism of a beneficial Azospirillum-plant interaction.

Phytostimulatory effect of Azospirillum brasilense wild type and mutant strains altered in IAA production on wheat

Azospirilla are free-living rhizobacteria that are able to promote plant growth and increase yields in many crops of agronomic importance. It is assumed that the bacteria affect plant growth mainly by the production of plant growth promoting substances, which leads to an improvement in root development and an increase in the rate of water and mineral uptake. In the present review, we discuss the physiological responses of the plant roots to inoculation with Azospirillum, and report on field and greenhouse experiments carried out with these bacteria during 1994-2001 in Belgium, Uruguay, Mexico and Israel.

Responses of agronomically important crops to inoculation with Azospirillum

The production of phytohormones by plant-growth promoting rhizobacteria is considered to be an important mechanism by which these bacteria promote plant growth. In this study the importance of indole-3-acetic acid (IAA) produced by Azospirillum brasilense Sp245 in the observed plant growth stimulation was investigated by using Sp245 strains genetically modified in IAA production. Firstly wild-type A. brasilense Sp245 and an ipdC knock-out mutant which produces only 10% of wild-type IAA levels (Vande Broek et al., J Bacteriol 181:1338–1342, 1999) were compared in a greenhouse inoculation experiment for a number of plant parameters, thereby clearly demonstrating the IAA effect in plant growth promotion. Secondly, the question was addressed whether altering expression of the ipdC gene, encoding the key enzyme for IAA biosynthesis in A. brasilense, could also contribute to plant growth promotion. For that purpose, the endogenous promoter of the ipdC gene was replaced by either a constitutive or a plant-inducible promoter and both constructs were introduced into the wild-type strain. Based on a greenhouse inoculation experiment it was found that the introduction of these recombinant ipdC constructs could further improve the plant-growth promoting effect of A. brasilense. These data support the possibility of constructing Azospirillum strains with better performance in plant growth promotion.

Effects of Azospirillum brasilense indole-3-acetic acid production on inoculated wheat plants

Under the controlled conditions of the greenhouse and by varying some biotic and abiotic factors, we tried to identify some of the factors critical to obtain successful Azospirillum inoculation. Spring wheat and grain maize were inoculated with different concentrations of the wild type strains A. brasilense Sp245 and A. irakense KBC1, and grown in a substrate with varying concentrations of organic matter (OM) and N fertiliser. The inoculum concentration was one of the factors that influenced most the outcome of an inoculation experiment on wheat, with lower inoculum concentrations (105–106 cfu plant–1) stimulating root development and plant dry weight and higher inoculum concentrations (107–108 cfu plant–1) having no effect or sometimes even inhibiting root development. The effect of inoculation was most pronounced at low to intermediate N fertilisation levels, while the OM content of the substrate had no effect. Inoculation was found to affect early plant and root development, plant and root dry weight, grain yield and the N-uptake efficiency of plants. However, inoculation did not change the N concentration in plants or grains. In addition, a difference in the ability of both strains to stimulate plant growth and N uptake of wheat and maize was observed, with A. brasilense Sp245 having most effect on spring wheat and A. irakense KBC1 being more effective on grain maize. The significance of the obtained results for agriculture is discussed.

Effect of inoculation with wild type Azospirillum brasilense and A. irakense strains on development and nitrogen uptake of spring wheat and grain maize

To visualize rice root colonization by two Azospirillum species, A. irakense KBC1 was equipped with a plasmid expressing the enhanced green fluorescent protein (EGFP) and A. brasilense Sp7 was equipped with a plasmid expressing the enhanced yellow fluorescent protein (EYFP). In both cases, intensive fluorescence was observed under the epifluorescent microscope. Striking differences for association with roots of rice seedlings were observed between the two species: (i) A. irakense cells attached faster than A. brasilense to rice roots following inoculation; (ii) A. irakense attached to rice roots as vibroid cells, while A. brasilense occurred as rounded cyst-like cells; (iii) A. irakense cells were mainly found on root hairs, whereas A. brasilense cells were mainly concentrated on root surfaces. The two Azospirillum species obviously do not compete with each other for colonization of rice roots. These results demonstrate that the two Azospirillum species differ in their mode of rice root colonization. As the two Azospirillum species are extensively studied for unravelling mechanisms of plant root colonization and plant growth promotion, labelling with fluorescent protein is a useful additional tool for these studies.

Sofie Dobbelaere

Papers

Phytostimulatory effect of Azospirillum brasilense wild type and mutant strains altered in IAA production on wheat

Responses of agronomically important crops to inoculation with Azospirillum

Effects of Azospirillum brasilense indole-3-acetic acid production on inoculated wheat plants

Effect of inoculation with wild type Azospirillum brasilense and A. irakense strains on development and nitrogen uptake of spring wheat and grain maize

Use of green fluorescent protein to visualize rice root colonization by Azospirillum irakense and A. brasilense.