The soil represents heterogenous habitat in which the environmental conditions can differ markedly from one microhabitat to the next. These different micro-habitats in the soil correspond to a large number of ecological niches, in which different microorganisms are present. Therefore, the microbial biodiversity of the soil ecosystem is very high. Soil microorganisms with certain traits of interest have been isolated from soil and are already used as inoculants (Table 1). However, the natural diversity of the microbial community of the soil has been little explored until recently and soil microorganisms represent a useful source for the isolation of new strains that could be exploited as microbial inoculants in agriculture or for industrial applications.

Selective cultivation media can be used to discriminate between microorganisms present in the rhizosphere.
Bacteria currently used as agricultural inoculants in the field and new bacteria developed by genetic modification for improved performance.
Wild-type bacteria |
Crop inoculated | Usage |
Anabaena-Azolla |
Rice | Biofertilizer |
Bradyrhizobium japonicum | Forage and grain legumes | Biofertilizer |
Frankia spp. | Non-leguminous trees (Alnus) | Biofertilizer |
Bacillus subtilis and B.
thuringiensis | Different crops | Biopesticide |
Improved bacteria |
Modified trait | Goal of modification |
Agrobacterium radiobacter |
Deletion of transfer genes | Safe use for biological control of crown gall |
Clavibacter spp. | Addition of endotoxin from Bacillus thuringiensis | Biological control of insect damage to crops |
Bradyrhizobium japonicum |
Additional copies of nif gene | Increased nitrogen fixation |
Pseudomonas syringae | Deletion of ice nucleation gene |
Control of frost damage to crops |
Rhizobium meliloti | Additional copies of nif and/or dct genes | Increased nitrogen fixation |
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