Intensive cultivation of plants in the monoculture field system in order to feed the continuously growing human population creates a need for their protection from the variety of natural competitors such as: bacteria, fungi, insects as well as other plants. The increase in the use of chemical substances in the 20th century has brought many effective solutions for the agriculture. However, it was extremely difficult to obtain a substance, which would be directed solely against a specific plant pathogen and would not be harmful for the environment. In the late 1900's scientists began trying to use natural antagonisms between resident soil organism to protect plants. This phenomenon was named biocontrol. Biological control of plants by microorganisms is a very promising alternative to an extended use of pesticides, which are often expensive and accumulate in plants or soil, having adverse effects on humans. Nonpathogenic soil bacteria living in association with roots of higher plants enhance their adaptive potential and, moreover, they can be beneficial for their growth. Here, we present the current status of the use of Bacillus subtilis in biocontrol. This prevalent inhabitant of soil is widely recognized as a powerful biocontrol agent. Naturally present in the immediate vicinity of plant roots, B. subtilis is able to maintain stable contact with higher plants and promote their growth. In addition, due to its broad host range, its ability to form endospores and produce different biologically active compounds with a broad spectrum of activity, B. subtilis as well as other Bacilli are potentially useful as biocontrol agents.

The ability to colonize the host plants’ rhizospheres is a crucial feature to study in the case of Plant Growth Promoting Rhizobacteria (PGPRs) with potential agricultural applications. In this work, we have created GFP-tagged derivatives of three candidate PGPRs: Bacillus subtilis MB73/2, Pseudomonas sp. P482 and Ochrobactrum sp. A44. The presence of these strains in the rhizosphere of soil-grown potato (Solanum tuberosum L.) was detected with a classical fluorescence microscope and a confocal laser scanning microscope (CLSM). In this work, we have used a broad-field-of-view CLMS device, dedicated to in vivo analysis of macroscopic objects, equipped with an automated optical zoom system and tunable excitation and detection spectra. We show that features of this type of CLSM microscopes make them particularly well suited to study root colonization by microorganisms. To facilitate the detection of small and scattered bacterial populations, we have developed a fast and user-friendly enrichment method for root sample preparation. The described method, thanks to the in situ formation of mini-colonies, enables visualization of bacterial colonization sites on large root fragments. This approach can be easily modified to study colonization patterns of other fluorescently tagged strains. Additionally, dilution plating of the root extracts was performed to estimate the cell number of MB73/2, P482 and A44 in the rhizosphere of the inoculated plants.