Polish Journal of Microbiology 2014, Vol. 63, No 3, 291–298 ORIGINAL PAPER Introduction Progress in organic agriculture makes it necessary to develop new bioproducts that are suitable for the cul- tivation of fruit plants and contribute at the same time to improving the quality of soils under perennial crops, such as fruit orchards. To develop such bioproducts, it is necessary to acquire and isolate strains of beneficial bacteria from the soil environment. Among the bacteria that produce favourable efects on plants there are many strains belonging to the genus Pseudomonas. It has been established that strains of Pseudomonas spp. are important microorganisms in the rhizosphere, and that is why considerable research work is being conducted to exploit the potential of these bacteria for improving the quality of soils and the growth, yielding and protection of plants (Choudhary et al., 2009). Pseudomonas spp. are aerobic, Gram-negative bac- teria, ubiquitous in agricultural soils, and well-adapted to growing in the rhizosphere (Weller, 2007). Bacteria of the genus Pseudomonas are oten found in cultivated soils, including the rhizosphere of plants, or in other substrates, such as oil-contaminated sand (McSpadden Gardener et al., 2000; Mavrodi et al., 2001; Susilowati et al., 2010; Mulet et al., 2011). Pseudomonas bacteria have many valuable attributes that make them highly suitable for use in bioproducts. hese bacteria quickly colonize the rhizosphere and plant roots, produce bioactive metabolites, such as antibiotics and sidero- phores (compounds stimulating plant growth), inhibit the growth of pathogenic microorganisms, increase the resistance of plants to diseases, and, moreover, they can be multiplied in the laboratory (Weller, 2007; Choud- hary et al., 2009). Pseudomonas bacteria are character- ized by a broad spectrum of beneficial efects on plants; their action is oten synergistic with other rhizosphere bacteria and mycorrhizal fungi beneficial to plants. Pseudomonas luorescens and Pseudomonas putida strains have the ability to promote plant growth and drive developmental plasticity in the roots of Arabidop- sis thaliana by inhibiting primary root elongation and promoting the formation of lateral roots and root hairs (Zamioudis et al., 2013). Pseudomonas bacteria have been found to stimulate the growth and increase fruit Identification and Assessment of Genetic Similarity of Soil Bacterial Isolates of Pseudomonas spp. Using Molecular Techniques ANNA LISEK*, LIDIA SAS PASZT AND PAWEŁ TRZCIŃSKI Research Institute of Horticulture, Skierniewice, Poland Submitted 12 March 2014, revised 23 May 2014, accepted 25 May 2014 Abstract Bacteria of the genus Pseudomonas are oten components of bioproducts designed to enhance the condition of the soil and plants. he use of Pseudomonas bacteria in bioproducts must be preceded by the acquisition, characterization and selection of beneficial strains living in the soil. A prerequisite for the selection of bacterial strains for use in bioproducts is to be able to identify the isolates rapidly and accurately. To identify and diferentiate 15 bacterial isolates obtained from the soil surrounding the roots of sour cherry trees and to assess their genetic similarity, the rep-PCR technique and restriction analysis of the 16S rRNA gene and the 16S-ITS-23S rRNA operon were used. In addition, a sequence analysis of the 16S rRNA gene was performed. he analyses made it possible to divide the isolates into four clusters and to confirm their affiliation with the Pseudomonas species. RFLP analysis of the 16S-ITS-23S rRNA operon enabled greater diferentiation of the isolates than RFLP of the 16S rRNA gene. he greatest diferentiation of isolates within the clusters was obtained ater using the rep-PCR technique. However, none of the techniques was able to discriminate all the isolates, which indicates very high genetic similarity of the Pseudomonas isolates found in the same sample of soil from around the roots of sour cherry trees. he tests performed will find application for distinguishing and identifying Pseudomonas strains collected from the soil in order to select the most valuable bacterial strains that produce beneficial efects on plants. Key words: 16S rRNA, 16S-ITS-23S rRNA operon, RFLP, rep-PCR * Corresponding author: A. Lisek, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland; e-mail: anna.lisek@inhort.pl