Variability of the 16S–23S rRNA gene internal transcribed spacer inPseudomonas avellanaestrains

Abstract

The 16S-23S rRNA gene internal transcribed spacer region (ITS1) from 34 strains of Pseudomonas avellanae and some strains of Pseudomonas syringae pathovars was amplified and assessed by restriction fragment length polymorphism (RFLP) using 10 restriction enzymes. In addition, the ITS1 region of four representative P. avellanae strains was sequenced and compared by the neighbour-joining algorithm with that of P. syringae pathovars. Two main groups of P. avellanae strains were observed that did not correlate with their origin. The ITS1 region sequencing revealed a high similarity with the P. syringae complex. One group of P. avellanae strains showed high similarity to P. s. pv. actinidiae and P. s. pv. tomato; another group showed similarity with P. s. pv. tabaci and P. s. pv. glycinea. Two strains clustered with P. s. pv. pisi. The difficulties to unambiguously classify the strains associated with hazelnut decline in Greece and Italy are discussed.

Molecular identification and assessment of genetic diversity of fluorescent pseudomonads based on different polymerase chain reaction (PCR) methods

“…This was largely due to the limited number of bands in each group, which did not provide sufficient characters for confident differentiation of all genomovars (Dawson et al, 2002). In order to increase the number of comparable characters, other authors have found that ITS-PCR typing can be improved by the digestion of the PCR products with the restriction endonucleases (Natalini and Scortichini, 2007;Scarpellini et al, 2004).…”

Intercistronic heterogeneity of the 16S–23S rRNA spacer region among Pseudomonas strains isolated from subterranean seeds of hog peanut (Amphicarpa bracteata)

“…ITS1 varies considerably among different operons (Naimi et al, 1997;Gurtler, 1999;Iteman et al, 2000) without a remarkable length difference. In the genus Pseudomonas, intercistronic heterogeneity of the ITS1 reported to date is primarily due to insertions and/or deletions of nucleotide blocks outside the tRNA genes (Milyutina et al, 2004;Natalini & Scortichini, 2007). Milyutina et al (2004) identified eight ITS1 types among 14 strains of P. syringae and P. fluorescens with similar sequence lengths except for one strain exhibiting about 8 % length difference among its copies.…”

Reverse Transcription of 16S rRNA To Monitor Ribosome-Synthesizing Bacterial Populations in the Environment

“…This suggests that the DHPLC method is able to differentiate bacteria at the species level based on the pre-16S rRNA sequences, which is an important complement for 16S rRNA gene sequencing for the study of bacterial diversity and phylogeny. Studies have shown that pre-16S rRNA genes exhibit higher degrees of sequence and length variation that can be exploited to compare closely related bacterial strains than 16S rRNA genes (13,25). Second, most bacteria can harbor multiple rrn operons which have sequence heterogeneities.…”

“…could be used for in situ measurement of nitrite-oxidizing activity to improve implementation of traditional nitrification (17). Furthermore, pre-16S 3Ј rRNA sequence information has been very important in taxonomic and ecological studies (16) and has been used to differentiate closely related strains in a broad diversity of bacterial genera and species, such as Sphingomonas (37), Frankia (15), and Pseudomonas avellanae (25).…”