Pseudomonas cyclaminis sp. nov., a pathogen causing bacterial bud blight of cyclamen in Japan

Abstract

Five phytopathogenic bacterial strains, MAFF 301449T, MAFF 301450, MAFF 301451, MAFF 301452, and MAFF 301453, which were isolated from bud blight lesions of cyclamen (Cyclamen persicum Mill.) in Miyagi, Japan, were subjected to polyphasic taxonomic characterisation. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one to five polar flagella, and rod-shaped. Analysis of 16S rRNA gene sequences showed that they belong to the genus Pseudomonas , with Pseudomonas extremaustralis 14-3T (99.79 % sequence similarity), Pseudomonas trivialis DSM 14937T (99.79 %), Pseudomonas poae DSM 14936T (99.72 %), and Pseudomonas antarctica CMS 35T (99.72 %) as their relatives. The genomic DNA G+C content was 60.3 mol% and the major fatty acids (>5 % of the total fatty acids) were C16 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), and C17 : 0 cyclo. Phylogenetic analysis using the rpoD gene sequences and phylogenomic analyses based on the whole genome sequences demonstrated that the strains are members of the Pseudomonas fluorescens subgroup, but form a monophyletic and robust clade separated from their relatives. Average nucleotide identity and digital DNA–DNA hybridisation analyses with the closely related Pseudomonas species corroborated their novel species status. The strains were differentiated from their relatives by phenotypic characteristics, pathogenicity towards cyclamen, cellular fatty acid composition, and whole-cell MALDI-TOF mass spectrometry profiles. Based on the phenotypic, chemotaxonomic, and genotypic data obtained, we conclude that the strains represent a novel Pseudomonas species, for which we propose the name Pseudomonas cyclaminis sp. nov.; the type strain is MAFF 301449T (=ICMP 23720T).

Pseudomonas petroselini sp. nov., a pathogen causing bacterial rot of parsley in Japan

“…The presence of C 10:0 3OH and C 12:0 3OH in MAFF 311094 T was consistent with the fatty acid profiles reported for the Pseudomonas species [11]. The fatty acid components (Table 3) observed were similar between MAFF 311094 T and the type strains of its phylogenetic neighbours [6,26,27]. However, C 19:0 cyclo ω8c was not detected in P. sivasensis, P. kitaguniensis and P. antarctica but was detected in MAFF 311094 T , P. cyclaminis and P. extremaustralis.…”

“…Data for P. petroselini were obtained in this study. The other data were from Sawada et al[6], Sawada et al[26] and Duman et al[27], under the same analytical conditions used in this study. tr, Trace amount (<1%); -, not detected.…”

Pseudomonas lactucae sp. nov., a pathogen causing bacterial rot of lettuce in Japan

“…grimontii and P. extremaustralis , which were found to be closely related to the lettuce isolates by the genome analyses (Figs 1 and 2, ), the data of their phenotypic characteristics obtained in our previous studies [24, 25] were used for comparison with those of the isolates (). The strains were cultured routinely at 27 °C and checked for purity on standard methods agar plates (Nissui).…”

“…These six strains were selected for comparison with the isolates in the subsequent analyses, because they showed the highest 16S rRNA gene sequence similarities to sequences of the isolates (Table 1). In addition, for P. grimontii and P. extremaustralis, which were found to be closely related to the lettuce isolates by the genome analyses (Figs 1 and 2, Table 1), the data of their phenotypic characteristics obtained in our previous studies [24,25] were used for comparison with those of the isolates (Table 2). The strains were cultured routinely at 27 °C and checked for purity on standard methods agar plates (Nissui).…”

“…Their nucleotide sequences were then subjected to concatenation, followed by multiple alignment using mafft [20] and elimination of poorly aligned positions and divergent regions using Gblocks [21] with default parameters. Based on the resultant alignment (total alignment length was 955 853 bp), a maximum-likelihood tree was inferred with RAxML [22] using the general time-reversible substitution model and a gamma model of rate heterogeneity were obtained from our previous studies [24,25], under the same analytical conditions used in this study. Characteristics have been scored as follows: +, positive reaction; -, negative reaction; w, weakly positive reaction; nd, no data.…”