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

Abstract

Phytopathogenic bacterial strains (MAFF 311094T, MAFF 311095, MAFF 311096 and MAFF 311097), which were isolated from rot lesions of parsley (Petroselinum crispum) sampled in Miyagi, Japan, were subjected to polyphasic characterization to determine their taxonomic position. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one or two polar flagella and rod-shaped. The 16S rRNA gene sequences analyses revealed that the strains belong to the genus Pseudomonas , exhibiting the highest sequence similarity to Pseudomonas sivasensis P7T (99.93% sequence similarity), Pseudomonas cyclaminis MAFF 301449T (99.93 %), Pseudomonas extremaustralis 14-3T (99.86 %), Pseudomonas kitaguniensis MAFF 212408T (99.86 %) and Pseudomonas antarctica CMS 35T (99.79 %). The genomic DNA G+C content was 60.1 mol%, and the major cellular 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. The rpoD sequence-based phylogenetic and whole genome-based phylogenomic analyses demonstrated that the strains are a member of the Pseudomonas fluorescens subgroup, but their phylogenetic position does not match those of any members of this subgroup. The average nucleotide identity and digital DNA–DNA hybridization values between the strains and their closely related species were ≤90.64% and ≤41.9 %, respectively, which were below the thresholds for prokaryotic species delineation (95–96 and 70%, respectively). Phenotypic characteristics, pathogenicity toward parsley and cellular fatty acid composition could differentiate the strains from their closest relatives. The phenotypic, chemotaxonomic and genotypic data presented in this study revealed that the strains constitute a novel Pseudomonas species, for which we propose the name Pseudomonas petroselini sp. nov., with MAFF 311094T (=ICMP 24279T) being the type strain.

Pseudomonas aegrilactucae sp. nov. and Pseudomonas morbosilactucae sp. nov., pathogens causing bacterial rot of lettuce in Japan

“…The major fatty acids (>5 % of the total fatty acids) in MAFF 302030 T were summed feature 3 (30.9 %), C 16:0 (29.7 %), summed feature 8 (12.5 %) and C 17 : 0 cyclo (9.0 %). Similar fatty acid compositions were found between MAFF 302030 T and the type strains of its phylogenetic neighbours (7,12,15,(35)(36)(37). However, C 18 : 0 and C 19:0 cyclo ω8c were not detected in P. sivasensis and P. arsenicoxydans (Table 6).…”

“…The genomes of MAFF 301350 T , MAFF 302030 T and MAFF 302046 were sequenced using an Ion S5 sequencer (Thermo Fisher Scientific) according to the methods described in our previous studies [7,8]. The sequence reads obtained were assembled using the CLC Genomics Workbench version 21 (Qiagen) [15]. The draft genomes were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (www.ncbi.nlm.nih.gov/genome/annotation_prok).…”

“…Data for P. morbosilactucae and P. rhodesiae were obtained in this study. The other data were from Sawada et al[15], Sawada et al[7], Sawada et al[35], Sawada et al[12], Duman et al[36] and Duman et al[37], under the same analytical conditions used in this study. tr, Trace amount (<1%); -, not detected.…”

Dismantling and reorganizingPseudomonas marginalissensu lato

“… Note : The results obtained in our previous studies (Sawada et al, 2019; Sawada, Fujikawa, & Horita, 2020; Sawada, Fujikawa, Nishiwaki, et al, 2020; Sawada, Fujikawa, Osada, et al, 2021, 2022; Sawada, Fujikawa, & Satou, 2021, 2022; Sawada, Fujikawa, Tsuji, et al, 2021; Sawada, Horita, Nishimura, et al, 2020) are summarized in this table. Characteristics have been scored as follows: +, positive reaction; −, negative reaction; w, weakly positive reaction; *, slight variation in results for one or a few strains; NT, not tested. …”

“…marginalis at the Genebank Project (NARO Genebank; https://www.gene.affrc.go.jp/databases-micro_search_en.php), which is a culture collection operated by NARO (National Agriculture and Food Research Organization, Japan). In this article, we provide a brief overview of the results obtained since the start of the study in 2017 (Sawada et al, 2019; Sawada, Fujikawa, & Horita, 2020; Sawada, Fujikawa, Nishiwaki, et al, 2020; Sawada, Fujikawa, Osada, et al, 2021, 2022; Sawada, Fujikawa, & Satou, 2021, 2022; Sawada, Fujikawa, Tsuji, et al, 2021; Sawada, Horita, Nishimura, et al, 2020), and discuss some of the remaining issues.…”