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

Abstract

Phytopathogenic bacterial strains (MAFF 301350T, MAFF 302030T and MAFF 302046), isolated from lettuce (Lactuca sativa var. capitata) with bacterial rot disease in Japan, were subjected to polyphasic characterization to determine their taxonomic affiliations. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with polar flagella and rod-shaped. The results of similarity searches and phylogenetic analyses based on the 16S rRNA gene sequences, as well as the analysis results of the cellular fatty acid composition and genomic DNA G+C content indicated that these strains belong to the genus Pseudomonas . Phylogenetic analyses using the rpoD gene sequences and phylogenomic analyses of the whole genome sequences grouped them into the Pseudomonas putida group (MAFF 301350T) and the Pseudomonas fluorescens group (MAFF 302030T and MAFF 302046), but the phylogenetic positions of the strains did not match those of any known Pseudomonas species. The average nucleotide identity and digital DNA–DNA hybridization values between the strains and their closely related species were lower than the thresholds for prokaryotic species delineation (95–96 and 70 %, respectively). Phenotypic characteristics, pathogenicity toward lettuce, cellular fatty acid composition and whole-cell MALDI-TOF mass spectrometry profiles could differentiate the strains from their closest relatives. The phenotypic, chemotaxonomic and genotypic data obtained in this study showed that the strains represent two novel species of the genus Pseudomonas , Pseudomonas aegrilactucae sp. nov. for MAFF 301350T and Pseudomonas morbosilactucae sp. nov. for MAFF 302030T and MAFF 302046. The respective type strains are MAFF 301350T (= ICMP 23989T) and MAFF 302030T (= ICMP 24377T).

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. …”

“…aegrilactucae and P . morbosilactucae ; Sawada, Fujikawa, & Satou, 2021, 2022). In addition, it was revealed that P .…”

“…fluorescens subgroup (Girard et al, 2021; Rudra & Gupta, 2021), it was located outside any known subgroups within the P . fluorescens group in the phylogenomic trees, suggesting that it may represent a novel subgroup (Sawada, Fujikawa, & Satou, 2022).…”

“…marginalis sensu lato strains, preserved in the NARO Genebank, that do not fall under the category of P . marginalis sensu stricto (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). However, thus far, the taxonomic affiliations of only some of these strains have been clarified (Table 1), and many related issues still remain.…”

“…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.…”