Two Bremia lactucae isolates were obtained from infected lettuce (Lactuca sativa) plants in fields in Kagawa Prefecture. The two isolates exhibited distinct reaction phenotypes compared to those of races in Hyogo Prefecture previously characterized by the International Bremia Evaluation Board, suggesting the presence of unreported races in Japan. Some commercial lettuce cultivars with resistance genes supported minimal sporulation of an isolate, confirming their effectiveness for disease control. When wild L. serriola collected from three regions was inoculated with the other isolate, the isolate only sporulated on plants from Hiroshima Prefecture. L. sativa cotyledons inoculated with sporangia of the isolate from L. serriola also sporulated, providing evidence of cross-infection of L. sativa and L. serriola by B. lactucae in Japan. The presence of new B. lactucae races and the regional susceptibility of L. serriola to B. lactucae may be influenced by practices such as weed management and crop rotation, including paddy rice cultivation.

Phytopathogenic bacteria (MAFF 311311T and MAFF 311313) were isolated from sugarcane plants exhibiting leaf stripe symptoms associated with red stripe disease in Okinawa Prefecture, Japan. The strains were Gram-reaction-negative, aerobic, motile with one polar flagellum, rod-shaped and non-spore-forming. The genomic DNA G+C content was 69.0 mol%, and the major cellular fatty acids (>10 % of the total fatty acids) included summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), C16 : 0 and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c). Phylogenomic analyses using whole-genome sequences consistently placed these strains within the genus Acidovorax. However, their phylogenetic positions did not correspond to any known species within this genus. Comparative analyses, including average nucleotide identity and digital DNA-DNA hybridization with closely related species, yielded values below the thresholds for prokaryotic species delineation (95-96 and 70 %, respectively), with the highest values observed for Acidovorax oryzae ATCC 19882T (93.98 and 54.3 %, respectively). Phenotypic characteristics, cellular fatty acid composition and a repertoire of secretion systems and their effectors can differentiate these strains from their closest relatives. The phenotypic, chemotaxonomic and genotypic data obtained in this study indicate that MAFF 311311T and MAFF 311313 constitute a novel species within the genus Acidovorax, for which we propose the name Acidovorax sacchari sp. nov., with MAFF 311311T (=ICMP 25276T) designated as the type strain.

Here, we report the complete genome sequences of four strains of Pseudomonas allii (MAFF 301514, MAFF 302050, MAFF 730042, and MAFF 730146) that represent pathogens causing bacterial rot in onion, lettuce, Chinese yam, and tomato, respectively, in Japan.

Bacterial strains, designated DD3 T and DDX28, were isolated from field soil in Japan. The strains had the ability to use 2,4-dichlorophenoxyacetic acid as the sole carbon source. They were Gram-reaction-negative, oxidase-positive, weakly catalase-positive, aerobic and non-spore-forming. Their cells were rod-shaped and often lacked flagella, but some exhibited motility due to the presence of one or two polar flagella. The genomic DNA G+C content was 58.8 mol%, and the major cellular fatty acids (>10% of the total fatty acids) were summed feature 8 (C 18 : 1 ω7c and/or C 18 : 1 ω6c ), C 18 : 0 and C 17 : 0 cyclo. Phylogenetic analyses based on gyrB gene sequences and phylogenomic analysis using whole-genome sequences confirmed that the strains belong to the genus Afipia ; however, their phylogenetic position did not match that of any known species of this genus. Comparative studies of the average nucleotide identity and digital DNA–DNA hybridization with closely related species revealed values lower than the thresholds used for prokaryotic species delineation (95–96 and 70%, respectively), with the highest values observed for Afipia broomeae ATCC 49717 T (79.92 and 21.5%, respectively). Phenotypic characteristics, cellular fatty acid composition and specific metabolic processes and biosynthetic gene clusters could differentiate the strains from their closest relatives. Our phenotypic, chemotaxonomic and genotypic data indicate that DD3 T /DDX28 constitute a novel Afipia species, for which we propose the name Afipia dichlorophenoxyacetatis sp. nov., with DD3 T (MAFF 311804 T =ICMP 25015 T ) as the type strain.

Bacterial wilt disease, caused by Ralstonia solanacearum species complex phylotype I, severely affects the cultivation of solanaceous vegetables (tomato, eggplant, etc.) in Japan. In this study, we report the complete genome sequences of 96 strains of the pathogen isolated from solanaceous vegetables in various parts of Japan.

Two Bremia lactucae isolates were obtained from infected lettuce ( Lactuca sativa ) plants cultivated in fields in Kagawa Prefecture, Japan. The two isolates exhibited distinct reaction phenotypes compared to those of races previously characterized by the International Bremia Evaluation Board and detected in Hyogo Prefecture, suggesting the presence of previously unreported races in Japan. Commercial lettuce cultivars with resistance genes showed minimal sporulation, confirming their effectiveness for disease control. Cross-inoculation experiments with B. lactucae on wild Lactuca serriola collected from three regions reveled sporulation only on plants from Hiroshima Prefecture. Furthermore, L. sativa cotyledons inoculated with conidia from L. serriola also developed sporulation, providing evidence of cross-infection of B. lactucae between L. sativa and L. serriola in Japan. The detection of new B. lactucae races, as well as the regional susceptibility of L. serriola to B. lactucae , may be influenced by factors such as weed management and crop rotation practices, including paddy rice cultivation in Japan, compared to field crops in other countries.

Phytopathogenic bacteria (MAFF 302110T and MAFF 302107) were isolated from lesions on Japanese angelica trees affected by bacterial soft rot in Yamanashi Prefecture, Japan. The strains were Gram-reaction-negative, facultatively anaerobic, motile with peritrichous flagella, rod-shaped, and non-spore-forming. The genomic DNA G+C content was 51.1 mol % and the predominant cellular fatty acids included summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 2 (comprising any combination of C12 : 0 aldehyde, an unknown fatty acid with an equivalent chain length of 10.928, C16 : 1 iso I, and C14 : 0 3OH), and C12 : 0. Phylogenetic analyses based on 16S rRNA and gyrB gene sequences, along with phylogenomic analysis utilizing whole-genome sequences, consistently placed these strains within the genus Pectobacterium. However, their phylogenetic positions did not align with any known species within the genus. Comparative studies involving average nucleotide identity and digital DNA–DNA hybridization with the closely related species indicated values below the thresholds employed for the prokaryotic species delineation (95–96 % and 70 %, respectively), with the highest values observed for Pectobacterium polonicum DPMP315T (92.10 and 47.1 %, respectively). Phenotypic characteristics, cellular fatty acid composition, and a repertoire of secretion systems could differentiate the strains from their closest relatives. The phenotypic, chemotaxonomic, and genotypic data obtained in this study show that MAFF 302110T/MAFF 302107 represent a novel species of the genus Pectobacterium, for which we propose the name Pectobacterium araliae sp. nov., designating MAFF 302110T (=ICMP 25161T) as the type strain.

Until recently, it had been a common practice in the field of plant disease control to identify bacterial strains with the following characteristics as Pseudomonas marginalis: fluorescent; oxidase-, potato soft rot- and arginine dihydrolase-positive; soft rot-causing (here referred to as P. marginalis sensu lato). In contrast, as phylogenetic and genomic analyses have been introduced into the bacterial taxonomy, it became clear that P. marginalis sensu lato is heterogeneous, suggesting that it might be a species complex containing many cryptic species. Therefore, a preliminary survey was performed targeting the P. marginalis sensu lato strains preserved in the NARO (National Agriculture and Food Research Organization, Japan) Genebank to sort these into strains corresponding to P. marginalis sensu stricto (i.e., strains that would be included in the same species range as the type strain of P. marginalis) and strains that might not fit this category. Since then, attempts have been made to examine the taxonomic affiliations of the latter by using a polyphasic approach. As a result, some strains were proven to differ from any known species and are described as the following novel species: Pseudomonas kitaguniensis, Pseudomonas allii, Pseudomonas cyclaminis, Pseudomonas petroselini, Pseudomonas brassicae, Pseudomonas lactucae, Pseudomonas aegrilactucae and Pseudomonas morbosilactucae. In this article, the profiles of each of these novel species and a scheme for their identification are briefly introduced. In addition to the problem of cryptic species, reorganizing P. marginalis sensu lato still faces various challenges, which we discuss.

Two phytopathogenic bacteria, MAFF 301380T and MAFF 301381, isolated from rot lesions of lettuce (Lactuca sativa L. var. capitata L.) in Japan, were characterized using a polyphasic approach. The cells were Gram-reaction-negative, aerobic, non-spore-forming, rod-shaped and motile with one to three polar flagella. Analysis of the 16S rRNA gene sequences showed that the strains belong to the genus Pseudomonas and are closely related to Pseudomonas cedrina subsp. cedrina CFML 96-198T (99.72 %), Pseudomonas cedrina subsp. fulgida P515/12T (99.65 %), Pseudomonas gessardii DSM 17152T (99.51 %), Pseudomonas synxantha DSM 18928T (99.44 %), Pseudomonas libanensis CIP 105460T (99.44 %) and Pseudomonas lactis DSM 29167T (99.44 %). The genomic DNA G+C content was 60.4 mol% and the major fatty acids consisted of summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c), C16 : 0 and summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c). 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 formed a monophyletic and robust clade separated from their closest relatives. The average nucleotide identity and digital DNA-DNA hybridization values between the strains and their closely related species were 88.65 % or less and 36.3 % or less, respectively. The strains could be distinguished from their closest relatives by phenotypic characteristics, pathogenicity towards lettuce and whole-cell MALDI-TOF MS profiles. The evidence presented in this study supports the classification of the strains as representing a novel Pseudomonas species, for which we propose the name Pseudomonas lactucae sp. nov., with the type strain MAFF 301380T (=ICMP 23838T).

Six phytopathogenic bacterial strains, MAFF 301512, MAFF 301513, MAFF 301514T, MAFF 301515, MAFF 301516 and MAFF 301517, were isolated from soft rot lesions of onion (Allium cepa L.) in Japan. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one or two polar flagella and rod-shaped. Analysis of their 16S rRNA gene sequences showed that they belong to the genus Pseudomonas, with the highest similarities to Pseudomonas poae DSM 14936T (99.86 %), Pseudomonas simiae OLiT (99.85 %), Pseudomonas trivialis DSM 14937T (99.79 %) and Pseudomonas extremorientalis KMM 3447T (99.79 %). Their genomic DNA G+C content was 60.9 mol% and the major fatty acids (>5 % of the total fatty acids) present 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 and phylogenomic analyses based on the rpoD gene and whole genome sequences, respectively, demonstrated that the strains belong to the Pseudomonas fluorescens subgroup, but form a monophyletic and robust clade, with Pseudomonas azotoformans as their neighbour. Between the strains and P. azotoformans, the average nucleotide identity scores were 95.63-95.70 %, whereas the digital DNA-DNA hybridization scores of the strains against their closest relatives, including P. azotoformans, were 65.4 % or less, which are lower than the 70 % cut-off for prokaryotic species delineation. The strains were differentiated from their closest relatives by phenotypic characteristics, pathogenicity in onion and cellular fatty acid composition. The phenotypic, chemotaxonomic and genotypic data showed that the strains represent a novel Pseudomonas species, proposed to be named Pseudomonas allii sp. nov., with MAFF 301514T (=ICMP 23680T) being the type strain.