Approved strains of the soft rot-causing species derived from Pseudomonas marginalis sensu lato

Until recently, bacterial strains exhibiting the following properties had been identified as Pseudomonas marginalis in the field of plant disease control: fluorescent, oxidase-, potato soft rot-, and arginine dihydrolase-positive, soft rot-causing (referred to as “P. marginalis sensu lato” here). On the other hand, in recent years, as the phylogenetic and genomic analyses have been introduced into the bacterial taxonomy, it has become clear that P. marginalis sensu lato is heterogeneous, suggesting that it might be a species complex including many cryptic species.

In 2017, a preliminary survey was performed, targeting the P. marginalis sensu lato strains preserved in the NARO Genebank, to sort them into strains corresponding to “P. marginalis sensu stricto” (= strains included in the same species range as the type strain of P. marginalis) and strains that might not fit this category. Subsequent examination of the taxonomic affiliations of the latter using a polyphasic approach confirmed that a part of them differ from any known species, for which we have proposed the following eight novel species: P. aegrilactucae, P. allii, P. brassicae, P. cyclaminis, P. kitaguniensis, P. lactucae, P. morbosilactucae, and P. petroselini. In contrast, among the latter, some strains have been found to correspond to the “known species other than P. marginalis sensu stricto” (e.g., P. grimontii, P. salomonii, etc.). Therefore, for each species mentioned above, we chose some strains with typical characteristics as the approved strains and decided to show them here with related information.

Reference Sawada, H., Fujikawa, T. and Satou, M. (2023). Dismantling and reorganizing Pseudomonas marginalis sensu lato. Plant Pathology 72: 654-666. [10.1111/ppa.13690]

Strains that served as the basis for proposing the novel species
MAFF No.*1	Scientific Name	Source	Reference*2	Gene Regions	Genome Data	Distribution
301350 ^T	Pseudomonas aegrilactucae	Lettuce	a	16S rpoD	JAHTBI000000000	Order
301512	Pseudomonas allii	Onion	b	16S rpoD	JABUHS000000000	Order
301514 ^T	Pseudomonas allii	Onion	b	16S rpoD	JABUHT000000000	Order
212427 ^T	Pseudomonas brassicae	Broccoli	c	16S gyrB rpoB rpoD	JAAHBU000000000	Order
212428	Pseudomonas brassicae	Broccoli	c	16S gyrB rpoB rpoD	JAAHBV000000000	Order
301449 ^T	Pseudomonas cyclaminis	Common cyclamen	d	16S rpoD	JADDUM00000000	Order
301451	Pseudomonas cyclaminis	Common cyclamen	d	16S rpoD	JADDUN00000000	Order
212408 ^T	Pseudomonas kitaguniensis	Welsh onion	e	16S gyrB rpoB rpoD	VUAZ00000000	Order
730085	Pseudomonas kitaguniensis	Welsh onion	e	16S gyrB rpoB rpoD	VUBA00000000	Order
301380 ^T	Pseudomonas lactucae	Lettuce	f	16S rpoD	JAFHKI000000000	Order
301381	Pseudomonas lactucae	Lettuce	f	16S rpoD	JAFHKJ000000000	Order
302030 ^T	Pseudomonas morbosilactucae	Lettuce	a	16S rpoD	JALQCW00000000	Order
302046	Pseudomonas morbosilactucae	Lettuce	a	16S rpoD	JALQCX00000000	Order
311094 ^T	Pseudomonas petroselini	Parsley	g	16S rpoD	JAJOZG000000000	Order
311095	Pseudomonas petroselini	Parsley	g	16S rpoD	JAJOZH000000000	Order
311096	Pseudomonas petroselini	Parsley	g	16S rpoD	JAJOZI000000000	Order
311097	Pseudomonas petroselini	Parsley	g	16S rpoD	JAJOZJ000000000	Order

Strains found to correspond to the known species other than *Pseudomonas marginalis* sensu stricto
MAFF No.	Scientific Name	Source	Reference	Gene Regions	Distribution
212084	Pseudomonas grimontii	Turnip	h	16S gyrB rpoB rpoD	Order
212085	Pseudomonas grimontii	Turnip	h	16S gyrB rpoB rpoD	Order
212397	Pseudomonas salomonii	Garlic	i	16S gyrB rpoB rpoD	Order
212398	Pseudomonas salomonii	Garlic	i	16S gyrB rpoB rpoD	Order

Strains found to be included in the same species range as the type strain of *Pseudomonas marginalis*
MAFF No.	Scientific Name	Source	Reference	Gene Regions	Distribution
302028	Pseudomonas marginalis	Lettuce	h	16S gyrB rpoB rpoD	Order
302034	Pseudomonas marginalis	Lettuce	h	16S gyrB rpoB rpoD	Order
302055	Pseudomonas marginalis	Persian buttercup	h	16S gyrB rpoB rpoD	Order
302097	Pseudomonas marginalis	Dutch iris	h	16S gyrB rpoB rpoD	Order
302098	Pseudomonas marginalis	Dutch iris	h	16S gyrB rpoB rpoD	Order

*1 T, type strain of the species.
*2 The papers that served as the basis for selecting each strain as the approved strain are as follows:
- a Sawada H. et al. (2022). International Journal of Systematic and Evolutionary Microbiology 72(11): 005599. [10.1099/ijsem.0.005599]
- b Sawada H. et al. (2021). International Journal of Systematic and Evolutionary Microbiology 71(1): 004582. [10.1099/ijsem.0.004582]
- c Sawada H. et al. (2020). International Journal of Systematic and Evolutionary Microbiology 70(10): 5319-5329. [10.1099/ijsem.0.004412]
- d Sawada H. et al. (2021). International Journal of Systematic and Evolutionary Microbiology 71(3): 004723. [10.1099/ijsem.0.004723]
- e Sawada H. et al. (2020). International Journal of Systematic and Evolutionary Microbiology 70(5): 3018-3026. [10.1099/ijsem.0.004123]
- f Sawada H. et al. (2021). International Journal of Systematic and Evolutionary Microbiology 71(7): 004917. [10.1099/ijsem.0.004917]
- g Sawada H. et al. (2022). International Journal of Systematic and Evolutionary Microbiology 72(6): 005424. [10.1099/ijsem.0.005424]
- h Sawada H. et al. (2019). Journal of General Plant Pathology 85(6): 413-423. [10.1007/s10327-019-00869-3]
- i Sawada H. et al. (2020). Journal of General Plant Pathology 86(3): 180-192. [10.1007/s10327-020-00909-3]

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