Pseudomonas salomonii, another causal agent of garlic spring rot in Japan

Sawada, Hiroyuki; Horita, Harukuni; Nishimura, Fumihiro; Mori, Motoyuki

doi:10.1007/s10327-020-00909-3

Cited by 9 publications

(22 citation statements)

References 18 publications

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“…Phylogenetic analysis based on the 16S rRNA gene sequences was conducted as described previously [9,18], targeting the five Welsh onion isolates and the type strains of the top 32 Pseudomonas species that were found to be highly close to the isolates based on 16S rRNA gene sequence similarities. Their 16S rRNA gene sequences, and that of P. aeruginosa JCM 5962 T selected as an outgroup, were subjected to analysis using mega x [19], where the data were aligned with muscle, positions with gaps or ambiguous bases were excluded, and the remaining 1327 bp were subjected to calculation of evolutionary distance based on the Maximum Composite Likelihood method [20].…”

Section: Pseudomonas Kitaguniensis Sp Nov a Pathogen Causing Bactementioning

confidence: 99%

“…Multilocus sequence analysis (MLSA) using the sequences of the rpoD, gyrB and rpoB genes was performed as in a previous report [18], aiming to more accurately determine the phylogenetic positions of the Welsh onion isolates. The sequences of their rpoD (611 bp), gyrB (705 bp), and rpoB (1112 bp) genes were determined by the direct sequencing method, using primer sets PsEG30F/PsEG790R [21], gyrB+271ps/ gyrB-1022ps [22] and VIC4/LAPS27 [3], respectively.…”

Section: Pseudomonas Kitaguniensis Sp Nov a Pathogen Causing Bactementioning

confidence: 99%

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Pseudomonas kitaguniensis sp. nov., a pathogen causing bacterial rot of Welsh onion in Japan

Sawada

Fujikawa

Nishiwaki

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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Five Gram-reaction-negative, aerobic, motile with one to three polar flagella, rod-shaped bacterial strains, MAFF 212408T, MAFF 212409, MAFF 212410, MAFF 301498 and MAFF 730085, were isolated from diseased Welsh onion (Allium fistulosum L.) in Japan. Analysis of their 16S rRNA gene sequences showed that they belong to the genus Pseudomonas with the highest similarity to Pseudomonas extremaustralis 14-3T (99.86 %), Pseudomonas antarctica CMS 35T (99.79 %) and Pseudomonas poae DSM 14936T (99.72%). The genomic DNA G+C content was 59.5 mol% and the major fatty acids (>5 %) were summed feature 3, C16 : 0, summed feature 8 and C12 : 0 2-OH. Multilocus sequence analysis using the rpoD, gyrB and rpoB gene sequences and phylogenomic analysis based on the 90 core genes demonstrated that the strains are members of the P. fluorescens subgroup, but are distant from all closely related species. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) analysis confirmed low genomic relatedness to their closest relatives [below the recommended thresholds of 95 % (ANI) and 70 % (dDDH) for prokaryotic species delineation]. The strains were characterized by using API 20NE and Biolog GEN III tests, and inoculation tests in Welsh onion, showing that they are phenotypically differentiated from their closest relatives. Based on the genetic and phenotypic evidence, the strains should be classified as representing a novel species, for which the name Pseudomonas kitaguniensis sp. nov. is proposed. The type strain is MAFF 212408T (=ICMP 23530T).

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Section: Pseudomonas Kitaguniensis Sp Nov a Pathogen Causing Bactementioning

confidence: 99%

Section: Pseudomonas Kitaguniensis Sp Nov a Pathogen Causing Bactementioning

confidence: 99%

Pseudomonas kitaguniensis sp. nov., a pathogen causing bacterial rot of Welsh onion in Japan

Sawada

Fujikawa

Nishiwaki

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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“…Whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) assays were performed to assess protein-based relatedness among the broccoli isolates and the type strains of the most closely related species. The strains were grown on standard method agar plates (Nissui) at 27 °C for 24 h, and five colonies of each strain were analysed using the direct smear method and the Bruker MALDI Biotyper system [41]. Briefly, a small amount of bacterial cells was transferred onto a spot of a steel target plate (Bruker) using a toothpick, air-dried, and overlaid with 1 µl of a saturated α-cyano-4-hydroxycinnamic acid (HCCA) matrix solution in 50 % (v/v) acetonitrile-2.5 % (v/v) trifluoroacetic acid (Bruker).…”

Section: Chemotaxonomic Analysesmentioning

confidence: 99%

“…The target plate was then inserted into a Microflex LT mass spectrometer (Bruker) to acquire the mass spectral data of proteins within the mass range of 2000-20000 Da, using the flexControl 3.4.135.0 and MBT Compass 4.1.70 software (Bruker) at default settings [42]. To visually evaluate the dissimilarity and dispersion of the mass spectral data among the strains, MBT Compass Explorer 4.1.70 (Bruker) was used to perform cluster analysis [39,41]. Five independent spectra obtained from each strain were reduced to a consensus spectrum, and Pearson's correlation coefficient was calculated for every combination of the consensus spectra to generate a distance matrix.…”

Section: Chemotaxonomic Analysesmentioning

confidence: 99%

Pseudomonas brassicae sp. nov., a pathogen causing head rot of broccoli in Japan

Sawada

Fujikawa

Horita

2020

International Journal of Systematic and Evolutionary Microbiology

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Phytopathogenic bacteria, MAFF 212426, MAFF 212427T, MAFF 212428 and MAFF 212429, were isolated from head rot lesions of broccoli (Brassica oleracea L. var. italica Plenck) in Hokkaido, Japan, and subjected to polyphasic taxonomic characterization. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one or two polar flagella, rod-shaped and formed pale yellow colonies. Results of 16S rRNA gene sequence analysis showed that they belong to the genus Pseudomonas with the highest similarity to ‘Pseudomonas qingdaonensis’ JJ3T (99.86 %), Pseudomonas laurentiana GSL-010T (99.22 %), Pseudomonas huaxiensis WCHPs060044T (99.01 %), Pseudomonas japonica NBRC 103040T (98.87 %) and Pseudomonas alkylphenolica KL28T (98.73 %). The genomic DNA G+C content was 63.4 mol% and the major fatty acids (>5 % of the total fatty acids) were summed feature 3 (C16 : 1 ω7c / C16 : 1 ω6c), C16 : 0, summed feature 8 (C18 : 1 ω7c / C18 : 1 ω6c) and C17 : 0 cyclo. Multilocus sequence analysis using the partial rpoD, gyrB and rpoB gene sequences and phylogenomic analyses based on the whole genome sequences demonstrated that the strains are members of the Pseudomonas putida group, but form a monophyletic, robust clade separated from their closest relatives. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values corroborated their novel species status, with 88.39 % (ANI) and 35.8 % (dDDH) as the highest scores with ‘P. qingdaonensis’ JJ3T. The strains were differentiated from their closest relatives by phenotypic characteristics, pathogenicity on broccoli, and whole-cell MALDI-TOF mass spectrometry profiles. The phenotypic, chemotaxonomic and genotypic data showed that the strains represent a novel Pseudomonas species, for which the name Pseudomonas brassicae sp. nov. is proposed. The type strain is MAFF 212427T (=ICMP 23635T).

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“…Although garlic is regarded as very easy to grow, various diseases threaten the yield and quality of garlic. Bacteria such as Pantoea, Pseudomonas, Burkholderia, and Xanthomonas species cause flower stalk and leaf necrosis, leaf spot, slippery skin, and leaf blot symptoms in the infected garlic [1][2][3]. The well-known fungal diseases for garlic are white rot by Sclerotium cepivorum, vegetable rot by Penicillium, Mucor or Rhizopus species, fusarium bulb and basal rot by Fusarium species, botrytis neck ort caused by Botrytis porri, embellisia skin blotch by Embellisia allii, and rust by Puccinia allii [4][5][6][7][8][9].…”

Section: Introductionmentioning

confidence: 99%

Using RNA-Sequencing Data to Examine Tissue-Specific Garlic Microbiomes

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Kim

et al. 2021

IJMS

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Garlic (Allium sativum) is a perennial bulbous plant. Due to its clonal propagation, various diseases threaten the yield and quality of garlic. In this study, we conducted in silico analysis to identify microorganisms, bacteria, fungi, and viruses in six different tissues using garlic RNA-sequencing data. The number of identified microbial species was the highest in inflorescences, followed by flowers and bulb cloves. With the Kraken2 tool, 57% of identified microbial reads were assigned to bacteria and 41% were assigned to viruses. Fungi only made up 1% of microbial reads. At the species level, Streptomyces lividans was the most dominant bacteria while Fusarium pseudograminearum was the most abundant fungi. Several allexiviruses were identified. Of them, the most abundant virus was garlic virus C followed by shallot virus X. We obtained a total of 14 viral genome sequences for four allexiviruses. As we expected, the microbial community varied depending on the tissue types, although there was a dominant microorganism in each tissue. In addition, we found that Kraken2 was a very powerful and efficient tool for the bacteria using RNA-sequencing data with some limitations for virome study.

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Pseudomonas salomonii, another causal agent of garlic spring rot in Japan

Cited by 9 publications

References 18 publications

Pseudomonas kitaguniensis sp. nov., a pathogen causing bacterial rot of Welsh onion in Japan

Pseudomonas kitaguniensis sp. nov., a pathogen causing bacterial rot of Welsh onion in Japan

Pseudomonas brassicae sp. nov., a pathogen causing head rot of broccoli in Japan

Using RNA-Sequencing Data to Examine Tissue-Specific Garlic Microbiomes

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