Paenibacillus doosanensis sp. nov., isolated from soil

Kim, Jong-Hwa; Kang, Hyeonji; Kim, Wonyong

doi:10.1099/ijs.0.050716-0

Cited by 16 publications

(6 citation statements)

References 42 publications

(55 reference statements)

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“…Strain C4-5 T revealed a fatty acid profile that consisted of saturated branched and straight-chain fatty acids, with anteiso-C 15 : 0 (44.70 %), iso-C 16 : 0 (15.83 %) and C 16 : 0 (14.16 %) as the major fatty acids (.10 % of the total), which was similar to those of the reference strains used in this study, albeit with minor differences (Table 2). The DNA G+C content of strain C4-5 T was 54.8 mol%, slightly higher than those of P. contaminans (51.2 mol%) and P. doosanensis (48.3 mol%) reported previously (Chou et al, 2009;Kim et al, 2014). Strain C4-5…”

Section: Strain C4-5mentioning

confidence: 88%

Paenibacillus cavernae sp. nov., isolated from soil of a natural cave

Lee

2016

International Journal of Systematic and Evolutionary Microbiology

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A Gram-reaction-variable, strictly aerobic, motile, rod-shaped bacterium, designated strain C4-5 T , was isolated from soil of a natural cave. Cells were oxidase-and catalase-positive and formed endospores in sporangia. The 16S rRNA gene sequence comparison showed that the organism formed a distinct clade within the genus Paenibacillus and was most closely related to Paenibacillus contaminans CKOBP-6 T (5KCTC 13623 The genus Paenibacillus was created for rRNA group 3 bacilli on the basis of 16S rRNA gene sequence study with Paenibacillus polymyxa as the type species (Ash et al., 1993) and was later assigned to the family Paenibacillaceae as the type genus . During the past two decades since the creation of the genus, continuous reclassification of some species of the genus Bacillus together with descriptions of novel species have explosively increased the number of species of the genus Paenibacillus, and at the time of writing, this genus contained 162 species with validly published names (http://www.bacterio.net/ paenibacillus.html). Members of the genus Paenibacillus have been recovered from diverse environmental habitats, and are aerobic or facultatively anaerobic, endosporeforming, motile, rod-shaped bacteria that possess mesodiaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, anteiso-C 15 : 0 as the major fatty acid, MK-7 as the predominant menaquinone and DNA G+C contents of 39-59 mol% (Shida et al., 1997;Priest, 2009;Yao et al., 2014). In this study, a novel bacterial strain was recovered from soil of a cave and its taxonomic position was examined by a polyphasic approach including morphological, physiological, chemotaxonomic and phylogenetic analyses, resulting in the proposal of a novel species of the genus Paenibacillus.Strain C4-5 T was isolated from a soil sample of a natural cave in Jeju, Republic of Korea. The sample was collected at a distance of 3 m from the entrance of the cave. One gram of soil sample was placed in 9 ml sterile distilled water and mixed for 30 min at 30 8C. After serial dilution of the mixture, aliquots (100 ml) of the supernatant were transferred onto plates of starch-casein agar (1 % soluble starch, 0.03 % casein, 0.2 % KNO 3 , 0.2 % NaCl, 0.002 % CaCO 3 , 0.005 % MgSO 4 . 7H 2 O, 0.001 % FeSO 4 . 7H 2 O and 1.8 % agar; pH 7.2) and incubated under aerobic conditions at 30 8C for 2 weeks. The pure culture was maintained in 20 % (v/v) glycerol suspensions at 220 8C and 280 8C. For phenotypic comparison, Paenibacillus contaminans KCTC 13623 T and Paenibacillus doosanensis KCTC 33036 T were grown on nutrient agar (NA; BD) at 30 8C for 3 days. According to proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria (Logan et al., 2009), P. polymyxa KCTC 3627 T , the type species of the genus Paenibacillus, was also included in this study.

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Section: Strain C4-5mentioning

confidence: 88%

Paenibacillus cavernae sp. nov., isolated from soil of a natural cave

Lee

2016

International Journal of Systematic and Evolutionary Microbiology

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“…At first, we compared 16S rRNA sequence similarity of the two novel strains and found that similarity is 97.94 %, which is below the previously described threshold for species demarcation 98.6% [32,33]. This result indicates that the novel strains were not from the same supergroup.…”

Section: Results and Discussion: Sequence Similarity And Phylogenetic...mentioning

confidence: 71%

Assigning new supergroups V and W to the Wolbachia diversity

Som¹

2023

Bioinformation

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Wolbachia are endosymbiotic and alphaproteobacteria that belong to the order Rickettsiales. They are known to infect half of the insect population and cause host manipulation, and have been categorized into 19 monophyletic lineages called supergroups. Recently, two strains, wCfeJ and wCfeT were isolated from cat fleas (Ctenocephalides felis), but their supergroup relationships were not assigned. In this article, we have attempted to classify these two novel strains and establish their evolutionary lineage (i.e., supergroup designation). For this we performed 16S rRNA similarity analysis and reconstructed 16S rRNA phylogeny of 52 Wolbachia strains (including two novel strains) belong to 19 supergroups. We also performed average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) studies to measure genomic similarity between the two novel genomes. The results revealed that 16S rRNA similarity between the two novel strains is 97.94%, which is below the threshold value of 98.6% and phylogeny shows that they are placed at the two different positions (i.e., showing distinct evolutionary lineages). Further, genomic similarity analysis revealed that the novel genomes have ANI and dDDH values 79% and 22.4% respectively, which were below the threshold value of ANI (95%) and dDDH (70%). These results suggested that the novel strains neither shared a species boundary between them nor with any other previously identified supergroups, which designate them as two new supergroups, namely supergroup V (strain wCfeJ) and supergroup W (strain wCfeT).

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“…At the time of writing in October 2019, there are over 249 recognized species and four subspecies (www.bacterio.net/paenibacillus.html) [2]. Species of the genus Paenibacillus have been isolated from diverse habitats, such as soil [3–6], fresh water [7, 8], human faeces [9], pit mud [10], saline silt [11], warm springs [12], lake sediment [13] and plant rhizosphere [14–16]. Members of the genus Paenibacillus share the common characteristics of having spore-forming cells containing menaquinone 7 as a major or sole respiratory quinone and anteiso-C 15 : 0 as the major fatty acid.…”

Section: Full-textmentioning

confidence: 99%

Paenibacillus solisilvae sp. nov., isolated from birch forest soil

Kong

Zhang

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-positive, motile, rod-shaped bacterium, designated strain LAM7113 T , was isolated from soil sample collected from a birch forest in Xinjiang Uygur Autonomous Region, PR China. Strain LAM7113 T grew optimally at pH 8.0, 30 °C and in the presence of 1.0 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain LAM7113 T was closely related to members of the genus Paenibacillus, with the highest similarity to Paenibacillus baekrokdamisoli Back-11 T (96.2 %). The genomic DNA G+C content was 43.4 mol%. The values of average nucleotide identity and DNA-DNA hybridization were 66.1 and 27.0 %, respectively, by comparing the draft genome sequences of strain LAM7113 T and P. baekrokdamisoli Back-11 T. Anteiso-C 15 : 0 and iso-C 15 : 0 were identified as the major cellular fatty acids. Menaquinone-7 was detected as the predominant respiratory quinone. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, three unidentified aminophospholipids, three unidentified glycolipids, one unidentified phospholipid and two unknown polar lipids. Based on its phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM7113 T is proposed to represent a novel species of the genus Paenibacillus with the name Paenibacillus solisilvae sp. nov. The type strain is LAM7113 T (=CGMCC 1.16619 T =JCM 32513 T).

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Paenibacillus doosanensis sp. nov., isolated from soil

Abstract: A Gram-stain-positive, aerobic, endospore-forming bacterium, designated CAU 1055 T , was isolated from soil and its taxonomic position was investigated using a polyphasic approach.

Cited by 16 publications

References 42 publications

Paenibacillus cavernae sp. nov., isolated from soil of a natural cave

Paenibacillus cavernae sp. nov., isolated from soil of a natural cave

Assigning new supergroups V and W to the Wolbachia diversity

Paenibacillus solisilvae sp. nov., isolated from birch forest soil

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