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

Abstract

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.

Paenibacillus cymbidii sp. nov., isolated from Cymbidium goeringii roots

“…This polar lipid profile is similar to those of its closest relatives P. cavernae C4-5 T [27] and P. contaminans CKOBP-6 T [28].…”

“…In the neighbour-joining tree based on 16S rRNA gene sequences, strain R196 T formed a tight subclade with P. cavernae C4-5 T [27] and P. contaminans CKOBP-6 T () [28].…”

“…The presence of anteiso-C 15 : 0 as the major fatty acid is typical of members of the genus Paenibacillus . The differences between the fatty acid profiles of strain R196 T and the reference strains were found to be among minor constituents [27, 28]. Strain R196 T contained a menaquinone with seven isoprene units (MK-7) as the predominant isoprenoid quinone.…”

“…Strain R196 T contained a menaquinone with seven isoprene units (MK-7) as the predominant isoprenoid quinone. MK-7 is also the major menaquinone in species of the genus Paenibacillus [27]. The main polar lipids of strain R196 T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids, two unidentified aminophospholipids and an unidentified aminolipid (Fig.…”

Description of Paenibacillus tepidiphilus sp. nov., isolated from a tepid spring

“…[5] to accommodate rod-shaped, motile, endospore-forming bacteria, and at the time of writing the genus comprises more than 230 species (www.bacterio.net/paenibacillus.html) [6]. Members of this genus have been reported from a wide range of environments, such as soil [7], marine sediment [8], cave samples [9], food-packaging paperboard [10], etc., and have been reported to produce a wide range of bioactive molecules [7, 11]. Due to the low 16S rRNA gene sequence identity of SYSU G01001 T and SY-13 and wide applications of members of the genus Paenibacillus , the present study was conducted to establish the taxonomic positions of SYSU G01001 T and SY-13.…”