Bacillus paraflexus sp. nov., isolated from compost

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4735-4743 ◽  
Author(s):  
Piyush Chandna ◽  
Shanmugam Mayilraj ◽  
Ramesh Chander Kuhad

A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium capable of growing at 15–42 °C (optimum 30 °C) and at pH 5–11 (optimum pH 7) was isolated from compost. Its taxonomic position was deduced using a polyphasic approach and the strain was designated RC2T. 16S rRNA gene sequence analysis showed that the isolate belongs to the division Firmicutes , forming a clade within the cluster containing Bacillus flexus IFO 15715T, and showed highest similarity to B. flexus IFO 15715T (98.1 %). The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. The major cellular fatty acids of the novel strain were iso-C15:0 (36.83 %), anteiso-C15:0 (49.19 %) and C16:0 (5.19 %). DNA–DNA hybridization between strain RC2T and B. flexus DSM 1320T showed a level of relatedness of 54.5 %. The polar lipid profile of strain RC2T showed the presence of phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The predominant isoprenoid quinone was MK-7 and the G+C content of strain RC2T was 37.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and the results of biochemical and physiological tests, strain RC2T was clearly distinguished from closely related members of the genus, and the strain is assigned to a novel species, for which the name Bacillus paraflexus sp. nov. is proposed. The type strain is RC2T ( = MTCC 9831T = MCC 2100T = KCTC 13724T = CCM 7754T).

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1421-1425 ◽  
Author(s):  
Syed G. Dastager ◽  
Rahul Mawlankar ◽  
Poonam Mual ◽  
Ashish Verma ◽  
Srinivasan Krishnamurthi ◽  
...  

A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium designated SGD-V-25T was isolated from Veraval sediment sample, India. Strain SGD-V-25T was capable of growing at 25–50 °C (optimum 37 °C), pH 6–12 (optimum pH 7.0) and with 0–5 % (w/v) NaCl. The taxonomic position of this strain was deduced using a polyphasic approach and the 16S rRNA gene sequence analysis showed that the isolate belongs to the phylum Firmicutes , forming the cluster with Bacillus badius MTCC 1548T, with which it shares highest similarity of 99.1 % with 13 nt differences. Other type strains of the genus Bacillus showed less than 96 % similarity. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. The polar lipid profile of strain SGD-V-25T showed the presence of diphosphatidylglycerol, phosphatidylglycerol, phsophoglycolipid and two aminophospholipids. The predominant isoprenoid quinone was MK-7. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0, C16 : 1ω11c and C16 : 0. The genomic DNA G+C content of strain SGD-V-25T was 37.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA hybridization, strain SGD-V-25T could be clearly distinguished from closely related members of the genus Bacillus , and the name Bacillus encimensis sp. nov., is proposed to accommodate this strain. The type strain is SGD-V-25T ( = NCIM 5513T = DSM 28241T).


2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2484-2489 ◽  
Author(s):  
Peter Kämpfer ◽  
Stefanie P. Glaeser ◽  
Iris Grün-Wollny ◽  
Hans-Jürgen Busse

A Gram-positive, non-spore-forming bacterium (GW-12028T) of unknown origin showing filamentous growth and producing spherical sporangia was studied for its taxonomic allocation. The 16S rRNA gene sequence analysis and subsequent similarity studies showed that strain GW-12028T belongs to the genus Streptosporangium , and is most closely related to Streptosporangium pseudovulgare DSM 43181T (99.9 %) and Streptosporangium nondiastaticum DSM 43848T (99.6 %) and more distantly related to Streptosporangium fragile IFO 14311T (98.4 %) and other species of the genus Streptosporangium (95.8 to 98 %). Chemotaxonomic analyses showed that the peptidoglycan diamino acid was meso-diaminopimelic acid. Whole-cell hydrolysates contained madurose as the diagnostic sugar and exhibited a quinone system that contained predominantly menaquinones with nine isoprenoic units in the side chain [MK-9, MK-9(H2), MK-9(H4)]. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phoshatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol-mannosides, four unidentified glycolipids, a phospholipid and an aminolipid. The polyamine pattern contained the major compounds spermine and spermidine. The major fatty acids were 10-methyl C17 : 0, iso-C16 : 0 and C15 : 0. These chemotaxonomic traits are common to other species of the genus Streptosporangium . DNA–DNA hybridizations and physiological and biochemical tests in comparison with the type strains of the most closely related species, S. nondiastaticum and S. pseudovulgare , allowed genotypic and phenotypic differentiation of strain GW-12028T. This strain represents a novel species, for which we propose the name Streptosporangium sandarakinum sp. nov., with the type strain GW-12028T ( = LMG 27062T  = DSM 45763T).


2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3063-3068 ◽  
Author(s):  
Van-An Hoang ◽  
Yeon-Ju Kim ◽  
Ngoc-Lan Nguyen ◽  
Deok-Chun Yang

A novel Gram-staining-positive, aerobic bacterium, designed DCY80T, was isolated from soil of a ginseng field in the Republic of Korea. 16S rRNA gene sequence analysis revealed that strain DCY80T belonged to the genus Brachybacterium (95.8–98.2 % similarity) and was most closely related to Brachybacterium faecium DSM 4810T (98.2 %). Colonies were circular, entire, low-convex, opaque and 0.5–1.0 mm in diameter after growth for 2 days on TSA at 30 °C. Growth occurred at 4–34 °C (optimum, 25 °C), at pH 5.0–10.0 (optimum, pH 6.5–7.0) and in the presence of 0–7.0 % NaCl. Strain DCY80T produced siderophores and was sensitive to penicillin G, erythromycin, cefazolin, oleandomycin, ceftazidime, vancomycin, tetracycline, novobiocin, carbamicillin, rifampicin and neomycin. The DNA G+C content was 71.0 mol%. Levels of DNA–DNA relatedness between strain DCY80T and B. faecium DSM 4810T, B. paraconglomeratum KCTC 9916T, B. saurashtrense DSM 23186T and B. conglomeratum KCTC 9915T were 46.9±0.5, 28.9±0.6, 20.4±0.9 and 17.3±0.4 %, respectively. The cell-wall peptidoglycan of strain DCY80T contained meso-diaminopimelic acid as the diagnostic diamino acid. The menaquinones were MK-7 (85.8 %) and MK-8 (14.2 %). The major cellular fatty acids were anteiso-C15 : 0 (69.1 %) and anteiso-C17 : 0 (12.2 %). Phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid, two unidentified phospholipids and five unidentified polar lipids were found. On the basis of our phenotypic and genotypic analyses, strain DCY80T represents a novel species of the genus Brachybacterium , for which the name Brachybacterium ginsengisoli sp. nov. is proposed (type strain DCY80T = KCTC 29226T = JCM 19356T).


Author(s):  
Hans-Jürgen Busse ◽  
Peter Kämpfer ◽  
Michael P. Szostak ◽  
Joachim Spergser

Strain F2AT, isolated from the cricket Acheta domesticus, was subjected to a polyphasic taxonomic characterization. Cells of the strain were rod-shaped, Gram-stain-negative and catalase- and oxidase-positive. It did not assimilate any carbohydrates. The strain's 16S rRNA gene sequence showed highest similarity to Entomomonas moraniae QZS01T (96.4 %). The next highest similarity values were found to representatives of related genera (<93 %). The genome size of strain F2AT was 3.2 Mbp and the G+C content was 36.4 mol%. Average nucleotide identity values based on blast and MUMmer and average amino acid identity values between strain F2AT and E. moraniae QZS01T were 74.29/74.43, 83.88 and 74.70 %, respectively. The quinone system predominantly contained ubiquinone Q-8. In the polar lipid profile, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid were detected. The polyamine pattern consisted of the major compounds putrescine and spermidine. Major fatty acids were C18 : 1 ω7c and C16 : 0 and the hydroxyl acids were C12 : 0 3-OH, C14 : 0 2-OH and C14 : 0 3-OH. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. Due to its association with the only species of the genus Entomomonas but its distinctness from E. moraniae we here propose the novel species Entomomonas asaccharolytica sp. nov. F2AT (=CCM 9136T=LMG 32211T).


2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 901-906 ◽  
Author(s):  
Jung-Hye Choi ◽  
Chang-Jun Cha

A Gram-staining-positive, motile, facultatively anaerobic, endospore-forming and rod-shaped bacterium, designated strain CJ32T, was isolated from ginseng soil at Geumsan in Korea. The isolate grew optimally at 30 °C, 2 % (w/v) NaCl and pH 7.0. Colonies of strain CJ32T were beige and circular with an entire margin on LB agar plates. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CJ32T was associated with the genus Bacillus and was most closely related to Bacillus graminis YC6957T (97.3 % similarity) and Bacillus lentus IAM 12466T (97.1 %). DNA–DNA hybridization with closely related strains was below 31.3 %. The major respiratory isoprenoid quinone was MK-7. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The polar lipid profile of strain CJ32T consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unidentified lipids, including phospholipids, aminolipids and aminophospholipids. The predominant fatty acids of strain CJ32T were iso-C15 : 0 and anteiso-C15 : 0. The G+C content of the genomic DNA was 35.1 mol%. Based on phenotypic, genotypic and phylogenetic data, strain CJ32T should be classified within a novel species of the genus Bacillus , for which the name Bacillus panacisoli sp. nov. is proposed. The type strain is strain CJ32T ( = KACC 17503T = JCM 19226T).


2020 ◽  
Vol 70 (10) ◽  
pp. 5425-5431 ◽  
Author(s):  
Jin-Soo Son ◽  
Soo-Yeong Lee ◽  
Ye-Ji Hwang ◽  
Jae-Ho Shin ◽  
Sa-Youl Ghim

An actinobacterial strain, designated KUDC0627T, was isolated from rhizospheric soil that contained Elymus tsukushiensis on the Dokdo Islands, Republic of Korea. Cells were Gram-stain-positive, facultative anaerobic, non-motile and non-endospore-forming cocci. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain KUDC0627T belongs to the genus Microlunatus and is most closely related to Microlunatus soli DSM 21800T (98.5 %), Microlunatus endophyticus DSM 100019T (97.7 %) and Microlunatus ginsengisoli Gsoil 633T (96.5 %). The average nucleotide identity scores and average amino acid identity values were all below the 95.0 % cut-off point. In silico DNA–DNA hybridization, using the Genome-to-Genome Distance Calculator, estimated that there is 22.3 % DNA relatedness between KUDC0627T and M. soli DSM 21800T. The genomic DNA G+C content was 66.9 mol%. The major menaquinone was MK-9(H4) and the major diagnostic diamino acid in the cell-wall peptidoglycan was ll-diaminopimelic acid. The polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipids, unidentified glycolipids and unidentified lipids. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0. Based on phenotypic, chemotaxonomic, and phylogenetic data, strain KUDC0627T (=KCTC 39853T=JCM 32702T) represents a novel species, for which the name Microlunatus elymi sp. nov. is proposed.


2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1945-1951 ◽  
Author(s):  
Yong-Guang Zhang ◽  
Qing Liu ◽  
Hong-Fei Wang ◽  
Dao-Feng Zhang ◽  
Yuan-Ming Zhang ◽  
...  

A facultatively alkaliphilic actinomycete strain, designated EGI 80088T, was isolated from a saline-alkali soil sample from Xinjiang province, north-west China, and subjected to a polyphasic taxonomic characterization. Strain EGI 80088T formed fragmented aerial hyphae and short spore chains, and rod-like spores aggregated at maturity. Whole-cell hydrolysates of the isolate contained ll-diaminopimelic acid as the diagnostic diamino acid, and glucosamine, mannose, galactose, glucose and rhamnose as the marker sugars. The major fatty acids identified (>5 %) were anteiso-C15 : 0, iso-C15 : 0, summed feature 4 (iso-C17 : 1I/anteiso-C17 : 1B), iso-C16 : 0 and anteiso-C17 : 0. The predominant menaquinone was MK-9(H4). The G+C content of the genomic DNA of strain EGI 80088T was 70.6 mol%. EGI 80088T showed the highest 16S rRNA gene sequence similarity to its closest phylogenetic neighbour Haloactinopolyspora alba YIM 93246T (98.5 %). The DNA–DNA relatedness value of the strain EGI 80088T and H. alba YIM 93246T was 59.3±5.2 %. On the basis of morphological, chemotaxonomic and phylogenetic characteristics and DNA–DNA hybridization data, strain EGI 80088T represents a novel species of the genus Haloactinopolyspora , for which the name Haloactinopolyspora alkaliphila sp. nov. (type strain EGI 80088T = BCRC 16946T = JCM 19128T) is proposed. The description of the genus Haloactinopolyspora has also been emended.


2019 ◽  
Vol 69 (4) ◽  
pp. 1075-1080 ◽  
Author(s):  
Leni Sun ◽  
Yan Chen ◽  
Wei Tian ◽  
Lunguang Yao ◽  
Zhaojin Chen ◽  
...  

A Gram-stain-positive, rod-shaped, motile bacterial strain, designated 3-2-2T, was isolated from field topsoil collected from a western suburb of Nanyang city, Henan province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 3-2-2T was a member of the genus Bacillus and most closely related to Bacillus fortis R-6514T (98.9 % similarity), Bacillus terrae RA9T (98.0 %) and Bacillus fordii R-7190T (97.7 %). A draft genome sequence determined for strain 3-2-2T revealed a DNA G+C content of 42.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between 3-2-2T and the closely related Bacillus species ranged 79.4–84.2 % and 23.4–24.6 %. The major fatty acids of strain 3-2-2T were iso-C15 : 0, anteiso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The major isoprenoid quinone was MK-7. meso-Diaminopimelic acid was detected in the peptidoglycan. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. The results of phylogenetic analyses, in silico genomic comparisons, and chemotaxonomic and phenotypic analyses clearly indicated that strain 3-2-2T represents a novel species within the genus Bacillus , for which the name Bacillus acidinfaciens sp. nov. is proposed. The type strain is 3-2-2T (=CGMCC 1.13685T=LMG 30839T).


2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2997-3002 ◽  
Author(s):  
Neha Niharika ◽  
Swati Jindal ◽  
Jasvinder Kaur ◽  
Rup Lal

A bacterial strain, designated Dd16T, was isolated from a hexachlorocyclohexane (HCH) dumpsite at Lucknow, India. Cells of strain Dd16T were Gram-stain-negative, non-motile, rod-shaped and yellow-pigmented. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain belonged to the genus Sphingomonas in the family Sphingomonadaceae , as it showed highest sequence similarity to Sphingomonas asaccharolytica IFO 15499T (95.36 %), Sphingosinicella vermicomposti YC7378T (95.30), ‘Sphingomonas humi’ PB323 (95.20 %), Sphingomonas sanxanigenens NX02T (95.14 %) and Sphingomonas desiccabilis CP1DT (95.00 %). The major fatty acids were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) C14 : 0 2-OH, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The polar lipid profile of strain Dd16T also corresponded to those reported for species of the genus Sphingomonas (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, and a sphingoglycolipid), again supporting its identification as a member of the genus Sphingomonas . The predominant respiratory quinone was ubiquinone Q10, and sym-homospermidine was the major polyamine observed. The total DNA G+C content of strain Dd16T was 65.8 mol%. The results obtained on the basis of phenotypic characteristics and phylogenetic analysis and after biochemical and physiological tests, clearly distinguished strain Dd16T from closely related members of the genus Sphingomonas . Thus, strain Dd16T represents a novel species of the genus Sphingomonas for which the name Sphingomonas indica sp. nov. is proposed. The type strain is Dd16T ( = DSM 25434T = CCM 7882T).


Author(s):  
Xiaoya Peng ◽  
Yumin Zhang ◽  
Yijing Lu ◽  
Xueyin Zhou ◽  
Zhourui Wei ◽  
...  

A rod-shaped, yellow-pigmented, Gram-stain-negative, non-motile and aerobic bacterium, designated 7-3AT, was isolated from soil from King George Island, maritime Antarctica, and subjected to a polyphasic taxonomic study. Growth occurred at 4–37 °C (optimum, 20°C) and at pH 5.0–9.0 (optimum, pH 7.0–8.0). Tolerance to NaCl was up to 4 % (w/v) with optimum growth in the absence of NaCl. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 7-3AT represented a member of the family Flavobacteriaceae . Strain 7-3AT showed the highest sequence similarities with Kaistella yonginensis HMD 1043T (96.65 %), Kaistella carnis NCTC 13525T (96.53 %), Kaistella chaponensis DSM 23145T (96.27 %), Kaistella antarctica LMG 24720T (96.13 %) and Kaistella jeonii DSM 17048T (96.06 %). A whole genome-level comparison of 7-3AT with K. jeonii DSM 17048T, K. antarctica LMG 24720T, K. chaponensis DSM 23145T, and Kaistella palustris DSM 21579T revealed average nucleotide identity (ANI) values of 79.03, 82.25, 78.12, and 74.42 %, respectively. The major respiratory isoprenoid quinone was identified as MK-6 and a few ubiquinones Q-10 were identified. In addition, flexirubin-type pigments were absent. The polar lipid profile of 7-3AT was found to contain one phosphatidylethanolamine, six unidentified aminolipids (AL) and two unidentified lipids (L). The G+C content of the genomic DNA was determined to be 34.54 mol%. The main fatty acids were iso-C15 : 0, summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl), anteiso-C15 : 0, iso-C13 : 0 and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). On the basis of the evidence presented in this study, a novel species of the genus Kaistella , Kaistella flava sp. nov., is proposed, with the type strain 7-3AT (=CCTCC AB 2016141T= KCTC 52492T). Emended descriptions of Kaistella yonginensis , Kaistella jeonii , Kaistella antarctica and Kaistella chaponensis are also given.


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