Chryseomicrobium amylolyticum sp. nov., isolated from a semi-arid tropical soil, and emended descriptions of the genus Chryseomicrobium and Chryseomicrobium imtechense

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2612-2617 ◽  
Author(s):  
P. Shalem Raj ◽  
Ch. Sasikala ◽  
E. V. V. Ramaprasad ◽  
Y. Subhash ◽  
H.-J. Busse ◽  
...  

A rod-shaped, non-motile, Gram-stain-positive, catalase-positive, starch-hydrolysing strain, JC16T, was isolated from a semi-arid tropical soil from India. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain JC16T clustered with the type species of the genus Chryseomicrobium, Chryseomicrobium imtechense MW 10T, a member of the family Planococcaceae within the phylum Firmicutes with 99.3 % sequence similarity. Major (>10 %) fatty acids of strain JC16T were iso-C15 : 0 and iso-C16 : 0. Minor (<10 and >1 %) amounts of C16 : 0, iso-C14 : 0, anteiso-C15 : 0, iso-C17 : 0, anteiso-C17 : 0, iso-C17 : 1ω10c and C16 : 1ω11c are present in strain JC16T. Polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phospholipids (PL2–4), aminolipids (AL1, 2) and an unknown lipid. Cell wall peptidoglycan was of the type l-Orn–d-Glu. The quinone system was composed of MK-7, MK-8 and MK-6. Genomic DNA G+C content of strain JC16T was 57.6 mol%. Distinct physiological, chemotaxonomic and genotypic differences (37 % reassociation based on DNA–DNA hybridization) from Chryseomicrobium imtechense MW 10T support the classification of strain JC16T as a representative of a novel species in the genus Chryseomicobium, for which the name Chryseomicrobium amylolyticum sp. nov. (type strain JC16T = DSM 23442T = NBRC 105215T) is proposed.

2005 ◽  
Vol 55 (2) ◽  
pp. 747-751 ◽  
Author(s):  
Zubair Aslam ◽  
Wan-Taek Im ◽  
Myung Kyum Kim ◽  
Sung-Taik Lee

A Gram-negative, rod-shaped, non-spore-forming bacterium (designated strain Kw05T) was isolated from granules used in the wastewater treatment plant of a beer-brewing factory in Kwang-Ju, Republic of Korea. On the basis of 16S rRNA gene sequence similarity, strain Kw05T was shown to belong to the family Flavobacteriaceae, and was most closely related to Flavobacterium limicola (96·6 %), Flavobacterium hibernum (96·3 %), Flavobacterium hydatis (96·1 %) and Flavobacterium xinjiangense (96·1 %). The G+C content of the genomic DNA of strain Kw05T was 36·2 mol%, within the range of 32–37 mol% for the genus Flavobacterium. Chemotaxonomic data (major menaquinone MK-6; major fatty acids iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and iso-C17 : 1 ω9c) supported the classification of strain Kw05T within the genus Flavobacterium. Kw05T therefore represents a novel species, for which the name Flavobacterium granuli sp. nov. is proposed. The type strain is Kw05T (=KCTC 12201T=IAM 15099T).


2010 ◽  
Vol 60 (4) ◽  
pp. 866-870 ◽  
Author(s):  
G. S. N. Reddy ◽  
Suman Pradhan ◽  
Ruth Manorama ◽  
S. Shivaji

Strain RuGl7T was isolated from a soil sample collected at the periphery of the glacial Lake Roopkund in the Himalayan mountain range, India. Cells of RuGl7T were Gram-positive, aerobic, rod-shaped, motile and grew optimally between 15 and 18 °C. Cells of RuGl7T contained 2,4-diaminobutyric acid in the cell-wall peptidoglycan and the major menaquinones were MK-10, MK-11 and MK-12. The polar lipids present were diphosphatidylglycerol and phosphatidylglycerol and an unknown lipid and the major fatty acid was anteiso-C15 : 0. Based on the above characteristics, strain RuGl7T was assigned to the genus Cryobacterium. Strain RuGl7T shared a 16S rRNA gene sequence similarity of 97.0 and 99.0 % with Cryobacterium psychrotolerans JCM 13925T and Cryobacterium psychrophilum JCM 1463T, respectively. However, DNA–DNA relatedness values between strain RuGl7T and C. psychrotolerans and C. psychrophilum were 28 and 23 %, respectively. Furthermore, strain RuGl7T exhibited several phenotypic and genotypic differences when compared with C. psychrotolerans, C. psychrophilum and Cryobacterium mesophilum. Based on these differentiating characteristics, strain RuGl7T was identified as a novel species of the genus Cryobacterium for which the name Cryobacterium roopkundense sp. nov. is proposed. The type strain is RuGl7T (=DSM 21065T=JCM 15131T).


2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4113-4120 ◽  
Author(s):  
Holed Juboi ◽  
Ann Anni Basik ◽  
Sunita Sara Gill Shamsul ◽  
Phil Arnold ◽  
Esther K. Schmitt ◽  
...  

The taxonomic position of an actinobacterium strain, C296001T, isolated from a soil sample collected in Sarawak, Malaysia, was established using a polyphasic approach. Phylogenetically, strain C296001T was closely associated with the genus Luteipulveratus and formed a distinct monophyletic clade with the only described species, Luteipulveratus mongoliensis NBRC 105296T. The 16S rRNA gene sequence similarity between strain C296001T and L. mongoliensis was 98.7 %. DNA–DNA hybridization results showed that the relatedness of strain C296001T to L. mongoliensis was only 21.5 %. The DNA G+C content of strain C296001T was 71.7 mol%. Using a PacBio RS II system, whole genome sequences for strains C296001T and NBRC 105296T were obtained. The genome sizes of 4.5 Mbp and 5.4 Mbp determined were similar to those of other members of the family Dermacoccaceae. The cell-wall peptidoglycan contained lysine, alanine, aspartic acid, glutamic acid and serine, representing the peptidoglycan type A4α l-Lys-l-Ser-d-Asp. The major menaquinones were MK-8(H4), MK-8 and MK-8(H2). Phosphatidylglycerol, phosphatidylinositol, diphosphatidylglycerol and phosphoglycolipid were the polar lipids, while the whole-cell sugars were glucose, fucose and lesser amounts of ribose and galactose. The major fatty acids were iso-C16 : 0, anteiso-C17 : 0, iso-C16 : 1 H, anteiso-C17 : 1ω9c, iso-C18 : 0 and 10-methyl C17 : 0. Chemotaxonomic analyses showed that C296001T had typical characteristics of members of the genus Luteipulveratus, with the main differences occurring in phenotypic characteristics. On the basis of the phenotypic and chemotaxonomic evidence, it is proposed that strain C296001T be classified as a representative of a novel species in the genus Luteipulveratus, for which the name Luteipulveratus halotolerans sp. nov. is recommended. The type strain is C296001T ( = ATCC TSD-4T = JCM 30660T).


2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4546-4551 ◽  
Author(s):  
Salam Nimaichand ◽  
Yong-Guang Zhang ◽  
Juan Cheng ◽  
Li Li ◽  
Dao-Feng Zhang ◽  
...  

Strain MBRL 34T, isolated from a sample of limestone quarry located at Hundung, Manipur, India, was characterized by polyphasic taxonomy. The strain showed the highest 16S rRNA gene sequence similarity with Micromonospora echinaurantica DSM 43904T (98.4 %), but formed a monophyletic clade with Micromonospora coerulea DSM 43143T (98.3 %) in the neighbour-joining tree. DNA–DNA hybridization experiments gave a DNA–DNA relatedness value of 53.1 % between MBRL 34T and M. coerulea DSM 43143T. Strain MBRL 34T contained meso-diaminopimelic acid, galactose and glucose in the whole-cell hydrolysates along with small amounts of mannose, xylose, rhamnose and ribose. The major polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannoside, along with an unknown lipid. MK-10(H6), MK-10(H2) MK-11(H4) and MK-10(H4) were the predominant menaquinones detected. The major fatty acids were iso-C16 : 0 and iso-C15 : 0. The G+C content of the genomic DNA was 73.5 %. Based on the taxonomic characteristics from a polyphasic study, strain MBRL 34T merits recognition as a representative of a novel species of the genus Micromonospora for which the name Micromonospora kangleipakensis sp. nov. is proposed; the type strain is MBRL 34T ( = DSM 45612T = JCM 17696T).


2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2835-2843 ◽  
Author(s):  
Hong Chen ◽  
Mareike Jogler ◽  
Manfred Rohde ◽  
Hans-Peter Klenk ◽  
Hans-Jürgen Busse ◽  
...  

‘ Caulobacter leidyi ’ DSM 4733T has been shown to be affiliated with the family Sphingomonadaceae instead of the Caulobacteraceae , and due to its poor characterization has been omitted from the current edition of Bergey’s Manual of Systematic Bacteriology and removed to limbo. We isolated a novel sphingoglycolipid-containing dimorphic prosthecate bacterium, designated strain 247, from a pre-alpine freshwater lake. Strain 247 and ‘ Caulobacter leidyi ’ DSM 4733T were characterized in detail. The rod-shaped cells were Gram-stain-negative, aerobic, catalase- and oxidase-positive, and formed a stalk or polar flagellum. Both strains grew optimally at 28–30 °C, and pH 6.0–8.0. The major fatty acids were C18 : 1ω7c, C16 : 0 and 11-methyl C18 : 1ω7c. C14 : 0 2-OH represents the major 2-hydroxy fatty acid. Q-10 was the major respiratory quinone and the major polar lipids were diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylcholine, three glycolipids, two phosphoaminolipids and two unidentified sphingoglycolipids. The major polyamine was sym-homospermidine. The G+C content of genomic DNA of strains 247 and DSM 4733T was 67.6 mol% and 67.0 mol%, respectively. According to 16S rRNA gene sequence analysis and DNA–DNA hybridization, strains DSM 4733T and 247 were phylogenetically closely related (99.6 % 16S rRNA gene sequence similarity, 82.9 % DNA–DNA hybridization value) and affiliated to the genus Sphingomonas . The closest recognized species was Sphingomonas aquatilis DSM 15581T (98.1 % sequence similarity). In addition, the presence of cystine arylamidase, absence of β-galactosidase, and the inability to utilize l-arabinose, galactose and sucrose distinguished strains DSM 4733T and 247 from most other members of the family Sphingomonadaceae . So far, the dimorphic life cycle that involves a prosthecate and a flagellated stage is unique for strains DSM 4733T and 247 among all members of the family Sphingomonadaceae . Therefore, Caulobacter leidyi is reclassified as Sphingomonas leidyi, with the type strain DSM 4733T ( = ATCC 15260T = CIP 106443T = VKM B-1368T) and strain 247 (DSM 25078 = LMG 26658) as an additional strain of this species.


2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3807-3811 ◽  
Author(s):  
Heung-Min Son ◽  
Jung-Eun Yang ◽  
Eun-Ji Yi ◽  
YongJin Park ◽  
Kyung-Hwa Won ◽  
...  

A Gram-reaction-negative, aerobic, motile by one polar flagellum, yellow-pigmented, rod-shaped bacterium, designated strain THG-B117T, was isolated from soil of a cornus fruit field of Hoengseong province in South Korea and its taxonomic position was investigated by a polyphasic study. Strain THG-B117T grew well at 25–30 °C and at pH 6.0–8.0 in the absence of NaCl on nutrient agar. On the basis of 16S rRNA gene sequence similarity, strain THG-B117T was shown to belong to the family Xanthomonadaceae and be related to Dyella japonica XD53T (98.7 % similarity), Dyella terrae JS14-6T (98.0 %), Dyella koreensis BB4T (96.9 %), Dyella soli JS12-10T (96.9 %) and Dyella thiooxydans ATSB10T (96.7 %). DNA–DNA hybridization experiments showed that DNA relatedness between strain THG-B117T and its phylogenetically closest neighbours was below 45.1 %. The G+C content of the genomic DNA of strain THG-B117T was 64.8 mol%. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, unidentified aminolipids, unidentified aminophospholipids and unidentified phospholipids. Phenotypic and chemotaxonomic data (major ubiquinone was Q-8, and major fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and iso-C17 : 1ω9c) supported the affiliation of strain THG-B117T with the genus Dyella . The results of physiological and biochemical tests suggested that strain THG-B117T was different genotypically and phenotypically from recognized species of the genus Dyella , and represents a novel species of this genus. The name Dyella kyungheensis sp. nov. is proposed, with the type strain THG-B117T ( = KACC 16981T = JCM 18747T).


2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 663-667 ◽  
Author(s):  
Jangho Lee ◽  
Banghyo Park ◽  
Sung-Geun Woo ◽  
Juyoun Lee ◽  
Joonhong Park

A Gram-stain-negative, fusiform-shaped, facultatively anaerobic bacterial strain, designated EBTL04T, was isolated from activated sludge using algal metabolites and taxonomically characterized through polyphasic investigation. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain EBTL04T belongs to the family Verrucomicrobiaceae , class Verrucomicrobiae , and is closely related to Prosthecobacter dejongeii DSM 12251T (98.6 % sequence similarity), Prosthecobacter fusiformis ATCC 25309T (97.9 %), Prosthecobacter debontii DSM 14044T (97.5 %), Prosthecobacter vanneervenii DSM 12252T (94.7 %) and Prosthecobacter fluviatilis KCTC 22182T (93.7 %). The G+C content of the genomic DNA of strain EBTL04T was 62.7 mol%. The menaquinone MK-6 was detected as the predominant quinone. Strain EBTL04T contained phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine as major polar lipids. A fatty acid profile with C16 : 1ω5c, iso-C14 : 0, C16 : 0, anteiso-C15 : 0 and C14 : 0 as the major components supported the classification of strain EBTL04T in the genus Prosthecobacter . Based on several phenotypic, genotypic and chemotaxonomic features, strain EBTL04T was clearly differentiated from its phylogenetic neighbours. Therefore, strain EBTL04T should be considered to represent a novel species of the genus Prosthecobacter , for which the name Prosthecobacter algae sp. nov. is proposed. The type strain is EBTL04T ( = KCTC 23681T = JCM 18053T).


2011 ◽  
Vol 61 (7) ◽  
pp. 1617-1621 ◽  
Author(s):  
Heng-Lin Cui ◽  
Xia Gao ◽  
Xin Yang ◽  
Xue-Wei Xu

Two extremely halophilic archaeal strains, TBN21T and TBN49, were isolated from the Taibei marine solar saltern near Lianyungang city, Jiangsu province, China. Cells of the two strains were pleomorphic and Gram-negative and colonies were red. Strains TBN21T and TBN49 were able to grow at 25–50 °C (optimum 37 °C), at 1.4–5.1 M NaCl (optimum 3.4–3.9 M) and at pH 5.5–9.5 (optimum pH 7.0–7.5) and neither strain required Mg2+ for growth. Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 8 % (w/v). The major polar lipids of the two strains were phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and eight glycolipids; three of these glycolipids (GL3, GL4 and GL5) were chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1), galactosyl mannosyl glucosyl diether (TGD-1) and mannosyl glucosyl diether (DGD-1), respectively. Phylogenetic analysis revealed that strains TBN21T and TBN49 formed a distinct clade with their closest relative, Halobaculum gomorrense JCM 9908T (89.0–89.5 % 16S rRNA gene sequence similarity). The DNA G+C contents of strains TBN21T and TBN49 were 64.8 and 62.7 mol%, respectively. DNA–DNA hybridization between strains TBN21T and TBN49 was 90.1 %. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strains TBN21T and TBN49 represent a novel species in a new genus within the family Halobacteriaceae, for which the name Halolamina pelagica gen. nov., sp. nov. is proposed. The type strain of Halolamina pelagica is TBN21T ( = CGMCC 1.10329T  = JCM 16809T).


2011 ◽  
Vol 61 (8) ◽  
pp. 1829-1836 ◽  
Author(s):  
H. Christensen ◽  
B. M. Korczak ◽  
A. M. Bojesen ◽  
P. Kuhnert ◽  
W. Frederiksen ◽  
...  

To allow classification of bacteria previously reported as the SP group and the Stewart–Letscher group, 35 isolates from rodents (21), rabbits (eight), a dog and humans (five) were phenotypically and genotypically characterized. Comparison of partial rpoB sequences showed that 34 of the isolates were closely related, demonstrating at least 97.4 % similarity. 16S rRNA gene sequence comparison of 20 selected isolates confirmed the monophyly of the SP group and revealed 98.5 %–100 % similarity between isolates. A blast search using the 16S rRNA gene sequences showed that the highest similarity outside the SP group was 95.5 % to an unclassified rat isolate. The single strain, P625, representing the Stewart–Letscher group showed the highest 16S rRNA gene similarity (94.9–95.5 %) to members of the SP group. recN gene sequence analysis of 11 representative strains resulted in similarities of 97–100 % among the SP group strains, which showed 80 % sequence similarity to the Stewart–Letscher group strain. Sequence similarity values based on the recN gene, indicative for whole genome similarity, showed the SP group being clearly separated from established genera, whereas the Stewart–Letscher group strain was associated with the SP group. A new genus, Necropsobacter gen. nov., with only one species, Necropsobacter rosorum sp. nov., is proposed to include all members of the SP group. The new genus can be separated from existing genera of the family Pasteurellaceae by at least three phenotypic characters. The most characteristic properties of the new genus are that haemolysis is not observed on bovine blood agar, positive reactions are observed in the porphyrin test, acid is produced from (+)-l-arabinose, (+)-d-xylose, dulcitol, (+)-d-galactose, (+)-d-mannose, maltose and melibiose, and negative reactions are observed for symbiotic growth, urease, ornithine decarboxylase and indole. Previous publications have documented that both ubiquinones and demethylmenaquinone were produced by the proposed type strain of the new genus, Michel A/76T, and that the major polyamine of representative strains (type strain not included) of the genus is 1,3-diaminopropane, spermidine is present in moderate amounts and putrescine and spermine are detectable only in minor amounts. The major fatty acids of strain Michel A/76T are C14 : 0, C16 : 0, C16:1ω7c and summed feature C14 : 0 3-OH/iso-C16 : 1 I. This fatty acid profile is typical for members of the family Pasteurellaceae. The G+C content of DNA of strain Michel A/76T was estimated to be 52.5 mol% in a previous investigation. The type strain is P709T ( = Michel A/76T  = CCUG 28028T  = CIP 110147T  = CCM 7802T).


2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2132-2137 ◽  
Author(s):  
Y. Subhash ◽  
L. Tushar ◽  
Ch. Sasikala ◽  
Ch. V. Ramana

Two bacterial strains (JA744T and JA745) were isolated from dry soil samples collected from solar salterns at Humma, Odisha, India. Both strains were Gram-stain-negative, catalase- and oxidase-positive, motile rods. Major fatty acids in both strains included C18 : 1ω7c, C18 : 0 and C16 : 0, while minor amounts of C10 : 0 3-OH, C12 : 0, C12 : 0 3-OH, C14 : 0 and C16 : 0 were also present. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, an unidentified glycolipid, five unidentified lipids, an unidentified aminolipid and an unidentified phospholipid made up the polar lipids of both strains. Both strains had bacteriohopane derivatives (BHD1,2) and diploptene as major hopanoids. Mean genomic DNA G+C content was 75±1 mol% and the two strains were closely related (mean DNA–DNA hybridization >90 %). Phylogenetic analysis based on the 16S rRNA gene sequence showed that the two strains clustered with species of the genus Rhodobacter belonging to the family Rhodobacteraceae of the class Alphaproteobacteria . The highest sequence similarity was observed with Rhodobacter sphaeroides ATH2.4.1T (96 %) and other members of the genera Rhodobacter and Pseudorhodobacter (<96 %). However, the two strains were positioned distinctly outside the group formed by the other genera of the family Rhodobacteraceae . Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of these isolates as representatives of a novel species in a new genus, for which the name Falsirhodobacter halotolerans gen. nov., sp. nov. is proposed. The type strain of Falsirhodobacter halotolerans is JA744T ( = KCTC 32158T  = NBRC 108897T).


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