scholarly journals Bacillus luteus sp. nov., isolated from soil

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1580-1586 ◽  
Author(s):  
Y. Subhash ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Bacterial Strains ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type

Two bacterial strains (JC167T and JC168) were isolated from a soil sample collected from Mandpam, Tamilnadu, India. Colonies of both strains were orange and cells Gram-stain-positive. Cells were small rods, and formed terminal endospores of ellipsoidal to oval shape. Both strains were positive for catalase, oxidase and hydrolysis of starch/gelatin, and negative for chitin hydrolysis, H2S production, indole production and nitrate reduction activity. Major fatty acids of both strains (>5 %) were anteiso-C15 : 0, iso-C16 : 0, iso-C15 : 0, anteiso-C17 : 0, iso-C14 : 0 and C16 : 0 with minor (<5 but >1 %) amounts of iso-C17 : 0, anteiso-C17 : 0 B/iso-C17 : 0 I and C16 : 1ω11c. Diphosphatydilglycerol, phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids of both strains. Cell wall amino acids were l-alanine, d-alanine, d-glutamic acid and meso-diaminopimelic acid. β-Carotene and five unidentified carotenoids were present in both strains. Mean genomic DNA G+C content was 53.4±1 mol% and the two strains were closely related (mean DNA–DNA hybridization >90 %). 16S rRNA gene sequence comparisons of both strains indicated that they represent species of the genus Bacillus within the family Bacillaceae of the phylum Firmicutes . Both strains had a sequence similarity of 97.6 % with Bacillus saliphilus 6AGT and <96.8 % with other members of the genus Bacillus . Sequence similarity between strain JC167T and 168 was 100 %. Strain JC167T showed 25.8±1 % reassociation (based on DNA–DNA hybridization) with B. saliphilus DSM 15402T ( = 6AGT). Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain JC167T as a representative of a novel species of the genus Bacillus , for which the name Bacillus luteus sp. nov. is proposed. The type strain is JC167T ( = KCTC 33100T = LMG 27257T).

scholarly journals Nonomuraea antri sp. nov., an actinomycete isolated from cave soil in Thailand

2020 ◽  
Vol 70 (10) ◽  
pp. 5296-5303 ◽  
Author(s):  
Kenika Lipun ◽  
Wee Fei Aaron Teo ◽  
Paweena Suksaard ◽  
Wasu Pathom-aree ◽  
Kannika Duangmal
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Whole Cell ◽  
Content Type ◽  
Link Type ◽  
Diamino Acid ◽  
Reference Strains

A novel actinobacterium, designated strain NN258T, was isolated from a cave soil sample collected from a karst cave at Khao No-Khao Kaeo, Nakhon Sawan province, Thailand. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with its classification in the genus Nonomuraea . Strain NN258T showed the highest 16S rRNA gene sequence similarity values to Nonomuraea candida HMC10T, Nonomuraea mesophila 6K102T, Nonomuraea rubra DSM 43768T, Nonomuraea diastatica KC712T and Nonomuraea helvata IFO 14681T. The strain formed an extensively branched substrate and aerial mycelia. The whole-cell hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid, with glucose, madurose, mannose and ribose as the whole-cell sugars. The polar lipids were diphosphatidylglycerol, phosphotidylmethylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylmonomethylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, two unidentified phospholipids, three unidentified sugar-containing phosphoaminolipids, an unidentified glycolipid and two unidentified lipids. The predominant menaquinone was MK-9(H4), with minor amounts of MK-9(H0), MK-9(H2) and MK-9(H6). Major cellular fatty acids (>10%) were iso-C16 : 0 and 10-methyl-C17 : 0. The G+C content of the genomic DNA was 71.0 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain NN258T and the reference strains were 79.9–80.9 % and 26.1–27.0 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strain NN258T represents a novel species of the genus Nonomuraea , for which the name Nonomuraea antri sp. nov. is proposed. The type strain is NN258T (=TBRC 11478T=NBRC 114269T).

Brevibacillus composti sp. nov., isolated from hyperthermophilic compost

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Rong Tang ◽  
Qi Zhang ◽  
Yin Ye ◽  
Shang Yang ◽  
Tao Fu ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Shanxi Province ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
Maximum Similarity

Two aerobic, Gram-stain-positive, rod-shaped, endospore-forming, thermophilic bacterial strains, designated FJAT-54423T and FJAT-54424, were isolated from hyperthermophilic compost sampled in Shanxi Province, PR China. Growth was observed at 30–60 °C (optimum, 50 °C) and pH 6.0–9.0 (optimum, pH 7.0), with up to 2.0 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence similarity between FJAT-54423T and FJAT-54424 was 99.9%, and the maximum similarity to a valid taxon was observed with Brevibacillus borstelensis (98.3%). Further, in phylogenetic and phylogenomic trees, strains FJAT-54423T and FJAT-54424 branched with members of the genus Brevibacillus . The menaquinone was MK-7, and the major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The main polar lipids included phosphatidylmethylethanolamine, phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The cell-wall peptidoglycan was found to contain meso-diaminopimelic acid. The DNA G+C content of strains FJAT-54423T and FJAT-54424 were 54.3 and 54.4 mol%, respectively. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values of strain FJAT-54423T and its most closely related reference strain B. borstelensis DSM 6347T were 77.7 and 21.5 %, respectively, which were lower than the recommended species delineation thresholds of ANI (95%) and dDDH (70%). Based on the observed physiological properties, chemotaxonomic characteristics and ANI and dDDH values, FJAT-54423T and FJAT-54424 belong to a novel species of the genus Brevibacillus , for which the name Brevibacillus composti sp. nov. is proposed. The type strain is FJAT-54423T (=GDMCC 1.2054T=KCTC 43273T).

Lonsdalea quercina subsp. populi subsp. nov., isolated from bark canker of poplar trees

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2309-2313 ◽  
Author(s):  
Tímea Tóth ◽  
Tamás Lakatos ◽  
András Koltay
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Content Type ◽  
Link Type ◽  
Poplar Trees ◽  
Distinct Lineage

Seven Gram-negative bacterial strains were isolated from oozing bark canker of poplar (Populus×euramericana) trees in Hungary. They showed high (>98.3 %) 16S rRNA gene sequence similarity to Lonsdalea quercina ; however, they differed from this species in several phenotypic characteristics. Multilocus sequence analysis based on three housekeeping genes (gyrB, atpD and infB) revealed, and DNA–DNA hybridization analysis confirmed, that this group of bacterial strains forms a distinct lineage within the species Lonsdalea quercina . A detailed study of phenotypic and physiological characteristics confirmed the separation of isolates from poplars from other subspecies of L. quercina ; therefore, a novel subspecies, Lonsdalea quercina subsp. populi, type strain NY060T ( = DSM 25466T = NCAIM B 02483T), is proposed.

scholarly journals Kitasatospora acidiphila sp. nov., isolated from pine grove soil, exhibiting antimicrobial potential

2020 ◽  
Vol 70 (10) ◽  
pp. 5567-5575 ◽  
Author(s):  
Min Ji Kim ◽  
Su Gwon Roh ◽  
Min-Kyeong Kim ◽  
Changwoo Park ◽  
Seil Kim ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Acidic Conditions ◽  
Phosphatidylinositol Mannosides

A polyphasic study was carried out to establish the taxonomic position of an acidophilic isolate designated MMS16-CNU292T (=JCM 32302T) from pine grove soil, and provisionally assigned to the genus Kitasatospora . On the basis of 16S rRNA gene sequence similarity, the strain formed a novel evolutionary lineage within Kitasatospora and showed highest similarities to Kitasatospora azatica KCTC 9699T (98.75 %), Kitasatospora kifunensis IFO 15206T (98.74 %), Kitasatospora purpeofusca NRRL B-1817T (98.61 %) and Kitasatospora nipponensis HKI 0315T (98.42 %), respectively. Strain MMS16-CNU292T possessed MK-9(H6) and MK-9(H8) as the major menaquinones, and a major amount of meso-diaminopimelic acid in the cell-wall peptidoglycan. The whole-cell hydrolysates were rich in galactose, glucose and mannose, and the polar lipids mainly consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol and phosphatidylinositol mannosides. The major fatty acids were anteiso-C15 : 1-A, anteiso-C15 : 0, and iso-C15 : 0, and the DNA G+C content was 71.5 mol%. The strain exhibited antibacterial activity against a number of bacterial strains, and the activity was generally greater when grown in acidic conditions. The phylogenetic, chemotaxonomic and phenotypic properties enabled distinction of MMS16-CNU292T from related species, and thus the isolate should be recognized as a new species of the genus Kitasatospora , for which the name Kitasatospora acidiphila sp. nov. (type strain=MMS16-CNU292T=KCTC 49011T=JCM 32302T) is proposed.

Micromonospora kangleipakensis sp. nov., isolated from a sample of limestone quarry

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4546-4551 ◽  
Author(s):  
Salam Nimaichand ◽  
Yong-Guang Zhang ◽  
Juan Cheng ◽  
Li Li ◽  
Dao-Feng Zhang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Limestone Quarry ◽  
Link Type ◽  
Unknown Lipid

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).

Pontibacter ruber sp. nov. and Pontibacter deserti sp. nov., isolated from the desert

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 1006-1011 ◽  
Author(s):  
Y. Subhash ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Major Polar Lipid ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Hydrolysed Casein

Two strains of bacteria, JC213T and JC215T, were isolated from desert soil. Colonies were red to pink and cells Gram-stain-negative. Both strains were oxidase- and catalase-positive and hydrolysed casein. In both strains, phosphatidylethanolamine was the major polar lipid, iso-C15 : 0 was the major fatty acid and the bacteriohopane derivative, BHD1, was the major hopanoid. The genomic DNA G+C contents of strains JC213T and JC215T were 52.7 and 46.3 mol%, respectively. 16S rRNA gene sequence comparisons indicated that both strains belong to the genus Pontibacter within the family Cytophagaceae and the phylum Bacteroidetes . Strain JC213T showed the highest sequence similarity to Pontibacter populi HLY7-15T (96.6 %) and with other species of the genus Pontibacter sequence similarity was less than 96 %. Strain JC215T exhibited highest sequence similarity with Pontibacter lucknowensis DM9T (95.1 %) and shared 95 % or less sequence similarity with other species of the genus Pontibacter . The sequence similarity between strains JC213T and JC215T was 95.8 %. Distinct morphological, physiological and genotypic differences from previously described taxa support JC213T and JC215T being representatives of two novel species of the genus Pontibacter , for which the names Pontibacter ruber sp. nov. and Pontibacter deserti sp. nov. are proposed and the type strains are JC213T ( = KCTC 32442T = LMG 27669T) and JC215T ( = KCTC 32443T = LMG 27670T), respectively.

scholarly journals Streptomyces lasalocidi sp. nov. (formerly ‘Streptomyces lasaliensis’), an actinomycete isolated from soil which produces the polyether antibiotic lasalocid

2020 ◽  
Vol 70 (5) ◽  
pp. 3076-3083 ◽  
Author(s):  
Gary S. Erwin ◽  
Jouni Heikkinen ◽  
Pauliina Halimaa ◽  
Christopher L. Haber
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Description

Strain ATCC 31180T was isolated from soil collected in Hyde Park, Massachusetts (USA), and found to produce the polyether antibiotic lasalocid. The name ‘Streptomyces lasaliensis’ has been in common use since 1974, without a recognized taxonomic description. The most closely related type cultures determined by rRNA gene sequence similarity were Streptomyces longwoodensis DSM 41677T (100 %) and Streptomyces galbus DSM 40089T (100 %). OrthoANI values with S. longwoodensis and S. galbus were 95.50 and 94.41 %, respectively. Chemotaxonomic characteristics supported inclusion within the genus Streptomyces . The cell wall peptidoglycan contained ll-diaminopimelic acid, and the major whole-cell sugars were glucose and ribose. Polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol, one unidentified lipid and one unidentified glycolipid. The major menaquinones detected were MK9(H4), MK9(H6) and MK9(H8). The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0, iso-C15 : 0 and anteiso-C17 : 1. Its DNA had a G+C content of 72.6 %. Differentiation of ATCC 31180T from the closely related species was evident from digital DNA–DNA hybridization values of 61.80 and 56.90 % for S. longwoodensis and S. galbus respectively. Significant differences were seen in the polyphasic phenotypic analyses. ATCC 31180T produced lasalocid, grew from 10 to 45 °C, pH4-8 and in the presence of 0–10 % NaCl, 0.01 % NaN3 and 1 % phenol. Melanin was produced; H2S and indole were not. Nitrate was not reduced. Spore chains were retinaculum-apertum and spore surfaces were smooth. Spore colour, mycelia colour and soluble pigment production were medium-dependent. The proposed name is Streptomyces lasalocidi sp. nov.; the type strain being ATCC 31180T (=NRRL 3382T=DSM 46487T).

Salinimicrobium sediminis sp. nov., isolated from a deep-sea sediment

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 984-988 ◽  
Author(s):  
Y. Subhash ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Major Polar Lipid ◽  
Sequence Comparisons ◽  
Content Type ◽  
Deep Sea Sediment ◽  
Link Type

Strain JC207T was isolated from a deep (265 m) sea sediment, and appeared as dark yellow colonies on agar plates with cells staining Gram-negative. Catalase, oxidase and caseinase were positive, while chitinase, gelatinase and amylase were negative. Major (>5 %) fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 1ω9c, iso-C16 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH, iso-C14 : 0 and iso-C15 : 1G. Strain JC207T contained phosphatidylethanolamine as the major polar lipid, with minor amounts of five unidentified lipids. A bacterial hopane derivative, diplopterol and adenosylhopane were the major hopanoids. Genomic DNA G+C content was 47.5 mol%. 16S rRNA gene sequence comparisons indicated that strain JC207T represented a member of the genus Salinimicrobium within the family Flavobacteriaceae of the phylum Bacteroidetes . Strain JC207T had sequence similarity with Salinimicrobium terrae YIM-C338T (98 %), Salinimicrobium xinjiangense BH206T (97.6 %) and other members of the genus Salinimicrobium (<96.8 %). However, strain JC207T showed an average of 23.6±4 and 37±4 relatedness (based on DNA–DNA hybridization) with Salinimicrobium terrae CGMCC 1.6308T ( = YIM-C338T) and Salinimicrobium xinjiangense KCTC 12883T ( = BH206T), respectively. Morphological, physiological and genotypic differences from the previously described taxa support the classification of strain JC207T as a representative of a novel species in the genus Salinimicrobium , for which the name Salinimicrobium sediminis sp. nov. is proposed. The type strain is JC207T ( = KCTC 32444T = CGMCC 1.12641T).

Bacillus thermocopriae sp. nov., isolated from a compost

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3024-3029 ◽  
Author(s):  
Luchao Han ◽  
Guiqin Yang ◽  
Xuemei Zhou ◽  
Dehui Yang ◽  
Pei Hu ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Hybridization Experiment ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph

A Gram-reaction-positive, facultatively anaerobic, motile, endospore-forming, rod-shaped strain, designated SgZ-7T, was isolated from a windrow compost pile and was characterized by means of a polyphasic approach. Growth occurred with 0–3 % (w/v) NaCl (optimum 1 %), at pH 6.0–10.0 (optimum pH 7.2) and at 40–60 °C (optimum 50 °C). The main respiratory quinone was MK-7. The predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The DNA G+C content was 46.6 mol%. The phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain SgZ-7T should be assigned to the genus Bacillus and was related most closely to Bacillus drentensis LMG 21831T (sequence similarity 97.2 %). The result of the DNA–DNA hybridization experiment revealed a low relatedness (27.2 %) between the isolate and B. drentensis LMG 21831T. The results of phenotypic, chemotaxonomic and genotypic analyses clearly indicated that strain SgZ-7T represents a novel species, for which the name Bacillus thermocopriae sp. nov. is proposed. The type strain is SgZ-7T ( = CCTCC AB 2012030T = KACC 16700T).

scholarly journals Sphingopyxis italica sp. nov., isolated from Roman catacombs

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2565-2569 ◽  
Author(s):  
Cynthia Alias-Villegas ◽  
Valme Jurado ◽  
Leonila Laiz ◽  
Cesareo Saiz-Jimenez
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Dna Base ◽  
Physiological Tests

A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, strain SC13E-S71T, was isolated from tuff, volcanic rock, where the Roman catacombs of Saint Callixtus in Rome, Italy, was excavated. Analysis of 16S rRNA gene sequences revealed that strain SC13E-S71T belongs to the genus Sphingopyxis , and that it shows the greatest sequence similarity with Sphingopyxis chilensis DSM 14889T (98.72 %), Sphingopyxis taejonensis DSM 15583T (98.65 %), Sphingopyxis ginsengisoli LMG 23390T (98.16 %), Sphingopyxis panaciterrae KCTC 12580T (98.09 %), Sphingopyxis alaskensis DSM 13593T (98.09 %), Sphingopyxis witflariensis DSM 14551T (98.09 %), Sphingopyxis bauzanensis DSM 22271T (98.02 %), Sphingopyxis granuli KCTC 12209T (97.73 %), Sphingopyxis macrogoltabida KACC 10927T (97.49 %), Sphingopyxis ummariensis DSM 24316T (97.37 %) and Sphingopyxis panaciterrulae KCTC 22112T (97.09 %). The predominant fatty acids were C18 : 1ω7c, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), C14 : 0 2-OH and C16 : 0. The predominant menaquinone was MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. These chemotaxonomic data are common to members of the genus Sphingopyxis . However, a polyphasic approach using physiological tests, DNA base ratios, DNA–DNA hybridization and 16S rRNA gene sequence comparisons showed that the isolate SC13E-S71T belongs to a novel species within the genus Sphingopyxis , for which the name Sphingopyxis italica sp. nov. is proposed. The type strain is SC13E-S71T ( = DSM 25229T = CECT 8016T).

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