scholarly journals Isolation and Identification of Microvirga thermotolerans HR1, a Novel Thermo-Tolerant Bacterium, and Comparative Genomics among Microvirga Species

2020 ◽  
Vol 8 (1) ◽  
pp. 101 ◽  
Author(s):  
Jiang Li ◽  
Ruyu Gao ◽  
Yun Chen ◽  
Dong Xue ◽  
Jiahui Han ◽  
...  
Keyword(s):  
Root Nodule ◽  
Functional Differentiation ◽  
High Ratio ◽  
Nodule Formation ◽  
Rrna Gene ◽  
Isolation And Identification ◽  
Growth Optimum ◽  
Gene Sequence Analysis ◽  
Radiation Resistant ◽  
Ph Range

Members of the Microvirga genus are metabolically versatile and widely distributed in Nature. However, knowledge of the bacteria that belong to this genus is currently limited to biochemical characteristics. Herein, a novel thermo-tolerant bacterium named Microvirga thermotolerans HR1 was isolated and identified. Based on the 16S rRNA gene sequence analysis, the strain HR1 belonged to the genus Microvirga and was highly similar to Microvirga sp. 17 mud 1-3. The strain could grow at temperatures ranging from 15 to 50 °C with a growth optimum at 40 °C. It exhibited tolerance to pH range of 6.0–8.0 and salt concentrations up to 0.5% (w/v). It contained ubiquinone 10 as the predominant quinone and added group 8 as the main fatty acids. Analysis of 11 whole genomes of Microvirga species revealed that Microvirga segregated into two main distinct clades (soil and root nodule) as affected by the isolation source. Members of the soil clade had a high ratio of heat- or radiation-resistant genes, whereas members of the root nodule clade were characterized by a significantly higher abundance of genes involved in symbiotic nitrogen fixation or nodule formation. The taxonomic clustering of Microvirga strains indicated strong functional differentiation and niche-specific adaption.

scholarly journals Fuchsiella ferrireducens sp. nov., a novel haloalkaliphilic, lithoautotrophic homoacetogen capable of iron reduction, and emendation of the description of the genus Fuchsiella

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2432-2440 ◽  
Author(s):  
Tatyana N. Zhilina ◽  
Daria G. Zavarzina ◽  
Ekaterina N. Detkova ◽  
Ekaterina O. Patutina ◽  
Boris B. Kuznetsov
Keyword(s):  
Dna Hybridization ◽  
Iron Reduction ◽  
Gene Sequence ◽  
Soda Lake ◽  
Chloride Ions ◽  
Electron Donors ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequence Analysis ◽  
Ph Range

Two strains of haloalkaliphilic homoacetogenic bacteria capable of iron reduction, Z-7101T and Z-7102, were isolated from soda lake Tanatar III (Altai, Russia). Cells of both strains were flexible, motile, Gram-negative, spore-forming rods. The strains were mesophilic and obligately alkaliphilic: the pH range for growth was 8.5–10.2 (pHopt 9.8). Growth depended on carbonate and chloride ions. The strains were able to grow chemolithoautotrophically on H2+CO2, producing acetate as the only metabolic product. In medium with carbonates as the only potential electron acceptor, the following substrates were utilized for chemo-organotrophic growth: pyruvate, lactate, ethanol, 1-propanol, ethylene glycol and 1-butanol. Strain Z-7101T was able to reduce nitrate, selenate, thiosulfate and anthraquinone 2,6-disulfonate with ethanol as an electron donor. It was also able to reduce synthesized ferrihydrite to siderite with molecular hydrogen or organic compounds, including acetate and formate, as electron donors. It was able to reduce S0 with acetate or formate as electron donors. The DNA G+C content of strain Z-7101T was 34.6 mol%. 16S rRNA gene sequence analysis showed that strains Z-7101T and Z-7102 were members of the order Halanaerobiales and family Halobacteroidaceae, clustering with Fuchsiella alkaliacetigena Z-7100T (98.9–98.4 % similarity). DNA–DNA hybridization was 63.0 % between strain Z-7101T and F. alkaliacetigena Z-7100T. Based on morphological and physiological differences from F. alkaliacetigena Z-7100T and the results of phylogenetic analysis and DNA–DNA hybridization, it is proposed to assign strains Z-7101T and Z-7102 ( = DSM 26052 = VKM B-2790) to the novel species Fuchsiella ferrireducens sp. nov. The type strain is strain Z-7101T ( = DSM 26031T = VKM B-2766T).

Isolation and Identification of a New Pathogen Causing Mulberry Bacterial Wilt Disease

2011 ◽  
Vol 282-283 ◽  
pp. 526-530
Author(s):  
Xing Jiang ◽  
Fu An Wu ◽  
Shui Qin Fang ◽  
Yan Dong Zhang ◽  
Jun Wang ◽  
...  
Keyword(s):  
Plant Disease ◽  
Gene Sequence ◽  
Hypersensitive Reaction ◽  
Wilt Disease ◽  
Rrna Gene ◽  
Isolation And Identification ◽  
Physiological Characterization ◽  
Bacterial Wilt Disease ◽  
Gene Sequence Analysis ◽  
The 16S Rrna Gene

To identify the pathogen of Mulberry wilt disease, a tested strain WJ-1 was isolated from a naturally infected mulberry in Guangzhou, Guangdong province, P. R. China. Hypersensitive reaction, along with Koch’s postulates, morphological, biochemical and physiological characterization, light microscope observation and molecular identification were performed on WJ-1. The results indicated that WJ-1 was a Gram-negative, short-rod shaped bacterium. Based on morphology and the 16S rRNA gene sequence analysis, WJ-1 strain was identified as members of the genusEnterobacter. The phylogenetic tree revealed that WJ-1 shared the highest homology withEnterobacter cloacaestrain M5. It was another evidence on plant disease caused byEnterobacterspecies. We found thatEnterobacterspecies could cause mulberry wilt disease in Guangzhou.

scholarly journals Thermococcus thioreducens sp. nov., a novel hyperthermophilic, obligately sulfur-reducing archaeon from a deep-sea hydrothermal vent

2007 ◽  
Vol 57 (7) ◽  
pp. 1612-1618 ◽  
Author(s):  
Elena V. Pikuta ◽  
Damien Marsic ◽  
Takashi Itoh ◽  
Asim K. Bej ◽  
Jane Tang ◽  
...  
Keyword(s):  
Hydrothermal Vent ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Black Smoker ◽  
Separate Species ◽  
Gene Sequence Analysis ◽  
Nacl Concentration ◽  
Mid Atlantic Ridge ◽  
Casamino Acids ◽  
Ph Range

A hyperthermophilic, sulfur-reducing, organo-heterotrophic archaeon, strain OGL-20PT, was isolated from ‘black smoker’ chimney material from the Rainbow hydrothermal vent site on the Mid-Atlantic Ridge (36.2°N, 33.9°W). The cells of strain OGL-20PT have an irregular coccoid shape and are motile with a single flagellum. Growth was observed within a pH range of 5.0−8.5 (optimum pH 7.0), an NaCl concentration range of 1–5 % (w/v) (optimum 3 %) and a temperature range of 55–94 °C (optimum 83–85 °C). The novel isolate is strictly anaerobic and obligately dependent upon elemental sulfur as an electron acceptor, but it does not reduce sulfate, sulfite, thiosulfate, Fe(III) or nitrate. Proteolysis products (peptone, bacto-tryptone, Casamino acids and yeast extract) are utilized as substrates during sulfur reduction. Strain OGL-20PT is resistant to ampicillin, chloramphenicol, kanamycin and gentamicin, but sensitive to tetracycline and rifampicin. The G+C content of the DNA is 52.9 mol%. The 16S rRNA gene sequence analysis revealed that strain OGL-20PT is closely related to Thermococcus coalescens and related species, but no significant homology by DNA–DNA hybridization was observed between those species and the new isolate. On the basis of physiological and molecular properties of the new isolate, we conclude that strain OGL-20PT represents a new separate species within the genus Thermococcus, for which we propose the name Thermococcus thioreducens sp. nov. The type strain is OGL-20PT (=JCM 12859T=DSM 14981T=ATCC BAA-394T).

scholarly journals Paenibacillus medicaginis sp. nov. a chitinolytic endophyte isolated from a root nodule of alfalfa (Medicago sativa L.)

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3853-3860 ◽  
Author(s):  
Wei-An Lai ◽  
Asif Hameed ◽  
Shih-Yao Lin ◽  
Mei-Hua Hung ◽  
Yi-Han Hsu ◽  
...  
Keyword(s):  
Medicago Sativa ◽  
Root Nodule ◽  
Sequence Similarity ◽  
Endophytic Bacterium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
Diamino Acid

A Gram-stain-variable, short-rod-shaped, endospore-forming, strictly aerobic, non-motile, chitinolytic and endophytic bacterium, designated strain CC-Alfalfa-19T, exhibiting unusual bipolar appendages was isolated from a root nodule of alfalfa (Medicago sativa L.) in Taiwan and subjected to a polyphasic taxonomic study. Based on 16S rRNA gene sequence analysis, strain CC-Alfalfa-19T was found to be most closely related to Paenibacillus puldeungensis CAU 9324T (95.2 %), whereas other species of the genus Paenibacillus shared ≤ 95.0 % sequence similarity. The phylogenetic analysis revealed a distinct phyletic lineage established by strain CC-Alfalfa-19T with respect to other species of the genus Paenibacillus. Fatty acids comprised predominantly anteiso-C15 : 0, C16 : 0, anteiso-C17 : 0 and iso-C16 : 0. Menaquinone 7 (MK-7) was identified as the sole respiratory quinone and the genomic DNA G+C content was 42.7 mol%. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, an unidentified glycolipid and an unidentified lipid. The diagnostic diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. Based on the polyphasic taxonomic evidence that was in line with the genus Paenibacillus and additional distinguishing characteristics, strain CC-Alfalfa-19T is considered to represent a novel species, for which the name Paenibacillus medicaginis sp. nov. (type strain CC-Alfalfa-19T = BCRC 80441T = JCM 18446T) is proposed.

scholarly journals Chromohalobacter sarecensis sp. nov., a psychrotolerant moderate halophile isolated from the saline Andean region of Bolivia

2004 ◽  
Vol 54 (6) ◽  
pp. 1921-1926 ◽  
Author(s):  
Jorge Quillaguamán ◽  
Osvaldo Delgado ◽  
Bo Mattiasson ◽  
Rajni Hatti-Kaul
Keyword(s):  
Gene Sequence ◽  
Rrna Gene ◽  
Moderate Halophile ◽  
Bolivian Andes ◽  
Gene Sequence Analysis ◽  
Nutritional Characteristics ◽  
Laguna Verde ◽  
Bacterium Strain ◽  
Ph Range ◽  
Type Strains

A moderately halophilic, aerobic, motile, Gram-negative, rod-shaped bacterium (strain LV4T) was isolated from saline soil around the lake Laguna Verde in the Bolivian Andes. The organism is a heterotroph, able to utilize various carbohydrates as a carbon source. It showed tryptophan deaminase, oxidase and catalase activity, but was unable to produce indole or H2S; nitrate was not reduced. The G+C content of the genomic DNA was 56·1 mol%. The pH range for growth was 5–10, temperature range was 0–45 °C and the range of NaCl concentrations was 0–25 % (w/v). On the basis of 16S rRNA gene sequence analysis, strain LV4T was found to be closely related to Chromohalobacter canadensis DSM 6769T and Pseudomonas beijerinckii DSM 7218T; however, its DNA–DNA relatedness with these type strains was low. Strain LV4T resembled other Chromohalobacter species with respect to various physiological, biochemical and nutritional characteristics but also exhibited differences. Thus, a novel species, Chromohalobacter sarecensis sp. nov., is proposed, with LV4T (=CCUG 47987T=ATCC BAA-761T) as the type strain.

scholarly journals Natrinema ejinorense sp. nov., isolated from a saline lake in Inner Mongolia, China

2006 ◽  
Vol 56 (11) ◽  
pp. 2683-2687 ◽  
Author(s):  
A. M. Castillo ◽  
M. C. Gutiérrez ◽  
M. Kamekura ◽  
Y. Xue ◽  
Y. Ma ◽  
...  
Keyword(s):  
Inner Mongolia ◽  
Saline Lake ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Growth Optimum ◽  
The Family ◽  
Hypotonic Treatment ◽  
Extremely Halophilic Archaeon ◽  
Ph Range ◽  
Derivatives Of

A Gram-negative, non-motile, neutrophilic, pleomorphic and extremely halophilic archaeon, strain EJ-57T, was isolated from saline Lake Ejinor in Inner Mongolia, China. Strain EJ-57T was able to grow at 25–50 °C, required at least 1.8 M NaCl for growth (optimum at 3.4 M NaCl) and grew over a pH range from 6.0 to 8.5 (optimum at pH 7.0). Hypotonic treatment with less than 1.5 M NaCl caused cell lysis. Analysis of the almost complete 16S rRNA gene sequence indicated that the isolate represented a member of the genus Natrinema in the family Halobacteriaceae. Strain EJ-57T was most closely related to Natrinema versiforme JCM 10478T (96.2 % sequence similarity), Natrinema pallidum NCIMB 777T (95.9 % sequence similarity), Natrinema altunense JCM 12890T (95.8 % sequence similarity) and Natrinema pellirubrum NCIMB 786T (95.5 % sequence similarity). However, DNA–DNA hybridization experiments showed that strain EJ-57T was not related to these species, with levels of DNA–DNA relatedness equal to or below 39 %. The major polar lipids of the isolate were C20C20 and C20C25 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and the disulfated glycolipid S2-DGA-1. The G+C content of the genomic DNA was 64.7 mol%. Comparative analysis of phenotypic characteristics between strain EJ-57T and recognized Natrinema species supported the conclusion that EJ-57T represents a novel species within this genus, for which the name Natrinema ejinorense sp. nov. is proposed. The type strain is EJ-57T (=CECT 7144T=JCM 13890T=CGMCC 1.6202T).

scholarly journals Deinobacterium chartae gen. nov., sp. nov., an extremely radiation-resistant, biofilm-forming bacterium isolated from a Finnish paper mill

2011 ◽  
Vol 61 (3) ◽  
pp. 540-548 ◽  
Author(s):  
Jaakko V. Ekman ◽  
Mari Raulio ◽  
Hans-Jürgen Busse ◽  
David P. Fewer ◽  
Mirja Salkinoja-Salonen
Keyword(s):  
Polar Lipid ◽  
Paper Mill ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Separate Branch ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Novel Genus And Species ◽  
Radiation Resistant

A rod-shaped, non-spore-forming, non-motile, aerobic, oxidase and catalase-positive and radiation-resistant bacterium (designated strain K4.1T) was isolated from biofilm collected from a Finnish paper mill. The bacterium grew as pale pink colonies on oligotrophic medium at 12 to 50 °C (optimum 37 to 45 °C) and at pH 6 to 10.3. The DNA G+C content of the strain was 66.8 mol%. According to 16S rRNA gene sequence analysis, strain K4.1T was distantly related to the genus Deinococcus, sharing highest similarity with Deinococcus pimensis (90.0 %). In the phylogenetic tree, strain K4.1T formed a separate branch in the vicinity of the genus Deinococcus. The peptidoglycan type was A3β with l-Orn–Gly–Gly and the quinone system was determined to be MK-8. The polar lipid profile of strain K4.1T differed markedly from that of the genus Deinococcus. The predominant lipid of strain K4.1T was an unknown aminophospholipid and it did not contain the unknown phosphoglycolipid predominant in the polar lipid profiles of deinococci analysed to date. Two of the predominant fatty acids of the strain, 15 : 0 anteiso and 17 : 0 anteiso, were lacking or present in small amounts in species of the genus Deinococcus. Phylogenetic distinctness and significant differences in the polar lipid and fatty acid profiles suggest classification of strain K4.1T as a novel genus and species in the family Deinococcaceae, for which we propose the name Deinobacterium chartae gen. nov., sp. nov. The type strain is K4.1T (=DSM 21458T =HAMBI 2721T).

scholarly journals Methylotenera mobilis gen. nov., sp. nov., an obligately methylamine-utilizing bacterium within the family Methylophilaceae

2006 ◽  
Vol 56 (12) ◽  
pp. 2819-2823 ◽  
Author(s):  
Marina G. Kalyuzhnaya ◽  
Sarah Bowerman ◽  
Jimmie C. Lara ◽  
Mary E. Lidstrom ◽  
Ludmila Chistoserdova
Keyword(s):  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Methylamine Dehydrogenase ◽  
Carbon And Nitrogen ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Lake Washington ◽  
Ribulose Monophosphate Cycle ◽  
Ph Range ◽  
Single Flagellum

A novel obligate methylamine utilizer (strain JLW8T), isolated from Lake Washington sediment, was characterized taxonomically. The isolate was an aerobic, Gram-negative bacterium. Cells were rod-shaped and motile by means of a single flagellum. Reproduction was by binary fission and no resting bodies were formed. Growth was observed within a pH range of 5–8.5, with optimum growth at pH 7.5. It utilized methylamine as a single source of energy, carbon and nitrogen. Methylamine was oxidized via methylamine dehydrogenase and formaldehyde was assimilated via the ribulose monophosphate cycle. The cellular fatty acid profile was dominated by C16 : 0 ω7c and C16 : 0 and the major phospholipid was phosphatidylethanolamine. The DNA G+C content was 54 mol%. 16S rRNA gene sequence analysis indicated that the new isolate was closely related (97–98 % similarity) to a broad group of sequences from uncultured or uncharacterized Betaproteobacteria, but only distantly related (93–96 % similarity) to known methylotrophs of the family Methylophilaceae. Strain JLW8T (=ATCC BAA-1282T=DSM 17540T) is proposed as the type strain of a novel species in a new genus within the family Methylophilaceae, Methylotenera mobilis gen. nov., sp. nov.

scholarly journals Isolation and Identification of Streptomyces spp. from Desert and Savanna Soils in Sudan

2020 ◽  
Vol 17 (23) ◽  
pp. 8749
Author(s):  
Mohamed E. Hamid ◽  
Adil Mahgoub ◽  
Abdulrhman J. O. Babiker ◽  
Hussein A. E. Babiker ◽  
Mohammed A. I. Holie ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Antibiotic Production ◽  
Rrna Gene ◽  
Isolation And Identification ◽  
Streptomyces Sp ◽  
Ecological Zones ◽  
Streptomyces Spp ◽  
Gene Sequence Analysis ◽  
Unique Species

The purpose of this study was to investigate streptomycete populations in desert and savanna ecozones in Sudan and to identify species based on 16S rRNA gene sequences. A total of 49 different Streptomyces phenotypes (22 from sites representing the desert and semi-desert ecozone; 27 representing the savanna ecozone) have been included in the study. The isolates were characterized phenotypically and confirmed using 16S rRNA gene sequence analysis. The two ecozones showed both similarities and uniqueness in the types of isolates. The shared species were in cluster 1 (Streptomyces (S.) werraensis), cluster 2 (Streptomyces sp.), cluster 3 (S. griseomycini-like), and cluster 7 (S. rochei). The desert ecozone revealed unique species in cluster 9 (Streptomyces sp.) and cluster 10 (S. griseomycini). Whereas, the savanna ecozone revealed unique species in cluster 4 (Streptomyces sp.), cluster 5 (S. albogriseolus/ S. griseoincarnatus), cluster 6 (S. djakartensis), and cluster 8 (Streptomyces sp.). Streptomycetes are widely distributed in both desert and the savanna ecozones and many of these require full descriptions. Extending knowledge on Streptomyces communities and their dynamics in different ecological zones and their potential antibiotic production is needed.

scholarly journals Carnobacterium pleistocenium sp. nov., a novel psychrotolerant, facultative anaerobe isolated from permafrost of the Fox Tunnel in Alaska

2005 ◽  
Vol 55 (1) ◽  
pp. 473-478 ◽  
Author(s):  
Elena V. Pikuta ◽  
Damien Marsic ◽  
Asim Bej ◽  
Jane Tang ◽  
Paul Krader ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Optimum Growth ◽  
Facultative Anaerobe ◽  
Phenotypic Characteristics ◽  
Gene Sequence Analysis ◽  
Ph Range

A novel, psychrotolerant, facultative anaerobe, strain FTR1T, was isolated from Pleistocene ice from the permafrost tunnel in Fox, Alaska. Gram-positive, motile, rod-shaped cells were observed with sizes 0·6–0·7×0·9–1·5 μm. Growth occurred within the pH range 6·5–9·5 with optimum growth at pH 7·3–7·5. The temperature range for growth of the novel isolate was 0–28 °C and optimum growth occurred at 24 °C. The novel isolate does not require NaCl; growth was observed between 0 and 5 % NaCl with optimum growth at 0·5 % (w/v). The novel isolate was a catalase-negative chemoorganoheterotroph that used as substrates sugars and some products of proteolysis. The metabolic end products were acetate, ethanol and CO2. Strain FTR1T was sensitive to ampicillin, tetracycline, chloramphenicol, rifampicin, kanamycin and gentamicin. 16S rRNA gene sequence analysis showed 99·8 % similarity between strain FTR1T and Carnobacterium alterfunditum, but DNA–DNA hybridization between them demonstrated 39±1·5 % relatedness. On the basis of genotypic and phenotypic characteristics, it is proposed that strain FTR1T (=ATCC BAA-754T=JCM 12174T=CIP 108033T) be assigned to the novel species Carnobacterium pleistocenium sp. nov.

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