scholarly journals Degradation and Mineralization of Nanomolar Concentrations of the Herbicide Dichlobenil and Its Persistent Metabolite 2,6-Dichlorobenzamide by Aminobacter spp. Isolated from Dichlobenil-Treated Soils

2006 ◽  
Vol 73 (2) ◽  
pp. 399-406 ◽  
Author(s):  
Sebastian R. Sørensen ◽  
Maria S. Holtze ◽  
Allan Simonsen ◽  
Jens Aamand
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Selective Advantage ◽  
Fatty Acid Analysis ◽  
Rrna Gene ◽  
Chlorobenzoic Acid ◽  
Carbon And Nitrogen ◽  
Plant Nursery ◽  
Rrna Gene Sequencing ◽  
Related Compounds ◽  
Type Strains

ABSTRACT 2,6-Dichlorobenzamide (BAM), a persistent metabolite from the herbicide 2,6-dichlorobenzonitrile (dichlobenil), is the pesticide residue most frequently detected in Danish groundwater. A BAM-mineralizing bacterial community was enriched from dichlobenil-treated soil sampled from the courtyard of a former plant nursery. A BAM-mineralizing bacterium (designated strain MSH1) was cultivated and identified by 16S rRNA gene sequencing and fatty acid analysis as being closely related to members of the genus Aminobacter, including the only cultured BAM degrader, Aminobacter sp. strain ASI1. Strain MSH1 mineralized 15 to 64% of the added [ring-U-14C]BAM to 14CO2 with BAM at initial concentrations in the range of 7.9 nM to 263.1 μM provided as the sole carbon, nitrogen, and energy source. A quantitative enzyme-linked immunoassay analysis with antibodies against BAM revealed residue concentrations of 0.35 to 18.05 nM BAM following incubation for 10 days, corresponding to a BAM depletion of 95.6 to 99.9%. In contrast to the Aminobacter sp. strain ASI1, strain MSH1 also mineralized the herbicide itself along with several metabolites, including ortho-chlorobenzonitrile, ortho-chlorobenzoic acid, and benzonitrile, making it the first known dichlobenil-mineralizing bacterium. Aminobacter type strains not previously exposed to dichlobenil or BAM were capable of degrading nonchlorinated structural analogs. Combined, these results suggest that closely related Aminobacter strains may have a selective advantage in BAM-contaminated environments, since they are able to use this metabolite or structurally related compounds as a carbon and nitrogen source.

scholarly journals Nocardia amamiensis sp. nov., isolated from a sugar-cane field in Japan

2007 ◽  
Vol 57 (7) ◽  
pp. 1599-1602 ◽  
Author(s):  
Hideki Yamamura ◽  
Tomohiko Tamura ◽  
Yayoi Sakiyama ◽  
Shigeaki Harayama
Keyword(s):  
Sugar Cane ◽  
16S Rrna Gene Sequencing ◽  
Treatment Method ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Sequencing Studies ◽  
Actinomycete Strain ◽  
Pre Treatment ◽  
Rrna Gene Sequencing ◽  
Type Strains

An actinomycete, strain TT 00-78T, was isolated from soil from a sugar-cane field on Amami Island in Japan, using an SDS/yeast extract pre-treatment method, and the taxonomy was studied using a polyphasic approach. The chemotaxonomic and morphological characterizations clearly demonstrated that the strain belongs to the genus Nocardia. 16S rRNA gene sequencing studies showed that the strain was closely related to the type strains of Nocardia pneumoniae (98.6 %), Nocardia araoensis (98.1 %), Nocardia arthritidis (97.9 %) and Nocardia beijingensis (97.7 %). However, the results of DNA–DNA hybridization and physiological and biochemical tests showed that strain TT 00-78T could be differentiated from its closest phylogenetic relatives both genotypically and phenotypically. Therefore this strain represents a novel species of the genus Nocardia, for which the name Nocardia amamiensis sp. nov. is proposed. The type strain is TT 00-78T (=NBRC 102102T=DSM 45066T=KCTC 19208T).

Methanoculleus horonobensis sp. nov., a methanogenic archaeon isolated from a deep diatomaceous shale formation

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4320-4323 ◽  
Author(s):  
Satoru Shimizu ◽  
Akio Ueno ◽  
Shuji Tamamura ◽  
Takeshi Naganuma ◽  
Katsuhiko Kaneko
Keyword(s):  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Shale Formation ◽  
Rrna Gene Sequencing ◽  
Type Strains

A methanogenic organism from the domain Archaea , designated strain T10T, was isolated from groundwater sampled from a deep diatomaceous shale formation located in Horonobe, Hokkaido, Japan. The strain utilized H2/CO2 and formate as substrates for methanogenesis. Cells were strictly anaerobic, Gram-negative-staining, flagellated, irregular coccoids, 0.7–1.6 µm in diameter, and occurred singly. The strain grew at 25–45 °C (optimum 37–42 °C), at pH 5.8–8.2 (optimum pH 6.7–6.8) and in the presence of 0–1.3 M NaCl (optimum 0.1–0.2 M NaCl). The G+C content of the genomic DNA was 62.9 mol%. 16S rRNA gene sequencing revealed that, although the strain is a member of the genus Methanoculleus , it clearly differed from all described species of this genus (95.5–98.3 % sequence similarity). Values for DNA–DNA hybridization with type strains of closely related Methanoculleus species were less than 50 %. Phenotypic and phylogenetic features of strain T10T clearly indicate that it represents a novel species of the genus Methanoculleus , for which the name Methanoculleus horonobensis sp. nov. is proposed. The type strain is T10T ( = DSM 21626T = JCM 15517T).

scholarly journals Biodecolorization of Azo Dye Acid Blue 113 by Soil Bacterium Klebsiella variicola RMLP1

2021 ◽  
Vol 21 (2) ◽  
pp. 64
Author(s):  
Pradeep Kumar Singh ◽  
Pankaj Singh ◽  
Rajat Pratap Singh ◽  
Ram Lakhan Singh
Keyword(s):  
Azo Dye ◽  
Textile Wastewater ◽  
16S Rrna Gene Sequencing ◽  
Optimum Process ◽  
Rrna Gene ◽  
Carbon And Nitrogen ◽  
Physico Chemical ◽  
Rrna Gene Sequencing ◽  
Acid Blue 113 ◽  
Acid Blue

The present study was aimed to isolate a new bacterial strain for the degradation/decolorization of azo dye Acid Blue 113 (AB 113). The physico-chemical method is inadequate for degradation of azo dyes; therefore, an environmental friendly and competent method such as use of the biological organism was studied for decolorization of AB 113. Bushnell and Hass (BHM) medium containing AB 113 dye were used to perform the decolorization study. 16S rRNA gene sequencing approach was used for identification of bacterial isolate as a <em>Klebsiella variicola</em>. The optimum process parameters for the decolorization of AB 113 were found at pH 8, 35°C temperature and 100 mg/L dye concentration during 72 h incubation. Glucose and ammonium sulphate was the carbon and nitrogen source suited well for the decolorization of dye. The results proved that the <em>Klebsiella variicola</em>, offer huge ability in treating textile wastewater containing the color AB 113.

scholarly journals Fulvivirga kasyanovii gen. nov., sp. nov., a novel member of the phylum Bacteroidetes isolated from seawater in a mussel farm

2007 ◽  
Vol 57 (5) ◽  
pp. 1046-1049 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Seung Bum Kim ◽  
Dong Sung Shin ◽  
Irina A. Beleneva ◽  
Valery V. Mikhailov
Keyword(s):  
Marine Bacterium ◽  
New Genus ◽  
Novel Species ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequencing ◽  
Taxonomic Approach ◽  
Type Strains

A novel, strictly aerobic, heterotrophic, gliding, Gram-negative, oxidase-, catalase-, β-galactosidase- and alkaline phosphatase-positive marine bacterium, designated strain KMM 6220T, was isolated from seawater and studied by using a polyphasic taxonomic approach. The DNA G+C content of strain KMM 6220T was 59.9 mol%. The predominant fatty acids were iso-C15 : 1, iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and C16 : 1 ω7/iso-C15 : 0 2-OH. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that strain KMM 6220T formed a cluster with the misclassified strains [Flexibacter] aggregans NBRC 15974 and [Flexibacter] tractuosus NBRC 16035 and with the type strains of Reichenbachiella agariperforans and Roseivirga ehrenbergii with levels of similarity of 95.9, 94.4, 92.0 and 91.8 %, respectively. On the basis of its phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, strain KMM 6220T is considered to represent a novel species of a new genus in the phylum Bacteroidetes, for which the name Fulvivirga kasyanovii gen. nov., sp. nov. is proposed. The type strain of the type species is KMM 6220T (=CCTCC AB 206119T=KCTC 12832T).

scholarly journals Characterization of Rhizobial Bacteria Nodulating Astragalus corrugatus and Hippocrepis areolata in Tunisian Arid Soils

2016 ◽  
Vol 65 (3) ◽  
pp. 331-339 ◽  
Author(s):  
Mosbah Mahdhi ◽  
Nadia Houidheg ◽  
Neji Mahmoudi ◽  
Abdelhakim Msaadek ◽  
Mokhtar Rejili ◽  
...  
Keyword(s):  
Host Plants ◽  
Root Nodules ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Carbon And Nitrogen ◽  
16S Rdna Pcr ◽  
Pcr Rflp ◽  
Phenotypic Features ◽  
Rrna Gene Sequencing

Fifty seven bacterial isolates from root nodules of two spontaneous legumes (Astragalus corrugatus and Hippocrepis areolata) growing in the arid areas of Tunisia were characterized by phenotypic features, 16S rDNA PCR-RFLP and 16S rRNA gene sequencing. Phenotypically, our results indicate that A. corrugatus and H. areolata isolates showed heterogenic responses to the different phenotypic features. All isolates were acid producers, fast growers and all of them used different compounds as sole carbon and nitrogen source. The majority of isolate grew at pHs between 6 and 9, at temperatures up to 40°C and tolerated 3% NaCl concentrations. Phylogenetically, the new isolates were affiliated to four genera Sinorhizobium, Rhizobium, Mesorhizobium and Agrobacterium. About 73% of the isolates were species within the genera Sinorhizobium and Rhizobium. The isolates which failed to nodulate their host plants of origin were associated to Agrobacterium genus (three isolates).

scholarly journals Cat Scratch Disease: the Rare Role ofAfipia felis

1998 ◽  
Vol 36 (9) ◽  
pp. 2499-2502 ◽  
Author(s):  
Michael Giladi ◽  
Boaz Avidor ◽  
Yehudith Kletter ◽  
Suzy Abulafia ◽  
Leonard N. Slater ◽  
...  
Keyword(s):  
Lymph Node ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bartonella Henselae ◽  
16S Rrna Gene Sequencing ◽  
Fatty Acid Analysis ◽  
Rrna Gene ◽  
Cat Scratch Disease ◽  
Rrna Gene Sequencing

Since its isolation in 1988, Afipia felis has been associated with cat scratch disease (CSD) in only one report and its role in CSD has been questioned. We have cultured A. felisfrom a lymph node of a patient with CSD. 16S rRNA gene sequencing, DNA relatedness studies, fatty acid analysis, and PCR of the A. felis ferredoxin gene showed that the isolate is identical to the previously reported A. felis isolate. To determine the role of A. felis in CSD, PCR of the 16S rRNA gene followed by hybridizations with specific probes were performed with lymph node specimens from CSD patients. All 32 specimens tested positive forBartonella henselae and negative for A. felis. We conclude that A. felis is a rare cause of CSD. Diagnostic tests not conducive to the identification of A. felis might cause the diagnosis of CSD due to A. felis to be missed.

scholarly journals hsp65 Sequencing for Identification of Rapidly Growing Mycobacteria

1999 ◽  
Vol 37 (3) ◽  
pp. 852-857 ◽  
Author(s):  
H. Ringuet ◽  
C. Akoua-Koffi ◽  
S. Honore ◽  
A. Varnerot ◽  
V. Vincent ◽  
...  
Keyword(s):  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Mycobacterium Abscessus ◽  
Rrna Gene ◽  
Mycobacterium Fortuitum ◽  
Mycobacterium Chelonae ◽  
Rapidly Growing Mycobacteria ◽  
Rrna Gene Sequencing ◽  
Human Infections ◽  
Type Strains

Partial sequencing of the hsp65 gene was used for the identification of rapidly growing mycobacteria (RGM). A 441-bp fragment (A. Telenti, F. Marchesi, M. Balz, F. Bally, E. Böttger, and T. Bodmer, J. Clin. Microbiol. 31:175–178, 1993) was amplified and sequenced by an automated fluorescence-based method involving capillary electrophoresis. Type strains of 10 RGM species were first studied. Each species had a unique nucleotide sequence, distinguishing it clearly from the other species. A panel of strains from the four main RGM species responsible for human infections, Mycobacterium abscessus, Mycobacterium chelonae,Mycobacterium fortuitum, and Mycobacterium peregrinum, was also studied. There were few sequence differences within each of these species (<2% of bases were different from the type strain sequence), and they had no effect on species assignment.hsp65 sequencing unambiguously differentiated M. chelonae and M. abscessus, two species difficult to identify by classical methods and 16S rRNA gene sequencing. The devised procedure is a rapid and reliable tool for the identification of RGM species.

scholarly journals Chryseobacterium taiwanense sp. nov., isolated from soil in Taiwan

2006 ◽  
Vol 56 (8) ◽  
pp. 1771-1776 ◽  
Author(s):  
Chun-Ju Tai ◽  
Hsiao-Ping Kuo ◽  
Fwu-Ling Lee ◽  
Han-Ken Chen ◽  
Akira Yokota ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Fatty Acid Analysis ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Rrna Gene Sequencing

Among a large collection of Taiwanese soil isolates, a novel Gram-negative, rod-shaped, non-spore-forming, yellow-pigmented bacterial strain, Soil-3-27T, was isolated from farmland soil in Wu-Feng, Taiwan. The isolate was subjected to a polyphasic study including 16S rRNA gene sequencing, DNA–DNA hybridization, fatty acid analysis and comparative phenotypic characterization. The 16S rRNA gene sequence analysis indicated that the organism belongs to the genus Chryseobacterium. The organism contains menaquinone MK-6 as the predominant isoprenoid quinone and 15 : 0 iso (43 %), 17 : 1 isoω9c (17.5 %) and 17 : 0 iso 3-OH (16.6 %) as the major fatty acids. Phylogenetically, the closest relatives of strain Soil-3-27T are Chryseobacterium daecheongense, Chryseobacterium defluvii and Chryseobacterium taichungense with 96.7–97.2 % sequence similarity. DNA–DNA hybridization showed relatedness values of 8.5–24.2 % with these species. The DNA G+C content is 36.8 mol%. Strain Soil-3-27T is clearly distinguishable from other Chryseobacterium species and represents a novel species, for which the name Chryseobacterium taiwanense sp. nov. is proposed. The type strain is strain Soil-3-27T (=BCRC 17412T=IAM 15317T=LMG 23355T).

scholarly journals Production and Characterization of Keratinolytic Protease from New Wool-DegradingBacillusSpecies Isolated from Egyptian Ecosystem

2013 ◽  
Vol 2013 ◽  
pp. 1-14 ◽  
Author(s):  
Mohamed A. Hassan ◽  
Bakry M. Haroun ◽  
Amro A. Amara ◽  
Ehab A. Serour
Keyword(s):  
Serine Protease ◽  
16S Rrna Gene Sequencing ◽  
Maximum Activity ◽  
Rrna Gene ◽  
Carbon And Nitrogen ◽  
Degrading Bacteria ◽  
Rrna Gene Sequencing ◽  
Potential Use ◽  
Wool Industry

Novel keratin-degrading bacteria were isolated from sand soil samples collected from Minia Governorate, Egypt. In this study, the isolates were identified asBacillus amyloliquefaciensMA20 andBacillus subtilisMA21 based on morphological and biochemical characteristics as well as 16S rRNA gene sequencing.B. amyloliquefaciensMA20 andB. subtilisMA21 produced alkaline keratinolytic serine protease when cultivated in mineral medium containing 1% of wool straight off sheep as sole carbon and nitrogen source. The two strains were observed to degrade wool completely to powder at pH 7 and 37°C within 5 days. Under these conditions the maximum activity of proteases produced byB. amyloliquefaciensMA20 andB. subtilisMA21 was 922 and 814 U/ml, respectively. The proteases exhibited optimum temperature and pH at 60°C and 9, respectively. However, the keratinolytic proteases were stable in broad range of temperature and pH values towards casein Hammerstein. Furthermore the protease inhibitor studies indicated that the produced proteases belong to serine protease because of their sensitivity to PMSF while they were inhibited partially in presence of EDTA. The two proteases are stable in most of the used organic solvents and enhanced by metals suggesting their potential use in biotechnological applications such as wool industry.

scholarly journals Aerococcus urinae in Urinary Tract Infections

2000 ◽  
Vol 38 (4) ◽  
pp. 1703-1705 ◽  
Author(s):  
Qing Zhang ◽  
Christopher Kwoh ◽  
Silvia Attorri ◽  
Jill E. Clarridge
Keyword(s):  
Urinary Tract ◽  
16S Rrna Gene Sequencing ◽  
Fatty Acid Analysis ◽  
Rrna Gene ◽  
Elderly Males ◽  
Aerococcus Urinae ◽  
Potential Pathogen ◽  
Rrna Gene Sequencing ◽  
Biochemical Testing ◽  
Tract Infections

Aerococcus urinae is a rarely reported pathogen, possibly due to difficulties in the identification of the organism.A. urinae is a gram-positive coccus that grows in pairs and clusters, produces alpha-hemolysis on blood agar, and is negative for catalase and pyrrolidonyl aminopeptidase. Some of these characteristics and its being absent from the databases of most commercial identification systems could allow A. urinae to be misidentified as a streptococcus, enterococcus, or staphylococcus. We report two cases of urinary tract infection (UTI) caused by A. urinae and characterize these isolates by morphology, biochemical testing, whole-cell fatty acid analysis, 16S rRNA gene sequencing, and antibiotic susceptibilities. Most patients infected with A. urinae are elderly males with predisposing conditions who present initially with UTI. Because A. urinae is resistant to sulfonamides, treatment could be inappropriate, with infections resulting in serious complications, including death. It is important for the clinician and the microbiologist to consider A. urinae a potential pathogen and proceed with thorough microbiological identification.

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