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1.
Environ Monit Assess ; 190(11): 692, 2018 10 31.
Artículo en Inglés | MEDLINE | ID: mdl-30382408

RESUMEN

The original version of this article unfortunately contained an error in the affiliation section.

2.
Environ Monit Assess ; 190(10): 605, 2018 Sep 24.
Artículo en Inglés | MEDLINE | ID: mdl-30251083

RESUMEN

Inland pollution sources of Doam bay were investigated from August to October in 2013. A total of 210 sources including rivers, streams, domestic, agricultural and industrial discharge points were identified along the coast, including 32 sources that had outflow. Agricultural sources were the largest inland pollution sources (139, 66.2%). Fecal coliform concentrations were measured. These data were combined with water discharge data to determine daily loads of pollutants discharged from each source into the bay. Fecal coliform concentrations were the highest in domestic discharges. However, they only had slight influence because their discharge volume was small. The most significant pollution source was Tamjin River (St.85) due to large amount of discharge volume. The influence of St.85 reached almost half of Doam bay. Fecal coliform levels of streams increased after rainfall, but decreased overtime. Domestic pollution sources were not affected upon rain event.


Asunto(s)
Enterobacteriaceae/aislamiento & purificación , Monitoreo del Ambiente/métodos , Contaminación Ambiental/análisis , Lluvia/microbiología , Ríos/microbiología , Agua de Mar/microbiología , Agricultura , Bahías , Heces/microbiología , República de Corea , Encuestas y Cuestionarios , Agua/análisis , Microbiología del Agua
3.
Int J Syst Evol Microbiol ; 63(Pt 2): 755-760, 2013 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-22561594

RESUMEN

A strictly aerobic, Gram-stain-negative bacterium, designated strain No.6(T), was isolated from a lichen (Cladonia sp.) collected in Geogeum Island, Korea, and its taxonomic status was established by a polyphasic study. Cells of strain No.6(T) were non-motile, catalase- and oxidase-positive, non-spore-forming rods. Growth was observed at 15-35 °C (optimum, 25-30 °C), at pH 5.0-10.0 (optimum, pH 6.0-8.0) and with 0-3 % NaCl (optimum, 0-2 %). The predominant cellular fatty acids were summed feature 3 (comprising iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c, 41.5 %), iso-C(15 : 0) (26.7 %) and C(16 : 0) (9.6 %), and menaquinone MK-7 was the only respiratory quinone. The G+C content of the genomic DNA of strain No.6(T) was 36.8 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain No.6(T) fell within the evolutionary group encompassed by the genus Sphingobacterium. Levels of 16S rRNA gene sequence similarity between the novel strain and the type strains of recognized Sphingobacterium species ranged from 92.1 to 99.1 %, the highest values being with Sphingobacterium siyangense SY1(T) (99.1 %) and Sphingobacterium multivorum IAM 14316(T) (98.5 %). DNA-DNA relatedness between strain No.6(T) and these two type strains were 32.0 and 5.7 %, respectively. The polar lipids found in strain No.6(T) were phosphatidylethanolamine, two unidentified phospholipids, three unidentified aminophospholipids, one glycolipid and four unidentified lipids. One unidentified sphingolipid was also found. On the basis of phenotypic and genotypic data, strain No.6(T) represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium cladoniae sp. nov. is proposed. The type strain is No.6(T) ( = KCTC 22613(T) = JCM 16113(T)). An emended description of Sphingobacterium siyangense is also proposed.


Asunto(s)
Líquenes/microbiología , Filogenia , Sphingobacterium/clasificación , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/análisis , Datos de Secuencia Molecular , ARN Ribosómico 16S/genética , República de Corea , Análisis de Secuencia de ADN , Sphingobacterium/genética , Sphingobacterium/aislamiento & purificación , Vitamina K 2/análogos & derivados , Vitamina K 2/análisis
4.
Int J Syst Evol Microbiol ; 62(Pt 2): 409-413, 2012 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-21460141

RESUMEN

A gram-negative, pink-pigmented, non-motile, strictly aerobic rod, designated CNU040(T), was isolated from seawater from the coast of Jeju Island in Korea. The temperature, pH and NaCl ranges for growth were 4-30 °C, pH 5.5-10.0 and 0-5.0 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CNU040(T) belonged to a distinct lineage in the genus Algoriphagus and exhibited high sequence similarity with Algoriphagus terrigena DS-44(T) (98.3 %) and Algoriphagus alkaliphilus AC-74(T) (96.6 %) and lower sequence similarity (<96.0 %) with all other members of the genus Algoriphagus. DNA-DNA relatedness between strain CNU040(T) and A. terrigena KCTC 12545(T) was 44.5 %. The DNA G+C content of the isolate was 48.5 mol% and the major respiratory quinone was menaquinone-7. The major cellular fatty acids were iso-C(15 : 0) (28.6 %) and summed feature 3 (consisting of iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c; 24.0 %). The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, one unknown amino lipid, one unknown aminophospholipid and three unknown polar lipids. On the basis of phenotypic, phylogenetic and genotypic data, strain CNU040(T) represents a novel species within the genus Algoriphagus, for which the name Algoriphagus jejuensis sp. nov. is proposed. The type strain is CNU040(T) ( = KCTC 22647(T)  = JCM 16112(T)).


Asunto(s)
Bacteroidetes/clasificación , Bacteroidetes/aislamiento & purificación , Agua de Mar/microbiología , Técnicas de Tipificación Bacteriana , Bacteroidetes/química , Bacteroidetes/genética , Composición de Base , ADN Bacteriano/análisis , ADN Ribosómico/análisis , Ácidos Grasos/análisis , Genes de ARNr , Genotipo , Lípidos/análisis , Datos de Secuencia Molecular , Fenotipo , Filogenia , ARN Ribosómico 16S/genética , República de Corea , Análisis de Secuencia de ADN , Especificidad de la Especie , Vitamina K 2/análisis
5.
Int J Syst Evol Microbiol ; 62(Pt 2): 414-419, 2012 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-21460140

RESUMEN

A Gram-staining-negative, strictly aerobic and rod-shaped bacterium, designated strain CNURIC013(T), was isolated from seawater collected on the coast of Jeju Island, South Korea. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CNURIC013(T) belonged to the genus Tenacibaculum, within the family Flavobacteriaceae. Sequence similarities between the novel strain and the type strains of recognized species of the genus Tenacibaculum were 93.6-96.0 %, the highest value being with Tenacibaculum litopenaei B-I(T) (96 %). The DNA G+C content of the novel strain was 34.5 mol% and the major respiratory quinone was menaquinone-6. The major fatty acids were summed feature 3 (comprising C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH; 26.0 %), iso-C(15 : 0) (24.4 %), iso-C(15 : 1) G (18.5 %) and iso-C(17 : 0) 3-OH (8.1 %). The polar lipids consisted of phosphatidylethanolamine, one unknown aminophospholipid and nine unknown polar lipids. On the basis of the phenotypic, phylogenetic and genotypic data, strain CNURIC013(T) represents a novel species within the genus Tenacibaculum, for which the name Tenacibaculum jejuense sp. nov. is proposed. The type strain is CNURIC013(T) ( = KCTC 22618(T) = JCM 15975(T)).


Asunto(s)
Agua de Mar/microbiología , Tenacibaculum/clasificación , Tenacibaculum/aislamiento & purificación , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/análisis , ADN Ribosómico/análisis , Ácidos Grasos/análisis , Genes de ARNr , Genotipo , Lípidos/análisis , Datos de Secuencia Molecular , Fenotipo , Filogenia , ARN Ribosómico 16S/genética , República de Corea , Análisis de Secuencia de ADN , Especificidad de la Especie , Tenacibaculum/química , Tenacibaculum/genética , Vitamina K 2/análisis
6.
Int J Syst Evol Microbiol ; 61(Pt 6): 1425-1429, 2011 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-20622053

RESUMEN

A strictly aerobic, orange-pigmented and Gram-staining-negative bacterium, designated K17-16(T), was isolated from seawater of Gangjin Bay, Korea. Comparative 16S rRNA gene sequence analysis revealed that strain K17-16(T) was a member of the genus Polaribacter in the family Flavobacteriaceae and showed 94.0-95.6 % sequence similarity with the type strains of recognized species of the genus Polaribacter. The G+C content of the genomic DNA was 34.6 mol% and the major respiratory lipoquinone was MK-6. The major polar lipids detected were phosphatidylethanolamine, three unidentified amino-group-containing lipids and an unidentified aminophospholipid. The predominant cellular fatty acids were iso-C(15 : 0) (15.4 %), C(15 : 0) (12.4 %), summed feature 3 (comprising iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c; 10.6 %), C(15 : 1)ω6c (9.8 %) and iso-C(15 : 0) 3-OH (8.6 %). On the basis of phenotypic and genotypic data, strain K17-16(T) represents a novel species in the genus Polaribacter, for which the name Polaribacter gangjinensis sp. nov. is proposed. The type strain is K17-16(T) ( = KCTC 22729(T) = JCM 16152(T)).


Asunto(s)
Flavobacteriaceae/clasificación , Flavobacteriaceae/aislamiento & purificación , Agua de Mar/microbiología , Aerobiosis , Composición de Base , Análisis por Conglomerados , ADN Bacteriano/química , ADN Bacteriano/genética , ADN Ribosómico/química , ADN Ribosómico/genética , Ácidos Grasos/análisis , Flavobacteriaceae/genética , Flavobacteriaceae/fisiología , Corea (Geográfico) , Datos de Secuencia Molecular , Fosfolípidos/análisis , Filogenia , Quinonas/análisis , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN
7.
Int J Syst Evol Microbiol ; 61(Pt 7): 1539-1543, 2011 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-20656809

RESUMEN

A novel gram-negative, orange-pigmented, rod-shaped, strictly aerobic, gliding, oxidase- and catalase-positive bacterial strain, A73(T), was isolated from seawater collected off Jeju, South Korea. 16S rRNA gene sequence similarity between A73(T) and type strains of Winogradskyella species with validly published names ranged from 94.1 to 96.2 %. The dominant fatty acids of strain A73(T) were iso-C(15 : 1) G (19.1 %), iso-C(15 : 0) (13.3 %), iso-C(17 : 0) 3-OH (10.0 %) and iso-C(15 : 0) 3-OH (7.2 %). The DNA G+C content of strain A73(T) was 36.0 mol% and its major respiratory quinone was MK-6. On the basis of combined data from phenotypic and phylogenetic analyses, strain A73(T) represents a novel species of the genus Winogradskyella, for which the name Winogradskyella lutea sp. nov. is proposed. The type strain is A73(T) ( = KCTC 23237(T)  = DSM 22624(T)). An emended description of the genus Winogradskyella is also provided.


Asunto(s)
Flavobacteriaceae/clasificación , Filogenia , Agua de Mar/microbiología , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , Flavobacteriaceae/genética , Flavobacteriaceae/aislamiento & purificación , Datos de Secuencia Molecular , Pigmentación , ARN Ribosómico 16S/genética , República de Corea , Análisis de Secuencia de ADN , Vitamina K 2/análogos & derivados , Vitamina K 2/química , Microbiología del Agua
8.
Int J Syst Evol Microbiol ; 61(Pt 2): 325-329, 2011 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-20228204

RESUMEN

A novel strictly aerobic, orange-pigmented, Gram-stain-negative bacterium, designated strain GJ16(T), was isolated from coastal seawater of Gangjin Bay, the southernmost part of the Korean peninsula, and subjected to a polyphasic taxonomic study. It grew optimally at 25-30 °C, at pH 7.0-8.0 and in the presence of 3 % NaCl. Comparative 16S rRNA gene sequence analysis revealed that strain GJ16(T) formed a distinct lineage within the family Flavobacteriaceae and shared less than 91.2 % 16S rRNA gene sequence similarity with members of the genera Leptobacterium, Zhouia, Winogradskyella, Dokdonia and Krokinobacter. The predominant cellular fatty acids were iso-C(15 : 0) (40.2 %), iso-C(15 : 1) G (12.8 %), iso-C(17 : 0) 3-OH (11.2 %) and C(15 : 0) (6.6 %). The G+C content of the genomic DNA was 39.4 mol% and the major respiratory isoprenoid quinone was MK-6. On the basis of phenotypic and genotypic data, strain GJ16(T) represents a novel species in a new genus in the family Flavobacteriaceae, for which the name Gangjinia marincola gen. nov., sp. nov. is proposed; the type strain is GJ16(T) (=KCTC 22649(T) =JCM 16082(T)).


Asunto(s)
Flavobacteriaceae/clasificación , Filogenia , Agua de Mar/microbiología , Microbiología del Agua , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/análisis , Flavobacteriaceae/genética , Flavobacteriaceae/aislamiento & purificación , Genotipo , Datos de Secuencia Molecular , Fenotipo , ARN Ribosómico 16S/genética , República de Corea , Análisis de Secuencia de ADN , Vitamina K 2/análogos & derivados , Vitamina K 2/análisis
9.
Int J Syst Evol Microbiol ; 60(Pt 12): 2719-2723, 2010 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-20061499

RESUMEN

A novel Gram-negative, aerobic, motile, short rod-shaped bacterium, designated MS-3(T), was isolated from a crude oil-contaminated seashore in Taean, Korea. Strain MS-3(T) grew at 4-30 °C, at pH 6.0-9.5 and with 0-5 % NaCl and was oxidase- and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MS-3(T) was most similar to Pseudomonas marincola KMM 3042(T) (97.9 % 16S rRNA gene sequence similarity), P. cuatrocienegasensis 1N(T) (97.8 %), P. borbori R-20821(T) (97.3 %) and P. lundensis ATCC 49968(T) (97.1 %). Relatively low levels of DNA-DNA relatedness were found between strain MS-3(T) and P. cuatrocienegasensis LMG 24676(T) (57.2 %), P. borbori LMG 23199(T) (39.7 %), P. marincola KMM 3042(T) (32.2 %) and P. lundensis KACC 10832(T) (32.1 %), which support the classification of strain MS-3(T) within a novel species of the genus Pseudomonas. The G+C content of the genomic DNA of strain MS-3(T) was 57.6 mol% and the major isoprenoid quinone was Q-9. Strain MS-3(T) contained summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c; 38.0 %), C(16 : 0) (24.4 %), C(18 : 1)ω7c (12.8 %), C(12 : 0) (9.6 %) and C(10 : 0) 3-OH (4.9 %) as the major cellular fatty acids. On the basis of the phenotypic, genotypic and phylogenetic data, strain MS-3(T) represents a novel species of the genus Pseudomonas, for which the name Pseudomonas taeanensis sp. nov. is proposed. The type strain is MS-3(T) (=KCTC 22612(T) =KACC 14032(T) =JCM 16046(T) =NBRL 105641(T)).


Asunto(s)
Contaminación por Petróleo , Petróleo/microbiología , Filogenia , Pseudomonas/clasificación , Agua de Mar/microbiología , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , ADN Ribosómico/genética , Ácidos Grasos/química , Datos de Secuencia Molecular , Hibridación de Ácido Nucleico , Pseudomonas/genética , Pseudomonas/aislamiento & purificación , ARN Ribosómico 16S/genética , República de Corea , Análisis de Secuencia de ADN , Ubiquinona/química
10.
J Microbiol Biotechnol ; 20(11): 1524-8, 2010 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-21124057

RESUMEN

Antioxidant properties of 46 lichen species collected from high-UV exposed alpine areas of southwestern China were evaluated for their therapeutic utilization. Anti-linoleic acid peroxidation activity, 1, 1-diphenyl-2-picryl-hydrazyl (DPPH) scavenging activity, reducing power and the total phenolic contents were assessed in methanol extract of the lichens in vitro. Extracts of Peltigera praetextata and Sticta nylanderiana exhibited potent activity in all antioxidant tests. Especially, extracts of S. nylanderiana exhibited 1.37 times higher anti-linoleic acid peroxidation activity than ascorbic acid used as a positive control. It also showed the strongest free radical scavenging activity among all the tested species with an inhibition of 90.4% at the concentration of 330microgram/ml. Potent reducing power was also detected in the lichen extract compared with BHA. Generally, the antioxidant lichens contained large amount of phenolic contents. The activity-guided bioautographic TLC and HPLC analysis are used to find out the compounds responsible for the potent antioxidant activities of S. nylanderiana extract. The analysis demonstrated that lecanoric acid is one of the effective antioxidant compounds in S. nylanderiana. The results suggested that several highland lichens can be used as a novel bioresource for natural antioxidants.


Asunto(s)
Antioxidantes/análisis , Líquenes/química , Antioxidantes/farmacología , China , Ácido Linoleico/química , Peroxidación de Lípido/efectos de los fármacos
11.
Biotechnol Lett ; 31(8): 1245-51, 2009 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-19404744

RESUMEN

Exiguobacterium sp. CNU020, an alkaliphile and extremohalophile bacterium, is resistant to 20 mM H(2)O(2), a concentration that is lethal to most bacteria. Representative antioxidant genes of catalase and superoxide dismutase (SOD), obtained by PCR amplification of the genomic DNA, were characterized: the 252-bp catalase gene shared 77% similarity in the deduced amino acid sequence to that of E. oxidotolerans T-2-2(T). The 420-bp SOD gene had the closest similarity (94.3%) to the manganese-SOD of E. sibiricum 255-15. Through activity-staining analysis, stain CNU020 had at least four catalase isoforms: C1, C2, C3 and C4. Expression of each catalase isoform was dependent on the growth phase and oxidants but two catalases (C3 and C4) were always induced and expressed at a similar rate, indicating that they were constitutively expressed. RT-PCR-based expression analysis at the transcriptional level suggested that the catalase gene is strongly expressed in response to 2 mM H(2)O(2), 0.2 mM Paraquat and 0.2 mM menadione. However, the SOD gene exhibited no observable expression pattern with 2 mM H(2)O(2) despite its strong expression when exposed to Paraquat and menadione.


Asunto(s)
Antioxidantes/metabolismo , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Bacterias Grampositivas/genética , Antibacterianos/antagonistas & inhibidores , Antibacterianos/farmacología , Catalasa/genética , Catalasa/metabolismo , Perfilación de la Expresión Génica , Regulación Bacteriana de la Expresión Génica , Regulación Enzimológica de la Expresión Génica , Bacterias Grampositivas/efectos de los fármacos , Peróxido de Hidrógeno/antagonistas & inhibidores , Peróxido de Hidrógeno/farmacología , Oxidantes/antagonistas & inhibidores , Oxidantes/farmacología , Paraquat/metabolismo , Homología de Secuencia de Aminoácido , Superóxido Dismutasa/genética , Superóxido Dismutasa/metabolismo , Vitamina K 3/metabolismo
12.
OMICS ; 11(3): 280-94, 2007.
Artículo en Inglés | MEDLINE | ID: mdl-17883339

RESUMEN

Bacterial biodegradation (bioremediation) is the use of microorganisms to break down organic materials into simpler compounds; it plays a pivotal role in the clean-up of hazardous wastes in the environment. Following the completion of genome sequencing in bacteria capable of biodegradation, functional genomic studies have played a major role in obtaining information on bacterial biodegradation pathways. Novel proteomics technologies have recently been developed to make it possible to analyze global protein expression. Proteomics can also provide important information on the life cycle, regulation, and post-translational modification of proteins induced under specific conditions. Proteomics technologies have been applied to the comprehensive study of bacterial biodegradation. In this paper, we introduce the proteomics technologies applicable to bacterial biodegradation studies, review the results of the proteomics analysis of representative biodegrading bacteria, and discuss the potential use of proteomics technologies in future biodegradation studies.


Asunto(s)
Bacterias/metabolismo , Biodegradación Ambiental , Contaminantes Ambientales/metabolismo , Proteómica/métodos , Acinetobacter/metabolismo , Secuencia de Aminoácidos , Contaminantes Ambientales/química , Datos de Secuencia Molecular , Pentaclorofenol/química , Pentaclorofenol/metabolismo , Pseudomonas/metabolismo , Tolueno/química , Tolueno/metabolismo
13.
J Microbiol Biotechnol ; 17(9): 1460-8, 2007 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-18062223

RESUMEN

In this study, an approx. 2.5-kb gene fragment including the catalase gene from Rhodospirillum rubrum S1 was cloned and characterized. The determination of the complete nucleotide sequence revealed that the cloned DNA fragment was organized into three open reading frames, designated as ORF1, catalase, and ORF3 in that order. The catalase gene consisted of 1,455 nucleotides and 484 amino acids, including the initiation and stop codons, and was located 326 bp upstream in the opposite direction of ORF1. The catalase was overproduced in Escherichia coli UM255, a catalase-deficient mutant, and then purified for the biochemical characterization of the enzyme. The purified catalase had an estimated molecular mass of 189 kDa, consisting of four identical subunits of 61 kDa. The enzyme exhibited activity over a broad pH range from pH 5.0 to pH 11.0 and temperature range from 20 degrees C to 60 degrees C. The catalase activity was inhibited by 3-amino-1,2,4-triazole, cyanide, azide, and hydroxylamine. The enzyme's K(m) value and V(max) of the catalase for H2O2 were 21.8 mM and 39,960 U/mg, respectively. Spectrophotometric analysis revealed that the ratio of A406 to A280 for the catalase was 0.97, indicating the presence of a ferric component. The absorption spectrum of catalase-4 exhibited a Soret band at 406 nm, which is typical of a heme-containing catalase. Treatment of the enzyme with dithionite did not alter the spectral shape and revealed no peroxidase activity. The combined results of the gene sequence and biochemical characterization proved that the catalase cloned from strain S1in this study was a typical monofunctional catalase, which differed from the other types of catalases found in strain S1.


Asunto(s)
Catalasa/genética , Rhodospirillum rubrum/enzimología , Catalasa/aislamiento & purificación , Catalasa/metabolismo , Clonación Molecular , ADN Bacteriano , Estabilidad de Enzimas , Escherichia coli/metabolismo , Genes Bacterianos , Peróxido de Hidrógeno/química , Concentración de Iones de Hidrógeno , Peroxidasas/metabolismo , Rhodospirillum rubrum/genética , Rhodospirillum rubrum/metabolismo
14.
J Microbiol ; 55(2): 90-95, 2017 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-28120194

RESUMEN

An aerobic, Gram-negative bacterium, designated strain SD70T, was isolated from sea cucumber aquaculture farm sediment in Taean, Korea, and its taxonomic status was established by undertaking a polyphasic study. Cells of strain SD70T were non-motile, catalase-, and oxidase-positive, non-spore-forming, and horseshoe-shaped. Optimal growth was observed under 25-30°C, pH 7.0-8.0, and 3.0-5.0% (w/v) NaCl conditions. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain SD70T fell within an evolutionary group comprising species of the genus Cyclobacterium. Strain SD70T shared 92.1-98.5% 16S rRNA sequence similarity values with the type strains of species of the genus Cyclobacterium. Relatively low levels of DNA-DNA relatedness were found between strain SD70T and C. marinum DSM 745T (40.2%) and C. amurskyense KMM 6143T (15.8%). The predominant cellular fatty acids were iso-C15:0 (32.1%), and anteiso-C15:0 (9.1%). Menaquinone MK-7 was the only respiratory quinone. The G+C content of the genomic DNA was 36 mol%. The polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, and seven unidentified lipids. On the basis of phenotypic and genotypic data, strain SD70T represents a novel species of the genus Cyclobacterium, for which the name Cyclobacterium sediminis sp. nov. is proposed. An emended description of the genus Cyclobacterium is also provided.


Asunto(s)
Bacteroidetes/clasificación , Bacteroidetes/aislamiento & purificación , Pepinos de Mar/microbiología , Animales , Acuicultura , Técnicas de Tipificación Bacteriana , Bacteroidetes/genética , Bacteroidetes/metabolismo , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/análisis , Sedimentos Geológicos/microbiología , Filogenia , República de Corea , Análisis de Secuencia de ADN , Vitamina K 2/análisis
15.
J Microbiol ; 44(6): 671-3, 2006 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-17205047

RESUMEN

A new 4.87 kb Escherichia-Pseudomonas shuttle vector has been constructed by inserting a 1.27 kb DNA fragment with a replication origin of a Pseudomonas plasmid pRO1614 into the 3.6 kb E. coli plasmid pBGS18. This vector, designated pJH1, contains an aminoglycoside phosphotransferase gene (aph) from Tn903, a lacZ'' gene for alpha-complementation and a versatile multiple cloning site possessing unique restriction sites for EcoRI, SacI, KpnI, SmaI, BamHI, XbaI, SalI, BspMI, PstI, SphI, and HindIII. When pJH1 was transformed into E. coli DH5alpha and into P. putida HK-6, it was episomally and stably maintained in both strains. In addition, the enhanced green fluorescent protein (EGFP) gene which was transcriptionally cloned into pJH1 rendered E. coli cells fluorescence when its transformants were illuminated at 488 nm.


Asunto(s)
Escherichia/genética , Vectores Genéticos/genética , Kanamicina Quinasa/genética , Operón Lac , Pseudomonas/genética , Antibacterianos/farmacología , Clonación Molecular , Farmacorresistencia Bacteriana , Escherichia/enzimología , Prueba de Complementación Genética , Kanamicina/farmacología , Plásmidos , Pseudomonas/enzimología
16.
J Microbiol ; 44(6): 632-40, 2006 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-17205041

RESUMEN

In this study, the biodegradative activities of monocyclic aromatic compounds were determined from the multi-drug resistant (MDR) Acinetobacter baumannii, which were studied in the form of clinical isolates from a hospital in Korea. These bacteria were capable of biodegrading monocyclic aromatic compounds, such as benzoate and p-hydroxybenzoate. In order to determine which pathways are available for biodegradation in these stains, we conducted proteome analyses of benzoate and p-hydroxybenzoate-cultured A. baumannii DU202, using 2-DE/MS analysis. As genome DB of A. baumannii was not yet available, MS/MS analysis or de novo sequencing methods were employed in the identification of induced proteins. Benzoate branch enzymes [catechol 1,2-dioxygenase (CatA) and benzoate dioxygenase alpha subunit (BenA)] of the beta-ketoadipate pathway were identified under benzoate culture condition and p-hydroxybenzoate branch enzymes [protocatechuate 3,4-dioxygenase alpha subunit (PcaG) and 3-carboxy-cis,cis-muconate cycloisomerase (PcaB)] of the beta-ketoadipate pathway were identified under p-hydroxybenzoate culture condition, respectively, thereby suggesting that strain DU202 utilized the beta-ketoadipate pathway for the biodegradation of monocyclic aromatic compounds. The sequence analysis of two purified dioxygenases (CatA and PcaGH) indicated that CatA is closely associated with the CatA of Acinetobacter radiresistance, but PcaGH is only moderately associated with the PcaGH of Acinetobacter sp. ADP1. Interestingly, the fused form of PcaD and PcaC, carboxymuconolactone decarboxylase (PcaCD), was detected on benzoate-cultured A. baumannii DU202. These results indicate that A. baumannii DU202 exploits a different beta-ketoadipate pathway from other Acinetobacter species.


Asunto(s)
Acinetobacter baumannii/efectos de los fármacos , Adipatos/metabolismo , Proteínas Bacterianas/metabolismo , Farmacorresistencia Bacteriana Múltiple , Regulación Bacteriana de la Expresión Génica , Parabenos/metabolismo , Proteoma , Acinetobacter baumannii/genética , Acinetobacter baumannii/crecimiento & desarrollo , Acinetobacter baumannii/metabolismo , Anciano , Secuencia de Aminoácidos , Antibacterianos/farmacología , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Benzoatos/metabolismo , Humanos , Pruebas de Sensibilidad Microbiana , Persona de Mediana Edad , Datos de Secuencia Molecular
17.
J Microbiol ; 43(6): 572-6, 2005 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-16410776

RESUMEN

This study focused on detecting catabolic genes for polycyclic aromatic hydrocarbons (PAHs) distributed in the reed rhizosphere of Sunchon Bay, Korea. These marsh and mud environments were severely affected by human activities, including agriculture and fisheries. Our previous study on microbial roles in natural decontamination displayed the possibility that PAH-degrading bacteria, such as Achromobacter sp., Alcaligenes sp., Burkholderia sp. and Pseudomonas sp. play an important decontamination role in a reed rhizosphere. In order to gain further fundamental knowledge on the natural decontamination process, catabolic genes for PAH metabolism were investigated through PCR amplification of dioxygenase genes using soil genomic DNA and sequencing. Comparative analysis of predicted amino acid sequences from 50 randomly selected dioxygenase clones capable of hydroxylating inactivated aromatic nuclei indicated that these were divided into three groups, two of which might be originated from PAH-degrading bacteria. Amino acid sequences of each dioxygenase clone were a part of the genes encoding enzymes for initial catabolism of naphthalene, phenanthrene, or pyrene that might be originated from bacteria in the reed rhizosphere of Sunchon Bay.


Asunto(s)
Bacterias/genética , ADN Bacteriano/análisis , ADN Bacteriano/genética , Genes Bacterianos , Poaceae/microbiología , Microbiología del Suelo , Secuencia de Aminoácidos , Bacterias/metabolismo , Proteínas Bacterianas/genética , Biodegradación Ambiental , Dioxigenasas/genética , Corea (Geográfico) , Datos de Secuencia Molecular , Estructura Molecular , Filogenia , Raíces de Plantas/microbiología , Hidrocarburos Policíclicos Aromáticos/metabolismo , Reacción en Cadena de la Polimerasa , Análisis de Secuencia de ADN , Homología de Secuencia
18.
Mol Biotechnol ; 57(9): 781-92, 2015 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-25943044

RESUMEN

Two genes encoding lipolytic enzymes were isolated from a metagenomic library constructed from oil-polluted mud flats. An esterase gene, est3K, encoded a protein of 299 amino acids (ca. 32,364 Da). Est3K was a family IV esterase with typical motifs, HGGG, and HGF. Although est3K showed high identity to many genes with no information on their enzymatic properties, Est3K showed the highest identity (36 %) to SBLip5.1 from forest soil metagenome when compared to the enzymes with reported properties. A lipase gene, lip3K, encoded a protein of 616 amino acids (ca. 64,408 Da). Lip3K belonged to family I.3 lipase with a C-terminal secretion signal and showed the highest identity (93 %) to the lipase of Pseudomonas sp. MIS38. The presence of several newly identified conserved motifs in Est3K and Lip3K are suggested. Both Est3K and Lip3K exerted their maximal activity at pH 9.0 and 50 °C. The activity of Lip3K was significantly increased by the presence of 30 % methanol. The ability of the enzymes to retain activities in the presence of methanol and the substrates may offer a merit to the biotechnological applications of the enzymes such as transesterification. The activity and the thermostability of Lip3K were increased by Ca(2+). Est3K and Lip3K preferred p-nitrophenyl butyrate (C4) and octanoate (C8), respectively, as the substrate and acted independently on the substrates with no synergistic effect.


Asunto(s)
Esterasas/metabolismo , Lipasa/metabolismo , Metagenoma/genética , Activación Enzimática/genética , Activación Enzimática/fisiología , Esterasas/genética , Lipasa/genética
19.
Genome Announc ; 3(1)2015 Feb 19.
Artículo en Inglés | MEDLINE | ID: mdl-25700396

RESUMEN

We report here the draft genome sequence of Arthrobacter sp. MWB30 strain, isolated from a crude oil-contaminated seashore in Tae-an, South Korea, which is able to degrade the crude oil and its derivatives. The draft genome sequence of 4,647,008 bp provides a resource for the identification of crude oil-degrading mechanisms in strain MWB30.

20.
J Microbiol ; 42(4): 292-8, 2004 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-15650685

RESUMEN

This study reports, for the first time, the investigation of the distribution of Korean saxicolous lichens in the coastal rocks of U-do islet, which is known as an unpolluted zone in Jeju. More than thirty lichens were obtained and investigated from the coastal rocks frequently contacted by seawater. A molecular analysis using PCR amplification of the rRNA ITS regions revealed the coastal rock lichens could be placed into 8 families and 14 genera, Ramalinaceae (Bacidia, Ramalina), Physciaceae (Buellia, Dirinaria, Phaeophyscia, Physcia, Pyxine), Lecanoraceae (Candelaria, Lecanora), Parmeliaceae (Xanthoparmelia), Graphidaceae (Graphis), Pertusariaceae (Pertusaria), Rhizocarpaceae (Rhizocarpon), and Teloschistaceae (Caloplaca), showing a diversity of lichens, with foliose (flat leaf-like), crustose (crust-like), and fruticose (miniature shrub-like) life forms might be distributed in the coastal rocks. These findings suggested the possibility that the lichens identified in the present work might be resistant to a salty environment.


Asunto(s)
Microbiología Ambiental , Sedimentos Geológicos/microbiología , Líquenes/aislamiento & purificación , Sedimentos Geológicos/análisis , Corea (Geográfico) , Líquenes/clasificación , Líquenes/genética , Filogenia , Reacción en Cadena de la Polimerasa , Agua de Mar
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