Antibiotic resistance among aquatic bacteria in natural freshwater environments of Korea

2015 ◽  
Vol 13 (4) ◽  
pp. 1085-1097 ◽  
Author(s):  
Tae Woon Kim ◽  
Yochan Joung ◽  
Ji-Hye Han ◽  
Wonwha Jung ◽  
Seung Bum Kim
Keyword(s):  
Antibiotic Resistance ◽  
Bacterial Communities ◽  
Gene Sequence ◽  
Taxonomic Diversity ◽  
Taxonomic Composition ◽  
Rrna Gene ◽  
Freshwater Environment ◽  
Gene Sequence Analysis ◽  
Environmental Bacteria ◽  
Low Levels

The taxonomic diversity and antibiotic resistance among freshwater bacterial communities in the major water bodies of Korea was examined using 437 penicillin-resistant, and 110 tetracycline-resistant bacterial isolates. Based on 16S rRNA gene sequence analysis, most isolates were assigned to Proteobacteria, which was then followed by Bacteroidetes. Strains of Aeromonas were found as the most abundant penicillin-resistant populations, whereas those affiliated to diverse species including enteric groups were found as the most abundant tetracycline-resistant populations. Most strains exhibited multiple antibiotic resistance, and all tested strains were resistant to penicillin and hygromycin. High levels of resistance were observed for antibiotics acting on cell wall synthesis, whereas low levels were for those acting on DNA replication or transcription in general. It is apparent from this study that penicillin resistance is widespread among environmental bacteria, although the antibiotic has been generally non-detectable in the environment. It is also likely from the taxonomic composition of the resistant communities that various sources including terrestrial animals and humans may contribute to antibiotic resistance in the freshwater environment.

Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil

2010 ◽  
Vol 60 (11) ◽  
pp. 2577-2582 ◽  
Author(s):  
Myungjin Lee ◽  
Sung-Geun Woo ◽  
Joonhong Park ◽  
Soon-Ae Yoo
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Degrading Bacterium ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Low Levels

A Gram-negative, non-motile, aerobic bacterial strain, designated MJ20T, was isolated from farm soil near Daejeon (South Korea) and was characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ20T belongs to the family Cytophagaceae, class Sphingobacteria, and was related most closely to Dyadobacter fermentans DSM 18053T (98.9 % sequence similarity), Dyadobacter beijingensis JCM 14200T (98.0 %) and Dyadobacter ginsengisoli KCTC 12589T (96.4 %). The G+C content of the genomic DNA of strain MJ20T was 48.5 mol%. The detection of MK-7 as the predominant menaquinone and a fatty acid profile with summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, C16 : 0 and C16 : 1 ω5c as major components supported the affiliation of strain MJ20T to the genus Dyadobacter. The new isolate exhibited relatively low levels of DNA–DNA relatedness with respect to D. fermentans DSM 18053T (mean±sd of three determinations, 47±7 %) and D. beijingensis JCM 14200T (38±8 %). On the basis of its phenotypic and genotypic properties together with phylogenetic distinctiveness, strain MJ20T (=KCTC 22481T =JCM 16232T) should be classified in the genus Dyadobacter as the type strain of a novel species, for which the name Dyadobacter soli sp. nov. is proposed.

scholarly journals Physiology and Molecular Phylogeny of Bacteria Isolated from Alkaline Distillery Lime

2015 ◽  
Vol 64 (4) ◽  
pp. 369-377 ◽  
Author(s):  
Agnieszka Kalwasińska ◽  
Tamas Felfoldi ◽  
Maciej Walczak ◽  
Przemysław Kosobucki
Keyword(s):  
Gene Sequence ◽  
Biochemical Properties ◽  
Taxonomic Composition ◽  
Aerobic Bacteria ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Genus Bacillus ◽  
Gene Sequence Analysis ◽  
Number Of Bacteria

This paper presents the results of the research on the number, taxonomic composition, and biochemical properties of bacterial strains isolated from the alkaline Solvay distillery lime, deposited at the repository in Janikowo (central Poland). Fifteen strains out of 17 were facultative alkaliphiles and moderate halophiles, and two were alkalitolerants and moderate halophiles. The number of aerobic bacteria cultured in alkaline lime was approximately 105 CFU ml-1, and the total number of bacteria was 107 cells g-1. According to 16S rRNA gene sequence analysis, nine strains belonged to the genus Bacillus, six to the genus Halomonas, one to the genus Planococcus, and one to the genus Microcella. Strains that hydrolyse starch and protein were the most numerous. Esterase (C4) and esterase lipase (C8) were detected in the majority of bacterial strains. Twelve strains exhibited α-glucosidase activity and nine, naphtol-AS-BI-phosphohydrolase activity. The present study proves that alkaliphilic bacteria of this type may constitute a source of potentially useful extremozymes.

Pusillimonas soli sp. nov., isolated from farm soil

2010 ◽  
Vol 60 (10) ◽  
pp. 2326-2330 ◽  
Author(s):  
Myungjin Lee ◽  
Sung-Geun Woo ◽  
Myoungsoo Chae ◽  
Leonid N. Ten
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Low Levels

A Gram-negative, motile, non-spore-forming bacterial strain, designated MJ07T, was isolated from a farm soil and was characterized to determine its taxonomic position by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ07T belongs to the family Alcaligenaceae, class Betaproteobacteria, and is related most closely to Pusillimonas ginsengisoli KCTC 22046T (98.6 % sequence similarity) and Pusillimonas noertemannii BN9T (96.9 %). The levels of 16S rRNA gene sequence similarity between strain MJ07T and members of all other recognized species of the family Alcaligenaceae were below 95.2 %. The G+C content of the genomic DNA of strain MJ07T was 59.4 mol%. The detection of a quinone system with ubiquinone Q-8 as the major respiratory lipoquinone, putrescine as the predominant polyamine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unknown aminolipids as major polar lipids and a fatty acid profile with C16 : 0 (32.0 %), C17 : 0 cyclo (24.7 %) and C19 : 0 cyclo ω8c (11.5 %) as the major components supported the affiliation of strain MJ07T to the genus Pusillimonas. Strain MJ07T exhibited relatively low levels of DNA–DNA relatedness with respect to P. ginsengisoli KCTC 22046T (50±8 %) and P. noertemannii KACC 13183T (18±7 %). On the basis of its phenotypic and genotypic properties together with its phylogenetic distinctiveness, strain MJ07T (=KCTC 22455T =JCM 16386T) should be classified in the genus Pusillimonas as the type strain of a novel species, for which the name Pusillimonas soli sp. nov. is proposed.

Aquimarina addita sp. nov., isolated from seawater

2011 ◽  
Vol 61 (10) ◽  
pp. 2445-2449 ◽  
Author(s):  
Hana Yi ◽  
Jongsik Chun
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Gliding Motility ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Phenotypic Characteristics ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Low Levels ◽  
Type Strains

An orange-coloured, rod-shaped, non-motile, Gram-reaction-negative, strictly aerobic bacterial strain, designated JC2680T, was isolated from a seawater sample of Jeju Island, Korea. The isolate required sea salts for growth. Flexirubin-type pigments were absent. 16S rRNA gene sequence analysis indicated that the test strain belonged to the genus Aquimarina within the family Flavobacteriaceae, but shared relatively low levels of similarity (93.6–95.9 %) with the type strains of recognized Aquimarina species. The predominant cellular fatty acids [iso-C17 : 0 3-OH, iso-C15 : 0 and summed feature 9 (comprising 10-methyl C16 : 0 and/or iso-C17 : 1ω9c) and DNA G+C content (35 mol%) were consistent with the assignment of strain JC2680T to the genus Aquimarina. However, a number of phenotypic characteristics, namely inability to grow under microaerophilic conditions, differences in enzyme reactions, and absence of flexirubin-type pigments and gliding motility, clearly distinguished strain JC2680T from recognized species of the genus Aquimarina. The data presented thus indicate that strain JC2680T represents a novel species of the genus Aquimarina, for which the name Aquimarina addita sp. nov. is proposed. The type strain is JC2680T ( = KACC 14156T  = JCM 17106T).

scholarly journals Paenibacillus qingshengii sp. nov., isolated from a lead–zinc tailing

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2161-2166 ◽  
Author(s):  
Ling Chen ◽  
Lu Wang ◽  
Xia-Fang Sheng
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Polar Lipid Profile ◽  
Gene Sequence Analysis ◽  
Lead Zinc ◽  
Total Dna ◽  
Low Levels ◽  
Type Strains

A novel bacterial strain, S1-9T, was isolated from a lead–zinc tailing in Nanjing, Jiangsu Province, China. Cells of strain S1-9T were Gram-stain-negative, ellipsoidal endospore-forming, aerobic rods and motile by means of peritrichous flagella. On the basis of 16S rRNA gene sequence analysis, strain S1-9T was shown to belong to the genus Paenibacillus and the closest phylogenetic relatives were Paenibacillus glucanolyticus DSM 5162T (96.8 % similarity), Paenibacillus lautus NRRL NRS-666T (96.5 %) and Paenibacillus lactis MB 1871T (95.4 %). The predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C15:0 and iso-C16:0. The polar lipid profile contained phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, two unknown phospholipids and two unknown lipids. The total DNA G+C content of strain S1-9T was 49.9 mol%. Based on the low levels of DNA–DNA relatedness (ranging from 21.8 to 48.4 %) to the type strains of the above species of the genus Paenibacillus and unique phenotypic characteristics, strain S1-9T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus qingshengii sp. nov. is proposed. The type strain is S1-9T ( = CCTCC AB 2014290T = JCM 30613T).

scholarly journals Castellaniella daejeonensis sp. nov., isolated from soil

2010 ◽  
Vol 60 (9) ◽  
pp. 2056-2060 ◽  
Author(s):  
Myungjin Lee ◽  
Hae-Min Jung ◽  
Sung-Geun Woo ◽  
Soon-Ae Yoo ◽  
Leonid N. Ten
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Low Levels

A Gram-negative, non-spore-forming, motile, facultatively anaerobic bacterium, designated strain MJ06T, was isolated from oil-contaminated soil and was characterized taxonomically by using a polyphasic approach. Strain MJ06T contained ubiquinone Q-8 as the major respiratory lipoquinone, putrescine as the predominant polyamine and phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol as major polar lipids. The G+C content of the genomic DNA of strain MJ06T was 66.2 mol%. The major fatty acids were summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 32.5 %), C16 : 0 (22.8 %) and summed feature 7 (one or more of C18 : 1 ω7c, C18 : 1 ω9t and C18 : 1 ω12t; 14.9 %). Comparative 16S rRNA gene sequence analysis showed that strain MJ06T belonged to the family Alcaligenaceae, class Betaproteobacteria, and joined the evolutionary radiation enclosed by the genus Castellaniella. Levels of 16S rRNA gene sequence similarity between strain MJ06T and its phylogenetically closest relatives, Castellaniella denitrificans NKNTAUT, Castellaniella defragrans 54PinT, Castellaniella ginsengisoli DCY36T and Castellaniella caeni Ho-11T, were 98.6, 98.3, 97.8 and 97.3 %, respectively. Levels of similarity between strain MJ06T and the type strains of all other recognized species in the family Alcaligenaceae were below 95.0 %. Strain MJ06T exhibited relatively low levels of DNA–DNA relatedness with respect to C. defragrans DSM 12141T (52 %), C. denitrificans DSM 11046T (31 %), C. ginsengisoli KCTC 22398T (18 %) and C. caeni KCTC 12197T (15 %). On the basis of its phenotypic and genotypic properties together with phylogenetic distinctiveness, strain MJ06T is considered to represent a novel species of the genus Castellaniella, for which the name Castellaniella daejeonensis sp. nov. is proposed. The type strain is MJ06T (=KCTC 22454T =JCM 16240T).

scholarly journals Shinella daejeonensis sp. nov., a nitrate-reducing bacterium isolated from sludge of a leachate treatment plant

2011 ◽  
Vol 61 (9) ◽  
pp. 2123-2128 ◽  
Author(s):  
Myungjin Lee ◽  
Sung-Geun Woo ◽  
Leonid N. Ten
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Treatment Plant ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Leachate Treatment ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Low Levels

A Gram-negative-staining, motile, rod-shaped, aerobic bacterial strain, designated MJ02T, was isolated from sludge of a leachate treatment plant in Daejeon (South Korea) and was characterized to determine its taxonomic position by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ02T belonged to the family Rhizobiaceae, class Alphaproteobacteria, and was most closely related to Shinella yambaruensis MS4T (97.6 % sequence similarity) and Shinella fusca DC-196T (97.5 %). The G+C content of the genomic DNA of strain MJ02T was 64.3 mol%. The detection of a quinone system with ubiquinone Q-10 as the predominant respiratory lipoquinone and a fatty acid profile with C18 : 1ω7c (45.8 %) and C16 : 0 (21.8 %) as the major components supported the affiliation of strain MJ02T to the genus Shinella. However, strain MJ02T exhibited relatively low levels of DNA–DNA relatedness with respect to S. fusca DSM 21319T (17±7 %) and S. yambaruensis KACC 14483T (12±6 %), showing clearly that the isolate constituted a new genospecies. Strain MJ02T could be clearly differentiated from its phylogenetic neighbours on the basis of several phenotypic, genotypic and chemotaxonomic features. Therefore, strain MJ02T is considered to represent a novel species of the genus Shinella, for which the name Shinella daejeonensis sp. nov. is proposed. The type strain is MJ02T ( = KCTC 22450T = JCM 16236T).

scholarly journals Microbial Diversity of Septic Tank Effluent and a Soil Biomat

2009 ◽  
Vol 75 (10) ◽  
pp. 3348-3351 ◽  
Author(s):  
Jill Tomaras ◽  
Jason W. Sahl ◽  
Robert L. Siegrist ◽  
John R. Spear
Keyword(s):  
Sequence Analysis ◽  
Microbial Diversity ◽  
Gene Sequence ◽  
Septic Tank ◽  
Rrna Gene ◽  
Control Soil ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Site Water ◽  
Septic Tank Effluent

ABSTRACT Microbial diversity of septic tank effluent (STE) and the biomat that is formed as a result of STE infiltration on soil were characterized by 16S rRNA gene sequence analysis. Results indicate that microbial communities are different within control soil, STE, and the biomat and that microbes found in STE are not found in the biomat. The development of a stable soil biomat appears to provide the best on-site water treatment or protection for subsequent groundwater interactions of STE.

scholarly journals Actinocorallia cavernae sp. nov., isolated from a natural cave in Jeju, Korea

2006 ◽  
Vol 56 (5) ◽  
pp. 1085-1088 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Dilution Method ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Polar Lipid Profile ◽  
Phylogenetic Cluster ◽  
Gene Sequence Analysis ◽  
Actinomycete Strain

A novel actinomycete, strain N3-7T, was isolated from a natural cave in Jeju, Republic of Korea, using a dilution method and was subjected to characterization using polyphasic taxonomy. A 16S rRNA gene sequence analysis revealed that the organism belonged to the phylogenetic cluster of the genus Actinocorallia and was most closely related to Actinocorallia glomerata and Actinocorallia longicatena (97.6 and 97.5 % similarity, respectively). The main chemotaxonomic properties of strain N3-7T, such as the principal amino acid of the peptidoglycan, the predominant menaquinone and the polar lipid profile, supported classification in the genus Actinocorallia. The organism was readily differentiated from Actinocorallia species with validly published names on the basis of a broad range of phenotypic properties. Thus the isolate represents a novel species of the genus Actinocorallia, for which the name Actinocorallia cavernae sp. nov. is proposed. The type strain is strain N3-7T (=JCM 13278T=NRRL B-24429T).

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