scholarly journals Alteromonas litorea sp. nov., a slightly halophilic bacterium isolated from an intertidal sediment of the Yellow Sea in Korea

2004 ◽  
Vol 54 (4) ◽  
pp. 1197-1201 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Soo-Hwan Yeo ◽  
Tae-Kwang Oh ◽  
Yong-Ha Park
Keyword(s):  
16S Rdna ◽  
Phylogenetic Analyses ◽  
Halophilic Bacterium ◽  
The Yellow Sea ◽  
Intertidal Sediment ◽  
Phenotypic Properties ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Slightly Halophilic Bacterium ◽  
Type Strains

A Gram-negative, motile, non-spore-forming, rod-shaped bacterium, designated strain TF-22T, was isolated from an intertidal sediment in Korea. This organism grew optimally at 30–37 °C and in the presence of 2–5 % (w/v) NaCl. It did not grow without NaCl or in the presence of more than 14 % (w/v) NaCl. Strain TF-22T was characterized chemotaxonomically as having ubiquinone-8 as the predominant respiratory lipoquinone and C16 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and C18 : 1 ω7c as the major fatty acids. The DNA G+C content of strain TF-22T was 46·0 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-22T falls within the γ-subclass of the Proteobacteria and forms a coherent cluster with Alteromonas macleodii and Alteromonas marina. Levels of 16S rDNA similarity between strain TF-22T and the type strains of two Alteromonas species were in the range 98·1–98·6 %. The level of DNA–DNA relatedness between strain TF-22T and the type strains of two Alteromonas species was 15·7–18·5 %. Therefore, on the basis of phenotypic properties, phylogeny and genomic distinctiveness, strain TF-22T should be placed in the genus Alteromonas as a novel species, for which the name Alteromonas litorea sp. nov. is proposed. The type strain is TF-22T (=KCCM 41775T=JCM 12188T).

scholarly journals Shewanella gaetbuli sp. nov., a slight halophile isolated from a tidal flat in Korea

2004 ◽  
Vol 54 (2) ◽  
pp. 487-491 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Kook Hee Kang ◽  
Tae-Kwang Oh ◽  
Yong-Ha Park
Keyword(s):  
16S Rdna ◽  
Tidal Flat ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Phenotypic Properties ◽  
16S Rdna Sequence ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Isoprenoid Quinones ◽  
Type Strains

A Gram-negative, motile, non-spore-forming, rod-shaped strain, TF-27T (=KCCM 41648T=JCM 11814T), was isolated from a tidal flat in Korea. This organism grew well at 25–35 °C, with optimum growth at 30 °C. Strain TF-27T grew optimally in the presence of 2 % NaCl; it did not grow without NaCl or in the presence of >8 % NaCl. Strain TF-27T simultaneously contained both menaquinones and ubiquinones as isoprenoid quinones. The predominant menaquinone was MK-7 and the predominant ubiquinones were Q-7 and Q-8. The major fatty acids in strain TF-27T were iso-C15 : 0 (20·6 %) and iso-C15 : 0 2-OH and/or C16 : 1 ω7c (21·1 %). The DNA G+C content of strain TF-27T was 42 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-27T falls within the radiation of the cluster that is encompassed by the genus Shewanella. Levels of 16S rDNA sequence similarity between strain TF-27T and the type strains of Shewanella species were 93·2–96·8 %. On the basis of phenotypic properties and phylogenetic data, strain TF-27T should be placed in the genus Shewanella as a novel species, for which the name Shewanella gaetbuli sp. nov. is proposed.

scholarly journals Microbulbifer maritimus sp. nov., isolated from an intertidal sediment from the Yellow Sea, Korea

2004 ◽  
Vol 54 (4) ◽  
pp. 1111-1116 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
In-Gi Kim ◽  
Tae-Kwang Oh ◽  
Yong-Ha Park
Keyword(s):  
16S Rdna ◽  
Yellow Sea ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Halophilic Bacterium ◽  
Major Fatty Acid ◽  
The Yellow Sea ◽  
Intertidal Sediment ◽  
Phenotypic Properties ◽  
Type Strains

A Gram-negative, rod-shaped, non-spore-forming, slightly halophilic bacterium (strain TF-17T) was isolated from an intertidal sediment from the Yellow Sea, Korea. Pigment of strain TF-17T was similar to that of Microbulbifer elongatus, but different from those of Microbulbifer hydrolyticus and Microbulbifer salipaludis. Strain TF-17T was distinguishable from M. elongatus by some phenotypic properties, including motility, optimal growth temperature and others. Phylogenetic analysis based on 16S rDNA sequences showed that strain TF-17T clustered with the type strains of the three Microbulbifer species with validly published names. Strain TF-17T exhibited 16S rDNA sequence similarity levels of 95·1–95·7 % to the type strains of the three Microbulbifer species. The predominant respiratory lipoquinone found in strain TF-17T was ubiquinone-8. The major fatty acid was iso-C15 : 0 and significant amounts of iso-C11 : 0 3-OH and iso-C17 : 1 ω9c were also present. The DNA G+C content of strain TF-17T was 59·9 mol%. Levels of DNA–DNA relatedness between strain TF-17T and the type strains of the three Microbulbifer species were in the range 10·0–13·0 %. On the basis of phenotypic and phylogenetic data and genotypic distinctiveness, strain TF-17T (=KCCM 41774T=JCM 12187T) is proposed as the type strain of a novel species of the genus Microbulbifer, Microbulbifer maritimus sp. nov.

Bacillus hwajinpoensis sp. nov. and an unnamed Bacillus genomospecies, novel members of Bacillus rRNA group 6 isolated from sea water of the East Sea and the Yellow Sea in Korea

2004 ◽  
Vol 54 (3) ◽  
pp. 803-808 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
In-Gi Kim ◽  
Kook Hee Kang ◽  
Tae-Kwang Oh ◽  
Yong-Ha Park
Keyword(s):  
16S Rdna ◽  
Yellow Sea ◽  
Sea Water ◽  
Diaminopimelic Acid ◽  
East Sea ◽  
The Yellow Sea ◽  
Phenotypic Properties ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Group 6

Two Gram-positive or -variable, endospore-forming, slightly halophilic strains (SW-72T and SW-93) were isolated from sea water of the East Sea and the Yellow Sea in Korea, respectively, and subjected to polyphasic taxonomic study. Both strains had cell-wall peptidoglycan that was based on meso-diaminopimelic acid and MK-7 as the predominant menaquinone. The two strains contained large amounts of saturated and branched fatty acids, with anteiso-C15 : 0 as the major fatty acid. The DNA G+C contents of strains SW-72T and SW-93 were 40·9 and 41·0 mol%, respectively. Phylogenetic analysis based on 16S rDNA sequences showed that strains SW-72T and SW-93 fall within the radiation of the cluster that comprises members of the genus Bacillus, particularly Bacillus rRNA group 6. There were five nucleotide differences between the 16S rDNA sequences of strains SW-72T and SW-93. The mean level of DNA–DNA relatedness between strains SW-72T and SW-93 was 21·5 %. Strains SW-72T and SW-93 showed 93·1–95·2 % 16S rDNA sequence similarity to the type strains of Bacillus species that are assigned to rRNA group 6. Strains SW-72T and SW-93 could not be differentiated clearly by using their phenotypic properties. On the basis of phenotypic properties, phylogeny and genomic data, it is proposed that strain SW-72T (=KCCM 41641T=JCM 11807T) should be placed in the genus Bacillus as the type strain of a novel species, Bacillus hwajinpoensis sp. nov., and that strain SW-93 (=KCCM 41640=JCM 11806) should be placed in the genus Bacillus as an unnamed Bacillus genomospecies.

Human intestinal spirochetosis diagnosed with colonoscopy and analysis of partial 16S rDNA sequences of involved spirochetes

2001 ◽  
Vol 2 (1) ◽  
pp. 111-116 ◽  
Author(s):  
Wolfgang Kraatz ◽  
Ulf Thunberg ◽  
Bertil Pettersson ◽  
Claes Fellström
Keyword(s):  
16S Rdna ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rdna Sequences ◽  
Intestinal Spirochetosis ◽  
16S Rdna Sequences ◽  
Pcr Products ◽  
Human Intestinal Spirochetosis ◽  
Type Strains ◽  
Rrna Sequences

AbstractDNA was extracted from colonic biopsies of 33 patients with and three without evidence of intestinal spirochetosis (IS) in the large bowel. The biopsies were subjected to PCR. A pair of primers, generating a 207 bp fragment, were designed to detect specifically the 16S rDNA gene ofBrachyspira. PCR products of the expected size were obtained from 33 samples with histologic evidence of IS. The PCR amplicons were used for sequencing. The sequences obtained were aligned to the corresponding 16S rRNA sequences of five type strains ofBrachyspira. The sequences of 23 PCR products were 99–100% identical with the correspond-ingB.aalborgitype strain sequence. Two cases showed 99–100% sequence similarity with the type strain ofB.pilosicoliP43/6/78. Six cases could not be referred to any of the known species ofBrachyspira. Two PCR products gave incomplete sequences.

scholarly journals Clover Proliferation Group (16SrVI) Subgroup A (16SrVI-A) Phytoplasma is a Probable Causal Agent of Potato Purple Top Disease in Washington and Oregon

Plant Disease ◽  
2004 ◽  
Vol 88 (4) ◽  
pp. 429-429 ◽  
Author(s):  
I.-M. Lee ◽  
K. D. Bottner ◽  
J. E. Munyaneza ◽  
G. A. Secor ◽  
N. C. Gudmestad
Keyword(s):  
16S Rdna ◽  
Phylogenetic Analyses ◽  
Nested Polymerase Chain Reaction ◽  
Axillary Shoots ◽  
Rdna Sequences ◽  
Etiological Role ◽  
16S Rdna Sequences ◽  
Purple Top Disease ◽  
Potato Purple Top ◽  
Potato Seedlings

An epidemic of purple top disease of potato (Solanum tuberosum) occurred in the Columbia Basin Region of Washington and Oregon in 2002 and 2003, causing great economic loss in the potato industry (1). Symptoms of potato purple top (PPT) were characterized by upright terminal shoots, upward leaf rolling, chlorosis, red or purplish discoloration of new leaves, proliferation of axillary shoots with basal swelling, and the formation of aerial tubers. Preliminary studies on PPT disease suggested phytoplasma as a possible cause (1). In this study, 78 potato samples (including five asymptomatic) were collected from five fields throughout the region. A nested polymerase chain reaction (PCR) with primer pair P1/P7 in the first amplification followed with primer pair R16F2n/R16R2 was performed to detect the presence of phytoplasmas in infected plants (2). Restriction fragment length polymorphism (RFLP) and phylogenetic analyses of amplified 16S rDNA sequences were used for phytoplasma identification. Eighty-four percent (63% in the first amplification) of the symptomatic samples and 60% (0% in the first amplification) of the asymptomatic samples tested positive. Low phytoplasma titers and the presence of PCR inhibitors accounts for the low detection rate in the first PCR amplifications. RFLP analyses of 16S rDNA with enzymes MseI, AluI, HhaI, RsaI, and HpaII indicated that the phytoplasma associated with PPT belonged to the clover proliferation (CP) group (16SrVI) subgroup A (16SrVI-A) (2). 16SrVI-A currently consists of three members, CP (GenBank Accession No. AY500130), potato witches'-broom (GenBank Accession No. AY500818), and vinca virescence (VR) (GenBank Accession No. AY500817), a strain of beet leafhopper-transmitted virescence agent (BLTVA) phytoplasma (2). The taxonomic affiliation of PPT phytoplasma was confirmed by phylogenetic analysis of cloned 16S rDNA (GenBank Accession Nos. PPT4, AY496004; PPT8, AY496005). The 16S rDNA sequences of the PPT strains were closely related to VR with 99.7% sequence homology compared with 99.2% with CP. A high correlation between the symptoms and the presence of 16SrVI-A phytoplasmas in the potato plants suggests that these phytoplasmas play an etiological role in PPT disease. To gain further evidence, a modified test of Koch's postulates was conducted. Infected tissues from four phytoplasma-positive potato samples (including PPT4 and PPT8) were grafted onto healthy potato seedlings. Within 60 days after grafting, the potato seedlings developed symptoms similar to those in the original diseased samples. The newly infected plants were maintained through cuttings. RFLP analysis of 16S rDNA indicated that the phytoplasmas detected in each of the seedlings and cuttings were identical to those in the scions. These results confirmed the probable etiological role of CP group, subgroup 16SrVI-A phytoplasma strains in PPT disease in Washington and Oregon. There are two other confirmed cases of phytoplasmas (BLTVA and aster yellows phytoplasma) associated with PPT disease in Utah (4) and Mexico (3). References: (1) P. B. Hamm et al. Potato Prog. Vol. 3, No. 1, 2003. (2) I.-M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (3) N. E. Leyva-Lopez et al. Can. J. Microbiol. 48:1062, 2002. (4) C. D. Smart et al. Phytopathology 83:1399, 1993.

scholarly journals 16S rDNA sequences and phylogenetic analyses ofMicrocystisstrains with and without phycoerythrin

1998 ◽  
Vol 164 (1) ◽  
pp. 119-124 ◽  
Author(s):  
Shigeto Otsuka ◽  
Shoichiro Suda ◽  
Renhui Li ◽  
Masayuki Watanabe ◽  
Hiroshi Oyaizu ◽  
...  
Keyword(s):  
16S Rdna ◽  
Phylogenetic Analyses ◽  
Rdna Sequences ◽  
16S Rdna Sequences

Monophyly and phylogenetic relationships of Thereva and therevine genus-groups (Insecta:Diptera:Therevidae) based on EF-1α, 28S rDNA and mitochondrial 16S rDNA sequences

2007 ◽  
Vol 21 (3) ◽  
pp. 279 ◽  
Author(s):  
Kevin C. Holston ◽  
Michael E. Irwin ◽  
Brian M. Wiegmann
Keyword(s):  
16S Rdna ◽  
Phylogenetic Relationships ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
28S Rdna ◽  
Partial Recovery ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Holarctic Region ◽  
Species Groups

Phylogenetic analyses using 28S rDNA, elongation factor (EF)-1α, and mt 16S rDNA sequences were performed to test the monophyly of Thereva Latreille. Two of the three Afrotropical Thereva species groups lack the genitalia characters that unambiguously diagnose Thereva in the Holarctic Region, but phylogenetic relationships among Thereva species groups and therevine genera are poorly understood. Using an extensive taxonomic sample (39 of the 62 therevine genera) and Thereva, sensu lato (15 spp.), simultaneous analyses of all three gene partitions recovered Nearctic and Palaearctic Thereva species in a well supported clade that includes the Afrotropical seminitida-group but excludes the Afrotropical analis- and turneri-groups. Stronger phylogenetic signal from the EF-1α partition, measured by the skewness statistic and proportion of total parsimony informative characters, dominated conflicting signal from the 16S partition and weaker, but more congruent, signal from 28S. Reducing the taxonomic sample in analyses of Therevinae reduced homoplasy, increased phylogenetic structure and partitioned Bremer support values and reduced incongruence with 28S for the 16S partition. Although molecular analyses yielded partial recovery of informal therevine genus-groups, morphological diagnoses of higher-level groups are poorly supported with the exception of Cyclotelini. The ‘Holarctic radiation’ refers to a diverse clade of genera closely related to Pandivirilia Irwin & Lyneborg and Acrosathe Irwin & Lyneborg widely distributed throughout the Holarctic Region that is the sister-group to Thereva, sensu stricto. Results from these analyses underscore the importance of male and female genitalia characters in recognising monophyletic groups and regional endemism in therevine diversification.

scholarly journals Herbaspirillum chlorophenolicum sp. nov., a 4-chlorophenol-degrading bacterium

2004 ◽  
Vol 54 (3) ◽  
pp. 851-855 ◽  
Author(s):  
Wan-Taek Im ◽  
Hee-Sung Bae ◽  
Akira Yokota ◽  
Sung Taik Lee
Keyword(s):  
16S Rdna ◽  
Sequence Similarity ◽  
Rdna Sequence ◽  
The Novel ◽  
Comamonas Testosteroni ◽  
16S Rdna Sequence ◽  
Rdna Sequences ◽  
Degrading Bacterium ◽  
16S Rdna Sequences ◽  
Type Strains

A 4-chlorophenol-degrading bacterial strain, formerly designated as a strain of Comamonas testosteroni, was reclassified as a member of the genus Herbaspirillum based on its phenotypic and chemotaxonomic characteristics, as well as phylogenetic analysis using 16S rDNA sequences. Phylogenetic inference based on 16S rDNA sequences showed that strain CPW301T clusters in a phylogenetic branch that contains Herbaspirillum species. 16S rDNA sequence similarity of strain CPW301T to species of the genus Herbaspirillum with validly published names is in the range 98·7–98·9 %. Despite the considerably high 16S rDNA sequence similarity, strain CPW301T could be distinguished clearly from type strains of Herbaspirillum species with validly published names by DNA–DNA relatedness values, which were <15·7 %. The genomic DNA G+C content of strain CPW301T is 61·3 mol%. The predominant ubiquinone is Q-8 and the major cellular fatty acids are C16 : 0 and cyclo-C17 : 0. The strain does not fix nitrogen and is not plant-associated. It is an aerobic rod with one unipolar flagellum. On the basis of these characteristics, a novel Herbaspirillum species, Herbaspirillum chlorophenolicum sp. nov., is proposed. The type strain of the novel species is strain CPW301T (=KCTC 12096T=IAM 15024T).

scholarly journals Phylogenetic Analysis of Nonthermophilic Members of the Kingdom Crenarchaeota and Their Diversity and Abundance in Soils

1998 ◽  
Vol 64 (11) ◽  
pp. 4333-4339 ◽  
Author(s):  
Daniel H. Buckley ◽  
Joseph R. Graber ◽  
Thomas M. Schmidt
Keyword(s):  
16S Rrna ◽  
16S Rdna ◽  
Phylogenetic Analyses ◽  
Pcr Primers ◽  
Soil Samples ◽  
Molecular Techniques ◽  
Rrna Gene ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Long Term Ecological Research

ABSTRACT Within the last several years, molecular techniques have uncovered numerous 16S rRNA gene (rDNA) sequences which represent a unique and globally distributed lineage of the kingdom Crenarchaeotathat is phylogenetically distinct from currently characterized crenarchaeotal species. rDNA sequences of members of this novel crenarchaeotal group have been recovered from low- to moderate-temperature environments (−1.5 to 32°C), in contrast to the high-temperature environments (temperature, >80°C) required for growth of the currently recognized crenarchaeotal species. We determined the diversity and abundance of the nonthermophilic members of the Crenarchaeota in soil samples taken from cultivated and uncultivated fields located at the Kellogg Biological Station’s Long-Term Ecological Research site (Hickory Corners, Mich.). Clones were generated from 16S rDNA that was amplified by using broad-specificity archaeal PCR primers. Twelve crenarchaeotal sequences were identified, and the phylogenetic relationships between these sequences and previously described crenarchaeotal 16S rDNA sequences were determined. Phylogenetic analyses included nonthermophilic crenarchaeotal sequences found in public databases and revealed that the nonthermophilic Crenarchaeota group is composed of at least four distinct phylogenetic clusters. A 16S rRNA-targeted oligonucleotide probe specific for all known nonthermophilic crenarchaeotal sequences was designed and used to determine their abundance in soil samples. The nonthermophilicCrenarchaeota accounted for as much as 1.42% ± 0.42% of the 16S rRNA in the soils analyzed.

scholarly journals CDC Group IV c-2: a New RalstoniaSpecies Close to Ralstonia eutropha

1999 ◽  
Vol 37 (6) ◽  
pp. 1777-1781 ◽  
Author(s):  
Didier Moissenet ◽  
Christophe P. Goujon ◽  
Antoine Garbarg-Chenon ◽  
Hoang Vu-Thien
Keyword(s):  
16S Rdna ◽  
Biochemical Characterization ◽  
Ralstonia Eutropha ◽  
Rapd Analysis ◽  
Group Iv ◽  
Clinical Isolates ◽  
Rdna Sequences ◽  
Rdna Sequencing ◽  
16S Rdna Sequences ◽  
Type Strains

CDC group IV c-2, an environmental gram-negative bacillus recently proposed for inclusion in the genus Ralstonia, has been isolated in several human infections. Biochemical characterization and 16S ribosomal DNA (rDNA) sequencing with phylogenetic analysis were used to characterize eight clinical isolates and four type strains. Other typing tools, such as pulsed-field gel electrophoresis (PFGE) and randomly amplified polymorphic DNA (RAPD) analysis, were also used. PFGE typing of clinical isolates was unsuccessful because the DNA was degraded, and RAPD analysis was poorly discriminatory. In contrast, the type strains were clearly distinguished with both PFGE and RAPD analysis. All of the 16S rDNA sequences were identical. Comparison of the 16S rDNA sequences to the GenBank sequences showed that they were consistent with CDC group IV c-2 belonging to the genusRalstonia. The closest matches were obtained withRalstonia eutropha. However, four differences in 32 biochemical tests separated R. eutropha from CDC group IV c-2, which suggests that CDC group IV c-2 is a new species of the genusRalstonia.

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