• Environmental Engineering Research
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• v.19 no.4
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• pp.317-329
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• 2014

The diversity of cyanobacteria in Sri Lanka was studied in different water reservoirs, paddy fields, brackish water and tsunami affected areas using light microcopy, 16S rRNA sequences, followed by phylogenetic analysis. Based on light microscopy, 24 genera were identified from environmental samples belonging to the orders Chroococcales, Oscillatoriales, Pleurocapsales and Nostocales. In cultures, 33 genera were identified from all five cyanobacterial orders, including Stigonematales. Based on 16S rRNA gene sequences and their morphology, two isolates were identified up to species level, 72 to genus level, one isolate up to family and 11 up to order level. Twelve isolates couldn't be assigned to any taxonomic level. The results of 16S rRNA gene sequences along with the phylogenetic analysis indicated that some cyanobacterial isolates could be accommodated to genus or order level. The 16S rRNA sequence analysis data in this study confirmed that order Nostocales and order Pleurocapsales cyanobacteria are monophyletic while orders Chroococcales, Oscillatoriales and Stigonematales cyanobacteria are polyphyletic. Polyphasic approach including the combination of light microscopy, cultures and the analysis of 16S rRNA gene sequences provide a promising approach to ascertain the diversity of cyanobacteria in different habitats.

• Korean Journal of Microbiology
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• v.46 no.3
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• pp.296-302
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• 2010

Microcystis (Cyanobacteria, Chroococcales) is one of the green tide-causing organisms in freshwaters, and some species produce microcystin that is hepatotoxin. In the aspects of freshwater quality controls and health concerns, therefore it is necessary to manage the harmful organisms. In the present study, RNA polymerase beta subunit (rpoB) gene sequences of Microcystis were determined and characterized in order to use a potential marker for the molecular detections of the species. Microcystis rpoB showed high divergences of DNA similarity and genetic distances when compared with those of 16S rRNA, and the molecular differences were statistically significant (Student t-test, p<0.05). Parsimony analyses showed the rpoB gene evolves more than 2-fold faster than 16S rRNA. In addition, phylogeny of the rpoB gene separated each M. aeruginosa strain more clearly compared with a 16S rRNA tree. This study found that the order Chroococcales, including Microcystis, has approximately two rRNA operons and single copy of the rpoB gene in their chromosomes. These results suggest that the rpoB gene is a useful marker for the molecular phylogenetics and the detection of Microcystis.

• Korean Journal of Microbiology
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• v.45 no.4
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• pp.430-434
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• 2009

Bacterial 16S rRNA gene sequences have been widely used for the studies on molecular phylogeny, evolutional history, and molecular detections. Bacterial genomes have multiple rRNA operons, of which gene sequences sometimes are variable. In the present study, heterogeneity of the Vibrio 16S rRNA gene sequences were investigated. Vibrio 16S rRNA sequences were obtained from GenBank databases, considering the completion of gene annotation of Vibrio genome sequences. These included V. cholerae, V. harveyi, V. parahaemolyticus, V. splendidus, and V. vulnificus. Chromosome 1 of the studied Vibrio had 7~10 copies of the 16S rRNA gene, and their intragenomic variations were less than 0.9% dissimilarity (more than 99.1% DNA similarity). Chromosome 2 had none or single 16S rRNA gene. Intragenomic 16S rRNA genotypes were detected at least 5 types (V. vulnificus #CMCP6) to 8 types (V. parahaemolyticus #RIMD 2210633, V. harveyi #ATCC BAA-1116). These suggest that Vibrio has high heterogeneity of the 16S rRNA gene sequences.

• Korean Journal of Microbiology
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• v.47 no.3
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• pp.268-274
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• 2011

Anabaena (Cyanobacteria, Nostocales) are important for water quality controls, because they are often responsible for freshwater green tides; moreover, some species are reported to produce hepatotoxin. In this study, we sequenced RNA polymerase beta subunit (rpoB) gene of Anabaena, and evaluated their sequences for the potential use of a molecular taxonomic marker in this taxon. Anabaena rpoB showed low DNA similarity and high genetic divergences when compared those of 16S rRNA, and the molecular differences were statistically significant (Student t-test, p<0.01). Parsimony analyses showed the rpoB gene evolves 4.8-fold faster than 16S rRNA. In addition, phylogeny of the rpoB gene separated each Anabaena strain more clearly compared with a 16S rRNA tree. These results suggest that the rpoB gene is a useful marker for the molecular phylogenetics and the species discrimination of Anabaena.

• Journal of Microbiology
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• v.44 no.5
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• pp.566-571
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• 2006

An archaeal 16S rRNA gene library was constructed from mangrove soil. Phylogenetic analysis revealed archaea in mangrove soil including the Crenarchaeota (80.4%) and Euryarchaeota (19.6%) phyla. The archaeal community in mangrove soil appears to be a mixture of organisms found in a variety of environments with the majority being of marine origin.

• International Journal of Industrial Entomology and Biomaterials
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• v.2 no.1
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• pp.37-53
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• 2001

Two regions of mtDNA genome, cytochrome oxidase subunit I (COI) and 165 ribosomal RNA (165 rRNA) genes, were sequenced for 15 species of the long-horned beetle belonging to four subfamilies and geographic samples of mulberry longicorn beetle, Apriona germari, from two localities in Korea. Ten samples of A. germari collected from Suwon and Busan revealed three COI haplotypes ranging in nucleotide divergence of 0.3% to 0.5%, and the two populations shared one common COI haplotype (80%). The sequence divergence among 15 species of the long-horned beetle was much higher in COI gene (12.3%∼39.4%) than 16S rRNA gene (7.2% to 23.1), and the maximum value in the COI gene is exceptional compared with other relevant studies, including that of Coleoptera. The greatly increased divergence in the COI gene, in facto was stemmed from a peculiar sequence of Prionus insularis belonging to Prioninne, divergence of which ranges from 31.2% to 39.3% from other species. We discussed possible reason of the divergence in this species. Due to the abnormality of COI gene divergence, decrease in phylogenetic signal was severe in COI nucleotide and, subsequently, the converted amino acid sequences, rendering us to put more confidence on the 16S5 rRNA gene data. Although the molecular phylogeny confidently supports the monophyletic origin of Lepturinae, the presence of discrepancy between molecular data and traditional taxonomic views also is a testable hyothesis. One such discrepancy includes taxonomic position of Sophronica obrioides and Theophilea cylindricollis belonging to Lamiinae.

• Molecules and Cells
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• v.27 no.1
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• pp.55-66
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• 2009

The phylogeny of the family Tephritidae (Diptera: Tephritidae) was reconstructed from mitochondrial 12S, 16S, and COII gene fragments using 87 species, including 79 tephritid and 8 outgroup species. Minimum evolution and Bayesian trees suggested the following phylogenetic relationships: (1) A sister group relationship between Ortalotrypeta and Tachinisca, and their basal phylogenetic position within Tephritidae; (2) a sister group relationship between the tribe Acanthonevrini and Phytalmiini; (3) monophyly of Plioreocepta, Taomyia and an undescribed new genus, and their sister group relationship with the subfamily Tephritinae; (4) a possible sister group relationship of Cephalophysa and Adramini; and (5) reconfirmation of monophyly for Trypetini, Carpomyini, Tephritinae, and Dacinae. The combination of 12S, 16S, and COII data enabled resolution of phylogenetic relationships among the higher taxa of Tephritidae.

• Journal of Life Science
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• v.13 no.6
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• pp.856-864
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• 2003

The 16S rRNA gene is the most common gene in the phylogenetic analysis of procaryotes. However very high conservative of 16S rRNA has limitation in the discrimination of highly related organisms, hence other molecule was applied in this study and the result was compared with that of 16S rRNA. Three COGs (Clusters of Orthologous of protein) were only detected in 42 procaryotes ; transcription elongation facto. (COG0195), bacterial DNA primase (COG0358) and uridylate kinase (COG0528). Uridylate kinase gene was selected because of the similarity and one single copy number in each genome. Bacteria, belong to same genus, and Archaebacteria were same position with high bootstrap value in phylogenetic tree like the tree of 16S rRNA. However, alpha and epsilon Proteobcteria showed different position and Spirochaetales of Eubarteria was grouped together with Archaebacteria unlike the result of 16S rRNA. Uridylate kinase may compensate the problem of very high conservative of 16S rRNA gene and it would help to access more accurate discrimination and phylogenetic analysis of bacteria.

• Proceedings of the Microbiological Society of Korea Conference
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• 2003.05a
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• pp.19-21
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• 2003

• Journal of Microbiology
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• v.40 no.4
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• pp.335-339
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• 2002

Partial sequences of 16S rRNA gene of five chroococcalian blue-green algal strains, Aphanothece nidulans KCTC AG10041, Aphanothece naegelii KCTC AG10042, Microcystis aeruginosa KCTC AG10159, Microcystis ichthyoblabe KCTC AG10160, and Microcystis viridis KCTC AG10198, which were isolated from water from the Geumgang River, were determined and were inferred their phylogenetic and taxonomic positions among taxa of order Chroococcales. Most taxa of Chroococcales whose partial 16S rRNA gene sequences were aligned in this study, are clustered with other related taxa. Aphanothece nidulans KCTC AG10041 and Aphanothece naegelii KCTC AG10042 made a cluster with other European species of these genera, which supported 100% of the bootstrap trees with a very high sequence similarity (97.4-99.4%) in this study. Three strains, Microcystis aeruginosa KCTC AG10159, M. ichthyoblabe KCTC AG10160, and M. viridis KCTC AG10198, formed a cluster with other Microcystis spp. supported 100 % of the bootstrap trees with a similarity of 97.0-99.9% except for two strains. However, this phylogentic tree made no resolution among the species of Microcystis spp. The topology of the tree reconfirmed the taxonomic status of three species of Microcystis, identified in this study based on the morphology, as three colonial types of Microcystis aeruginosa com. nov. Otsuka et al. (1999c). The genera of chroococcalian cyanophytes are heterogeneously clustered in these sequence analyses. We suggest that more molecular studies on the genera of Chroococcales with reference strains, widely collected from restricted geographic or environmental ranges, get accurate taxonomic or phylogenetic determinations.