• Korean Journal of Microbiology
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• v.53 no.1
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• pp.29-38
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• 2017

In this study, we investigated the phylogenetic diversity of the bacterial community and isolation of extremely halophilic bacteria using culturomics in a gray solar saltern. The number of bacterial living cells, enumerated in a gray solar saltern by direct fluorescence microscopy was three to four orders of magnitude greater than those enumerated by plate counts, suggesting the distribution of 'viable but non-culturable bacteria'. The biodiversity of bacterial communities in a gray solar saltern was investigated by pyrosequencing, 1,778 OTUs of bacteria were comprised of 18 phyla 46 classes 85 orders 140 families 243 genera with 6.16 diversity index. Archaea communities were composed of 3 phyla 6 classes 7 orders 7 families 38 genera with 4.95 diversity index from 643 OTUs. Totally 137 isolates were isolated by 59 different cultural methods based on culturomics considering culture media and conditions suitable for the growth of extremely halophilic bacteria. Phylogenetic analyses of extremely halophilic isolates based on 16S rRNA gene sequences, extremely halophilic isolates were composed of 4 phyla and 11 genera. Haloterrigena and Haloferax can be successfully isolated from culturomics. These culturomics were effective methods for collection of diversity of extremely halophilic bacteria.

• Korean Journal of Soil Science and Fertilizer
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• v.35 no.1
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• pp.12-26
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• 2002

The phylogenetic relationships for 33 strains belonging to the genera Azorhizobium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium were conducted by the sequence analyses of the ITS regions. The sequence homologies of these strains showed the high variations(28.0 - 94.9%). According to the phylogenetic analysis of ITS regions. 37 ITS clones from 33 strains of 32 species were classified into four groups. Group I included all strains of the genus Sinorhizobium as core members and R. giardinii as a peripheral member. The genus Rhizobium strains were clustered into group II which was very heterogeneous and the tree toplogy of this group were very unstable. Among the members of group II. the taxonomic position of R. radiobacter and R. rubi was not clearly identified on the basis of ITS I regions. R. undicola and R. vitis were remotely related with other Rhizobium strains including R. leguminosarum, R. galegae, R. gallicum, R. mongolense, R. tropici, R. hainanense, R. rhizogense and R. huautlense of group II were supposed to be loosely related to R. leguminosarum. While the stains of the genera Bradyrhizobium constituted group III with Azorhizobium caulindans, the strains of the genus Mesorhizobium formed group IV on the relatively high sequence homology level.

• Journal of Veterinary Science
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• v.22 no.4
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• pp.43.1-43.10
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• 2021

Background: The H5 avian influenza viruses (AIVs) of clade 2.3.4.4 circulate in wild and domestic birds worldwide. In 2017, nine strains of H5N6 AIVs were isolated from aquatic poultry in Xinjiang, Northwest China. Objectives: This study aimed to analyze the origin, reassortment, and mutations of the AIV isolates. Methods: AIVs were isolated from oropharyngeal and cloacal swabs of poultry. Identification was accomplished by inoculating isolates into embryonated chicken eggs and performing hemagglutination tests and reverse transcription polymerase chain reaction (RT-PCR). The viral genomes were amplified with RT-PCR and then sequenced. The sequence alignment, phylogenetic, and molecular characteristic analyses were performed by using bioinformatic software. Results: Nine isolates originated from the same ancestor. The viral HA gene belonged to clade 2.3.4.4B, while the NA gene had a close phylogenetic relationship with the 2.3.4.4C H5N6 highly pathogenic avian influenza viruses (HPAIVs) isolated from shoveler ducks in Ningxia in 2015. The NP gene was grouped into an independent subcluster within the 2.3.4.4B H5N8 AIVs, and the remaining six genes all had close phylogenetic relationships with the 2.3.4.4B H5N8 HPAIVs isolated from the wild birds in China, Egypt, Uganda, Cameroon, and India in 2016-2017, Multiple basic amino acid residues associated with HPAIVs were located adjacent to the cleavage site of the HA protein. The nine isolates comprised reassortant 2.3.4.4B HPAIVs originating from 2.3.4.4B H5N8 and 2.3.4.4C H5N6 viruses in wild birds. Conclusions: These results suggest that the Northern Tianshan Mountain wetlands in Xinjiang may have a key role in AIVs disseminating from Central China to the Eurasian continent and East African.

• Journal of Life Science
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• v.30 no.12
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• pp.1063-1069
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• 2020

Two crucian carp species (Carassius auratus and C. cuvieri) inhabit Lake Yedang in South Korea, and C. auratus is known to be native to Korea. Classification of these two freshwater fish species is often confused because of their morphological similarity. To distinguish the two species, we conducted phylogenetic and population genetic analyses of C. auratus and C. cuvieri based on their mitochondrial DNA sequences of the cytochrome b gene (CYTB). We also compared our partial CYTB sequence (<1,056 bp) with 10 Chinese, nine Japanese, and two Russian crucian carp fishes. The results of our phylogenetic analysis showed that C. auratus and C. cuvieri were clearly divided into two phylogroups. The nucleotide diversity (π) of C. auratus from Korea, China, and Japan showed a range of 0.146%~0.421%, while the range of π of C. cuvieri from Korea and Japan was lower than those of C. auratus (0.0%~0.054%). Moreover, the comparison of CYTB divergence among crucian carp fishes in China, Japan, and Korea indicated that Korean Carassius fishes were distantly related to those from China and Japan, with two exceptions: the pairwise Fst value between Korean C. auratus and northern Chinese C. auratus was not significantly different. In addition, no significant genetic divergence between Korean and Japanese C. cuvieri was detected. We conclude that, despite the morphological similarities, C. auratus and C. cuvieri should be considered as separate freshwater fish resources in conservation efforts for genetic diversity.

• Korean Journal of Ichthyology
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• v.34 no.4
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• pp.231-243
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• 2022

To investigate the taxonomic status of undescribed species Acheilognathus sp. HR from Korean Acheilognathidae discovered from the Dalcheon River, a tributary of the Hangang River, molecular phylogenetic and morphological characteristics were compared and analyzed with previous studies. As a result of molecular phylogenetic analysis, A. sp. HR formed the same genetic clade as the five subspecies of Acheilognathus tabira, but formed a separate monophyletic group based on the unique genotype, showing clear differences. As a result of morphological analyses, the dorsal fin color in males is grayish and the nuptial coloration of the outer edge of the anal fin is white. The outer edges of the dorsal and anal fins are convexly rounded. A black blotch is present on the dorsal fin of the juvenile, but there is a black blotch absent on the dorsal fin of the small adult female. In the counts, the number of branched dorsal rays is 12~13. In the measurements, the length of the barbels is short and the body depth is deep. Therefore, the A. sp. HR of Hangang River is considered at the level of a distinct species distinguished from each other by the five subspecies of A. tabira by molecular phylogenetic, morphological, and limited distributional characteristics.

• The Korean Journal of Mycology
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• v.24 no.2 s.77
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• pp.155-165
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• 1996

This study was carried out to identify the phylogenetic relationship among several isolates of Pleurotus species by comparing ITS II region of ribosomal DNA(rDNA) repeat unit. Two primers from ribosomal DNA sequences were chosen to amplify the specific internal transcribed spacer (ITS) II region of Pleurotus spp. The exact ITS II region with an unique band from six species of Pleurotus genus could be amplified using the two primers taken from at the 3'-end of 5.8S rDNA and 5'-end of 28S rDNA. Six representative species of the Pleurotus genus were easily characterized according to the length differences of ITS II region. Furthermore, within P. ostreatus species, different sizes of ITS II region could be observed in the isolates of ASI 2025 and ASI 2095 although they were classified as P. ostreatus by the conventional observation. The nucleotide sequence analyses of PCR-amplified ITS II region indicated that the isolates ASI 2025 and ASI 2095 were different from other Pleurotus spp. When the nucleotide sequences of six Pleurotus species were compared, three typical ITS II regions were highly variable especially at both ends of this region. The phylogenetic tree obtained by the Neighbor program of Felsenstein PHYLIP package with all the nucleotide sequence of Pleurotus spp. indicated that P. ostreatus, P. florida, P. sajor-caju and P. eryngii were closely related to one phylogenetic branch and P. cystidious was related to other branch with P. cornucopiae. The isolates ASI 2025 and 2038, however, were not closely related to any other Pleurotus spp. and formed their own individual branches.

• Journal of fish pathology
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• v.33 no.1
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• pp.15-21
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• 2020

We found skin flukes in snubnose pompano (Trachinotus blochii) from a public aquarium and attempted clear identification of them to the species level by morphology and molecular analyses. Skin flukes were collected from snubnose pompano showing dyspnea, anorexia and mild hemorrhage on the skin. All the fish samples (n=2) were infected with the flukes on the skin, gill and eyes, covered with excessive mucus. The isolated worms were transferred for making slide specimen and PCR amplification targeting 18S rDNA, 28S rDNA, mitochondrial cytochrome c oxidase subunit 1 (mt cox1) and cytochrome b (Cytb) genes for further analyses. Morphology and measurements data of our slide specimen coincided with those of Neobenedenia girellae. The sequence data of 2 genes (28S rDNA and Cytb) and the phylogenetic trees revealed that our specimen consistently belonged to the N. girellae clade. For 18S rDNA and mt cox1 genes, there was no sequence of either of these 2 Neobenedenia species from the type host available in GenBank. This is the first record of N. girellae in snubnose pompano, but it is still unclear if the snubnose pompano is a natural host for N. girellae or not because N. girellae is known to have an unusual broad host range and the host-switching can occur particularly in captive conditions such as aquarium or aquaculture facilities.

• Journal of Microbiology and Biotechnology
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• v.20 no.1
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• pp.21-29
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• 2010

The phenolic compounds are a major contaminant class often found in industrial wastewaters and the biological treatment is an alternative tool commonly employed for their removal. In this sense, monitoring microbial community dynamics is crucial for a successful wastewater treatment. This work aimed to monitor the structure and activity of the bacterial community during the operation of a laboratory-scale continuous submerged membrane bioreactor (SMBR), using PCR and RT-PCR followed by denaturing gradient gel electrophoresis (DGGE) and 16S rRNA libraries. Multivariate analyses carried out using DGGE profiles showed significant changes in the total and metabolically active dominant community members during the 4-week treatment period, explained mainly by phenol and ammonium input. Gene libraries were assembled using 16S rDNA and 16S rRNA PCR products from the fourth week of treatment. Sequencing and phylogenetic analyses of clones from the 16S rDNA library revealed a high diversity of taxa for the total bacterial community, with predominance of Thauera genus (ca. 50%). On the other hand, a lower diversity was found for metabolically active bacteria, which were mostly represented by members of Betaproteobacteria (Thauera and Comamonas), suggesting that these groups have a relevant role in the phenol degradation during the final phase of the SMBR operation.

• Journal of Microbiology and Biotechnology
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• v.22 no.1
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• pp.1-12
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• 2012

The present study examines the effects of 30 mg/kg butachlor on the cyanobacterial diversity of rice fields in Eastern Uttar Pradesh and Western Bihar in India. A total of 40 samples were grouped into three classes [(i) acidic, (ii) neutral, and (iii) alkaline soils], based on physicochemical and principle component analyses. Acidic soils mainly harbored Westillopsis, Trichormus, Anabaenopsis, and unicellular cyanobacteria; whereas Nostoc, Anabaena, Calothrix, Tolypothrix, and Aulosira were found in neutral and alkaline soils. Molecular characterization using 16S rRNA PCR and DGGE revealed the presence of 13 different phylotypes of cyanobacteria in these samples. Butachlor treatment of the soil samples led to the disappearance of 5 and the emergence of 2 additional phylotypes. A total of 40 DGGE bands showed significant reproducible changes upon treatment with butachlor. Phylogenetic analyses divided the phylotypes into five major clusters exhibiting interesting links with soil pH. Aulosira, Anabaena, Trichormus, and Anabaenopsis were sensitive to butachlor treatment, whereas uncultured cyanobacteria, a chroococcalean member, Westillopsis, Nostoc, Calothrix, Tolypothrix, Rivularia, Gloeotrichia, Fischerella, Leptolyngbya, and Cylindrospermum, appeared to be tolerant against butachlor at their native soil pH. Butachlor-induced inhibition of nitrogen fixation was found to be 65% (maximum) and 33% (minimum) in the soil samples of pH 9.23 and 5.20, respectively. In conclusion, low butachlor doses may prove beneficial in paddy fields having a neutral to alkaline soil pH.

• Korean Journal of Poultry Science
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• v.44 no.2
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• pp.75-81
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• 2017

A total of 340 individuals from seven duck populations were studied using 24 polymorphic microsatellite (MS) markers to identify plumage colors with genetic diversity. The estimated average number of alleles (Na), polymorphic information content (PIC) value, and expected heterozygosity (He) per locus of all populations were 11.5, 0.602, and 0.635, respectively. The calculated population genetic distance (Fst), inbreeding coefficient of individuals within duck populations (Fis), and total inbreeding among populations (Fit) were 0.135, 0.105, and 0.229, respectively. Statistical analyses for each population using 24 marker combinations, revealed that the estimated average number of effective alleles (Ne), observed heterozygosity (Ho), and fixation index of inbreeding within populations (F) were 3.129, 0.505, and 0.104, respectively. The results of genetic distance and phylogenetic analysis revealed that Korean native duck populations were clearly separated from all Bangladeshi duck populations. Moreover, all populations clustered well according to their genetic distance, but could not be clearly separated according to black and white plumage colors or plumage color pattern. The combination of these 24 MS markers can be used for discrimination and determination of the genetic diversity of native duck breeds in further investigations for conservation and special development purposes.