• Journal of Species Research
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• v.7 no.2
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• pp.97-103
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• 2018

In 2016, as a subset study to discover indigenous prokaryotic species in Korea, a total of 15 bacterial strains were isolated and assigned to the class Betaproteobacteria. From the high 16S rRNA gene sequence similarity (>98.8%) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that these 15 species have been described in Korea; therefore, 1 strain of the Aquitalea, 5 strains of the Paraburkholderia, 2 strains of the Comamonas, 1 strain of the Cupriavidus, 1 strain of the Diaphorobacter, 2 strains of the Hydrogenophaga, 1 strain of the Iodobacter, 1 strain of the Massilia and 1 strain of the Rhodoferax within the Betaproteobacteria are described for unreported bacterial species in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, and isolation sources are also described in the species description section.

• Journal of Species Research
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• v.7 no.2
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• pp.161-180
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• 2018

Fourteen bacterial strains, low10-4-1, J11015, 17J27-22, 17G22-9, 17G9-4, 17Bio_15, 17gy_33, 17SD1_21, Strain8, 17Sr1_17, J21014T, H31021, 17J49-9, and 17J80-6 assigned to the phylum Actinobacteria, Bacteroidetes, Deinococcus-Thermus, and Firmicutes were isolated from soil samples. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strains low10-4-1, J11015, 17J27-22, 17G22-9, 17G9-4, 17Bio_15, 17gy_33, 17SD1_21, Strain8, 17Sr1_17, J21014T, H31021, 17J49-9, and 17J80-6 were most closely related to Marmoricola aurantiacus (98.9%), Calidifontibacter indicus (99.8%), Gordonia soli (98.8%), Rhodococcus globerulus (99.5%), Pseudarthrobacter siccitolerans (99.1%), Hymenobacter qilianensis (98.7%), Hymenobacter terrae (99.0%), Deinococcus yunweiensis (99.2%), Deinococcus proteolyticus (99.7%), Domibacillus indicus (99.2%), Exiguobacterium mexicanum (100.0%), Kurthia senegalensis (99.1%), Lysinibacillus composti (99.6%), and Bacillus loiseleuriae (99.3%). These fourteen species have never been reported in Korea, therefore we report them here for the first time.

• Journal of Species Research
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• v.7 no.2
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• pp.135-150
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• 2018

Eleven bacterial strains 17SD2_15, 17Sr1_23, 17SD2_13, 17Sr1_31, 17gy_18, 16B15D, 16B02D, 16B04G, 16B01D, 17U4-2 and 17J28-10 assigned to the phylum Proteobacteria were isolated from soil samples collected from Seoul Women's University, in South Korea. The Belnapia species, strain 17SD2_15 was cocci-shaped and pink-colored. The Methylobacterium species, strain 17Sr1_23, 17SD2_13, 17Sr1_31, and 16B15D were short rod-shaped and pink-colored. The Microvirga species, strain 17gy_18, and 16B02D were short rod-shaped and pink-colored. The Oxalicibacterium species, strain 16B04G was short rod-shaped and pink-colored. The Sphingomonas species, strain 16B01D was short rod-shaped and yellow-colored. The Variovorax species, strain 17U4-2 was cocci-shaped and yellow-colored. The Paracoccus species, 17J28-10 was cocci-shaped and orange-colored. Phylogenetic analysis based on 16S rRNA gene sequence showed that strains 17SD2_15, 17Sr1_23, 17SD2_13, 17Sr1_31, 17gy_18, 16B15D, 16B02D, 16B04G, 16B01D, 17U4-2 and 17J28-10 were most closely related to Belnapia soli (with 99.9% similarity), Methylobacterium gregans (99.1%), Methylobacterium isbiliense (99.6%), Methylobacterium oxalidis (99.9%), Microvirga aerilata (98.7%), Methylobacterium aerolatum (99.0%), Microvirga vignae (100.0%), Noviherbaspirillum canariense (100.0%), Sphingomonas desiccabilis (100.0%), Variovorax humicola (99.6%), and Paracoccus acridae (99.1%), respectively. This is the first report of these eleven species in Korea.

• Journal of Species Research
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• v.7 no.2
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• pp.104-113
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• 2018

In order to investigate indigenous prokaryotic species diversity in Korea, various environmental samples from diverse ecosystems were examined. Isolated bacterial strains were identified based on 16S rRNA gene sequences, and those exhibiting at least 98.7% sequence similarity with known bacterial species, but not reported in Korea, were selected as unrecorded species. 28 unrecorded bacterial species belonging to the phylum Bacteroidetes were discovered from various habitats including wastewater, freshwater, freshwater sediment, wet land, reclaimed land, plant root, bird feces, seawater, sea sand, tidal flat sediment, a scallop, marine algae, and seaweed. The unrecorded species were assigned to 18 different genera in five families: Flavobacterium, Epilithonimonas, Dokdonia, Gillisia, Flavicella, Chryseobacterium, Algibacter, Aquimarina, Lacinutrix, Gaetbulibacter, Cellulophaga, Tenacibaculum, and Maribacter of Flavobacteriaceae, Dyadobacter of Cytophagaceae, Draconibacterium of Draconibacterium_f, Sunxiuqinia of Prolixibacteraceae, and Fulvivirga of Fulvivirga_f. The selected isolates were subjected to further taxonomic characterization including analysis of Gram reaction, cellular and colonial morphology, biochemical activities, and phylogenetic trees. Descriptive information of the 28 unrecorded species is provided.

• Korean Journal of Microbiology
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• v.45 no.2
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• pp.170-176
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• 2009

Culture-independent 16S rDNA-DGGE profiling and phylogenetic analysis were used to examine the predominant bacterial communities associated with the two sponges, Dictyonella sp. and Spirastrella abata from Jeju island. The culture-independent approach involved extraction of total bacterial DNA, PCR amplification of the 16S ribosomal DNA using primer pair 341f-GC and 518r, and separation of the amplicons on a denaturing gradient gel. Denaturing gradient gel electrophoresis banding patterns indicated 8 and 7 bands from the two sponge species, Dictyonella sp. and Spirastrella abata, respectively. There were not common major bands in two different sponges. Comparative sequence analysis of variable DGGE bands revealed from 93% to 98% similarity to the known published sequences. The dominant bacterial group of Dictyonella sp. belonged to uncultured Gammaproteobacteria, while, that of Spirastrella abata belonged to uncultured Alphaproeobacteria and Firmicutes. DGGE analysis indicated predominant communities of the sponge-associated bacteria differ in the two sponges from the same geographical location. This result revealed that bacterial community profiles of the sponges were host species-specific.

• The Plant Pathology Journal
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• v.34 no.2
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• pp.150-156
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• 2018

The genome sequences of two novel monopartite RNA viruses were identified in a common eelgrass (Zostera marina) transcriptome dataset. Sequence comparison and phylogenetic analyses revealed that these two novel viruses belong to the genus Amalgavirus in the family Amalgaviridae. They were named Zostera marina amalgavirus 1 (ZmAV1) and Zostera marina amalgavirus 2 (ZmAV2). Genomes of both ZmAV1 and ZmAV2 contain two overlapping open reading frames (ORFs). ORF1 encodes a putative replication factory matrix-like protein, while ORF2 encodes a RNA-dependent RNA polymerase (RdRp) domain. The fusion protein (ORF1+2) of ORF1 and ORF2, which mediates RNA replication, was produced using the +1 programmed ribosomal frameshifting (PRF) mechanism. The +1 PRF motif sequence, UUU_CGN, which is highly conserved among known amalgaviruses, was also found in ZmAV1 and ZmAV2. Multiple sequence alignment of the ORF1+2 fusion proteins from 24 amalgaviruses revealed that +1 PRF occurred only at three different positions within the 13-amino acid-long segment, which was surrounded by highly conserved regions on both sides. This suggested that the +1 PRF may be constrained by the structure of fusion proteins. Genome sequences of ZmAV1 and ZmAV2, which are the first viruses to be identified in common eelgrass, will serve as useful resources for studying evolution and diversity of amalgaviruses.

• Journal of Mushroom
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• v.8 no.1
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• pp.27-32
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• 2010

This study was carried out to analyze the genetic relationships among 22 strains of Sparassis crispa, which were collected from various regions of worldwide. The cleaved amplified polymorphic sequence were obtained from the ribosomal DNA ITS regions of each strain. Based on the sequence analysis, the presence of five different groups were observed. Most strains shared the high nucleotide sequence similarity (about 90%) to each other, except only one strain, KACC50866. Nucleotide sequence similarity of KACC50866 was below 10% to other strains, indicating the genetic relatedness of strain KACC50866 was low compared to other strains. More works such as mitochondria genome analysis should help to determine the precise genetic diversity of S. crispa strains.

• The Plant Pathology Journal
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• v.29 no.3
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• pp.260-273
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• 2013

The incidence and distribution of Tobacco mosaic virus (TMV) and related tobamoviruses was determined using an enzyme-linked immunosorbent assay on 1,926 symptomatic horticultural crops and 107 asymptomatic weed samples collected from 78 highly infected fields in the major horticultural crop-producing areas in 17 provinces throughout Iran. The results were confirmed by host range studies and reverse transcription-polymerase chain reaction. The overall incidence of infection by these viruses in symptomatic plants was 11.3%. The coat protein (CP) gene sequences of a number of isolates were determined and disclosed to be a high identity (up to 100%) among the Iranian isolates. Phylogenetic analysis of all known TMV CP genes showed three clades on the basis of nucleotide sequences with all Iranian isolates distinctly clustered in clade II. Analysis using the complete CP amino acid sequence showed one clade with two subgroups, IA and IB, with Iranian isolates in both subgroups. The nucleotide diversity within each subgroup was very low, but higher between the two clades. No correlation was found between genetic distance and geographical origin or host species of isolation. Statistical analyses suggested a negative selection and demonstrated the occurrence of gene flow from the isolates in other clades to the Iranian population.

• The Plant Pathology Journal
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• v.29 no.3
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• pp.223-233
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• 2013

Rice stripe virus (RSV) is one of the most destructive viruses of rice, and greatly reduces rice production in China, Japan, and Korea, where mostly japonica cultivars of rice are grown. RSV is transmitted by the small brown plant-hopper (SBPH) in a persistent and circulative-propagative manner. Several methods have been developed for detection of RSV, which is composed of four single-stranded RNAs that encode seven proteins. Genome sequence data and comparative phylogenetic analysis have been used to identify the origin and diversity of RSV isolates. Several rice varieties resistant to RSV have been selected and QTL analysis and fine mapping have been intensively performed to map RSV resistance loci or genes. RSV genes have been used to generate several genetically modified transgenic rice plants with RSV resistance. Recently, genome-wide transcriptome analyses and deep sequencing have been used to identify mRNAs and small RNAs involved in RSV infection; several rice host factors that interact with RSV proteins have also been identified. In this article, we review the current statues of RSV research and propose integrated approaches for the study of interactions among RSV, rice, and the SBPH.

• Journal of Species Research
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• v.5 no.2
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• pp.241-253
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• 2016

In 2014, as a subset study to discover indigenous prokaryotic species in Korea, a total of 33 bacterial strains assigned to the class Gammaproteobacteria were isolated from diverse environmental samples collected from soil, tidal flat, freshwater, seawater, oil-contaminated soil, and guts of animal. From the high 16S rRNA gene sequence similarity (>98.5%) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that these 33 species have been described in Korea; therefore, 1 strain of the Aeromonadales, 6 strains of the Alteromonadales, 3 strains of the Chromatiales, 5 strains of the Enterobacteriales, 4 strains of the Oceanospirillales, 11 strains of the Pseudomonadales, and 3 strains of the Xanthomonadales within the Gammaproteobacteria are described for unreported bacterial species in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, and isolation sources are also described in the species description section.