• The Plant Pathology Journal
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• 제28권1호
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• pp.20-31
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• 2012

Endophytic bacterial communities of tidal flat plants antagonistic to oomycete plant pathogens were studied by the isolation of 256 root colonizing endophytic bacteria from surface-disinfected root tissues of six plants ($Rosa$ $rugosa$, $Suaeda$ $maritima$, $Vitex$ $rotundifolia$, $Carex$ $scabrifolia$, $Glehnia$ $littoralis$ and $Elymus$ $mollis$) growing in a tidal flat area of Namhae Island, Korea. To understand the antagonistic potential, an $in$ $vitro$ antagonistic assay was performed to characterize and identify strains that were antagonistic to the oomycete plant pathogens $Phytophthora$ $capsici$ and $Pythium$ $ultimum$ from the total population. Nine percent of the total number of isolated bacteria exhibited in vitro inhibitory activity against target plant pathogenic oomycetes. Taxonomic and phylogenetic placement of the antagonistic bacteria was investigated by analysis of the 16S rRNA gene sequences. The sequence analysis classified the antagonistic strains into four major classes of the domain bacteria ($Firmicutes$, ${\alpha}-Proteobacteria$, ${\gamma}-Proteobacteria$ and $Actinomycetes$) and 10 different genera. Further production of secondary metabolites, hydrolytic enzymes and plant growth promoting traits were determined for the putative new species of antagonistic endophytic bacteria. These new strains could not be identified as known species of ${\alpha}-Proteobacteria$, and so may represent novel bacterial taxa. The unexpected high antagonistic bacterial diversity associated with the tidal flat plants may be indicative of their importance in tidal flat plants as a promising source of novel antimicrobial compounds and biocontrol agents.

• Journal of Microbiology and Biotechnology
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• 제7권2호
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• pp.114-120
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• 1997

Microorganisms producing xylanase were screened for the enzymatic production of xylo-oligo saccharides from xylan. One of the bacteria isolated from compost produced an endoxylanase extracellularly. The bacterium was identified as Bacillus sp. according to its taxonomic characteristics examined. Xylanase production reached upto 5 U/ml after 22 h of culture in LB medium at $30^{\circ}C$. The xylanase was purified by ammonium sulfate precipitation and gel filtration. The molecular weight of the xylanase was estimated to be 20,400 by SDS-PAGE. Optimal temperature and pH for the xylanase activity was $60^{\circ}C$ and 6.5, respectively. The enzyme was stable at temperatures upto $40^{\circ}C$ and pH values from 4 to 10. The xylanase was completely inhibited by the addition of 2 mM mercury ion. Apparent $K_m$ and $V_max$ values for oat spelt xylan were 9.2 mg/ml and 1954 U/mg protein, respectively. For birchwood xylan, the values were 6.3 mg/ml and 1009 U/mg protein. The predominant products of the xylan hydrolysis were xylobiose, xylotriose and xylotetraose, indicating that the enzyme is an endoxylanase. Upto $85{\%}$ of the initially added enzyme (2 U/ml) was bound to 50 mg/ml of the insoluble fraction of oat spelt xylan after incubation at $30^{\circ}C$ for 30 min.

• Asian-Australasian Journal of Animal Sciences
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• 제28권4호
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• pp.584-591
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• 2015

This study characterized the fecal bacterial community structure and inter-individual variation in 30-week-old Duroc pigs, which are known for their excellent meat quality. Pyrosequencing of the V1-V3 hypervariable regions of the 16S rRNA genes generated 108,254 valid reads and 508 operational taxonomic units at a 95% identity cut-off (genus level). Bacterial diversity and species richness as measured by the Shannon diversity index were significantly greater than those reported previously using denaturation gradient gel electrophoresis; thus, this study provides substantial information related to both known bacteria and the untapped portion of unclassified bacteria in the population. The bacterial composition of Duroc pig fecal samples was investigated at the phylum, class, family, and genus levels. Firmicutes and Bacteroidetes predominated at the phylum level, while Clostridia and Bacteroidia were most abundant at the class level. This study also detected prominent inter-individual variation starting at the family level. Among the core microbiome, which was observed at the genus level, Prevotella was consistently dominant, as well as a bacterial phylotype related to Oscillibacter valericigenes, a valerate producer. This study found high bacterial diversity and compositional variation among individuals of the same breed line, as well as high abundance of unclassified bacterial phylotypes that may have important functions in the growth performance of Duroc pigs.

• Journal of Species Research
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• 제4권2호
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• pp.127-136
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• 2015

As an outcome of the study on the bacterial species diversity in Korea, we report 24 unrecorded bacterial species of Korea belonging to the phylum Firmicutes. The unrecorded species excavated through this study were assigned to 12 different genera of 7 families, namely Bacillus, Halobacillus, Lysinibacillus and Thalassobacillus of Bacillaceae, Brevibacillus and Paenibacillus of Paenibacillaceae, Viridibacillus of Planococcaceae, Salinicoccus and Staphylococcus of Staphylococcaceae, Enterococcus of Enterococcaceae, Lactobacillus of Lactobacillaceae, and Lactococcus of Streptococcaceae, respectively. The bacterial isolates were obtained from various ecosystems in Korea. The isolates were identified based on 16S rRNA gene sequences, and those exhibiting at least 99% sequence similarity with known bacterial species but never reported in Korea were selected as unrecorded species. The selected isolates were subjected to further taxonomic characterization including the analysis of cell shape and fine structure using electron microscope, colony color and shapes, enzyme activities and carbon source utilization. The descriptive information on the 24 unrecorded species are provided.

• Journal of Species Research
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• 제7권2호
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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.

• 환경생물
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• 제38권3호
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• pp.433-449
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• 2020

Nine fish and one clam species were collected from freshwater environments in Korea, including four lakes, two streams, and the Nakdong River, to investigate the host-associated bacteria. Hundreds of bacterial strains were isolated from the samples using a cell sorter and a dilution plating method. After identification of the bacterial strains using 16S rRNA gene sequences, 42 strains with greater than 98.7% sequence similarity with validly published species were determined to be unrecorded bacterial species in Korea. These strains were phylogenetically diverse and assigned to four phyla, six classes, 17 orders, 27 families, and 32 genera. At the genus level, the unrecorded species were classified as Corynebacterium, Mycobacterium, Mycolicibacterium, Gordonia, Williamsia, Modestobacter, Brachybacterium, Sanquibacter, Arthrobacter, and Mycolicibacterium of the class Actinobacteria; Empedobacter, and Flavobacterium of the class Flavobacteriia; Fictibacillus, Psychrobacillus, Cohnella, Paenibacillus, Rummeliibacillus, Enterococcus, and Vagococcus of the class Bacilli; Aquamicrobium, Paracoccus, and Sphingomonas of the class Alphaproteobacteria; Achromobacter, Delftia, and Deefgea of the class Betaproteobacteria; and Aeromonas, Providencia, Yersinia, Marinomonas, Acinetobacter, and Pseudomonas of the class Gammaproteobacteria. The 42 unrecorded species were subjected to further taxonomic characterization using gram staining, cellular and colony morphological determination, biochemical analyses, and phylogenetic analyses. This paper provides detailed descriptions of the 42 previously unrecorded bacterial species.

• Journal of Species Research
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• 제9권4호
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• pp.362-374
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• 2020

A total of 35 bacterial strains were isolated from various sediment samples. From 16S rRNA gene sequence similarities higher than 98.7% and the formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to independent and predefined bacterial species. No previous official reports have described these 35 species in Korea. The unrecorded species were assigned to 6 phyla, 10 classes, 18 orders, 23 families, and 31 genera. At the genus level, the unrecorded species were affiliated with Terriglobus of the phylum Acidobacteria, as well as with Mycobacterium, Rhodococcus, Kineococcus, Phycicoccus, Agromyces, Cryobacterium, Microbacterium, and Arthrobacter; Catellatospora of the class Actinomycetia; Lacibacter of the class Chitinophagia; Algoriphagus and Flectobacillus of the class Cytophagia; Flavobacterium and Maribacter of the class Flavobacteriia; Bacillus, Cohnella, Fontibacillus, Paenibacillus, Lysynibacillus, and Paenisporosarcina of the class Bacilli; Bradyrhizobium, Gemmobacter, Loktanella, and Altererythrobacter of the class Alphaproteobacteria; Acidovorax of the class Betaproteobacteria; Aliiglaciecola, Cellvibrio, Arenimonas, and Lysobacter of class Gammaproteobacteria; and Roseimicrobium of the class Verrucomicrobia. The selected strains were subjected to further taxonomic characterization, including Gram reaction, cellular and colonial morphology, and biochemical properties. This paper provides detailed descriptions of the 35 previously unrecorded bacterial species.

• 미생물학회지
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• 제36권3호
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• pp.167-172
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• 2000

제주도의 여섯 지역과 인천 작약도 근해의 해수로부터 내염성 그람양성 세균 25균주를 분리하여 화학 분류학적 특징과 표현형적 특성을 조사하였다. 분리된 균주들은 화학 분류학적 특징에 의거하여 4개의 group으로 구분되었다. Group1은 40.~49.9 mol% 의 G+C함량과 MK-7의 menaquinome type, peptidoglycan의 주요 아미노산으로 meso-A2pm을 함유하며 Bacillus pumilus와 Bacillus licheniformis, Bacillu megaterium, bacillus subtilis로 동정되었으며, Group 2는 63.9~66.4 mol% 의 G+C 함량과 MK-8을 함유하는 Arthrobacter속 세균이었으며 , Group 3은 31.0~37.6 mol%의 G+G 함량과 MK-7을 함유하며 Staphylococcus haemolyticus, Staphylococcus saprophyticyus, Staphylococcus intermedius 로 , Group 4는 72.0 mol% 의 G+C 함량과 MK-8을 주요 quinone으로 함유하는 Micrococcus luteus로 동정되었다. 분리된 세균들 중 Bacillus 속 세균들은 68%로 우세한 분포를 나타내었다.

• 한국임상수의학회지
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• 제38권2호
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• pp.75-81
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• 2021

An aquariid nematode, Desportesius invaginatus, was found in the proventriculus of an Egretta garzetta and a Bubulcus ibis from Chuncheon in the Republic of Korea. The worms were identified by light and scanning electron microscopy based on important taxonomic characteristics (body length, esophagus length, cordons, spicules, caudal alae of males, position of the vulva) and then phylogenetically analyzed using the 18S rRNA encoding gene. The nematodes were characterized by a body length of 7.0-8.0 mm in males and 10.2-13.1 mm in females, and two pairs of cordons recurrent in the anterior direction, and cordons were anastomosed by a longitudinal cuticular ridge that externally delimits a longitudinal canal. The widest cuticular plates of cordons bears over 20 posterior spines. The length of the spicules in males was also significantly different. The right spicule measured 742-821 (794) ㎛ in length and 40-45 (42) ㎛ in width, and the left spicule measured 493-556 (541) ㎛ in length and 11-13 (12) ㎛ in width. The caudal alae of males are inflated and vesicular in appearance. The vulva was situated at 56-71 (58.3) ㎛ from the posterior extremity. Although the 18S rRNA sequences of worms were similar to the Synhimantus species, some genetic divergences were observed in comparison. In this study, the worms were recognized with genus Desportesius because genus Desportesius was considered a subgenus of Synhimantus. This is the first record of D. invaginatus in the Republic of Korea.

• 한국미생물·생명공학회지
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• 제47권3호
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• pp.401-411
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• 2019

All Idiomarina species are isolated from saline environments; microorganisms in such extreme habitats develop metabolic adaptations and can produce compounds such as proteases with an industrial potential. ARDRA and 16S rRNA gene sequencing are established methods for performing phylogenetic analysis and taxonomic identification. However, 16S-23S ITS is more variable than the 16S rRNA gene within a genus, and is therefore, used as a marker to achieve a more precise identification. In this study, ten protease producing Idiomarina strains isolated from the Peruvian salterns were characterized using biochemical and molecular methods to determine their bacterial diversity and industrial potential. In addition, comparison between the length and nucleotide sequences of a 16S-23S ITS region allowed us to assess the inter and intraspecies variability. Based on the 16S rRNA gene, two species of Idiomarina were identified (I. zobellii and I. fontislapidosi). However, biochemical tests revealed that there were differences between the strains of the same species. Moreover, it was found that the ITS contains two tRNA genes, $tRNA^{Ile(GAT)}$ and $tRNA^{Ala(TGC)}$, which are separated by an ISR of a variable size between strains of I. zobellii. In one strain of I. zobellii (PM21), we found nonconserved nucleotides that were previously not reported in the $tRNA^{Ala}$ gene sequences of Idiomarina spp. Thus, based on the biochemical and molecular characteristics, we can conclude that protease producing Idiomarina strains have industrial potential; only two I. zobellii strains (PM48 and PM72) exhibited the same properties. The differences between the other strains could be explained by the presence of subspecies.