• The Plant Pathology Journal
• /
• v.39 no.4
• /
• pp.397-408
• /
• 2023

Fire blight disease, caused by Erwinia amylovora, is a devastating affliction in apple cultivation worldwide. Chemical pesticides have exhibited limited effectiveness in controlling the disease, and biological control options for treating fruit trees are limited. Therefore, a relatively large-scale survey is necessary to develop microbial agents for apple trees. Here we collected healthy apple trees from across the country to identify common and core bacterial taxa. We analyzed the endophytic bacterial communities in leaves and twigs and discovered that the twig bacterial communities were more conserved than those in the leaves, regardless of the origin of the sample. This finding indicates that specific endophytic taxa are consistently present in healthy apple trees and may be involved in vital functions such as disease prevention and growth. Furthermore, we compared the community metabolite pathway expression rates of these endophyte communities with those of E. amylovora infected apple trees and discovered that the endophyte communities in healthy apple trees not only had similar community structures but also similar metabolite pathway expression rates. Additionally, Pseudomonas and Methylobacterium-Methylorobrum were the dominant taxa in all healthy apple trees. Our findings provide valuable insights into the potential roles of endophytes in healthy apple trees and inform the development of strategies for enhancing apple growth and resilience. Moreover, the similarity in cluster structure and pathway analysis between healthy orchards was mutually reinforcing, demonstrating the power of microbiome analysis as a tool for identifying factors that contribute to plant health.

• The Korean Journal of Community Living Science
• /
• v.18 no.2
• /
• pp.241-246
• /
• 2007

This study was conducted to select and screen for an antifungal bacterial strain showing pathogen inhibitory activity against Diaporthe actinidiae, which causes stem-end rot in kiwi fruit. Four bacterial strains were isolated which strongly inhibit Diaporthe actinidiae from among two hundred and fifty bacterial strains screened from the soil where kiwi fruit were grown. By co-culturing bacterial strain #72 and the pathogen causing the stem-end rot of kiwi fruit, bacterial strain #72 showed 81.0% antifungal activity against Diaporthe actinidiae. Bacterial strain #72 was identified to be from the genus Bacillus sp. based on morphological and biochemical characterization. The bacterialization of culture broth for Bacillus sp. #72 which was sterilized at $121^{\circ}C$ for 15 minutes and than purified by $0.45{\mu}m$ membrane filter showed almost all of the antagonistic activity against Diaporthe actinidiae. We have also confirmed that in vitro treatment of Bacillus sp. #72 cultured in SD+B+P(sugar 5%, soy sauce 3%, beef extract 0.2%, peptone 0.2%) medium efficiently inhibited the growth of Diaporthe actinidiae responsible for stem-end rot in kiwi fruit.

• Korean Journal of Microbiology
• /
• v.25 no.4
• /
• pp.318-327
• /
• 1987

Taxonomic composition and diversity were wxamined by statistical analysis for bacterial communities in surface waters of the Sudong Stream, a tributary of North Han River. For total 282 isolates, Flavobacterium, Aeromonas and Enterobacteriaceae was identified by the deterministic schemes as a major group above 50% of total isolates in all sampling sites. Morphological, biochemical and physiological characteristics were numerically analyzed for bacterial isolates from each site and clustered into 15-28 groups. Not all statistically clustered groups were identical to the groups derived from deterministic identification. Especially, consistent relationship was not found in dendrograms for the groups with each a single strain which gas peculiar sugar-degrading activity. At a level of 80% similarity, bacterial diversity (H) was ranged as 2.37-3.14, and it was suggested that the research area was oligotrophic-mesotrophic status. Regional distribution of bacterial community was most heterogeneous at the site where large input of allochthonous materials or bacteria were occurred. And that was the significant factor for the compositions of bacterial communities in the Sudong stream.

• Korean Journal of Microbiology
• /
• v.38 no.3
• /
• pp.192-197
• /
• 2002

Fluorescent in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes was used to compare the community structures of free-living and aggregated bacteria at thawing period in Lake Baikal. Targeted groups were Eubacteria, $\alpha$-, $\beta$-, $\gamma$- proteobacteria groups, Cytophaga-Flavobacterium group and Planctomycetales. Total bacterial numbers of free-living bacteria were ranged from $0.2{\times}10^6\cells{\cdot}ml^-1$ to $3.2{\times}10^6\cells{\cdot}ml^-1$, which were decreasing with depth, while the aggregated bacterial numbers were dramatically increasing from $0.4{\times}10^4 to 3.3{\times}10^4 \cells{\cdot}ml^-1$ with depth. The ratios of EUB probe binding cells to DAPI counts were ranged from 52.3 to 74.1% in free-living bacteria, and from 39.6 to 66.7% in the aggregated bacteria, respectively. Community structures of the aggregated bacteria were very different from each free-living bacteria at every depth. At 25 m depth, where the chlorophyll a concentration was highest, both structures were quite different from those of surface layers, rendering the fact that the community structures might be affected by phytoplankton. The vertical profile of community structure of aggregated bacteria is particular. The proportion of $\beta$-proteobacteria group was increasing with depth and it was 51.8% at 100 m, but the dominant group was $\gamma$-pro-teobacteria group at 250 m. Taken together, the biodiversity and succession of aggregated bacteria are quite different from free-living bacteria.

• Clinical and Experimental Pediatrics
• /
• v.52 no.3
• /
• pp.283-288
• /
• 2009

Pneumonia remains the leading cause of mortality in children. Diagnosis depends on a combination of factors, including clinical assessment, radiological and laboratory findings. Although Streptococcus pneumoniae remains the most important cause of childhood bacterial pneumonia, the great majority of cases of community-acquired pneumonia (CAP) are of viral etiology. A new, rapid, and inexpensive test that differentiates viral from bacterial pneumonia is needed to decide empiric antibiotic treatment. Antibiotics effective against the expected bacterial pathogens should be instituted where necessary. The role of emerging pathogens and the effect of pneumococcal resistance and heptavalent conjugate pneumococcal vaccines are to be considered in practice. There are reports supporting the valid and highly efficacious use of penicillin as a first-line drug for treating CAP. This review raises the issue of the overuse of unnecessary antibiotics in viral CAPs and the use of second or third-line antibiotics for non-complicated pneumonias in most clinical settings.

• Korean Journal of Microbiology
• /
• v.45 no.2
• /
• pp.119-125
• /
• 2009

To understand the ecological function of heterotrophic bacterial community in water column of large freshwater lakes in the permafrost zone, we investigated the structure and function of bacterial community in Lake Khuvsgul, Mongolia. Species composition of overall bacterial community was analyzed by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments, and bacteria that can be cultured at 10oC were isolated and characterized. Based on the depth profile of environmental parameters, thermocline and chemocline were recognized at the 5~10 m zone of the water column. The stratified DGGE profile indicated that the discontinuity of water properties might influence the structure of bacterial community: band profiles in the 0~5 m zone were diverse with large change by depth, but the profile was relatively stable at the $\geq$10 m zone, with predominance of the band identified as Acidovorax facilis. Bacterial cultures were screened for protease, cellulase, amylase and lipase activity, and 23 isolates were selected for high activity of the hydrolytic enzymes. The isolates were identified based on their 16S rRNA gene sequences. In the surface water (zero meter depth), Acidovorax defluvii and Sphingobacterium faecium with high cellulase activity were present. Flavobacterium succinicans, Mycoplana bullata and A. facilis were stably predominant isolates at 2 m, 5 m, and $\geq$10 m depths, respectively. F. succinicans isolates showed high protease activity while M. bullata isolates showed moderate levels of protease and celluase activity. A. facilis isolates showed either cellulase or lipase activity, exclusively to each other. According to the profile of growth rates of the isolates in the temperature range of $0\sim42^{\circ}C$, the surface-zone (0~5 m) isolates were facultative psychrophiles while isolates from $\geq$10 m depth were typical mesophiles. This stratification is believed to be due to stratified availability of organic materials to the bacterial decomposers. In the water column below the chemoline, the environment is extremely oligotrophic so that the trait of rapid growth in low temperature might not be demanded by deep-lake decomposers. The stratified distribution of community composition and decomposer activity in Lake Khuvsgul implies that ecological functions of bacterial community in lakes of cold region are sharply divided by water column stratification.

• Korean Journal of Microbiology
• /
• v.47 no.3
• /
• pp.275-280
• /
• 2011

In order to evaluate the diversity and change of bacterial population during the manufacturing process of traditional soybean paste (doenjang), bacterial communities were analyzed using 16S rRNA gene-based pyrosequencing. In rice straw, the most important inoculum source for fermentation, the bacterial sequences with a relative abundance greater than 1% were assigned to four phyla, Proteobacteria (71%), Actinobacteria (20.6%), Bacteroidetes (4.2%), and Firmicutes (1.3%). Unlike bacterial community composition of rice straw, a different pattern of bacterial population in meju was observed with predominantly high abundance (99.1%) of Firmicutes. Phylum composition in young doenjang was almost same as that of meju. Major genera in young doenjang were Bacillus (81.3%), Clostridium (6.9%) and Enterococcus (6.3%) and the predominant species among bacterial population was B. amyloliquefaciens (63.6%). Abundance of the phylum Firmicutes in mature doenjang was 99.98%, which was even higher value than those in meju and young doenjang. Predominant species in mature doenjang were B. amyloliquefaciens (67.3%), B. atrophaeus (12.7%), B. methylotrophicus (6.5%), B. mojavensis (3.2%), and B. subtilis. (2.5%), which were also identified as major species of the microbial flora in meju. These results suggested that rice straw was a primary source for supplement of Bacillus species in manufacturing the traditional doenjang and that some species of Bacillus strains were mainly involved in the fermentation process of traditional doenjang.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2017.06a
• /
• pp.161-161
• /
• 2017

Seed endophytes are very remarkable groups of bacteria for their unique abilities of being vertically transmitted and conserved. As plants attain hybrid vigor and heterosis in the process of crossbreeding, this might also lead to the changes in the community structure and diversity of plant endophytes in the hybrid plants ultimately affecting the endophytes of the seeds. It would be interesting to characterize how seed endophyte composition change over time. The objective of this study is to gain insights into the influence of natural crossbreeding and parental lineage in the seed bacterial endophytic communities of two pure inbred lines exploring contributions of the two most important sources of plant endophytes - colonization from external sources and vertical transmission via seeds. Total genomic DNA was isolated from rice seeds and bacterial DNA was selectively amplified by PCR. The diversity of endophytic bacteria was studied through Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis. Diversity between the original parents and the pure inbred line may show significant differences in terms of richness, evenness and diversity indices. Heat maps reveal astonishing contributions of both or either parents (IR29 ${\times}$ Pokkali and AT401 ${\times}$ IR31868) in the shaping of the bacterial seed endophytes of the hybrid, FL478 and IC32, respectively. Most of the T-RFs of the subsequent pure inbred line could be traced to any or both of the parents. Comparison of common and genotype-specific T-RFs of parents and their offspring reveals that majority of the T-RFs are shared suggesting higher transmission of bacterial communities common to both parents. The parents influence the bacterial community of their offspring. Unique T-RFs of the offspring also suggest external sources of colonization particularly as the seeds are cultivated in different ecogeographical locations. This study showed that host parental lines contributed greatly in the shaping of bacterial seed endophytes of their offspring. It also revealed transmission and potential conservation of core seed bacterial endophytes that generally become the dominant microbiota in the succeeding generations of plant hosts.

• The Korean Journal of Ecology
• /
• v.22 no.6
• /
• pp.337-342
• /
• 1999

Rotifer grazing rates in both species and community levels on bacteria and phytoplankton were determined by using representative models (fluorescent beads: 0.75$\mu m$ for bacteria and 10 $\mu m$ for phytoplankton) at biweekly intervals. One-year study at the lower part of the Nakdong River (Mulgum) indicated that the seasonal pattern of rotifer biomass was similar to that of total zooplankton biomass. Total mean biomass of rotifers was significantly higher than that of other groups (rotifers, 148$\pm $327 $\mu g$C/l; cladoceran. 25$\pm 69$$\mu g$C/l; copepodids. 58$\pm 159$$\mu g$C/l). For laboratory grazing experiments. mean specific filtering rate (SFR: $ml\cdot \; l^{-1}\cdot \; day^{-1}$) for rotifers varied from 0.001 to 0.726, and > 90% individuals of rotifer species took up fluorescent microspheres. The high SFRs were achieved by Brachionus angularis, B. calyciflorus, and Filinia longiseta. Community filtering rates (CFRs, $ml\cdot \; l^{-1}\cdot \; day^{-1}$) varied in the range from 2 ~ 1,670. Rotifer filtering rates on phytoplankton were much higher than bacterial filtering rates, especially in the late growing season (May. June, and November). Rotifers appear to be important in transferring both bacterial and phytoplankton carbon to higher trophic levels at the lower Nakdong River.

• The Plant Pathology Journal
• /
• v.34 no.2
• /
• pp.143-149
• /
• 2018

Flowers of kiwifruit are morphologically hermaphroditic and survivable binucleate pollen is produced by the male flowers. In this study, we investigated microbial diversity in kiwifruit pollens by analyzing amplicon sequences of 16S rRNA. Four pollen samples were collected: 'NZ' was imported from New Zealand, 'CN' from China in year of 2014, respectively. 'KR13' and 'KR14' were collected in 2013' and 2014' in South Korea. Most of the identified bacterial phyla in the four different pollens were Proteobacteria, Actinobacteria and Firmicutes. However, the imported and the domestic pollen samples showed different aspects of microbial community structures. The domestic pollens had more diverse in diversity than the imported samples. Among top 20 OTUs, Pseudomonas spp. was the most dominant specie. Interestingly, a bacterial pathogen of kiwifruit canker, Pseudomonas syringae pv. actinidiae was detected in 'NZ' by the specific PCR. This study provides insights microbial distribution and community structure information in kiwifruit pollen.