• Journal of Microbiology and Biotechnology
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• v.13 no.1
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• pp.15-21
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• 2003

Two microbial communities of activated sludge in the same municipal wastewater, but treated with different systems, were studied and compared using molecular microbiological approaches. The bacterial 16S rDNA sequences from 124 clones were analyzed, however, the majority of them were not closely related to any known species, and found to belong to 8 different phylogenetic groups and 3 different unidentified groups. The relative frequencies of each group were similar between the two microbial communities. Fingerprinting using terminal restriction fragment length polymorphism (T-RFLP) showed that the putative Nitrospira-related populations were more diverse and quantitatively higher in the KNR process system than in the other system using a conventional activated sludge process. The relationship between the bacterial community composition and the higher removal efficiency of nitrogen and phosphorus in the KNR process is discussed.

• Journal of Microbiology and Biotechnology
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• v.12 no.3
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• pp.382-388
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• 2002

In order to assess the effects of organic fertilizer on soil microbial community structure and diversity in the greenhouse fields, fatty acid methyl ester (FAME) was analyzed by the MIDI (Microbial ID, Inc., Newark, DE, U.S.A.) system and enumerations were performed. In relation to bacterial division of each sample, low GC Gram-positive bacteria were predominant among bacteria cultured on aerobic bacteria media. On the other hand, alpha subdivision was predominant on proteobacteria of control and OM (organic matter) 1 treated plot, and Flavobacterium spp. existed in OM2 plot on crystal violet media of all samples. Shannon-weaver Index (H) of OM1 plot varied most by 1.9 and 5.0 among bacteria cultured on aerobic bacteria media and crystal violet media, respectively. Our results revealed that addition of the organic wastes to soil led to a highly diverse microbial community, but the excessive amounts of organic and mineral fertilizer applied in the greenhouse fields produced excess nutrients in soil and led to simplification on bacterial populations.

• The Plant Pathology Journal
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• v.38 no.6
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• pp.692-699
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• 2022

Bacterial wilt caused by Ralstonia solanacearum is considered one of the most harmful diseases of pepper plants. Recently, research on plant disease control through the rhizosphere microbiome has been actively conducted. In this study, the relationship with disease occurrence between the neighboring plant confirmed by analyzing the physicochemical properties of the rhizosphere soil and changes in the microbial community. The results confirmed that the microbial community changes significantly depending on the organic matters, P₂O₅, and clay in the soil. Despite significant differences in microbial communities according to soil composition, Actinobacteriota at the phylum level was higher in healthy plant rhizosphere (mean of relative abundance, D: 8.05 ± 1.13; H: 10.06 ± 1.59). These results suggest that Actinobacteriota may be associated with bacterial wilt disease. In this study, we present basic information for constructing of healthy soil in the future by presenting the major microbial groups that can suppress bacterial wilt.

• Fisheries and Aquatic Sciences
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• v.26 no.10
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• pp.593-604
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• 2023

Post-harvest handling and hygienic level of aquatic products significantly affect the quality and level of safety. Cold chain control is one of the determining factors for the quality of fish and the bacterial community that grows on the fish. Identification of spoilage bacteria and pathogens in aquatic products must be made because it will determine the physical and chemical quality. A molecular identification method with high sensitivity is the solution. This study aims to identify the quality of fish and bacterial communities that grow. The research procedures included sample collection, pH measurement, drip loss measurement, transportation and cold storage treatment, DNA extraction, DNA sequencing, sequence analysis, and bioinformatics analysis. The conclusion obtained from this study is that the simulation of the cold chain system applied to eastern little tuna does not significantly affect changes in the water activity value, pH, and drip loss. The insignificant change indicates that the eastern little tuna samples are still in good quality. The bioinformatics analysis showed the highest diversity and abundance of the bacterial community came from the Gammaproteobacterial class.

• Journal of Microbiology
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• v.38 no.1
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• pp.11-17
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• 2000

A new method was developed for the rapid analysis of diverse bacterial species in the natural environment. Our method is based on PCR-single-strands-conformation polymorphism (PCR-SSCP) and selective isolation technique of single-stranded DNA. Variable V3 fragments of 16S rDNA were amplified by PCR with bacterial 16S rDNA primers, where one of the primers was biotinylated at the 5'-end. The biotinylated strands of the PCR products were selectively isolated by using streptavidin paramagnetic particles and a magnetic stand, to prevent SSCP analysis producing heteroduplexes from heterogeneous DNA samples. The selected strands were separated by electrophoresis on a polyacrylamide gel, and detected by silver staining. Analysis of PCR products from 8 bacterial strains demonstrated their characteristic DNA band patterns. In addition, changes in the structure of the bacterial community and species diversity in the microcosm treated with phenol could be monitored. After 3 weeks of incubation, phenol and its intermediate, 2-hydroxy-muconic-semialdehyde, were degraded by indigenous bacteria. These dominating bacterial populations were identified as strong bands on an SSCP gel. Therefore, this study provides useful tools for microbial community analysis of natural habitats.

• The Plant Pathology Journal
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• v.35 no.4
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• pp.362-371
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• 2019

Plant phenotype is affected by a community of associated microorganisms which requires dissection of the functional fraction. In this study, we aimed to culture the functionally active fraction of an upland soil microbiome, which can suppress tomato bacterial wilt. The microbiome fraction (MF) from the rhizosphere of Hawaii 7996 treated with an upland soil or forest soil MF was successively cultured in a designed modified M9 (MM9) medium partially mimicking the nutrient composition of tomato root exudates. Bacterial cells were harvested to amplify V3 and V4 regions of 16S rRNA gene for QIIME based sequence analysis and were also treated to Hawaii 7996 prior to Ralstonia solanacearum inoculation. The disease progress indicated that the upland MM9 $1^{st}$ transfer suppressed the bacterial wilt. Community analysis revealed that species richness was declined by successive cultivation of the MF. The upland MM9 $1^{st}$ transfer harbored population of phylum Proteobacteria (98.12%), Bacteriodetes (0.69%), Firmicutes (0.51%), Actinobacteria (0.08%), unidentified (0.54%), Cyanobacteria (0.01%), FBP (0.001%), OD1 (0.001%), Acidobacteria (0.005%). The family Enterobacteriaceae of Proteobacteria was the dominant member (86.76%) of the total population of which genus Enterobacter composed 86.76% making it a potential candidate to suppress bacterial wilt. The results suggest that this mixed culture approach is feasible to harvest microorganisms which may function as biocontrol agents.

• Journal of Microbiology and Biotechnology
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• v.24 no.7
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• pp.888-897
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• 2014

A bacterial community analysis of the gut of Tenebrio molitor larvae was performed using pyrosequencing of the 16S rRNA gene. A predominance of genus Spiroplasma species in phylum Tenericutes was observed in the gut samples, but there was variation found in the community composition between T. molitor individuals. The gut bacteria community structure was not significantly affected by the presence of antibiotics or by the exposure of T. molitor larvae to a highly diverse soil bacteria community. A negative relationship was identified between bacterial diversity and ampicillin concentration; however, no negative relationship was identified with the addition of kanamycin. Ampicillin treatment resulted in a reduction in the bacterial community size, estimated using the 16S rRNA gene copy number. A detailed phylogenetic analysis indicated that the Spiroplasma-associated sequences originating from the T. molitor larvae were distinct from previously identified Spiroplasma type species, implying the presence of novel Spiroplasma species. Some Spiroplasma species are known to be insect pathogens; however, the T. molitor larvae did not experience any harmful effects arising from the presence of Spiroplasma species, indicating that Spiroplasma in the gut of T. molitor larvae do not act as a pathogen to the host. A comparison with the bacterial communities found in other insects (Apis and Solenopsis) showed that the Spiroplasma species found in this study were specific to T. molitor.

• Korean Journal of Soil Science and Fertilizer
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• v.32 no.3
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• pp.319-325
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• 1999

A culture-dependent survey of bacterial community in the soil-root system of red pepper and tomato was conducted by dilution plate count method. The bacterial community within soil was not different from that of rhizoplane. However, the populations of fluorescent, pseudomonads were higher in rhizoplanes than in soils and higher in healthy rhizoplanes than in Phytophthora disease-infested rhizoplanes. The bacterial community of the pepper cropped soil and rhizoplanes was very similar to that of the tomato-cropped soil and rhizoplanes. Among 285 identified bacterial colonies, most colonies were belong to two groups by fatty acid analyses: 52% of the 285 colonies were belong to low G + C gram positive bacteria group. Bacillus spp. and 33% were belong to high G + C gram positive bacteria group. In order to use beneficial microorganisms to agro-ecosystem, these data of field trials should be intensively accumulated.

• Korean Journal of Microbiology
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• v.40 no.3
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• pp.244-247
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• 2004

To investigate the effects of elevated $CO_2$ on the denitrifying bacterial community structure in a wetland soil, dynamics of bacterial community structure was explored in an artificial wetland ecosystem with one of three plant species (T. latifolia, S. lacustris, and 1. effusus) under two levels of $CO_2$(370 ppm or 740 ppm) after 110day incubation. For the analysis of bacterial community structure, functional genes such as nitrite reductase genes (nirS) were PCR-amplified followed by cloning of PCR products and screening by restriction fragment length polymorphism (RFLP). nirS gene fragments were amplified in all analyzed soil samples. Species richness estimated by the number of distinct phylotypes were 83 and 95 in the ambient $CO_2$ treatment and the elevated treatment, respectively. Two phylotypes (type 1 and type 2) were dominant in both of the treatments. Elevated $CO_2$ treatment increased species richness of denitrifying as well as changed a large proportion of denitrifier phylotypes compared to those of the ambient treatment. Overall, the data in this study suggested that the denitrifying communities in the wetland soil are diverse and that the richness of denitrifying bacterial community might be affected by elevated $CO_2$ treatment.

• Korean Journal of Microbiology
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• v.40 no.4
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• pp.307-312
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• 2004

Diversity of the bacterial communities and the relation between community structure and components of waste­water were analyzed by 16S rRNA-based molecular techniques. Clone libraries of the 16S rDNAs from the sludges were constructed by PCR and cloning. The 1,151 clones from a sludge sample of sewage treatment plant were clustered into 699 RFLP phylotypes and the 1,228 clones from the wastewater disposal plant of chemical industry were clustered into 300 RFLP phylotypes. Shannon-Weiner diversity indices of two sampling sites were 8.7 and 6.1, indicating that the bacterial community structure of sewage treatment plant was more diverse than that of wastewater disposal plant of chemical industry. Forty clones belonging to predominant RFLP types were selected and sequenced. Seventy percent (28 clones) of the sequenced clones were related to the uncultured bacteria in public databases. The ${\beta}-Proteobacteria$ dominated in the bacterial communities of investigated two sludge samples. 16S rDNA sequences of the sewage treatment plant were similar to those of other activated sludges, while the bacterial community in wastewater disposal plant of chemical industry rep­resented the strains identified from high-temperature, anaerobic, hydrocarbon-rich, and sulfur-rich environ­ments. This result suggested that bacterial communities depended upon the components of wastewater.