• Journal of Microbiology and Biotechnology
• /
• v.15 no.2
• /
• pp.376-383
• /
• 2005

Alcaligenes sp. JMP228 carrying 2,4­dichlorophenoxyacetic acid (2,4-D) degradative plasmid pJP4 was inoculated into natural soil, and transfer of the plasmid pJP4 to indigenous soil bacteria was investigated with and without 2,4-D amendment. Plasmid pJP4 transfer was enhanced in the soils treated with 2,4-D, compared to the soils not amended with 2,4-D. Several different transconjugants were isolated from the soils treated with 2,4-D, while no indigenous transconjugants were obtained from the unamended soils. Inoculation of the soils with both the donor Alcaligenes sp. JMP228/pJP4 and a recipient Burkholderia cepacia DBO 1 produced less diverse transconjugants than the soils inoculated with the donor alone. Repetitive extragenic palindromic-polymerase chain reaction (REP-PCR) analysis of the transconjugants exhibited seven distinct genomic DNA fingerprints. Analysis of 16S rDNA sequences indicated that the transconjugants were related to members of the genera Burkholderia and Pandoraea. Denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA genes revealed that inoculation of the donor caused clear changes in the bacterial community structure of the 2,4-D­amended soils. The new 16S rRNA gene bands in the DGGE profile corresponded with the 16S rRNA genes of 2,4-D­degrading transconjugants isolated from the soil. The results indicate that introduction of the 2,4-D degradative plasmid as Alcaligenes sp. JMP228/pJP4 has a substantial impact on the bacterial community structure in the 2,4-D-amended soil.

• Journal of Microbiology and Biotechnology
• /
• v.20 no.5
• /
• pp.862-870
• /
• 2010

Cyperus rotundus L. is a perennial herb that was found to be dominating an area in northeast Brazil previously contaminated with petroleum. In order to increase our knowledge of microorganism-plant interactions in phytoremediation, the bacterial community present in the rhizosphere and roots of C. rotundus was evaluated by culture-dependent and molecular approaches. PCR-DGGE analysis based on the 16S rRNA gene showed that the bacterial community in bulk soil, rhizosphere, and root samples had a high degree of similarity. A complex population of alkane-utilizing bacteria and a variable nitrogen-fixing population were observed via PCR-DGGE analysis of alkB and nifH genes, respectively. In addition, two clone libraries were generated from alkB fragments obtained by PCR of bulk and rhizosphere soil DNA samples. Statistical analyses of these libraries showed that the compositions of their respective populations were different in terms of alkB gene sequences. Using culturedependent techniques, 209 bacterial strains were isolated from the rhizosphere and rhizoplane/roots of C. rotundus. Dot-blot analysis showed that 17 strains contained both alkB and nifH gene sequences. Partial 16S rRNA gene sequencing revealed that these strains are affiliated with the genera Bosea, Cupriavidus, Enterobacter, Gordonia, Mycoplana, Pandoraea, Pseudomonas, Rhizobium, and Rhodococcus. These isolates can be considered to have great potential for the phytoremediation of soil with C. rotundus in this tropical soil area.

• Journal of Microbiology and Biotechnology
• /
• v.23 no.1
• /
• pp.76-84
• /
• 2013

A polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) technique followed by sequencing of the 16S rDNA fragments eluted from the bands of interest on denaturing gradient gels was used to monitor changes in the bacterial microflora of two commercial kimchi, salted cabbage, and ingredient mix samples during 30 days of fermentation at $4^{\circ}C$ and $10^{\circ}C$. Leuconostoc (Lc.) was the dominant lactic acid bacteria (LAB) over Lactobacillus (Lb.) species at $4^{\circ}C$. Weissella confusa was detected in the ingredient mix and also in kimchi samples throughout fermentation in both samples at $4^{\circ}C$ and $10^{\circ}C$. Lc. gelidum was detected as the dominant LAB at $4^{\circ}C$ in both samples. The temperature affected the LAB profile of kimchi by varing the pH, which was primarily caused by the temperature-dependent competition among different LAB species in kimchi. At $4^{\circ}C$, the sample variations in pH and titratable acidity were more conspicuous owing to the delayed growth of LAB. Temperature affected only initial decreases in pH and initial increases in viable cell counts, but affected both the initial increases and final values of titratable acidity. The initial microflora in the kimchi sample was probably determined by the microflora of the ingredient mix, not by that of the salted cabbage. The microbial distributions in the samples used in this study resembled across the different kimchi samples and the different fermentation temperatures as the numbers of LAB increased and titratable acidity decreased.

• Korean Journal of Microbiology
• /
• v.46 no.1
• /
• pp.33-37
• /
• 2010

Rhizobacterial strain isolated from barren soil, Bacillus subtilis RFO41 exhibits a high level of phosphate solubilizing activity and produces some phytohormones. Its promoting effect on the growth of Xanthium italicum Moore, a wild plant growing at lakeside barren land and thus a good candidate plant for revegetation of barren lakeside was evaluated in the in situ test for 19 weeks at Lake Paro, Kangwon-do. Strain RFO41 could enhance the dry weight of X. italicum by 67.7%. It also increased the shoot length of X. italicum plant by 21.1% compared to that of uninoculated control. Both growth enhancements had statistical significance. However, the inoculation did not show any effect on the root growth, which might be due to the breakage of tiny root. Denaturing gradient gel electrophoresis analysis showed that the inoculated bacteria were maintained in the soils, and the indigenous bacterial community did not exhibit any significant change. This plant growth promoting capability may be utilized as an environment-friendly and low cost revegetation method, especially for the sensitive areas such as barren lakeside lands.

• Journal of Microbiology and Biotechnology
• /
• v.15 no.5
• /
• pp.1087-1093
• /
• 2005

The population diversity and seasonal changes of bacterial communities in rice soils were monitored using both culture-dependent approaches and molecular methods. The rice field plot consisted of twelve subplots planted with two genetically-modified (GM) rice and two non-GM rice plants in three replicates. The DGGE analysis revealed that the bacterial community structures of the twelve subplot soils were quite similar to each other in a given month, indicating that there were no significant differences in the structure of the soil microbial populations between GM rice and non-GM rice during the experiment. However, the DGGE profiles of June soil after a sudden flooding were quite different from those of the other months. The June profiles exhibited a few intense DNA bands, compared with the others, indicating that flooding of rice field stimulated selective growth of some indigenous microorganisms. Phylogenetic analysis of l6S rDNA sequences from cultivated isolates showed that, while the isolates obtained from April soil before flooding were relatively evenly distributed among diverse genera such as Arthrobacter, Streptomyces, Terrabacter, and Bacillus/Paenibacillus, those from June soil after flooding mostly belonged to the Arthrobacter species. Phylogenetic analysis of 16S rDNA sequences obtained from the soil by cloning showed that April, August, and October had more diverse microorganisms than June. The results of this study indicated that flooding of rice fields gave a significant impact on the indigenous microbial community structure; however, the initial structure was gradually recovered over time after a sudden flooding.

• Journal of Microbiology and Biotechnology
• /
• v.18 no.2
• /
• pp.207-218
• /
• 2008

The impacts of planted transgenic rice varieties on bacterial communities in paddy soils were monitored using both cultivation and molecular methods. The rice field plot consisted of eighteen subplots planted with two genetically modified (GM) rice and four non-GM rice plants in three replicates. Analysis with denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA genes revealed that the bacterial community structures were quite similar to each other in a given month, suggesting that there were no significant differences in bacterial communities between GM and non-GM rice soils. The bacterial community structures appeared to be generally stable with the seasons, as shown by a slight variation of microbial population levels and DGGE banding patterns over the year. Comparison analysis of 16S rDNA clone libraries constructed from soil bacterial DNA showed that there were no significant differences between GM and non-GM soil libraries but revealed seasonal differences of phyla distribution between August and December. The composition profile of phospholipid fatty acids (PLFA) between GM and non-GM soils also was not significantly different to each other. When soil DNAs were analyzed with PCR by using primers for the bar gene, which was introduced into GM rice, positive DNA bands were found in October and December soils. However, no bar gene sequence was detected in PCR analysis with DNAs extracted from both cultured and uncultured soil bacterial fractions. The result of this study suggested that, in spite of seasonal variations of bacterial communities and persistence of the bar gene, the bacterial communities of the experimental rice field were not significantly affected by cultivation of GM rice varieties.

• Journal of Microbiology and Biotechnology
• /
• v.17 no.2
• /
• pp.253-261
• /
• 2007

Molecular and cultivation techniques were used to characterize the bacterial communities of biobead reactor biofilms in a sewage treatment plant to which an Aerated Up-Flow Biobead process was applied. With this biobead process, the monthly average values of various chemical parameters in the effluent were generally kept under the regulation limits of the effluent quality of the sewage treatment plant during the operation period. Most probable number (MPN) analysis revealed that the population of denitrifying bacteria was abundant in the biobead #1 reactor, denitrifying and nitrifying bacteria coexisted in the biobead #2 reactor, and nitrifying bacteria prevailed over denitrifying bacteria in the biobead #3 reactor. The results of the MPN test suggested that the biobead #2 reactor was a transition zone leading to acclimated nitrifying biofilms in the biobead #3 reactor. Phylogenetic analysis of 16S rDNA sequences cloned from biofilms showed that the biobead #1 reactor, which received a high organic loading rate, had much diverse microorganisms, whereas the biobead #2 and #3 reactors were dominated by the members of Proteobacteria. DGGE analysis with the ammonia monooxygenase (amoA) gene supported the observation from the MPN test that the biofilms of September were fully developed and specialized for nitrification in the biobead reactor #3. All of the DNA sequences of the amoA DGGE bands were very similar to the sequence of the amoA gene of Nitrosomonas species, the presence of which is typical in the biological aerated filters. The results of this study showed that organic and inorganic nutrients were efficiently removed by both denitrifying microbial populations in the anaerobic tank and heterotrophic and nitrifying bacterial biofilms well-formed in the three functional biobead reactors in the Aerated Up-Flow Biobead process.

• Journal of the Korea Organic Resources Recycling Association
• /
• v.24 no.4
• /
• pp.77-83
• /
• 2016

The objectives of this study was to investigate the difference between organic-farming and conventional-farming soils relatives to soil chemical properties and microbial flora. Fifteen soil sampling sites were chosen from the certified organic upland farm, considered with its location, crop and application of organic compost types. Soil chemical properties were analyzed by standard methods established by National Institute of Agricultural Sciences, Rural Development Administration. For the soil chemical properties, the values of pH were ranged from 4.5 to 7.3. The values of electrical conductivity (EC) in the sampling sites were below 2 dS/m of convention cultivation soil. For analyzing the microbial flora, the bacillus(16S rDNA) and cladothricosis(18S rDNA) were analyzed by using PCR-DGGE (Denaturing Gradient Gel Electrophoresis) in the soil of 15 sampling sites. Cluster analysis of biodiversity index was performed by using pattern of DGGE. DGGE patterns and clustering analysis of bacterial DNA from soil extracts revealed that the bacterial community was differentiated between less than 5 years and more than 5 years depending on the cultivation history. But there was no consistent tendency between cultivation history and regional trend in the case of molds. Therefore, it would be very effective to analyze bacterial clusters of organically cultivated soils in long - term cultivated soil for more than 5 years.

• Microbiology and Biotechnology Letters
• /
• v.45 no.1
• /
• pp.71-80
• /
• 2017

Tea is the most popular beverage in the world. The three main types are green, black, and post-fermented. Post-fermented teas are produced by the microbial fermentation of sun-dried green tea leaves (Camellia sinensis). In this study, the composition of the bacterial communities involved in the production of traditional oriental post-fermented teas (Korean algacha, dancha, and Chinese pu-erh) were investigated using 16S rRNA gene analysis. The dominant microorganisms present in the post-fermented teas included the ${\alpha}$-proteobacteria Rhodobacteraceae and Sphingomonas, and the ${\gamma}$-proteobacteria Pantoea. Cluster analysis confirmed that the microbial populations present in both Korean and Chinese post-fermented teas grouped into the same class. Interestingly, the dominant microorganism present in the Korean post-fermented teas was a bacterium, while for the Chinese post-fermented tea, it was a fungus.

• Microbiology and Biotechnology Letters
• /
• v.32 no.1
• /
• pp.91-95
• /
• 2004

For the detection of the oil-degrading bacterium, Nocardia sp. Hl7-1, inoculated during the bioremediation of oil-contaminated soil, a species-specific primer was constructed based on the 16S rDNA sequence of this strain. Two forward primers and two reverse primers were designed and tested against both closely and distantly related bacterial strains. All the primers designed were specific to the Nocardia sp. H17-1. Particularly, primer sets NH169F-NH972R and NH575F-NH972R could be used to detect 50 fg of template DNA and TEX>$1.2${\times}$10^4$ CFU/g of sandy soil. These two PCR primer sets successfully detected the H 17-1 strain in the oil-con-laminated soil samples containing heterogeneous DNA. We also conformed the primer specificity by restriction-enzyme cleavage of the PCR products and denaturing gradient gel electrophoresis.