• Journal of Microbiology and Biotechnology
• /
• v.13 no.2
• /
• pp.236-242
• /
• 2003

A culture-independent and -dependent survey of the bacterial community structure in the rhizosphere and soil samples from hot pepper plants was conducted using 16S rDNA clone library and FAME analyses. Out of the 78 clones sequenced, 56% belonged to Proteobacteria, 4% to high G+C Gram- positive group, 3% to Cytophyga-Flexibacter-Bacreroides, and 32% could not be grouped with any known taxonomic division. Among the 127 FAME isolates identified, 66% belonged to low G+C Gram-positive bacteria (Baciilus spp.) and 26% to high G+C Gram-positive bacteria. In a cluster analysis, the results for both methods were found to be strikingly dissimilar. The current study is the first comparative study of FAME and 165 rDNA clonal analyses performed on the same set of soil, rhizosphere soil, and root samples.

• Korean Journal of Environmental Biology
• /
• v.22 no.1
• /
• pp.213-219
• /
• 2004

The bacterial community of water stream, soil and guano in Gossi cave was examined by using PCR amplified the 16S rDNA-denaturing gradient gel electrophoyesis (DGGE). In this study, the genetic diversity and the similarity of bacterial community between open area and non - open area toy cave tour were investigated, and the seasonable variation pattern was compared each other. DGGE is attractive technique, as it sepayate same length dsDNA according to sequence variation typical 16S rDNA genes. The diversity and similarity of bacterial community in cave was analyzed by GC341f and PRUN518r primer sets foy amplification of V3 region of eubacteria 16S rDNA. The specific DGGE band profile of the cave water gives the possibility that the specific bacterial cell can be adapting to the specific cave environment and living in the cave. The DGGE band profiles of all samples with guano were compared and analyzed by image analyzer, in which mutual band profile was compared to be and the band intensity of guano was the highest. From these result, it is thought that the guano was main nutrient source and influenced on the community structure of the cave environment where is nutritionally limited. Pseudomonas sp. NZ060, Pseudomonas pseudoalcaligenes, uncultured Variovorax sp. and soli bacterium NS7 were identified to be on some sample from analysing DNA sequence of some DGGE band.

• Journal of Microbiology and Biotechnology
• /
• v.17 no.4
• /
• pp.668-672
• /
• 2007

A microcosmal experiment using a metagenomic technique was designed to assess the effect of BTEX (benzene, toluene, ethylbenzene, and xylenes) on an indigenous bacterial community in a Daejeon forest soil. A compositional shift of bacterial groups in an artificial BTEX-contaminated soil was examined by the 16S rDNA PCR-DGGE method. Phylogenetic analysis of 16S rDNAs in the dominant DGGE bands showed that the number of Actinobacteria and Bacillus populations increased. To confirm these observations, we performed PCR to amplify the 23S rDNA and 16S rDNA against the sample metagenome using Actinobacteria-targeting and Bacilli-specific primer sets, respectively. The result further confirmed that a bacterial community containing Actinobacteria and Bacillus was affected by BTEX.

• 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.22 no.9
• /
• pp.1264-1270
• /
• 2012

The ecotoxicological effects of nanomaterials on animal, plant, and soil microorganisms have been widely investigated; however, the nanotoxic effects of plant-soil interactive systems are still largely unknown. In the present study, the effects of ZnO nanoparticles (NPs) on the soil-plant interactive system were estimated. The growth of plant seedlings in the presence of different concentrations of ZnO NPs within microcosm soil (M) and natural soil (NS) was compared. Changes in dehydrogenase activity (DHA) and soil bacterial community diversity were estimated based on the microcosm with plants (M+P) and microcosm without plants (M-P) in different concentrations of ZnO NPs treatment. The shoot growth of M+P and NS+P was significantly inhibited by 24% and 31.5% relative to the control at a ZnO NPs concentration of 1,000 mg/kg. The DHA levels decreased following increased ZnO NPs concentration. Specifically, these levels were significantly reduced from 100 mg/kg in M-P and only 1,000 mg/kg in M+P. Different clustering groups of M+P and M-P were observed in the principal component analysis (PCA). Therefore, the M-P's soil bacterial population may have more toxic effects at a high dose of ZnO NPs than M+P's. The plant and activation of soil bacteria in the M+P may have a less toxic interactive effect on each of the soil bacterial populations and plant growth by the ZnO NPs attachment or absorption of plant roots surface. The soil-plant interactive system might help decrease the toxic effects of ZnO NPs on the rhizobacteria population.

• Journal of Microbiology and Biotechnology
• /
• v.26 no.1
• /
• pp.89-98
• /
• 2016

Endophytes play an important role in the growth and development of the host. However, the study of endophytes is mostly focused on plants, and reports on bacteria associated with fungi are relatively rare. We studied the bacteria associated with fruiting bodies of Tricholoma matsutake picked from seven main T. matsutake-producing areas in Sichuan, China, by barcoded pyrosequencing. About 8,272 reads were obtained per sample, representing 40 phyla, 103 classes, and 495 genera of bacteria and archaea, and 361-797 operational taxonomic units were observed at a 97% similarity level. The bacterial community was always both more abundant and more diverse than the archaeal community. UniFrac analysis showed there were some difference of bacterial communities among the samples sites. Three bacterial phyla, Proteobacteria, Bacteroidetes, and Firmicutes, were dominant in all samples. Correlation analysis showed there was a significant correlation between some soil properties and bacterial community associated with T. matsutake. This study demonstrated that the bacteria associated with T. matsutake fruiting bodies were diversified. Among these bacteria, we may find some strains that can promote the growth of T. matsutake.

• Journal of Microbiology and Biotechnology
• /
• v.16 no.5
• /
• pp.704-715
• /
• 2006

Oil spill was found in 1999 from a diesel storage facility located near the top of Baekun Mountain in Uiwang City. Application of bioremediation techniques was very relevant in removing oil spills in this site, because the geological condition was not amenable for other onsite remediation techniques. For efficient bioremediation, bacterial communities of the contaminated site and the uncontaminated control site were compared using both molecular and cultivation techniques. Soil bacterial populations were observed to be stimulated to grow in the soils contaminated with diesel hydrocarbon, whereas fungal and actinomycetes populations were decreased by diesel contamination. Most of the dieseldegrading bacteria isolated from contaminated forest soils were strains of Pseudomonas, Ralstonia, and Rhodococcus species. Denaturing gradient gel electrophoresis (DGGE) analysis revealed that the profiles were different among the three contaminated sites, whereas those of the control sites were identical to each other. Analysis of 16S rDNA sequences of dominant isolates and clones showed that the bacterial community was less diverse in the oil-contaminated site than at the control site. Sequence analysis of the alkane hydroxylase genes cloned from soil microbial DNAs indicated that their diversity and distribution were different between the contaminated site and the control site. The results indicated that diesel contamination exerted a strong selection on the indigenous microbial community in the contaminated site, leading to predominance of well-adapted microorganisms in concurrence with decrease of microbial diversity.

• Korean Journal of Soil Science and Fertilizer
• /
• v.47 no.1
• /
• pp.28-35
• /
• 2014

Due to recent interest of the consumers on safe farm products and the government's political support for eco-friendly agriculture, organic fruit production has been growing continuously. This research was conducted in order to study the effect of cover plants on soil microbial community on cover plants and establish an organic fruit cultivation method through choosing optimal cover plant. As a result of investigating soil microbial population density, the bacterial density in soil showed an increasing trend in June compared to April, and there was a decreasing trend in bacterial density of the soil in August compared to June. The density of actinomycetes in soil increased around 1.6 times in June compared to April when the soil was covered with hairy vetch. The increase of filamentous fungus in crimson clover group was 6.1 times higher in June compared to April and in hairy vetch group, the increase was 4.9 times higher in June compared to April. As a result of analyzing DNA extracted from the soil categorized by different types of cover plants using DGGE method, soil collected from April had higher number of bands detected from different locations according to different types of cover plants. Diversity of the bands from the soil collected from August showed higher range of reduction. As a result of analyzing soil microbial community by different period and the types of cover plants using Pyrosequencing method, microbes were detected in the order of Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Firmicutes. Distribution rate of Firmicutes increased in the soil collected in August compared to June and this was shown in all types of cover plants by twice the amount.

• Journal of Korean Society of Forest Science
• /
• v.106 no.2
• /
• pp.121-129
• /
• 2017

The soil microbiome plays important roles in material cycling and plant growth in forest ecosystem. Although a lot of researches on forest soil fungi in Korea have been performed, the studies on forest soil bacterial communities have been limited. In this study, we conducted next generation sequencing (NGS) targeting 16S rRNA gene to investigate the soil bacterial communities from natural red pine (Pinus densiflora) forest in Mt. Janggunbong, Bonghwa-gun, Gyeongbuk, Korea. Our results showed that the entire bacterial communities in the study sites include the phyla Proteobacteria, Acidobacteria, Actinobacteria, Planctomycetes, which have been typically observed in forest soils. The composition ratio of Proteobacteria was the highest in the soil bacteria community. The results reflect that Proteobacteria is copiotroph, which generally favors relatively nutrient-rich conditions with abundant organic matter. Some rhizobia species such as Burkholderia, Bradyrhizobium, Rhizobium, which are known to contribute to soil nitrogen-fixation, exist in the study sites. As a result of correlation analysis between soil physicochemical characteristics and bacteria communities, the soil pH was significantly correlated with the soil bacteria compositions.

• 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.