• Animal cells and systems
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• v.14 no.3
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• pp.225-236
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• 2010

We compared the composition of phospholipid fatty acids (PLFA) to assess the microbial community structure in the soil and rhizosphere community of non-transgenic watermelons and transgenic watermelons in Miryang farmlands in Korea during the spring and summer of 2005. The PLFA data were seasonally examined for the number of PLFA to determine whether there is any difference in the microbial community in soils from two types of watermelons, non-transgenic and transgenic. We identified 78 PLFAs from the rhizosphere samples of the two types of watermelons. We found eight different PLFAs for the type of plants and sixteen PLFAs for the interaction of plant type and season. The PLFA data were analyzed by analysis of variance separated by plant type (P<0.0085), season (P<0.0154), and the plant type${\times}$season interaction (P<0.1595). Non-parametric multidimensional scaling (NMS showed a small apparent difference but multi-response permutation procedures (MRPP) confirmed that there was no difference in microbial community structure for soils of both plant types. Conclusively, there was no significant adverse effect of transgenic watermelon on bacterial and fungal relative abundance as measured by PLFA. We could reject our hypothesis that there might be an adverse effect from transgenic watermelon with our statistical results. Therefore, we can suggest the use of this PLFA methodology to examine the adverse effects of transgenic plants on the soil microbial community.

• Journal of Microbiology and Biotechnology
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• v.31 no.7
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• pp.978-989
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• 2021

Allyl isothiocyanate (AITC), as a fumigant, plays an important role in soil control of nematodes, soil-borne pathogens, and weeds, but its effects on soil microorganisms are unclear. In this study, the effects of AITC on microbial diversity and community composition of Capsicum annuum L. soil were investigated through Illumina high-throughput sequencing. The results showed that microbial diversity and community structure were significantly influenced by AITC. AITC reduced the diversity of soil bacteria, stimulated the diversity of the soil fungal community, and significantly changed the structure of fungal community. AITC decreased the relative abundance of dominant bacteria Planctomycetes, Acinetobacter, Pseudodeganella, and RB41, but increased that of Lysobacter, Sphingomonas, Pseudomonas, Luteimonas, Pseudoxanthomonas, and Bacillus at the genera level, while for fungi, Trichoderma, Neurospora, and Lasiodiplodia decreased significantly and Aspergillus, Cladosporium, Fusarium, Penicillium, and Saccharomyces were higher than the control. The correlation analysis suggested cellulase had a significant correlation with fungal operational taxonomic units and there was a significant correlation between cellulase and fungal diversity, while catalase, cellulose, sucrase, and urease were the major contributors in the shift of the community structure. Our results will provide useful information for the use of AITC in the assessment of environmental and ecological security.

• Journal of Microbiology and Biotechnology
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• v.15 no.6
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• pp.1286-1298
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• 2005

The genus Paenibacillus is a new group of bacilli separated from the genus Bacillus, and most of species have been isolated from soil. In the present study, we collected 450 spore-forming bacilli from the roots of winter crops, such as barley, wheat, onion, green onion, and Chinese cabbage, which were cultivated in the southern part of Korea. Among these 450 isolates, 104 Paenibacillus-like isolates were selected, based on their colony shape, odor, color, and endospore morphology, and 41 isolates were then finally identified as Paenibacillus spp. by 16S rDNA sequencing. Among the 41 Paenibacillus isolates, 23 were classified as P. polymyxa, a type species of the genus Paenibacillus, based on comparison of the 16S rDNA sequences with those of 32 type strains of the genus Paenibacillus from the GenBank database. Thirty-five isolates among the 41 Paenibacillus isolates exhibited antagonistic activity towards plant fungal and bacterial pathogens, whereas 24 isolates had a significant growth-enhancing effect on cucumber seedlings, when applied to the seeds. An assessment of the root-colonization capacity under gnotobiotic conditions revealed that all 41 isolates were able to colonize cucumber roots without any significant difference. Twenty-one of the Paenibacillus isolates were shown to contain the nifH gene, which is an indicator of $N_{2}$ fixation. However, the other 20 isolates, including the reference strain E681, did not incorporate the nifH gene. To investigate the diversity of the isolates, a BOX-PCR was performed, and the resulting electrophoresis patterns allowed the 41 Paenibacillus isolates to be divided into three groups (Groups A, B, and C). One group included Paenibacillus strains isolated mainly from barley or wheat, whereas the other two groups contained strains isolated from diverse plant samples. Accordingly, the present results showed that the Paenibacillus isolates collected from the rhizosphere of winter crops were diverse in their biological and genetic characteristics, and they are good candidates for further application studies.

• Proceedings of the Microbiological Society of Korea Conference
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• 2005.05a
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• pp.196.1-196
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• 2005

• Journal of Life Science
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• v.16 no.1
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• pp.22-29
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• 2006

Effect of microbial products made of Bacillus stearothermophilus DL-3 on growth of chickens and pigs was investigated. Two types of microbial product were made in this study. One is the microbial product made of culture broth of B. stearothemophilus DL-3 and rice bran which named as the microbial product A. The other is the microbial product made of culture broth of B. stearothermophilus DL-3, apple pomace, soybean pomace and rice bran which named as the microbial product B. Chickens were divided into three groups and each group was fed with $100\%$ general feed, $90\%$ general feed supplemented with $10\%$ microbial product A or $90\%$ general feed supplemented with $10\%$ microbial product B. The average chicken weight of each group was $41.1{\pm}2.5g,\;41.6{\pm}3.2g\;and\;42.3{\pm}2.9g$ and those after 28 days was $547.7{\pm}91.7g,\;560.1{\pm}17.2g\;and\;562.2{\pm}32.5g$, respectively. The average weight gain for each group was 506.6 g, 518.6 g and 519.9 g, respectively, and weight increases of groups fed with $90\%$ general feeder and $10\%$ microbial product A and B were $2.4\%\;and\;2.6\%$ higher than the group fed with $100\%$ general feed. Pigs were also divided into three groups and each group was fed like chickens. The average weight of each group was $9.3{\pm}1.0kg,\;9.4{\pm}1.1kg\;and\;9.6{\pm}1.0kg$ and those after 37 days was $19.3{\pm}4.1kg,\;20.2{\pm}3.9kg\;and\;20.8{\pm}4.2kg$, respectively. The average Weight gain for each group was 10.65 kg, 10.82 kg and 11.20 kg, respectively, and weight increases of groups fed with $90\%$ general feeder and $10\%$ microbial product A and B were $1.6\%$ and $5.2\%$ higher than the group fed with $100\%$ general feed.

• Journal of Microbiology and Biotechnology
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• v.17 no.1
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• pp.162-167
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• 2007

A genetic transfer system for introducing foreign genes to biomining microorganisms is urgently needed. Thus, a conjugative gene transfer system was investigated for a moderately thermophilic, extremely acidophilic biomining bacterium, Acidithiobacillus caldus MTH-04. The broad-hostrange IncP plasmids RP4 and R68.45 were transferred directly into A. caldus MTH-04 from Escherichia coli by conjugation at relatively high frequencies. Additionally the broad-hostrange IncQ plasmids pJRD215, pVLT33, and pVLT35 were also transferred into A. caldus MTH-04 with the help of plasmid RP4 or strains with plasmid RP4 integrated into their chromosome, such as E. coli SM10. The $Km^r\;and\;Sm^r$ selectable markers from these plasmids were successfully expressed in A. caldus MTH-04. Futhermore, the IncP and IncQ plasmids were transferred back into E. coli cells from A. caldus MTH-04, thereby confirming the initial transfer of these plasmids from E. coli to A. caldus MTH-04. All the IncP and IncQ plasmids studied were stable in A. caldus MTH-04. Consequently, this development of a conjugational system for A. caldus MTH-04 will greatly facilitate its genetic study.

• Journal of Microbiology and Biotechnology
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• v.30 no.8
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• pp.1195-1206
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• 2020

Beringraja pulchra, Cham-hong-eo in Korean, is a mottled skate which is belonging to the cartilaginous fish. Although this species is economically valuable in South Korea as an alkaline-fermented food, there are few microbial studies on such fermentation. Here, we analyzed microbial changes and pH before, during, and after fermentation and examined the effect of inoculation by a skin microbiota mixture on the skate fermentation (control vs. treatment). To analyze microbial community, the V4 regions of bacterial 16S rRNA genes from the skates were amplified, sequenced and analyzed. During the skate fermentation, pH and total number of marine bacteria increased in both groups, while microbial diversity decreased after fermentation. Pseudomonas, which was predominant in the initial skate, declined by fermentation (Day 0: 11.39 ± 5.52%; Day 20: 0.61 ± 0.9%), while the abundance of Pseudoalteromonas increased dramatically (Day 0: 1.42 ± 0.41%; Day 20: 64.92 ± 24.15%). From our co-occurrence analysis, the Pseudoalteromonas was positively correlated with Aerococcaceae (r = 0.638) and Moraxella (r = 0.474), which also increased with fermentation, and negatively correlated with Pseudomonas (r = -0.847) during fermentation. There are no critically significant differences between control and treatment. These results revealed that the alkaline fermentation of skates dramatically changed the microbiota, but the initial inoculation by a skin microbiota mixture didn't show critical changes in the final microbial community. Our results extended understanding of microbial interactions and provided the new insights of microbial changes during alkaline fermentation.

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

• Microbiology and Biotechnology Letters
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• v.48 no.2
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• pp.138-147
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• 2020

Various microorganisms play important roles in food fermentation, food spoilage, and agriculture. In this study, the biotype of 54 yeast and bacterial strains having high potential for utilization in food and agriculture, including Candida spp., Lactobacillus spp., and Acetobacter spp., were characterized by matrix-assisted laser desorption/ionization time-of flight mass spectrometry (MALDI-TOF MS). This characterization using a fast and robust method provides much-needed information on the selected microorganisms and will facilitate effective usage of these strains in various applications. Importantly, the unique protein profile of each microbial species obtained from this study was used to create a database of fingerprints from these species. The database was validated using microbial strains of the same species by comparing the mass spectra with the created database through pattern matching. The created reference database provides crucial information and is useful for further utilization of a large number of valuable microorganisms relevant to food and agriculture.

• Journal of Microbiology and Biotechnology
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• v.25 no.5
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• pp.612-619
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• 2015

We have synthesized gold nanoparticles (GNPs) using chicken feathers (poultry waste) and Bacillus subtilis RSE163. Disulfide reductase and keratinase produced by Bacillus subtilis during the degradation of chicken feather has been used to reduce Au³⁺ from HAuCl₄ precursor to produce gold nanoparticles. The synthesized biogenic GNPs were characterized by UV-visible spectroscopy, transmission electron microscopy (TEM), and zeta potential measurements. Fourier transform infrared (FTIR) spectroscopy indicated the presence of protein capping on synthesized GNPs, imparting multifunctionality to the GNP surface. Furthermore, the nontoxic nature of biogenic GNPs was insured by interaction with Escherichia coli (ATCC11103), where TEM images and enhancement of growth rate of E. coli in log phase signified their nontoxic nature. The results indicate that the synthesis of biocompatible GNPs using poultry waste may find potential applications in drug delivery and sensing.