• Journal of Korean Society on Water Environment
• /
• v.22 no.6
• /
• pp.1014-1021
• /
• 2006

SMMIAR (Submerged Moving Media Intermittent Aeration Reactor) Process is a very efficient system which remove ammonia to nitrogen gas in one reactor. In this study, we determined the diversity of ammonia oxidizing bacteria and denitrifying bacteria using specific PCR amplification and the clone library construction. An ammonia monooxygenase gene(amoA) was analyzed to investigate the diversity of nitrifiers. Most of amoA gene fragments (27/29, 93%) were same types and they are very similar (>99%) to the sequences of Nitrosomonas europaea and other clones isolated from anoxic ammonia oxidizing reactors. ANAMMOX related bacteria have not determined by specific PCR amplification. A nitrite reductase gene(nirK) was analyzed to investigate the diversity of denitrifying bacteria. About half (9/20, 45%) of denitrifiers were clustered with Rhodobacter and most of others were clustered with Mesorhizobium (6/20, 30%) and Rhizobium (3/20, 15%). All of these nirK gene clones were clustered in alpha-Proteobacteria and this result is coincide with other system which also operate nitrification and denitrification in one reactor. The molecular monitoring of the population of nitrifiers and denitrifiers would be helpful for the system stabilization and scale-up.

• Microbiology and Biotechnology Letters
• /
• v.52 no.3
• /
• pp.233-254
• /
• 2024

The microorganisms that live under extreme conditions on Earth are known as extremophiles. They possess an extraordinary capability to endure extreme conditions, including salinity, temperature variations, pH, desiccation, and nutrient scarcity, among others. These organisms, including a vast array of bacteria, eukarya, and archaea, have evolved specialized structural and functional adaptations that make them capable of thriving in extremely selective environments in such a way that they showcase remarkable adaptations that push the limits of what we consider habitable. This capability results in valuable compounds with great potential for developing novel pharmaceuticals and biotechnological innovations. The present review paper aims to summarize current knowledge on the diversity of extremophilic microorganisms and the adaptive strategies employed to face such a range of extreme conditions. Particular attention will be given to temperature, salinity, pH, and desiccation adaptation. The review also highlights their potential applications, specifically focusing on pharmaceutical and biotechnological applications.

• Journal of Microbiology and Biotechnology
• /
• v.30 no.5
• /
• pp.633-641
• /
• 2020

Microbial rhodopsins are a superfamily of photoactive membrane proteins with the covalently bound retinal cofactor. Isomerization of the retinal chromophore upon absorption of a photon triggers conformational changes of the protein to function as ion pumps or sensors. After the discovery of proteorhodopsin in an uncultivated γ-proteobacterium, light-activated proton pumps have been widely detected among marine bacteria and, together with chlorophyll-based photosynthesis, are considered as an important axis responsible for primary production in the biosphere. Rhodopsins and related proteins show a high level of phylogenetic diversity; we focus on a specific class of bacterial rhodopsins containing the '3 omega motif.' This motif forms a stack of three non-consecutive aromatic amino acids that correlates with the B-C loop orientation and is shared among the phylogenetically close ion pumps such as the NDQ motif-containing sodium-pumping rhodopsin, the NTQ motif-containing chloride-pumping rhodopsin, and some proton-pumping rhodopsins including xanthorhodopsin. Here, we reviewed the recent research progress on these 'omega rhodopsins,' and speculated on their evolutionary origin of functional diversity.

• Journal of Microbiology
• /
• v.43 no.5
• /
• pp.383-390
• /
• 2005

The diversity of the denitrifying bacterial populations in Daejeon Sewage Treatment Plant was examined using a culture-dependent approach. Of the three hundred and seventy six bacterial colonies selected randomly from agar plates, thirty-nine strains that showed denitrifying activity were selected and subjected to further analysis. According to the morphological and biochemical properties, the thirty nine isolates were divided into seven groups. This grouping was supported by an unweighted pair group method, using an arithmetic mean (UPGMA) analysis with fatty acid profiles. Restriction pattern analysis of 16S rDNA with four endonucleases (AluI, BstUI, MspI and RsaI) again revealed seven distinct groups, consistent with those defined from the morphological and biochemical properties and fatty acid profiles. Through the phylogenetic analysis using the 16S rDNA partial sequences, the main denitrifying microbial populations were found to be members of the phylum, Proteobacteria; in particular, classes Gammaproteobacteria (Aeromonas, Klebsiella and Enterobacter) and Betaproteobacteria (Acidovorax, Burkholderia and Comamonas), with Firmicutes, represented by Bacillus, also comprised a major group.

• Journal of Life Science
• /
• v.22 no.1
• /
• pp.110-116
• /
• 2012

Nuruk plays a significant role in the flavor and quality of Takju and Yakju, which are produced through saccharification and alcohol fermentation by various microorganisms. In this study, we identified microbial strains isolated from a plate count and PCR-denaturing gradient gel electrophoresis (DGGE) analysis targeting the 16S and 28S rRNA genes, in order to characterize bacterial and fungal diversity in Sansung Nuruk. The numbers of bacteria and fungi in Nuruk were $1.5{\times}10^9$ CFU/g and $2.2{\tims}10^8$ CFU/g, respectively. The 16S rRNA gene sequence indicated that the predominant bacteria in the isolates and PCR-DGGE profile of Nuruk were Kocuria spp., Pantoea spp., Lactobacillus spp., Pediococcus spp., Weissella spp., Staphylococcus spp., endophytic bacterium, uncultured Gamma-proteobacteria, uncultured Cyanobacteria, and Actinobacteria. Dominant bacteria from the PCR-DGGE profile were Pediococcous pentosaceus and uncultured Cyanobacteria. The 28S rRNA gene sequence indicated the predominant fungi in the isolates and PCR-DGGE profile to be Trichomonascus spp. Pichia spp., Torulaspora spp., Wickerhamomyces spp., Sacharomycopsis spp., Lichtheimia spp., Mucor spp., Rhizopus spp. Aspergillus spp., and Cladosporium spp. Dominant fungi from the PCR-DGGE profile were Pichia kudriavzevii and Aspergillus oryzae. The PCR-DGGE technique was used for the first time in this study to assess a microbial community in Nuruk and proved to be an effective protocol for profiling microbial diversity.

• Microbiology and Biotechnology Letters
• /
• v.30 no.1
• /
• pp.79-85
• /
• 2002

Ecological characteristics of microorganisms in tideland soils were studied by investigation of microbial diversity and population. Twenty soil samples were taken at surface, 10, 20 and 30 cm depth each. Bacteria, actinomycetes and fungi were isolated on each selective isolation medium containing different concentration of NaCl. Actinomycetes were the most isolated from soil samples taken at 10 cm depth and isolated by humic acid-vitamin (HV) medium without sea water or salt. Twenty nine strains of actinomycetes were isolated at surface soil and 74, 39, 37 strains were at 10, 20, and 30 cm depth, respectively. All these isolates were analysed and grouped by random amplified polymorphic DNA (RAPD)-PCR analysis. Many of the isolates were clustered into Microtetraspora and Pseudonocardia. Fungal isolates were highly distributed at the surface soil and isolated well on potato dextrose agar (PDA) medium with sea water. Bacterial isolates were higly distributed at surface soil and isolated well by nutrient medium without sea water or salt. Soil samples taken at 10 cm depth showed the highest microbial diversity and population.

• Journal of Animal Science and Technology
• /
• v.66 no.2
• /
• pp.353-365
• /
• 2024

Rumen cannulation is a surgical technique used to collect rumen contents from ruminants. However, rumen cannulation surgery may potentially impact the composition of the rumen microbiota. This study aimed to examine the longitudinal alterations in the rumen microbiota composition of Hanwoo steers after cannulation surgery. In this study, eight Hanwoo steers were used; four steers underwent rumen cannulation surgery (cannulation group), while the remaining four were left intact (control group). Rumen samples were collected from all eight steers using the stomach tubing method on the day before surgery (day 0) and on postoperative days 1, 4, 7, 10, 14, 17, 21, 24, and 28, resulting in 80 samples (10 timepoints × 8 animals). The microbiota of all 80 samples were analyzed using 16S rRNA gene amplicon sequencing with Quantitative Insights into Microbial Ecology version 2 (QIIME2). There were no significant differences (p > 0.05) in all major phyla and most major genera representing at least 0.5% of total sequences across all 80 samples between the control and cannulation groups on the preoperative and postoperative days. However, while the alpha diversity indices did not differ (p > 0.05) between the two groups on the preoperative day, they significantly differed (p < 0.05) between the two groups on the postoperative days. Further, the overall microbial distribution based on both unweighted and weighted principal coordinate analysis plots significantly differed (p < 0.05) between the two groups on both the preoperative and postoperative days. Orthogonal polynomial contrasts indicated that major genera and microbial diversity in the cannulation group decreased following surgery but returned to their initial states by postoperative day 28. In conclusion, this study demonstrates that rumen cannulation surgery affects some major taxa and microbial diversity, suggesting that the rumen cannulation method can alter the composition of rumen microbiota in Hanwoo steers.

• The Korean Journal of Mycology
• /
• v.43 no.3
• /
• pp.158-164
• /
• 2015

A total of 509 rice panicle samples were collected at harvest time from fields in 8 provinces from 2010 to 2014. One hundred five grains per sample were plated on potato dextrose agar and 6,658 Fusarium isolates were obtained; among them, 67 were identified as Fusarium armeniacum by sequencing the translation elongation factor $1{\alpha}$ ($EF-1{\alpha}$) and confirmed by their morphological and cultural characteristics. Considerable variation in conidial size, colony color and $EF-1{\alpha}$ sequences was observed among the fungal isolates. The ability of 24 F. armeniacum isolates to produce T-2 and HT-2 toxin in potato sucrose agar was determined using liquid chromatography-mass spectrometry. Twenty one isolates produced T-2 and HT-2 toxin, resulting in varying toxin levels among the isolates. The results show that Korean isolates of F. armeniacum have diversity with respect to morphological, cultural, genetic, and toxigenic properties.

• Korean Journal of Soil Science and Fertilizer
• /
• v.42 no.4
• /
• pp.257-265
• /
• 2009

The long-term effects of soil management history on microbial communities are still poorly understood. Our objectives were to determine the impact of long-term application of soil amendments on microbial communities in rice paddy fields. The treatments selected were control where crops were grown without any nutrient application (CON); nitrogen-phosphorus-potassium (NPK); NPK plus compost (CNPK); NPK plus lime (LNPK); and NPK plus silicate (WNPK). The long-term addition of organic and inorganic amendments significantly changed soil chemical properties. The amount of organic carbon increased in the treatments with fertilizer and amendments over that in the soil without inputs. However, we could not observe the differences of bacterial population among the treatments, but the number of aerobic bacteria increased by the addition of amendments. Isolates from the rice paddy soils before irrigation were Dactylosporangium, Ewingella, Geobacillus, Kocuria, Kurthia, Kytococcus, Lechevalieria, Micrococcus, Micromonospora, Paenibacillus, Pedobacter, Pseudomonas, Pseudoxanthomonas, Rhodococcus, Rothia, Sphingopyxis, Stenotrophomonas, and Variovorax. Dominant genera were Arthrobacter, Kocuria, Kurthia, and Bacillus in the long-term field. Microbial biomass was the highest in the compost treatment (CNPK), and was the lowest in the CON. Dehydrogenase activity in soils treated with rice compost straw was the highest and the activity showed an increasing trend according to treatment as follows: CON < WNPK < NPK = LNPK < CNPK. These results demonstrate that soil management practice, such as optimal application of fertilizer and amendment, that result in accumulations of organic carbon may increase microbial biomass and dehydrogenase activity in long-term rice paddy soils.

• The Korean Journal of Mycology
• /
• v.49 no.3
• /
• pp.303-313
• /
• 2021

Peanuts in storage were estimated for mycotoxigenic fungi and mycotoxins. Peanut samples collected from storages in Gochang were mainly contaminated with Fusarium (17.2±28.0%), Penicillium (12.4±28.0%), and Aspergillus (8.0±7.6%). Other genera, including Talaromyces, Rhizopus, Rhizoctonia, Trichocladium, Clonostachys, Mucor, Chaetomium, Trametes, Epicoccum, and Humicola, were also found. Although aflatoxins were not detected in the peanut samples, 29 strains of Aspergillus flavus were identified using molecular marker genes. Among them, 17 selected isolates produced aflatoxins in solid culture media ranging from 0.61-187.82 ㎍/kg. All of them could produce both aflatoxin B₁ and B₂ and some (n=5) produced additional G₁, G₂, or both. This study is the first report that A. flavus stains obtained from Korean stored peanut are aflatoxigenic.