• Microbiology and Biotechnology Letters
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• v.49 no.3
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• pp.391-402
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• 2021

Earthworms play an important role in soil fertilization, interacting continually with microorganisms. This study aims to demonstrate the existence of beneficial microorganisms living in the earthworm's immune system, the coelomic fluid. To achieve this goal, a molecular identification technique was performed, using cytochrome c oxidase I (COI) barcoding to identify abundant endogenic earthworms inhabiting the temperate zone of Rabat, Morocco. Then, 16S rDNA and ITS sequencing techniques were adopted for bacteria and fungi, respectively. Biochemical analysis, showed the ability of bacteria to produce characteristic enzymes and utilize substrates. Qualitative screening of plant growth-promoting traits, including nitrogen fixation, phosphate and potassium solubilization, and indole acetic acid (IAA) production, was also performed. The result of mitochondrial COI barcoding allowed the identification of the earthworm species Aporrectodea molleri. Phenotypic and genotypic studies of the sixteen isolated bacteria and the two isolated fungi showed that they belong to the Pseudomonas, Aeromonas, Bacillus, Buttiauxella, Enterobacter, Pantoea, and Raoultella, and the Penicillium genera, respectively. Most of the isolated bacteria in the coelomic fluid showed the ability to produce β-glucosidase, β-glucosaminidase, Glutamyl-β-naphthylamidase, and aminopeptidase enzymes, utilizing substrates like aliphatic thiol, sorbitol, and fatty acid ester. Furthermore, three bacteria were able to fix nitrogen, solubilize phosphate and potassium, and produce IAA. This initial study demonstrated that despite the immune property of earthworms' coelomic fluid, it harbors beneficial microorganisms. Thus, the presence of resistant microorganisms in the earthworm's immune system highlights a possible selection process at the coelomic fluid level.

• Journal of Microbiology and Biotechnology
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• v.32 no.8
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• pp.967-975
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• 2022

Kombucha mutualistic community (KMC) is composed by acetic acid bacteria and yeasts, producing fermented tea with health benefits. As part of the BIOlogy and Mars EXperiment (BIOMEX) project, the effect of Mars-like conditions on the KMC was analyzed. Here, we analyzed metagenome-assembled genomes (MAGs) of the Komagataeibacter, which is a predominant genus in KMC, to understand their roles in the KMC after exposure to Mars-like conditions (outside the International Space Station) based on functional genetic elements. We constructed three MAGs: K. hansenii, K. rhaeticus, and K. oboediens. Our results showed that (i) K. oboediens MAG functionally more complex than K. hansenii, (ii) K. hansenii is a keystone in KMCs with specific functional features to tolerate extreme stress, and (iii) genes related to the PPDK, betaine biosynthesis, polyamines biosynthesis, sulfate-sulfur assimilation pathway as well as type II toxin-antitoxin (TA) system, quorum sensing (QS) system, and cellulose production could play important roles in the resilience of KMC after exposure to Mars-like stress. Our findings show the potential mechanisms through which Komagataeibacter tolerates the extraterrestrial stress and will help to understand minimal microbial composition of KMC for space travelers.

• Journal of Animal Science and Technology
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• v.64 no.5
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• pp.937-949
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• 2022

Health concern of dogs is the most important issue for pet owners. People who have companied the dogs long-term provide the utmost cares for their well-being and healthy life. Recently, it was revealed that the population and types of gut microbiota affect the metabolism and immunity of the host. However, there is little information on the gut microbiome of dogs. Hericium erinaceus (H. erinaceus; HE) is one of the well-known medicinal mushrooms and has multiple bioactive components including polyphenol, β-glucan, polysaccharides, ergothioneine, hericerin, erinacines, etc. Here we tested a pet food that contained H. erinaceus for improvement in the gut microbiota environment of aged dogs. A total of 18 dogs, each 11 years old, were utilized. For sixteen weeks, the dogs were fed with 0.4 g of H. erinaceus (HE-L), or 0.8 g (HE-H), or without H. erinaceus (CON) per body weight (kg) with daily diets (n = 6 per group). Taxonomic analysis was performed using metagenomics to investigate the difference in the gut microbiome. Resulting from principal coordinates analysis (PCoA) to confirm the distance difference between the groups, there was a significant difference between HE-H and CON due to weighted Unique fraction metric (Unifrac) distance (p = 0.047), but HE-L did not have a statistical difference compared to that of CON. Additionally, the result of Linear discriminate analysis of effect size (LEfSe) showed that phylum Bacteroidetes in HE-H and its order Bacteroidales increased, compared to that of CON, Additionally, phylum Firmicutes in HE-H, and its genera (Streptococcus, Tyzzerella) were reduced. Furthermore, at the family level, Campylobacteraceae and its genus Campylobacter in HE-H was decreased compared to that of CON. Summarily, our data demonstrated that the intake of H. erinaceus can regulate the gut microbial community in aged dogs, and an adequate supply of HE on pet diets would possibly improve immunity and anti-obesity on gut-microbiota in dogs.

• Korean Journal of Environmental Biology
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• v.40 no.1
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• pp.54-69
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• 2022

We conducted a field survey from 2018 to 2020 to analyze the spatial distribution of phytoplankton communities at 13 stations in the East Sea. The diatom Chaetoceros curvisetus appeared as the dominant species in winter, and small flagellates less than 20 ㎛ prevailed in all seasons except winter. The seasonal average range of the micro (>20 ㎛), nano (20 ㎛≥Chl-a>3 ㎛), and picophytoplankton (≤3 ㎛) was 20.6-26.2%, 27.1-35.9%, and 40.8-49.0%, respectively. The composition ratio of nano and picophytoplankton was high at the surface mixed layer from spring to autumn when the water columns were strongly stratified. Especially, the stability of the water mass was increased when the summer surface water temperature was higher than that of the previous year. As a result, the nutrient inflow from the lower layer to the surface was reduced as the ocean stratification layer was strengthened. Therefore, the composition ratio of nano and picophytoplankton was the highest at 77.9% at the surface mixed layer. In conclusion, the structure of the phytoplankton community in the East Sea has been miniaturized, which is expected to form a complex microbial food web structure and lower the carbon transfer rate to the upper consumer stage.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.8 no.1
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• pp.44-57
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• 2003

Seasonal variations of bacterial abundance and production, heterotrophic nanoflagellate (HNF) abundance and HNF ingestion rates on bacteria using FLB together with environmental variables were investigated at intervals of a month in Kyeonggi Bay from December 1991 to November 1998. Bacterial abundance and production ranged from 0.38$\times$10$^{9}$ ~ 3.25$\times$10$^{9}$ cells 1$^{-1}$ (average 1.19$\pm$0.69$\times$10$^{9}$ cells 1$^{-1}$ ) and from 1.51 to 20.4 cells 1$^{-1}$ h$^{-1}$ (average 6.04$\pm$ 1.88$\times$10$^{6}$ cells 1$^{-1}$ h$^{-1}$ ), respectively. Bacterial abundance and production showed no differences at the high tide and low tide, and bacterial abundances were not different with depth, but bacterial production decreased with depth. Seasonal variation of bacterial abundance showed almost similar fluctuation pattern to those of DOC (dissolved organic carbon). HNF abundances ranged from 388 to 4,374 cells ml$^{-1}$ (average 1,344$\pm$130 cells ml$^{-1}$ ), were high in March, April, July and August. HNF abundance showed no difference between the high tide and low tide, and was not different with depth. The ingestion rates of HNF on bacteria were 1.0 to 6.3$\pm$10$^{6}$ bacteria 1$^{-1}$ h$^{-1}$ (average 3.12$\pm$0.55$\times$10$^{6}$ bacteria 1$^{-1}$ h$^{-1}$ ), resulting ingestion rates of HNF removed 19.4 to 141.4 %(average 62.3$\pm$12.0%) of bacterial production. Ingestion rates and grazing pressure of HNF on bacteria showed high correlation with HNF abundance. Although we cannot exactly discussion about seasonal variation of bacteria community in this study area where physical and chemical parameters were very complex, the results indicate that bacterial abundance and production were mainly controlled by resources supply as dissolved organic carbon and chlorophyll-a(bottom-up) except March which bacterial abundance and production uncoupled chlorophyll-a because of low dissolved organic carbon and low temperature, and were controlled by HNF grazing pressure(top-down) in the warm seasons except the winter.

• Journal of Life Science
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• v.23 no.6
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• pp.796-803
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• 2013

Property changes and bacterial characterizations by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) were investigated during the fermentation of Makgeollies by 5 isolated yeast strains. Changes of pH were large between day 0 (pH 6) and day 2 (pH 3) and showed less variation after then. ANOVA analyses revealed that pHs were statistically different with fermentation times (p<0.001), while strains (p=0.60) did not. Acidities were changed from 0.19 to 1.04% and showed rather high increase from day 2, and fermentation times (p<0.001) and strains (p=0.006) represented statistical differences. All strains showed less than 0.150% at amino-type nitrogen contents except S strain showed 0.442% at day 8, and there were no statistical differences with fermentation times (p=0.4558) and strains (p=0.3513). Saccharinities of C strain were higher from day 4, and fermentation times (p<0.0001) and strains (p=0.007) showed statistical differences. Large variation of alcohol concentrations (%) were observed between day 0 (0%) and day 2 (10%) and showed less variation after day 2, and there was no statistical difference with strains. Dominant prokaryotes were Lactobacillus fermentum and Pediococcus pentosaceus, which producing acids and functional materials. Dominant eukaryote was Saccharomyces cerevisiae, which might be resulted from addition of yeasts.

• Korean Journal of Environmental Biology
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• v.35 no.2
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• pp.198-206
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• 2017

From June 2007 to May 2008, seasonal variations of bacterial abundance and heterotrophic nanoflagellate (HNF), together with environmental factors, were investigated at weekly and monthly intervals in Kyeonggi Bay. During the study period, the water temperature and salinity varied from $1.9^{\circ}C{\sim}29.0^{\circ}C$ and 31~35.1 psu, respectively. The concentration of ammonia, nitrate+nitrite, phosphate, and silicate ranged from 0.01 to $3.22{\mu}M$, 2.03 to $15.34{\mu}M$, 0.06 to $1.82{\mu}M$, and 0.03 to $18.3{\mu}M$, respectively. The annual average concentration of Chl. a varied from $0.86{\mu}g\;L^{-1}$ to $37.70{\mu}g\;L^{-1}$; the concentration was twice as much at the surface than at the deeper layers. The abundance of bacteria and HNF ranged from $0.29{\times}10^6$ to $7.62{\times}10^6cells\;mL^{-1}$ and $1.00{\times}10^2$ to $1.26{\times}10^3cells\;mL^{-1}$, respectively. In particular, there were significant correlations between bacteria and HNF abundance (p<0.05), and then the high abundance of HNF was frequently observed with an increase of bacterial abundance in summer (p<0.001). Our results therefore indicate that bacterial abundance in the bay was mainly controlled by resources supplied as organic and inorganic substances from Lake Shihwa due to the daily water exchange after dike construction. Also, the bacterial abundance was significantly controlled by HNF grazing pressure (top-down) in the warm seasons, i.e. excluding winter, in the Kyeonggi Bay.

• Korean Journal of Environmental Biology
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• v.34 no.4
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• pp.304-313
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• 2016

One of the issues currently facing nuclear power plants is how to store spent nuclear waste materials which are contaminated with radionuclides such as $^{134}Cs$, $^{135}Cs$, and $^{137}Cs$. Bioremediation processes may offer a potent method of cleaning up radioactive cesium. However, there have only been limited reports on $Cs^+$ tolerant bacteria. In this study, we report the isolation and identification of $Cs^+$ tolerant bacteria in environmental soil and sediment. The resistant $Cs^+$ isolates were screened from enrichment cultures in R2A medium supplemented with 100 mM CsCl for 72 h, followed by microbial community analysis based on sequencing analysis from 16S rRNA gene clone libraries(NCBI's BlastN). The dominant Bacillus anthracis Roh-1 and B. cereus Roh-2 were successfully isolated from the cesium enrichment culture. Importantly, B. cereus Roh-2 is resistant to 30% more $Cs^+$ than is B. anthracis Roh-1 when treated with 50 mM CsCl. Growth experiments clearly demonstrated that the isolate had a higher tolerance to $Cs^+$. In addition, we investigated the adsorption of $0.2mg\;L^{-1}$ $Cs^+$ using B. anthracis Roh-1. The maximum $Cs^+$ biosorption capacity of B. anthracis Roh-1 was $2.01mg\;g^{-1}$ at pH 10. Thus, we show that $Cs^+$ tolerant bacterial isolates could be used for bioremediation of contaminated environments.

• Korean Journal of Soil Science and Fertilizer
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• v.41 no.4
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• pp.260-266
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• 2008

Small lysimeter experiment under rain shelter plastic film house was conducted to investigate the effect of soil characteristics on the leaching and soil solution concentration of nitrate and phosphate. Three soils were obtained from different agricultural sites of Korea: Soil A (mesic family of Typic Dystrudepts), Soil B (mixed, mesic family of Typic Udifluvents), and Soil C (artificially disturbed soils under greenhouse). Organic-C contents were in the order of Soil C ($32.4g\;kg^{-1}$) > Soil B ($15.0g\;kg^{-1}$) > Soil A ($8.1g\;kg^{-1}$). Inorganic-N concentration also differed significantly among soils, decreasing in the order of Soil B > Soil C > Soil A. Degree of P saturation (DPS) of Soil C was 178%, about three and fifteen times of Soil B (38%) and Soil A (6%). Prior to treatment, soils in lysimeters (dia. 300 mm, soil length 450 mm) were tabilized by repeated drying and wetting procedures for two weeks. After urea at $150kg\;N\;ha^{-1}$ and $KH_2PO_4$ at $100kg\;P_2O_5\;ha^{-1}$ were applied on the surface of each soil, total volume of irrigation was 213 mm at seven occasions for 65 days. At 13, 25, 35, 37, and 65 days after treatment, soil solution was sampled using rhizosampler at 10, 20, and 30 cm depth and leachate was sampled by free drain out of lysimeter. The volume of leachate was the highest in Soil C, and followed by the order of Soils A and B, whereas the amount of leached nitrate had a reverse trend, i.e. Soil B > Soil A > Soil C. Soil A and B had a significant increase of the nitrate concentration of soil solution at depth of 10 cm after urea-N treatment, but Soil C did not. High nitrate mobility of Soil B, compared to other soils, is presumably due to relatively high clay content, which could induce high extraction of nitrate of soil matrix by anion exclusion effect and slow rate of water flow. Contrary to Soil B, high organic matter content of Soil C could be responsible for its low mobility of nitrate, inducing preferential flow by water-repellency and rapid immobilization of nitrate by a microbial community. Leached phosphate was detected in Soil C only, and continuously increased with increasing amount of leachate. The phosphate concentration of soil solution in Soil B was much lower than in Soil C, and Soil A was below detection limit ($0.01mg\;L^{-1}$), overall similar to the order of degree of P saturation of soils. Phosphate mobility, therefore, could be largely influenced by degree of P saturation of soils but connect with apparent leaching loss only more than any threshold of P accumulation.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.31 no.6
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• pp.920-926
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• 1998

To investigate the effects of yellow loess on the microbial community after applying into C. polykrikoides as a red tide centrol method during decomposition process, we conducted this study using microcosm experiments, which consisted of sediment collected from Jinhae and Masan bay. The composition, number of bacteria and respiratory electron transport system activity (ETSA) were analyzed. The number of heterotrophic bacteria examined in the samples of both stations reached maximum value within 12 hrs with $10^7$ cells/dry g, independent with the yellow loess applied. In addition, a differenee in the variation of heterotrophic bacterial composition was not observed by adding the yellow loess, and Vibrio spp. always appeared during the culture periods, However, in day 8 culture, the sulfate reducing bacteria was $3.8\times10^7$ cells/dry g in Masan bay and $5.5\times10^6$ cells/dry g in Jinhae bay samples without yellow loess, and these were 120, 350 fold-and 160, 420 fold-increased when yellow loess was added (1 : 1, 1 : 2). The average ETSA was 6.8$\~$7.6 $\mu$g formazan $h^{-1}$ dry $g^{-1}$ independently with yellow loess in aerobic condition for both samples, but activity was decreased by addition of yellow loess in anaerobic. Thus the addition of yellow loess to marine sediment seems to have an effect to inhibit the anaerobic decomposition process and growth of sulfate reducing bacteria which lead to the bad condition of marine environments.