• ALGAE
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• v.21 no.2
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• pp.235-243
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• 2006

Benthic sediment samples ranging from poorly aggregated sand to complex, stratified mats were collected from six hypersaline ponds from March and July 1995 in the British Virgin Islands. Assemblages were analyzed with respect to species composition and abundance within visibly distinct layers in each mat sample. In individual ponds there was no apparent association between changing depth and the development of the benthic mats. Some species were present in all samples (e.g. Oscillatoria sp.) while others were restricted to single sites (e.g. Johannesbaptistia pellucida). Primary species included Microcoleus chthonoplastes, Phormidium spp., Coccochloris stagnina, and purple sulfur bacteria. Quantitative analysis of community structure included cluster and principal component analysis. Samples from individual ponds were often clustered; however, this was subject to seasonal variation. Mats collected in March were generally thicker and contained more layers than those in July. Variation among sites was not explained by the measured variation in environmental factors such as average pond salinity, depth, and oxygen concentration (mg/L). This study provides a detailed analysis of mat communities in hypersaline ponds and compares them with similar mat communities from other areas.

• Korean Journal of Organic Agriculture
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• v.19 no.spc
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• pp.149-152
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• 2011

To improve the soil condition for no-tillage organic pepper cultivation, four different green manure crops were cultivated. Fertilizer supply was depended on the biomass of the cultivated green manure crops, nitrogen supplies were 314kg in Vicia villosa and 341kg $ha^{-1}$ in Vicia angustifolia. In the microbial community analyzed by phospholipid fatty acid (PLFA) method, soil microbe populations were different among the green manure crops and fungi group was increased at Vicia angustifloia and Vicia villosa. The biological ratio indexes of fatty acids in the soils, the ratio of Gram-negative to Gram-positive bacterial PLFA and Ratio of aerobes to anaerobes were high at Vicia hirsute and Vicia tetrasperma suggesting the enrich of the aerobic conditions. The ratio of saturated to unsaturated fatty acids increased at Vicia angustifloia and Vicia villosa suggesting anaerobic conditions. Abundant biomass and uncomposted organic matter, the ratio of fungi to bacteria was increased at Vicia angustifloia and Vicia villosa.

• Journal of Ginseng Research
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• v.40 no.2
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• pp.97-104
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• 2016

Background: Rhizobacteria play an important role in plant defense and could be promising sources of biocontrol agents. This study aimed to screen antagonistic bacteria and develop a biocontrol system for root rot complex of Panax notoginseng. Methods: Pure-culture methods were used to isolate bacteria from the rhizosphere soil of notoginseng plants. The identification of isolates was based on the analysis of 16S ribosomal RNA (rRNA) sequences. Results: A total of 279 bacteria were obtained from rhizosphere soils of healthy and root-rot notoginseng plants, and uncultivated soil. Among all the isolates, 88 showed antagonistic activity to at least one of three phytopathogenic fungi, Fusarium oxysporum, Fusarium solani, and Phoma herbarum mainly causing root rot disease of P. notoginseng. Based on the 16S rRNA sequencing, the antagonistic bacteria were characterized into four clusters, Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetesi. The genus Bacillus was the most frequently isolated, and Bacillus siamensis (Hs02), Bacillus atrophaeus (Hs09) showed strong antagonistic activity to the three pathogens. The distribution pattern differed in soil types, genera Achromobacter, Acidovorax, Brevibacterium, Brevundimonas, Flavimonas, and Streptomyces were only found in rhizosphere of healthy plants, while Delftia, Leclercia, Brevibacillus, Microbacterium, Pantoea, Rhizobium, and Stenotrophomonas only exist in soil of diseased plant, and Acinetobacter only exist in uncultivated soil. Conclusion: The results suggest that diverse bacteria exist in the P. notoginseng rhizosphere soil, with differences in community in the same field, and antagonistic isolates may be good potential biological control agent for the notoginseng root-rot diseases caused by F. oxysporum, Fusarium solani, and Panax herbarum.

• Food Science of Animal Resources
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• v.26 no.3
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• pp.402-409
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• 2006

Although microorganisms are, in fact, the most diverse and abundant type of organism on Earth, the ecological functions of microbial populations remains poorly understood. A variety of bacteria including marine Vibrios encounter numerous ecological challenges, such as UV light, predation, competition, and seasonal variations in seawater including pH, salinity, nutrient levels, temperature and so forth. In order to survive and proliferate under variable conditions, they have to develop elaborate means of communication to meet the challenges to which they are exposed. In bacteria, a range of biological functions have recently been found to be regulated by a population density-dependent cell-cell signaling mechanism known as quorum-sensing (QS). In other words, bacterial cells sense population density by monitoring the presence of self-produced extracellular autoinducers (AI). N-acylhomoserine lactone (AHL)-dependent quorum-sensing was first discovered in two luminescent marine bacteria, Vibrio fischeri and Vibrio harveyi. The LuxI/R system of V. fischeriis the paradigm of Gram-negative quorum-sensing systems. At high population density, the accumulated signalstrigger the expression of target genes and thereby initiate a new set of biological activities. Several QS systems have been identified so far. Among them, an AHL-dependent QS system has been found to control biofilm formation in several bacterial species, including Pseudomonas aeruginosa, Aeromonas hydrophila, Burkholderia cepacia, and Serratia liquefaciens. Bacterial biofilm is a structured community of bacterial cells enclosed in a self-produced polymeric matrix that adheres to an inert or living surface. Extracellular signal molecules have been implicated in biofilm formation. Agrobacterium tumefaciens strain NT1(traR, tra::lacZ749) and Chromobacterium violaceum strain CV026 are used as biosensors to detect AHL signals. Quorum sensing in lactic acid bacteria involves peptides that are directly sensed by membrane-located histidine kinases, after which the signal is transmitted to an intracellular regulator. In the nisin autoregulation process in Lactococcus lactis, the NisK protein acts as the sensor for nisin, and NisR protein as the response regulator activatingthe transcription of target genes. For control over growth and survival in bacterial communities, various strategies need to be developed by which receptors of the signal molecules are interfered with or the synthesis and release of the molecules is controlled. However, much is still unknown about the metabolic processes involved in such signal transduction and whether or not various foods and food ingredients may affect communication between spoilage or pathogenic bacteria. In five to ten years, we will be able to discover new signal molecules, some of which may have applications in food preservation to inhibit the growth of pathogens on foods.

• Journal of Microbiology and Biotechnology
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• v.26 no.11
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• pp.1951-1964
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• 2016

1,4-Dioxane-degrading bacterial consortia were enriched from forest soil (FS) and activated sludge (AS) using a defined medium containing 1,4-dioxane as the sole carbon source. These two enrichments cultures appeared to have inducible tetrahydrofuran/dioxane and propane degradation enzymes. According to qPCR results on the 16S rRNA and soluble di-iron monooxygenase genes, the relative abundances of 1,4-dioxane-degrading bacteria to total bacteria in FS and AS were 29.4% and 57.8%, respectively. For FS, the cell growth yields (Y), maximum specific degradation rate ($V_{max}$), and half-saturation concentration ($K_m$) were 0.58 mg-protein/mg-dioxane, $0.037mg-dioxane/mg-protein{\cdot}h$, and 93.9 mg/l, respectively. For AS, Y, $V_{max}$, and $K_m$ were 0.34 mg-protein/mg-dioxane, $0.078mg-dioxane/mg-protein{\cdot}h$, and 181.3 mg/l, respectively. These kinetics data of FS and AS were similar to previously reported values. Based on bacterial community analysis on 16S rRNA gene sequences of the two enrichment cultures, the FS consortium was identified to contain 38.3% of Mycobacterium and 10.6% of Afipia, similar to previously reported literature. Meanwhile, 49.5% of the AS consortium belonged to the candidate division TM7, which has never been reported to be involved in 1,4-dioxane biodegradation. However, recent studies suggested that TM7 bacteria were associated with degradation of non-biodegradable and hazardous materials. Therefore, our results showed that previously unknown 1,4-dioxane-degrading bacteria might play an important role in enriched AS. Although the metabolic capability and ecophysiological significance of the predominant TM7 bacteria in AS enrichment culture remain unclear, our data reveal hidden characteristics of the TM7 phylum and provide a perspective for studying this previously uncultured phylotype.

• Environmental Engineering Research
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• v.13 no.3
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• pp.125-130
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• 2008

Free ammonia ($NH_3$-N) inhibition of nitrite-oxidizing bacteria (NOB) has been widely studied for partial nitrification (or nitrite accumulation) and denitrification via nitrite ($NO_2^-$-N) as a low-cost treatment of ammonium containing wastewater. The literature on $NH_3$-N inhibition of NOB, however, shows disagreement about the threshold $NH_3$-N concentration and its degree of inhibition. In order to clarify the confusion, a simple and cheap respirometric method was devised to investigate the effect of free ammonia inhibition of NOB. Sludge samples from an autotrophic nitrifying reactor were exposed to various $NH_3$-N concentrations to measure the maximum specific nitrite oxidation rate ($\hat{K}_{NO}$) using a respirometer. NOB biomass was estimated from the yield values in the literature. Free ammonia inhibition of nitrite oxidizing bacteria was reversible and the specific nitrite oxidation rate ($K_{NO}$) decreased from 0.141 to 0.116, 0.100, 0.097 and 0.081 mg $NO_2^-$-N/mg NOB h, respectively, as the $NH_3$-N concentration increased from 0.0 to 1.0, 4.1, 9.7 and 22.9 mg/L. A nonlinear regression based on the noncompetitive inhibition mode gave an estimate of the Inhibition concentration ($K_I$) of free ammonia to be 21.3 mg $NH_3$-N/L. Previous studies gave $\hat{K}_{NO}$ of Nitrobacter and Nitrospira as 0.120 and 0.032 mg/mg VSS h. The free ammonia concentration which inhibits Nitrobacter was $30{\sim}50\;mg$ $NH_3$-N/L and Nitrospira was inhibited at $0.04{\sim}0.08\;mg$ $NH_3$-N/L. The results support the fact that Nitrobacter is the dominant NOB in the reactor. The variations in the reported values of free ammonia inhibition may be due to the different species of nitrite oxidizers present in the reactors. The respirometric method provides rapid and reliable analysis of the behavior and community of the nitrite oxidizing bacteria.

• 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 Mushroom
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• v.22 no.1
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• pp.27-30
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• 2024

As a member of ectomycorrhizal fungi, Tricholoma matsutake has a symbiotic relationship with its host, Pinus densiflora. To cultivate T. matsutake artificially, the co-cultivation of T. matsutake mycelia and bacteria from shiro was introduced. In this study, bacteria were isolated from soil samples in Bonghwa-gun, and seven bacterial isolates (B22_7_B05, B22_7_B06, B22_7_B07, B22_7_B08, B22_7_B10, B22_7_B13, and B22_7_B14) promoted the growth of T. matsutake mycelia (147.48, 232.11, 266.72, 211.43, 175.17, 154.62, and 177.92%, respectively). Sequencing of the 16S rRNA region of the isolated bacteria was performed. B22_7_B05 and B22_7_B10 were identified as Bacillus toyonensis, B22_7_B06 and B22_7_B08 as Paenibacillus taichungensis, B22_7_B07 and B22_7_B14 as P. gorilla, and B22_7_B13 as P. odorifer. These bacterial isolates were associated with the shiro community and are expected to contribute to the cultivation of T. matsutake.

• Journal of Korean Society of Forest Science
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• v.101 no.3
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• pp.501-508
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• 2012

This study was carried out to compare species diversity of soil bacteria from Baekdudaegan mountain forests (Bonghwa-gun, Mungyeong-si and Sangju-si) in Gyeongsangbuk-do and to analyze the effects of soil environments on diversity and population of soil bacteria. Soil bacteria were isolated from soil samples by streak plate method, and identified by DNA extaction and 16S rDNA sequence analyses. The population of soil bacteria from the soil samples of Bonghwa-gun was the highest with $5.1{\times}10^5cfu/g$, and followed by those from Mungyeong-si and Sangju-si with $1.9{\times}10^5cfu/g$ and $1.1{\times}10^5cfu/g$, respectively. The population of soil bacteria from surface layer soil was the highest, and then gradually decreased according to soil depth. The increase in population of soil bacteria from soil samples of different sites was correlated with the increase of the altitude of soil sampling site, depth of A horizon, liquid phase among three phases of soil, water content and bulk density of soil. Two hundreds and sixty eight bacterial colonies from Bonghwa-gun were classified into 10 species, 8 genera. One hundred and thirty four bacterial colonies from Mungyeong-si were classified into 15 species, 9 genera. Forty four bacterial colonies from Sangju-si were classified into 5 species, 2 genera. The dominant species (occupancy rate) from Bonghwa-gun and Mungyeong-si were Bacillus weihenstephanensis (36% and 40%, respectively), and Sangju-si was Bacillus cereus (39%). The relationships between soil environment and community structure of soil bacteria were analyzed statistically by using ecological indices. The diversity, evenness and dominance indices of soil bacteria were 6.30, 2.04 and 0.59 in Bonghwa-gun, 9.09, 2.94 and 0.51 in Mungyeong-si, and 4.55, 2.34 and 0.71 in Sangju-si, respectively. The diversity and evenness indices were increased by the increase of water content, drainage condition and gravel content of soil, while the dominance index was decreased.

• Journal of Korean Society of Environmental Engineers
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• v.30 no.9
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• pp.939-947
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• 2008

PCR-DGGE method was applied to analyze changes of microbial community in simultaneous nitrification and denitrification (SND) bioreactor with various DO concentrations. In the analysis of eubacterial community, band profiles of DGGE were similar with 2 or 1 mg/L DO concentrations in the reactor. Experimental results led to 16 different bacteria being identified, including 5 dominant strains(3 strains of Uncultured Bacterium, 1 strains of Bacillus, 1 strains of Uncultured Bacteroidetes). DGGE results at 0.5 mg/L DO concentration led to 12 strains being identified, including 7 dominant strains(5 strains of Uncultured Bacterium, 2 strains of Zoogloea sp.). DGGE results at 0.1 mg/L DO concentration led to 11 strains being identified, including 3 dominant strains(1 strains of Uncultured Bacterium, 2 strains of Zoogloea sp.). In DGGE band profiles of $\beta$-AOB($\beta$-Ammonia Oxidizing Bacteria), only one band was observed. This band had 97% similarity with Nitrosomonas sp. done DNB Y20. This band was clearly observed at the 2, 1 and 0.5 mg/L DO concentrations, while the brightness of the band at 0.1 mg/L DO concentration was mostly dimmed. In DGGE band profiles of denitrification process, 5 bands(3 strains of Uncultured organism containing nirS, 2 strains of Uncultured organism containing nirK) were observed. Among those bands, the brightness of one band was gradually increased at the lower DO concentrations. This band has 86% identity with Uncultured organism clone eS1 cd1 nirS gene, partial cds. Based on this result, it could be concluded that Uncultured organism clone eS1 cd1 nirS gene, partial cds is a predominant microorganism in the denitrification process.