• BMB Reports
• /
• v.32 no.5
• /
• pp.480-485
• /
• 1999

Tyrosine phenol-lyase of thermophilic Symbiobacterium sp. SC-1, which is obligately and symbiotically dependent on thermophilic Bacillus sp. SK-1, was purified and characterized. The enzyme is composed of four identical subunits and contains approximately 1 mol of pyridoxal 5'-phosphate (PLP) per mol subunit as a cofactor. The enzyme showed absorption maxima at 330 and 420 nm, and lost this absorption profile by treatment with phenylhydrazine. The apparent dissociation constsnt, $K'_D$, for PLP was determined with the apoenzyme to be about $1.2\;{\mu}M$. The isoelectric point was 4.9. The optimal temperature and pH for the $\alpha,\beta$-elimination of L-tyrosine were found to be $80^{\circ}C$ and pH 8.0, respectively. The substrate specificity of the enzyme was very broad: L-amino acids including L-tyrosine, 3,4-dihydroxyphenyl-L-alanine (L-DOPA), L-cysteine, L-serine, S-methyl-L-cysteine, $\beta$-chloro-L-alanine, and S-(o-nitrophenyl)-L-cysteine all served as substrates. D-Tyrosine and D-serine were also decomposed into pyruvic acid and ammonia at rates of 7% and 31% relative to their corresponding L-enantiomers, respectively. D-Alanine, which was inert as a substrate in a, $\beta$-elimination, was the only D-amino acid racemized by the enzyme. The $K_m$ values for L-tyrosine, L-DOPA, S-(o-nitrophenyl)-L-cysteine, $\beta$-chloro-L-alanine, and S-methyl-L-cysteine were 0.19, 9.9, 0.36, 12, and 5.5 mM, respectively.

• Journal of Microbiology and Biotechnology
• /
• v.19 no.12
• /
• pp.1547-1556
• /
• 2009

A novel thermostable $\alpha$-glucosidase (TtGluA) from Thermoanaerobacter tengcongensis MB4 was successfully expressed in E. coli and characterized. The TtgluA gene contained 2,253 bp, which encodes 750 amino acids. The native TtGluA was a trimer with monomer molecular mass of 89 kDa shown by SDS-PAGE. The purified recombinant enzyme showed hydrolytic activity on maltooligosaccharides, p-nitrophenyl-$\alpha$-D-glucopyranide, and dextrin with an exotype cleavage manner. TtGluA showed preference for short-chain maltooligosaccharides and the highest specific activity for maltose of 3.26 units/mg. Maximal activity was observed at $60^{\circ}C$ and pH 5.5. The half-life was 2 h at $60^{\circ}C$. The enzyme showed good tolerance to urea and SDS but was inhibited by Tris. When maltose with the concentration over 50 mM was used as substrate, TtGluA was also capable of catalyzing transglycosylation to produce $\alpha$-1,4-linked maltotriose and $\alpha$-1,6-linked isomaltooligosaccharides. More importantly, TtGluA showed exclusive regiospecificity with high yield to produce $\alpha$-1,6-linked isomaltooligosaccharides when the reaction time extended to more than 10 h.

• Korean Journal of Environmental Biology
• /
• v.38 no.3
• /
• pp.433-449
• /
• 2020

Nine fish and one clam species were collected from freshwater environments in Korea, including four lakes, two streams, and the Nakdong River, to investigate the host-associated bacteria. Hundreds of bacterial strains were isolated from the samples using a cell sorter and a dilution plating method. After identification of the bacterial strains using 16S rRNA gene sequences, 42 strains with greater than 98.7% sequence similarity with validly published species were determined to be unrecorded bacterial species in Korea. These strains were phylogenetically diverse and assigned to four phyla, six classes, 17 orders, 27 families, and 32 genera. At the genus level, the unrecorded species were classified as Corynebacterium, Mycobacterium, Mycolicibacterium, Gordonia, Williamsia, Modestobacter, Brachybacterium, Sanquibacter, Arthrobacter, and Mycolicibacterium of the class Actinobacteria; Empedobacter, and Flavobacterium of the class Flavobacteriia; Fictibacillus, Psychrobacillus, Cohnella, Paenibacillus, Rummeliibacillus, Enterococcus, and Vagococcus of the class Bacilli; Aquamicrobium, Paracoccus, and Sphingomonas of the class Alphaproteobacteria; Achromobacter, Delftia, and Deefgea of the class Betaproteobacteria; and Aeromonas, Providencia, Yersinia, Marinomonas, Acinetobacter, and Pseudomonas of the class Gammaproteobacteria. The 42 unrecorded species were subjected to further taxonomic characterization using gram staining, cellular and colony morphological determination, biochemical analyses, and phylogenetic analyses. This paper provides detailed descriptions of the 42 previously unrecorded bacterial species.

• Journal of Microbiology and Biotechnology
• /
• v.9 no.4
• /
• pp.429-435
• /
• 1999

An adenosine 5'-monophosphate deaminase (AMP aminohydrolase, EC 3.5.4.6) was purified to homogeneity from the cell-free extract of Saccharomyces cerevisiae DKCTC7248. The molecular mass of subunit was estimated to be 80 kDa on SDS-PAGE, and that of the holoenzyme was shown to be 240 kDa by gel filtration. The isoelectric point of the enzyme (AMP deaminase D) was determined to be 6.2. The AMP deaminase D was specific towards AMP with an apparent $K_m$ value of 4.1 mM and a Hill coefficient, $n_H$, of 2.2. Both ATP and ADP were positive allosteric effectors of the AMP deaminase D: The apparent $K_{m}$ was decreased to 1.6 mM and 3.3 mM in the presence of 0.1 mM ATP and ADP, respectively, lowering $n_{H}$ to 1.0. Univalent cations like $K^+, Na^+ and Li^ +$ activated the enzyme but some divalent cations such as $Cu^{ 2+} and Cd^{2+}$ showed strong inhibitory effects. This enzyme displayed optimum activity at $30^{\circ}C$ and pH 7.0. In addition, it was stable up to $45^{\circ}C$ and over a wide pH range(pH 5.5-9.0). Amino acid sequences of its N-terminal region were analyzed to be ADYKMQMFADDA.

• Korean Journal of Soil Science and Fertilizer
• /
• v.46 no.3
• /
• pp.173-181
• /
• 2013

Livestock wastes are considered as major environmental pollutants because they contain high concentration of organic materials. In 2001, The Environmental Department reported that stock farmers were increasing as 5.1%/year, which resulted in a gradual increase in livestock wastes generation. The direct disposal of livestock wastes create several environmental problems. Thus, several countries banned the disposal of livestock wastes in environment including aquatic systems. Recently, aeration-based liquid fertilization was considered as potential way for the disposal of livestock wastes. In this study, next generation sequencing (NGS) analysis was used to understand the microbial community changes during liquid fertilization of livestock wastes. Microbial community was compared with liquid fertilizer physicochemical analysis such as $BOD_5$, $COD_{Mn}$ pH, N (Nitrogen), P (Phosphorus), K (Potassium) etc. The physicochemical parameters and bacterial community results pave the way for producing effective livestock-based fertilizer. By comparing the physical characteristics of the manure with microbial community changes, it is possible to optimize the conditions for producing effective fertilizer.

• Journal of Veterinary Science
• /
• v.22 no.3
• /
• pp.37.1-37.14
• /
• 2021

Background: Ticks are one of the most common external parasites in dogs, and are associated with the transmission of a number of major zoonoses, which result in serious harm to human health and even death. Also, the increasing number of pet dogs and pet owners in China has caused concern regarding human tick-borne illnesses. Accordingly, studies are needed to gain a complete understanding of the bacterial composition and diversity of the ticks that parasitize dogs. Objectives: To date, there have been relatively few reports on the analysis of the bacterial community structure and diversity in ticks that parasitize dogs. The objective of this study was to investigate the microbial composition and diversity of parasitic ticks of dogs, and assessed the effect of tick sex and geographical region on the bacterial composition in two tick genera collected from dogs in China. Methods: A total of 178 whole ticks were subjected to a 16S ribosomal RNA (rRNA) next generation sequencing analysis. The Illumina MiSeq platform targeting the V3-V4 region of the 16S rRNA gene was used to characterize the bacterial communities of the collected ticks. Sequence analysis and taxonomic assignment were performed using QIIME 2 and the GreenGene database, respectively. After clustering the sequences into taxonomic units, the sequences were quality-filtered and rarefied. Results: After pooling 24 tick samples, we identified a total of 2,081 operational taxonomic units, which were assigned to 23 phyla and 328 genera, revealing a diverse bacterial community profile. The high, moderate and low prevalent taxa include 46, 101, and 182 genera, respectively. Among them, dominant taxa include environmental bacterial genera, such as Psychrobacter and Burkholderia. Additionally, some known tick-associated endosymbionts were also detected, including Coxiella, Rickettsia, and Ricketssiella. Also, the potentially pathogenic genera Staphylococcus and Pseudomonas were detected in the tick pools. Moreover, our preliminary study found that the differences in microbial communities are more dependent on the sampling location than tick sex in the tick specimens collected from dogs. Conclusions: The findings of this study support the need for future research on the microbial population present in ticks collected from dogs in China.

• Microbiology and Biotechnology Letters
• /
• v.47 no.4
• /
• pp.621-629
• /
• 2019

In this study we attempted to screen bacteria and fungi that generate electricity while treating wastewater using optimized double-chamber microbial fuel cell (MFC) system parameters. Optimization was carried out for five best exoelectrogenic isolates (two bacteria and three fungi) at pH values of 6.0, 7.5, 8.5, and 9.5, and temperatures of 30, 35, 40, and 45℃; the generated power densities were measured using a digital multimeter (DT9205A). The isolates were identified using molecular characterization, followed by the phylogenetic analysis of isolates with known exoelectrogenic microorganisms. The bacterium, Proteus species, N6 (KX548358.1) and fungus, Candida parapsilosis, S10 (KX548360) produced the highest power densities of 1.59 and 1.55 W/m² (at a pH of 8.5 and temperatures of 35 and 40℃) within 24 h, respectively. Other fungi-Clavispora lusitaniae, S9 (KX548359.1) at 40℃, Clavispora lusitaniae, S14 (KX548361.1) at 35℃-and bacterium-Providencia species, N4 (KX548357.1) at 40℃-produced power densities of 1.51, 1.46, and 1.44 W/m², respectively within 24 h. The MFCs achieved higher power densities at a pH of 8.5, temperature of 40℃ within 24 h. The bacterial isolates have a close evolutionary relationship with other known exoelectrogenic microorganisms. These findings helped us determine the optimal pH, temperature, evolutionary relationship, and exoelectrogenic fungal species other than bacteria that enhance MFC performance.

• Journal of Microbiology and Biotechnology
• /
• v.24 no.11
• /
• pp.1484-1489
• /
• 2014

A novel esterase gene, est01, was successfully unearthed from a biogas digester microbiota metagenomic library. The 1,194 bp est01 gene encodes a protein of 44,804 Da (designated Est01). The amino acid sequence of Est01 shows only moderate (33%) identity to a lipase/esterase. Phylogenetic analysis and biochemical characterization confirmed that Est01 is a new member of family VIII esterases. The purified Est01 from recombinant Escherichia coli BL21 (DE3) showed high hydrolytic activity against short-chain fatty acid esters, suggesting that it is a typical carboxylesterase rather than a lipase. Furthermore, the Est01 was even active at $10^{\circ}C$ (43% activity remained), with the optimal temperature at $20^{\circ}C$, and had a broad pH range from 5.0 to 10.0, with the optimal pH of 8.0. These properties suggest that Est01 is a cold-adaptive esterase and could have good potential for low-temperature hydrolysis application.

• Animal Bioscience
• /
• v.34 no.12
• /
• pp.1921-1929
• /
• 2021

Objective: The intestinal microbiota enhances nutrient absorption in the host and thus promotes heath. Qinghai semi-fine wool sheep is an important livestock raised in the Qinghai-Tibetan Plateau; however, little is known about the bacterial microbiota of its intestinal tract. The aim of this study was to detect the microbial characterization in the intestinal tract of the Qinghai semi-fine wool sheep. Methods: The bacterial profiles of the six different intestinal segments (duodenum, jejunum, ileum, cecum, colon and rectum) of Qinghai semi-fine wool sheep were studied using 16S rRNA V3-V4 hypervariable amplicon sequencing. Results: A total of 2,623,323 effective sequences were obtained, and 441 OTUs shared all six intestinal segments. The bacterial diversity was significantly different among the different intestinal segments, and the large intestine exhibited higher bacterial diversity than the small intestine. Firmicutes, Bacteroidetes, and Patescibacteria were the dominant phyla in these bacterial communities. Additionally, at the genus level, Prevotella_1, Candidatus_Saccharimonas, and Ruminococcaceae_UCG-005 were the most predominant genus in duodenal segment, jejunal and ileal segments, and cecal, colonic, and rectal segments, respectively. We predicted that the microbial functions and the relative abundance of the genes involved in carbohydrate metabolism were overrepresented in the intestinal segments of Qinghai semi-fine wool sheep. Conclusion: The bacterial communities and functions differed among different intestinal segments. Our study is the first to provide insights into the composition and biological functions of the intestinal microbiota of Qinghai semi-fine wool sheep. Our results also provide useful information for the nutritional regulation and production development in Qinghai semi-fine wool sheep.

• Journal of Ecology and Environment
• /
• v.46 no.4
• /
• pp.282-291
• /
• 2022

Background: The Arctic permafrost stores enormous amount of carbon (C), about one third of global C stocks. However, drastically increasing temperature in the Arctic makes the stable frozen C stock vulnerable to microbial decomposition. The released carbon dioxide from permafrost can cause accelerating C feedback to the atmosphere. Soil organic matter (SOM) composition would be the basic information to project the trajectory of C under rapidly changing climate. However, not many studies on SOM characterization have been done compared to quantification of SOM stocks. Thus, the purpose of our study is to determine soil properties and molecular compositions of SOM in four different Arctic regions. We collected soils in different soil layers from 1) Cambridge Bay, Canada, 2) Council, Alaska, USA, 3) Svalbard, Norway, and 4) Zackenberg, Greenland. The basic soil properties were measured, and the molecular composition of SOM was analyzed through pyrolysis-gas chromatography/mass spectrometry (py-GC/MS). Results: The Oi layer of soil in Council, Alaska showed the lowest soil pH and the highest electrical conductivity (EC) and SOM content. All soils in each site showed increasing pH and decreasing SOC and EC values with soil depth. Since the Council site was moist acidic tundra compared to other three dry tundra sites, soil properties were distinct from the others: high SOM and EC, and low pH. Through the py-GC/MS analysis, a total of 117 pyrolysis products were detected from 32 soil samples of four different Arctic soils. The first two-axis of the PCA explained 38% of sample variation. While short- and mid-hydrocarbons were associated with mineral layers, lignins and polysaccharides were linked to organic layers of Alaska and Cambridge Bay soil. Conclusions: We conclude that the py-GC/MS results separated soil samples mainly based on the origin of SOM (plants- or microbially-derived). This molecular characteristics of SOM can play a role of controlling SOM degradation to warming. Thus, it should be further investigated how the SOM molecular characteristics have impacts on SOM dynamics through additional laboratory incubation studies and microbial decomposition measurements in the field.