• Title/Summary/Keyword: sediment characterization

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Identification and Characterization of an Antifungal Protein, AfAFPR9, Produced by Marine-Derived Aspergillus fumigatus R9

  • Rao, Qi;Guo, Wenbin;Chen, Xinhua
    • Journal of Microbiology and Biotechnology
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    • v.25 no.5
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    • pp.620-628
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    • 2015
  • A fungal strain, R9, was isolated from the South Atlantic sediment sample and identified as Aspergillus fumigatus. An antifungal protein, AfAFPR9, was purified from the culture supernatant of Aspergillus fumigatus R9. AfAFPR9 was identified to be restrictocin, which is a member of the ribosome-inactivating proteins (RIPs), by MALDI-TOF-TOF-MS. AfAFPR9 displayed antifungal activity against plant pathogenic Fusarium oxysporum, Alternaria longipes, Colletotrichum gloeosporioides, Paecilomyces variotii, and Trichoderma viride at minimum inhibitory concentrations of 0.6, 0.6, 1.2, 1.2, and 2.4 μg/disc, respectively. Moreover, AfAFPR9 exhibited a certain extent of thermostability, and metal ion and denaturant tolerance. The iodoacetamide assay showed that the disulfide bridge in AfAFPR9 was indispensable for its antifungal action. The cDNA encoding for AfAFPR9 was cloned from A. fumigatus R9 by RT-PCR and heterologously expressed in E. coli. The recombinant AfAFPR9 protein exhibited obvious antifungal activity against C. gloeosporioides, T. viride, and A. longipes. These results reveal the antifungal properties of a RIP member (AfAFPR9) from marine-derived Aspergillus fumigatus and indicated its potential application in controlling plant pathogenic fungi.

Characterization of Biological Degradation Cypermethrin by Bacillus amyloliquefaciens AP01 (Bacillus amyloliiquefaciens AP01 균주에 의한 사이퍼메트린의 생물학적 분해 특성)

  • Lee, Yong-Suk;Lee, Je-Hoon;Hwang, Eun-Jung;Lee, Hyo-Jung;Kim, Jae-Hoon;Heo, Jae Bok;Choi, Yong-Lark
    • Journal of Applied Biological Chemistry
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    • v.59 no.1
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    • pp.9-12
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    • 2016
  • Strain AP01 was isolated for the biological cypermethrin degradation from soil and sediment in Busan. This strain was identified on the basis of phylogenetic analysis of the 16s rDNA sequence and assigned as Bacillus amyloliquefaciens AP01. AP01 could degrade about 45% of cypermethrin in the mineral medium at $30^{\circ}C$ and 180 rpm for 5 days. Furthermore when 2% glucose was added in the medium, the degradation rate of cypermethrin by strain AP01 was increased upto about 60%. Therefore, AP01 may serve as a promising strain in the bioremediation of soil polluted with cypermethrin.

Distributive Characterization of Estrogenic Activity in Sediments from Gwangyang Bay, Korea (광양만 퇴적물에서의 에스트로겐 활성분포 특성)

  • Han, Sang-Kuk;Park, Ji-Young
    • Journal of the Korean Society for Marine Environment & Energy
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    • v.10 no.2
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    • pp.86-92
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    • 2007
  • In this study, we tried to quantitatively study the distribution of estrogenic activity in sediment from Gwangyang Bay by E-screen assay. Besides, we compared the estrogenic activity and the concentration of chemical pollutants. The highest estrogenic activity was recorded at the stations(GY6 and GY8) close to industrial complex and the river mouth of Seomjin. These results obtained from the E-screen assay similar to those of simultaneous analytical detection of 310 chemicals. In particular, GY6 and GY8 sites are confirmed as the full agonist sites because of their RPE values were over 90% having strong estrogenic effect. Also, their EEQ(Estradiol Equivalency Quantity) values are 35.6 ng/g and 14.6 ng/g, low than that of other sites, and these results suggests that have relatively high estrogenic efficiency in Gwangyang Bay. From these results, we can estimate that the stations close to industrial complex and the river mouth of Seomjin are major sources of endocrine disrupter in Gwangyang Bay. On the other hand, when we tried to compare the endocrine disrupter activity and $COD_{Mn}$ value, that is not correlated.

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Isolation of a Novel Freshwater Agarolytic Cellvibrio sp. KY-YJ-3 and Characterization of Its Extracellular ${\beta}$-Agarase

  • Rhee, Young-Joon;Han, Cho-Rong;Kim, Won-Chan;Jun, Do-Youn;Rhee, In-Ku;Kim, Young-Ho
    • Journal of Microbiology and Biotechnology
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    • v.20 no.10
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    • pp.1378-1385
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    • 2010
  • A novel agarolytic bacterium, KY-YJ-3, producing extracellular agarase, was isolated from the freshwater sediment of the Sincheon River in Daegu, Korea. On the basis of Gram-staining data, morphology, and phylogenetic analysis of the 16S rDNA sequence, the isolate was identified as Cellvibrio sp. By ammonium sulfate precipitation followed by Toyopearl QAE-550C, Toyopearl HW-55F, and MonoQ column chromatographies, the extracellular agarase in the culture fluid could be purified 120.2-fold with a yield of 8.1%. The specific activity of the purified agarase was 84.2 U/mg. The molecular mass of the purified agarase was 70 kDa as determined by dodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The optimal temperature and pH of the purified agarase were $35^{\circ}C$ and pH 7.0, respectively. The purified agarase failed to hydrolyze the other polysaccharide substrates, including carboxymethyl-cellulose, dextran, soluble starch, pectin, and polygalacturonic acid. Kinetic analysis of the agarose hydrolysis catalyzed by the purified agarase using thin-layer chromatography showed that the main products were neoagarobiose, neoagarotetraose, and neoagarohexaose. These results demonstrated that the newly isolated freshwater agarolytic bacterium KY-YJ-3 was a Cellvibrio sp., and could produce an extracellular ${\beta}$-agarase, which hydrolyzed agarose to yield neoagarobiose, neoagarotetraose, and neoagarohexaose as the main products.

Isolation and characterization of acid-resistanct and halophilic bacteria using cultivation technique in Jeju island (배양기법을 활용한 제주도내 내산 및 호염성 미생물의 분리 및 특성 분석)

  • Han, Bit;Kim, Minji;Ryu, Dajung;Lee, Ki-Eun;Lee, Byoung-Hee;Lee, Eun-Young;Park, Soo-Je
    • Korean Journal of Microbiology
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    • v.55 no.3
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    • pp.248-257
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    • 2019
  • In this study, we isolated about 70 bacterial strains from terrestrial and marine environments in Jeju island, and finally, total 21 strains were obtained based on the 16S ribosomal RNA gene sequence analysis. These isolated strains were classified into 16 genera of 5 classes and were identified as an unrecorded species in the Republic of Korea. As a result of the substrate utilization and capability for polymer degradation, the physiological phenotypes for acid resistance and halophilic bacteria were observed to be distinct from each other, except for some acid resistance strains. This study might provide basic information on utilization for indigenous microorganisms.

Advanced Analytical Techniques for Dissolved Organic Matter and Their Applications in Natural and Engineered Water Treatment Systems (최근 용존 유기물 분석 기법 및 자연환경과 수 처리 시스템 내 활용방안)

  • Lee, Yun Kyung;Hur, Jin
    • Journal of Korean Society on Water Environment
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    • v.38 no.1
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    • pp.31-42
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    • 2022
  • Dissolved organic matter (DOM), which changes according to various factors, is ubiquitously present from natural environments to engineered treatment systems. Only limited information is available regarding the environmental functions of DOM after bulk analyses are only applied for characterization. In this paper, latest DOM analytical techniques are briefly introduced, which include fluorescence excitation-emission matrix with parallel factor analysis (EEM-PARAFAC), size-exclusion chromatography with an organic carbon detector (SEC-OCD), carbon/nitrogen stable-isotope ratio, and Fourier transform-ion cyclotron resonance-mass spectroscopy (FT-ICR-MS). Recent examples of using advanced analyses to interpret the phenomena associated with DOM occurring in natural and engineered systems are presented here. Through EEM-PARAFAC, different components like protein-like, fulvic-like, and humic-like can be identified and tracked individually through the investigated systems. SEC-OCD allows researchers to quantify different size fractions. FT-ICR-MS provides thousands of molecular formulas present in bulk DOM samples. Lastly, carbon/nitrogen stable-isotope ratio offers reasonable tools for tracking the sources in environments. We also discuss the advantages and weakness of the above-mentioned characterizing tools. Specifically, they focus on single environmental factors (different sourced-DOM and interaction of sediment-pore water) or simple changes after individual treatment processes. Through collaboration with the advanced techniques later, they help the researchers to better understand environmental behaviors in aquatic systems and serve as essential tools for addressing various pending problems associated with DOM.

Biochemical Characterization of a Novel Thermostable Esterase from the Metagenome of Dokdo Islets Marine Sediment (독도 심해토 메타게놈 유래 신규 내열성 에스테라아제의 생화학적 특성규명)

  • Lee, Chang-Muk;Seo, Sohyeon;Kim, Su-Yeon;Song, Jaeeun;Sim, Joon-Soo;Hahn, Bum-Soo;Kim, Dong-Hern;Yoon, Sang-Hong
    • Microbiology and Biotechnology Letters
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    • v.45 no.1
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    • pp.63-70
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    • 2017
  • A functional screen of 60,672 fosmid metagenomic clones amplified from marine sediment obtained from the Dokdo islets in Korea identified the gene EstES1, whose product, EstES1, displayed lipolytic properties on tributyrin-supplemented media. EstES1 is a 576 amino acid protein with a predicted molecular weight of 59.4 kDa including 37 N-terminal leader amino acids. EstES1 exhibited the highest sequence similarity (44%) to a carboxylesterase found in Haliangium ochraceum DSM14365. Phylogenetic analysis indicated that EstES1 belongs to a currently uncharacterized family of lipases. Within the conserved domain, EstES1 retains the catalytic triad that consists of the consensus penta-peptide motif, GESAG. EstES1 demonstrated a broad substrate specificity toward the long acyl group of ethyl esters (C2-C12), and its optimal activity was recorded toward p-Nitrophenyl butyrate (C4) at pH 9.0 and $40^{\circ}C$ (specific activity of 255.4 U/mg). The enzyme remained stable in the ranges of $60-65^{\circ}C$ and pH 9.0-10.5 and in the presence of methanol, ethanol, isopropanol, and dimethyl sulfoxide. Therefore, EstES1 has potential for use in industrial applications involving high temperature, organic solvents, and/or alkaline conditions.

Initial Risk Assessment of Acetanilide with Respect to Ecological Integrity (아세트아닐리드의 초기 환경위해성 평가)

  • Lee, Su-Rae;Park, Seon-Ju;Lee, Mi-Kyung;Nam, U-Kyung;Chung, Sun-Hwa;Seog, Geum-Su;Park, Kwang-Sik;Kim, Kyun;Kim, Yong-Hwa
    • Environmental Analysis Health and Toxicology
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    • v.15 no.1_2
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    • pp.19-29
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    • 2000
  • Acetanilide may be released into the environment through air and wastewater from its production and use sites as an intermediate in the synthesis of pharmaceuticals and dyes. Acetanilide is biodegraded rapidly under aerobic conditions and decomposed by indirect photolysis in the presence of OH radicals. An estimated bioconcentration factor of 4.5 suggests that bioaccumulation in aquatic organisms is low. Ecotoxicological data on acetanilide exist on acute toxicity to fishes of 4 species only. According to the EUSES system, the lowest PNEC (Predicted no effect concentration) in fishes is 0.01 mg/1 and PEC (Predicted environmental concentration) for surface water on a regional scale is 9.1$\times$10$\^$-5/mg/l as the worst case. RCR (Risk characterization ratio) of acetanilide for surface water on a regional scale was estimated as 9.1$\times$10-3, which is safe enough for fishes, RCR on a local basis slightly exceeds the value 1 in water and sediment; that is, 1.3 and 1.6, respectively, which suggests the existence of ecotoxicological risk at the vicinity of the manufacturing site. For the refinement of environmental risk assessment on acetanilide, more data should be collected regarding prolonged fish toxicity, acute toxicity toward daphnia and algae. It is, therefore, recommended that acetanilide should be a candidate for further work to supplement the lacking data until it is proved to be safe in the ecotoxicological aspects.

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Isolation of marine algicidal bacteria from surface seawater and sediment samples associated with harmful algal blooms in Korea (유해조류번성 주변의 해수와 침전물에서 살조균의 분리)

  • Kristyanto, Sylvia;Kim, Jaisoo
    • Korean Journal of Microbiology
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    • v.52 no.1
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    • pp.40-48
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    • 2016
  • This study mainly focused on isolation of marine algicidal bacteria associated with phytoplankton blooms and characterization of algicidal activity against harmful algae. Harmful algal blooms (HABs) found naturally in surface waters have caused many environmental problems worldwide. In this study, forty bacterial strains that have capability of inhibiting harmful algal growth were isolated from Masan Bay, Jinhae Bay, Dol Island, Jangmok Bay, and the Tongyeong Sea, Republic of Korea. The bacteria were screened furthermore for the characteristics on algicidal activities against Cochlodinium polykrikoides, Chattonella marina, Skeletonema costatum, Heterosigma akashiwo, Heterocapsa triquetra, Prorocentrum minimum, and Scrippsiella trochoidea. As a result, the algicidal bacteria that were screened from double over layer agar and microscopic counts tests belonged to genera Pseudomonas, Vibrio, Bacillus, Pseudoalteromonas, Ruegeria, Joostella, Marinomonas, Stakelama, Porphyrobacter, and Albirhodobacter. One of the most important HAB species is Co. polykrikoides and the strongest algicidal activity against the dinoflagellate was 94.00% after 6 h treatment with 10% bacterial culture filtrate. In this study, Marinomonas sp. M Jin 1-8, Stakelama sp. ZB Yeonmyeong 1-11 & 1-13, Porphyrobacter sp. M Yeonmyeong 2-22, and Albirhodobacter sp. 6-R Jin 6-1 were found to be as new genera of bacteria having anti-algal activity. These results suggest that these bacteria might play an important role in controlling phytoplankton blooms.

Taxonomical Characterization and Antimicrobial Activity of Red Pigment-Producing Marine Bacterium Strain JE-34 (적색색소를 생산하는 해양미생물 JE-34 균주의 분류학적 특성 및 항균활성)

  • Kim, Ju-Sang;Kim, Man-Chul;Harikrishnan, Ramasamy;Han, Yong-Jae;Heo, Moon-Soo
    • Korean Journal of Microbiology
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    • v.45 no.4
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    • pp.368-376
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    • 2009
  • A red pigment-producing bacterial strain was isolated from sediment sample of the East China Sea. The isolate was identified by analysis based on 16S rDNA sequence and morphological, physiological properties, biochemical characteristics and fatty acid composition. Phylogenetic analysis based on 16S rDNA sequence showed that isolate represent a phyletic lineage within the genus Zooshikella, and this strain was most closely related to Zooshikella ganghwensis KCTC $12044^T$ (AY130994) (99.79%). The strain was Gram-negative, aerobic and required NaCl at 0.5~8.0% for growth. The predominant cellular fatty acids were saturated and monounsaturated straight-chain fatty acids. Consequently, this strain was identified as a member of the genus Zooshikella and designated as Zooshikella sp. JE-34. The pigment showed characteristics similar to prodigiosin, a well-known red pigment previously detected in Serratia marcescens. The antimicrobial activity of Zooshikella sp. JE-34 bacterial pigment was tested against 18 microorganisms, which were fish and human pathogens. The Zooshikella sp. JE-34 red pigment showed high antimicrobial activity against Streptococcus iniae, S. parauberis, S. mutans, Staphylococcus aureus, and Propionibacterium acnes.