An Effective Method for Extracting DNA from Contaminated Soil Due to Industrial Waste

Hinoue, Mitsuo; Fukuda, Kazumasa; Wan, Yan; Yamauchi, Kenta; Ogawa, Hiroaki; Taniguchi, Hatsumi

doi:10.7888/juoeh.26.13

Cited by 5 publications

(4 citation statements)

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“…The major contaminants coprecipitating with the isolated environmental DNA are humic acids, phenolics and heavy metals (Hinoue et al . ). They interfere with biotechnological processing of the isolated DNA, such as PCR amplification (Tsai and Olson ; Smalla et al .…”

Section: Introductionmentioning

confidence: 97%

“…However, ineffective cell disruption, smaller size of isolated DNA, unbiased representation of all microbial genomes and above all coprecipitation of contaminants are some of the bottlenecks in successful studies of metagenomics. The major contaminants coprecipitating with the isolated environmental DNA are humic acids, phenolics and heavy metals (Hinoue et al 2004). They interfere with biotechnological processing of the isolated DNA, such as PCR amplification (Tsai and Olson 1992;Smalla et al 1993), restriction digestion (Porteous and Armstrong 1991) and transformation (Holben et al 1988) thus hampering the downstream processing of DNA.…”

Section: Introductionmentioning

confidence: 99%

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An efficient and economical method for extraction of DNA amenable to biotechnological manipulations, from diverse soils and sediments

Sharma

Kuhad

2014

J Appl Microbiol

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Aims: An attempt was made to optimize a new protocol for isolation of pure metagenomic DNA from soil samples. Methods and Results: Various chemicals (FeCl 3 , MgCl 2 , CaCl 2 and activated charcoal) were tested for their efficacy in isolation of metagenomic DNA from different soil and compost samples. Among these trials, charcoal and MgCl 2 when used in combination yielded highly pure DNA free from humic acids and other contaminants. The DNA extracted with the optimized protocol was readily digested, amplified and cloned. Moreover, compared with a wellestablished commercial DNA isolation kit (UltraClean TM Soil DNA Isolation Kit), our method for DNA isolation was found to be economical. This demonstrated that the method developed can be applied to a wide variety of soil samples and allows handling of multiple samples at a given time. Conclusions: The optimized protocol developed has successfully yielded pure metagenomic DNA amenable to biotechnological manipulations. Significance and Impact of the Study: A user-friendly and economical protocol for isolation of DNA from soil and compost samples has been developed.

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Section: Introductionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

An efficient and economical method for extraction of DNA amenable to biotechnological manipulations, from diverse soils and sediments

Sharma

Kuhad

2014

J Appl Microbiol

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“…Perubahan komunitas bakteri dianalisis dengan metode PCR-DGGE. Ekstraksi total DNA bakteri dilakukan dengan menggunakan metode modifikasi ekstraksi DNA dari tanah terkontaminasi limbah (Hinoue et al, 2004). Lisis sel dilakukan dengan menggunakan 300 μl bufer lisis (10 mM tris-Cl, 100 mM NaCl, 1 mM EDTA, 20 mg/mL lisozim) dan dibiarkan selama 10 menit pada suhu ruang, kemudian ditambahkan 5 μl proteinase K(11 mg/mL) dan 50 μl 10%SDS.…”

Section: Analisis Komunitas Bakteri Pereduksi Sulfatunclassified

Pengaruh Nitrat terhadap Biokorosi Logam oleh Konsorsium Bakteri Pereduksi Sulfat dari PLTA Saguling

Afianti¹,

Astuti

2021

OLDI

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<div><strong>The Influence of Nitrate in Metal Biocorrosion caused by Sulfate Reducing Bacteria from Saguling Hydropower</strong>. The corrosion facilitated and accelerated by the activities of microorganism is called biocorrosion. Sulfate reducing bacteria (SRB) is known as the bacteria that cause biocorrosion in anaerobic condition by using sulfate as the final electron acceptor. Biocorrosion reduces equipment lifetime and increases maintenance cost in industry. In the cooling system in Saguling hydropower, corrosion was commonly caused by utilization of contaminated water due to anorganic and organic waste, especially sulfate. In this research, sulfate reducing bacteria was isolated from biofilms in the cooling system of Saguling Hydropower. Molecular analysis using PCR-DGGE method with dsrB gene (350 bp) as molecular markers showed that SRB consortium contained 12 bands and assumed as different species of SRB. SRB consortium was tested to determine its biocorrosion activity over metal material of ST37 (carbon steel) and SUS304 (stainless steel). The consortium then treated with 7 different nitrate concentrations to determine its effect against the sulfate reducing bacteria activity. SRB consortium caused higher corrosion to ST37 than SUS304L, with the corrosion rate of 0.07660 mm/year and 0.00265 mm/year, respectively. Concentration of 10 mM nitrate effectively inhibited corrosion rate on ST37 and caused the changes in sulfate reducing bacteria communities, indicated by the disappearance of 6 bands in DGGE profile</div>

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“…DNA extraction DNA was extracted from kefir using variations of the modified lysozyme (Hinoue et al 2004), CTAB (Wu et al 2001) and sonication (Li et al 2007a) methods.…”

Section: Preparation Of Kefirmentioning

confidence: 99%

Comparison of DNA extraction methods for the PCR-single-strand-conformation polymorphism analysis of kefir

Chen

Wang

Han

et al. 2010

World J Microbiol Biotechnol

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Experiments were performed to determine the influence of three DNA extraction methods (i.e. lysozyme, sonication and CTAB methods) from kefir on the microbial diversity analysis by PCR-single strand conformation polymorphism (PCR-SSCP). The results showed that the band of DNA extracted using CTAB was clearer than that using other methods. In addition, the yield and purity of DNA extracted using CTAB were the highest and reached, respectively, 915 lg/ml and 1.694.The results from the experiments indicated that the CTAB-based DNA extraction method was the most efficient method for DNA extraction from kefir. The heterogeneity of PCR products, amplified from community DNA with universal primers spanning the V3 region of 16S rRNA genes, was analysed by using SSCP. The results showed that the SSCP profile based on the sonication method gave the highest microbial diversity of kefir. One conclusion from these results was that the DNA extraction method was an important factor affecting the SSCP-based microbial diversity analysis of kefir.

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An Effective Method for Extracting DNA from Contaminated Soil Due to Industrial Waste

Abstract: Recently, labor accidents caused by toxic gas production such as HiS and CH4 have happened at some waste disposal sites and illegal dumping sites in Japan.The gas production has been known to be end products of bacterial respiration.

Cited by 5 publications

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An efficient and economical method for extraction of DNA amenable to biotechnological manipulations, from diverse soils and sediments

An efficient and economical method for extraction of DNA amenable to biotechnological manipulations, from diverse soils and sediments

Pengaruh Nitrat terhadap Biokorosi Logam oleh Konsorsium Bakteri Pereduksi Sulfat dari PLTA Saguling

Comparison of DNA extraction methods for the PCR-single-strand-conformation polymorphism analysis of kefir

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