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HomeInternational Letters of Natural SciencesInternational Letters of Natural Sciences Vol. 60An Improved Procedure of the Metagenomic DNA...

An Improved Procedure of the Metagenomic DNA Extraction from Saline Soil, Sediment and Salt

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Abstract:

A new modified protocol has been developed for extracting pure community inhibitors-free DNA from saline soils, sediments and salts. Amplification of DNA from soil and sediment is often inhibited by copurified contaminants. A rapid, inexpensive, large-scale DNA extraction method involving minimal purification has been developed that is applicable to saline samples. Using a widely used a newly modified direct DNA extraction method proposed in this report, DNA was extracted from samples of Urmia Lake in diverse geological location in Iran and quantity of the DNA were examined. We developed an improved method to extract DNA include the combination of physical, chemical and mechanical lysis methods from saline samples. In the earlier reports, skim milk as an adsorption competitor was added to buffer DNA extract. In current study, we added skim milk to buffer DNA extraction. The results showed that skim milk was useful as an additive for extract DNA from saline samples. This method is applicable to molecular community analysis of saline samples which strongly adsorb DNA. The methods appear to have wide applicability in investigating molecular diversity and exploring functional genes from the total DNA. The extracted DNA was used to successfully amplify 16SrRNA region and functional genes. The amplicons were suitable for further applications such as diversity based analysis by denaturing gradient gel electrophoresis (DGGE) and cloning library.

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Periodical:

International Letters of Natural Sciences (Volume 60)

Pages:

38-45

DOI:

https://doi.org/10.56431/p-6t69gc

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Online since:

November 2016

Authors:

Fereshteh Jookar Kashi*

Keywords:

DNA, DNA Extraction, Metagenome, Molecular Methods, Saline Sample

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Creative Commons CC BY 4.0

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* - Corresponding Author

[1] P. Robe et al., Extraction of DNA from soil, European J. Soil Bio. 39 (2003) 183–190.

[2] G.M. Luna, A. Dell'Anno, R. Danovaro, DNA extraction procedure: a critical issue for bacterial diversity assessment in marine sediments, Environ. Microbiol. 8(2) (2006) 308–320.

DOI: 10.1111/j.1462-2920.2005.00896.x

[3] T. Hattori, Soil aggregates as microhabitats of microorganisms, Biol. Fertil. Soils. 6 (1988) 189–203.

[4] L. Ranjard et al., A single procedure to recover DNAfrom the surface or inside aggregates and in various size fractions of soil suitable for PCR-based assays of bacterial communities, Eur. J. Soil Biol. 34 (1998) 89–97.

DOI: 10.1016/s1164-5563(99)90006-7

[5] T.H. Yuko, M. Naouki, An improved DNA extraction method using skim milk from soils that strongly adsorb DNA, Microbes Environment. 19(1) (2004) 13-19.

DOI: 10.1264/jsme2.19.13

[6] T.H. Yuko, M. Naouki, Skim Milk Drastically Improves the Efficacy of DNA Extraction from Andisol, a Volcanic Ash Soil, Japan Agricultural Research Quarterly. 39(4) (2005) 247–252.

DOI: 10.6090/jarq.39.247

[7] K.Y. Kweku, R.S. Todd, Strategy for Extracting DNA from Clay Soil and Detecting a Specific Target Sequence via Selective Enrichment and Real-Time(Quantitative) PCR Amplification, Appl. Environment. Microbiol. (2009) 6017–6021.

DOI: 10.1128/aem.00211-09

[8] J. Li et al., A rapid DNA extraction method for PCR amplification from wetland soils, Lett. Appl. Microbiol. 52 (2011) 626–633.

DOI: 10.1111/j.1472-765x.2011.03047.x

[9] T. Miao et al., A method suitable for DNA extraction from humus-rich soil, Biotechnol. Lett. 36(11) (2014) 2223-2228.

DOI: 10.1007/s10529-014-1591-5

[10] A. Panigrahy et al., Development of a metagenomic DNA extraction procedure and PCR detection of human enteric bacteria in vegetable salad tissues, Res. Biotechnol. 2(1) (2011) 11-19.

[11] J.S. Rajesh, K. Sivasubramani, S. Jayalakhsmi, Simple, Rapid Method For Direct Isolation Of Metagenomic Dna From Pichavaram Mangrove Sediment, Int. J. Res. Biotechnol. Biochem. 3(1) (2013) 19-21.

[12] M.A. Schneegurt, S.Y. Dore, C.F.J. Kulpa, Direct Extraction of DNA from Soils for Studies in Microbial Ecology, Curr. Issues. Mol. Biol. 5 (2003) 1-8.

[13] J.D. Rhoades, Soluble Salts, In: A.L. Page et al. (ed.), Methods of soil analysis, Part 2, Chemical and microbiological properties - Agronomy. 9 (1982) 167-179.

DOI: 10.2134/agronmonogr9.2.2ed.c10

[14] H.W. Doughty, Mohr's method for the determination of silver and halogens in other than neutral solutions, J. Am. Chem. Soc. 46(12) (1924) 2707–2709.

DOI: 10.1021/ja01677a014

[15] R.T. Sheen, H.L. Kahler, Effects of Ions on mohr method for chloride determination, Ind. Eng. Chem. Anal. Ed. 10 (1983) 628-629.

DOI: 10.1021/ac50127a004

[16] S. Turner, K.M. Pryer, V.P.W. Miao, J.D. Palmer, Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis, J. Eukaryot. Microbiol. 46 (1999) 327-338.

DOI: 10.1111/j.1550-7408.1999.tb04612.x

[17] D.J. Lane et al., Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses, Proc. Natl. Acad. Sci. 82 (1985) 6955-6959.

DOI: 10.1073/pnas.82.20.6955

[18] G. Muyzer, E.C. Waal, A. Uitterlinden, Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction amplified genes encoding for 16Sr DNA, Applied Environment Microbiology, 59 (1993) 695–700.

DOI: 10.1128/aem.59.3.695-700.1993

[19] R.T. Papke et al., Diversity of bacteriorhodopsins in different hypersaline waters from a single Spanish saltern, Environ. Microbiol. 5 (2003) 1039–1045.

DOI: 10.1046/j.1462-2920.2003.00501.x

[20] M. Tianjin et al., A method suitable for DNA extraction from humus-rich soil, Biotechnol. Lett. 36 (2014) 2223–2228.

DOI: 10.1007/s10529-014-1591-5

[21] M.P. Vinardell, M.R. Infante, The relationship between the chain length of non-ionic surfactants and their hemolytic action on human erythrocytes, Comparative Biochemistry and Physiology Part C: Pharmacology, Toxicology and Endocrinology. 124(2) (1999) 117-120.

DOI: 10.1016/s0742-8413(99)00057-2

[22] K. Saeki, M. Sakai, T. Kunito, Effect of α-casein on DNA adsorption by Andosols and by soil components, Biol. Fertil. Soils. 48 (2012) 469–474.

DOI: 10.1007/s00374-011-0640-7