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Modified pretreatment method for total microbial DNA extraction from contaminated river sediment

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Abstract

Extraction of high-quality microbial DNA from contaminated environmental samples is an essential step in microbial ecological study. Based on previously published methods for soil and sediment samples, a modified pretreatment method was developed for extracting microbial DNA from heavily contaminated river sediment samples via selection of optimal pretreatment parameters (i.e., reagent solution, reaction duration, and temperature). The pretreatment procedure involves washing the river sediment sample for three times with a solution containing 0.1 mol·L−1 ethylene diamine tetraacetic acid (EDTA), 0.1 mol·L−1 Tris (pH 8.0), 1.5 mol·L−1 NaCl, 0.1 mol·L−1 NaH2PO4, and Na2HPO4 at 65°C with 180 r·min−1 for 15 min to remove humic materials and heavy metals prior to the employment of standard DNA extraction procedures. We compared the results of standard procedure DNA extraction following pretreatment, without pretreatment, and with using a commercial PowerSoil™ DNA Isolation Kit. The results indicated that the pretreatment significantly improved the DNA quality based on DNA yield, DNA fragment length, and determination of prokaryotic diversity. Prokaryotic diversity exhibited in the DNA with the pretreatment was also considerably higher than that extracted with the PowerSoil™ DNA Isolation Kit only. The pretreatment method worked well even with a small amount of sediment sample (0.25 g or even lower). The method provides a novel, simple, cost-effective tool for DNA extraction for microbial community analysis in environmental monitoring and remediation processes.

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References

  1. Cai J N, Cao Y Z, Tan H J, Wang Y M, Luo J Q. Fractionation and ecological risk of metals in urban river sediments in Zhongshan City, Pearl River Delta. Journal of Environmental Monitoring, 2011, 13(9): 2450–2456

    Article  CAS  Google Scholar 

  2. Mehler W T, Li H Z, Lydy M J, You J. Identifying the causes of sediment-associated toxicity in urban waterways of the Pearl River Delta, China. Environmental Science & Technology, 2011, 45(5): 1812–1819

    Article  CAS  Google Scholar 

  3. Santhiya G, Lakshumanan C, Selvin J, Asha D. Microbiological analysis of seawater and sediments in urban shorelines: occurrence of heavy metals resistance bacteria on Chennai beaches, Bay of Bengal. Microchemical Journal, 2011, 99(2): 197–202

    Article  CAS  Google Scholar 

  4. Wu L, Kellogg L, Devol A H, Tiedje J M, Zhou J. Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico. Applied and Environmental Microbiology, 2008, 74(14): 4516–4529

    Article  CAS  Google Scholar 

  5. Pires A C C, Cleary D F R, Almeida A, Cunha Â, Dealtry S, Mendonça-Hagler L C S, Smalla K, Gomes N C M. Denaturing gradient gel electrophoresis and barcoded pyrosequencing reveal unprecedented archaeal diversity in mangrove sediment and rhizosphere samples. Applied and Environmental Microbiology, 2012, 78(16): 5520–5528

    Article  CAS  Google Scholar 

  6. Hollister E B, Engledow A S, Hammett A J M, Provin T L, Wilkinson H H, Gentry T J. Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments. ISME Journal, 2010, 4(6): 829–838

    Article  CAS  Google Scholar 

  7. Bowman J S, Rasmussen S, Blom N, Deming J W, Rysgaard S, Sicheritz-Ponten T. Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene. The ISME Journal, 2012, 6(1): 11–20

    Article  CAS  Google Scholar 

  8. Ning J, Liebich J, Kästner M, Zhou J, Schäffer A, Burauel P. Different influences of DNA purity indices and quantity on PCR-based DGGE and functional gene microarray in soil microbial community study. Applied Microbiology and Biotechnology, 2009, 82(5): 983–993

    Article  CAS  Google Scholar 

  9. Delmont T O, Robe P, Clark I, Simonet P, Vogel TM. Metagenomic comparison of direct and indirect soil DNA extraction approaches. Journal of Microbiological Methods, 2011, 86(3): 397–400

    Article  CAS  Google Scholar 

  10. Amorim J H, Macena T N S, Lacerda-Junior G V, Rezende R P, Dias J C T, Brendel M, Cascardo J C M. An improved extraction protocol for metagenomic DNA from a soil of the Brazilian Atlantic Rainforest. Genetics and Molecular Research, 2008, 7(4): 1226–1232

    Article  CAS  Google Scholar 

  11. Fitzpatrick K A, Kersh G J, Massung R F. Practical method for extraction of PCR-quality DNA from environmental soil samples. Applied and Environmental Microbiology, 2010, 76(13): 4571–4573

    Article  CAS  Google Scholar 

  12. Fortin N, Beaumier D, Lee K, Greer C W. Soil washing improves the recovery of total community DNA from polluted and high organic content sediments. Journal of Microbiological Methods, 2004, 56(2): 181–191

    Article  CAS  Google Scholar 

  13. Purohit H J, Kapley A, Moharikar A A, Narde G. A novel approach for extraction of PCR-compatible DNA from activated sludge samples collected from different biological effluent treatment plants. Journal of Microbiological Methods, 2003, 52(3): 315–323

    Article  CAS  Google Scholar 

  14. Sagova-Mareckova M, Cermak L, Novotna J, Plhackova K, Forstova J, Kopecky J. Innovative methods for soil DNA purification tested in soils with widely differing characteristics. Applied and Environmental Microbiology, 2008, 74(9): 2902–2907

    Article  CAS  Google Scholar 

  15. Leuko S, Goh F, Ibáñez-Peral R, Burns B P, Walter M R, Neilan B A. Lysis efficiency of standard DNA extraction methods for Halococcus spp. in an organic rich environment. Extremophiles, 2008, 12(2): 301–308

    Article  CAS  Google Scholar 

  16. Zhou J, Bruns M A, Tiedje J M. DNA recovery from soils of diverse composition. Applied and Environmental Microbiology, 1996, 62(2): 316–322

    CAS  Google Scholar 

  17. Braida M D, Daniels L M, Kitts C L. Removal of PCR inhibitors from soil DNA by chemical flocculation. Journal of Microbiological Methods, 2003, 52(3): 383–393

    Google Scholar 

  18. Leff L G, Dana J R, McArthur J V, Shimkets L J. Comparison of methods of DNA extraction from stream sediments. Applied and Environmental Microbiology, 1995, 61(3): 1141–1143

    CAS  Google Scholar 

  19. Miller D N, Bryant J E, Madsen E L, Ghiorse W C. Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Applied and Environmental Microbiology, 1999, 65(11): 4715–4724

    CAS  Google Scholar 

  20. Rojas-Herrera R, Narváez-Zapata J, Zamudio-Maya M, Mena-Martínez ME. A simple silica-based method for metagenomic DNA extraction from soil and sediments. Molecular Biotechnology, 2008, 40(1): 13–17

    Article  CAS  Google Scholar 

  21. Lakay F M, Botha A, Prior B A. Comparative analysis of environmental DNA extraction and purification methods from different humic acid-rich soils. Journal of Applied Microbiology, 2007, 102(1): 265–273

    Article  CAS  Google Scholar 

  22. Liu J, Deng D Y, Xu M Y, Sun G P. Characteristics of organic pollutants in the sediments from a typical electronics industrial zone. Environmental Sciences (China), 2013, 34(3): 326–333 (in Chinese)

    CAS  Google Scholar 

  23. Deng D Y, Sun G P, Guo J, Zhang H T, Zhang Q, Xu M Y. Investigation on the distribution and potential ecological risk of heavy metal in the sediments from typical electrical industrial zone. Environmental Sciences (China), 2012, 33(5): 1700–1766 (in Chinese)

    Google Scholar 

  24. Fu J, Mai B, Sheng G, Zhang G, Wang X, Peng P, Xiao X, Ran R, Cheng F, Peng X, Wang Z, Wa Tang U. Persistent organic pollutants in environment of the Pearl River Delta, China: an overview. Chemosphere, 2003, 52(9): 1411–1422

    Article  CAS  Google Scholar 

  25. Enright M J, Scott E E, Chang K. Regional Powerhouse: The Greater Pearl River Delta and the Rise of China. Chichester: Wiley, 2005

    Google Scholar 

  26. Csaikl U, Bastian H, Brettschneider R, Gauch S, Meir A, Schauerte M, Scholz F, Sperisen C, Vornam B, Ziegenhagen B. Comparative analysis of different DNA extraction protocols: a fast, universal maxi-preparation of high quality plant DNA for genetic evaluation and phylogenetic studies. Plant Molecular Biology Reporter, 1998, 16(1): 69–86

    Article  CAS  Google Scholar 

  27. Watson R J, Blackwell B. Purification and characterization of a common soil component which inhibits the polymerase chain reaction. Canadian Journal of Microbiology, 2000, 46(7): 633–642

    Article  CAS  Google Scholar 

  28. Lahiri D K, Schnabel B. DNA isolation by a rapid method from human blood samples: effects of MgCl2, EDTA, storage time, and temperature on DNA yield and quality. Biochemical Genetics, 1993, 31(7–8): 321–328

    Article  CAS  Google Scholar 

  29. Wang G C, Wang Y. Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes. Applied and Environmental Microbiology, 1997, 63(12): 4645–4650

    CAS  Google Scholar 

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Authors and Affiliations

  1. Guangdong Institute of Microbiology, Guangzhou, 510070, China

    Yun Fang, Meiying Xu, Xingjuan Chen, Guoping Sun & Jun Guo

  2. School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China

    Yun Fang & Xueduan Liu

  3. Key Laboratory of Biometallurgy of Ministry of Education, Changsha, 410083, China

    Yun Fang & Xueduan Liu

  4. State Key Laboratory of Applied Microbiology (Ministry-Guangdong Province Jointly Breeding Base), Guangzhou, 510070, China

    Yun Fang, Meiying Xu, Xingjuan Chen, Guoping Sun & Jun Guo

  5. Department of Civil & Environmental Engineering, Center for Sustainable Development & Global Competitiveness, Stanford University, Stanford, CA, 94305, USA

    Weimin Wu

Authors
  1. Yun Fang
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  2. Meiying Xu
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  3. Xingjuan Chen
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  4. Guoping Sun
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Correspondence to Meiying Xu or Xueduan Liu.

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Fang, Y., Xu, M., Chen, X. et al. Modified pretreatment method for total microbial DNA extraction from contaminated river sediment. Front. Environ. Sci. Eng. 9, 444–452 (2015). https://doi.org/10.1007/s11783-014-0679-4

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  • DOI: https://doi.org/10.1007/s11783-014-0679-4

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