Development of pretreatment protocol for DNA extraction from biofilm attached to biologic activated carbon (BAC) granules

  • Shuting Zhang
  • Bo Wei
  • Xin Yu
  • Bing Liu
  • Zhuoying Wu
  • Li Gu
Research Article

Abstract

The biologic activated carbon (BAC) process is widely used in drinking water treatments. A comprehensive molecular analysis of the microbial community structure provides very helpful data to improve the reactor performance. However, the bottleneck of deoxyribonucleic acid (DNA) extraction from BAC attached biofilm has to be solved since the conventional procedure was unsuccessful due to firm biomass attachment and adsorption capacity of the BAC granules. In this study, five pretreatments were compared, and adding skim milk followed by ultrasonic vibration was proven to be the optimal choice. This protocol was further tested using the vertical BAC samples from the full-scale biofilter of Pinghu Water Plant. The results showed the DNAyielded a range of 40 μg·g−1 BAC (dry weight) to over 100 μg·g−1 BAC (dry weight), which were consistent with the biomass distribution. All results suggested that the final protocol could produce qualified genomic DNA as a template from the BAC filter for downstream molecular biology researches.

Keywords

bacterial DNA extraction biological activated carbon (BAC) biofilm water treatment pretreatment protocol 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Nishijima W, Kim W, Shoto E, Okada M. The performance of an ozonation-biological activated carbon process under long term operation. Water Science and Technology, 1998, 38(6): 163–169CrossRefGoogle Scholar
  2. 2.
    Graham N J D. Removal of humic substances by oxidation/biofiltration processes-A review. Water Science and Technology, 1999, 40(9): 141–148CrossRefGoogle Scholar
  3. 3.
    Xu B, Gao N Y, Sun X F, Xia S J, Simonnot M O, Causserand C, Rui M, Wu H H. Characteristics of organic material in Huangpu River and treatability with the O3-BAC process. Separation and Purification Technology, 2007, 57(2): 348–355CrossRefGoogle Scholar
  4. 4.
    Kim W, Nishijima W, Baes A, Okada M. Micropollutant removal with saturated biological activated carbon(BAC) in ozonation-BAC process. Water Science and Technology, 1997, 36(12): 283–298CrossRefGoogle Scholar
  5. 5.
    Cheng L, Gao N Y, Cai Y L. Influence of the disinfectants on the biological stability of the drinking water. Journal of Xi’an University of Architecture & Technology (Natural Science Edition), 2007, 39(2): 263–267Google Scholar
  6. 6.
    Sirotkin A, Koshkina L, Ippolitov K. The BAC-process for treatment of waste water containing non-ionogenic synthetic surfactants. Water Research, 2001, 35(13): 3265–3271CrossRefGoogle Scholar
  7. 7.
    Lin W, Weber A. Aerobic biological activated carbon (BAC) treatment of a phenolic wastewater. Environment and Progress, 1992, 11(2): 145–154Google Scholar
  8. 8.
    Chung Y C, Lin Y Y, Tseng C P. Operational characteristics of effective removal of H2S and NH3 waste gases by activated carbon biofilter. Journal of the Air & Waste Management Association, 2004, 54(4): 450–458Google Scholar
  9. 9.
    Duan H, Yan R, Koe L C. Investigation on the mechanism of H2S removal by biological activated carbon in a horizontal biotrickling filter. Applied Microbiology and Biotechnology, 2005, 69(3): 350–357CrossRefGoogle Scholar
  10. 10.
    Lin C K, Tsai T Y, Liu J C, Chen M C. Enhanced biodegradation of petrochemical wastewater using ozonation and BAC advanced treatment system. Water Research, 2001, 35(3): 699–704CrossRefGoogle Scholar
  11. 11.
    Kim W H, Nishijima W, Shoto E, Okada M. Pilot plant study on ozonation and biological activated carbon process for drinking water treatment. Water Science and Technology, 1997, 35(8): 21–28CrossRefGoogle Scholar
  12. 12.
    Simpson D R. Biofilm processes in biologically active carbon water purification. Water Research, 2008, 42(12): 2839–2848CrossRefGoogle Scholar
  13. 13.
    Rompré A, Servais P, Baudart J, de-Roubin M, Laurent P. Detection and enumeration of coliforms in drinking water: current methods and emerging approaches. Journal of Microbiological Methods, 2002, 49(1): 31–54CrossRefGoogle Scholar
  14. 14.
    DeVet W W J M, Dinkla I J T, Muyzer G, Rietveld L C, van Loosdrecht M C M. Molecular characterization of microbial populations in groundwater sources and sand filters for drinking water production. Water Research, 2009, 43(1): 182–194CrossRefGoogle Scholar
  15. 15.
    Fonseca A C, Summers R S, Hernandez M T. Comparative measurements of microbial activity in drinking water biofilters. Water Research, 2001, 35(16): 3817–3824CrossRefGoogle Scholar
  16. 16.
    Steele J, Ozis F, Fuhrman J A, Devinny J S. Structure of microbial communities in ethanol biofilters. Chemical Engineering Journal, 2005, 113(2–3): 135–143CrossRefGoogle Scholar
  17. 17.
    Liu X L, Liu W J. Microbial community structure in bio-ceramics and biological activated carbon analyzed by PCR-SSCP technique. Huan Jing Ke Xue, 2007, 28(4): 924–928 (in Chinese)Google Scholar
  18. 18.
    Kyotani T. Control of pore structure in carbon. Carbon, 2000, 38(2): 269–286CrossRefGoogle Scholar
  19. 19.
    Li L, Quinlivan P, Knappe D. Effects of activated carbon surface chemistry and pore structure on the adsorption of organic contaminants from aqueous solution. Carbon, 2002, 40(12): 2085–2100CrossRefGoogle Scholar
  20. 20.
    Frostegard A, Courtois S, Ramisse V, Clerc S, Bernillon D, Le Gall F, Jeannin P, Nesme X, Simonet P. Quantification of bias related to the extraction of DNA directly from soils. Applied and Environmental Microbiology, 1999, 65(12): 5409–5420Google Scholar
  21. 21.
    Volossiouk T, Robb E J, Nazar R N. Direct DNA extraction for PCR-mediated assays of soil organisms. Applied and Environmental Microbiology, 1995, 61(11): 3972–3976Google Scholar
  22. 22.
    García-Pedrajas M D, Bainbridge B W, Heale J B, Perez-Artes E, Jimenez-Diaz R M. A simple PCR-based methods for the detection of the chickpea-wilt pathogen Fusarium oxysporum f.sp.ciceria in artificial and natural soils. European Journal of Plant Pathology, 1999, 105(3): 251–259CrossRefGoogle Scholar
  23. 23.
    Takada-Hoshino Y, Matsumoto N. An improved DNA extraction method using skim milk from soils that strongly adsorb DNA. Microbes and Environments, 2004, 19(1): 13–19CrossRefGoogle Scholar
  24. 24.
    Ikeda S, Tsurumaru H, Wakai S, Noritake C, Fujishiro K, Akasaka M, Ando K. Evaluation of the effects of different additives in improving the DNA extraction yield and quality from Andosol. Microbes and Environments, 2008, 23(2): 159–166CrossRefGoogle Scholar
  25. 25.
    Zhou J, BrunsM A, Tiedje J M. DNA recovery from soils of diverse composition. Applied and Environmental Microbiology, 1996, 62(2): 316–322Google Scholar
  26. 26.
    Buesing N, Gessner M O. Comparison of detachment procedures for direct counts of bacteria associated with sediment particles, plant litter and epiphytic biofilms. Aquatic Microbial Ecologys, 2002, 27(1): 29–36CrossRefGoogle Scholar
  27. 27.
    Frey J C, Angert E R, Pell A N. Assessment of biases associated with profiling simple, model communities using terminal-restriction fragment length polymorphism-based analyses. Journal of Microbiological Methods, 2006, 67(1): 9–19CrossRefGoogle Scholar
  28. 28.
    Griffiths R I, Whiteley A S, O’Donnell A G, Bailey M J. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Applied and Environmental Microbiology, 2000, 66(12): 5488–5491CrossRefGoogle Scholar
  29. 29.
    Uzel A, Ozdemir G. Metal biosorption capacity of the organic solvent tolerant Pseudomonas fluorescens TEM08. Bioresource Technology, 2009, 100(2): 542–548CrossRefGoogle Scholar
  30. 30.
    Yu X, Zhang X, Wang Z. Biomass determination using Lipid-P method for drinking water biological treatment. Water and Wastewater Engineering, 2002, 28(5): 1–5 (in Chinese)Google Scholar
  31. 31.
    Wang J Z, Summers R S, Miltner R J. Biofiltration Performance: Part 1, Relationship to Biomass. Journal AWWA, 1995, 87(12): 55–63Google Scholar
  32. 32.
    Ogram A V, Mathot M L, Harsh J B, Boyle J, Pettigrew C A. Effects of DNA polymer length on its adsorption to soils. Applied and Environmental Microbiology, 1994, 60(2): 393–396Google Scholar
  33. 33.
    Paget E, Monrozier L J, Simonet P. Adsorption of DNA on clay minerals: protection against Dnase I and influence on gene transfer. FEMS Microbiology Letters, 1992, 97(1–2): 31–39CrossRefGoogle Scholar
  34. 34.
    Ogram A, Sayler G S, Barkay T. The extraction and purification of microbial DNA from sediments. Journal of Microbiological Methods, 1987, 7(2–3): 57–66CrossRefGoogle Scholar

Copyright information

© Higher Education Press and Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Shuting Zhang
    • 1
  • Bo Wei
    • 1
  • Xin Yu
    • 1
  • Bing Liu
    • 1
  • Zhuoying Wu
    • 1
  • Li Gu
    • 1
  1. 1.Key Laboratory of Urban Environment and Health, Institute of Urban EnvironmentChina Academy of SciencesXiamenChina

Personalised recommendations