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

doi:10.1007/s11783-010-0249-3

Front Envir Sci Eng Chin

2010, Vol. 4

Issue (4) : 459-465 https://doi.org/10.1007/s11783-010-0249-3

RESEARCH ARTICLE

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

Key Laboratory of Urban Environment and Health, Institute of Urban Environment, China Academy of Sciences, Xiamen 361021, China

Download: PDF(196 KB) HTML
Export: BibTeX | EndNote | Reference Manager | ProCite | RefWorks

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 DNA yielded 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

Corresponding Author(s): YU Xin,Email:xyu@iue.ac.cn

Issue Date: 05 December 2010

Cite this article:

Shuting ZHANG,Bo WEI,Xin YU, et al. Development of pretreatment protocol for DNA extraction from biofilm attached to biologic activated carbon (BAC) granules[J]. Front Envir Sci Eng Chin, 2010, 4(4): 459-465.

URL:

https://academic.hep.com.cn/fese/EN/10.1007/s11783-010-0249-3
https://academic.hep.com.cn/fese/EN/Y2010/V4/I4/459

Fig.1

1% agarose gel electrophoresis results of five different pretreatments. M: DL2000 DNA marker (TaKaRa)

Fig.2

Results of recovered DNA concentration (μg·g^-1 [wet wt]) by spectrophotometer

Fig.3

Results of PCR tests of recovered DNA extracted by five pretreatments. M: DL2000 DNA marker

Fig.4

1% agarose gel electrophoresis results of adding different doses of skim milk in DNA extraction M: DL2000 DNA marker

Fig.5

Agarose gel electrophoresis bands of DNA extracted from samples of different depth in BAC filter. M: DL2000 DNA marker

Fig.6

DNA yields (µg·g^-1 [dry wt]) determined by spectrophotometer and biomass determined using lipid-P method of six-depth samples. (a) DNA yields; (b) biomass

Tab.1

Influent and effluent of the BAC biofilter (2008.7.16-2009.5.15)

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): 163–169 doi: 10.1016/S0273-1223(98)00578-2
2	Graham N J D. Removal of humic substances by oxidation/biofiltration processes–A review. Water Science and Technology , 1999, 40(9): 141–148 doi: 10.1016/S0273-1223(99)00650-2
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): 348–355 doi: 10.1016/j.seppur.2007.03.019
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): 283–298 doi: 10.1016/S0273-1223(97)00722-1
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): 263–267
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): 3265–3271 doi: 10.1016/S0043-1354(01)00029-X
7	Lin W, Weber A. Aerobic biological activated carbon (BAC) treatment of a phenolic wastewater. Environment and Progress , 1992, 11(2): 145–154
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): 450–458
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): 350–357 doi: 10.1007/s00253-005-0057-z
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): 699–704 doi: 10.1016/S0043-1354(00)00254-2
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): 21–28 doi: 10.1016/S0273-1223(97)00147-9
12	Simpson D R. Biofilm processes in biologically active carbon water purification. Water Research , 2008, 42(12): 2839–2848 doi: 10.1016/j.watres.2008.02.025
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): 31–54 doi: 10.1016/S0167-7012(01)00351-7
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): 182–194 doi: 10.1016/j.watres.2008.09.038
15	Fonseca A C, Summers R S, Hernandez M T. Comparative measurements of microbial activity in drinking water biofilters. Water Research , 2001, 35(16): 3817–3824 doi: 10.1016/S0043-1354(01)00104-X
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): 135–143 doi: 10.1016/j.cej.2005.04.011
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)
18	Kyotani T. Control of pore structure in carbon. Carbon , 2000, 38(2): 269–286 doi: 10.1016/S0008-6223(99)00142-6
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): 2085–2100 doi: 10.1016/S0008-6223(02)00069-6
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): 5409–5420
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): 3972–3976
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): 251–259 doi: 10.1023/A:1008711313840
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): 13–19 doi: 10.1264/jsme2.19.13
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): 159–166 doi: 10.1264/jsme2.23.159
25	Zhou J, Bruns M A, Tiedje J M. DNA recovery from soils of diverse composition. Applied and Environmental Microbiology , 1996, 62(2): 316–322
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 Ecology , 2002, 27(1): 29–36 doi: 10.3354/ame027029
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): 9–19 doi: 10.1016/j.mimet.2006.02.011
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): 5488–5491 doi: 10.1128/AEM.66.12.5488-5491.2000
29	Uzel A, Ozdemir G. Metal biosorption capacity of the organic solvent tolerant Pseudomonas fluorescens TEM08. Bioresource Technology , 2009, 100(2): 542–548 doi: 10.1016/j.biortech.2008.06.032
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)
31	Wang J Z, Summers R S, Miltner R J. Biofiltration Performance: Part 1, Relationship to Biomass. Journal AWWA , 1995, 87(12): 55–63
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): 393–396
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): 31–39 doi: 10.1111/j.1574-6968.1992.tb05435.x
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): 57–66 doi: 10.1016/0167-7012(87)90025-X

[1]	Kangying Guo, Baoyu Gao, Jie Wang, Jingwen Pan, Qinyan Yue, Xing Xu. Flocculation behaviors of a novel papermaking sludge-based flocculant in practical printing and dyeing wastewater treatment[J]. Front. Environ. Sci. Eng., 2021, 15(5): 103-.
[2]	Shujuan Meng, Rui Wang, Kaijing Zhang, Xianghao Meng, Wenchao Xue, Hongju Liu, Dawei Liang, Qian Zhao, Yu Liu. Transparent exopolymer particles (TEPs)-associated protobiofilm: A neglected contributor to biofouling during membrane filtration[J]. Front. Environ. Sci. Eng., 2021, 15(4): 64-.
[3]	Yunping Han, Lin Li, Ying Wang, Jiawei Ma, Pengyu Li, Chao Han, Junxin Liu. Composition, dispersion, and health risks of bioaerosols in wastewater treatment plants: A review[J]. Front. Environ. Sci. Eng., 2021, 15(3): 38-.
[4]	Wenyue Li, Min Chen, Zhaoxiang Zhong, Ming Zhou, Weihong Xing. Hydroxyl radical intensified Cu₂O NPs/H₂O₂ process in ceramic membrane reactor for degradation on DMAc wastewater from polymeric membrane manufacturer[J]. Front. Environ. Sci. Eng., 2020, 14(6): 102-.
[5]	Yang Yang. Recent advances in the electrochemical oxidation water treatment: Spotlight on byproduct control[J]. Front. Environ. Sci. Eng., 2020, 14(5): 85-.
[6]	Haiyan Yang, Shangping Xu, Derek E. Chitwood, Yin Wang. Ceramic water filter for point-of-use water treatment in developing countries: Principles, challenges and opportunities[J]. Front. Environ. Sci. Eng., 2020, 14(5): 79-.
[7]	Jianfeng Zhou, Ting Wang, Cecilia Yu, Xing Xie. Locally enhanced electric field treatment (LEEFT) for water disinfection[J]. Front. Environ. Sci. Eng., 2020, 14(5): 78-.
[8]	Kun Wan, Wenfang Lin, Shuai Zhu, Shenghua Zhang, Xin Yu. Biofiltration and disinfection codetermine the bacterial antibiotic resistome in drinking water: A review and meta-analysis[J]. Front. Environ. Sci. Eng., 2020, 14(1): 10-.
[9]	Luxi Zou, Huaibo Li, Shuo Wang, Kaikai Zheng, Yan Wang, Guocheng Du, Ji Li. Characteristic and correlation analysis of influent and energy consumption of wastewater treatment plants in Taihu Basin[J]. Front. Environ. Sci. Eng., 2019, 13(6): 83-.
[10]	Jiuhui Qu, Hongchen Wang, Kaijun Wang, Gang Yu, Bing Ke, Han-Qing Yu, Hongqiang Ren, Xingcan Zheng, Ji Li, Wen-Wei Li, Song Gao, Hui Gong. Municipal wastewater treatment in China: Development history and future perspectives[J]. Front. Environ. Sci. Eng., 2019, 13(6): 88-.
[11]	Yuhan Zheng, Zhiguo Su, Tianjiao Dai, Feifei Li, Bei Huang, Qinglin Mu, Chuanping Feng, Donghui Wen. Identifying human-induced influence on microbial community: A comparative study in the effluent-receiving areas in Hangzhou Bay[J]. Front. Environ. Sci. Eng., 2019, 13(6): 90-.
[12]	Aoshuang Jing, Tao Liu, Xie Quan, Shuo Chen, Yaobin Zhang. Enhanced nitrification in integrated floating fixed-film activated sludge (IFFAS) system using novel clinoptilolite composite carrier[J]. Front. Environ. Sci. Eng., 2019, 13(5): 69-.
[13]	Muhammad Kashif Shahid, Yunjung Kim, Young-Gyun Choi. Adsorption of phosphate on magnetite-enriched particles (MEP) separated from the mill scale[J]. Front. Environ. Sci. Eng., 2019, 13(5): 71-.
[14]	Xuemin Hao, Guanlong Wang, Shuo Chen, Hongtao Yu, Xie Quan. Enhanced activation of peroxymonosulfate by CNT-TiO₂ under UV-light assistance for efficient degradation of organic pollutants[J]. Front. Environ. Sci. Eng., 2019, 13(5): 77-.
[15]	Tiezheng Tong, Kenneth H. Carlson, Cristian A. Robbins, Zuoyou Zhang, Xuewei Du. Membrane-based treatment of shale oil and gas wastewater: The current state of knowledge[J]. Front. Environ. Sci. Eng., 2019, 13(4): 63-.

Viewed

Full text

Abstract

Cited

Shared

Discussed