RAPD
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Cheap and does not require prior knowledge. |
It has poor reproducibility, and requires strict standardization of PCR conditions. Different final results can be obtained due to variations in DNA polymerase, DNA template and primer amount and annealing temperatures. |
Municipal wastewater [3030 Qu F, Jin W, Zhou X, Wang M, Chen C, Tu R, et al. Nitrogen ion beam implantation for enhanced lipid accumulation of Scenedesmus obliquus in municipal wastewater. Biomass and Bioenergy. 2020 Mar 1;134:105483. – 3131 Calheiros CSC, Pereira SIA, Brix H, Rangel AOSS, Castro PML. Assessment of culturable bacterial endophytic communities colonizing Canna flaccida inhabiting a wastewater treatment constructed wetland. Ecol Eng. 2017 Jan 1;98:418–26.]; Pharmaceutical wastewater [3232 Zhang XX, Jia HY, Wu B, Zhao DY, Li WX, Cheng SP. Genetic analysis of protoplast fusant Xhhh constructed for pharmaceutical wastewater treatment. Bioresour Technol. 2009 Mar 1;100(6):1910–4.]; Industrial wastewater [1717 Li J, Jin Z, Yu B. Changes in the structure and diversity of bacterial communities during the process of adaptation to organic wastewater. Can J Microbiol. 2010 Apr;56(4):352–5., 3333 Swaileh KM, Barakat SO, Hussein RM. RAPD assessment of in vivo induced genotoxicity of raw and treated wastewater to albino rat. Bull Environ Contam Toxicol. 2013 May;90(5):621–5. –3434 Eneroth Å, Ahrné S, Molin G. Contamination routes of Gram-negative spoilage bacteria in the production of pasteurised milk, evaluated by randomly amplified polymorphic DNA (RAPD). Int Dairy J. 2000 Jan 1;10(5–6):325–31.]. |
DGGE TGGE
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Good sensibility and it is possible to excise band from gel for amplification and sequencing. |
Dissimilar DNA sequences of different bacteria species can display the same separation as a result of the same GC contents. |
Municipal wastewater [3030 Qu F, Jin W, Zhou X, Wang M, Chen C, Tu R, et al. Nitrogen ion beam implantation for enhanced lipid accumulation of Scenedesmus obliquus in municipal wastewater. Biomass and Bioenergy. 2020 Mar 1;134:105483., 3535 Silveira DD, Filho PB, Philippi LS, Cantão ME, Foulquier A, Bayle S, et al. In-depth assessment of microbial communities in the full-scale vertical flow treatment wetlands fed with raw domestic wastewater. Environ Technol (United Kingdom). 2020. –3737 Moura A, Tacão M, Henriques I, Dias J, Ferreira P, Correia A. Characterization of bacterial diversity in two aerated lagoons of a wastewater treatment plant using PCR-DGGE analysis. Microbiol Res. 2009 Sep 29;164(5):560–9.]; Industrial wastewater [1717 Li J, Jin Z, Yu B. Changes in the structure and diversity of bacterial communities during the process of adaptation to organic wastewater. Can J Microbiol. 2010 Apr;56(4):352–5., 3838 Karray R, Karray F, Loukil S, Mhiri N, Sayadi S. Anaerobic co-digestion of Tunisian green macroalgae Ulva rigida with sugar industry wastewater for biogas and methane production enhancement. Waste Manag. 2017 Mar 1;61:171–8. – 3939 Nguyen YT, Kieu HTQ, West S, Dang YT, Horn H. Community structure of a sulfate-reducing consortium in lead-contaminated wastewater treatment process. World J Microbiol Biotechnol. 2017 Jan 1;33(1).]. |
ARDRA
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It is a fast, simple and accurate molecular tool to determine the environmental population profile. |
It has lower discriminatory power compared to other fingerprinting techniques such as DDGE, TGGE, T-RFLP, RISA and SSCP. |
Municipal wastewater [4040 Błaszczyk D, Bednarek I, Machnik G, Sypniewski D, Sołtysik D, Loch T, et al. Amplified Ribosomal DNA Restriction Analysis (ARDRA) as a Screening Method for Normal and Bulking Activated Sludge Sample Differentiation. Polish J Environ Stud. 2011;20(1):29–36.]; Industrial wastewater [4141 Princy S, Sathish SS, Cibichakravarthy B, Prabagaran SR. Hexavalent chromium reduction by Morganella morganii (1Ab1) isolated from tannery effluent contaminated sites of Tamil Nadu, India. Biocatal Agric Biotechnol. 2020 Jan 1;23:101469.–4242 Sarti A, Pozzi E, Zaiat M. Characterization of immobilized biomass by amplified rDNA restriction analysis (ARDRA) in an anaerobic sequencing-batch biofilm reactor (ASBBR) for the treatment of industrial wastewater. Brazilian Arch Biol Technol. 2012;55(4):623–9., 8585 Stets MI, Etto RM, Galvão CW, Ayub RA, Cruz LM, Steffens MBR, et al. Microbial community and performance of slaughterhouse wastewater treatment filters. Genet Mol Res. 2014 Jun;13(2):4444–55.]. |
T-RFLP
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It gives the relative amounts of bacteria of a sample with good sensibility by using fluorochome. |
The identification of different bacteria depends of the restriction enzymes that are used. |
Municipal wastewater [4343 Fredriksson NJ, Hermansson M, Wilén BM. Diversity and dynamics of Archaea in an activated sludge wastewater treatment plant. BMC Microbiol. 2012;12:140. – 4646 Matsuda M, Inoue D, Anami Y, Tsutsui H, Sei K, Soda S, et al. Comparative analysis of DNA-based microbial community composition and substrate utilisation patterns of activated sludge microorganisms from wastewater treatment plants operated under different conditions. Water Sci Technol. 2010;61(11):2843–51.]; Industrial wastewater [4747 Joshi SM, Inamdar SA, Telke AA, Tamboli DP, Govindwar SP. Exploring the potential of natural bacterial consortium to degrade mixture of dyes and textile effluent. Int Biodeterior Biodegrad. 2010 Oct 1;64(7):622–8. – 4848 Cheng HH, Liu CB, Lei YY, Chiu YC, Mangalindan J, Wu CH, et al. Biological treatment of DMSO-containing wastewater from semiconductor industry under aerobic and methanogenic conditions. Chemosphere. 2019 Dec 1;236:124291.]. |
RISA
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It has good discriminatory power and is less likely to produce inconsistent results. |
Detects only differences in ISR fragment length. Different bacteria with the same ISR length will not be discriminated. |
Industrial wastewater [2525 Yu Z, Mohn WW. Bacterial Diversity and Community Structure in an Aerated Lagoon Revealed by Ribosomal Intergenic Spacer Analyses and 16S Ribosomal DNA Sequencing. Appl Environ Microbiol. 2001 Apr;67(4):1565–74.–2727 Smith NR, Yu Z, Mohn WW. Stability of the bacterial community in a pulp mill effluent treatment system during normal operation and a system shutdown. Water Res. 2003 Dec 1;37(20):4873–84.,4949 Qu YY, Zhou JT, Wang J, Xing LL, Jiang N, Gou M, et al. Population dynamics in bioaugmented membrane bioreactor for treatment of bromoamine acid wastewater. Bioresour Technol. 2009 Jan;100(1):244–8.–5050 Silva-Bedoya LM, Sánchez-Pinzón MS, Cadavid-Restrepo GE, Moreno-Herrera CX. Bacterial community analysis of an industrial wastewater treatment plant in Colombia with screening for lipid-degrading microorganisms. Microbiol Res. 2016 Nov;192:313–25.]; Pharmaceutical wastewater [5151 Duarte P, Almeida CMR, Fernandes JP, Morais D, Lino M, Gomes CR, et al. Bioremediation of bezafibrate and paroxetine by microorganisms from estuarine sediment and activated sludge of an associated wastewater treatment plant. Sci Total Environ. 2019 Mar;655:796–806.]. |
SSCP
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It is quick, simple and cost-effective. |
There is currently no theoretical model for predicting the exact conformation of a DNA fragment under different parameters such as mutation, size of DNA fragment, G and C content, porosity of gel matrix, DNA concentration, ionic strength and pH. |
Municipal wastewater [5252 Braun F, Hamelin J, Gèvaudan G, Patureau D. Development and application of an enzymatic and cell flotation treatment for the recovery of viable microbial cells from environmental matrices such as anaerobic sludge. Appl Environ Microbiol. 2011 Dec;77(24):8487–93.]; Industrial wastewater [5353 Jabari L, Gannoun H, Khelifi E, Cayol JL, Godon JJ, Hamdi M, et al. Bacterial ecology of abattoir wastewater treated by an anaerobic digestor. Brazilian J Microbiol. 2016 Jan;47(1):73–84. – 5454 Zhao Y, Zhao Y, Wang A, Ren N. Microbial community structure in different wastewater treatment processes characterized by single-strand conformation polymorphism (SSCP) technique. Front Environ Sci Eng China. 2008 Mar;2(1):116–21.]; Gelatinaceous wastewater [5555 Mostafa A, El-Dissouky A, Fawzy A, Farghaly A, Peu P, Dabert P, et al. Magnetite/graphene oxide nano-composite for enhancement of hydrogen production from gelatinaceous wastewater. Bioresour Technol. 2016 Sep;216:520–8.]. |