A Rapid and Reproducible Genomic DNA Extraction Protocol for Sequence-Based Identification of Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and Green Algae
AbstractBackground: Sequence-based identification of various microorganisms including Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and green algae necessitates an efficient and reproducible genome extraction procedure though which a pure template DNA is yielded and it can be used in polymerase chain reactions (PCR). Considering the fact that DNA extraction from these microorganisms is time consuming and laborious, we developed and standardized a safe, rapid and inexpensive miniprep protocol. Methods: According to our results, amplification of various genomic regions including SSU, LSU, ITS, β-tubulin, actin, RPB2, and EF-1 resulted in a reproducible and efficient DNA extraction from a wide range of microorganisms yielding adequate pure genomic material for reproducible PCR-amplifications. Results: This method relies on a temporary shock of increased concentrations of detergent which can be applied concomitant with multiple freeze-thaws to yield sufficient amount of DNA for PCR amplification of multiple or single fragments(s) of the genome. As an advantage, the recipe seems very flexible, thus, various optional steps can be included depending on the samples used.Conclusion: Having the needed flexibility in each step, this protocol is applicable on a very wide range of samples. Hence, various steps can be included depending on the desired quantity and quality.
Komárek, Modern classification of cyanobacteria. Cyanobacteria: an economic perspective. John Wiley & Son, West Sussex, UK, 2014.
Clerck O, Guiry MD, Leliaert F, et al. Algal taxonomy: a road to nowhere?. J Phycol 2013; 49: 215-225.
Hibbett DS, Binder M, Bischoff JF, et al. A higher-level phylogenetic classification of the Fungi. Mycol res 2007; 111: 509-547.
Mc Guire KL, Fierer N, Bateman C, et al. Fungal community composition in neotropical rain forests: the influence of tree diversity and precipitation. Microb Ecol 2012; 63: 804-812.
Dean AJ, Steneck RS, Tager D, et al. Distribution, abundance and diversity of crustose coralline algae on the Great Barrier Reef. Coral Reefs 2015; 34: 581-594.
Dighton J, White JF, Oudemans PV. The fungal community: its organization and role in the ecosystem. CRC Press, New York, USA, 2005.
Doyle JJ. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 1987; 19: 11-15.
Lodhi MA, Ye G, Weeden NF, et al. A simple and efficient method for DNA extraction from grapevine cultivars and Vitis species. Plant Mol Biol Rep 1994; 12: 6-13.
Sachinandan D, Gurpreet K, Amit R, et al. A simple method for the efficient isolation of genomic DNA from lactobacilli isolated from traditional Indian fermented milk (dahi). Indian J Microbiol 2010; 50: 412-418.
Griffin DW, Kellogg C, Peak K, et al. A rapid and efficient assay for extracting DNA from fungi. Lett Appl Microbiol 2002; 34: 210-214.
Zhu H, Qu F, Zhu L. Isolation of genomic DNAs from fungi using benzyl chloride. Acta Mycol. 1994; 13: 34.
Müller FMC, Werner KE, Kasai M, et al. Rapid extraction of genomic DNA from medically important yeasts and filamentous fungi by high-speed cell disruption. J Clin Microbiol 1998; 36: 1625-1629.
Zhang Y, Zhang S, Liu X, et al. A simple method of genomic DNA extraction suitable for analysis of bulk fungal strains. Lett Appl Microbiol 2010; 51: 114-118.
Goodwin D and Lee SB. Microwave miniprep of total genomic DNA from fungi, plants, protists and animals for PCR. Biotechniques 1993; 15: 441-432.
Liu D, Coloe S, Baird R, et al. Rapid mini-preparation of fungal DNA for PCR. J Clin Microbiol 2000; 38: 471-471.
Cenis J. Rapid extraction of fungal DNA for PCR amplification. Nucleic Acids Res 1992; 20(9): 2380.
Papizadeh M and Roayaei Ardakani M. Bio filtration of volatile sulphurous hydrocarbon-polluted air by hydrocarbon degrading Pseudomonas NISOC-11. J Biotechnol 2010: 150; 209-210.
Papizadeh M, Roayaei Ardakani M, Ebrahimipour G, et al. Utilization of dibenzothiophene as sulfur source by Microbacterium sp. NISOC-06. World J Microbiol Biotechnol 2010: 26; 1195-1200.
Saba F, Noroozi M, Ghahremaninejad F, et al. Isolation, Purification, and Identification of three Diatom species (Bacillariophyceae) from Gomishan wetland using Phylogeny and Silica-wall Ultra-Structure Analysis. Rostaniha 2016: 17(1); 28-39.