title: DNA extraction from benthic Cyanobacteria: comparative assessment and optimization.
abstract: OBJECTIVE
  Benthic Cyanobacteria produce toxic and odorous compounds similar to their planktonic counterparts, challenging the quality of drinking water supplies. The biofilm that benthic algae and other micro-organisms produce is a complex and protective matrix. Monitoring to determine the abundance and identification of Cyanobacteria, therefore, relies on molecular techniques, with the choice of DNA isolation technique critical. This study investigated which DNA extraction method is optimal for DNA recovery in order to guarantee the best DNA yield for PCR-based analysis of benthic Cyanobacteria.
  
  
  RESULTS
  The conventional phenol-chloroform extraction method was compared with five commercial kits, with the addition of chemical and physical cell-lysis steps also trialled. The efficacy of the various methods was evaluated by measuring the quantity and quality of DNA by UV spectrophotometry and by quantitative PCR (qPCR) using Cyanobacteria-specific primers. The yield and quality of DNA retrieved with the commercial kits was significantly higher than that of DNA obtained with the phenol-chloroform protocol.
  
  
  CONCLUSIONS
  Kits including a physical cell-lysis step, such as the MO BIO Power Soil and Biofilm kits, were the most efficient for DNA isolation from benthic Cyanobacteria.
  
  
  CONCLUSIONS
  These commercial kits allow greater recovery and the elimination of dangerous chemicals for DNA extraction, making them the method of choice for the isolation of DNA from benthic mats. They also facilitate the extraction of DNA from benthic Cyanobacteria, which can help to improve the characterization of Cyanobacteria in environmental studies using qPCRs or population composition analysis using next-generation sequencing.
authors: Ecology and Environmental Sciences, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.
authors: V
authors: V
authors: Gaget
authors: Ecology and Environmental Sciences, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.
authors: A
authors: A
authors: Keulen
authors: Australian Water Quality Centre, South Australia Water Corporation, Adelaide, SA, Australia.
authors: M
authors: M
authors: Lau
authors: Ecology and Environmental Sciences, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.|Australian Water Quality Centre, South Australia Water Corporation, Adelaide, SA, Australia.
authors: P
authors: P
authors: Monis
authors: Ecology and Environmental Sciences, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.
authors: J D
authors: JD
authors: Brookes
mesh_terms: D053000:Analytic Sample Preparation Methods / Q000379:methods*; D018441:Biofilms; D000458:Cyanobacteria / Q000737:chemistry / Q000235:genetics* / Q000502:physiology; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification*; D060888:Real-Time Polymerase Chain Reaction
chemical_list: D004269:DNA, Bacterial
keywords: 
  MO BIO
  ; DNA extraction; Qiagen; benthic Cyanobacteria; epilithic biofilm; phenol-chloroform