Optimization of a Rapid DNA Extraction and Purification Protocol for Wastewater Biosolids

Hongping Chen, Yen-chih Chen

Research output: Contribution to journalArticle

Abstract

The aim is to optimize a rapid DNA extraction protocol for biosolids that provides high recovery and purity, and to evaluate potential biases on both quantitative and qualitative microbial analyses. A protocol with 3-step sequential DNA extractions using a modified lysis buffer and purification by a commercial DNA kit was developed and compared to a previously known high recovery solvent-based extraction method, a commercial soil DNA kit with single extraction, and the same commercial kit protocol except extracted with the modified lysis buffer. The developed protocol showed more than 7 times DNA recovery compared to the commercial kit, and comparable E. coli concentrations to the solvent-based method. Direct adoption of the commercial soil kit showed significantly lower recovery and underestimation of E. coli compared to the high recovery protocols. A simple switch of the lysis buffer also improved the DNA recovery by 5 times. Species diversity indexes from pyrosequencing analysis on the other hand showed scatter results from all protocols and only as much as 76% similarity was observed among any paired protocols. Phylogenetic analysis showed a shift of dominance as DNA recovery increases. Overall, this work shows that the developed protocol allows extraction of high quality and quantity DNA within 3 hr. However, qualitative comparisons of species structure may still vary.

Original languageEnglish (US)
Pages (from-to)1-9
Number of pages9
JournalJournal of Residuals Science and Technology
Volume10
Issue number1
StatePublished - May 21 2013

Fingerprint

Biosolids
biosolid
Purification
purification
Wastewater
DNA
wastewater
Recovery
lysis
Buffers
Escherichia coli
Soils
protocol
Biodiversity
extraction method
diversity index
species diversity
soil
Switches
phylogenetics

All Science Journal Classification (ASJC) codes

  • Environmental Engineering
  • Environmental Chemistry
  • Waste Management and Disposal

Cite this

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Optimization of a Rapid DNA Extraction and Purification Protocol for Wastewater Biosolids. / Chen, Hongping; Chen, Yen-chih.

In: Journal of Residuals Science and Technology, Vol. 10, No. 1, 21.05.2013, p. 1-9.

Research output: Contribution to journalArticle

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