Comparative analysis of environmental DNA extraction and purification methods from different humic acid-rich soils.
OBJECTIVE
To establish a rapid, improved soil environmental DNA extraction and purification protocol.


RESULTS
Three different soil DNA isolation and four purification strategies were compared on different soil samples with variable rates of success. Bead beating extraction gave significantly higher DNA yields than microwave-based and liquid nitrogen grinding DNA extraction methods. The inclusion of soil washing prior to cell lysis decreased the amount of purification steps required. Although these soil types differed, polyvinylpolypyrrolidone (PVPP)-sepharose 2B column elution was sufficient for all three samples, yielding DNA pure enough for successful application in molecular studies. One soil sample retained 80% of the initial DNA after successful purification.


CONCLUSIONS
Optimization of a purification protocol confirmed that only a combination of previously described methods proved sufficient in yielding pure environmental DNA from humic-rich soils. Total processing time for DNA extraction and subsequent purification from multiple samples was considerably more rapid than the previously described methods.


CONCLUSIONS
This study developed a new optimized soil DNA extraction and purification protocol that is suitable for different environmental sources that are rich in humic acid content.
Lakay
F M
FM
Department of Microbiology, University of Stellenbosch, Matieland, South Africa. FLakay@csir.co.za
Botha
A
A
Prior
B A
BA
D001407:Bacillus / Q000737:chemistry; D004247:DNA / Q000032:analysis* / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000032:analysis / Q000302:isolation & purification; D004271:DNA, Fungal / Q000032:analysis / Q000302:isolation & purification; D004492:Edetic Acid / Q000737:chemistry; D005821:Genetic Techniques; D006812:Humic Substances; D008872:Microwaves; D009584:Nitrogen / Q000737:chemistry; D016133:Polymerase Chain Reaction / Q000379:methods; D011205:Povidone / Q000031:analogs & derivatives / Q000737:chemistry; D012685:Sepharose / Q000737:chemistry; D012987:Soil / Q000032:analysis; D012988:Soil Microbiology; D015003:Yeasts / Q000737:chemistry
D004269:DNA, Bacterial; D004271:DNA, Fungal; D006812:Humic Substances; D012987:Soil; C077842:polyvinylpolypyrrolidone; D004247:DNA; D012685:Sepharose; D004492:Edetic Acid; D011205:Povidone; D009584:Nitrogen