Evaluation of DNA Extraction Efficiency in Diverse Algae Strains Using Commercial Kits and Lysis Approaches
- Sandia National Laboratories (SNL-CA), Livermore, CA (United States)
Efficient DNA extraction is essential for accurately monitoring microalgae communities in large-scale cultivation systems such as raceway ponds and wastewater ponds. Traditional phenol chloroform extracts are a staple in microbiology but are obsolete for routine sampling due to its high toxicity reagents and time intensive setups. Commercial DNA extraction kits are more favorable for the microbes found in these ponds, but lack specific kits made for these communities. Little is known about which kits perform the best, leading researchers to use a variety of different kits with inconsistent results. This project compared one precipitation based commercial kit (Lucigen Masterpure) and five wash based kits (Monarch, Zymo Quick-DNA, and three Qiagen DNeasy kits) using four brackish algae strains to determine which methods yield the greatest quantity and quality of genomic DNA. Extractions were evaluated using the manufacturers protocol, and additional pretreatment options were administered before a single kit to compare its potential in being added routinely before extractions. Pretreatment options included both cryogenic freeze-thawing and heat incubation using enzymes. DNA was quantified using Qubit fluorometry and NanoDrop purity ratios. Overall, the Qiagen PowerWater kit provided the highest DNA yield and purity, but at a significantly higher cost then the precipitation-based kit (MasterPure). It was also noted that while the precipitation-based kit was significantly cheaper, provided similar results, it took significantly more time to complete a single run. Cryogenic pretreatment (6x cycles) increased average DNA yields by up to 80%, whereas enzymatic pretreatment most improved purity ratios without substantially improving quantity. The results suggest that it may be more cost and time efficient to use Qiagen kits with the addition of lysis pretreatments to procure better results. Future works includes developing a better system to efficiently collect multi variable data, and to upscale to artificial polycultures using similar methodologies alongside sequencing to confirm kit results.
- Research Organization:
- Sandia National Laboratories (SNL-CA), Livermore, CA (United States)
- Sponsoring Organization:
- USDOE Office of Energy Efficiency and Renewable Energy (EERE)
- DOE Contract Number:
- NA0003525
- OSTI ID:
- 2586983
- Report Number(s):
- SAND--2025-10546R; 1787306
- Country of Publication:
- United States
- Language:
- English
Similar Records
Report on Qiagen Columns with Precipitation versus Packed Bed Technology for Trace Amounts of DNA
Technical Report
·
Mon Feb 04 23:00:00 EST 2008
·
OSTI ID:929531