1. Assessing impacts of DNA extraction methods on next generation sequencing of water and wastewater samples
- Author
-
Wen Zhang, Franck Carbonero, and Connie Walden
- Subjects
DNA, Bacterial ,0301 basic medicine ,Microbiology (medical) ,Trickling filter ,030106 microbiology ,Wastewater ,Real-Time Polymerase Chain Reaction ,Microbiology ,DNA sequencing ,Feces ,03 medical and health sciences ,Bioreactors ,Gemmatimonadetes ,Molecular Biology ,Bacteria ,biology ,business.industry ,Moving bed biofilm reactor ,Soil dna ,Analytic Sample Preparation Methods ,High-Throughput Nucleotide Sequencing ,Pulp and paper industry ,biology.organism_classification ,Isolation (microbiology) ,DNA extraction ,Biotechnology ,Biofilms ,Water Microbiology ,business - Abstract
Next Generation Sequencing (NGS) is increasingly affordable and easier to perform. However, standard protocols prior to the sequencing step are only available for few selected sample types. Here we investigated the impact of DNA extraction methods on the consistency of NGS results. Four commercial DNA extraction kits (QIAamp DNA Mini Kit, QIAamp DNA Stool Mini Kit, MO BIO Power Water Kit, and MO BIO Power Soil DNA Isolation Kit) were used on sample sources including lake water and wastewater, and sample types including planktonic and biofilm bacteria communities. Sampling locations included a lake water reservoir, a trickling filter, and a moving bed biofilm reactor (MBBR). Unique genera such as Gemmatimonadetes, Elusimicrobia, and Latescibacteria were found in multiple samples. The Stool Mini Kit was least efficient in terms of diversity in sampling results with freshwater lake samples, and surprisingly the Power Water Kit was the least efficient across all sample types examined. Detailed NGS beta diversity comparisons indicated that the Mini Kit and PowerSoil Kit are best suited for studies that extract DNA from a variety of water and wastewater samples. We ultimately recommend application of Mini Kit or PowerSoil Kit as an improvement to NGS protocols for these sampling environments. These results are a step toward achieving accurate comparability of complex samples from water and wastewater environments by applying a single DNA extraction method, further streamlining future investigations.
- Published
- 2017
- Full Text
- View/download PDF