Modified pretreatment method for total microbial DNA extraction from contaminated river sediment

Extraction of high-quality microbial DNA from contaminated environmental samples is an essential step in microbial ecological study. Based on previously published methods for soil and sediment samples, a modified pretreatrnent method was developed for extracting microbial DNA from heavily contaminated river sediment samples via selection of optimal pretreatment parameters （i.e., reagent solution, reaction duration, and temperature）. The pretreatment procedure involves wash ing the river sediment sample for three times with a solution containing 0.1 mol.L-1 ethylene diamine tetra- acetic acid （EDTA）, 0.1 mol- L-1 Tris （pH 8.0）, 1.5 mol. L1 NaC1, 0.1 mol. L-1 NaH2PO4, and Na2HPO4 at 65~C with 180r.min-1 for 15min to remove humic materials and heavy metals prior to the employment of standard DNA extraction procedures. We compared the results of standard procedure DNA extraction following pretreatrnent, without pretreatment, and with using a commercial PowerSoilTM DNA Isolation Kit. The results indicated that the pretreatment significantly improved the DNA quality based on DNA yield, DNA fragment length, and determination of prokaryotic diversity. Prokaryotic diversity exhibited in the DNA with the pretreatment was also considerably higher than that extracted with the Power- SoilTM DNA Isolation Kit only. The pretreatment method worked well even with a small amount of sediment sample （0.25 g or even lower）. The method provides a novel, simple, cost-effective tool for DNA extraction for microbial community analysis in environmental monitoring and remediation processes.