Direct cell extraction from fresh and stored soil samples: Impact on microbial viability and community compositions

The direct extraction of viable microbes from soil samples is critical for the application many single-cell related technologies. However, there are aspects technologies that can impact viability and diversity extractable cells fresh or stored samples. In this study, physical dispersion method, chemical Nycodenz density gradient medium concentration were optimized with two sequential rounds cell four having diverse physicochemical properties. Cell was quantified fluorescence staining flow cytometry. microbial community compositions in assessed after selective removal DNA dead cells. Among different purification methods, a protocol included blending, Tween 20 treatment, centrifugation 80% Nycodenz, had highest yield. Repeated increased yield but reduced viability. over- under-represented taxa might contribute to bias communities. Using procedure, effect storage conditions (4 °C, ?80 air-drying) on yield, viability, composition assessed. decreased all samples, significant decreases only observed air-dried Microbial changed significantly least changes at 4 confirming °C short-term suitable highly efficient extraction. Taken together, developed method offers great potential advancing our analyses understanding ecology role individual microbes.