The contamination of microRNA of soil microbes in microRNA of rice's root

[Cheah Boon Huat]

I plan to sequence the small RNA from rice root by using Illumina next generation sequencing. I will grow the rice plants in pots. Since, there is a lot of microbes existing in the soil. It is highly possible that the microbes' RNA will be extracted together with that of rice root. Therefore, the output of the sequencing will have the noise or contaminated reads from the microbes. With this noise, it is difficult to decide whether a small RNA comes from the rice root or microbes, especially if the small RNA is new to us.Is there any realistic way in bioinformatics to solve this problem?

I only can think of the preventive approach in the wet lab, that is by treating the root with detergent to sterilize it before performing RNA extraction.