Hello Luisa,
Welcome to the forums! :qiime2:
I've got good news and bad news...
The good news: you are asking all the right questions! 
I'm glad you are thinking about the tradeoff between read quality and sampling depth, and about sequencing artifacts that could sneak into your data.
The bad news: if you want 
quality answers, you need positive controls.
How many positive controls did you include? What is their composition?
Colin