Option 1 -> The passage does not mention testing microbes in nutrient-rich environments to confirm their origin.
Option 2 -> DNA comparison to surface microbes is not mentioned as the confirmation method used.
Option 3 -> The passage explicitly states "DNA staining and imaging with advanced microscopes confirmed the microbes were indigenous, with intact cell walls."
Option 4 -> Clay deposits provided nutrients but were not used to confirm the microbes were indigenous.
Hence, Option 3 -> The researchers used DNA staining combined with advanced microscopy to verify the microbes were native to the rock and not contamination, as evidenced by their intact cell walls and cellular structure -> correct