Read the passage given below and answer the four questions that follow:-

Microorganisms were discovered in tiny cracks within 2-billion-year-old rock in South Africa, making it the oldest rock known to host life. This finding offers insights into Earth's early life and the search for extraterrestrial life.

Deep within Earth's crust, billions of resilient microbes survive in extreme isolation, far removed from sunlight, oxygen, and food sources, growing at a glacial pace over thousands or millions of years. Previously, the oldest microbial traces were found in 100- million-year-old seafloor sediments. However, Yohey Suzuki and his team at Tokyo University have pushed this record back by 2 billion years.

They extracted a 30-cm cylindrical rock core from the Bushveld Igneous Complex in South Africa, a 2-billion-year-old volcanic region. Upon slicing the core, they found microbial cells in tiny fractures. DNA staining and imaging with advanced microscopes confirmed the microbes were indigenous, with intact cell walls, suggesting they were active.

The researchers hypothesise that the microorganisms were carried into the rock via water shortly after its formation. Clay deposits in the fractures may have provided nutrients. These microbes, primitive in evolutionary terms, offer clues about Earth's earliest life forms and their evolution.

The study also has implications for Mars exploration. Suzuki notes similarities between the Bushveld rocks and Martian rocks, suggesting the same techniques could identify life on Mars.

"This underscores the deep subsurface as a crucial environment for microbial life," says Manuel Reinhardt from the University of Göttingen, while noting that microorganisms colonised the rocks after crack formation; the timing needs investigation.

How were the microbes in the rock confirmed to be indigenous?

By staining their DNA and using advanced microscopes to rule out contamination.

The correct answer is Option (3) → By staining their DNA and using advanced microscopes to rule out contamination.

The passage describes the confirmation process: "DNA staining and imaging with advanced microscopes confirmed the microbes were indigenous, with intact cell walls, suggesting they were active."

This method—using advanced microscopic techniques and DNA staining—was used to verify the microbes' presence inside the cracks and confirm that they were original inhabitants, not recent contaminants.