The article discusses the importance of transitioning to clean and sustainable energy sources to combat climate change and improve energy efficiency. Carbon Capture, Utilization, and Storage (CCUS), geothermal energy, and hydrogen geological storage are highlighted as effective options to reduce carbon emissions and slow down climate change. However, these subsurface applications face challenges related to technology maturity, monitoring fluid flow paths, and economic feasibility. The article emphasizes the significance of monitoring deep subsurface fluid flow paths throughout the entire process to ensure safety and efficiency. Advancements in DNA sequencing technology offer practical solutions for monitoring microbial ecosystems and fluid flow pathways in CCUS, geothermal, and hydrogen storage. By integrating DNA sequencing with traditional monitoring techniques, such as seismic and electromagnetic methods, the efficiency and safety of subsurface applications can be enhanced. This comprehensive approach can address challenges related to monitoring, uncertainty in geological description, and high costs, guiding us towards sustainable energy solutions and a cleaner, low-carbon world.