I am looking for soil microbial community which aids in green house gases (methane and nitrous oxide), which specific genes should i need to target in order to get the picture of microorganisms involve in these gases.
You can get more information about the archaeal 16S gene or mcrA gene. Because methane is produced by methanogens. And for nitrous oxide, you can read about ammnox and denitrifying bacteria ammonia oxidising bacteria or archaea and denitrification genes like nirK, nirS, nosZ. And after getting all information about the type of analysis you want and marker, you can decide what is best marker for your needs.