Carl Zimmer does a great job discussing the role the role that microbes play in global carbon cycling here.  He focuses on how microbial carbon cycling relates to climate change.  Through their metabolism, these organisms are responsible for moving a huge amount of carbon around the planet (cool semi-related fact: marine microbes produce more oxygen than all land plants put together), but we barely understand who they are and what, exactly, they do.  This is one reason that predicting climate change is so difficult!