Immediate thought: What happens when that bioengineered E. coli or whatever, which you're hoping evolution will make work even more efficiently, leaves your carbon-sequestering vats and starts reproducing in the wild? Eventually you reach a point where we're getting record low CO2 levels. Hello, new Ice Age.
(I am sure there are many reasons this would not happen but it certainly makes for a nice bullshit explanation if I wanted to write a story set in a far-future ice planet.)