Inhospitable places on our planet, from steaming hot springs to the

A. (same as above) ---- places is the subject of the second clause—wrong
B. that seem to flourish with these extreme conditions and ------ places is the subject of the second clause; also the second clause misses that; wrong
C. that seem to flourish in these extreme conditions and that are --- best
D. seeming to flourish in these extreme conditions and are ----- same as A
E. seeming to flourish with these extreme conditions and that are --- that is missing in the first clause

The first thing is that extremophiles refers to a phylum of organisms rather than places; Therefore, we are necessitated to use relative clauses introduced by the connector that to modify the nearest noun microbes; Else, the second clause will be using the places as its subject and will thus be materially incorrect.
Second, these modifiers need to be equal and parallel;