Penelope Boston, the director of NASA's Astrobiology Institute, and her team have spent years exploring Mexico's Naica Mine in Chihuahua looking for extremophiles, which contain caves as large as cathedrals. Is it just because English isn't my first language, or does that sentence sound weird to native speakers too? Like the extremophiles contain "caves as large as cathedrals"
It should rather be "Looking for extremophiles Penelope Boston, the director of NASA's Astrobiology Institute, and her team have spent years exploring Mexico's Naica Mine in Chihuahua, which contains caves as large as cathedrals." and even then it's quite cumbersome to read because there are too many modifiers.
Sentences like that should simply be split up in order to avoid such problems and to be more comprehensible. Unfortunately, many writers seem to equate long sentences with sounding intelligent (speaking from personal experience here ... school and academia can teach you bad writing habits that take some time to unlearn).