Cymbals are reversed through most of the intro. Sounds to me like they used the low E on the rhythm guitar (single string note) tuned down to D or E flat and then used knob tuning to bring it up into the full E for that first note. Distortion on the guitar is heavy with weight in the low and mid frequencies.
It doesn't sound like a bass to me (sound would be rounder with more depth from the thicker strings) - that's the sound of a long neck guitar, possibly an Ibanez RG series. The low end on them sounds quite close to a light bass.