The more I listen to Pneuma I swear I hear a reverb on some parts. It's so hard to tell and it's probably just the delay. Justin's parts are a little understated on this album but like always the subtleties and variations make his lines much more complex than they seem at first.
Toolbassplayer just put his video up for Pneuma.
No reverb, but plenty of delay and a bit with some chorus at the end.
I still hear a whammy like tone on the intro around 50 seconds, and i don't think it's Adam. Brad does not play during that part in the video though.