Gas in gravel

Hi Everyone. I moved to a new apartment this weekend along with my 29 gallon reef. I took as much old water with me as I could, leaving about 2 inches of water above the crushed coral substrate. Everything is doing great, but I'm noticing some gas bubbles in the substrate. I'm sure stuff died. Is this is some kind of gas left behind from that? Should I take a gravel vac and suck them out? Any help would be great!
 
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