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Petrified wood is usually made of silicates (like agate and quartz) and therefore is rather inert in a tank. Other chemical elements are often included such as iron which can give it lovely red and browns and copper which can give it greens and blues. These other elements are pretty locked up into the rock and don't leach out in any noticeable amount.
I've had a large chunk of nice agatized petrified wood with red and green in it for almost 30 years now and haven't had any problems. It's temping to turn it into slabs and cabs, but I've resisted so far.

Anther rock I use a lot in my aquariums is quartz. It's hard, pretty and inert.
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