Many varietals of wood are used in aquascaping. The majority soften after being submerged, releasing tannins and tree sap. These tannins tint the water brown while the sugars from residual tree sap often give rise to fungi/mould.
While potentially unsightly, neither tannin-stained water nor fungi / mould are particularly harmful. However these substances can start clogging filters if present in very large quantities, typically only in aquascapes that utilize a lot of wood, as the one shown in the picture above.
Above: White / translucent gooey fungi feed on the tannins and sap released when dried driftwood is submerged. This is normal and clears up naturally after a few weeks if the tank has good filtration and is properly cycled.
In working with wood, the best approach depends on the amount of wood you are using.
A few small pieces
If you are only using a small amount of wood, the easiest way is to have them in the tank during the cycling phase (lights off, filter on) which should typically take around 3 to 4 weeks (yes, longer than we prefer!)
During that time, the water might turn a little brown and fungus may appear on the wood. It is perfectly normal. Simply change water every few days.
The tannin stains and fungi should disappear naturally after the tank has been properly cycled, and ready for planting.
A moderate amount
If you are using a moderate amount of wood, it may be good to soak the wood first, which means submerging it in water, either in the tank or in a separate bucket, for a few days or a couple of weeks (depending on how much staining and fungus develops).
If soaked in the tank itself, we would typically keep both lights and filter off at this soaking stage.
Water should be changed every few days, until the water is considerably clearer and there is far less fungi.
At this stage we turn on the filter, and the normal cycling process begins. This prevents choking the filter with debris/tannins.
A large amount
If using a large amount of wood, it is generally a good idea to soak them first. This means simply soaking them either in the tank or in a separate container, no lights and filter, for as long as it takes for the tannins to leech out and the fungus to clear.
We generally would not recommend boiling the wood as it can break down and soften the internal structures of the wood. For certain wood types like Malayan driftwood that is very tough, boiling can indeed be one way to accelerate tannin release without the integrity of the wood being affected much.
However for more delicate wood types like Senggani wood, boiling them beforehand can accelerate their break down.
Boiling the wood isn't necessary in the majority of cases.
Above: It is usual for new tanks to have diatoms. This can be reduced by giving time to cycle a tank before planting, but even then may occur to some degree. The right course of action is really to do nothing at this stage. The diatoms would naturally disappear after a few weeks, leaving the plants unscathed. We can speed up the process by changing water the 2Hr Way more frequently during the first few weeks.
Expect wood to release water-staining tannins and trigger fungi growth after being submerged. They can be unsightly, but are relatively harmless.
If using a moderate or large amount of wood, soaking them to remove excess tannins and sap is a good step before the usual tank cycling process.
In new tanks, Diatoms are unsightly but relatively benign and generally disappears by itself. You can minimise their occurrence by giving time for the tank to cycle before planting and adding livestock.