I have containers made of pine with hardwood bases. What is the best way to sterilize the pine wood and hardwood in the containers so that any fungus harboured in the wood (we had early blight last summer for the 3d year in a row) is killed. The first year, the plants were in raised beds (with triple mix soil); for the second year, I moved to new soil (black earth) and food grade plastic containers; last year, I built the wood containers and used new triple mix soil (1/3 topsoil, 1/3 compost, 1/3 composted manure). It appears that this fungus is airborne, as I’ve changed my strategy each year, to no avail.
Some gardeners prefer not to plant anything directly into a wooden planter, since the wood will eventually break down and you’ll need a new planter. A better solution might be to line the planters with plastic (e.g., cut-up, heavy-duty plastic bags that the soil is sold in) – this prevents the soil from touching the wood. Make sure you punch drainage holes in the bottom of the bag (and the planter too, of course).
You did not mention if the containers were stained/waterproofed. They are likely quite absorbent (e.g., if they have not been stained, or the stain is wearing off), and you could scrub and disinfect each one with a 10% chlorine bleach solution to disinfect the surface. However, although the water penetrates the wood, the bleach itself may remain on the surface, so may not attack the mould or fungus roots that are located below the surface – so it won’t kill the mould. Chlorine bleach is generally best for hard, non-porous surfaces. As well, since you have had this problem for 3 years, it might be a good idea to consider a few other issues, including the following:
• Start with new soil, one more time- Potting mixes should be of uniform texture, drain well, be lightweight, have good water holding capacity and be free of
pests and diseases.
• Make sure your compost is well-rotted and that you know where it came from – compost could be the source of the “bad” fungus.
• Do you have drainage holes in the containers?
• Make sure any stain you use on the boxes is mildew-resistant (note that mildew fungi love to eat linseed oil stain and could grow on the wood).