Not sure about a fungal infection, as such, but certainly it's possible that fungal spores are present, the ones that produce various mushrooms and toadstools - most compost these days contains lots of semi rotted wood material which does tend to produce crops of mini toadstools, as I've discovered for myself this year with this very compost. However, as you're growing them in a trough, it's also possible that the depth of soil is not sufficient, and that may be causing the problem, troughs usually being fairly shallow at between 6 and 8 inches deep.