Weather stains are caused by mould that grows in dark, moist conditions. Weather stains are not harmful to synthetic cloth types, but they do cause damage natural fibres such as cotton.
Mould feeds on small microscopic organisms in the air, water, or cloth surface. It is very easily spread through the air and through contact. Thus, even rainwater can be a contaminated food source.
TIP: Have you cleaned your tent or boat cover? Then ensure you also clean the pegs, poles, etc. These will certainly contain mould spores.