Rust on Phaseolus beans is caused by the fungus Uromyces appendiculatus. It is unrelated to broad bean rust, which is caused by the fungus Uromyces viciae-fabae and infects Vicia beans.
The rust fungi are described as biotrophs; that is, they grow within the living tissues of the plant and extract nutrients from the cells. Although they do not kill tissues rapidly, heavy attacks by rusts can cause tissues to collapse and die prematurely and this is the case with the bean rusts. Some rusts require two different plant hosts in order to complete their life cycle but both of the bean rusts spend their entire life on the bean host.
The different coloured pustules seen on the plants as the summer progresses are the result of the rust fungi producing different types of spore. The brown pustules contain summer spores that can spread the disease very rapidly under suitable wet weather conditions, whilst the black pustules contain overwintering spores. These can survive on leaf debris to affect the following season’s crop.