If the metabolites of any member of any of these groups were useful they would be beneficial but if they were to be toxic then they would be harmful.
No member of any of these groups is either harmful or beneficial to humans as such.
Some species may colonise a large complex organism and the two could develop a symbiotic relationship,or the larger organism,human in this case would remain unaffected.
Some species from all three kingdoms here are parasites and in some situations they couls overwhelm the human immune system.They would then be regarded as pathogenic and harmful.
Some species produce metabolites that can be exploited by humans to their benefit in various ways and would then be called beneficial.
Here are a few examples of beneficial and harmful organisms from the three kingdoms: The beneficial followed by the harmful.
Fungi:Edible mushrooms, Aspergillus oryzae helps make soya sauce.Penicillin the first antibiotic to be discovered.
Many fungi like Ascomycetesare sapropytic and are responsible for food spoilage.
Some are parasitic on plants and cause damage to foodcrops. Candida causes human disease.
Monera: Escherichia coli lives in human guts and aids in digestion.Most fibrous food would remain undigested if we had no gut bacteria. Lactobacillis acidophilus helps make yoghurt out of milk and there are combinations of monerans that are used to make cheese, wine and other foods that require fermentation.
Streptomyces is used to make antibiotics.
Pneumonia and tuberculosis are caused by bacteria, as are all diseases that could be treated with antibiotics.
Protists: Phytoplankton ,the single celled green organisms are the earliest producers of oxygen on Earth. Their fossil remains on the ocean floors are our source of deep sea petroleum.
Brown algae serve as sources of iodine and alginate a thickening agent in foods.
The most famous harmful protist is Plasmodium the malarial parasite.Trypanosoma and amoba are two other pathogenic protists.