The process by which microorganisms (bacteria and fungi) break down complex organic nitrogen compounds in dead plants, animals, and waste materials is called ammonification. This process releases simpler inorganic forms, primarily ammonia (NH\(_3\)). In the soil, this ammonia reacts with water to form ammonium ions.

B. trioxonitrate(V) is formed in a later stage of the nitrogen cycle called nitrification, where nitrifying bacteria convert the initial ammonia/ammonium into nitrites and then nitrates.

C. ammonium salts are formed in the soil after ammonia is produced and dissolves in water, forming ammonium ions which are a component of the salts. However, the initial conversion of the organic material itself yields ammonia.

D. dioxonitrate(III) is an intermediate compound in the nitrification process, produced when ammonia is converted by bacteria like Nitrosomonas. It is then further converted to trioxonitrate(V) by Nitrobacter.

The correct answer is ammonia - option A