Early microbial ecologists knew that hydrogen gas is oxidized in soil and that ammonia is oxidized in sewage. how did these scientists determine that microbes are responsible for these ecological reactions?

Scientist applied heat and antimicrobial treatment to sewage samples and then observed that nitrate was no longer formed in that conditions (in absence of bacteria).

Explanation:

The first step to prove anything is to actually build a hypothesis to explain why a natural phenomenon occurs.

In this particular case, microbial ecologists knew that hydrogen gas is oxidized in soil and that ammonia is oxidized in sewage as they this can be observed and measured directly by them chemically.

Then, they built and hypothesis of what could be happening that led to the oxidized of ammonia into the soil. One possibility, among others, is to postulate (hypothesize) that microbial metabolism is responsible for the ammonia being oxidized in sewage.

Indeed, at least one experiment must be done to test this hypothesis. For example, one would eliminate microbial from sewage; then:

In real world, ecologist did this experiment and obtained that no nitrate is formed when bacteria are removed from siege.