If a large population of helpful bacteria is in a place where a smaller population of harmful bacteria lives the species have several options for interaction:
- No interaction (neutralism): this means that there is no effect of one species on the other (very unlikely in this case)
- Positive interaction (commensalism or mutualism): one species helps the other to survive where either one or both benefits (think of an anemone and clownfish)
- Negative interaction (competition, ammensalism, or antagonism/predation): harm is caused to one species by another
The thinking behind this solution is that there will be a negative interaction between the two species. Since they need the same resources to survive, the species will be in direct competition. If a large enough population of helpful bacteria is introduced, the harmful bacteria will be outcompeted for resources, leading the species to either die off or be so small that the effect they have is negligible.
This is a very common species interaction in an environment and often leads to extinction or endangerment of a particular organism in an ecosystem. A common example of interspecific competition is cheetahs and lions. They have the same prey, so when both exist in an area one or bot populations is hurt by lack of resources.
Hope that helps!