A team of University of East London (UEL) researchers believe the airborne bugs may be behind the formation of clouds and rainfall.
The ability to manipulate the environment in this way would facilitate the microbes' dispersal and reproduction, the UK scientists claim.
Using a £130,000 grant the team plans to spend 18 months testing the theory that a self-sustaining ecosystem exists in clouds.
The study will also help scientists understand the movement of airborne pathogens like foot-and-mouth.
Early tests
Team leader Dr Bruce Moffett said a revolutionary "cyclonic cloud catcher" would be used to collect samples of cloud water from uplands across the UK.
The samples will then be analysed to discover the composition and activity of any microbes present.
Early tests around Oxford have already shown the presence of micro-organisms in low-lying cumulus clouds.
Dr Moffett said: "We are looking for evidence that microbial metabolism could have a major influence on patterns of climate and weather today.
"A really exciting possibility is that microbes have evolved ways of triggering cloud formation and rainfall to facilitate their own dispersal and reproduction.
"In other words, they could be controlling the weather."
Natural defences
Dr Moffet hopes the research could be significant for scientists working in the medical and biotechnology fields.
He believes some of the microbes which may be discovered by his team could have natural defences against ultraviolet rays.
Until now, scientists have been unable to accurately detect, identify and analyse microbial communities in harsh conditions.
Funding for the project has been provided by the Natural Environment Research Council.