Abstract
Airborne microorganisms connect Earth's habitats, yet a central question in microbial ecology remains: do airborne communities simply reflect what is released from the surfaces below, or does local environmental context shape them? Methane oxidation offers a tractable test, because methane monooxygenase genes are restricted to defined bacterial lineages and methane is directly measurable. Pairing aerosol and underlying soil or water metagenomes across a 35-fold methane range, we show that these genes were present in every soil and water sample, yet detected in aerosols only above the landfill and dairy farm, and not above the three wetlands. The soil did not predict the air; instead, gene detection tracked local methane availability. Aerosol cell concentrations spanned 1,000 to 1,000,000 cells per cubic metre, and bacterial communities tracked their sources whereas eukaryotes were enriched in spore-dispersing fungi. Predicting what airborne microbiomes carry will therefore require accounting for local environmental context, not passive dispersal alone.