Clouds boost microbial activity in the atmosphere

The atmosphere transports biological material including living microorganisms. Whereas their survival is impaired during atmospheric transport due to desiccation and UV notably, certain organisms maintain metabolic activity and interact with physicochemical processes. This has especially been studied in clouds for its potential impacts on chemical processes such as the degradation of organic compounds and the oxidant capacity. However, it is still unknown whether the functioning of airborne microorganisms in clouds is specific and differs from the rest of the atmosphere; this question was investigated here. We developed a metagenomic/metratranscriptomic approach to investigate the in-situ functioning of airborne microbial communities and decipher its environmental drivers, notably the impacts of the presence of condensed water in clouds. Aerosol and clouds samples were collected from puy de Dôme mountain summit (1465 m asl, France) using series of high flow rate impingers, into a fixative agent to preserve nucleic acids (DNA and RNA), i.e. the identity and instantaneous functional signature of organisms. A bioinformatics pipeline was developed specifically to analyze these unprecedented and complex datasets. Comparative analyses revealed that clouds are genuine oases for living microorganisms in the atmosphere: although their microbial biodiversity is similar as that during clear atmospheric situations, droplets provide shelters especially against oxidative stress, which is found to characterize the metabolic functioning of airborne microbes in dry aerosols. The presence of condensed water boosts many biological functions, and functions related with starvation toward carbon and nitrogen notably indicate increased biological needs and evidence the existence of numerous interactions with chemical processes and atmospheric biogeochemical cycles. Regarding microbial ecology, the reactivation of metabolic functions in airborne microorganisms transiting through clouds could facilitate their settlement in their new environment.