The only constant is change: Endogenous circadian rhythms of soil microbial activities

Soil microbial community rhythms are a foundational mechanism that underpins soil microbial ecological processes, but evidence of endogenous circadian rhythms in these communities which are regulated by microbial molecular oscillations is lacking. In this study we used soil total and potentially active microbial communities to explore endogenous circadian rhythms excluded diurnal environmental fluctuations. Even though the communities were sampled from constantly dark, flooded paddy soil conditions, the potentially active microbial community structures were significantly different between the surface soil's ‘day’ and ‘night’. Seven taxa were identified as circadian indicators from the presence of circadian clock genes. The circadian indicators contributed to endogenous circadian rhythms by regulating community diversity, species interactions, and community assembly. These findings emphasize the importance of diurnal-scale perspective in understanding microbial ecological processes and, more practically, in the design of microbial ecology experiments. • Soil microbial community activities showed endogenous circadian rhythms under a constant environment. • Rare OTUs contributed more in community circadian rhythms than abundant OTUs. • Seven OTUs were identified as circadian indicators possessing circadian genes potentially. • Circadian indicators regulated community endogenous circadian rhythms directly and indirectly.