Keystone microbes affect the evolution and ecological coexistence of the community via species/strain specificity

Microbial communities exhibit different diversity and fluctuations in the ecological functions due to time and environmental migration. Despite a long history of research and a plethora of data, the factors determining the biodiversity and stability of ecosystems is still elusive.

Here, the Chinese Xiaoqu fermentation system was used as a template to explore the mechanism in which the species specificity and strain in the initial phase affect the community structure and metabolites in the subsequent micro-ecosystem. The micro-ecosystem has been applied for hundreds of years, and the main metabolic function can be reproduced and traced.

The result proved that Rhizopus spp. is a keystone microbe with a species/strain specificity affecting the trophic interaction niche and function of modules in the complex community through glucose. The fungal community was demonstrated to have a high sealing and stability, while the bacterial community was generally found to change the community structure, physiological function, and interaction relationship, producing strains with connector functions to adapt to fluctuations.

This study shows that the taxonomic level of key microbial strains can be changed to affect the evolution of coexistence and functional realisation of the community.