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Although the recognition of archaea as one of the three kingdoms in the tree of life has been nearly a half-century long, the comparative investigations on their ecological adaptations with bacteria have been limited. The mechanisms of their community assembly and diversity maintenance in hot springs have not been addressed. The mechanistic study is critical not only for understanding the hot-spring microbiome structure and dynamics, but also for shedding light on their evolutionary adaptations. We applied the neutral theory model and species sorting paradigm of metacommunity theory to investigate how hot-spring microbial communities were assembled, how their diversities were maintained, and how the temperature and pH influence these mechanisms. Through rigorous statistical tests based on the neutral theory and species sorting paradigm, we found ( i ) According to the neutral theory, archaeal and bacterial communities are assembled differently, with stochastic neutral force playing a more significant role in archaeal communities than in bacterial communities (neutrality-rate = 52.9 vs. 15.8%,  p -value < 0.05). ( ii ) Temperature and pH account for rather limited (<10%) variations in hot-spring microbiomes based on the species sorting paradigm. The pH has more significant influences than temperature on archaeal communities, and both pH and temperature have similarly low influences on bacterial community structure. ( iii ) We postulate that the differences between archaea and bacteria are likely due to the longer evolutionary history and better adaptation of archaea to host spring environments.

Species Sorting and Neutral Theory Analyses Reveal Archaeal and Bacterial Communities Are Assembled Differently in Hot Springs