Fitness equalizing mechanisms, such as trade-offs, are recognized as one
of the main factors promoting species coexistence in community ecology.
However, they have rarely been explored in microbial communities.
Although microbial communities are highly diverse, the coexistence of
their multiple taxa is largely attributed to niche differences and high
dispersal rates, following the principle “everything is everywhere, but
the environment selects”. We use a dynamical stochastic model based on
the Theory of Island Biogeography to study highly diverse microbial
communities over time across three different systems (soils, alpine
lakes, and shallow saline lakes). Here we report for the first time a
colonization-persistence trade-off in natural microbial communities. We
conclude that this trade-off is mainly driven by rare taxa, which are
occasional and more likely to follow independent colonization/extinction
dynamics. Our work also emphasizes the fundamental value of dynamical
models for understanding temporal patterns and processes in highly