The mechanisms of species coexistence make ecologists fascinated, although theoretical work show that omnivory can promote coexistence of species and food web stability, it is still a lack of the general mechanisms for species coexistence in the real food webs, and is unknown how omnivory affects the interactions between competitor and predator. In this work, we first establish an omnivorous food web model with a competitor based on two natural ecosystems (the plankton community and fig-fig wasp system). We analyze the changes of both food web structure and stability under the different resource levels and predation preference of the generalist/top predator. The results of model analyses show that weak predation strength can promote stable coexistence of predators and prey. Moreover, evolutionary trend of food web structure changes with the relative predation strength is more diversity than the relative competition strength, and an integration of both omnivory, increased competition, top-down control and bottom-up control can promote species diversity and food web stability. Our theoretical predictions are consistent with empirical data in the plankton community: the lower concentration of nutrient results in a more stable population dynamics. Our theoretical work could enrich the general omnivorous theory on species coexistence and system stability in the real food webs.
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