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The mechanisms of species coexistence make ecologists fascinated, although theoretical work shows 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, the evolutionary trend of food web structure changes with the relative predation strength is more diverse 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.

Understanding plankton dynamics in marine and lake ecosystems under eutrophication is currently a hot topic in the literature. Simple theoretical models predict appearance of large amplitude oscillations of species densities in nutrient-rich waters; however, such predictions do not always correspond to field observations. Recent models taking into account heterogeneity of the growth rate of phytoplankton and active food-searching behavior of zooplankton demonstrated that grazers can efficiently control phytoplankton densities at low values even for a high nutrient stock. In this paper, we extend the previous modeling findings on the role of fast-moving plankton grazers by exploring a more realistic case where the limiting nutrient is a dynamical variable. Thus, the growth of phytoplankton across the water column depends on both light attenuation and dynamical depletion of nutrients. We also consider a more realistic scenario of a depth-dependent vertical turbulent diffusion. Most of the previous results on stabilization of planktonic ecosystems still hold; however, some alternative mechanisms of bloom suppression can also be possible. In particular, we demonstrate that the foraging of zooplankton according to the ideal free distribution (IFD) of food (which was previously considered to be a crucial condition for stabilization) may be less stabilizing than random foraging of zooplankton. We also show that stable top-down control in the ecosystem would be highly dependent on values of vertical diffusion and on the nutrient concentration in deep layers.