Biodiversity, or the relative abundance of species, measures the persistence of an ecosystem. To better understand its modulation, we analyzed the spatial and temporal dynamics of a synthetic, chemical-mediated ecosystem that consisted of two engineered Escherichia coli populations. Depending on the specific experimental conditions implemented, the dominant interaction between the two populations could be competition for nutrients or predation due to engineered communication. While the two types of interactions resulted in different spatial patterns, they demonstrated a common trend in terms of the modulation of biodiversity. Specifically, biodiversity decreased with increasing cellular motility if the segregation distance between the two populations was comparable to the length scale of the chemical-mediated interaction. Otherwise, biodiversity was insensitive to cellular motility. Our results suggested a simple criterion for predicting the modulation of biodiversity by habitat partitioning and cellular motility in chemical-mediated ecosystems.