SRP311552 PRJNA715957 Study of Bacterial predator-prey interactions A fundamental question in community ecology is the role of predator-prey interactions in food-web stability and species coexistence. Although microbial microcosms offer powerful systems to investigate it, interrogating the environment is much more arduous. Here, using a high-throughput sequencing approach, we show in a one-year survey that in the naturally complex, species-rich environments of wastewater treatment plants, the obligate predators Bdellovibrio and like organisms (BALOs) regulate prey populations in a density-dependent manner. However, as BALO strains differed in prey range, abundant as well as rarer prey populations were affected, leading to an oscillating predatory landscape shifting at various temporal scales in which the total population remained stable. Shifts, along with differential prey range explained co-existence of the numerous predators through niche partitioning. These sequence-based findings were validated by single cell sorting combined with fluorescent hybridization and community sequencing. The novel approach should be applicable for deciphering community interactions at large.