Community and single cell analyses reveal complex predatory interactions between bacteria in high-diversity systems

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.
Conclusion:
Here, using a high-throughput sequencing approach, we show in a one-year survey that in the naturally complex, species-rich environments formed by wastewateof wastewater treatment r plants, the obligate predators Bdellovibrio and like organisms (BALOs) controlregulate prey bacterial 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. Fluorescent beads 1 µm blue FluoSpheres (F8815 (350/440), Molecular Probes Eugene, Oregon, USA), 2 µm yellow-green FluoSpheres (F-8827 (505/515), Molecular Probes Eugene, Oregon, USA) were used to align the instrument in the linear range and blue fluorescent beads Fluoresbrite BB Carboxylate microspheres 0.5 μm (360/407, lot no.: 552744, PolyScience, Niles, Illinois, USA), 1 μm (360/407, lot no.: 499344, PolyScience, Niles, Illinois, USA) were used to align the instrumental settings in the logarithmic range, in addition 0.5 µm yellow-green fluorescent Fluoresbrite - Carboxylate Microspheres (Polysciences, 15700, Warrington, PA, USA), and 0.2 µm crimson fluorescent Fluospheres - Carboxylate Microspheres (ThermoFisher Scientific, F-8806, Waltham, MA, USA) - daily.