Bacteriophage predation regulates microbial abundance and diversity in a full-scale bioreactor treating industrial wastewater

Changes in the microbial community composition of a full-scale membrane bioreactor treating industrial wastewater were studied over a period of 462 days using a series of 16S rRNA gene clone libraries. Frequent changes in the relative abundance of specific taxonomic groups were observed, which could not be explained by changes in the reactor's conditions or wastewater composition. Phage activity was proposed to drive some of the observed changes. Bacterial hosts were isolated from a biomass sample obtained towards the end of the study period, and specific phage counts were carried out for some of the isolated hosts using stored frozen biomass samples as the phage inocula. Plaque-forming unit concentrations were shown to change frequently over the study period, in correlation with changes in the relative abundance of taxonomic groups closely related by 16S rRNA gene sequence to the isolated strains. Quantitative PCR was used to verify changes in the abundance of a taxonomic group closely related to one of the isolated hosts, showing good agreement with the changes in relative abundance in the clone libraries of that group. The emerging pattern was consistent with the killing the winner hypothesis, although alternative interaction mechanisms could not be ruled out. This is the first time that phage-host interactions in a complex microbial community are demonstrated over an extended period, and possibly the first in situ demonstration of killing the winner stochastic behavior.