Regardless of the significant differences in the environments created by each of the aeration cycles, comparison of amoA DGGE profiles showed that AOB species were rather similar among the reactors. This suggests that factors other than the operating parameters tested had a stronger influence on AOB species. The concomitant increase in AOB species diversity in all reactors during the last phase of the investigation suggests that AOB species diversity was affected by an environmental factor common to all reactors. Given that temperature, pH,and aeration cycles remained unchanged, influent characteristics are probably the strongest factor affecting AOB species diversity. Since the influent was collected from an anaerobic lagoon treating swine wastewater, it was impossible to control numerous potential factors affecting AOB species, such as ammonia concentrations, wastewater salinity, metal concentrations,organic matter, and solids content. Previous studies have shown that the microbial community in identically operated
laboratory-scale reactors can differ significantly while showing similar performances (22). Therefore, when assessing the effect of environmental parameters on the microbial communities in
laboratory-scale experiments, it is desirable to test reproducibility by either running duplicates or operating the reactors for long periods (a total of 1 year in this study).