Integrated 'omic' analyses provide evidence that a Ca. Accumulibacter phosphatis strain performs denitrification under micro-aerobic conditions

ABSTRACT The unique and complex metabolism of Candidatus Accumulibacter phosphatis has been used for decades for efficiently removing phosphorus during wastewater treatment in reactor configurations that expose the activated sludge to cycles of anaerobic and aerobic conditions. The ability of Accumulibacter to grow and remove phosphorus during cyclic anaerobic and anoxic conditions has also been investigated as a metabolism that could lead to simultaneous removal of nitrogen and phosphorus by a single organism. However, although phosphorus removal under cyclic anaerobic and anoxic conditions has been demonstrated, elucidating the role of Accumulibacter in this process has been challenging, since experimental research describes contradictory findings and none of the published Accumulibacter genomes show the existence of a complete pathway for denitrification. In this study, we use an integrated omics analysis to elucidate the physiology of an Accumulibacter strain enriched in a reactor operated under cyclic anaerobic and micro-aerobic conditions. The reactor’s performance suggested the ability of the enriched Accumulibacter (clade IC) to simultaneously use oxygen and nitrate as electron acceptors under micro-aerobic conditions. A draft genome of this organism was assembled from metagenomic reads (hereafter referred to as Accumulibacter UW-LDO-IC) and used as a reference to examine transcript abundance throughout one reactor cycle. The genome of UW-LDO-IC revealed the presence of a full denitrification pathway. The observed patterns of transcript abundance showed evidence of co-regulation of the denitrifying genes along with a cbb3 cytochrome, which is characterized as having high affinity for oxygen, thus supporting the hypothesis that UW-LDO-IC can simultaneously respire nitrate and oxygen. Furthermore, we identified an FNR-like binding motif upstream of the coregulated genes, suggesting transcriptional level regulation of the expression of both denitrifying and respiratory pathways in Accumulibacter UW-LDO-IC. Taken together, the omics analysis provides strong evidence that Accumulibacter UW-LDO-IC simultaneously uses oxygen and nitrate as electron acceptors under micro-aerobic conditions. IMPORTANCE Candidatus Accumulibater phosphatis is widely found in full-scale wastewater treatment plants, where it has been identified as the key organism for biological removal of phosphorus. Since aeration can account for 50% of the energy use during wastewater treatment, micro-aerobic conditions for wastewater treatment have emerged as a cost-effective alternative to conventional biological nutrient removal processes. Our study provides strong genomics-based evidence that Accumulibacter is not only the main organism contributing to phosphorus removal under micro-aerobic conditions, but also that this organism simultaneously respires nitrate and oxygen in this environment, consequently removing nitrogen and phosphorus from the wastewater. Such activity could be harnessed in innovative designs for cost-effective and energy-efficient optimization of wastewater treatment systems.