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Algal–bacterial water treatment is more effective for better harvesting and promotes energy savings than other traditional treatments, while the relationships between them are multifarious. Among all the interactions, quorum sensing plays an essential ecological role. However, the relative contributions of signaling in the interaction between algae and bacteria are not clear. To elucidate the role of quorum sensing by indole-3-acetic acid (IAA) in terms of the algal–bacterial interaction during the nitrogen removal process, the bioreactors, respectively, inoculated with  Chlorella ,  Phormidium,  and both of them were started. We manifest the existence of multiple signaling-related proteins by alignment with the constructed database, and the signaling was analyzed using metagenomic sequence data obtained during bioreactor operation. We found that IAA was mainly synthetized depending on indole-3-acetamide (IAM) and indole-3-pyruvic acid (IPA) pathways by calculating the gene abundance of IAA synthetase. Both  Chlorella  and the co-culture reactor possessed higher nitrogen removal rate (NRR) than the  Phormidium  reactor, and the abundance profile of the signaling-related gene is similar with the NRR. The signaling-related gene abundance increased in  Chlorella  and co-culture reactors but decreased in the  Phormidium  reactor.  Pseudomonas ,  Hydrogenophaga,  and  Zoogloea  are the dominant signaled bacteria.  Chlorella  is the dominant signaled algae. The relative abundance of total signaled bacteria in the whole bacterial community increased during the start-up in  Chlorella  and co-culture reactors. According to the network analysis, phytoplankton prefers to positively correlate with signaled bacteria than non-signaled bacteria, which indicated that the signaling influences the algal–bacterial interaction. These findings hint at the significance of algal–bacterial signaling in this interkingdom interaction during nitrogen removal.

Metagenomic Approaches to Explore the Quorum Sensing-Mediated Interactions Between Algae and Bacteria in Sequence Membrane Photo-Bioreactors