Microbes primarily exist in natural and engineered environments as multispecies consortia, particularly as biofilms. Using a synthetic biofilm community we have shown that such consortia display emergent properties, such as increased biomass and stress tolerance, compared to comparable single species biofilms. To better define how these interactions are mediated, a combination of targeted gene knockouts, transcriptomics and TraDIS approaches were used. The results show that community biofilms display altered metabolism as well as quorum sensing. Targeted deletions of quorum sensing genes demonstrate that both acylated homoserine lactone and auto-inducer-2 signalling pathways modulate community biofilm formation and mediate specific interactions between community members. TraDIS based analysis showed that two-component regulators, chemotaxis genes and nitrogen related metabolism were significantly altered in mixed species biofilms, but not in mixed species biofilms. Deletion of selected genes from the TraDIS analysis showed significant changes in either the host strain, P. protegens, or in co-occurring species, where the latter observation suggests changes in cooperative or competitive factors that drive community composition and function.