Time-series transcriptomic analysis reveals survival strategies of dominant strains in a domesticated community and their influence on polyhydroxyalkanoates synthesis in co-culture

Abstract

Mixed microbial cultures are increasingly employed to enhance the production of value-added metabolites like polyhydroxyalkanoates (PHA). However, the role of interspecies interactions in shaping PHA yield and monomer composition remains unclear. In this study, we investigated the impact of co-culturing two PHA-producing strains, Paracoccus shandongensis wg2 and Brevundimonas diminuta R79, which were enriched from activated sludge, on PHA production and gene expression under different carbon sources. When supplied with acetate, the mono-culture of wg2 yielded the highest PHA content, however, co-culturing wg2 with R79, led to reduced PHA accumulation, primarily due to substrate competition. R79 was unable to metabolize propionate and only exhibited transient growth sustained by internal reserves, thereby leaving wg2 as the dominant propionate consumer. Under mixed-carbon conditions, the co-culture demonstrated enhanced production of poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) and a higher proportion of 3-hydroxyvalerate (3HV) compared to wg2 mono-cultures, suggesting that interspecies interactions promote monomer diversification. Transcriptomic analysis revealed that co-culture conditions induced differential expression of key metabolic genes in wg2. Specifically, under acetate competition, genes associated with acetate assimilation (acs) and PHA biosynthesis (phaC) were upregulated. In mixed-carbon cultures, genes involved in propionate assimilation (prpE, aspC, leuA) showed increased expression. Overall, our findings underscore that species interactions modulate carbon flux distribution and monomer composition, suggesting that rationally designing microbial communities with complementary metabolic capabilities could serve as a promising strategy to enhance PHA production.