Microbial
communities are believed to outperform monocultures in
the complete catabolism of organic pollutants via reduced metabolic
burden and increased robustness to environmental challenges; however,
the interaction mechanism in functional microbiomes remains poorly
understood. Here, three functionally differentiated activated sludge
microbiomes (S1: complete catabolism of sulfamethoxazole (SMX); S2:
complete catabolism of the phenyl part of SMX ([phenyl]-SMX) with
stable accumulation of its heterocyclic product 3-amino-5-methylisoxazole
(3A5MI); A: complete catabolism of 3A5MI rather than [phenyl]-SMX)
were enriched. Combining time-series cultivation-independent microbial
community analysis, DNA-stable isotope probing, molecular ecological
network analysis, and cultivation-dependent function verification,
we identified key players involved in the SMX degradation process. Paenarthrobacter and Nocardioides were
primary degraders for the initial cleavage of the sulfonamide functional
group (−C–S–N– bond) and 3A5MI degradation,
respectively. Complete catabolism of SMX was achieved by their cross-feeding.
The co-culture of Nocardioides, Acidovorax, and Sphingobium demonstrated that the nondegraders Acidovorax and Sphingobium were involved
in the enhancement of 3A5MI degradation. Moreover, we unraveled the
internal labor division patterns and connections among the active
members centered on the two primary degraders. Overall, the proposed
methodology is promisingly applicable and would help generate mechanistic,
predictive, and operational understanding of the collaborative biodegradation
of various contaminants. This study provides useful information for
synthetic activated sludge microbiomes with optimized environmental
functions.