Microbial Interactions Drive the Complete Catabolism of the Antibiotic Sulfamethoxazole in Activated Sludge Microbiomes

Abstract

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.

Harnessing Paenarthrobacter ureafaciens YL1 and Pseudomonas koreensis YL2 Interactions to Improve Degradation of Sulfamethoxazole

“…The degradation of SMX by both isolated and enriched bacteria has been reported [ 26 , 27 , 28 , 29 , 30 , 31 , 32 ]. Co-cultures are superior to monocultures in biodegradation of SMX, because microorganisms can cooperate with each other to remove antibiotics [ 33 , 34 ]. Sulfonamides-degrading microbial populations have been evaluated by 16S rRNA-based molecular methods in some previous studies, however, the simple focus on the phylogenetic classification of the consortiums cannot lead to the fully understand their functions [ 35 , 36 ].…”

Anaerobic sulfamethoxazole‐degrading bacterial consortia in antibiotic‐contaminated wetland sediments identified by DNA‐stable isotope probing and metagenomics analysis

“…The biodegradation pathway of SMX under anaerobic conditions was different from that under aerobic conditions, because the transformation of SMX was initiated by hydrogenation with the cleavage of N-O bond on the isoxazole ring under anaerobic conditions, whereas the most common aerobic SA biotransformation pathway was initiated by ipso-hydroxylation with the cleavage of C-S bond (Deng et al, 2016;Ricken et al, 2013Ricken et al, , 2015. 3-amino-5-methyl-isoxazole, as the aerobic degradation product of SMX, usually could not be further converted under pure culture condition (Qi et al, 2021;Ricken et al, 2013), however, microbes can open the isoxazole rings under anaerobic conditions, and the hydrogenated products have potentials to be further assimilated and mineralized. Although the cleavage of the isoxazole N-O bond of SMX was found in sulfate-reducing activated sludge and anaerobic digestion, as well as in the aerobic culture of Acinetobacter sp.…”

“…To date, DNA‐SIP has been successfully used in the identification of active microbial populations involved in the degradation of numerous environmental contaminants, such as polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (Lerner et al ., 2020; Li et al ., 2017). Recently, the in situ aerobic SMX‐degraders have been also identified in both activated sludge and contaminated soils using DNA‐SIP (Ouyang et al ., 2019; Qi et al ., 2021; Song et al ., 2019). However, since sediments are mainly anoxic, anaerobic microbial degradation is more important for the cleanup of antibiotics, yet the active anaerobic SA‐degrading microbiota in contaminated sediments remains unknown.…”

Degrading Characterization of the Newly Isolated Nocardioides sp. N39 for 3-Amino-5-methyl-isoxazole and the Related Genomic Information

“…The strain N39 was isolated from the microbiomes A, which was described in detail previously [ 36 ]. LB agar plates were used for bacterial isolation.…”

“…In previous studies, Qi et al isolated a 3A5MI-degrading strain, Norcardiodes sp. N27, from activated sludge [ 36 ]. The genome character has also been reported [ 37 ].…”