Biodegradation of emerging pollutants and the functional bacteria in the microbial community

Abstract

This study was characterized by an emphasis on the biodegradation of emerging pollutants in the environment. Starting with the fate survey of typical emerging pollutants in sewage treatment plants, two sulfonamide antibiotics, sulfadiazine and sulfamethoxazole, were selected as model chemicals to develop a holistic approach for isolating sulfonamide-degrading specialist bacteria, deciphering the complexity of sulfonamide-degrading communities, as well as identifying the functionally significant bacteria and the corresponding catabolic genes which initiated the sulfonamide biodegradation. In addition, the implemented approach has been further demonstrated applicable in probing the bacterial populations that fulfill complete mineralization of two frequently encountered artificial sweeteners, i.e. saccharin and cyclamate. Initially, six selected pharmaceutical and personal care products were subjected to simulated treatment by activated sludge. Biodegradation played as the sole role in the removal of these pollutants in conventional activated sludge treatment. According to the observed batch results, the potential of the selected pollutants to biodegradation decreases as follow diclofenac > sulfamethoxazole = sulfadiazine > roxithromycin, while trimethoprim and carbamazepine were relatively persistant in the activated sludge treatment.

Subsequently, two aerobic sulfadiazine-degrading bacterial strains, D2 and D4, affiliated with the genus Arthrobacter, were isolated from sulfadiazine-enriched activated sludge. Half-life time of complete sulfadiazine degradation was 11.3 h for strain D2 and 46.4 h for strain D4. Both isolates could degrade sulfadiazine into 12 biodegradation products via three parallel pathways, of which 2-amino-4-hydroxypyrimidine was detected as the principal intermediate product toward the pyrimidine ring cleavage. The draft genomes of D2 and D4, with the same completeness of 99.7%, were compared to other genomes of related species.

Genome-resolved metagenomics was selected as the analysis approach to catalog strain-level diversities of two long-running sulfonamide enrichment communities. The isolated Arthrobacter sp. D2 and an as-yet uncultured Pimelobacter bacterium were found to be the most abundant organisms in two enrichment communities that stably performed complete sulfadiazine/sulfamethoxazole mineralization for over 2 years. Community responses to sole carbon source perturbations suggested that the functional difference of these two strains is the ecological niches required for 2-aminopyrimidine mineralization.

Metagenomics-guided isolation successfully resulted in obtaining the pure culture of the dominant Pimelobacter bacterium. Integration of metagenomic investigation with the physiology of the isolates conclusively demonstrated the sulfadiazine mineralization in a long-running enrichment culture is prominently mediated by primary sulfadiazine-degrading specialist strain D2 in association with the 2-aminopyrimidine-degrading partner strain LG209. Experimental evidences further demonstrated the ability to carry out effective degradation of sulfadiazine/ sulfamethoxazole to 2-aminopyrimidine/ 3-amino-5-methylisoxazole in strain D2 is unique among its closely phylogenetic relatives. Correlating the physiology with genomic base analyses, seven candidate genes which putatively initiate the sulfadiazine/sulfamethoxazole biodegradation were proposed.

Finally, the genome-resolved metagenomic analysis was extrapolated to the microbial communities fulfilling complete mineralization of two typical artificial sweeteners including saccharin and cyclamate.