The conversion of the nutrient condition alter the phenol degradation pathway by Rhodococcus biphenylivorans B403: A comparative transcriptomic and proteomic approach

Highly toxic phenol causes a threat to the ecosystem and human body. The development of bioremediation is a crucial issue in environmental protection. Herein, Rhodococcus biphenylivorans B403, which was isolated from the activated sludge of the sewage treatment plant, exhibited a good tolerance and removal efficiency to phenol. The degradation efficiency of phenol increased up to 62.27% in the oligotrophic inorganic medium (MM) containing 500-mg/L phenol at 18 h. R. biphenylivorans B403 cultured in the MM medium showed a higher phenol degradation efficiency than that in the eutrophic LB medium. On the basis of the transcriptomic and proteomic analysis, a total of 799 genes and 123 proteins showed significantly differential expression between two different culture conditions, especially involved in phenol degradation, carbon metabolism, and nitrogen metabolism. R. biphenylivorans B403 could alter the phenol degradation pathway by facing different culture conditions. During the phenol removal in the oligotrophic inorganic medium, muconate cycloisomerase, acetyl-CoA acyltransferase, and catechol 1,2-dioxygenase in the ortho-pathway for phenol degradation showed upregulation compared with those in the eutrophic organic medium. Our study provides novel insights into the possible pathway underlying the response of bacterium to environmental stress for phenol degradation.

Automated summary

Phenol poses a threat to the ecosystem and human health, highlighting the importance of bioremediation in environmental protection. The study demonstrated that Rhodococcus biphenylivorans B403 exhibited high tolerance and removal efficiency to phenol, and could alter the phenol degradation pathway under different culture conditions. Transcriptionomic and proteomic analysis revealed significant differential expression of genes and proteins related to phenol degradation, carbon metabolism, and nitrogen metabolism between different culture conditions.