Selective enrichment, identification, and isolation of diclofenac, ibuprofen, and carbamazepine degrading bacteria from a groundwater biofilm

Abstract

AbstractDiclofenac, ibuprofen, and carbamazepine are three of the most widely detected and most concerning pharmaceutical residues in aquatic ecosystems. The aim of this study was to identify bacteria that may be involved in their degradation from a bacterial biofilm. Selective enrichment cultures in mineral salt solution containing pharmaceutical compounds as sole source of carbon and energy were set up, and population dynamics were monitored using shotgun metagenome sequencing. Bacterial genomes were reconstructed using genome-resolved metagenomics. Thirty bacterial isolates were obtained, identified at species level, and tested regarding pharmaceutical biodegradation at an initial concentration of 1.5 mg l−1. The results indicated that most probably diclofenac biodegrading cultures consisted of members of generaFerrovibrio,Hydrocarboniphaga,Zavarzinia, andSphingopyxis, while in ibuprofen biodegradationNocardioidesandStarkeya, and in carbamazepine biodegradationNocardioides,Pseudonocardia, andSphingopyxismight be involved. During the enrichments, compared to the initial state the percentage relative abundance of these genera increased up to three orders of magnitude. ExceptStarkeya, the genomes of these bacteria were reconstructed and annotated. Metabolic analyses of the annotated genomes indicated that these bacteria harbored genes associated with pharmaceutical biodegradation.Stenotrophomonas humiDIC_5 andRhizobium daejeonenseIBU_18 isolates eliminated diclofenac and ibuprofen during the tests in the presence of either glucose (3 g l−1) or in R2A broth. Higher than 90% concentration reduction was observed in the case of both compounds.