Isolation and genomic characterization of the ibuprofen‐degrading bacterium Sphingomonas strain MPO218

Abstract

Summary The presence of pharmaceutical compounds in waters and soils is of particular concern because these compounds can be biologically active, even at environmental concentrations. Most pharmaceutical contaminants result from inefficient removal of these compounds during wastewater treatment. Although microorganisms able to biodegrade pharmaceuticals compounds have been described, the isolation and characterization of new bacterial strains capable of degrading drugs remain important to improve the removal of this pollutant. In this work, we describe the Sphingomonas wittichii strain MPO218 as able to use ibuprofen as the sole carbon and energy source. The genome of MPO218 consists of a circular chromosome and two circular plasmids. Our analysis shows that the largest plasmid, named pIBU218, is conjugative and can horizontally transfer the capability of growing on ibuprofen after conjugation with another related bacterium, Sphingopyxis granuli TFA. This plasmid appears to be unstable since it undergoes different deletions in absence of selection when growth on ibuprofen is not selected. This is the first described example of a natural and conjugative plasmid that enables growth on ibuprofen and is another example of how horizontal gene transfer plays a crucial role in the evolution of bacteria.

Genetic Characterization of the Ibuprofen-Degradative Pathway of Rhizorhabdus wittichii MPO218

“…To identify the genes affected by the transposons, we sequenced the DNA regions flanking the insertions. The results indicated that mutations were located in three main regions ( Table 1 ) as follows: (i) the noncolored mutants are affected in the ipf region previously described as necessary for IBU metabolism ( 15 , 16 ), which is located in pIBU218 (region III in Fig. 1 ); (ii) the dark mutants are affected in a region containing genes related to biodegradation of aromatic compounds and that is also located on pIBU218 ( 16 ) (region I in Fig.…”

“…The results indicated that mutations were located in three main regions ( Table 1 ) as follows: (i) the noncolored mutants are affected in the ipf region previously described as necessary for IBU metabolism ( 15 , 16 ), which is located in pIBU218 (region III in Fig. 1 ); (ii) the dark mutants are affected in a region containing genes related to biodegradation of aromatic compounds and that is also located on pIBU218 ( 16 ) (region I in Fig. 1 ); and (iii) the leaky mutant is affected in a gene annotated as a beta subunit of a propionyl-CoA carboxylase carboxyl transferase, located on the MPO218 chromosome.…”

“…Thus, while Ibu-2 accumulates a yellow intermediate while growing with IBU as the sole carbon and energy source, neither RW412 nor MPO218 develop any coloration under the same conditions. In addition, the doubling time of MPO218 growing on IBU was substantially shorter than that of RW412, around 3 h for MPO218 versus the 16 h described for RW412 ( 16 , 17 ). Murdoch et al ( 15 , 19 ) and Aguilar-Romero et al ( 17 ) have analyzed the metabolic pathway of ibuprofen biodegradation at the biochemical level showing that, in the first step, a CoA ligase binds coenzyme A to ibuprofen, which is then attacked by a dioxygenase system to form a dihydrodiol, which thereafter is cleaved by a retro-aldolase into propionyl-CoA and 4-isobutylcatechol.…”

“…Several studies have shown a toxic effect on aquatic and soil organisms exposed to IBU concentrations equivalent to those found in the environment ( 2 , 12 – 14 ), so improving wastewater treatment processes to eliminate this pollutant is a priority. Although several microorganisms capable of biodegrading IBU have been isolated to date, the metabolic pathways of this biodegradation and their genetic bases remain poorly understood ( 2 , 15 – 17 ). Although ibuprofen seems to be biodegradable, the fact that it is detected in such large amounts in the environment, and that it is detected in wastewater treatment plant (WWTP) effluents, indicates that there must be environmental factors limiting its biodegradation ( 2 , 7 , 11 , 18 ).…”

“…Within the Sphingomonadaceae family, three different strains sharing the same set of genes related to IBU biodegradation have been independently isolated worldwide. The ipf cluster, first described in the Sphingomonas ibu-2 strain by Murdoch et al ( 15 , 19 ), has been found highly conserved at the DNA level in two different strains, Rhizorhabdus wittichii MPO218 ( 16 ) (formerly Sphingomonas wittichii [ 20 ]) and Sphingopyxis granuli RW412 ( 17 ). Both MPO218 and RW412 carry the ipf genes on a large plasmid ( 16 , 17 ) that, in the case of the plasmid pIBU218 carried by R. wittichii strain MPO218, has been shown to be conjugative ( 16 ).…”