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Abstract:

Background: Mobile genetic elements (MGEs) like plasmids and transposons are often carriers of catabolic gene functions or antibiotic resistances. Therefore they represent a good target for metagenomic exploration of industrial desirable enzyme functions. Our aim is to increase metagenomic hit ratios through thorough environmental screening and selective targeting of MGEs in the metagenome. This work focused on the broad range IncP-1 plasmids and IS1071 composite transposons which often harbor xenobiotic catabolic genes and seem to play a key role in the adaptation of bacterial communities to degrade xenobiotic organic compounds. Whether the presence of specific recalcitrant compounds in an environment is correlated with the abundance of MGEs and its xenobiotic degradation capacity has not been studied. Therefore, we examined the prevalence of IncP-1 plasmids and IS1071 in different polluted environments. The ecosystems included material artificially polluted with pesticides in lab microcosms experiments, farm yard biopurification systems treating pesticide polluted wastewater, a woodland soil, a PAH contaminated soil and a Zn contaminated soil. Moreover, degradation capabilities of certain pesticides were evaluated in selected ecosystems. Material & Methods: The IncP-1 trfA gene and the IS1071 gene tnpA were amplified and amplicons were Southern hybridized with trfA or tnpA probes. MGE-content was quantified with qPCR targeting the IncP-1 gene korB gene and the IS1071 tnpA gene. Gene copy numbers were normalized to the bacterial 16S rRNA gene copy number. 92   Samples from selected ecosystems were suspended in minimal media containing either 14C-labeled atrazine, linuron, or metamitron and mineralization was followed based on cumulative 14CO2 production. Key Results: The microcosm data show that both IncP-1 and IS1071 increased in number after addition of pesticides. IS1071 is found in high contents in all other environments including non-contaminated ecosystems. IncP-1 on the other hand seems more associated with organic polluted ecosystems. Most biopurification systems were able to mineralize both linuron and metamitron, only one was able to mineralize the three pesticides. Mineralization of the easily degradable metamitron was observed in most samples even in the Zn polluted soil but not in the woodland soil and in pristine biopurification system material. Overall, non-organic xenobiotic polluted ecosystems showed less capacity to mineralize pesticides than organic xenobiotic polluted ecosystems. Conclusions: Higher contents of IncP-1 and IS1071 are found in samples exposed to high concentrations of pesticides. Environmental samples capable of degrading chloroaromatics show high IncP-1 and IS1071 contents. Prevalence of IS1071 is more general than first presumed. Probably other gene functions besides xenobiotic catabolic genes are transferred by IS1071 elements.