Bacterial communities of two contrasting soils reacted differently to lincomycin treatment

The antibiotic lincomycin an anthropogenic pollutant – may change the bacterial diversity and resistance of soil communities by increasing selection pressure in favour of resistant phenotypes. In a laboratory experiment, two forest soils of contrasting characteristics in both pH and clay content were examined for changes in their bacterial communities after lincomycin treatment. The two soils were incubated in beakers and treated with three dosages of lincomycin. Changes in bacterial community were assessed by (i) cultivation of bacteria on two different media, and percentage of resistant colonies at two lincomycin concentrations; (ii) analysis of putative actinomycete isolates for antibiotic activities and resistance; (iii) T-RFLP diversity profiles of the 16S rDNA and homologues of the resistance gene lmrB; and (iv) cloning-sequencing of PCR amplicons of both 16S rDNA and lmrB homologues. In cultivation, no increase in percentage of resistant strains in lincomycin-treated versus untreated soils was detected. Similar numbers of bacterial cells were determined by DAPI staining in the two, treated or untreated, soils; but significantly higher numbers of both total bacteria and actinomycetes were cultivated from all treatments of the high pH soil. Significantly higher numbers of antibiotic-producing bacteria as well as resistant bacteria were found in the low pH soil. Significant shifts in bacterial diversity (16S rRNA gene) were demonstrated after lincomycin treatment for the high pH soil, while the low pH soil with a higher percentage of actinomycetes and higher diversity of the lmrB homologue genes did not change after treatment. Finally, sequencing of 157 new clones of lmrB homologues revealed that the antibiotic treatment significantly influenced selection for lmrB homologues in both soils.