IS6100 proliferates in environments continuously exposed to pesticides

There is a rise in anthropogenic activities coming from industries, agricultural practices and roadside pollution. Microorganisms, especially bacteria, have evolved to withstand various environmental stressors. This adaptability happens by mobile genetic elements that can transfer genes among bacteria or within the genome. Insertion sequences facilitate this horizontal gene transfer and promote genetic diversity within microbial communities. IS6100 has been found to form composite transposons carrying genes responsible for antibiotic resistance and the catabolism of organic pollutants​​. These CTs, flanked by IS elements, are important in the spread of functional genes that enable bacteria to survive and adapt to contaminated environments.

In my thesis, I aimed to understand the role of IS6100 in the genetic adaptation of soil microbial communities in complex natural environments. For this I looked at the abundance and distribution of this element in Belgian soil samples and recover and identify the cargo genes IS6100 composite transposons carry by a novel established LR-PCR method that can amplify up to 25 kb. By exploring the complex dynamics of IS6100 related CTs within polluted soils, it was aimed to obtain a deeper insight into the function of these elements in microbial community adaptability and pollutant degradation.

Belgian soil samples were taken across various regions with exposures to different pollutions including pesticides, zink contamination, PFAS contamination and others. It was found that IS6100 was widespread and omnipresent in all samples. Notably, the highest abundance was found in samples from a bio-purification system, where there is a continuous exposure to pesticides. I could be concluded that soil samples continuously exposed to pesticides exhibited elevated IS6100 abundances compared to those with less clear contaminants. Examining the functionality of the genetic cargo that is carried by IS6100 CTs in the different soils might shed more light on the involvement of IS6100 in the local community adaptation. A novel approach using long-range PCR (LR-PCR) combined with long-read nanopore sequencing allowed for the identification of the cargo genes associated with IS6100 in these environments. It was confirmed that the amplicons were sequenced successfully and future analysis should investigate the function of these cargo genes.

The findings from these studies underscore the significant role of IS6100 in the adaptability of bacterial communities to anthropogenic stressors. By facilitating the horizontal transfer of essential adaptive genes, IS6100 not only promotes survival in polluted environments but also enhances the functional potential of microbial communities. 

Fig. 1. Relative abundances of IS6100 in the Belgian soils sampled from different environments exposed to various pollution types. BPS soil samples show the highest relative abundance, while the PFAS soil the lowest relative abundances. The soil samples showing a significant higher relative abundance of IS6100 compared to PFAS are circled in red (Conover, P<0.05). Samples are ordered by decreasing tnpA relative abundance (log(tnpA/106 16S rRNA)). The median was 2.578 log(tnpA/106 16S rRNA) in the IN sample from a field sprayed with pesticides.