Deciphering the role of IS6100 in microbial community adaptation to anthropogenic environmental stressors
Anthropogenic activities across various land uses (e.g. roadsides, industrial areas,
agricultural zones) have introduced xenobiotics, substances not natural to the
ecosystem, in the environment, affecting soil physiochemical characteristics and soil
bacterial communities. To adapt to this changing environment, bacteria have evolved
to withstand these harsh conditions. Insertion sequences (IS) can form composite
transposons that recruit and carry along passenger genes, including those involved in
the degradation of organic pollutants. However, studies examining IS elements
abundance and its cargo in bacterial communities within their natural context is limited.
The purpose of this thesis is to improve our knowledge of the role of the IS element
IS6100 in genetic adaptation within soil bacterial communities. This research focused
on two parts, the first part on Pakistani soil samples that determined how bacterial
community structure and abundance of IS6100 associates with land uses, spatial, and
environmental factors. Land use and location exerted significant influence on alpha
and beta diversity in soil ecosystems, notably with agricultural soil demonstrating
higher diversity due to increased disturbance. While environmental factors such as Cu,
total nitrogen, As, Cd, and total carbon contribute to soil bacterial community variability,
their impact is relatively small compared to land use in shaping soil bacterial
composition. Nevertheless, 86% unexplained variability suggests the presence of
additional important factors that were not measured in our study. IS6100 is
widespread, with no differences in abundance across various geographic Pakistani
samples with differing land use. While effects of environmental factors including
community diversity was low, some toxic contaminants like DiPCB and TriPCB
exhibited a negative correlation with IS6100 abundance. The second part examined
contaminated soils in Belgium, assessing IS6100 abundance by qPCR. Moreover, a
new long-range PCR (LR-PCR) method was applied to amplify the cargo of IS6100
associated CTs for functional analysis by nanopore sequencing. IS6100 was present
across all samples, with significant variations in relative abundance between soils.
Particularly, soil samples continuously exposed to pesticides exhibited elevated
IS6100 abundances compared to those with less clear contaminants. Regarding cargo
genes identification, clear bands in the AGE for every sample suggested that the LR
PCR IS6100 cargo genes were successfully and reproducibly amplified. The amplicons
were successfully sequenced by nanopore sequencing for future functional analysis.
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