Soil is recognized as the major reservoir of antibiotic
resistance
genes (ARGs), harboring the most diverse naturally evolved ARGs on
the planet. Multidrug resistance genes are a class of ARGs, and their
high prevalence in natural soil ecosystems has recently raised concerns.
Since most of these genes express proton motive force (PMF) driven
efflux pumps, studying whether soil pH is a determinant for the selection
of multidrug efflux pump genes and thus shaping the soil resistome
are of great interest. In this study, we collected 108 soils with
pH values ranging from 4.37 to 9.69 from multiple ecosystems and profiled
the composition of ARGs for metagenomes and metagenome-assembled genomes.
We observed the multidrug efflux pump genes enriched in the acidic
soil resistome, and their abundances have significant soil pH dependence.
This reflects the benefits of high soil proton activity on the multidrug
efflux pump genes, especially for the PMF-driven inner membrane transferase.
In addition, we preliminary indicate the putative microbial participants
in pH shaping the soil resistome by applying ecological analyzing
tools such as stepwise regression and random forest model fitting.
The decisive influence of proton activity on shaping the resistome
is more impactful than any other examined factors, and as the consequence,
we revisited the influence of edaphic factors on the soil resistome;
i.e., the deterministic selection of resistance mechanisms by edaphic
factors could lead to the bottom-up shaping of the ARG composition.
Such natural developing mechanisms of the resistome are herein suggested
to be considered in assessing human-driven ARG transmissions.