A machine learning approach to predict phyllosphere resistome abundance across urbanization gradients

Abstract

Recent studies reported an increased abundance of antibiotic resistance genes (ARGs) in urban greenspaces, yet the predictability of ARG variance along urbanization gradients remains unclear. We sampled paired soil and phyllosphere samples from the same site in wetland parks along urbanization gradients to assess the correlations of soil and phyllosphere ARG abundance with urbanization indices. Our results revealed that the abundance of phyllosphere resistomes correlated better with urbanization gradients than did that of soil resistomes and increased along urbanization gradients. Moreover, the phyllosphere presented more ARG-MGE (mobile gene element) pairs in metagenome-assembled genomes than soil, suggesting greater transmission potential than soil ARGs. Proximity to the built area and microbial diversity were the most important factors that significantly (p < 0.01) drove the variance in phyllosphere ARG abundance. By integrating population density, land use type, landscape metrics, and air quality data into machine learning models, we predicted phyllosphere ARG abundance at a 10-meter resolution. Among the five tested algorithms tested in the machine learning models (ridge regression, K-nearest neighbor, support vector machine, and neural network), the random forest algorithm achieved the highest accuracy with the lowest root mean square error (27.24 vs. 40.79–46.79 for the other models). These results demonstrate a strong association between phyllosphere ARG abundance and urbanization indices and provide predictions of the potential ARG risk along these gradients. The heightened transmission potential in urban greenspaces may facilitate the spread of antibiotic resistance spread to human pathogens, which poses significant public health threats.