Metagenomic Profiling of Antibiotic Resistomes in Soil Biocrusts from Urban Green Spaces at the Continental Scale: Driving Factors, Co-Occurrence Patterns, and Assembly Processes

Abstract

Soil is an essential sink for antibiotic resistance genes (ARGs). However, the distribution patterns of antibiotic resistomes in soil biological crusts (biocrusts) and the underlying factors influencing them remain poorly understood. Here, metagenomic sequencing was used to profile antibiotic resistomes in biocrusts of urban green space soils in 54 cities across China. The biocrust samples harbored ARGs associated with resistance against 21 classes of antibiotics such as betalactams, quinolones, aminoglycosides, and tetracyclines. The major ARG hosts were Proteobacteria and Actinobacteria (bacteria), while other less frequently identified hosts included Bacteroidetes, Acidobacteria, and Planctomycetes (bacteria) as well as Mucoromycota (fungi). Total ARG abundance was positively correlated with total phosphorus, available phosphorus, and lignin concentrations in biocrusts. Similarity in antibiotic resistomes exhibited a geographic distance-decay pattern, while being regulated by environmental factors (i.e., altitude, latitude, humification index, and available phosphorus concentration) and dissolved organic matter components (i.e., lignin concentration and unsaturated hydrocarbons). Moreover, the resistome profile was significantly correlated with biocrust bacterial community structure. Co-occurrence networks showed mainly positive correlations among the ARGs. Despite the contribution of deterministic processes was improved with increasing differences in geographical factors and dissolved organic matter components, stochastic processes still played a major role in resistome assembly. The findings of the present study demonstrate the ecological distribution of antibiotic resistomes in biocrusts of urban green spaces under different geographical, climatic, and soil environmental conditions over a continental scale. The results also provide a reference for public health risk management of antibiotic resistomes in future.

Keywords: antibiotic resistance gene, resistome assembly, dissolved organic carbon, geographical distribution, biological crust