A Comprehensive Profile of Antibiotic Resistance Genes in the Water Column of a Shallow-Sea Hydrothermal Vent Ecosystem

Abstract

Antibiotic resistance genes (ARGs) became an emerging contaminant, and were found to accumulate in natural and man-made environments. A comprehensive understanding of the diversity and abundance of ARGs in pristine environments is critical for defining the baseline levels of environmental ARGs. However, there is limited information available on the ARG profiles of pristine environments, especially for shallow-sea hydrothermal vents ecosystems. Here, we combined 16S rRNA gene full-length amplicon sequencing and high-throughput quantitative PCR (HT-qPCR) to study the bacterial communities, and ARG abundance and diversity in the shallow-sea hydrothermal vent ecosystem of the Kueishantao Islet. The results of the 16S rRNA gene amplicon sequencing showed that several sulfur-cycling related bacterial genera, including Thiomicrorhabdus, Thioreductor, Sulfurovum, Sulfurimonas and Lebetimonas, dominated in the water column of the shallow-sea system. Temperature was the significant factor shaping the bacterial communities. The results of HT-qPCR analysis showed that the Kueishantao shallow-sea system harbored the lowest diversity (average 10 ARG subtypes) and abundance (average 1.0 × 10−3 copy per bacterial cell) of ARGs compared with other pristine (i.e., Tibet lake sediments, marine water and sediments) and anthropogenic-disturbed (i.e., drinking water reservoirs, urban ponds and wastewater treatment plants) environments. Procrustes analysis demonstrated a concordant pattern between the compositions of bacterial communities and ARGs in the shallow-sea system, while variation partition analysis revealed that the shared effects of physicochemical and bacterial communities explained >80% of the variation in the composition of ARGs. These results suggest that the vent bacterial communities and local environmental factors played an important role in shaping the distribution of the ARG profiles. Our study provides the first comprehensive overview of the background level of ARGs in a shallow-sea hydrothermal vent ecosystem.