Insight into the spatiotemporal distribution of antibiotic resistance genes in estuarine sediments during long-term ecological restoration

Metagenomic analysis reveals the composition and sources of antibiotic resistance genes in coastal water ecosystems of the Yellow Sea and Yangtze River Delta

The rapid development of coastal areas has raised concerns about marine environmental pollution. In this study, metagenomics was employed to investigate antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial communities in the Yellow Sea and Yangtze River Delta in China. Multidrug resistance genes were the most abundant ARGs in these regions. Transposons and insertion_element_IS91 were the dominant MGEs, closely related to the horizontal gene transfer of ARGs. Temperature, dissolved oxygen, pH, and depth were identified as important environmental factors influencing the distribution of ARGs in seawater. Oil, agriculture, animal husbandry, and wastewater treatment plants are likely the primary sources of ARGs. From the perspective of ARG control, bacterial communities contributed the most to the development of the resistome and may carry ARGs, spreading from the Yangtze River Delta to the Yellow Sea along ocean currents. A comparison with Tara Oceans datasets revealed that the dominant ARG types and bacterial genera in coastal waters were consistent with global characteristics, with variations in ARG subtypes. This study expands knowledge on the distribution patterns of ARGs at an offshore scale and provides a reference for the prevention and control of resistant gene pollution in the Yellow Sea and Yangtze River Delta.

Antibiotic resistome dynamics in agricultural river systems: Elucidating transmission mechanisms and associated risk to water security

Usage of antibiotics in agriculture has increased dramatically recently, significantly raising the influx of antibiotic resistance genes (ARGs) into river systems through organic manure runoff, seriously threatening water security. However, the dynamics, transmission mechanisms, and potential water security risk of ARGs, as well as their response to land use spatial scale and seasonal variations in agricultural river systems remain unclear. To address these challenges, this work employed metagenomic technique to systematically evaluate the pollution and dissemination of ARGs in overlying water and sediment within a typical agricultural catchment in China. The results demonstrated significant differences between overlying water and sediment ARGs. Overlying water dominated by multidrug ARGs exhibited higher diversity, whereas sediment predominantly containing sulfonamide ARGs had higher abundance. The dynamics of ARGs in overlying water were more responsive to seasonal variations compared to sediment due to greater changes in hydrodynamics and nutrient conditions. The profiles of ARGs in overlying water were largely regulated by microbiota, whereas mobile genetic elements (MGEs) were the main forces driving the dissemination of ARGs in sediment. The variation in dissemination mechanisms led to different resistance risks, with sediment presenting a higher resistance risk than overlying water. Furthermore, Mantel test was applied to discover the impact of land use spatial scale and composition on the transmission of ARGs in river systems. The findings showed that cultivated land within 5 km of the riverbank was the key influencing factor. Cultivated land exacerbated ARGs spread by increasing MGEs abundance and nutrient concentrations, resulting in the abundance of ARGs in high-cultivated sites being twice that in low-cultivated sites, and raising the regional water security risk, with a more pronounced effect in sediment. These findings contribute to a better understanding of ARGs dissemination in agricultural watersheds, providing a basis for implementing effective resistance control measures and ensuring water security.

Overlooked interconversion between tetracyclines and their 4-epimers in soil and effects on soil resistome and bacterial community

With the widespread use of tetracycline antibiotics (TCs) and the application of manure fertilizer in farmland, TCs and their metabolites especially 4-epimers have been heavily detected in agricultural soil. However, existing studies have focused on the residual and environmental behavior of maternal TCs, and few studies have looked at the ecotoxicity of their 4-epimers in soil. In this study, the degradation and interconversion of tetracycline (TC), oxytetracycline (OTC) and their 4-epimers (4-epitetracycline, ETC; 4-epioxytetracycline, OTC) were revealed. Their effects on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and bacterial community in soil were also investigated in comparison. The results showed that the 4-epimers could be substantially transformed to their parents and degraded as a whole. The degradation rates of four selected pollutants are followed: TC > OTC > ETC > EOTC. This indicated that when TCs entered the soil, part of TCs transformed into slower-degraded 4-epimers, and these 4-epimers could also be converted back to their antibiotic parents, causing the long-term residue of TCs in soil. When added to the soil alone, TC and OTC significantly promoted the proliferation of most ARGs and MGEs, among them, trb-C, IS1247 and IS1111 were the top three genes in abundance. ETC and EOTC had little effect at the beginning. However, as the 4-epimers continuously converted into their parents after one month of cultivation, ETC and EOTC treatments showed similar promoting effect on ARGs and MGEs, indicating that the effect of ETC and EOTC on soil resistome was lagged and mainly caused by their transformed parents. Nocardioides, unclassified_Rhizobiaceae, norank_Sericytochromatia, Microlunatus, Solirubrobacter and norank_67-14 were the most frequent hosts of ARGs, Most of which belong to the phylum Actinobacteria. Due to their large transformation to TCs, slow degradation rate and potential effects on soil microbes and ARGs, the harm of TCs' 4-epimers on soil ecosystem cannot be ignored.

Seasonal hydrological dynamics affected the diversity and assembly process of the antibiotic resistome in a canal network

The significant threat of antibiotic resistance genes (ARGs) to aquatic environments health has been widely acknowledged. To date, several studies have focused on the distribution and diversity of ARGs in a single river while their profiles in complex river networks are largely known. Here, the spatiotemporal dynamics of ARG profiles in a canal network were examined using high-throughput quantitative PCR, and the underlying assembly processes and its main environmental influencing factors were elucidated using multiple statistical analyses. The results demonstrated significant seasonal dynamics with greater richness and relative abundance of ARGs observed during the dry season compared to the wet season. ARG profiles exhibited a pronounced distance-decay pattern in the dry season, whereas no such pattern was evident in the wet season. Null model analysis indicated that deterministic processes, in contrast to stochastic processes, had a significant impact on shaping the ARG profiles. Furthermore, it was found that Firmicutes and pH emerged as the foremost factors influencing these profiles. This study enhanced our comprehension of the variations in ARG profiles within canal networks, which may contribute to the design of efficient management approaches aimed at restraining the propagation of ARGs.