Identification of diverse antibiotic resistant bacteria in agricultural soil with H₂¹⁸O stable isotope probing and metagenomics

Abstract

Background: In this study, we aimed to identify bacteria able to grow in the presence of several antibiotics including the ultra-broad-spectrum antibiotic meropenem in a British agricultural soil, by combining DNA stable isotope probing (SIP) with high throughput sequencing. Soil was incubated with cefotaxime, meropenem, ciprofloxacin and trimethoprim in 18O-water. Metagenomes and the V4 region of the 16S rRNA gene from the labelled "heavy" and the unlabelled "light" SIP fractions were sequenced. Results: After incubations, an increase of the 16S rRNA copy numbers in the "heavy" fractions of the treatments with 18O-water compared with their controls was detected. The treatments resulted in differences in the community composition of bacteria. Members of the phyla Acidobacteriota (formally Acidobacteria) are highly abundant after two days of incubation with antibiotics. Several Pseudomonadota (formally Proteobacteria) including Stenotrophomonas were prominent after four days of incubation. Furthermore, a metagenome-assembled genome (MAG-1) from the genus Stenotrophomonas (90.7% complete) was retrieved from the heavy fraction. Finally, 11 antimicrobial resistance genes (ARGs) were identified in the unbinned-assembled heavy fractions, and 10 ARGs were identified in MAG-1. On the other hand, only two ARGs from the unbinned-assembled light fractions were identified. Conclusions: The results indicate that both non-pathogenic soil- dwelling bacteria as well as potential clinical pathogens are present in this agricultural soil, and several ARGs were identified from the labelled communities, but it is still unclear if horizontal gene transfer between these groups can occur.

Antimicrobial resistance in Arctic soils is mediated by competition and facilitation

“…Differences in the abundance of ARGs and ARB with soil age between the two glacier forefields with similar soil age profiles (Fig. 3, S1-S5; Table S1-S3) may arise from varying initial levels of AMR (including ARG abundance and microbial diversity) as well as inherent variability in soil characteristics between different glacier forefields (16,27,28). It has been hypothesised that the initial microbial diversity in recently deglaciated soils results from spatial variation in the paleoenvironment before and during glacier formation (29).…”