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Hernández, Marcela 
ORCID: https://orcid.org/0000-0002-1041-785X, Roy, Shamik ORCID: https://orcid.org/0000-0002-9916-5651, Keevil, C. William and Dumont, Marc G.
(2023)
Identification of diverse antibiotic resistant bacteria in agricultural soil with H218O stable isotope probing combined with high-throughput sequencing.
Environmental Microbiome, 18.
ISSN 2524-6372
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Abstract
Background: 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: 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) were highly abundant after two days of incubation with antibiotics. 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. In comparison, 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.
| Item Type: | Article |
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| Additional Information: | Data Availability Statement: Sequence data were deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA428598 for 16 S rRNA gene sequences, PRJNA602606 for raw metagenome data, and PRJNA778335 for MAG-1. Funding Information: This work was funded by a Natural Environmental Research Council (NERC, UK) award to Marc G. Dumont and C. William Keevil (NE/N02026X/1). Shamik Roy was supported by a NERC Discipline Hopping (DH) for Discovery Science grant awarded to Marcela Hernández (NE/X018180/1). Marcela Hernández was also supported by a Royal Society Dorothy Hodgkin Research Fellowship (DHF\R1\211076). |
| Faculty \ School: | Faculty of Science > School of Biological Sciences |
| UEA Research Groups: | Faculty of Science > Research Groups > Molecular Microbiology |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 01 Nov 2024 11:30 |
| Last Modified: | 04 Nov 2024 11:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97414 |
| DOI: | 10.1186/s40793-023-00489-7 |
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