Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem

Authors: ZHANG, YUJIE - Oak Ridge Institute For Science And Education (ORISE); KITAZUMI, AI - Texas Tech University; Liao, Yen-Te; DE LOS REYES, BENILDO - Texas Tech University; Wu, Vivian

Submitted to: Microbiology Spectrum
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/10/2023
Publication Date: 9/27/2023
Citation: Zhang, Y., Kitazumi, A., Liao, Y., De Los Reyes, B.G., Wu, V.C. 2023. Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem. Microbiology Spectrum. Article e00226-23. https://doi.org/10.1128/spectrum.00226-23.
DOI: https://doi.org/10.1128/spectrum.00226-23

Interpretive Summary: Foodborne outbreaks have become a continuous public health issue in the United States. People get sick from the consumption of pathogen-contaminated food. Previous studies indicated that contamination of fresh produce is largely from directly or indirectly contacting animal feces or contaminated water during food processing in farms. To eliminate pathogens, antibiotics were widely overused and misused in the production pipelines, resulting in the emergence of antibiotic resistance. Viruses, mostly bacteriophages, are important members of the natural agricultural microbiome and can co-exist and co-evolve with bacteria. In this study, the objective was to investigate the role of bacteriophages on the transmission of antibiotic resistance genes (ARGs) in natural agricultural environments. A total of 5 different sample types, including animal feces, soil, and surface water, were collected from an organic farm. Further, the profile of bacteria and viruses in each sample were genomically analyzed. The sequencing results showed that the most abundant bacteria and viruses were different between farm animal feces and agriculture environmental samples. Moreover, bacteriophages were found that contained diverse ARG types and had interactions with various ARG-associated bacteria in different samples. The finding from this study indicated the important roles of bacteriophages on ARG transmission across bacterial populations in natural agricultural environments.

Technical Abstract: Agricultural microbiomes are major reservoirs of antibiotic resistance genes (ARGs), posing continuous risks to human health. To understand the role of bacteriophages as vehicles for the horizontal transfer of ARGs in the agricultural microbiome, we investigated the diversity of bacterial and viral microbiota from biotic and abiotic samples in an organic farm. The profiles of bacteriome indicated the highest abundance of Bacteroidetes and Firmicutes phyla in animal feces with varying Bacteroidetes/Firmicutes ratios between herbivorous and omnivorous farm animals. The most predominant composition in abiotic samples was the phylum Proteobacteria. Compared to the bacteriome profiles, the trends in virome indicated much broader diversity with more specific signatures between the biotic and abiotic samples. Overall, viruses belonging to the Orders Picornavirales, Caudovirales, and Tubulavirales were the most predominant across the agricultural samples. Additionally, the similarities within and between biotic and abiotic components of the agricultural environment based on ARG-associated bacteria alone were much lower than that of total bacteriome composition. However, there were significant similarities in the profiles of ARG-associated viruses across the biotic and abiotic components. Moreover, the predictive models of phage-bacterial interactions on bipartite ARG transfer networks indicated that phages belonging to the Order Caudovirales, particularly in Siphoviridae family, contained diverse ARG types in different samples. Their interaction with various bacterial hosts further implied the important roles of bacteriophages on ARG transmission across bacterial populations. Our findings provided a novel insight into the potential mechanism of phage-mediated ARG transmission and their correlation with resistome evolution in natural agricultural environments.