Sub-MIC antibiotics influence the microbiome, resistome and structure of riverine biofilm communities
The effects of sub-minimum inhibitory concentrations (sub-MICs) of antibiotics on aquatic environments is not yet fully understood. Here, we explore these effects by employing a replicated microcosm system fed with river water where biofilm communities were continuously exposed over an eight-week pe...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-08-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1194952/full |
| _version_ | 1797767531718508544 |
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| author | Gabriela Flores-Vargas Darren R. Korber Jordyn Bergsveinson |
| author_facet | Gabriela Flores-Vargas Darren R. Korber Jordyn Bergsveinson |
| author_sort | Gabriela Flores-Vargas |
| collection | DOAJ |
| description | The effects of sub-minimum inhibitory concentrations (sub-MICs) of antibiotics on aquatic environments is not yet fully understood. Here, we explore these effects by employing a replicated microcosm system fed with river water where biofilm communities were continuously exposed over an eight-week period to sub-MIC exposure (1/10, 1/50, and 1/100 MIC) to a mix of common antibiotics (ciprofloxacin, streptomycin, and oxytetracycline). Biofilms were examined using a structure–function approach entailing microscopy and metagenomic techniques, revealing details on the microbiome, resistome, virulome, and functional prediction. A comparison of three commonly used microbiome and resistome databases was also performed. Differences in biofilm architecture were observed between sub-MIC antibiotic treatments, with an overall reduction of extracellular polymeric substances and autotroph (algal and cyanobacteria) and protozoan biomass, particularly at the 1/10 sub-MIC condition. While metagenomic analyses demonstrated that microbial diversity was lowest at the sub-MIC 1/10 antibiotic treatment, resistome diversity was highest at sub-MIC 1/50. This study also notes the importance of benchmarking analysis tools and careful selection of reference databases, given the disparity in detected antimicrobial resistance genes (ARGs) identity and abundance across methods. Ultimately, the most detected ARGs in sub-MICs exposed biofilms were those that conferred resistance to aminoglycosides, tetracyclines, β-lactams, sulfonamides, and trimethoprim. Co-occurrence of microbiome and resistome features consistently showed a relationship between Proteobacteria genera and aminoglycoside ARGs. Our results support the hypothesis that constant exposure to sub-MICs antibiotics facilitate the transmission and promote prevalence of antibiotic resistance in riverine biofilms communities, and additionally shift overall microbial community metabolic function. |
| first_indexed | 2024-03-12T20:41:14Z |
| format | Article |
| id | doaj.art-7a26cbc89d5c4fea94562d252da7f538 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-03-12T20:41:14Z |
| publishDate | 2023-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-7a26cbc89d5c4fea94562d252da7f5382023-08-01T09:14:03ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-08-011410.3389/fmicb.2023.11949521194952Sub-MIC antibiotics influence the microbiome, resistome and structure of riverine biofilm communitiesGabriela Flores-Vargas0Darren R. Korber1Jordyn Bergsveinson2Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, CanadaFood and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, CanadaWatershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Saskatoon, SK, CanadaThe effects of sub-minimum inhibitory concentrations (sub-MICs) of antibiotics on aquatic environments is not yet fully understood. Here, we explore these effects by employing a replicated microcosm system fed with river water where biofilm communities were continuously exposed over an eight-week period to sub-MIC exposure (1/10, 1/50, and 1/100 MIC) to a mix of common antibiotics (ciprofloxacin, streptomycin, and oxytetracycline). Biofilms were examined using a structure–function approach entailing microscopy and metagenomic techniques, revealing details on the microbiome, resistome, virulome, and functional prediction. A comparison of three commonly used microbiome and resistome databases was also performed. Differences in biofilm architecture were observed between sub-MIC antibiotic treatments, with an overall reduction of extracellular polymeric substances and autotroph (algal and cyanobacteria) and protozoan biomass, particularly at the 1/10 sub-MIC condition. While metagenomic analyses demonstrated that microbial diversity was lowest at the sub-MIC 1/10 antibiotic treatment, resistome diversity was highest at sub-MIC 1/50. This study also notes the importance of benchmarking analysis tools and careful selection of reference databases, given the disparity in detected antimicrobial resistance genes (ARGs) identity and abundance across methods. Ultimately, the most detected ARGs in sub-MICs exposed biofilms were those that conferred resistance to aminoglycosides, tetracyclines, β-lactams, sulfonamides, and trimethoprim. Co-occurrence of microbiome and resistome features consistently showed a relationship between Proteobacteria genera and aminoglycoside ARGs. Our results support the hypothesis that constant exposure to sub-MICs antibiotics facilitate the transmission and promote prevalence of antibiotic resistance in riverine biofilms communities, and additionally shift overall microbial community metabolic function.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1194952/fullantibioticsantibiotic resistancebiofilmsenvironmental resistomemicrobiomesub-MIC |
| spellingShingle | Gabriela Flores-Vargas Darren R. Korber Jordyn Bergsveinson Sub-MIC antibiotics influence the microbiome, resistome and structure of riverine biofilm communities Frontiers in Microbiology antibiotics antibiotic resistance biofilms environmental resistome microbiome sub-MIC |
| title | Sub-MIC antibiotics influence the microbiome, resistome and structure of riverine biofilm communities |
| title_full | Sub-MIC antibiotics influence the microbiome, resistome and structure of riverine biofilm communities |
| title_fullStr | Sub-MIC antibiotics influence the microbiome, resistome and structure of riverine biofilm communities |
| title_full_unstemmed | Sub-MIC antibiotics influence the microbiome, resistome and structure of riverine biofilm communities |
| title_short | Sub-MIC antibiotics influence the microbiome, resistome and structure of riverine biofilm communities |
| title_sort | sub mic antibiotics influence the microbiome resistome and structure of riverine biofilm communities |
| topic | antibiotics antibiotic resistance biofilms environmental resistome microbiome sub-MIC |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1194952/full |
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