Pond water microbiome antibiotic resistance genes vary seasonally with environmental pH and tannins
ABSTRACT Microbial communities of small freshwater bodies interact dynamically with environmental factors in unknown ways. Longitudinal sampling of four ponds in Knox County, Ohio, revealed relationships among antibiotic resistance genes (ARGs) and environmental factors such as pH and tannin concent...
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American Society for Microbiology
2025-05-01
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| Series: | Microbiology Spectrum |
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| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.03034-24 |
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| author | Maya Vaccaro Andrew M. Pilat Logan Gusmano Minh T. N. Pham Daniel Barich Audrey Gibson Mwï Epalle Dominick J. Frost Elianajoy Volin Zachary C. Slimak Chelsea C. Menke M. Siobhan Fennessy Joan L. Slonczewski |
| author_facet | Maya Vaccaro Andrew M. Pilat Logan Gusmano Minh T. N. Pham Daniel Barich Audrey Gibson Mwï Epalle Dominick J. Frost Elianajoy Volin Zachary C. Slimak Chelsea C. Menke M. Siobhan Fennessy Joan L. Slonczewski |
| author_sort | Maya Vaccaro |
| collection | DOAJ |
| description | ABSTRACT Microbial communities of small freshwater bodies interact dynamically with environmental factors in unknown ways. Longitudinal sampling of four ponds in Knox County, Ohio, revealed relationships among antibiotic resistance genes (ARGs) and environmental factors such as pH and tannin concentrations. For each site, microbial communities were collected by filtration, and metagenomes were analyzed by short-read sequencing. ARGs were quantified using the ShortBRED pipeline to detect and quantify hits to a marker set derived from the Comprehensive Antibiotic Resistance Database. The top 30 ARGs showed increased abundance at the end of the growing season. The top two ARGs with the largest marker hits encode components of a Stenotrophomonas drug efflux pump powered by proton-motive force (smeABC) and a mycobacterial global regulator that activates a drug pump and acid stress response (mtrA). The smeABC and mtrA prevalence showed a modest correlation with acidifying conditions (low pH and high tannic acids). Acidity amplifies the transmembrane pH difference component of the proton-motive force, thus increasing the cell’s energy available for pump function and ARG expression. Association with microbial taxa was tested by the Kraken2/Bracken predictor of taxa profiles. The ARG profiles showed the strongest acid dependence in ponds with a high proportion of Proteobacteria, whereas a pond with high Cyanobacteria showed the lowest ARG counts. Efflux pumps such as SmeABC and transcriptional activation by MtrA incur large energy expenditures whose function may be favored at low external pH, where the cell’s proton-motive force is maximal.IMPORTANCECompared to rivers and lakes, pond microbial ecosystems are understudied despite close contact with agriculture and recreation. Environmental microbes offer health benefits as well as hazards for human contact. Small water bodies may act as reservoirs for drug-resistant organisms and transfer of antibiotic resistance genes (ARGs). Yet, the public is rarely aware of the potential for exposure to ARG-carrying organisms in recreational water bodies. Little is known about the capacity of freshwater microbial communities to remediate drug pollution and which biochemical factors may select against antibiotic resistance genes. This study analyzes how aquatic ARG prevalence may depend on environmental factors such as pH and tannic acid levels. |
| format | Article |
| id | doaj-art-b0d521e8266c4f069fc7db2bff93af22 |
| institution | OA Journals |
| issn | 2165-0497 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | American Society for Microbiology |
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| series | Microbiology Spectrum |
| spelling | doaj-art-b0d521e8266c4f069fc7db2bff93af222025-08-20T02:14:45ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972025-05-0113510.1128/spectrum.03034-24Pond water microbiome antibiotic resistance genes vary seasonally with environmental pH and tanninsMaya Vaccaro0Andrew M. Pilat1Logan Gusmano2Minh T. N. Pham3Daniel Barich4Audrey Gibson5Mwï Epalle6Dominick J. Frost7Elianajoy Volin8Zachary C. Slimak9Chelsea C. Menke10M. Siobhan Fennessy11Joan L. Slonczewski12Department of Biology, Kenyon College, Gambier, Ohio, USADepartment of Biology, Kenyon College, Gambier, Ohio, USADepartment of Biology, Kenyon College, Gambier, Ohio, USADepartment of Biology, Kenyon College, Gambier, Ohio, USADepartment of Biology, Kenyon College, Gambier, Ohio, USADepartment of Biology, Kenyon College, Gambier, Ohio, USADepartment of Biology, Kenyon College, Gambier, Ohio, USADepartment of Biology, Kenyon College, Gambier, Ohio, USADepartment of Biology, Kenyon College, Gambier, Ohio, USADepartment of Biology, Kenyon College, Gambier, Ohio, USADepartment of Biology, Kenyon College, Gambier, Ohio, USADepartment of Biology, Kenyon College, Gambier, Ohio, USADepartment of Biology, Kenyon College, Gambier, Ohio, USAABSTRACT Microbial communities of small freshwater bodies interact dynamically with environmental factors in unknown ways. Longitudinal sampling of four ponds in Knox County, Ohio, revealed relationships among antibiotic resistance genes (ARGs) and environmental factors such as pH and tannin concentrations. For each site, microbial communities were collected by filtration, and metagenomes were analyzed by short-read sequencing. ARGs were quantified using the ShortBRED pipeline to detect and quantify hits to a marker set derived from the Comprehensive Antibiotic Resistance Database. The top 30 ARGs showed increased abundance at the end of the growing season. The top two ARGs with the largest marker hits encode components of a Stenotrophomonas drug efflux pump powered by proton-motive force (smeABC) and a mycobacterial global regulator that activates a drug pump and acid stress response (mtrA). The smeABC and mtrA prevalence showed a modest correlation with acidifying conditions (low pH and high tannic acids). Acidity amplifies the transmembrane pH difference component of the proton-motive force, thus increasing the cell’s energy available for pump function and ARG expression. Association with microbial taxa was tested by the Kraken2/Bracken predictor of taxa profiles. The ARG profiles showed the strongest acid dependence in ponds with a high proportion of Proteobacteria, whereas a pond with high Cyanobacteria showed the lowest ARG counts. Efflux pumps such as SmeABC and transcriptional activation by MtrA incur large energy expenditures whose function may be favored at low external pH, where the cell’s proton-motive force is maximal.IMPORTANCECompared to rivers and lakes, pond microbial ecosystems are understudied despite close contact with agriculture and recreation. Environmental microbes offer health benefits as well as hazards for human contact. Small water bodies may act as reservoirs for drug-resistant organisms and transfer of antibiotic resistance genes (ARGs). Yet, the public is rarely aware of the potential for exposure to ARG-carrying organisms in recreational water bodies. Little is known about the capacity of freshwater microbial communities to remediate drug pollution and which biochemical factors may select against antibiotic resistance genes. This study analyzes how aquatic ARG prevalence may depend on environmental factors such as pH and tannic acid levels.https://journals.asm.org/doi/10.1128/spectrum.03034-24antibiotic resistancefreshwatermetagenomicsenvironmental microbiology |
| spellingShingle | Maya Vaccaro Andrew M. Pilat Logan Gusmano Minh T. N. Pham Daniel Barich Audrey Gibson Mwï Epalle Dominick J. Frost Elianajoy Volin Zachary C. Slimak Chelsea C. Menke M. Siobhan Fennessy Joan L. Slonczewski Pond water microbiome antibiotic resistance genes vary seasonally with environmental pH and tannins Microbiology Spectrum antibiotic resistance freshwater metagenomics environmental microbiology |
| title | Pond water microbiome antibiotic resistance genes vary seasonally with environmental pH and tannins |
| title_full | Pond water microbiome antibiotic resistance genes vary seasonally with environmental pH and tannins |
| title_fullStr | Pond water microbiome antibiotic resistance genes vary seasonally with environmental pH and tannins |
| title_full_unstemmed | Pond water microbiome antibiotic resistance genes vary seasonally with environmental pH and tannins |
| title_short | Pond water microbiome antibiotic resistance genes vary seasonally with environmental pH and tannins |
| title_sort | pond water microbiome antibiotic resistance genes vary seasonally with environmental ph and tannins |
| topic | antibiotic resistance freshwater metagenomics environmental microbiology |
| url | https://journals.asm.org/doi/10.1128/spectrum.03034-24 |
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