Redox oscillation frequency reshapes antibiotic resistance-gene expression through metabolic and ecological selection in a freshwater community
- 1Vellore Institute of Technology, Vellore
Abstract
Aquatic environments can maintain and express antibiotic resistance genes even without antibiotic pressure, but the conditions that govern their activity remain poorly understood. Redox oscillations are pervasive in natural and engineered waters and strongly alter microbial metabolism, yet whether their frequency shapes resistance expression is unknown. We reanalyzed paired metagenomes and metatranscriptomes from a published chemostat experiment in which a sulfidic stream community was cycled between oxic and anoxic conditions at high, medium and low frequency (HF, MF, LF), with strain-resolved population genomics of the dominant Pseudomonas lineage. Resistance genes were broadly distributed across treatments, whereas transcription concentrated under fast cycling, reaching a median 168 TPM under HF against 38 under LF although no antibiotic was present, so genetic potential and expression diverged. Fast cycling induced ROS-generating flavoproteins, antioxidant defenses and transcription-coupled DNA repair, and Pseudomonas supplied 99% of resistance-gene transcripts under HF, chiefly through its intrinsic efflux systems. Within the dominant Pseudomonas genome, however, the four resistance genes carried no sequence variants under HF, where coverage was deepest, and no fixed difference from the reference in any sample. Genome-wide selection remained purifying throughout (pooled pN/pS 0.72 under HF against 0.12 under LF, both below 1), and the relaxation trended toward redox and central metabolism. Redox frequency therefore raises resistance expression by selecting a metabolically versatile, high-efflux lineage, while the resistance sequences themselves stay conserved. Resistance activity in aquatic systems responds to an abiotic driver, which argues for weighing expression alongside gene presence in environmental surveillance.
Related
- Rapid enhancement of antibiotic resistance and divergent remodeling of gene expression in single cells of bacteria
- A few genes modulate the ecological impact of a freshwater fish species on food webs and ecosystem functions
- Standardizing freshwater macroinvertebrate taxonomy: a Lithuanian operational taxa list for ecological quality assessments and biodiversity research.
- Ecological memory of prolonged plasmid persistence after transient antibiotic exposure
- Response to comment on “Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper”
BibTeX
@misc{manna2026redox,
title = {{Redox oscillation frequency reshapes antibiotic resistance-gene expression through metabolic and ecological selection in a freshwater community}},
author = {B. Manna and I. Keenum and Q. Liu and N. Singhal},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.29.755287},
url = {https://www.biorxiv.org/content/10.64898/2026.09.29.755287v1},
note = {CC BY-ND},
}
RIS
TY - UNPB
TI - Redox oscillation frequency reshapes antibiotic resistance-gene expression through metabolic and ecological selection in a freshwater community
AU - B. Manna
AU - I. Keenum
AU - Q. Liu
AU - N. Singhal
PY - 2026
DA - 2026/09/29
PB - bioRxiv
DO - 10.64898/2026.09.29.755287
UR - https://www.biorxiv.org/content/10.64898/2026.09.29.755287v1
AB - Aquatic environments can maintain and express antibiotic resistance genes even without antibiotic pressure, but the conditions that govern their activity remain poorly understood. Redox oscillations are pervasive in natural and engineered waters and strongly alter microbial metabolism, yet whether their frequency shapes resistance expression is unknown. We reanalyzed paired metagenomes and metatranscriptomes from a published chemostat experiment in which a sulfidic stream community was cycled between oxic and anoxic conditions at high, medium and low frequency (HF, MF, LF), with strain-resolved population genomics of the dominant Pseudomonas lineage. Resistance genes were broadly distributed across treatments, whereas transcription concentrated under fast cycling, reaching a median 168 TPM under HF against 38 under LF although no antibiotic was present, so genetic potential and expression diverged. Fast cycling induced ROS-generating flavoproteins, antioxidant defenses and transcription-coupled DNA repair, and Pseudomonas supplied 99% of resistance-gene transcripts under HF, chiefly through its intrinsic efflux systems. Within the dominant Pseudomonas genome, however, the four resistance genes carried no sequence variants under HF, where coverage was deepest, and no fixed difference from the reference in any sample. Genome-wide selection remained purifying throughout (pooled pN/pS 0.72 under HF against 0.12 under LF, both below 1), and the relaxation trended toward redox and central metabolism. Redox frequency therefore raises resistance expression by selecting a metabolically versatile, high-efflux lineage, while the resistance sequences themselves stay conserved. Resistance activity in aquatic systems responds to an abiotic driver, which argues for weighing expression alongside gene presence in environmental surveillance.
ER -