Publication Date

Fall 2025

Abstract

Harmful cyanobacterial blooms (C-HABs) are increasing as climate change and nutrient enrichment create favorable environments for cyanobacteria. Although bloom-forming cyanobacteria can persist in extreme and polluted conditions, and antimicrobial resistance (AMR) and metal resistance (MR) play significant roles in bloom persistence and response to treatments, both remain understudied. Currently, most AMR detection pipelines use clinical databases developed for human pathogens which routinely fail to detect resistance genes in environmental microbes. This study evaluated AMR and MR profiles in seven freshwater cyanobacteria using both clinical AMR pipelines (CARD, ResFinder, ARG-ANNOT) and a custom environmental resistance database specifically designed to include metal detoxification systems, environmental AMR families, and cyanobacteria-relevant homologs. Clinical AMR tools successfully detected resistance genes in positive controls but failed to identify any cyanobacterial genomes, confirming that pipeline failure, and not the absence of resistance genes, led to the lack of detection. In contrast, the custom database resulted in high-confidence AMR and MR homologs across all cyanobacteria. Bloom-forming species consistently possessed larger and more diverse resistance repertoires than low-bloom taxa. The presence of strong MR pathways suggests that bloom-forming cyanobacteria may already tolerate copper-based treatments, and repeated applications may further select for strain resistance. Overall, these findings demonstrate that current resistance database pipelines are ineffective at identifying resistance in environmental cyanobacteria. There is a rising need for tools that capture the diversity of environmental resistomes and cyanobacterial resistance.

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Life Sciences

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