From Biofilms to Biocontrol: Aquaculture Biofilms as a Reservoir of Pseudomonas spp. with Activity Against Fish and Human Pathogens

Abstract

The antimicrobial resistance crisis, driven by excessive use of antimicrobials in medical and agricultural settings, has spurred the search for alternative strategies. In the present study, we investigated surface biofilms from a rainbow trout aquaculture facility to identify bacteria with inhibitory activity against fish and human pathogens. A total of 906 isolates were obtained, of which 478 were taxonomically classified using full-length 16S rRNA gene sequencing, revealing Pseudomonas, Aeromonas, and Flavobacterium as the most abundant genera. Twenty-nine isolates, predominantly novel Pseudomonas species, inhibited one or more fish pathogen strains, with two P. aphyarum strains inhibiting every fish pathogen tested. All human pathogen strains were inhibited by at least one trout farm isolate. A biofilm assay identified strains capable of excluding F. columnare from established biofilms. Numerous strains reduced biofilm colonization, with P. aphyarum and P. idahonensis strains exhibiting the greatest reduction. Genome analysis and biosynthetic gene cluster (BGC) identification from a subset of isolates revealed shared and unique clusters with strong potential for antimicrobial production, correlating in part with observed inhibition patterns. Metabolomics profiling identified a suite of strain-specific siderophores that may mediate biofilm disruption. Additionally, co-culture of these isolates with the human pathogen Pseudomonas aeruginosa enhanced the production of specialized metabolites with reported antimicrobial activities. Collectively, these findings highlight trout farm biofilms as a promising source of bacteria that could be developed as probiotics or investigated for novel antimicrobial discovery. ImportanceDisease outbreaks in aquaculture facilities pose significant threats to food security and often rely on antibiotic treatments, contributing to antimicrobial resistance. This study identifies Pseudomonas isolates from native biofilms of a trout aquaculture facility that are capable of disrupting biofilms and inhibiting a wide range of fish and human pathogens. These Pseudomonas isolates produce a variety of siderophores that may mediate biofilm disruption, offering a promising avenue for developing probiotic applications or the discovery of new antimicrobials to improve aquaculture health and reduce reliance on antibiotics. The discovery of these biofilm-disrupting bacteria holds potential significance for combating antimicrobial resistance in both aquaculture and clinical settings.