Influence of Florfenicol Treatments on Marine-Sediment Microbiomes

Background/Objectives: Metagenomic analyses are an important tool for understanding ecological effects, particularly in sites exposed to antimicrobial treatments. Marine sediments host diverse microbial communities and may serve as reservoirs for microbial resistance. Although it is known that antimicrobials can alter microbial composition, specific impacts on sediments surrounding salmon farms remain poorly understood. This study analyzed bacterial community structure in marine sediments subjected to florfenicol treatment from salmon farms in the Los Lagos Region of southern Chile. Methods: Sediment samples were collected and examined through DNA extraction and PCR amplification of the 16S rRNA gene (V3–V4 region). Sequences were analyzed using a bioinformatics pipeline, and amplicon sequence variants were taxonomically classified with a Naïve Bayesian classifier. Results: Significant differences in bacterial phyla were observed between the control farm and two farms treated with florfenicol (17 mg kg-1 body weight per day) for 33 and 20 days, respectively. Farm 1 showed notable differences in phyla such as Bacteroidota, Bdellovibrionota, Crenarchaeota, Deferrisomatota, Desulfobacterota, Fibrobacterota, Firmicutes, and Fusobacteriota, while Farm 2 exhibited differences in the phyla Bdellovibrionota, Calditrichota, Crenarchaeota, Deferrisomatota, Desulfobacterota, Fusobacteriota, Nanoarchaeota, and Nitrospirota. Shannon Index analysis revealed reduced alpha diversity in treated farms. Conclusions: These findings highlight the considerable influence of florfenicol on sediment microbial communities and reinforce the need for sustainable management strategies to minimize ecological disruption and the spread of antimicrobial resistance.