Copper (Cu2+), though essential as a micronutrient, can pose significant ecotoxicological risks when introduced into aquatic environments at elevated levels, primarily due to anthropogenic sources such as industrial discharge, agricultural runoff, and urban effluents. This study investigated the long-term effects of environmentally relevant copper concentrations (0, 5, 10, and 20 μg/L) on Japanese medaka (Oryzias latipes) over a six-month exposure period, focusing on reproductive toxicity, oxidative stress, immune response, and gut microbiota alterations. Histopathological analysis revealed gonadal impairments, including disrupted testicular and ovarian structures, impaired spermatogenesis, and reduced oocyte maturation. Additionally, hormonal changes revealed elevated levels of luteinizing hormone (LH), follicle-stimulating hormone (FSH), and estradiol (E2), alongside reduced testosterone (T) levels, indicating interference with the hypothalamic–pituitary–gonadal (HPG) axis. Copper exposure also altered antioxidant enzyme activities, including sex-dependent modulation of superoxide dismutase (SOD), catalase (CAT), and malondialdehyde (MDA) levels, indicating oxidative imbalance and compensatory defense responses, along with upregulation of pro-inflammatory cytokines (IL-1β, IL-6, and TNF-α). Gut microbiota analysis via 16S rRNA sequencing revealed significant dysbiosis, characterized by marked reductions in alpha diversity indices and distinct beta diversity clustering. Taxonomic profiling showed a sharp decline in beneficial phyla such as Fusobacteriota, Firmicutes, and Actinobacteriota, coupled with an enrichment of potentially opportunistic Proteobacteria and shifts in Bacteroidota and Verrucomicrobiota, indicating compromised intestinal homeostasis. Collectively, these findings demonstrate that chronic exposure to copper ions induces multi-systemic toxicity in O. latipes, impairing reproductive function, provoking oxidative and inflammatory responses, and reshaping gut microbial communities in ways that may exacerbate host physiological stress.
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