Abstract
Glyphosate is one of the most widely used herbicides worldwide and has been increasingly reported in aquatic environments, including riverine, estuarine, and coastal systems. However, information on its intestinal effects in benthic marine invertebrates remains limited. In this study, we investigated dose-dependent intestinal responses of the sea cucumber Apostichopus japonicus following acute waterborne glyphosate exposure using integrated transcriptomic and metabolomic analyses. Sea cucumbers were exposed for 24 h to four nominal glyphosate concentrations: 0, 9.23, 46.15, and 230.77 mg/L. Mortality occurred only in the highest-concentration group, allowing phenotypic stratification of this group into high-dose survivors (HL) and high-dose dead individuals (HD) for downstream multi-omics comparisons. Principal component analysis and orthogonal partial least-squares discriminant analysis indicated clear exposure- and phenotype-associated shifts in intestinal molecular profiles. Differential expression analysis and pathway enrichment showed that low-dose exposure was mainly associated with metabolic and digestion-related adjustments, whereas higher exposure levels were characterized by broader perturbation of immune regulation, stress-response signaling, proteostasis-related processes, and cell fate-associated pathways. Metabolomic profiling further revealed progressive remodeling of lipid, amino acid, energy, redox, and transport-related pathways, with the most extensive alterations observed in HD. Integrated transcriptome–metabolome analysis supported increasingly structured cross-omics covariation with rising exposure severity, highlighting coordinated intestinal system disruption under high-dose glyphosate stress. Overall, these findings demonstrate that acute waterborne glyphosate exposure induces dose-dependent intestinal molecular reprogramming in A. japonicus, with marked divergence between surviving and dead individuals at the highest exposure level. This study provides mechanistic evidence for early intestinal responses to glyphosate in a representative marine deposit-feeding invertebrate and offers a basis for future studies linking controlled exposure experiments with environmentally relevant marine risk scenarios.