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Soil collembolans have been regarded as the effective bioindicator of environmental changes. However, the physiological mechanisms through which collembolans respond to agricultural activities are largely unknown. Given the plasticity and sensitivity to environmental changes, even subtle responses can be quantified via transcriptomics. Therefore, the relevant in situ soil ecosystem and numerically dominant collembolan species Entomobrya proxima Folsom was selected to explore the dynamic responses to fertilizer type and concentration using transcriptome sequencing over three periods (6 h, 24 h and 10 d). The results showed that exposure duration caused significant alterations in gene expression profiles. At day 10 after exposure, gene expression patterns differed remarkably between the two fertilizer types and the control. Relative to organic fertilizer, the number of DEGs was increased by 114.31% under inorganic fertilizer, which declined with increasing inorganic fertilizer concentrations. Functional enrichment analysis was indicative of enhanced fatty acid and carbohydrate metabolism and reduced disease occurrence by organic fertilizer; however, an inhibited lipid synthesis process promoted susceptibility to infection, triggered oxidative stress, etc. by inorganic fertilizer. Overall, fertilizer addition changed the transcriptional pattern of the collembolan, potentially causing shifts in pathways related to metabolism, immunity, etc. In comparison to inorganic fertilizer, organic fertilizer impacted less on the gene expression patterns, implying that organic fertilizer application may be more beneficial to soil animal health. Full article