Circulating exosome miRNAs, is it the connection cargo for cell communication and cross-kingdom communication by food chain in bivalves?

MicroRNAs (miRNAs) can efficiently regulate gene expression at intracellular and extracellular levels. Plant/food-derived miRNAs of the bio-environment are highly enriched in human serum or serum from phytophagous animals and play roles in the regulation of mammalian gene expression. However, the presence of food-derived miRNAs in Mollusca species is lacking evidence. In this study, we used the microalga Nannochloropsis oculata to feed the pearl oyster Pinctada fucata martensii, a bivalve species, and isolated exosomes from the serum to detect endogenous and food-derived miRNAs by RNA-seq. A total of 273 endogenous miRNAs were identified in all duplicate samples, and these participated in regulating cell proliferation and death, stress, energy metabolism, synthesis of unsaturated fatty acid, and protein synthesis and transport. Through the miRNA sequencing of the feeding N. oculata, we identified 23 microalga-derived miRNAs in the exosomes in the pearl oyster blood. Compared with endogenous miRNAs, most microalga-derived miRNAs showed high expression levels in both exosome and microalga cells and also exhibited apparent individual differences. These food-derived miRNAs were predicted to participate in endocytosis, apoptosis, signal transduction, energy metabolism, and biomineralization by targeting multiple genes. They were also closely related to energy metabolism and epigenetic regulation in N. oculata cells. These findings showed the phenomenon of cross-kingdom transport of miRNAs between a bivalve and feeding microalga and provided insights into functional molecule transmission through the food chain in an ecosystem.