The development of symbioses ensures formation of the super-organism systems for heredity (symbiogenomes) which represent the products of joint adaptations of partners towards an unfavorable environment. Using the examples of symbioses which enable plants and microorganisms to cooperatively overcome the limitations in the major biogenic elements (C, N, P) or impacts of the biotic and abiotic stresses we demonstrate that symbiosis involves not only the de novo formation (epigenesis) by plant of the ecological niches for hosting the microsymbionts, but also the reorganizations of relevant genetic systems in accordance to the partners' genotypes and environmental conditions. A possibility to address the ongoing processes in terms of epigenetics is evident when the microsymbionts occurring in the novel niches are included into the host reproduction cycle ensuring a stable maintenance of novel adaptation in the next generations suggesting that the newly formed symbiogenome have acquired the properties of a system for inheritance of the newly acquired adaptive traits.
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