Taxonomic structure of tissue endophytic bacterial microbiome in clonal apple rootstock grown on sod-podzolic soils with variant properties

Abstract

The taxonomic structure of tissue endophytic bacterial microbiome was comparatively studied in microplants (undifferentiated explant callus tissues, passage 25) and 5-year clonal apple rootstocks 57-490 and 54-118 cultured from corresponding tissues (passage 1) on sod-podzolic soils with variant granulometry, chemical, physical and physicochemical properties. Proteobacteria (91.6 %) predominated in vitro tissues among other endophytic bacterial phyla in rootstock 57-490, while Proteobacteria (52.5 %) and Firmicutes (47.4 %) — in rootstock 54-118. The endophytic Firmicutes ratio vs. in vitro tissues decreases (0.7-2.0 %) in roots and more severely (0-0.2 %) in leaves. Endophytic Actinobacteriota are revealed in 11.7 % in roots of the study rootstock in heavy loam soil, whilst in medium loam their ratio drops to 2.74.1 % in roots and 0.1-0.2 % in leaves. The phylogenetic diversity indices estimation for main endophytic bacterial phyla in apple rootstock tissue recovers their essentially lower diversity and evenness in culture endosphere (Shannon index 0.42-1.00) vs. open soil roots (1.34-2.08). The leaves Shannon index is typically low (0.06-0.13) indicating poor diversity and evenness of the main endophytic bacterial phyla.