Phylogenetic diversity of the endophytic bacterial component of the microbiome of apple clonal rootstocks during in vitro reproduction and cultivation under various agroecological conditions

Federal Horticultural Research Center for Breeding, Agrotechnology and Nursery, 4 str. Zagorievskaja, Moscow, 115598, Russia

^* Corresponding author: vstisp.agrochem@yandex.ru

Abstract

The phylogenetic diversity of the endophytic bacterial component of the clonal apple rootstock microbiome 57-490 and 54-118 was studied for microplants and 5-year-old plants grown from the same tissue culture and growing on sod-podzolic soils of different granulometric composition with different chemical, physicochemical and physical properties. Proteobacteria (91.6%) in rootstock 57-490, Proteobacteria (52.5%) and Firmicutes (47.4%) in rootstock 54-118 are the predominant phylum of endophytic bacteria in apple rootstock plant tissues in vitro culture. The relative amount of phylum Firmicutes endophytic bacteria, in comparison with in vitro culture, decreases in the roots to 0.7-2.0%, and even more significantly in the leaves (to 0-0.2%). At cultivation on heavy loamy soil, endophytic bacteria belonging to the phylum Actinobacteriota (11.7%) are found in the studied rootstock roots, the relative content of which, when grown on medium loamy soil, in the roots decreases to 2.7-4.1%, in the leaves – to 0,1-0.2%. The data show that in the endosphere of the culture in vitro, the diversity and uniformity of the community of endophytic bacteria is significantly lower (Shannon index 0.42-1.00) than in the roots of rootstocks grown in the outdoor growing (1.34-2.08). For leaves, the Shannon index is characterized by the lowest values (0.06-0.13).