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

Veronika Bobkova,Mikhail Upadyshev,Sergey Konovalov,E Egorov,E Yakimenko,I Ilina,N Zaporozhets

doi:10.1051/bioconf/20213404009

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).

Highlights

Endophytic bacteria are important for the growth, development, fruiting, adaptability of agricultural plants, as they have growth-stimulating, fungicidal and other useful properties [1,2]
Research of the taxonomic composition of the bacterial component of the microbiome of plant tissues of clonal rootstocks of apple trees 57-490 and 54-118 were carried out for microplants grown in tissue culture and on plants of apple rootstocks of 5 years of age, grown from the same tissue culture, and growing in different agroecological conditions, due to different granulometric composition and different chemical, physicochemical and physical properties of sod - podzolic soils of two plots located in Stupinsky and in Leninsky districts of the Moscow region
The study showed that 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 plant tissues of apple rootstocks in vitro culture

Summary

Introduction

Endophytic bacteria are important for the growth, development, fruiting, adaptability of agricultural plants, as they have growth-stimulating, fungicidal and other useful properties [1,2]. Among 55 isolates of cultivated endophytic bacteria isolated from the roots and leaves of apple varieties in the gardens of Canada [6], half of the bacteria belonged to the Bacillus species, of which 54 inhibited the growth of the apple scab pathogen Venturia inaequalis, and B. megaterium turned out to be the most effective. The species and quantitative composition of the bacterial component of the microbiome of plant tissues, of cultivated varieties, and of the rootstocks used is of great importance [16]. Different levels of fertility, redox regime, acid-base and other properties of the soil can affect the patterns of formation of the endophytic bacterial component of the microbiome of garden plants. It was concluded that anthropogenic activity significantly affects the structure of bacterial communities in soil and plant roots

Methods

Results

Conclusion