# Metagenomic Analysis of Wild Apple (Malus sieversii) Trees from Natural Habitats of Kazakhstan

## TL;DR

This study explores the bacterial communities in wild apple trees from Kazakhstan, revealing regional differences and the presence of both beneficial and harmful microbes.

## Contribution

The study provides a detailed metagenomic analysis of wild apple tree microbiomes in Kazakhstan, identifying region-specific bacterial patterns and their ecological implications.

## Key findings

- Microbiomes from Zhongar and Ile Alatau mountain ranges showed similar bacterial compositions dominated by Pseudomonadaceae and Enterobacteriaceae.
- Ketmen ridge samples had higher Enterobacteriaceae prevalence and additional bacterial families like Xanthomonadaceae and Brucellaceae.
- Beneficial bacteria like Pseudomonas veronii and phytopathogens like Pseudomonas viridiflava were identified, suggesting complex host-microbe interactions.

## Abstract

Kazakhstan’s rich biodiversity includes diverse apple populations, notably the wild apple tree (Malus sieversii) prized for traits like disease resistance and adaptability, potentially aiding breeding programs. Analyzing their microbiomes offers insights into bacterial diversity and how it influences apple tree development, making it a reliable method for understanding ecological interactions. In this research, 334 apple tree samples were collected from different mountain ranges in southeastern Kazakhstan. An analysis using nanopore-based 16S rRNA sequencing showed a distinct similarity in the microbiome compositions of samples from the Zhongar and Ile Alatau mountain ranges, with a predominance of Pseudomonadaceae, Enterobacteriaceae, and Microbacteriaceae. In contrast, samples from Ketmen ridge showed a higher prevalence of Enterobacteriaceae. Alongside the less represented Pseudomonadaceae family, in the Ketmen ridge region, bacteria of the Xanthomonadaceae, Alcaligenaceae, and Brucellaceae families were also present. Across all regions, beneficial plant-associated bacteria were identified, such as Pseudomonas veronii, Stenotrophomonas geniculata, and Kocuria rhizophila, potentially enhancing plant resilience. However, opportunistic phytopathogens were also detected, including Pseudomonas viridiflava and Serratia marcescens, particularly in the Ile Alatau region. These findings highlight the complex microbial interactions in M. sieversii, thus offering key insights into host—microbe relationships that can inform apple breeding and ecological preservation efforts.