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

Kazakhstan's rich biodiversity includes diverse apple populations, notably the wild apple tree (<i>Malus sieversii</i>) 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 <i>Pseudomonadaceae</i>, <i>Enterobacteriaceae</i>, and <i>Microbacteriaceae</i>. In contrast, samples from Ketmen ridge showed a higher prevalence of <i>Enterobacteriaceae</i>. Alongside the less represented <i>Pseudomonadaceae</i> family, in the Ketmen ridge region, bacteria of the <i>Xanthomonadaceae</i>, <i>Alcaligenaceae</i>, and <i>Brucellaceae</i> families were also present. Across all regions, beneficial plant-associated bacteria were identified, such as <i>Pseudomonas veronii</i>, <i>Stenotrophomonas geniculata</i>, and <i>Kocuria rhizophila</i>, potentially enhancing plant resilience. However, opportunistic phytopathogens were also detected, including <i>Pseudomonas viridiflava</i> and <i>Serratia marcescens</i>, particularly in the Ile Alatau region. These findings highlight the complex microbial interactions in <i>M. sieversii</i>, thus offering key insights into host-microbe relationships that can inform apple breeding and ecological preservation efforts.