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. 2025 May 18;14(10):1511.
doi: 10.3390/plants14101511.

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

Aruzhan Mendybayeva  1   2 , Alibek Makhambetov  1   3 , Kirill Yanin  1 , Aisha Taskuzhina  1   2   3 , Marina Khusnitdinova  1   2 , Dilyara Gritsenko  1   2   3
Affiliations

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

Aruzhan Mendybayeva et al. Plants (Basel). .

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.

Keywords: bacteria; malus sieversii; metagenomic analysis; microbiome.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
The most abundant bacterial colonies observed across the six populations. The dominant colonies exhibited a round shape and were white or beige in color, while yellow colonies appeared infrequently. Colony sizes ranged from 0.5 to 3 mm in diameter.
Figure 2
Figure 2
Bacterial microbiomes, expressed as percentages, in different regions. (A)—Zhongar Alatau: (a1)—phenological site; (a2)—genetic reserve of Siever’s wild apple trees. (B)—Ile Alatau: (b1)—Tau-Turgen; (b2)—genetic reserve of Siever’s wild apple trees. (C)—Ketmen ridge: (c1)—Sumbe; (c2)—Ketpentau.
Figure 3
Figure 3
Data discrepancies. Results from sequencing of three regions’ populations. (A) Ile Alatau region. (B) Zhongar Alatau region. (C) Ketpentau region. The colors denote distinct taxonomic groups.
Figure 4
Figure 4
A chart showing bacterial relationships. Red indicates a negative impact, green represents a beneficial impact, and blue signifies a neutral impact or a lack of substantial data.
Figure 5
Figure 5
Sampling sites on a map of Kazakhstan. Almaty region: A, B—Ile Alatau populations; C, D—Ketmen populations. Zhetysu region: E, F—Zhongar populations.
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