Evolution and Genetics of Plant–Microbe Interactions

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Protection and Biotic Interactions".

Deadline for manuscript submissions: closed (30 April 2025) | Viewed by 722

Special Issue Editors


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Guest Editor
Department of Agriculture, Food, Environment and Forestry, University of Florence, 50144 Firenze, Italy
Interests: genetic determinants involved in plant–microorganism interactions for the improvement of agricultural production; plant candidate genes involved in adaptation to abiotic stress; rhizosphere signaling; nitrogen-fixing symbiosis; protoplast metabolic characterization
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Guest Editor Assistant
Genexpress Laboratory of Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, 50019 Sesto Fiorentino, Italy
Interests: genetic determinants involved in legume–rhizobia symbiosis; screening and development of rhizobial inoculants; study of soil microbial ecology through next-generation sequencing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Ever since they first grew on land, plants and microorganisms have developed intricate and dynamic signaling systems to communicate and interact with each other efficiently. Indeed, thanks to these specific and strict associations, plants and their associated microbes can be considered a unique biological entity called the holobiont, the composition of which is shaped by selective pressure to improve plant fitness through the most robust mechanisms of cooperation.

The intimate interactions among plants and associated microorganisms can be beneficial for plants (i.e., synergy with rhizobia, mycorrhizal fungi, and/or plant growth-promoting microorganisms—PGPMs), allowing improved assimilation of nutrients, such as essential minerals and fixed nitrogen; however, some interactions can be detrimental to plant fitness, such as interactions with invading pathogenic microbes that can be saprophytic and lead to necrotrophy in colonized plants.

Co-evolution among plant and microorganisms is a hallmark of both benefic and harmful interactions, since it largely depends on features of the genomes of the interacting partners.

Indeed, if evolution drives beneficial interactions among plants and associated microorganisms toward a mutual improvement in fitness, then, in detrimental interactions, the two partners obtain different advantages: for pathogens, genetic alterations enhance their ability to evade or suppress plant defenses, while plants benefit from innovations that strengthen their immune responses.

This Special Issue will collect scientific contributions on the evolution of plant–microbe interactions, highlighting the most important genetic features shaped by evolutionary processes. Possible topics include, but are not limited to, the following: (i) genetic and molecular explorations of partner selection, encompassing both beneficial and detrimental interactions; (ii) the genetic determinants involved in interkingdom relationships; and (iii) the evolutionary dynamics that shape the holobiont.

Dr. Alice Checcucci
Guest Editor

Dr. Agnese Bellabarba
Guest Editor Assistant

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Keywords

  • plant–microbe interaction
  • microbiota
  • holobiont
  • evolutionary adaptation
  • co-adaptation

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Published Papers (1 paper)

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Research

16 pages, 3815 KiB  
Article
Metagenomic Analysis of Wild Apple (Malus sieversii) Trees from Natural Habitats of Kazakhstan
by Aruzhan Mendybayeva, Alibek Makhambetov, Kirill Yanin, Aisha Taskuzhina, Marina Khusnitdinova and Dilyara Gritsenko
Plants 2025, 14(10), 1511; https://doi.org/10.3390/plants14101511 - 18 May 2025
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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, [...] Read more.
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. Full article
(This article belongs to the Special Issue Evolution and Genetics of Plant–Microbe Interactions)
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