Evidence for host–microbiome co‐evolution in apple

Abstract

Plants evolved in association with a diverse community of microorganisms. The effect of plant phylogeny and domestication on host-microbiome co-evolutionary dynamics are poorly understood.Here we examined the effect of domestication and plant lineage on the composition of the endophytic microbiome of 11 Malus species, representing three major groups: domesticated apple (M. domestica), wild apple progenitors, and wild Malus species.The endophytic community of M. domestica and its wild progenitors showed higher microbial diversity and abundance than wild Malus species. Heirloom and modern cultivars harbored a distinct community composition, though the difference was not significant. A community-wide Bayesian model revealed that the endophytic microbiome of domesticated apple is an admixture of its wild progenitors, with clear evidence for microbiome introgression, especially for the bacterial community. We observed a significant correlation between the evolutionary distance of Malus species and their microbiome.This study supports co-evolution between Malus species and their microbiome during domestication. This finding has major implications for future breeding programs and our understanding of the evolution of plants and their microbiomes.

Plant genotype influence the structure of cereal seed fungal microbiome

“…Recent research suggests that, within some taxonomical groups, the structure of plant microbiomes reconciliates with the host’s phylogeny (i.e., phylogenetically closer hosts associate with more similar microbial communities). This link, named phylosymbiosis, has been recently found for example in the apples (Abdelfattah, Tack, et al 2021) and chloridoid grasses (Van Bel et al 2021). While we still do not know how common is phylosymbiosis among plants, it might be key to understand how different plant genotypes assemble their own microbial communities.…”

“…While we still do not know how common is phylosymbiosis among plants, it might be key to understand how different plant genotypes assemble their own microbial communities. This is particularly important considering that the vertical transmission of a portion of the plant microbiome has been found in several species, including oilseed rape (Wassermann et al 2022), tomato (Bergna et al 2018), wheat (Walsh et al 2021), and oak (Abdelfattah, Wisniewski, et al 2021).…”

The microbiome and resistome of apple fruits alter in the post-harvest period

“…The postharvest period was identified as a driver of the microbiome as well as the resistome, but not the cultivar. The latter is unexpected since cultivar and plant genotype effects on the plant microbiota are well documented [ 55 – 59 ], even for apples [ 28 , 60 – 62 ].…”

Bacterial Microbiome in the Phyllo-Endosphere of Highly Specialized Rock Spleenwort

“…Unfortunately, the holobiome of the vast majority of plants is still awaiting to be discovered, which applies particularly to the bacterial diversity in the endo-phyllosphere—meaning the niche spaces inside the leaves of land plants ( Vorholt, 2012 ; Khare et al, 2018 ; Cordovez et al, 2019 ; Harrison and Griffin, 2020 ; Chaudhry et al, 2021 ; Hawkes et al, 2021 ; Chialva et al, 2022 ). Many studies considered bacterial taxa enhancing plant defense ( Matsumoto et al, 2021 ; Cernava and Berg, 2022 ; Shalev et al, 2022 ) besides other plant growth-promoting functions ( Glick, 2012 ; Backer et al, 2018 ; Leontidou et al, 2020 ), but current studies expanded their focus on a wide range of ecological aspects such as the contribution of bacterial communities to the rapid adaption to local environments enforced by bacterial communities ( Li et al, 2021 ) that coincide with diversification patterns ( Abedlfattah et al, 2021 ) as argued in the SYMPHY proposal ( Tripp et al, 2017 ) and the Plant Holobiont Theory ( Lyu et al, 2021 ). Notable aspects studied include the enhanced resistance of plants to environmental stresses supported by endophytic bacteria, e.g., salt tolerance ( Vaishnav et al, 2019 ) and heavy metal tolerance ( Zhu et al, 2014 ; Xu et al, 2016 ; Gu et al, 2018 ; Banach et al, 2020 ; Yang et al, 2020 ; Antenozio et al, 2021 ) or even support the adaptation to extreme environments, e.g., deserts ( Zhang et al, 2019 ) and karst habitats ( Li F. et al, 2019 ).…”