Rhizosphere competent inoculants modulate the apple root–associated microbiome and plant phytoalexins

authored by: Kristin Hauschild, Nils Orth, Benye Liu, Adriana Giongo, Silvia Gschwendtner, Ludger Beerhues, Michael Schloter, Doris Vetterlein, Traud Winkelmann, Kornelia Smalla
Abstract: Abstract: Modulating the soil microbiome by applying microbial inoculants has gained increasing attention as eco-friendly option to improve soil disease suppressiveness. Currently, studies unraveling the interplay of inoculants, root-associated microbiome, and plant response are lacking for apple trees. Here, we provide insights into the ability of Bacillus velezensis FZB42 or Pseudomonas sp. RU47 to colonize apple root-associated microhabitats and to modulate their microbiome. We applied the two strains to apple plants grown in soils from the same site either affected by apple replant disease (ARD) or not (grass), screened their establishment by selective plating, and measured phytoalexins in roots 3, 16, and 28 days post inoculation (dpi). Sequencing of 16S rRNA gene and ITS fragments amplified from DNA extracted 28 dpi from different microhabitat samples revealed significant inoculation effects on fungal β-diversity in root-affected soil and rhizoplane. Interestingly, only in ARD soil, most abundant bacterial amplicon sequence variants (ASVs) changed significantly in relative abundance. Relative abundances of ASVs affiliated with Enterobacteriaceae were higher in rhizoplane of apple grown in ARD soil and reduced by both inoculants. Bacterial communities in the root endosphere were not affected by the inoculants but their presence was indicated. Interestingly and previously unobserved, apple plants responded to the inoculants with increased phytoalexin content in roots, more pronounced in grass than ARD soil. Altogether, our results indicate that FZB42 and RU47 were rhizosphere competent, modulated the root-associated microbiome, and were perceived by the apple plants, which could make them interesting candidates for an eco-friendly mitigation strategy of ARD.
Organisation(s): Institute of Horticultural Production Systems
External Organisation(s): Julius Kühn Institute - Federal Research Centre for Cultivated Plants (JKI)
Technische Universität Braunschweig
Helmholtz Zentrum München - German Research Center for Environmental Health
Helmholtz Centre for Environmental Research (UFZ)
Type: Article
Journal: Applied Microbiology and Biotechnology
Volume: 108
No. of pages: 20
ISSN: 0175-7598
Publication date: 12.2024
Publication status: Published
Peer reviewed: Yes
ASJC Scopus subject areas: Biotechnology, Applied Microbiology and Biotechnology
Electronic version(s): https://doi.org/10.1007/s00253-024-13181-8 (Access: Open)

BibTeX

@article{a58cbe2ee88a423d9df296b281127392,
title = "Rhizosphere competent inoculants modulate the apple root–associated microbiome and plant phytoalexins",
abstract = "Abstract: Modulating the soil microbiome by applying microbial inoculants has gained increasing attention as eco-friendly option to improve soil disease suppressiveness. Currently, studies unraveling the interplay of inoculants, root-associated microbiome, and plant response are lacking for apple trees. Here, we provide insights into the ability of Bacillus velezensis FZB42 or Pseudomonas sp. RU47 to colonize apple root-associated microhabitats and to modulate their microbiome. We applied the two strains to apple plants grown in soils from the same site either affected by apple replant disease (ARD) or not (grass), screened their establishment by selective plating, and measured phytoalexins in roots 3, 16, and 28 days post inoculation (dpi). Sequencing of 16S rRNA gene and ITS fragments amplified from DNA extracted 28 dpi from different microhabitat samples revealed significant inoculation effects on fungal β-diversity in root-affected soil and rhizoplane. Interestingly, only in ARD soil, most abundant bacterial amplicon sequence variants (ASVs) changed significantly in relative abundance. Relative abundances of ASVs affiliated with Enterobacteriaceae were higher in rhizoplane of apple grown in ARD soil and reduced by both inoculants. Bacterial communities in the root endosphere were not affected by the inoculants but their presence was indicated. Interestingly and previously unobserved, apple plants responded to the inoculants with increased phytoalexin content in roots, more pronounced in grass than ARD soil. Altogether, our results indicate that FZB42 and RU47 were rhizosphere competent, modulated the root-associated microbiome, and were perceived by the apple plants, which could make them interesting candidates for an eco-friendly mitigation strategy of ARD.",
keywords = "Apple replant disease, Bacillus velezensis FZB42, Pseudomonas sp. RU47, Rhizoplane, Root endosphere, Soil",
author = "Kristin Hauschild and Nils Orth and Benye Liu and Adriana Giongo and Silvia Gschwendtner and Ludger Beerhues and Michael Schloter and Doris Vetterlein and Traud Winkelmann and Kornelia Smalla",
note = "Publisher Copyright: {\textcopyright} The Author(s) 2024.",
year = "2024",
month = dec,
doi = "10.1007/s00253-024-13181-8",
language = "English",
volume = "108",
journal = "Applied Microbiology and Biotechnology",
issn = "0175-7598",
publisher = "Springer Verlag",
number = "1",
}