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

Research output: Contribution to journalArticleResearchpeer review

Authors

  • Kristin Hauschild
  • Nils Orth
  • Benye Liu
  • Adriana Giongo
  • Silvia Gschwendtner
  • Ludger Beerhues
  • Michael Schloter
  • Doris Vetterlein
  • Traud Winkelmann
  • Kornelia Smalla

External Research Organisations

  • 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)
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Details

Original languageEnglish
Article number344
Number of pages20
JournalApplied Microbiology and Biotechnology
Volume108
Issue number1
Early online date27 May 2024
Publication statusE-pub ahead of print - 27 May 2024

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

ASJC Scopus subject areas

Cite this

Rhizosphere competent inoculants modulate the apple root–associated microbiome and plant phytoalexins. / Hauschild, Kristin; Orth, Nils; Liu, Benye et al.
In: Applied Microbiology and Biotechnology, Vol. 108, No. 1, 344, 12.2024.

Research output: Contribution to journalArticleResearchpeer review

Hauschild, K, Orth, N, Liu, B, Giongo, A, Gschwendtner, S, Beerhues, L, Schloter, M, Vetterlein, D, Winkelmann, T & Smalla, K 2024, 'Rhizosphere competent inoculants modulate the apple root–associated microbiome and plant phytoalexins', Applied Microbiology and Biotechnology, vol. 108, no. 1, 344. https://doi.org/10.1007/s00253-024-13181-8
Hauschild, K., Orth, N., Liu, B., Giongo, A., Gschwendtner, S., Beerhues, L., Schloter, M., Vetterlein, D., Winkelmann, T., & Smalla, K. (2024). Rhizosphere competent inoculants modulate the apple root–associated microbiome and plant phytoalexins. Applied Microbiology and Biotechnology, 108(1), Article 344. Advance online publication. https://doi.org/10.1007/s00253-024-13181-8
Hauschild K, Orth N, Liu B, Giongo A, Gschwendtner S, Beerhues L et al. Rhizosphere competent inoculants modulate the apple root–associated microbiome and plant phytoalexins. Applied Microbiology and Biotechnology. 2024 Dec;108(1):344. Epub 2024 May 27. doi: 10.1007/s00253-024-13181-8
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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.",
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AU - Hauschild, Kristin

AU - Orth, Nils

AU - Liu, Benye

AU - Giongo, Adriana

AU - Gschwendtner, Silvia

AU - Beerhues, Ludger

AU - Schloter, Michael

AU - Vetterlein, Doris

AU - Winkelmann, Traud

AU - Smalla, Kornelia

N1 - Publisher Copyright: © The Author(s) 2024.

PY - 2024/5/27

Y1 - 2024/5/27

N2 - 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.

AB - 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.

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