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. KEY POINTS: • Rhizosphere competent inoculants modulated the microbiome (mainly fungi) • Inoculants reduced relative abundance of Enterobacteriaceae in the ARD rhizoplane • Inoculants increased phytoalexin content in roots, stronger in grass than ARD soil.
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Claims 8
Claim · model-written summary
Inoculation significantly changed fungal β-diversity in root-affected soil and rhizoplane.
- Taxon
- apple
Malus domesticat0 - Organ / stage
- rhizoplanee0
- Treatment
- inoculatione0
- Outcome
- fungal β-diversitye0
Not reportedComparatorDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“revealed significant inoculation effects on fungal β-diversity in root-affected soil and rhizoplane.”
t0“apple”
Claim · model-written summary
Abundant bacterial ASVs changed significantly in relative abundance only in ARD soil.
- Taxon
- appleMalus domesticat0
- Outcome
- most abundant bacterial amplicon sequence variants (ASVs) changed significantly in relative abundancee0
- Setting
- ARD soile0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“only in ARD soil, most abundant bacterial amplicon sequence variants (ASVs) changed significantly in relative abundance.”
t0“apple”
Claim · model-written summary
Enterobacteriaceae ASVs were more abundant in the apple rhizoplane in ARD soil.
- Taxon
- appleMalus domesticae0
- Organ / stage
- rhizoplanee0
- Outcome
- Relative abundances of ASVs affiliated with Enterobacteriaceaee0
- Direction
- highere0
- Setting
- ARD soile0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Relative abundances of ASVs affiliated with Enterobacteriaceae were higher in rhizoplane of apple grown in ARD soil”
t0“apple”
Claim · model-written summary
Both inoculants reduced Enterobacteriaceae ASVs in the rhizoplane.
- Taxon
- appleMalus domesticae0
- Organ / stage
- rhizoplanee0
- Treatment
- both inoculantse0
- Outcome
- Relative abundances of ASVs affiliated with Enterobacteriaceaee0
- Direction
- reducede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Relative abundances of ASVs affiliated with Enterobacteriaceae were higher in rhizoplane of apple grown in ARD soil and reduced by both inoculants.”
Claim · model-written summary
Inoculants did not affect bacterial communities in the root endosphere.
- Taxon
- appleMalus domesticat0
- Organ / stage
- root endospheree0
- Treatment
- inoculantse0
- Outcome
- Bacterial communities in the root endospheree0
- Direction
- not affectede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Bacterial communities in the root endosphere were not affected by the inoculants but their presence was indicated.”
t0“apple”
Claim · model-written summary
The presence of inoculants was indicated in the root endosphere.
- Taxon
- appleMalus domesticat0
- Organ / stage
- root endospheree0
- Outcome
- their presence was indicatede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Bacterial communities in the root endosphere were not affected by the inoculants but their presence was indicated.”
t0“apple”
Claim · model-written summary
Inoculants increased phytoalexin content in apple roots, more strongly in grass soil than ARD soil.
- Taxon
- appleMalus domesticae0
- Organ / stage
- rootse0
- Treatment
- inoculantse0
- Outcome
- phytoalexin contente0
- Direction
- increasede0
- Qualifier
- more pronounced in grass than ARD soile0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“apple plants responded to the inoculants with increased phytoalexin content in roots, more pronounced in grass than ARD soil.”
Claim · model-written summary
FZB42 and RU47 were rhizosphere competent.
- Taxon
- appleMalus domesticat0
- Outcome
- rhizosphere competente0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“FZB42 and RU47 were rhizosphere competent”
t0“apple”
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Claims are grouped by organism, treatment and what was measured or targeted. A paper counts as positive when any of its claims in the group is positive.