Coupling the endophytic microbiome with the host transcriptome in olive roots

Fernández-González, Antonio J.; Ramírez-Tejero, Jorge A.; Nevado-Berzosa, María Patricia; Luque, Francisco; Fernández‐López, Manuel; Mercado‐Blanco, Jesús

doi:10.1016/j.csbj.2021.08.035

Cited by 11 publications

(11 citation statements)

References 89 publications

(112 reference statements)

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“…GNC/GNF7 = 4/4. than diversity indexes for studying the influence of external factors/perturbations in microbial communities (Barberán et al, 2012;Karimi et al, 2017;Kong et al, 2019;Benidire et al, 2020;Fernández-González et al, 2021). Among these perturbations, the infection by pathogens and the introduction of bio-inoculants (e.g., BCA) have shown to exert clear effects on microbial interaction patterns (Kong et al, 2019;Benidire et al, 2020;Fernández-González et al, 2020;Hu et al, 2020;Qu et al, 2020;Zheng et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

“…The most significant alterations upon PICF7 inoculation were found in the interactions of microbial communities through co-occurrence network analysis. In recent years, these kinds of analysis have proved to be more effective and sensitive than diversity indexes for studying the influence of external factors/perturbations in microbial communities ( Barberán et al, 2012 ; Karimi et al, 2017 ; Kong et al, 2019 ; Benidire et al, 2020 ; Fernández-González et al, 2021 ). Among these perturbations, the infection by pathogens and the introduction of bio-inoculants (e.g., BCA) have shown to exert clear effects on microbial interaction patterns ( Kong et al, 2019 ; Benidire et al, 2020 ; Fernández-González et al, 2020 ; Hu et al, 2020 ; Qu et al, 2020 ; Zheng et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

“…Consequently, the plant and its associated microbial communities constitute a meta-organism, the so-called holobiont, which usually is also an important reservoir of beneficial microorganisms, including BCA ( Hassani et al, 2018 ). The plant-associated microbiome thus decisively contributes to the health, fitness, development, and productivity of the holobiont by, for instance, enhancing the tolerance to different (a)biotic stresses and/or promoting the growth of the host ( Mendes et al, 2013 ; Berg et al, 2017 ; Fernández-González et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

“…The microbiota present in a given plant holobiont forms a complex network whose components are continuously interacting among them ( Wassermann et al, 2019 ) and with the host transcriptome ( Fernández-González et al, 2021 ). Consequently, the application of a BCA will not only affect the host (e.g., triggering genetic defense responses) and/or the pathogen (e.g., antibiosis) but also likely have an impact on the composition, structure, and/or functionality of the host-associated microbiome.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Impacts of the Biocontrol Strain Pseudomonas simiae PICF7 on the Banana Holobiont: Alteration of Root Microbial Co-occurrence Networks and Effect on Host Defense Responses

et al. 2022

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The impact of the versatile biocontrol and plant-growth-promoting rhizobacteria Pseudomonas simiae PICF7 on the banana holobiont under controlled conditions was investigated. We examine the fate of this biological control agent (BCA) upon introduction in the soil, the effect on the banana root microbiota, and the influence on specific host genetic defense responses. While the presence of strain PICF7 significantly altered neither the composition nor the structure of the root microbiota, a significant shift in microbial community interactions through co-occurrence network analysis was observed. Despite the fact that PICF7 did not constitute a keystone, the topology of this network was significantly modified—the BCA being identified as a constituent of one of the main network modules in bacterized plants. Gene expression analysis showed the early suppression of several systemic acquired resistance and induced systemic resistance (ISR) markers. This outcome occurred at the time in which the highest relative abundance of PICF7 was detected. The absence of major and permanent changes on the banana holobiont upon PICF7 introduction poses advantages regarding the use of this beneficial rhizobacteria under field conditions. Indeed a BCA able to control the target pathogen while altering as little as possible the natural host-associated microbiome should be a requisite when developing effective bio-inoculants.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Impacts of the Biocontrol Strain Pseudomonas simiae PICF7 on the Banana Holobiont: Alteration of Root Microbial Co-occurrence Networks and Effect on Host Defense Responses

et al. 2022

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“…Amongst many of the bacteria, Porphyrobacter can produce indole-3-acetic acid and solubilize phosphate [32]. Actinophytocola members have been isolated from the rhizosphere and endosphere of several plants [33,34], and play an important role in stress adaptation [35,36]. Nocardia were identified from the root endosphere of halophytic plants [28] and are important facilitators of phytoremediation of VOCs as they can remove toxic compounds from the soil [37].…”

Section: Differential Analysis Identified Root Compartment-specific E...mentioning

confidence: 99%

Differed Growth Stage Dynamics of Root-Associated Bacterial and Fungal Community Structure Associated with Halophytic Plant Lycium ruthenicum

Yuan

et al. 2022

Microorganisms

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Lycium ruthenicum, a halophytic shrub, has been used to remediate saline soils in northwest China. However, little is known about its root-associated microbial community and how it may be affected by the plant’s growth cycle. In this study, we investigate the microbial community structure of L. ruthenicum by examining three root compartments (rhizosphere, rhizoplane, and endosphere) during four growth stages (vegetative, flowering, fruiting, and senescence). The microbial community diversity and composition were determined by Illumina MiSeq sequencing of the 16S V3–V4 and 18S ITS regions. Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, and Acidobacteria were the dominant bacterial phyla, while Ascomycota, Basidiomycota, and Mortierellomycota were the most dominant fungal phyla. The alpha diversity of the bacterial communities was highest in the rhizosphere and decreased from the rhizosphere to the endosphere compartments; the fungal communities did not show a consistent trend. The rhizosphere, rhizoplane, and endosphere had distinct bacterial community structures among the three root compartments and from the bulk soil. Additionally, PERMANOVA indicated that the effect of rhizocompartments explained a large proportion of the total community variation. Differential and biomarker analysis not only revealed that each compartment had unique biomarkers and was enriched for specific bacteria, but also that the biomarkers changed with the plant growth cycle. Fungi were also affected by the rhizocompartment, but to a much less so than bacteria, with significant differences in the community composition along the root compartments observed only during the vegetative and flowering stages. Instead, the growth stages appear to account for most of the fungal community variation as demonstrated by PCoA and NMDS, and supported by differential and biomarker analysis, which revealed that the fungal community composition in the rhizosphere and endosphere were dynamic in response to the growth stage. Many enriched OTUs or biomarkers that were identified in the root compartments were potentially beneficial to the plant, meanwhile, some harmful OTUs were excluded from the root, implying that the host plant can select for beneficial bacteria and fungi, which can promote plant growth or increase salt tolerance. In conclusion, the root compartment and growth stage were both determinant factors in structuring the microbial communities of L. ruthenicum, but the effects were different in bacteria and fungi, suggesting that bacterial and fungal community structures respond differently to these growth factors.

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Assessment of the rhizosphere fungi and bacteria recruited by sugarcane during smut invasion

et al. 2022

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Coupling the endophytic microbiome with the host transcriptome in olive roots

Abstract: Graphical abstract

Cited by 11 publications

References 89 publications

Impacts of the Biocontrol Strain Pseudomonas simiae PICF7 on the Banana Holobiont: Alteration of Root Microbial Co-occurrence Networks and Effect on Host Defense Responses

Impacts of the Biocontrol Strain Pseudomonas simiae PICF7 on the Banana Holobiont: Alteration of Root Microbial Co-occurrence Networks and Effect on Host Defense Responses

Differed Growth Stage Dynamics of Root-Associated Bacterial and Fungal Community Structure Associated with Halophytic Plant Lycium ruthenicum

Assessment of the rhizosphere fungi and bacteria recruited by sugarcane during smut invasion

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