Metabolomics in plant-microbe interactions in the roots

Chen, Li; Schwier, Melina; Krumbach, Jenna; Jacoby, Richard P.

doi:10.1016/bs.abr.2020.09.018

Cited by 16 publications

(17 citation statements)

References 111 publications

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“…However, SIP has been applied in the metabolite flux analysis through untargeted metabolomics to differentiate exogenous features in LC-MS to address questions such as the carbon source of microorganisms in marine sediments [90,91]. According to Chen et al [92], heavy isotope labelling should enable the identification of the origins of specific metabolites at the side of plant-microbe interactions. For instance, plants grown in 13 CO 2 metabolise that available which becomes incorporated into the photosynthates ultimately released as root exudates.…”

Section: Applications Of Metabolomics In Understanding Tripartite Pla...mentioning

confidence: 99%

Rhizosphere Tripartite Interactions and PGPR-Mediated Metabolic Reprogramming towards ISR and Plant Priming: A Metabolomics Review

Mashabela

Piater

Dubery

et al. 2022

Biology

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Plant growth-promoting rhizobacteria (PGPR) are beneficial microorganisms colonising the rhizosphere. PGPR are involved in plant growth promotion and plant priming against biotic and abiotic stresses. Plant–microbe interactions occur through chemical communications in the rhizosphere and a tripartite interaction mechanism between plants, pathogenic microbes and plant-beneficial microbes has been defined. However, comprehensive information on the rhizosphere communications between plants and microbes, the tripartite interactions and the biochemical implications of these interactions on the plant metabolome is minimal and not yet widely available nor well understood. Furthermore, the mechanistic nature of PGPR effects on induced systemic resistance (ISR) and priming in plants at the molecular and metabolic levels is yet to be fully elucidated. As such, research investigating chemical communication in the rhizosphere is currently underway. Over the past decades, metabolomics approaches have been extensively used in describing the detailed metabolome of organisms and have allowed the understanding of metabolic reprogramming in plants due to tripartite interactions. Here, we review communication systems between plants and microorganisms in the rhizosphere that lead to plant growth stimulation and priming/induced resistance and the applications of metabolomics in understanding these complex tripartite interactions.

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Section: Applications Of Metabolomics In Understanding Tripartite Pla...mentioning

confidence: 99%

Rhizosphere Tripartite Interactions and PGPR-Mediated Metabolic Reprogramming towards ISR and Plant Priming: A Metabolomics Review

Mashabela

Piater

Dubery

et al. 2022

Biology

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“…Plant root-associated microbiomes (collection of microbes living inside and around the roots) provide diverse functions that directly influence several plant traits and metabolites are the primary tools plants employ to actively shape their microbiome ( De Coninck et al, 2015 ; Pascale et al, 2020 ; Chen et al, 2021 ; Chouhan et al, 2021 ; Pang et al, 2021 ). Mechanistically, plant roots exude a cocktail of primary and secondary metabolites which work as growth substrates for some microbial families, exert toxic and antagonistic effects on others, or serve as signals that modulate the plant microbe interactions ( Lareen et al, 2016 ; Chen et al, 2021 ). Whilst some soil rhizosphere microbial species benefit the plant by acting as growth promoting rhizobacteria or symbionts in enhancing plant pathogen defense and nutrition, some microbes may be commensal or parasitic (reviewed in Lareen et al, 2016 ; Pascale et al, 2020 ; Chen et al, 2021 ).…”

Section: Phenomics Facilitated Improvement Of Crop Agronomic Traitsmentioning

confidence: 99%

“…Mechanistically, plant roots exude a cocktail of primary and secondary metabolites which work as growth substrates for some microbial families, exert toxic and antagonistic effects on others, or serve as signals that modulate the plant microbe interactions ( Lareen et al, 2016 ; Chen et al, 2021 ). Whilst some soil rhizosphere microbial species benefit the plant by acting as growth promoting rhizobacteria or symbionts in enhancing plant pathogen defense and nutrition, some microbes may be commensal or parasitic (reviewed in Lareen et al, 2016 ; Pascale et al, 2020 ; Chen et al, 2021 ). Therefore, dissecting these complex plant - soil rhizosphere - microbiome interactions is critical for designing new approaches for crop resilience to pathogenic and environmental stresses.…”

Section: Phenomics Facilitated Improvement Of Crop Agronomic Traitsmentioning

confidence: 99%

“…Moving ahead, plant root-associated microbiomes can be targeted as a source of variation in crop breeding and engineering microbial inoculants to support plant growth and suppress diseases (reviewed in Pascale et al, 2020 ). Especially, advanced and HTP techniques, such as stable isotope probing, amplicon sequencing, whole-genome shotgun sequencing and metabolomics, coupled with sophisticated bioinformatics softwares and tools (including QIIME, MEGAN, MOTHUR, etc., reviewed in Dubey et al, 2019b ; Pang et al, 2021 ), will become more routinely applied in unlocking the metabolite dialogs between plants and the microbes, and linking those metabolic footprints to key plant genes and phenotypic traits modulating microbiome recruitment or regulation ( Chen et al, 2021 ; Clouse and Wagner, 2021 ; Trivedi et al, 2021 ). Taken together, integrating phenomics with other multi-omics approaches provides an invaluable strategy to develop new disease- and climate resilient cultivars via the identification, characterization, manipulation and recruitment of plant rhizospheric microbes into crop breeding and bioengineering programs aimed at improving host plant‘s pathogen resistance and overall fitness and functionality under environmentally challenged conditions.…”

Section: Phenomics Facilitated Improvement Of Crop Agronomic Traitsmentioning

confidence: 99%

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Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value

et al. 2021

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Novel crop improvement approaches, including those that facilitate for the exploitation of crop wild relatives and underutilized species harboring the much-needed natural allelic variation are indispensable if we are to develop climate-smart crops with enhanced abiotic and biotic stress tolerance, higher nutritive value, and superior traits of agronomic importance. Top among these approaches are the “omics” technologies, including genomics, transcriptomics, proteomics, metabolomics, phenomics, and their integration, whose deployment has been vital in revealing several key genes, proteins and metabolic pathways underlying numerous traits of agronomic importance, and aiding marker-assisted breeding in major crop species. Here, citing several relevant examples, we appraise our understanding on the recent developments in omics technologies and how they are driving our quest to breed climate resilient crops. Large-scale genome resequencing, pan-genomes and genome-wide association studies are aiding the identification and analysis of species-level genome variations, whilst RNA-sequencing driven transcriptomics has provided unprecedented opportunities for conducting crop abiotic and biotic stress response studies. Meanwhile, single cell transcriptomics is slowly becoming an indispensable tool for decoding cell-specific stress responses, although several technical and experimental design challenges still need to be resolved. Additionally, the refinement of the conventional techniques and advent of modern, high-resolution proteomics technologies necessitated a gradual shift from the general descriptive studies of plant protein abundances to large scale analysis of protein-metabolite interactions. Especially, metabolomics is currently receiving special attention, owing to the role metabolites play as metabolic intermediates and close links to the phenotypic expression. Further, high throughput phenomics applications are driving the targeting of new research domains such as root system architecture analysis, and exploration of plant root-associated microbes for improved crop health and climate resilience. Overall, coupling these multi-omics technologies to modern plant breeding and genetic engineering methods ensures an all-encompassing approach to developing nutritionally-rich and climate-smart crops whose productivity can sustainably and sufficiently meet the current and future food, nutrition and energy demands.

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“…At the plant–microbe interface, the rhizosphere is a rich habitat of microorganisms that interact with plants, stimulate numerous signaling processes and contribute to material exchange 10 . Microorganisms and plants interact in a variety of ways that can result in neutral, synergistic, or undesirable consequences, with notable effects on the plants and the microbial population 11 . Plant growth-promoting bacteria (PGPB) are one of the important microorganisms that inhabit the rhizosphere in natural ecosystems.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of metabolites in Iranian Licorice accessions under salinity stress and Azotobacter sp. inoculation

Mousavi

Karami

Saharkhiz

et al. 2022

Sci Rep

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Licorice (Glycyrrhiza glabra L.) is an industrial medicinal plant that is potentially threatened by extinction. In this study, the effects of salinity (0 and 200 mM sodium chloride (NaCl)) and Azotobacter inoculation were evaluated on 16 licorice accessions. The results showed that salinity significantly reduced the fresh and dry biomass (FW and DW, respectively) of roots, compared to plants of the control group (a decrease of 15.92% and 17.26%, respectively). As a result of bacterial inoculation, the total sugar content of roots increased by 21.56% when salinity was applied, but increased by 14.01% without salinity. Salinity stress increased the content of glycyrrhizic acid (GA), phenols, and flavonoids in licorice roots by 104.6%, 117.2%, and 56.3%, respectively. Integrated bacterial inoculation and salt stress significantly increased the GA content in the accessions. Bajgah and Sepidan accessions had the highest GA contents (96.26 and 83.17 mg/g DW, respectively), while Eghlid accession had the lowest (41.98 mg/g DW). With the bacterial application, the maximum amounts of glabridin were obtained in Kashmar and Kermanshah accessions (2.04 and 1.98 mg/g DW, respectively). Bajgah and Kashmar accessions had higher amounts of rutin in their aerial parts (6.11 and 9.48 mg/g DW, respectively) when their roots were uninoculated. In conclusion, these results can assist in selecting promising licorice accessions for cultivation in harsh environments.

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Metabolomics in plant-microbe interactions in the roots

Cited by 16 publications

References 111 publications

Rhizosphere Tripartite Interactions and PGPR-Mediated Metabolic Reprogramming towards ISR and Plant Priming: A Metabolomics Review

Rhizosphere Tripartite Interactions and PGPR-Mediated Metabolic Reprogramming towards ISR and Plant Priming: A Metabolomics Review

Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value

Evaluation of metabolites in Iranian Licorice accessions under salinity stress and Azotobacter sp. inoculation

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