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Omics in Plant-Pathogen Interaction

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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Protection and Biotic Interactions".

Deadline for manuscript submissions: closed (31 May 2023) | Viewed by 33512

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Dr. Andreia Figueiredo

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Grapevine Pathogen Systems Lab, Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
Interests: systems biology; omics technologies; plant–pathogen interaction; grapevine; proteases; metabolism; lipids
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Dr. Walter Chitarra

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Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, TV, Italy
Interests: plant–microbe interactions; plant ecophysiology; grapevine; mycorrhiza; synthetic microbial communities

Dr. Luca Nerva

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Council for Agricultural Research and Economics, CREA-Research Centre for Viticulture and Enology, Viale XXVIII Aprile 26, 31015 Conegliano, Italy
Interests: genome editing; plant-microbe interactions; sustainability; agroecology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plants are sessile organisms that are continuously exposed to adverse biotic and abiotic environmental factors. Plant immunity involves a remarkable array of structural, chemical and protein-based layers of defense, which aim to stop pathogens before they cause irreversible damage.

Pathogen challenge is an elaborate defense system, beginning with the recognition of pathogen and microbial specific molecules (e.g., flagellin). When plant receptors perceive the invading pathogen activating signaling cascades, plant resistance is achieved through pathogen‐associated molecular‐pattern (PAMP)‐triggered immunity (PTI). If PTI is unsuccessful, a second layer of defense is activated: effector triggered immunity (ETI), which is mediated by resistance (R) proteins that recognize specific pathogen effector molecules, leading to a broader modulation of the plant defense system. This response is often accompanied by programmed cell death and pathogen restraint.

Over the last few decades, the study of plant–pathogen interaction was boosted by the advent of new technologies and the application of several OMIC platforms. Aside from the most well-known ‘OMIC technologies (transcriptomics, proteomics, and metabolomics), tremendous progress has been made in the development of newer ‘OMICs’ approaches, allowing a more comprehensive overview of plants’ defense systems. Moreover, the application of specialized OMIC’s technologies to specific cellular compartments (such as plant extracellular space, i.e., apoplast) offers exciting opportunities to improve our understanding of pathogen manipulation hubs and plants’ resistance mechanisms.

The focus of this Special Issue is on cutting-edge knowledge of plants defense mechanisms for different pathogens (e.g., bacteria, oomycetes, fungi, and nematodes) obtained from the application of OMICs approaches. Overviews of plant–pathogen interaction, including the role of plant symbionts (e.g., mycorrhizal and endophytic fungi or bacteria) on the modulation of plant defense responses, the action of pathogen effectors, or specific aspects of defense pathways (e.g., hormone signaling) will be considered.

We welcome all scientific works (original research papers, perspectives, hypotheses, opinions, reviews, modeling approaches, and methods) focused on the application of any OMICs technology to the study of plant–pathogen interactions.

Topics include (but are not limited to):

Omics studies to gain insight into plant disease resistance.
Omics applied to the study of plant and soil microbiomes and their impact on plant responses to pathogens.

The application of specialized OMIC research fields to the study of plant–pathogen interaction.
Studies that apply OMIC platforms to subcellular compartments (eg. apoplast) in plant–pathogen interaction.
Studies presenting new tools to support OMIC studies, including innovative bioinformatic approaches.

Prof. Dr. Andreia Figueiredo
Dr. Walter Chitarra
Dr. Luca Nerva
Guest Editors

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Keywords

plant immunity
OMIC platforms
programmed cell death
apoplast
systemic resistance
hormone crosstalk
signaling pathways
pathogenicity
microbiome

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Published Papers (8 papers)

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Research

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23 pages, 33507 KiB

Open AccessArticle

¹H-NMR Metabolomics Study after Foliar and Endo-Therapy Treatments of Xylella fastidiosa subsp. pauca Infected Olive Trees: Medium Time Monitoring of Field Experiments

by Mudassar Hussain, Chiara Roberta Girelli, Dimitri Verweire, Michael C. Oehl, Maier S. Avendaño, Marco Scortichini and Francesco Paolo Fanizzi

Plants 2023, 12(10), 1946; https://doi.org/10.3390/plants12101946 - 10 May 2023

Cited by 5 | Viewed by 1769

Abstract

Here we report the medium-term effects of foliar spray and endo-therapy treatments with different doses of a Cu/Zn citric acid biocomplex (Dentamet^®) in Xylella fastidiosa infected olive trees of Salento, Apulia region (South-east Italy). Leaf extract samples from field-treated 150 years old olive trees cvs Ogliarola salentina and Cellina di Nardò were studied by ¹H NMR-based metabolomics. The result of different applications of Dentamet^® endo-therapy after 60, 120 and 180 days in comparison with traditional foliar spray treatment and water injection as a control have been investigated. The metabolic profile analyses, performed by ¹H NMR-based metabolomic approach, indicated plant metabolites variations connected to the disease progression such as mannitol, quinic acid, and oleuropein related compounds. The best results, in terms of discrimination of the metabolic profiles with respect to water injection, were found for monthly endo-therapy treatments. Dentamet^® foliar application demonstrated more specific time related progressive effectiveness with respect to intravascular treatments. Therefore, besides a possible more effective performance of endo-therapy with respect to foliar treatments, the need of further doses/frequencies trimming to obtain long-term results was also assessed. The present field studies confirmed the indication of Dentamet^® effectiveness in metabolic variation induction, potentially linked with reducing the X. fastidiosa subspecies pauca related Olive Quick Decline Syndrome (OQDS) symptoms development. Full article

(This article belongs to the Special Issue Omics in Plant-Pathogen Interaction)

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23 pages, 3064 KiB

Open AccessArticle

A Metabolome Analysis and the Immunity of Phlomis purpurea against Phytophthora cinnamomi

by Dina Neves, Andreia Figueiredo, Marisa Maia, Endre Laczko, Maria Salomé Pais and Alfredo Cravador

Plants 2023, 12(10), 1929; https://doi.org/10.3390/plants12101929 - 9 May 2023

Cited by 1 | Viewed by 1994

Abstract

Phlomis purpurea grows spontaneously in the southern Iberian Peninsula, namely in cork oak (Quercus suber) forests. In a previous transcriptome analysis, we reported on its immunity against Phytophthora cinnamomi. However, little is known about the involvement of secondary metabolites in the P. purpurea defense response. It is known, though, that root exudates are toxic to this pathogen. To understand the involvement of secondary metabolites in the defense of P. purpurea, a metabolome analysis was performed using the leaves and roots of plants challenged with the pathogen for over 72 h. The putatively identified compounds were constitutively produced. Alkaloids, fatty acids, flavonoids, glucosinolates, polyketides, prenol lipids, phenylpropanoids, sterols, and terpenoids were differentially produced in these leaves and roots along the experiment timescale. It must be emphasized that the constitutive production of taurine in leaves and its increase soon after challenging suggests its role in P. purpurea immunity against the stress imposed by the oomycete. The rapid increase in secondary metabolite production by this plant species accounts for a concerted action of multiple compounds and genes on the innate protection of Phlomis purpurea against Phytophthora cinnamomi. The combination of the metabolome with the transcriptome data previously disclosed confirms the mentioned innate immunity of this plant against a devastating pathogen. It suggests its potential as an antagonist in phytopathogens’ biological control. Its application in green forestry/agriculture is therefore possible. Full article

(This article belongs to the Special Issue Omics in Plant-Pathogen Interaction)

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16 pages, 3480 KiB

Open AccessArticle

Peptidome and Transcriptome Analysis of Plant Peptides Involved in Bipolaris maydis Infection of Maize

by Pijie Sheng, Minyan Xu, Zhenzhen Zheng, Xiaojing Liu, Wanlu Ma, Ting Ding, Chenchen Zhang, Meng Chen, Mengting Zhang, Beijiu Cheng and Xin Zhang

Plants 2023, 12(6), 1307; https://doi.org/10.3390/plants12061307 - 14 Mar 2023

Cited by 2 | Viewed by 2203

Abstract

Southern corn leaf blight (SCLB) caused by Bipolaris maydis threatens maize growth and yield worldwide. In this study, TMT-labeled comparative peptidomic analysis was established between infected and uninfected maize leaf samples using liquid-chromatography-coupled tandem mass spectrometry. The results were further compared and integrated with transcriptome data under the same experimental conditions. Plant peptidomic analysis identified 455 and 502 differentially expressed peptides (DEPs) in infected maize leaves on day 1 and day 5, respectively. A total of 262 common DEPs were identified in both cases. Bioinformatic analysis indicated that the precursor proteins of DEPs are associated with many pathways generated by SCLB-induced pathological changes. The expression profiles of plant peptides and genes in maize plants were considerably altered after B. maydis infection. These findings provide new insights into the molecular mechanisms of SCLB pathogenesis and offer a basis for the development of maize genotypes with SCLB resistance. Full article

(This article belongs to the Special Issue Omics in Plant-Pathogen Interaction)

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21 pages, 4831 KiB

Open AccessArticle

Olive Cultivars Susceptible or Tolerant to Xylella fastidiosa Subsp. pauca Exhibit Mid-Term Different Metabolomes upon Natural Infection or a Curative Treatment

by Chiara Roberta Girelli, Laura Del Coco, Federica Angilè, Marco Scortichini and Francesco Paolo Fanizzi

Plants 2021, 10(4), 772; https://doi.org/10.3390/plants10040772 - 15 Apr 2021

Cited by 11 | Viewed by 2760

Abstract

Xylella fastidiosa subsp. pauca, is a bacterial phytopathogen associated with the “olive quick decline syndrome” (OQDS) causing severe economic losses to olive groves in Salento area (Apulia, Italy). In a previous work, we analyzed by ¹H-NMR the metabolic pattern of naturally infected Ogliarola salentina and Cellina di Nardò susceptible cultivars untreated and treated with a zinc-copper citric acid biocomplex and we observed the treatment related variation of the disease biomarker quinic acid. In this study, we focused also on the Leccino cultivar, known to exhibit tolerance to the disease progression. The ¹H-NMR-based metabolomic approach was applied with the aim to characterize the overall metabolism of tolerant Leccino in comparison with the susceptible cultivars Ogliarola salentina and Cellina di Nardò under periodic mid-term treatment. In particular, we studied the leaf extract molecular patterns of naturally infected trees untreated and treated with the biocomplex. The metabolic Leccino profiles were analyzed for the first time and compared with those exhibited by the susceptible Cellina di Nardò and Ogliarola salentina cultivars. The study highlighted a specificity in the metabolic response of the tolerant Leccino compared to susceptible cultivars. These differences provide useful information to describe the defensive mechanisms underlying the change of metabolites as a response to the infection, and the occurrence of different levels of disease, season and treatment effects for olive cultivars. Full article

(This article belongs to the Special Issue Omics in Plant-Pathogen Interaction)

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17 pages, 1370 KiB

Open AccessArticle

Grapevine–Downy Mildew Rendezvous: Proteome Analysis of the First Hours of an Incompatible Interaction

by Rita B. Santos, Rui Nascimento, Ana V. Coelho and Andreia Figueiredo

Plants 2020, 9(11), 1498; https://doi.org/10.3390/plants9111498 - 5 Nov 2020

Cited by 8 | Viewed by 2917

Abstract

Grapevine is one of the most relevant crops in the world being used for economically important products such as wine. However, relevant grapevine cultivars are heavily affected by diseases such as the downy mildew disease caused by Plasmopara viticola. Improvements on grapevine resistance are made mainly by breeding techniques where resistance traits are introgressed into cultivars with desired grape characteristics. However, there is still a lack of knowledge on how resistant or tolerant cultivars tackle the P. viticola pathogen. In this study, using a shotgun proteomics LC-MS/MS approach, we unravel the protein modulation of a highly tolerant grapevine cultivar, Vitis vinifera “Regent”, in the first hours post inoculation (hpi) with P. viticola. At 6 hpi, proteins related to defense and to response to stimuli are negatively modulated while at 12 hpi there is an accumulation of proteins belonging to both categories. The co-occurrence of indicators of effector-triggered susceptibility (ETS) and effector-triggered immunity (ETI) is detected at both time-points, showing that these defense processes present high plasticity. The results obtained in this study unravel the tolerant grapevine defense strategy towards P. viticola and may provide valuable insights on resistance associated candidates and mechanisms, which may play an important role in the definition of new strategies for breeding approaches. Full article

(This article belongs to the Special Issue Omics in Plant-Pathogen Interaction)

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30 pages, 8578 KiB

Open AccessEditor’s ChoiceArticle

Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling

by Ivan Tsers, Vladimir Gorshkov, Natalia Gogoleva, Olga Parfirova, Olga Petrova and Yuri Gogolev

Plants 2020, 9(9), 1176; https://doi.org/10.3390/plants9091176 - 10 Sep 2020

Cited by 20 | Viewed by 4216

Abstract

Soft rot caused by Pectobacterium species is a devastating plant disease poorly characterized in terms of host plant responses. In this study, changes in the transcriptome of tobacco plants after infection with Pectobacterium atrosepticum (Pba) were analyzed using RNA-Seq. To draw a comprehensive and nontrivially itemized picture of physiological events in Pba-infected plants and to reveal novel potential molecular “players” in plant–Pba interactions, an original functional gene classification was performed. The classifications present in various databases were merged, enriched by “missed” genes, and divided into subcategories. Particular changes in plant cell wall-related processes, perturbations in hormonal and other regulatory systems, and alterations in primary, secondary, and redox metabolism were elucidated in terms of gene expression. Special attention was paid to the prediction of transcription factors (TFs) involved in the disease’s development. Herewith, gene expression was analyzed within the predicted TF regulons assembled at the whole-genome level based on the presence of particular cis-regulatory elements (CREs) in gene promoters. Several TFs, whose regulons were enriched by differentially expressed genes, were considered to be potential master regulators of Pba-induced plant responses. Differential regulation of genes belonging to a particular multigene family and encoding cognate proteins was explained by the presence/absence of the particular CRE in gene promoters. Full article

(This article belongs to the Special Issue Omics in Plant-Pathogen Interaction)

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24 pages, 961 KiB

Open AccessReview

Legume Crops and Biotrophic Pathogen Interactions: A Continuous Cross-Talk of a Multilayered Array of Defense Mechanisms

by Davide Martins, Susana de Sousa Araújo, Diego Rubiales and Maria Carlota Vaz Patto

Plants 2020, 9(11), 1460; https://doi.org/10.3390/plants9111460 - 29 Oct 2020

Cited by 17 | Viewed by 4005

Abstract

Legume species are recognized for their nutritional benefits and contribution to the sustainability of agricultural systems. However, their production is threatened by biotic constraints with devastating impacts on crop yield. A deep understanding of the molecular and genetic architecture of resistance sources culminating in immunity is critical to assist new biotechnological approaches for plant protection. In this review, the current knowledge regarding the major plant immune system components of grain and forage legumes challenged with obligate airborne biotrophic fungi will be comprehensively evaluated and discussed while identifying future directions of research. To achieve this, we will address the multi-layered defense strategies deployed by legume crops at the biochemical, molecular, and physiological levels, leading to rapid pathogen recognition and carrying the necessary information to sub-cellular components, on-setting a dynamic and organized defense. Emphasis will be given to recent approaches such as the identification of critical components of host decentralized immune response negatively regulated by pathogens while targeting the loss-of-function of susceptibility genes. We conclude that advances in gene expression analysis in both host and pathogen, protocols for effectoromics pipelines, and high-throughput disease phenomics platforms are rapidly leading to a deeper understanding of the intricate host-pathogen interaction, crucial for efficient disease resistance breeding initiatives. Full article

(This article belongs to the Special Issue Omics in Plant-Pathogen Interaction)

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29 pages, 1361 KiB

Open AccessEditor’s ChoiceReview

Understanding Host–Pathogen Interactions in Brassica napus in the Omics Era

by Ting Xiang Neik, Junrey Amas, Martin Barbetti, David Edwards and Jacqueline Batley

Plants 2020, 9(10), 1336; https://doi.org/10.3390/plants9101336 - 10 Oct 2020

Cited by 32 | Viewed by 11084

Abstract

Brassica napus (canola/oilseed rape/rapeseed) is an economically important crop, mostly found in temperate and sub-tropical regions, that is cultivated widely for its edible oil. Major diseases of Brassica crops such as Blackleg, Clubroot, Sclerotinia Stem Rot, Downy Mildew, Alternaria Leaf Spot and White Rust have caused significant yield and economic losses in rapeseed-producing countries worldwide, exacerbated by global climate change, and, if not remedied effectively, will threaten global food security. To gain further insights into the host–pathogen interactions in relation to Brassica diseases, it is critical that we review current knowledge in this area and discuss how omics technologies can offer promising results and help to push boundaries in our understanding of the resistance mechanisms. Omics technologies, such as genomics, proteomics, transcriptomics and metabolomics approaches, allow us to understand the host and pathogen, as well as the interaction between the two species at a deeper level. With these integrated data in multi-omics and systems biology, we are able to breed high-quality disease-resistant Brassica crops in a more holistic, targeted and accurate way. Full article

(This article belongs to the Special Issue Omics in Plant-Pathogen Interaction)

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