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Special Issue "Plant Microbe Interaction 4.0"

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (31 January 2021).

Special Issue Editors

Prof. Dr. Jan Schirawski
E-Mail Website
Guest Editor
Microbial Genetics, Institute of Applied Microbiology, Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
Interests: fungus-plant interaction; biotrophic fungi; smut fungi; host selection; symptom formation; comparative genomics; effector function
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Michael H. Perlin
E-Mail Website
Guest Editor
Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY 40292, USA
Interests: host/pathogen interactions; smut fungi; evolution of disease; signal transduction; fungal dimorphism
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microbes interact with plants at many different levels, and plants have learned to deal with or even exploit available microbes. While some microbes impact plant growth without entering the plant, many microbes do enter and spread in various plant tissues. In recent years, small proteinaecous effectors secreted by interacting microbes into plant tissues have emerged as a unifying theme. Effector discovery has been tremendously aided by the availability of next-generation sequencing techniques, which have also improved the analysis of plant–microbe interactions at a system-wide level. The system-wide approach also shows that plant growth and development is highly dependent on orchestrating the appropriate responses to different microbial interactors. The development and orchestration of plant responses have been refined through continuous selection pressure during plant and microbe evolution.

This Special Issue calls for reviews as well as original research articles that address the progress and current understanding of different aspects of the vast field of plant–microbe interactions.

Prof. Dr. Jan Schirawski
Prof. Dr. Michael H. Perlin
Guest Editors

Manuscript Submission Information

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Keywords

  • mechanisms of biotrophy
  • endophytes
  • strategies of foliar pathogens
  • root colonizing microbes
  • rhizophere and plant development
  • regulation of plant defenses
  • functional elucidation of plant-microbe interactors
  • effects of microbes on plant development

Published Papers (8 papers)

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Research

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Article
Changes in Bacterial Endophyte Community Following Aspergillus flavus Infection in Resistant and Susceptible Maize Kernels
Int. J. Mol. Sci. 2021, 22(7), 3747; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22073747 - 03 Apr 2021
Viewed by 1019
Abstract
Aspergillus flavus (A. flavus)-mediated aflatoxin contamination in maize is a major global economic and health concern. As A. flavus is an opportunistic seed pathogen, the identification of factors contributing to kernel resistance will be of great importance in the development of [...] Read more.
Aspergillus flavus (A. flavus)-mediated aflatoxin contamination in maize is a major global economic and health concern. As A. flavus is an opportunistic seed pathogen, the identification of factors contributing to kernel resistance will be of great importance in the development of novel mitigation strategies. Using V3–V4 bacterial rRNA sequencing and seeds of A. flavus-resistant maize breeding lines TZAR102 and MI82 and a susceptible line, SC212, we investigated kernel-specific changes in bacterial endophytes during infection. A total of 81 bacterial genera belonging to 10 phyla were detected. Bacteria belonging to the phylum Tenericutes comprised 86–99% of the detected phyla, followed by Proteobacteria (14%) and others (<5%) that changed with treatments and/or genotypes. Higher basal levels (without infection) of Streptomyces and Microbacterium in TZAR102 and increases in the abundance of Stenotrophomonas and Sphingomonas in MI82 following infection may suggest their role in resistance. Functional profiling of bacteria using 16S rRNA sequencing data revealed the presence of bacteria associated with the production of putative type II polyketides and sesquiterpenoids in the resistant vs. susceptible lines. Future characterization of endophytes predicted to possess antifungal/ anti-aflatoxigenic properties will aid in their development as effective biocontrol agents or microbiome markers for maize aflatoxin resistance. Full article
(This article belongs to the Special Issue Plant Microbe Interaction 4.0)
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Article
Effector Profiles of Endophytic Fusarium Associated with Asymptomatic Banana (Musa sp.) Hosts
Int. J. Mol. Sci. 2021, 22(5), 2508; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22052508 - 02 Mar 2021
Cited by 1 | Viewed by 893
Abstract
During the infection of a host, plant pathogenic fungi secrete small proteins called effectors, which then modulate the defence response of the host. In the Fusarium oxysporum species complex (FOSC), the secreted in xylem (SIX) gene effectors are important for host-specific [...] Read more.
During the infection of a host, plant pathogenic fungi secrete small proteins called effectors, which then modulate the defence response of the host. In the Fusarium oxysporum species complex (FOSC), the secreted in xylem (SIX) gene effectors are important for host-specific pathogenicity, and are also useful markers for identifying the various host-specific lineages. While the presence and diversity of the SIX genes has been explored in many of the pathogenic lineages of F. oxysporum, there is a limited understanding of these genes in non-pathogenic, endophytic isolates of F. oxysporum. In this study, universal primers for each of the known SIX genes are designed and used to screen a panel of endophytically-associated Fusarium species isolated from healthy, asymptomatic banana tissue. SIX gene orthologues are identified in the majority of the Fusarium isolates screened in this study. Furthermore, the SIX gene profiles of these endophytic isolates do not overlap with the SIX genes present in the pathogenic lineages of F. oxysporum that are assessed in this study. SIX gene orthologues have not been commonly identified in Fusarium species outside of the FOSC nor in non-pathogenic isolates of F. oxysporum. The results of this study indicate that the SIX gene effectors may be more broadly distributed throughout the Fusarium genus than previously thought. This has important implications for understanding the evolution of pathogenicity in the FOSC. Full article
(This article belongs to the Special Issue Plant Microbe Interaction 4.0)
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Article
Leaf-to-Whole Plant Spread Bioassay for Pepper and Ralstonia solanacearum Interaction Determines Inheritance of Resistance to Bacterial Wilt for Further Breeding
Int. J. Mol. Sci. 2021, 22(5), 2279; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22052279 - 25 Feb 2021
Cited by 2 | Viewed by 790
Abstract
Bacterial wilt (BW) disease from Ralstonia solanacearum is a serious disease and causes severe yield losses in chili peppers worldwide. Resistant cultivar breeding is the most effective in controlling BW. Thus, a simple and reliable evaluation method is required to assess disease severity [...] Read more.
Bacterial wilt (BW) disease from Ralstonia solanacearum is a serious disease and causes severe yield losses in chili peppers worldwide. Resistant cultivar breeding is the most effective in controlling BW. Thus, a simple and reliable evaluation method is required to assess disease severity and to investigate the inheritance of resistance for further breeding programs. Here, we developed a reliable leaf-to-whole plant spread bioassay for evaluating BW disease and then, using this, determined the inheritance of resistance to R. solanacearum in peppers. Capsicum annuum ‘MC4′ displayed a completely resistant response with fewer disease symptoms, a low level of bacterial cell growth, and significant up-regulations of defense genes in infected leaves compared to those in susceptible ‘Subicho’. We also observed the spreading of wilt symptoms from the leaves to the whole susceptible plant, which denotes the normal BW wilt symptoms, similar to the drenching method. Through this, we optimized the evaluation method of the resistance to BW. Additionally, we performed genetic analysis for resistance inheritance. The parents, F1 and 90 F2 progenies, were evaluated, and the two major complementary genes involved in the BW resistance trait were confirmed. These could provide an accurate evaluation to improve resistant pepper breeding efficiency against BW. Full article
(This article belongs to the Special Issue Plant Microbe Interaction 4.0)
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Article
Visualization of Three Sclerotiniaceae Species Pathogenic on Onion Reveals Distinct Biology and Infection Strategies
Int. J. Mol. Sci. 2021, 22(4), 1865; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22041865 - 13 Feb 2021
Viewed by 755
Abstract
Botrytis squamosa, Botrytis aclada, and Sclerotium cepivorum are three fungal species of the family Sclerotiniaceae that are pathogenic on onion. Despite their close relatedness, these fungi cause very distinct diseases, respectively called leaf blight, neck rot, and white rot, which pose [...] Read more.
Botrytis squamosa, Botrytis aclada, and Sclerotium cepivorum are three fungal species of the family Sclerotiniaceae that are pathogenic on onion. Despite their close relatedness, these fungi cause very distinct diseases, respectively called leaf blight, neck rot, and white rot, which pose serious threats to onion cultivation. The infection biology of neck rot and white rot in particular is poorly understood. In this study, we used GFP-expressing transformants of all three fungi to visualize the early phases of infection. B. squamosa entered onion leaves by growing either through stomata or into anticlinal walls of onion epidermal cells. B. aclada, known to cause post-harvest rot and spoilage of onion bulbs, did not penetrate the leaf surface but instead formed superficial colonies which produced new conidia. S. cepivorum entered onion roots via infection cushions and appressorium-like structures. In the non-host tomato, S. cepivorum also produced appressorium-like structures and infection cushions, but upon prolonged contact with the non-host the infection structures died. With this study, we have gained understanding in the infection biology and strategy of each of these onion pathogens. Moreover, by comparing the infection mechanisms we were able to increase insight into how these closely related fungi can cause such different diseases. Full article
(This article belongs to the Special Issue Plant Microbe Interaction 4.0)
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Article
Diazotroph Paenibacillus triticisoli BJ-18 Drives the Variation in Bacterial, Diazotrophic and Fungal Communities in the Rhizosphere and Root/Shoot Endosphere of Maize
Int. J. Mol. Sci. 2021, 22(3), 1460; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22031460 - 02 Feb 2021
Cited by 3 | Viewed by 746
Abstract
Application of diazotrophs (N2-fixing microorganisms) can decrease the overuse of nitrogen (N) fertilizer. Until now, there are few studies on the effects of diazotroph application on microbial communities of major crops. In this study, the diazotrophic and endospore-forming Paenibacillus triticisoli BJ-18 [...] Read more.
Application of diazotrophs (N2-fixing microorganisms) can decrease the overuse of nitrogen (N) fertilizer. Until now, there are few studies on the effects of diazotroph application on microbial communities of major crops. In this study, the diazotrophic and endospore-forming Paenibacillus triticisoli BJ-18 was inoculated into maize soils containing different N levels. The effects of inoculation on the composition and abundance of the bacterial, diazotrophic and fungal communities in the rhizosphere and root/shoot endosphere of maize were evaluated by sequencing the 16S rRNA, nifH gene and ITS (Inter Transcribed Spacer) region. P. triticisoli BJ-18 survived and propagated in all the compartments of the maize rhizosphere, root and shoot. The abundances and diversities of the bacterial and diazotrophic communities in the rhizosphere were significantly higher than in both root and shoot endospheres. Each compartment of the rhizosphere, root and shoot had its specific bacterial and diazotrophic communities. Our results showed that inoculation reshaped the structures of the bacterial, diazotrophic and fungal communities in the maize rhizosphere and endosphere. Inoculation reduced the interactions of the bacteria and diazotrophs in the rhizosphere and endosphere, while it increased the fungal interactions. After inoculation, the abundances of Pseudomonas, Bacillus and Paenibacillus in all three compartments, Klebsiella in the rhizosphere and Paenibacillus in the root and shoot were significantly increased, while the abundances of Fusarium and Giberella were greatly reduced. Paenibacillus was significantly correlated with plant dry weight, nitrogenase, N2-fixing rate, P solubilization and other properties of the soil and plant. Full article
(This article belongs to the Special Issue Plant Microbe Interaction 4.0)
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Article
De Novo Transcriptome Sequencing of Rough Lemon Leaves (Citrus jambhiri Lush.) in Response to Plenodomus tracheiphilus Infection
Int. J. Mol. Sci. 2021, 22(2), 882; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22020882 - 17 Jan 2021
Cited by 1 | Viewed by 908
Abstract
Mal secco is one of the most severe diseases of citrus, caused by the necrotrophic fungus Plenodomus tracheiphilus. With the main aim of identifying candidate genes involved in the response of citrus plants to “Mal secco”, we performed a de novo transcriptome [...] Read more.
Mal secco is one of the most severe diseases of citrus, caused by the necrotrophic fungus Plenodomus tracheiphilus. With the main aim of identifying candidate genes involved in the response of citrus plants to “Mal secco”, we performed a de novo transcriptome analysis of rough lemon seedlings subjected to inoculation of P. tracheiphilus. The analysis of differential expressed genes (DEGs) highlighted a sharp response triggered by the pathogen as a total of 4986 significant DEGs (2865 genes up-regulated and 2121 down-regulated) have been revealed. The analysis of the most significantly enriched KEGG pathways indicated that a crucial role is played by genes involved in “Plant hormone signal transduction”, “Phenylpropanoid biosynthesis”, and “Carbon metabolism”. The main findings of this work are that under fungus challenge, the rough lemon genes involved both in the light harvesting and the photosynthetic electron flow were significantly down-regulated, thus probably inducing a shortage of energy for cellular functions. Moreover, the systemic acquired resistance (SAR) was activated through the induced salicylic acid cascade. Interestingly, RPM1 interacting protein 4, an essential positive regulator of plant defense, and BIR2, which is a negative regulator of basal level of immunity, have been identified thus representing useful targets for molecular breeding. Full article
(This article belongs to the Special Issue Plant Microbe Interaction 4.0)
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Article
Garlic Substrate Induces Cucumber Growth Development and Decreases Fusarium Wilt through Regulation of Soil Microbial Community Structure and Diversity in Replanted Disturbed Soil
Int. J. Mol. Sci. 2020, 21(17), 6008; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21176008 - 20 Aug 2020
Cited by 5 | Viewed by 1164
Abstract
Garlic substrate could influence plant growth through affecting soil microbiome structure. The relationship mechanism between changes in soil microbial communities, disease suppression and plant development, however, remains unclear, particularly in the degraded soil micro-ecological environment. In this study, garlic substrates as a soil [...] Read more.
Garlic substrate could influence plant growth through affecting soil microbiome structure. The relationship mechanism between changes in soil microbial communities, disease suppression and plant development, however, remains unclear, particularly in the degraded soil micro-ecological environment. In this study, garlic substrates as a soil amendment were incorporated with different ratios (1:100, 3:100 and 5:100 g/100 g of soil) in a replanted disturbed soil of long-term cucumber monoculture (annual double cropping system in a greenhouse). The results indicated that higher amount of C-amended garlic substrate significantly induced soil suppressiveness (35.9% greater than control (CK) against the foliar disease incidence rate. This inhibitory effect consequently improved the cucumber growth performance and fruit yield to 20% higher than the non-amended soil. Short-term garlic substrate addition modified the soil quality through an increase in soil organic matter (SOM), nutrient availability and enzymatic activities. Illumina MiSeq sequencing analysis revealed that soil bacterial and fungal communities in the garlic amendment were significantly different from the control. Species richness and diversity indices significantly increased under treated soil. The correlation-based heat map analysis suggested that soil OM, nutrient contents and biological activators were the primary drivers reshaping the microbial community structure. Furthermore, garlic substrate inhibited soil-borne pathogen taxa (Fusarium and Nematoda), and their reduced abundances, significantly affecting the crop yield. In addition, the host plant recruited certain plant-beneficial microbes due to substrate addition that could directly contribute to plant–pathogen inhibition and crop biomass production. For example, abundant Acidobacteria, Ascomycota and Glomeromycota taxa were significantly associated with cucumber yield promotion. Firmicutes, Actinobacteria, Bacteroidetes, Basidiomycota and Glomeromycota were the associated microbial taxa that possibly performed as antagonists of Fusarium wilt, with plant pathogen suppression potential in monocropped cucumber-planted soil. Full article
(This article belongs to the Special Issue Plant Microbe Interaction 4.0)
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Review

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Review
Understanding Plant Social Networking System: Avoiding Deleterious Microbiota but Calling Beneficials
Int. J. Mol. Sci. 2021, 22(7), 3319; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22073319 - 24 Mar 2021
Cited by 4 | Viewed by 1056
Abstract
Plant association with microorganisms elicits dramatic effects on the local phytobiome and often causes systemic and transgenerational modulation on plant immunity against insect pests and microbial pathogens. Previously, we introduced the concept of the plant social networking system (pSNS) to highlight the active [...] Read more.
Plant association with microorganisms elicits dramatic effects on the local phytobiome and often causes systemic and transgenerational modulation on plant immunity against insect pests and microbial pathogens. Previously, we introduced the concept of the plant social networking system (pSNS) to highlight the active involvement of plants in the recruitment of potentially beneficial microbiota upon exposure to insects and pathogens. Microbial association stimulates the physiological responses of plants and induces the development of their immune mechanisms while interacting with multiple enemies. Thus, beneficial microbes serve as important mediators of interactions among multiple members of the multitrophic, microscopic and macroscopic communities. In this review, we classify the steps of pSNS such as elicitation, signaling, secreting root exudates, and plant protection; summarize, with evidence, how plants and beneficial microbes communicate with each other; and also discuss how the molecular mechanisms underlying this communication are induced in plants exposed to natural enemies. Collectively, the pSNS modulates robustness of plant physiology and immunity and promotes survival potential by helping plants to overcome the environmental and biological challenges. Full article
(This article belongs to the Special Issue Plant Microbe Interaction 4.0)
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