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

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 37615

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Special Issue Editors

Dr. Yangrong Cao

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State Key Laboratory of Agriculture Microbiology, Hubei Hongshan Laboratory, Huazhong Agriculture University, Wuhan 430000, China
Interests: plant-microbe interactions; legume-rhizobial symbiosis; MAMP-trigged plant immunity
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Hari B. Krishnan

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Plant Genetics Research Unit, USDA-ARS, 108 Curtis Hall, University of Missouri, Columbia, MO 65211, USA
Interests: plant molecular biology; plant microbe interaction; soybean seed composition; biological nitrogen fixation; sulfur assimilation; plant biotechnology

Special Issue Information

Dear Colleagues,

One of the fundamental questions in biology is how plants, the sessile organisms, associate with different microbes that pose either pathogenesis, mutualism, or commensalism, as well as microbiota. Indeed, significant progress over the past thirty years has been made on the plant immune responses against pathogenic threats and the common signaling pathway for symbiotic interaction between plants and mutualistic microbes. However, both the ability of plants to distinguish friends from foes and the evolution of each specific type of plant–microbe interactions are unclear. This issue, entitled “Plant–Microbe Interactions”, will address questions including the molecular basis of plant–microbe interactions and the evolution of plant–microbe interactions.

Dr. Yangrong Cao
Prof. Dr. Hari B. Krishnan
Guest Editors

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Keywords

plant innate immunity
plant–microbe interactions
root nodule symbiosis
arbuscular mycorrhizal symbiosis
microbiota
microbiome

Published Papers (12 papers)

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19 pages, 4014 KiB

Open AccessArticle

Ectopic Expression of OsJAZs Alters Plant Defense and Development

by Baolong Sun, Luyue Shang, Yang Li, Qiang Zhang, Zhaohui Chu, Shengyang He, Wei Yang and Xinhua Ding

Int. J. Mol. Sci. 2022, 23(9), 4581; https://doi.org/10.3390/ijms23094581 - 21 Apr 2022

Cited by 6 | Viewed by 2345

Abstract

A key step in jasmonic acid (JA) signaling is the ligand-dependent assembly of a coreceptor complex comprising the F-box protein COI1 and JAZ transcriptional repressors. The assembly of this receptor complex results in proteasome-mediated degradation of JAZ repressors, which in turn bind and repress MYC transcription factors. Many studies on JAZs have been performed in Arabidopsis thaliana, but the function of JAZs in rice is largely unknown. To systematically reveal the function of OsJAZs, in this study, we compared the various phenotypes resulting from 13 OsJAZs via ectopic expression in Arabidopsis thaliana and the phenotypes of 12 AtJAZs overexpression (OE) lines. Phylogenetic analysis showed that the 25 proteins could be divided into three major groups. Yeast two-hybrid (Y2H) assays revealed that most OsJAZ proteins could form homodimers or heterodimers. The statistical results showed that the phenotypes of the OsJAZ OE plants were quite different from those of AtJAZ OE plants in terms of plant growth, development, and immunity. As an example, compared with other JAZ OE plants, OsJAZ11 OE plants exhibited a JA-insensitive phenotype and enhanced resistance to Pst DC3000. The protein stability after JA treatment of OsJAZ11 emphasized the specific function of the protein. This study aimed to explore the commonalities and characteristics of different JAZ proteins functions from a genetic perspective, and to screen genes with disease resistance value. Overall, the results of this study provide insights for further functional analysis of rice JAZ family proteins. Full article

(This article belongs to the Special Issue Plant-Microbe Interactions)

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17 pages, 4212 KiB

Open AccessArticle

Differential Response of Wheat Rhizosphere Bacterial Community to Plant Variety and Fertilization

by Lisa Cangioli, Marco Mancini, Marco Napoli, Camilla Fagorzi, Simone Orlandini, Francesca Vaccaro and Alessio Mengoni

Int. J. Mol. Sci. 2022, 23(7), 3616; https://doi.org/10.3390/ijms23073616 - 25 Mar 2022

Cited by 7 | Viewed by 2703

Abstract

The taxonomic assemblage and functions of the plant bacterial community are strongly influenced by soil and host plant genotype. Crop breeding, especially after the massive use of nitrogen fertilizers which led to varieties responding better to nitrogen fertilization, has implicitly modified the ability of the plant root to recruit an effective bacterial community. Among the priorities for harnessing the plant bacterial community, plant genotype-by-microbiome interactions are stirring attention. Here, we analyzed the effect of plant variety and fertilization on the rhizosphere bacterial community. In particular, we clarified the presence in the bacterial community of a varietal effect of N and P fertilization treatment. 16S rRNA gene amplicon sequence analysis of rhizospheric soil, collected from four wheat varieties grown under four N-P fertilization regimes, and quantification of functional bacterial genes involved in the nitrogen cycle (nifH; amoA; nirK and nosZ) were performed. Results showed that variety played the most important role and that treatments did not affect either bacterial community diversity or bacterial phyla abundance. Variety-specific response of rhizosphere bacterial community was detected, both in relation to taxa (Nitrospira) and metabolic functions. In particular, the changes related to amino acid and aerobic metabolism and abundance of genes involved in the nitrogen cycle (amoA and nosZ), suggested that plant variety may lead to functional changes in the cycling of the plant-assimilable nitrogen. Full article

(This article belongs to the Special Issue Plant-Microbe Interactions)

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16 pages, 5135 KiB

Open AccessArticle

A NAC Transcription Factor TuNAC69 Contributes to ANK-NLR-WRKY NLR-Mediated Stripe Rust Resistance in the Diploid Wheat Triticum urartu

by Yang Xu, Shenghao Zou, Hao Zeng, Wei Wang, Bin Wang, Huan Wang and Dingzhong Tang

Int. J. Mol. Sci. 2022, 23(1), 564; https://doi.org/10.3390/ijms23010564 - 5 Jan 2022

Cited by 10 | Viewed by 2839

Abstract

Stripe rust is one of the most devastating diseases in wheat. Nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domain receptors (NLRs) recognize pathogenic effectors and trigger plant immunity. We previously identified a unique NLR protein YrU1 in the diploid wheat Triticum urartu, which contains an N-terminal ANK domain and a C-terminal WRKY domain and confers disease resistance to stripe rust fungus Puccinia striiformis f. sp. Tritici (Pst). However, how YrU1 functions in disease resistance is not clear. In this study, through the RNA-seq analysis, we found that the expression of a NAC member TuNAC69 was significantly up-regulated after inoculation with Pst in the presence of YrU1. TuNAC69 was mainly localized in the nucleus and showed transcriptional activation in yeast. Knockdown TuNAC69 in diploid wheat Triticum urartu PI428309 that contains YrU1 by virus-induced gene silencing reduced the resistance to stripe rust. In addition, overexpression of TuNAC69 in Arabidopsis enhanced the resistance to powdery mildew Golovinomyces cichoracearum. In summary, our study indicates that TuNAC69 participates in the immune response mediated by NLR protein YrU1, and likely plays an important role in disease resistance to other pathogens. Full article

(This article belongs to the Special Issue Plant-Microbe Interactions)

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14 pages, 2698 KiB

Open AccessArticle

Studying the Function of Phytoplasma Effector Proteins Using a Chemical-Inducible Expression System in Transgenic Plants

by Keziah M. Omenge, Florian Rümpler, Subha Suvetha Kathalingam, Alexandra C. U. Furch and Günter Theißen

Int. J. Mol. Sci. 2021, 22(24), 13582; https://doi.org/10.3390/ijms222413582 - 18 Dec 2021

Cited by 3 | Viewed by 2877

Abstract

Phytoplasmas are bacterial pathogens that live mainly in the phloem of their plant hosts. They dramatically manipulate plant development by secreting effector proteins that target developmental proteins of their hosts. Traditionally, the effects of individual effector proteins have been studied by ectopic overexpression using strong, ubiquitously active promoters in transgenic model plants. However, the impact of phytoplasma infection on the host plants depends on the intensity and timing of infection with respect to the developmental stage of the host. To facilitate investigations addressing the timing of effector protein activity, we have established chemical-inducible expression systems for the three most well-characterized phytoplasma effector proteins, SECRETED ASTER YELLOWS WITCHES’ BROOM PROTEIN 11 (SAP11), SAP54 and TENGU in transgenic Arabidopsis thaliana. We induced gene expression either continuously, or at germination stage, seedling stage, or flowering stage. mRNA expression was determined by quantitative reverse transcription PCR, protein accumulation by confocal laser scanning microscopy of GFP fusion proteins. Our data reveal tight regulation of effector gene expression and strong upregulation after induction. Phenotypic analyses showed differences in disease phenotypes depending on the timing of induction. Comparative phenotype analysis revealed so far unreported similarities in disease phenotypes, with all three effector proteins interfering with flower development and shoot branching, indicating a surprising functional redundancy of SAP54, SAP11 and TENGU. However, subtle but mechanistically important differences were also observed, especially affecting the branching pattern of the plants. Full article

(This article belongs to the Special Issue Plant-Microbe Interactions)

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21 pages, 1620 KiB

Open AccessArticle

Potential of Trichoderma harzianum and Its Metabolites to Protect Wheat Seedlings against Fusarium culmorum and 2,4-D

by Julia Mironenka, Sylwia Różalska and Przemysław Bernat

Int. J. Mol. Sci. 2021, 22(23), 13058; https://doi.org/10.3390/ijms222313058 - 2 Dec 2021

Cited by 11 | Viewed by 2191

Abstract

Wheat is a critically important crop. The application of fungi, such as Trichoderma harzianum, to protect and improve crop yields could become an alternative solution to synthetic chemicals. However, the interaction between the fungus and wheat in the presence of stress factors at the molecular level has not been fully elucidated. In the present work, we exposed germinating seeds of wheat (Triticum aestivum) to the plant pathogen Fusarium culmorum and the popular herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) in the presence of T. harzianum or its extracellular metabolites. Then, the harvested roots and shoots were analyzed using spectrometry, 2D-PAGE, and MALDI-TOF/MS techniques. Although F. culmorum and 2,4-D were found to disturb seed germination and the chlorophyll content, T. harzianum partly alleviated these negative effects and reduced the synthesis of zearalenone by F. culmorum. Moreover, T. harzianum decreased the activity of oxidoreduction enzymes (CAT and SOD) and the contents of the oxylipins 9-Hode, 13-Hode, and 13-Hotre induced by stress factors. Under the influence of various growth conditions, changes were observed in over 40 proteins from the wheat roots. Higher volumes of proteins and enzymes performing oxidoreductive functions, such as catalase, ascorbate peroxidase, cytochrome C peroxidase, and Cu/Zn superoxide dismutase, were found in the Fusarium-inoculated and 2,4-D-treated wheat roots. Additionally, observation of the level of 12-oxo-phytodienoic acid reductase involved in the oxylipin signaling pathway in wheat showed an increase. Trichoderma and its metabolites present in the system leveled out the mentioned proteins to the control volumes. Among the 30 proteins examined in the shoots, the expression of the proteins involved in photosynthesis and oxidative stress response was found to be induced in the presence of the herbicide and the pathogen. In summary, these proteomic and metabolomic studies confirmed that the presence of T. harzianum results in the alleviation of oxidative stress in wheat induced by 2,4-D or F. culmorum. Full article

(This article belongs to the Special Issue Plant-Microbe Interactions)

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16 pages, 2037 KiB

Open AccessArticle

The Role of Pectobacterium atrosepticum Exopolysaccharides in Plant–Pathogen Interactions

by Bakhtiyar Islamov, Olga Petrova, Polina Mikshina, Aidar Kadyirov, Vladimir Vorob’ev, Yuri Gogolev and Vladimir Gorshkov

Int. J. Mol. Sci. 2021, 22(23), 12781; https://doi.org/10.3390/ijms222312781 - 26 Nov 2021

Cited by 12 | Viewed by 2045

Abstract

The phytopathogenic bacterium Pectobacterium atrosepticum (Pba), one of the members of the soft rot Pectobacteriaceae, forms biofilm-like structures known as bacterial emboli when colonizing the primary xylem vessels of the host plants. The initial extracellular matrix of the bacterial emboli is composed of the host plant’s pectic polysaccharides, which are gradually substituted by the Pba-produced exopolysaccharides (Pba EPS) as the bacterial emboli “mature”. No information about the properties of Pba EPS and their possible roles in Pba-plant interactions has so far been obtained. We have shown that Pba EPS possess physical properties that can promote the maintenance of the structural integrity of bacterial emboli. These polymers increase the viscosity of liquids and form large supramolecular aggregates. The formation of Pba EPS aggregates is provided (at least partly) by the acetyl groups of the Pba EPS molecules. Besides, Pba EPS scavenge reactive oxygen species (ROS), the accumulation of which is known to be associated with the formation of bacterial emboli. In addition, Pba EPS act as suppressors of the quantitative immunity of plants, repressing PAMP-induced reactions; this property is partly lost in the deacetylated form of Pba EPS. Overall, our study shows that Pba EPS play structural, protective, and immunosuppressive roles during Pba–plant interactions and thus should be considered as virulence factors of these bacteria. Full article

(This article belongs to the Special Issue Plant-Microbe Interactions)

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16 pages, 3837 KiB

Open AccessArticle

The THO/TREX Complex Active in Alternative Splicing Mediates Plant Responses to Salicylic Acid and Jasmonic Acid

by Nengxu Sun, Xiangjiu Kong, Yueyan Liu, Tingting Gong, Xiaoyong Gu and Lijing Liu

Int. J. Mol. Sci. 2021, 22(22), 12197; https://doi.org/10.3390/ijms222212197 - 11 Nov 2021

Cited by 4 | Viewed by 1747

Abstract

Salicylic acid (SA) and jasmonic acid (JA) are essential plant immune hormones, which could induce plant resistance to multiple pathogens. However, whether common components are employed by both SA and JA to induce defense is largely unknown. In this study, we found that the enhanced disease susceptibility 8 (EDS8) mutant was compromised in plant defenses to hemibiotrophic pathogen Pseudomonas syringae pv. maculicola ES4326 and necrotrophic pathogen Botrytis cinerea, and was deficient in plant responses to both SA and JA. The EDS8 was identified to be THO1, which encodes a subunit of the THO/TREX complex, by using mapping-by-sequencing. To check whether the EDS8 itself or the THO/TREX complex mediates SA and JA signaling, the mutant of another subunit of the THO/TREX complex, THO3, was tested. THO3 mutation reduced both SA and JA induced defenses, indicating that the THO/TREX complex is critical for plant responses to these two hormones. We further proved that the THO/TREX interacting protein SERRATE, a factor regulating alternative splicing (AS), was involved in plant responses to SA and JA. Thus, the AS events in the eds8 mutant after SA or JA treatment were determined, and we found that the SA and JA induced different alternative splicing events were majorly modulated by EDS8. In summary, our study proves that the THO/TREX complex active in AS is involved in both SA and JA induced plant defenses. Full article

(This article belongs to the Special Issue Plant-Microbe Interactions)

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10 pages, 1632 KiB

Open AccessArticle

Growth-Promoting Effect of Rhizobacterium (Bacillus subtilis IB22) in Salt-Stressed Barley Depends on Abscisic Acid Accumulation in the Roots

by Zarina Akhtyamova, Tatiana Arkhipova, Elena Martynenko, Tatyana Nuzhnaya, Ludmila Kuzmina, Guzel Kudoyarova and Dmitry Veselov

Int. J. Mol. Sci. 2021, 22(19), 10680; https://doi.org/10.3390/ijms221910680 - 1 Oct 2021

Cited by 14 | Viewed by 2170

Abstract

An ABA-deficient barley mutant (Az34) and its parental cultivar (Steptoe) were compared. Plants of salt-stressed Az34 (100 mmol m⁻³ NaCl for 10 days) grown in sand were 40% smaller than those of “Steptoe”, exhibited a lower leaf relative water content and lower ABA concentrations. Rhizosphere inoculation with IB22 increased plant growth of both genotypes. IB22 inoculation raised ABA in roots of salt-stressed plants by supplying ABA exogenously and by up-regulating ABA synthesis gene HvNCED2 and down-regulating ABA catabolic gene HvCYP707A1. Inoculation partially compensated for the inherent ABA deficiency of the mutant. Transcript abundance of HvNCED2 and related HvNCED1 in the absence of inoculation was 10 times higher in roots than in shoots of both mutant and parent, indicating that ABA was mainly synthesized in roots. Under salt stress, accumulation of ABA in the roots of bacteria-treated plants was accompanied by a decline in shoot ABA suggesting bacterial inhibition of ABA transport from roots to shoots. ABA accumulation in the roots of bacteria-treated Az34 was accompanied by increased leaf hydration, the probable outcome of increased root hydraulic conductance. Thereby, we tested the hypothesis that the ability of rhizobacterium (Bacillus subtilis IB22) to modify responses of plants to salt stress depends on abscisic acid (ABA) accumulating in roots. Full article

(This article belongs to the Special Issue Plant-Microbe Interactions)

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15 pages, 2134 KiB

Open AccessArticle

The Knockout of Enterobactin-Related Gene in Pectobacterium atrosepticum Results in Reduced Stress Resistance and Virulence towards the Primed Plants

by Vladimir Gorshkov, Olga Parfirova, Olga Petrova, Natalia Gogoleva, Evgeny Kovtunov, Vladimir Vorob’ev and Yuri Gogolev

Int. J. Mol. Sci. 2021, 22(17), 9594; https://doi.org/10.3390/ijms22179594 - 4 Sep 2021

Cited by 9 | Viewed by 2675

Abstract

Siderophores produced by microorganisms to scavenge iron from the environment have been shown to contribute to virulence and/or stress resistance of some plant pathogenic bacteria. Phytopathogenic bacteria of Pectobacterium genus possess genes for the synthesis of siderophore enterobactin, which role in plant-pathogen interactions has not been elucidated. In the present study we characterized the phenotype of the mutant strain of Pba deficient for the enterobactin-biosynthetic gene entA. We showed that enterobactin may be considered as a conditionally beneficial virulence factor of Pba. The entA knockout did not reduce Pba virulence on non-primed plants; however, salicylic acid-primed plants were more resistant to ΔentA mutant than to the wild type Pba. The reduced virulence of ΔentA mutant towards the primed plants is likely explained by its compromised resistance to oxidative stress. Full article

(This article belongs to the Special Issue Plant-Microbe Interactions)

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15 pages, 3928 KiB

Open AccessArticle

Molecular Characterization of Carbonic Anhydrase Genes in Lotus japonicus and Their Potential Roles in Symbiotic Nitrogen Fixation

by Longlong Wang, Jianjun Liang, Yu Zhou, Tao Tian, Baoli Zhang and Deqiang Duanmu

Int. J. Mol. Sci. 2021, 22(15), 7766; https://doi.org/10.3390/ijms22157766 - 21 Jul 2021

Cited by 9 | Viewed by 2613

Abstract

Carbonic anhydrase (CA) plays a vital role in photosynthetic tissues of higher plants, whereas its non-photosynthetic role in the symbiotic root nodule was rarely characterized. In this study, 13 CA genes were identified in the model legume Lotus japonicus by comparison with Arabidopsis CA genes. Using qPCR and promoter-reporter fusion methods, three previously identified nodule-enhanced CA genes (LjαCA2, LjαCA6, and LjβCA1) have been further characterized, which exhibit different spatiotemporal expression patterns during nodule development. LjαCA2 was expressed in the central infection zone of the mature nodule, including both infected and uninfected cells. LjαCA6 was restricted to the vascular bundle of the root and nodule. As for LjβCA1, it was expressed in most cell types of nodule primordia but only in peripheral cortical cells and uninfected cells of the mature nodule. Using CRISPR/Cas9 technology, the knockout of LjβCA1 or both LjαCA2 and its homolog, LjαCA1, did not result in abnormal symbiotic phenotype compared with the wild-type plants, suggesting that LjβCA1 or LjαCA1/2 are not essential for the nitrogen fixation under normal symbiotic conditions. Nevertheless, the nodule-enhanced expression patterns and the diverse distributions in different types of cells imply their potential functions during root nodule symbiosis, such as CO₂ fixation, N assimilation, and pH regulation, which await further investigations. Full article

(This article belongs to the Special Issue Plant-Microbe Interactions)

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Review

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11 pages, 628 KiB

Open AccessReview

Plant Executor Genes

by Zhiyuan Ji, Wei Guo, Xifeng Chen, Chunlian Wang and Kaijun Zhao

Int. J. Mol. Sci. 2022, 23(3), 1524; https://doi.org/10.3390/ijms23031524 - 28 Jan 2022

Cited by 14 | Viewed by 2896

Abstract

Executor (E) genes comprise a new type of plant resistance (R) genes, identified from host–Xanthomonas interactions. The Xanthomonas-secreted transcription activation-like effectors (TALEs) usually function as major virulence factors, which activate the expression of the so-called “susceptibility” (S) genes for disease development. This activation is achieved via the binding of the TALEs to the effector-binding element (EBE) in the S gene promoter. However, host plants have evolved EBEs in the promoters of some otherwise silent R genes, whose expression directly causes a host cell death that is characterized by a hypersensitive response (HR). Such R genes are called E genes because they trap the pathogen TALEs in order to activate expression, and the resulting HR prevents pathogen growth and disease development. Currently, deploying E gene resistance is becoming a major component in disease resistance breeding, especially for rice bacterial blight resistance. Currently, the biochemical mechanisms, or the working pathways of the E proteins, are still fuzzy. There is no significant nucleotide sequence homology among E genes, although E proteins share some structural motifs that are probably associated with the signal transduction in the effector-triggered immunity. Here, we summarize the current knowledge regarding TALE-type avirulence proteins, E gene activation, the E protein structural traits, and the classification of E genes, in order to sharpen our understanding of the plant E genes. Full article

(This article belongs to the Special Issue Plant-Microbe Interactions)

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28 pages, 4172 KiB

Open AccessReview

Diversity and Taxonomic Distribution of Endophytic Bacterial Community in the Rice Plant and Its Prospective

by Mohsin Ali, Qurban Ali, Muhammad Aamir Sohail, Muhammad Furqan Ashraf, Muhammad Hamzah Saleem, Saddam Hussain and Lei Zhou

Int. J. Mol. Sci. 2021, 22(18), 10165; https://doi.org/10.3390/ijms221810165 - 21 Sep 2021

Cited by 32 | Viewed by 7282

Abstract

Endophytic bacterial communities are beneficial communities for host plants that exist inside the surfaces of plant tissues, and their application improves plant growth. They benefit directly from the host plant by enhancing the nutrient amount of the plant’s intake and influencing the phytohormones, which are responsible for growth promotion and stress. Endophytic bacteria play an important role in plant-growth promotion (PGP) by regulating the indirect mechanism targeting pest and pathogens through hydrolytic enzymes, antibiotics, biocontrol potential, and nutrient restriction for pathogens. To attain these benefits, firstly bacterial communities must be colonized by plant tissues. The nature of colonization can be achieved by using a set of traits, including attachment behavior and motility speed, degradation of plant polymers, and plant defense evasion. The diversity of bacterial endophytes colonization depends on various factors, such as plants’ relationship with environmental factors. Generally, each endophytic bacteria has a wide host range, and they are used as bio-inoculants in the form of synthetic applications for sustainable agriculture systems and to protect the environment from chemical hazards. This review discusses and explores the taxonomic distribution of endophytic bacteria associated with different genotypes of rice plants and their origin, movement, and mechanism of PGP. In addition, this review accentuates compressive meta data of endophytic bacteria communities associated with different genotypes of rice plants, retrieves their plant-growth-promoting properties and their antagonism against plant pathogens, and discusses the indication of endophytic bacterial flora in rice plant tissues using various methods. The future direction deepens the study of novel endophytic bacterial communities and their identification from rice plants through innovative techniques and their application for sustainable agriculture systems. Full article

(This article belongs to the Special Issue Plant-Microbe Interactions)

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