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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 (23 April 2024) | Viewed by 13667

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Dr. Jiangyun Gao

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Guest Editor

Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
Interests: plant-fungi interactions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the past decades, the plant-fungus interactions, including mycorrhizal, parasitic or endophytic lifestyles, have been extensively studied at various aspects and have greatly improved our understanding. Among them, the symbiotic association of mycorrhiza is commonly found in most of vascular plants, mainly including arbuscular mycorrhiza, ectomycorrhiza, ericoid mycorrhiza and orchid mycorrhiza. Mycorrhizal fungi benefit most plants by enhancing their nutrient access and stress tolerance, and therefore strongly affect plant population and community biology by regulating seedling establishment and species coexistence. In this Topic, the interactions between plants and fungi will be considered. This includes but no limits, functional omics, molecular communication, coevolution, ecological adaption and nutrient modes of plant-fungi interactions, and applications of fungi for sustainable environmental management and plant conservation.

This Special Issue on “Advanced Research in Plant-Fungi Interactions” is open to all researchers studying this interaction at any level, from both the plant and the fungi side. Papers are welcome as original research articles, as well as review papers dealing with the advancement and current understanding of various aspects of plant-fungus interactions.

Dr. Jiangyun Gao
Guest Editor

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Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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Keywords

plant-fungus interactions
symbiotic association
endophytes
plant conservation
mycorrhizal symbioses

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Published Papers (10 papers)

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Research

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14 pages, 3724 KiB

Open AccessArticle

Unveiling the Role of RNA Recognition Motif Proteins in Orchestrating Nucleotide-Binding Site and Leucine-Rich Repeat Protein Gene Pairs and Chloroplast Immunity Pathways: Insights into Plant Defense Mechanisms

by Fengwei Gu, Zhikai Han, Xiaodi Zou, Huabin Xie, Chun Chen, Cuihong Huang, Tao Guo, Jiafeng Wang and Hui Wang

Int. J. Mol. Sci. 2024, 25(10), 5557; https://doi.org/10.3390/ijms25105557 - 20 May 2024

Viewed by 1058

Abstract

In plants, nucleotide-binding site and leucine-rich repeat proteins (NLRs) play pivotal roles in effector-triggered immunity (ETI). However, the precise mechanisms underlying NLR-mediated disease resistance remain elusive. Previous studies have demonstrated that the NLR gene pair Pik-H4 confers resistance to rice blast disease by interacting with the transcription factor OsBIHD1, consequently leading to the upregulation of hormone pathways. In the present study, we identified an RNA recognition motif (RRM) protein, OsRRM2, which interacted with Pik₁-H4 and Pik₂-H4 in vesicles and chloroplasts. OsRRM2 exhibited a modest influence on Pik-H4-mediated rice blast resistance by upregulating resistance genes and genes associated with chloroplast immunity. Moreover, the RNA-binding sequence of OsRRM2 was elucidated using systematic evolution of ligands by exponential enrichment. Transcriptome analysis further indicated that OsRRM2 promoted RNA editing of the chloroplastic gene ndhB. Collectively, our findings uncovered a chloroplastic RRM protein that facilitated the translocation of the NLR gene pair and modulated chloroplast immunity, thereby bridging the gap between ETI and chloroplast immunity. Full article

(This article belongs to the Special Issue Advanced Research in Plant-Fungi Interactions)

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19 pages, 4833 KiB

Open AccessArticle

OsCAMTA3 Negatively Regulates Disease Resistance to Magnaporthe oryzae by Associating with OsCAMTAPL in Rice

by Shibo Yu, Shengping Li, Wei Wang and Dingzhong Tang

Int. J. Mol. Sci. 2024, 25(9), 5049; https://doi.org/10.3390/ijms25095049 - 6 May 2024

Cited by 1 | Viewed by 1252

Abstract

Rice (Oryza sativa) is one of the most important staple foods worldwide. However, rice blast disease, caused by the ascomycete fungus Magnaporthe oryzae, seriously affects the yield and quality of rice. Calmodulin-binding transcriptional activators (CAMTAs) play vital roles in the response to biotic stresses. In this study, we showed that OsCAMTA3 and CAMTA PROTEIN LIKE (OsCAMTAPL), an OsCAMTA3 homolog that lacks the DNA-binding domain, functioned together in negatively regulating disease resistance in rice. OsCAMTA3 associated with OsCAMTAPL. The oscamta3 and oscamtapl mutants showed enhanced resistance compared to wild-type plants, and oscamta3/pl double mutants showed more robust resistance to M. oryzae than oscamta3 or oscamtapl. An RNA-Seq analysis revealed that 59 and 73 genes, respectively, were differentially expressed in wild-type plants and oscamta3 before and after inoculation with M. oryzae, including OsALDH2B1, an acetaldehyde dehydrogenase that negatively regulates plant immunity. OsCAMTA3 could directly bind to the promoter of OsALDH2B1, and OsALDH2B1 expression was decreased in oscamta3, oscamtapl, and oscamta3/pl mutants. In conclusion, OsCAMTA3 associates with OsCAMTAPL to regulate disease resistance by binding and activating the expression of OsALDH2B1 in rice, which reveals a strategy by which rice controls rice blast disease and provides important genes for resistance breeding holding a certain positive impact on ensuring food security. Full article

(This article belongs to the Special Issue Advanced Research in Plant-Fungi Interactions)

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16 pages, 3986 KiB

Open AccessArticle

Constitutive Overexpression of an NB-ARC Gene from Wild Chinese Vitis quinquangularis in Arabidopsis thaliana Enhances Resistance to Phytopathogenic Oomycete and Bacteria

by Xiangjing Yin, Qian Zha, Pengpeng Sun, Xiaojun Xi and Aili Jiang

Int. J. Mol. Sci. 2024, 25(6), 3221; https://doi.org/10.3390/ijms25063221 - 12 Mar 2024

Viewed by 956

Abstract

Resistance (R) genes were used to recognize pathogen effectors directly or indirectly in plants and activate defense signal pathways. Most of these R proteins consist of a nucleotide-binding adaptor (NB-ARC) domain, a leucine-rich repeat (LRR) domain and some also have a coiled-coil (CC) structure. In this study, we cloned a gene which encodes the CC-NB-ARC-LRR R protein (VqCNL) from Chinese wild grapevine Vitis. quinquangularis accession ‘Dan-2’. The transcript of VqCNL was obviously induced by inoculation with Plasmopara viticola and the salicylic acid (SA) treatment. The results of sequence analysis showed that the VqCNL gene contained a CC domain at the N-terminus, along with an NB-ARC and an LRR domain at the C-terminus. We transferred this gene into wildtype Arabidopsis and treated transgenic lines with Hyaloperonospora arabidopsidis (Hpa) and Pseudomonas syringae pv. tomato DC3000 (Pst DC3000); the results demonstrated that VqCNL promotes broad spectrum resistance to pathogens. Furthermore, qPCR analysis displayed that VqCNL may display a significant function in disease resistance via activating SA signaling pathways. In general, these conclusions primarily demonstrated that VqCNL enhances the disease resistance level in plants and contributes to future research of the R gene identification for grape breeding biotechnology. Full article

(This article belongs to the Special Issue Advanced Research in Plant-Fungi Interactions)

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17 pages, 3813 KiB

Open AccessArticle

Regulation of Disease-Resistance Genes against CWMV Infection by NbHAG1-Mediated H3K36ac

by Aizhu Tu, Mila Wu, Yaoyao Jiang, Lidan Guo, Yunfei Guo, Jinnan Wang, Gecheng Xu, Jingjing Shi, Jianping Chen, Jian Yang and Kaili Zhong

Int. J. Mol. Sci. 2024, 25(5), 2800; https://doi.org/10.3390/ijms25052800 - 28 Feb 2024

Viewed by 1123

Abstract

Post-translational modification of proteins plays a critical role in plant–pathogen interactions. Here, we demonstrate in Nicotiana benthamiana that knockout of NbHAG1 promotes Chinese wheat mosaic virus (CWMV) infection, whereas NbHAG1 overexpression inhibits infection. Transcriptome sequencing indicated that a series of disease resistance-related genes were up-regulated after overexpression of NbHAG1. In addition, cleavage under targets and tagmentation (Cut&Tag)-qPCR results demonstrated that NbHAG1 may activate the transcription of its downstream disease-resistance genes by facilitating the acetylation level of H3K36ac. Therefore, we suggest that NbHAG1 is an important positive regulator of resistance to CWMV infestation. Full article

(This article belongs to the Special Issue Advanced Research in Plant-Fungi Interactions)

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15 pages, 4422 KiB

Open AccessArticle

Hub Genes and Pathways Related to Lemon (Citrus limon) Leaf Response to Plenodomus tracheiphilus Infection and Influenced by Pseudomonas mediterranea Biocontrol Activity

by Angelo Sicilia, Riccardo Russo, Vittoria Catara and Angela Roberta Lo Piero

Int. J. Mol. Sci. 2024, 25(4), 2391; https://doi.org/10.3390/ijms25042391 - 17 Feb 2024

Cited by 2 | Viewed by 1206

Abstract

The lemon industry in the Mediterranean basin is strongly threatened by “mal secco” disease (MSD) caused by the fungus Plenodomus tracheiphlilus. Leaf pretreatments with Pseudomonas mediterranea 3C have been proposed as innovative tools for eco-sustainable interventions aimed at controlling the disease. In this study, by exploiting the results of previously performed RNAseq analysis, WCGNA was conducted among gene expression patterns in both inoculated (Pt) and pretreated and fungus-inoculated lemon plants (Citrus limon L.) (3CPt), and two indicators of fungal infection, i.e., the amount of fungus DNA measured in planta and the disease index (DI). The aims of this work were (a) to identify gene modules significantly associated with those traits, (b) to construct co-expression networks related to mal secco disease; (c) to define the effect and action mechanisms of P. mediterranea by comparing the networks. The results led to the identification of nine hub genes in the networks, with three of them belonging to receptor-like kinases (RLK), such as HERK1, CLAVATA1 and LRR, which play crucial roles in plant–pathogen interaction. Moreover, the comparison between networks indicated that the expression of those receptors is not induced in the presence of P. mediterranea, suggesting how powerful WCGNA is in discovering crucial genes that must undergo further investigation and be eventually knocked out. Full article

(This article belongs to the Special Issue Advanced Research in Plant-Fungi Interactions)

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16 pages, 3855 KiB

Open AccessArticle

The Beneficial Fungus Mortierella hyalina Modulates Amino Acid Homeostasis in Arabidopsis under Nitrogen Starvation

by Nataliia Svietlova, Michael Reichelt, Liza Zhyr, Anindya Majumder, Sandra S. Scholz, Veit Grabe, Anne Krapp, Ralf Oelmüller and Axel Mithöfer

Int. J. Mol. Sci. 2023, 24(22), 16128; https://doi.org/10.3390/ijms242216128 - 9 Nov 2023

Cited by 1 | Viewed by 1366

Abstract

Non-mycorrhizal but beneficial fungi often mitigate (a)biotic stress-related traits in host plants. The underlying molecular mechanisms are mostly still unknown, as in the interaction between the endophytic growth-promoting soil fungus Mortierella hyalina and Arabidopsis thaliana. Here, abiotic stress in the form of nitrogen (N) deficiency was used to investigate the effects of the fungus on colonized plants. In particular, the hypothesis was investigated that fungal infection could influence N deficiency via an interaction with the high-affinity nitrate transporter NRT2.4, which is induced by N deficiency. For this purpose, Arabidopsis wild-type nrt2.4 knock-out and NRT2.4 reporter lines were grown on media with different nitrate concentrations with or without M. hyalina colonization. We used chemical analysis methods to determine the amino acids and phytohormones. Experimental evidence suggests that the fungus does not modulate NRT2.4 expression under N starvation. Instead, M. hyalina alleviates N starvation in other ways: The fungus supplies nitrogen (¹⁵N) to the N-starved plant. The presence of the fungus restores the plants’ amino acid homeostasis, which was out of balance due to N deficiency, and causes a strong accumulation of branched-chain amino acids. We conclude that the plant does not need to invest in defense and resources for growth are maintained, which in turn benefits the fungus, suggesting that this interaction should be considered a mutualistic symbiosis. Full article

(This article belongs to the Special Issue Advanced Research in Plant-Fungi Interactions)

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20 pages, 6233 KiB

Open AccessArticle

Rhizosphere Microbe Affects Soil Available Nitrogen and Its Implication for the Ecological Adaptability and Rapid Growth of Dendrocalamus sinicus, the Strongest Bamboo in the World

by Peitong Dou, Qian Cheng, Ning Liang, Changyan Bao, Zhiming Zhang, Lingna Chen and Hanqi Yang

Int. J. Mol. Sci. 2023, 24(19), 14665; https://doi.org/10.3390/ijms241914665 - 28 Sep 2023

Cited by 4 | Viewed by 1336

Abstract

The interaction between soil microbes and plants has a significant effect on soil microbial structure and function, as well as plant adaptability. However, the effect of soil micro-organisms on ecological adaption and rapid growth of woody bamboos remains unclear. Here, 16S rRNA and ITS rRNA genes of rhizosphere micro-organisms were sequenced, and the soil properties of three different types of Dendrocalamus sinicus were determined at the dormancy and germination stages of rhizome buds. The result showed that each type of D. sinicus preferred to absorb ammonia nitrogen (NH₄⁺-N) rather than nitrate nitrogen (NO₃⁻-N) and required more NH₄⁺-N at germination or rapid growth period than during the dormancy period. In total, nitrogen fixation capacity of soil bacteria in the straight type was significantly higher than that in the introduced straight type, while the ureolysis capacity had an opposite trend. Saprophytic fungi were the dominant fungal functional taxa in habitat soils of both straight and introduced straight type. Our findings are of great significance in understanding how soil microbes affect growth and adaptation of woody bamboos, but also for soil management of bamboo forests in red soil. Full article

(This article belongs to the Special Issue Advanced Research in Plant-Fungi Interactions)

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14 pages, 4162 KiB

Open AccessArticle

Effects of Arbuscular Mycorrhizal Fungus on Sodium and Chloride Ion Channels of Casuarina glauca under Salt Stress

by Yihan Wang, Fengxin Dong, Hui Chen, Tingying Xu and Ming Tang

Int. J. Mol. Sci. 2023, 24(4), 3680; https://doi.org/10.3390/ijms24043680 - 12 Feb 2023

Cited by 6 | Viewed by 1664

Abstract

Casuarina glauca is an important coastal protection forest species, which is exposed to high salt stress all year round. Arbuscular mycorrhizal fungi (AMF) can promote the growth and salt tolerance of C. glauca under salt stress. However, the effects of AMF on the distribution of Na⁺ and Cl⁻ and the expression of related genes in C. glauca under salt stress need to be further explored. This study explored the effects of Rhizophagus irregularis on plant biomass, the distribution of Na⁺ and Cl⁻, and the expression of related genes in C. glauca under NaCl stress through pot simulation experiments. The results revealed that the mechanisms of Na⁺ and Cl⁻ transport of C. glauca under NaCl stress were different. C. glauca took a salt accumulation approach to Na⁺, transferring Na⁺ from roots to shoots. Salt accumulation of Na⁺ promoted by AMF was associated with CgNHX7. The transport mechanism of C. glauca to Cl⁻ might involve salt exclusion rather than salt accumulation, and Cl⁻ was no longer transferred to shoots in large quantities but started to accumulate in roots. However, AMF alleviated Na⁺ and Cl⁻ stress by similar mechanisms. AMF could promote salt dilution of C. glauca by increasing biomass and the content of K⁺, compartmentalizing Na⁺ and Cl⁻ in vacuoles. These processes were associated with the expression of CgNHX1, CgNHX2-1, CgCLCD, CgCLCF, and CgCLCG. Our study will provide a theoretical basis for the application of AMF to improve salt tolerance in plants. Full article

(This article belongs to the Special Issue Advanced Research in Plant-Fungi Interactions)

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14 pages, 5542 KiB

Open AccessArticle

Low Specificity but Dissimilar Mycorrhizal Communities Associating with Roots May Contribute to the Spatial Pattern of Four Co-Occurring Habenaria (Orchidaceae) Species

by Wenliu Zhang, Jiangyun Gao, Shicheng Shao and Taiqiang Li

Int. J. Mol. Sci. 2023, 24(1), 665; https://doi.org/10.3390/ijms24010665 - 30 Dec 2022

Cited by 3 | Viewed by 1785

Abstract

Fungi with orchid roots have been increasingly proven to play important roles in orchid growth, spatial distribution, and coexistence of natural communities. Here, we used 454 amplicon pyrosequencing with two different primer combinations to investigate the spatial variations in the community of OMF and endophytic fungi associates within the roots of four co-occurring Habenaria species. The results showed that all investigated Habenaria species were generalists and the different fungi communities may contribute to the spatial separation of the four Habenaria species. Firstly, the fungal OTUs identified in the roots of the four species overlapped but their presence differed amongst species and numerous distinct OMF families were unique to each species. Second, NMDS clustering showed samples clustered together based on associated species and PERMANOVA analyses indicated that fungi communities in the roots differed significantly between the Habenaria species, both for all endophytic fungi communities and for OMF communities. Third, the network structure of epiphytic fungi was highly specialized and modular but demonstrated lowly connected and anti-nested properties. However, it calls for more soil nutrition and soil fungal communities’ studies to elucidate the contribution of habitat-specific adaptations in general and mycorrhizal divergence. Full article

(This article belongs to the Special Issue Advanced Research in Plant-Fungi Interactions)

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Review

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21 pages, 1869 KiB

Open AccessReview

Endophytic Fungi from the Four Staple Crops and Their Secondary Metabolites

by Yinzhong Fan and Baobao Shi

Int. J. Mol. Sci. 2024, 25(11), 6057; https://doi.org/10.3390/ijms25116057 - 31 May 2024

Cited by 1 | Viewed by 760

Abstract

Endophytic fungi are present in every plant, and crops are no exception. There are more than 50,000 edible plant species on the planet, but only 15 crops provide 90 percent of the global energy intake, and “the big four”—wheat, rice, maize and potato—are staples for about 5 billion people. Not only do the four staple crops contribute to global food security, but the endophytic fungi within their plant tissues are complex ecosystems that have been under scrutiny. This review presents an outline of the endophytic fungi and their secondary metabolites in four staple crops: wheat, rice, maize and potato. A total of 292 endophytic fungi were identified from the four major crops, with wheat having the highest number of 157 endophytic fungi. Potato endophytic fungi had the highest number of secondary metabolites, totaling 204 compounds, compared with only 23 secondary metabolites from the other three crops containing endophytic fungi. Some of the compounds are those with specific structural and pharmacological activities, which may be beneficial to agrochemistry and medicinal chemistry. Full article

(This article belongs to the Special Issue Advanced Research in Plant-Fungi Interactions)

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