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Advances and New Perspectives in Plant-Microbe Interactions 2.0

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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 December 2023) | Viewed by 16976

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Dr. Marouane Baslam

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Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
Interests: plant–microorganism interactions, -omics; climate change; yield; sustainability
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Special Issue Information

Dear Colleagues,

Plants, due to their sessile nature, are constantly exposed to a myriad of microorganisms. Plant–microbe encounters can be friendly—beneficial—or hostile—harmful—depending on the interaction’s nature. Direct cooperative (symbiotic) plant–microbe relationships are dominant in many ecosystems. Synergistic interactions could determine crop health in the natural agroecosystem by providing numerous services to plants. In contrast, plants are also constantly exposed to fungal, bacterial, and/or viral pathogens, causing substantial economic losses, thereby leading to critical global food security pressure. As a result, in both relationships, a complex network of interactions has evolved within plants–microbes—and unique defense mechanisms to fight infections—mediated by a multitude of chemicals signals derived from both plants and microbes. Therefore, deciphering molecular aspects to reveal the principles/fundamental processes that orchestrate plant–microbe interactions is of great interest. Additionally, new research dealing with genome editing technology research, including newly emerged CRISPR/Cas systems, will be welcomed in the study of plant–microbe interactions.

Additionally, plant–microbe interactions are profoundly affected by external environmental conditions. Understanding this “triangle” and how environmental conditions modulate plant–microbe interactions is crucial to predict the performance of plant–microbe interactions, engineer effective biofertilizers and/or biocontrol agents, and design “dream” crop plants with increased resilience or synthetic microbe communities for reproducible beneficial outputs to address today’s challenges in the realm of human population growth, globalization, and current and future climate change.

This Special Issue will bring together an exciting body of recent research, reviews, methods, and opinion pieces addressing the latest knowledge, relationships, and significance of plant–microorganism interactions in the ecosystem and in the development of human society, and how they might contribute toward the global goals of food security, sustainability, and wellbeing. We welcome suggestions from the community by 30 June 2022 for potential articles covering all advancements and new perspectives within plant–microbe interaction research in the context of global change.

In particular, we welcome articles within (but not limited to) the following broad themes:

Agriculture, horticulture, and forestry;
Molecular plant sciences;
Climate change;
Microbiology.

Dr. Marouane Baslam
Guest Editor

Manuscript Submission Information

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.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

plant–microbe interaction (beneficial microbes/phytopathogens)
plant molecular biology
crop improvement
sustainable agriculture
climate change/environmental challenge
functional (plant/microbial) genomics
genetic tools
nutrients
biofertilizers
signaling networks

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Published Papers (7 papers)

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Research

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26 pages, 5591 KiB

Open AccessArticle

Combined Omics Approaches Reveal Distinct Mechanisms of Resistance and/or Susceptibility in Sugar Beet Double Haploid Genotypes at Early Stages of Beet Curly Top Virus Infection

by Paul J. Galewski, Rajtilak Majumdar, Matthew D. Lebar, Carl A. Strausbaugh and Imad A. Eujayl

Int. J. Mol. Sci. 2023, 24(19), 15013; https://doi.org/10.3390/ijms241915013 - 9 Oct 2023

Viewed by 1879

Abstract

Sugar beet is susceptible to Beet curly top virus (BCTV), which significantly reduces yield and sugar production in the semi-arid growing regions worldwide. Sources of genetic resistance to BCTV is limited and control depends upon insecticide seed treatments with neonicotinoids. Through double haploid production and genetic selection, BCTV resistant breeding lines have been developed. Using BCTV resistant (R) [KDH13; Line 13 and KDH4-9; Line 4] and susceptible (S) [KDH19-17; Line 19] lines, beet leafhopper mediated natural infection, mRNA/sRNA sequencing, and metabolite analyses, potential mechanisms of resistance against the virus and vector were identified. At early infection stages (2- and 6-days post inoculation), examples of differentially expressed genes highly up-regulated in the ‘R’ lines (vs. ‘S’) included EL10Ac5g10437 (inhibitor of trypsin and hageman factor), EL10Ac6g14635 (jasmonate-induced protein), EL10Ac3g06016 (ribosome related), EL10Ac2g02812 (probable prolyl 4-hydroxylase 10), etc. Pathway enrichment analysis showed differentially expressed genes were predominantly involved with peroxisome, amino acids metabolism, fatty acid degradation, amino/nucleotide sugar metabolism, etc. Metabolite analysis revealed significantly higher amounts of specific isoflavonoid O-glycosides, flavonoid 8-C glycosides, triterpenoid, and iridoid-O-glycosides in the leaves of the ‘R’ lines (vs. ‘S’). These data suggest that a combination of transcriptional regulation and production of putative antiviral metabolites might contribute to BCTV resistance. In addition, genome divergence among BCTV strains differentially affects the production of small non-coding RNAs (sncRNAs) and small peptides which may potentially affect pathogenicity and disease symptom development. Full article

(This article belongs to the Special Issue Advances and New Perspectives in Plant-Microbe Interactions 2.0)

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13 pages, 4009 KiB

Open AccessArticle

Diversity Analysis and Function Prediction of Bacterial Communities in the Different Colored Pericarp of Citrus reticulata cv. ‘Shatangju’ Due to ‘Candidatus Liberibacter asiaticus’ Infection

by Feiyan Wang, Congyi Zhu, Ruimin Zhang, Yongjing Huang, Wen Wu, Jiezhong Chen and Jiwu Zeng

Int. J. Mol. Sci. 2023, 24(14), 11472; https://doi.org/10.3390/ijms241411472 - 14 Jul 2023

Viewed by 1496

Abstract

Huanglongbing (HLB), caused by the Candidatus Liberibacter spp., is the most devastating disease in the citrus industry. HLB significantly affects and alters the microbial community structure or potential function of the microbial community of leaves and roots. However, it is unknown how the microbial community structure of the pericarp with different pigments is affected by Candidatus Liberibacter asiaticus (CLas). This study identified the enriched taxa of the microbial community in the citrus pericarp with normal or abnormal pigment and determine the effects of HLB on the pericarp microbial community using 16S rRNA-seq. The alpha and beta diversity and composition of microbial communities were significantly different between normal and abnormal pigment pericarp tissues of ripe fruits infected by CLas. Firmicutes, Actinobacteriota, Bacteroidota, Acidobacteriota, and Desulfobacterota dominated the pericarp microbiota composition in WDYFs (whole dark yellow fruits) samples. The relative abundance of most genera in WDYFs was higher than 1%, such as Burkholderia, and Pelomonas. However, with the exception of the HLB pathogen, the relative abundance of most genera in the abnormal-colored pericarp samples was less than 1%. CLas decreased the relative abundance of pericarp taxonomic. The predicted function of microbial was more plentiful and functional properties in the WDYF sample, such as translation, ribosomal structure and biogenesis, amino acid transport and metabolism, energy production and conversion, and some other clusters of orthologous groups (COG) except for cell motility. The results of this study offer novel insights into understanding the composition of microbial communities of the CLas-affected citrus pericarps and contribute to the development of biological control strategies for citrus against Huanglongbing. Full article

(This article belongs to the Special Issue Advances and New Perspectives in Plant-Microbe Interactions 2.0)

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17 pages, 8502 KiB

Open AccessArticle

Bacillus paralicheniformis RP01 Enhances the Expression of Growth-Related Genes in Cotton and Promotes Plant Growth by Altering Microbiota inside and outside the Root

by Jinzhi Xu, Lijun Qin, Xinyi Xu, Hong Shen and Xingyong Yang

Int. J. Mol. Sci. 2023, 24(8), 7227; https://doi.org/10.3390/ijms24087227 - 13 Apr 2023

Cited by 7 | Viewed by 3012

Abstract

Plant growth-promoting bacteria (PGPB) can promote plant growth in various ways, allowing PGPB to replace chemical fertilizers to avoid environmental pollution. PGPB is also used for bioremediation and in plant pathogen control. The isolation and evaluation of PGPB are essential not only for practical applications, but also for basic research. Currently, the known PGPB strains are limited, and their functions are not fully understood. Therefore, the growth-promoting mechanism needs to be further explored and improved. The Bacillus paralicheniformis RP01 strain with beneficial growth-promoting activity was screened from the root surface of Brassica chinensis using a phosphate-solubilizing medium. RP01 inoculation significantly increased plant root length and brassinosteroid content and upregulated the expression of growth-related genes. Simultaneously, it increased the number of beneficial bacteria that promoted plant growth and reduced the number of detrimental bacteria. The genome annotation findings also revealed that RP01 possesses a variety of growth-promoting mechanisms and a tremendous growth-promoting potential. This study isolated a highly potential PGPB and elucidated its possible direct and indirect growth-promoting mechanisms. Our study results will help enrich the PGPB library and provide a reference for plant–microbe interactions. Full article

(This article belongs to the Special Issue Advances and New Perspectives in Plant-Microbe Interactions 2.0)

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29 pages, 1441 KiB

Open AccessArticle

Proteomic Analysis of Proteins Related to Defense Responses in Arabidopsis Plants Transformed with the rolB Oncogene

by Yulia V. Vereshchagina, Anastasiya A. Mironova, Dmitry V. Bulgakov and Victor P. Bulgakov

Int. J. Mol. Sci. 2023, 24(3), 1880; https://doi.org/10.3390/ijms24031880 - 18 Jan 2023

Viewed by 2213

Abstract

During Agrobacterium rhizogenes–plant interaction, the rolB gene is transferred into the plant genome and is stably inherited in the plant’s offspring. Among the numerous effects of rolB on plant metabolism, including the activation of secondary metabolism, its effect on plant defense systems has not been sufficiently studied. In this work, we performed a proteomic analysis of rolB-expressing Arabidopsis thaliana plants with particular focus on defense proteins. We found a total of 77 overexpressed proteins and 64 underexpressed proteins in rolB-transformed plants using two-dimensional gel electrophoresis and MALDI mass spectrometry. In the rolB-transformed plants, we found a reduced amount of scaffold proteins RACK1A, RACK1B, and RACK1C, which are known as receptors for activated C-kinase 1. The proteomic analysis showed that rolB could suppress the plant immune system by suppressing the RNA-binding proteins GRP7, CP29B, and CP31B, which action are similar to the action of type-III bacterial effectors. At the same time, rolB plants induce the massive biosynthesis of protective proteins VSP1 and VSP2, as well as pathogenesis-related protein PR-4, which are markers of the activated jasmonate pathway. The increased contents of glutathione-S-transferases F6, F2, F10, U19, and DHAR1 and the osmotin-like defense protein OSM34 were found. The defense-associated protein PCaP1, which is required for oligogalacturonide-induced priming and immunity, was upregulated. Moreover, rolB-transformed plants showed the activation of all components of the PYK10 defense complex that is involved in the metabolism of glucosinolates. We hypothesized that various defense systems activated by rolB protect the host plant from competing phytopathogens and created an effective ecological niche for A. rhizogenes. A RolB → RACK1A signaling module was proposed that might exert most of the rolB-mediated effects on plant physiology. Our proteomics data are available via ProteomeXchange with identifier PXD037959. Full article

(This article belongs to the Special Issue Advances and New Perspectives in Plant-Microbe Interactions 2.0)

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19 pages, 3161 KiB

Open AccessArticle

Ustilaginoidea virens Nuclear Effector SCRE4 Suppresses Rice Immunity via Inhibiting Expression of a Positive Immune Regulator OsARF17

by Shanshan Qiu, Anfei Fang, Xinhang Zheng, Shanzhi Wang, Jiyang Wang, Jing Fan, Zongtao Sun, Han Gao, Jiyun Yang, Qingtao Zeng, Fuhao Cui, Wen-Ming Wang, Jianping Chen and Wenxian Sun

Int. J. Mol. Sci. 2022, 23(18), 10527; https://doi.org/10.3390/ijms231810527 - 10 Sep 2022

Cited by 10 | Viewed by 2499

Abstract

Rice false smut caused by the biotrophic fungal pathogen Ustilaginoidea virens has become one of the most important diseases in rice. The large effector repertory in U. virens plays a crucial role in virulence. However, current knowledge of molecular mechanisms how U. virens effectors target rice immune signaling to promote infection is very limited. In this study, we identified and characterized an essential virulence effector, SCRE4 (Secreted Cysteine-Rich Effector 4), in U. virens. SCRE4 was confirmed as a secreted nuclear effector through yeast secretion, translocation assays and protein subcellular localization, as well as up-regulation during infection. The SCRE4 gene deletion attenuated the virulence of U. virens to rice. Consistently, ectopic expression of SCRE4 in rice inhibited chitin-triggered immunity and enhanced susceptibility to false smut, substantiating that SCRE4 is an essential virulence factor. Furthermore, SCRE4 transcriptionally suppressed the expression of OsARF17, an auxin response factor in rice, which positively regulates rice immune responses and resistance against U. virens. Additionally, the immunosuppressive capacity of SCRE4 depended on its nuclear localization. Therefore, we uncovered a virulence strategy in U. virens that transcriptionally suppresses the expression of the immune positive modulator OsARF17 through nucleus-localized effector SCRE4 to facilitate infection. Full article

(This article belongs to the Special Issue Advances and New Perspectives in Plant-Microbe Interactions 2.0)

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Review

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17 pages, 2413 KiB

Open AccessReview

Plant-Growth-Promoting Rhizobacteria Modulate Carbohydrate Metabolism in Connection with Host Plant Defense Mechanism

by Fan Su, Bin Zhao, Sandrine Dhondt-Cordelier and Nathalie Vaillant-Gaveau

Int. J. Mol. Sci. 2024, 25(3), 1465; https://doi.org/10.3390/ijms25031465 - 25 Jan 2024

Cited by 6 | Viewed by 2346

Abstract

Plant-growth-promoting rhizobacteria (PGPR) could potentially enhance photosynthesis and benefit plant growth by improving soil nutrient uptake and affecting plant hormone balance. Several recent studies have unveiled a correlation between alterations in photosynthesis and host plant resistance levels. Photosynthesis provides materials and energy for plant growth and immune defense and affects defense-related signaling pathways. Photosynthetic organelles, which could be strengthened by PGPR inoculation, are key centers for defense signal biosynthesis and transmission. Although endophytic PGPRs metabolize plant photosynthates, they can increase soluble sugar levels and alternate sugar type and distribution. Soluble sugars clearly support plant growth and can act as secondary messengers under stressed conditions. Overall, carbohydrate metabolism modifications induced by PGPR may also play a key role in improving plant resistance. We provide a concise overview of current knowledge regarding PGPR-induced modulation in carbohydrate metabolism under both pathogen-infected and pathogen-free conditions. We highlight PGPR application as a cost-saving strategy amidst unpredictable pathogen pressures. Full article

(This article belongs to the Special Issue Advances and New Perspectives in Plant-Microbe Interactions 2.0)

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21 pages, 1444 KiB

Open AccessReview

Effector-Dependent and -Independent Molecular Mechanisms of Soybean–Microbe Interaction

by Jinhui Wang, Hejia Ni, Lin Chen, Jianan Zou, Chunyan Liu, Qingshan Chen, Pascal Ratet and Dawei Xin

Int. J. Mol. Sci. 2022, 23(22), 14184; https://doi.org/10.3390/ijms232214184 - 16 Nov 2022

Viewed by 2458

Abstract

Soybean is a pivotal staple crop worldwide, supplying the main food and feed plant proteins in some countries. In addition to interacting with mutualistic microbes, soybean also needs to protect itself against pathogens. However, to grow inside plant tissues, plant defense mechanisms ranging from passive barriers to induced defense reactions have to be overcome. Pathogenic but also symbiotic micro-organisms effectors can be delivered into the host cell by secretion systems and can interfere with the immunity system and disrupt cellular processes. This review summarizes the latest advances in our understanding of the interaction between secreted effectors and soybean feedback mechanism and uncovers the conserved and special signaling pathway induced by pathogenic soybean cyst nematode, Pseudomonas, Xanthomonas as well as by symbiotic rhizobium. Full article

(This article belongs to the Special Issue Advances and New Perspectives in Plant-Microbe Interactions 2.0)

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