International Journal of Molecular Sciences

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13 pages, 7053 KiB

Open AccessArticle

Floral Volatile Organic Compounds Change the Composition and Function of the Endophytic Fungal Community in the Flowers of Osmanthus fragrans

by Tingting Shi, Man Shi, Yunfang Ye, Yuanzheng Yue, Lianggui Wang and Xiulian Yang

Int. J. Mol. Sci. 2024, 25(2), 857; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms25020857 - 10 Jan 2024

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Abstract

Endophytic fungi in flowers influence plant health and reproduction. However, whether floral volatile organic compounds (VOCs) affect the composition and function of the endophytic fungal community remains unclear. Here, gas chromatography–mass spectrometry (GC–MS) and high-throughput sequencing were used to explore the relationship between [...] Read more.

Endophytic fungi in flowers influence plant health and reproduction. However, whether floral volatile organic compounds (VOCs) affect the composition and function of the endophytic fungal community remains unclear. Here, gas chromatography–mass spectrometry (GC–MS) and high-throughput sequencing were used to explore the relationship between floral VOCs and the endophytic fungal community during different flower development stages in Osmanthus fragrans ‘Rixiang Gui’. The results showed that the composition of the endophytic fungal community and floral VOCs shifted along with flowering development. The highest and lowest α diversity of the endophytic fungal community occurred in the flower fading stage and full blooming stage, respectively. The dominant fungi, including Dothideomycetes (class), Pleosporales (order), and Neocladophialophora, Alternaria, and Setophoma (genera), were enriched in the flower fading stage and decreased in the full blooming stage, demonstrating the enrichment of the Pathotroph, Saprotroph, and Pathotroph–Saprotroph functions in the flower fading stage and their depletion in the full blooming stage. However, the total VOC and terpene contents were highest in the full blooming stage and lowest in the flower fading stage, which was opposite to the α diversity of the endophytic fungal community and the dominant fungi during flowering development. Linalool, dihydro-β-ionone, and trans-linalool oxide(furan) were key factors affecting the endophytic fungal community composition. Furthermore, dihydro-β-ionone played an extremely important role in inhibiting endophytic fungi in the full blooming stage. Based on the above results, it is believed that VOCs, especially terpenes, changed the endophytic fungal community composition in the flowers of O. fragrans ‘Rixiang Gui’. These findings improve the understanding of the interaction between endophytic fungi and VOCs in flowers and provide new insight into the mechanism of flower development. Full article

(This article belongs to the Special Issue Molecular Plant-Microbe Interactions 2.0)

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22 pages, 3262 KiB

Open AccessArticle

Genomic and Metabolic Characterization of Plant Growth-Promoting Rhizobacteria Isolated from Nodules of Clovers Grown in Non-Farmed Soil

by Magdalena Wójcik, Piotr Koper, Kamil Żebracki, Małgorzata Marczak and Andrzej Mazur

Int. J. Mol. Sci. 2023, 24(23), 16679; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms242316679 - 23 Nov 2023

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Abstract

The rhizosphere microbiota, which includes plant growth-promoting rhizobacteria (PGPR), is essential for nutrient acquisition, protection against pathogens, and abiotic stress tolerance in plants. However, agricultural practices affect the composition and functions of microbiota, reducing their beneficial effects on plant growth and health. Among [...] Read more.

The rhizosphere microbiota, which includes plant growth-promoting rhizobacteria (PGPR), is essential for nutrient acquisition, protection against pathogens, and abiotic stress tolerance in plants. However, agricultural practices affect the composition and functions of microbiota, reducing their beneficial effects on plant growth and health. Among PGPR, rhizobia form mutually beneficial symbiosis with legumes. In this study, we characterized 16 clover nodule isolates from non-farmed soil to explore their plant growth-promoting (PGP) potential, hypothesizing that these bacteria may possess unique, unaltered PGP traits, compared to those affected by common agricultural practices. Biolog profiling revealed their versatile metabolic capabilities, enabling them to utilize a wide range of carbon and energy sources. All isolates were effective phosphate solubilizers, and individual strains exhibited 1-aminocyclopropane-1-carboxylate deaminase and metal ion chelation activities. Metabolically active strains showed improved performance in symbiotic interactions with plants. Comparative genomics revealed that the genomes of five nodule isolates contained a significantly enriched fraction of unique genes associated with quorum sensing and aromatic compound degradation. As the potential of PGPR in agriculture grows, we emphasize the importance of the molecular and metabolic characterization of PGP traits as a fundamental step towards their subsequent application in the field as an alternative to chemical fertilizers and supplements. Full article

(This article belongs to the Special Issue Molecular Plant-Microbe Interactions 2.0)

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17 pages, 1793 KiB

Open AccessArticle

Characterization of the Pyrroloquinoline Quinone Producing Rhodopseudomonas palustris as a Plant Growth-Promoting Bacterium under Photoautotrophic and Photoheterotrophic Culture Conditions

by Shou-Chen Lo, Shang-Yieng Tsai, Wei-Hsiang Chang, I-Chen Wu, Nga-Lai Sou, Shih-Hsun Walter Hung, En-Pei Isabel Chiang and Chieh-Chen Huang

Int. J. Mol. Sci. 2023, 24(18), 14080; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms241814080 - 14 Sep 2023

Cited by 2 | Viewed by 1107

Abstract

Rhodopseudomonas palustris is a purple non-sulfide bacterium (PNSB), and some strains have been proven to promote plant growth. However, the mechanism underlying the effect of these PNSBs remains limited. Based on genetic information, R. palustris possesses the ability to produce pyrroloquinoline quinone (PQQ). [...] Read more.

Rhodopseudomonas palustris is a purple non-sulfide bacterium (PNSB), and some strains have been proven to promote plant growth. However, the mechanism underlying the effect of these PNSBs remains limited. Based on genetic information, R. palustris possesses the ability to produce pyrroloquinoline quinone (PQQ). PQQ is known to play a crucial role in stimulating plant growth, facilitating phosphorous solubilization, and acting as a reactive oxygen species scavenger. However, it is still uncertain whether growth conditions influence R. palustris’s production of PQQ and other characteristics. In the present study, it was found that R. palustris exhibited a higher expression of genes related to PQQ synthesis under autotrophic culture conditions as compared to acetate culture conditions. Moreover, similar patterns were observed for phosphorous solubilization and siderophore activity, both of which are recognized to contribute to plant-growth benefits. However, these PNSB culture conditions did not show differences in Arabidopsis growth experiments, indicating that there may be other factors influencing plant growth in addition to PQQ content. Furthermore, the endophytic bacterial strains isolated from Arabidopsis exhibited differences according to the PNSB culture conditions. These findings imply that, depending on the PNSB’s growing conditions, it may interact with various soil bacteria and facilitate their infiltration into plants. Full article

(This article belongs to the Special Issue Molecular Plant-Microbe Interactions 2.0)

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14 pages, 4392 KiB

Open AccessArticle

Establishment of RNA Interference Genetic Transformation System and Functional Analysis of FlbA Gene in Leptographium qinlingensis

by Tian Gan, Huanli An, Ming Tang and Hui Chen

Int. J. Mol. Sci. 2023, 24(16), 13009; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms241613009 - 21 Aug 2023

Cited by 1 | Viewed by 988

Abstract

Leptographium qinlingensis is a pathogenic fungus of Pinus armandii that is epidemic in the Qinling Mountains. However, an effective gene interference strategy is needed to characterize the pathogenic genes in this fungus on a functional level. Using the RNA silencing vector pSilent-1 as [...] Read more.

Leptographium qinlingensis is a pathogenic fungus of Pinus armandii that is epidemic in the Qinling Mountains. However, an effective gene interference strategy is needed to characterize the pathogenic genes in this fungus on a functional level. Using the RNA silencing vector pSilent-1 as a template, we established an RNA interference genetic transformation system mediated by Agrobacterium tumefaciens GV3101, which is suitable for the gene study for Leptographium qinlingensis by homologous recombination and strain interference system screening. The LqFlbA gene was silenced using the RNA interference approach described above, and the resulting transformants displayed various levels of silencing with a gene silencing effectiveness ranging from 41.8% to 91.4%. The LqFlbA-RNAi mutant displayed altered colony morphology, sluggish mycelium growth, and diminished pathogenicity toward the host P. armandii in comparison to the wild type. The results indicate that this method provides a useful reverse genetic system for studying the gene function of L. qinlingensis, and that LqFlbA plays a crucial role in the growth, development, and pathogenicity of L. qinlingensis. Full article

(This article belongs to the Special Issue Molecular Plant-Microbe Interactions 2.0)

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18 pages, 2642 KiB

Open AccessArticle

Proteomic and Mutant Analysis of Hydrogenase Maturation Protein Gene hypE in Symbiotic Nitrogen Fixation of Mesorhizobium huakuii

by Songhua Long, Min Su, Xiaohong Chen, Aiqi Hu, Fuyan Yu, Qian Zou and Guojun Cheng

Int. J. Mol. Sci. 2023, 24(16), 12534; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms241612534 - 08 Aug 2023

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Abstract

Hydrogenases catalyze the simple yet important redox reaction between protons and electrons and H₂, thus mediating symbiotic interactions. The contribution of hydrogenase to this symbiosis and anti-oxidative damage was investigated using the M. huakuii hypE (encoding hydrogenase maturation protein) mutant. The hypE mutant grew a [...] Read more.

Hydrogenases catalyze the simple yet important redox reaction between protons and electrons and H₂, thus mediating symbiotic interactions. The contribution of hydrogenase to this symbiosis and anti-oxidative damage was investigated using the M. huakuii hypE (encoding hydrogenase maturation protein) mutant. The hypE mutant grew a little faster than its parental 7653R and displayed decreased antioxidative capacity under H₂O₂-induced oxidative damage. Real-time quantitative PCR showed that hypE gene expression is significantly up-regulated in all the detected stages of nodule development. Although the hypE mutant can form nodules, the symbiotic ability was severely impaired, which led to an abnormal nodulation phenotype coupled to a 47% reduction in nitrogen fixation capacity. This phenotype was linked to the formation of smaller abnormal nodules containing disintegrating and prematurely senescent bacteroids. Proteomics analysis allowed a total of ninety differentially expressed proteins (fold change > 1.5 or <0.67, p < 0.05) to be identified. Of these proteins, 21 are related to stress response and virulence, 21 are involved in transporter activity, and 18 are involved in energy and nitrogen metabolism. Overall, the HypE protein is essential for symbiotic nitrogen fixation, playing independent roles in supplying energy and electrons, in bacterial detoxification, and in the control of bacteroid differentiation and senescence. Full article

(This article belongs to the Special Issue Molecular Plant-Microbe Interactions 2.0)

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Review

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25 pages, 2154 KiB

Open AccessReview

Signaling in Legume–Rhizobia Symbiosis

by Julia Shumilina, Alena Soboleva, Evgeny Abakumov, Oksana Y. Shtark, Vladimir A. Zhukov and Andrej Frolov

Int. J. Mol. Sci. 2023, 24(24), 17397; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms242417397 - 12 Dec 2023

Cited by 2 | Viewed by 1584

Abstract

Legumes represent an important source of food protein for human nutrition and animal feed. Therefore, sustainable production of legume crops is an issue of global importance. It is well-known that legume-rhizobia symbiosis allows an increase in the productivity and resilience of legume crops. [...] Read more.

Legumes represent an important source of food protein for human nutrition and animal feed. Therefore, sustainable production of legume crops is an issue of global importance. It is well-known that legume-rhizobia symbiosis allows an increase in the productivity and resilience of legume crops. The efficiency of this mutualistic association strongly depends on precise regulation of the complex interactions between plant and rhizobia. Their molecular dialogue represents a complex multi-staged process, each step of which is critically important for the overall success of the symbiosis. In particular, understanding the details of the molecular mechanisms behind the nodule formation and functioning might give access to new legume cultivars with improved crop productivity. Therefore, here we provide a comprehensive literature overview on the dynamics of the signaling network underlying the development of the legume-rhizobia symbiosis. Thereby, we pay special attention to the new findings in the field, as well as the principal directions of the current and prospective research. For this, here we comprehensively address the principal signaling events involved in the nodule inception, development, functioning, and senescence. Full article

(This article belongs to the Special Issue Molecular Plant-Microbe Interactions 2.0)

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11 pages, 626 KiB

Open AccessReview

The Roles of N6-Methyladenosine Modification in Plant–RNA Virus Interactions

by Min He, Zhiqiang Li and Xin Xie

Int. J. Mol. Sci. 2023, 24(21), 15608; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms242115608 - 26 Oct 2023

Cited by 1 | Viewed by 943

Abstract

N⁶-methyladenosine (m⁶A) is a dynamic post-transcriptional RNA modification. Recently, its role in viruses has led to the study of viral epitranscriptomics. m⁶A has been observed in viral genomes and alters the transcriptomes of both the host cell [...] Read more.

N⁶-methyladenosine (m⁶A) is a dynamic post-transcriptional RNA modification. Recently, its role in viruses has led to the study of viral epitranscriptomics. m⁶A has been observed in viral genomes and alters the transcriptomes of both the host cell and virus during infection. The effects of m⁶A modifications on host plant mRNA can either increase the likelihood of viral infection or enhance the resistance of the host to the virus. However, to date, the regulatory mechanisms of m⁶A in viral infection and host immune responses have not been fully elucidated. With the development of sequencing-based biotechnologies, the study of m⁶A in plant viruses has received increasing attention. In this mini review, we summarize the positive and negative consequences of m⁶A modification in different RNA viral infections. Given its increasingly important roles in multiple viruses, m⁶A represents a new potential target for antiviral defense. Full article

(This article belongs to the Special Issue Molecular Plant-Microbe Interactions 2.0)

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25 pages, 795 KiB

Open AccessReview

Plants as the Extended Phenotype of Endophytes—The Actual Source of Bioactive Compounds

by Natalia Rutkowska, Piotr Drożdżyński, Małgorzata Ryngajłło and Olga Marchut-Mikołajczyk

Int. J. Mol. Sci. 2023, 24(12), 10096; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms241210096 - 13 Jun 2023

Cited by 3 | Viewed by 1971

Abstract

For thousands of years, plants have been used for their medicinal properties. The industrial production of plant-beneficial compounds is facing many drawbacks, such as seasonal dependence and troublesome extraction and purification processes, which have led to many species being on the edge of [...] Read more.

For thousands of years, plants have been used for their medicinal properties. The industrial production of plant-beneficial compounds is facing many drawbacks, such as seasonal dependence and troublesome extraction and purification processes, which have led to many species being on the edge of extinction. As the demand for compounds applicable to, e.g., cancer treatment, is still growing, there is a need to develop sustainable production processes. The industrial potential of the endophytic microorganisms residing within plant tissues is undeniable, as they are often able to produce, in vitro, similar to or even the same compounds as their hosts. The peculiar conditions of the endophytic lifestyle raise questions about the molecular background of the biosynthesis of these bioactive compounds in planta, and the actual producer, whether it is the plant itself or its residents. Extending this knowledge is crucial to overcoming the current limitations in the implementation of endophytes for larger-scale production. In this review, we focus on the possible routes of the synthesis of host-specific compounds in planta by their endophytes. Full article

(This article belongs to the Special Issue Molecular Plant-Microbe Interactions 2.0)

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30 pages, 1938 KiB

Open AccessReview

Fungal Effectoromics: A World in Constant Evolution

by Jewel Nicole Anna Todd, Karla Gisel Carreón-Anguiano, Ignacio Islas-Flores and Blondy Canto-Canché

Int. J. Mol. Sci. 2022, 23(21), 13433; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232113433 - 03 Nov 2022

Cited by 8 | Viewed by 2789

Abstract

Effectors are small, secreted molecules that mediate the establishment of interactions in nature. While some concepts of effector biology have stood the test of time, this area of study is ever-evolving as new effectors and associated characteristics are being revealed. In the present [...] Read more.

Effectors are small, secreted molecules that mediate the establishment of interactions in nature. While some concepts of effector biology have stood the test of time, this area of study is ever-evolving as new effectors and associated characteristics are being revealed. In the present review, the different characteristics that underly effector classifications are discussed, contrasting past and present knowledge regarding these molecules to foster a more comprehensive understanding of effectors for the reader. Research gaps in effector identification and perspectives for effector application in plant disease management are also presented, with a focus on fungal effectors in the plant-microbe interaction and interactions beyond the plant host. In summary, the review provides an amenable yet thorough introduction to fungal effector biology, presenting noteworthy examples of effectors and effector studies that have shaped our present understanding of the field. Full article

(This article belongs to the Special Issue Molecular Plant-Microbe Interactions 2.0)

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