Unraveling plant–microbe interactions: can integrated omics approaches offer concrete answers?

Journal of Experimental Botany, Год журнала: 2023, Номер 75(5), С. 1289 - 1313

Опубликована: Ноя. 9, 2023

Abstract Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help deeper insights into plant–microbe interactions a concerted way. Integrating multi-omics datasets transform our understanding of the microbiome from unspecified genetic influences interacting species specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies crop research review key aspects integration host microbial omics-based be used comprehensive outline complex crop–microbe We describe these technological advances have helped unravel crucial genes pathways that control beneficial, pathogenic, commensal identify knowledge gaps synthesize current limitations approaches. studies which multi-omics-based approaches led improved models community structure function. Finally, recommend holistic integrating achieve precision efficiency data analysis, for biotic abiotic stress contribution microbiota shaping fitness.

Язык: Английский

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Exploring Cereal Metagenomics: Unravelling Microbial Communities for Improved Food Security

Microorganisms, Год журнала: 2024, Номер 12(3), С. 510 - 510

Опубликована: Март 2, 2024

Food security is an urgent global challenge, with cereals playing a crucial role in meeting the nutritional requirements of populations worldwide. In recent years, field metagenomics has emerged as powerful tool for studying microbial communities associated cereal crops and their impact on plant health growth. This chapter aims to provide comprehensive overview its enhancing food through exploration beneficial pathogenic interactions. Furthermore, we will examine how integration other tools can effectively address adverse effects security. For this purpose, discuss metagenomic data machine learning providing novel insights into dynamic interactions shaping plant-microbe relationships. We also shed light potential applications leveraging diversity epigenetic modifications improving crop resilience yield sustainability. Ultimately, revolutionized by harnessing between microbiota, paving way sustainable agricultural practices.

Язык: Английский

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Epigenetic weapons of plants against fungal pathogens

BMC Plant Biology, Год журнала: 2024, Номер 24(1)

Опубликована: Март 6, 2024

Abstract In the natural environment, plants face constant exposure to biotic stress caused by fungal attacks. The plant’s response various stresses relies heavily on its ability rapidly adjust transcriptome. External signals are transmitted nucleus, leading activation of transcription factors that subsequently enhance expression specific defense-related genes. Epigenetic mechanisms, including histone modifications and DNA methylation, which closely linked chromatin states, regulate gene associated with defense against stress. Additionally, remodelers non-coding RNA play a significant role in plant stressors. These molecular enable exhibit enhanced resistance productivity under diverse environmental conditions. mechanisms also contribute stress-induced epigenetic memory priming plants, enabling them recall past experiences utilize this stored information for adaptation new arms race between fungi aspect is cross-kingdom RNAi mechanism, whereby sRNAs can traverse organismal boundaries. Fungi sRNA as an effector molecule silence genes, while transport sRNA, primarily through extracellular vesicles, pathogens order suppress virulence-related review, we summarize contemporary knowledge attack pathogenic fungi. during plant-fungus symbiotic interactions considered.

Язык: Английский

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Does ectomycorrhizal fungal biodiversity affect tree growth?

Fungal ecology, Год журнала: 2025, Номер 74, С. 101413 - 101413

Опубликована: Янв. 23, 2025

Язык: Английский

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A perspective on cross‐kingdom RNA interference in mutualistic symbioses

New Phytologist, Год журнала: 2023, Номер 240(1), С. 68 - 79

Опубликована: Июль 14, 2023

Summary RNA interference (RNAi) is arguably one of the more versatile mechanisms in cell biology, facilitating fine regulation gene expression and protection against mobile genomic elements, whilst also constituting a key aspect induced plant immunity. More recently, use this mechanism to regulate heterospecific partners – cross‐kingdom RNAi (ckRNAi) has been shown form critical part bidirectional interactions between hosts endosymbionts, regulating interplay microbial infection host Here, we review current understanding ckRNAi as it relates plants their pathogenic mutualistic with particular emphasis on evidence support arbuscular mycorrhizal symbiosis.

Язык: Английский

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The Silent Conversation: How Small RNAs Shape Plant–Microbe Relationships

International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(6), С. 2631 - 2631

Опубликована: Март 14, 2025

This review highlights the emerging role of cross-kingdom RNA interference in plant–microbe interactions, particularly transfer sRNAs from microbes to plants and vice versa, emphasizing importance this mechanism both mutualistic pathogenic contexts. As adapted terrestrial life, they formed symbiotic relationships with microbes, essential for nutrient uptake defense. Emerging evidence underscores sRNAs, including small interfering RNAs (siRNAs) microRNAs (miRNAs), as critical regulators gene expression immune responses interactions. In symbioses, such mycorrhizal fungi nitrogen-fixing bacteria associations, are hypothesized regulate exchange stability. scenarios, utilize undermine plant defenses, while employ strategies like host-induced silencing (HIGS) counteract these threats. We further explore extracellular vesicles (EVs) sRNA transport, which is facilitating interspecies communication Although potential ckRNAi interactions promising, need experimental validation establish its true significance relationships. By synthesizing current research, intricate molecular dialogues mediated by identifies gaps, proposing future research directions aimed at harnessing mechanisms agricultural advancements.

Язык: Английский

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Omics for Thriving Plant Microbiomes: Growing Food Security for a Sustainable Future

Опубликована: Янв. 1, 2025

Язык: Английский

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Epigenetic control during root development and symbiosis

PLANT PHYSIOLOGY, Год журнала: 2024, Номер 196(2), С. 697 - 710

Опубликована: Июнь 12, 2024

Abstract The roots of plants play multiple functions that are essential for growth and development, including anchoring to the soil as well water nutrient acquisition. These underground organs exhibit plasticity modify their root system architecture in response environmental cues, allowing adaptation change availability. In addition, enter mutualistic interactions with microorganisms, example, nodule symbiosis (RNS) established between a limited group nitrogen-fixing bacteria arbuscular mycorrhiza involving most land fungi Glomeromycetes phylum. past 20 years, genetic approaches allowed identification functional characterization genes required specific programs nodule, symbioses. studies provided evidence program RNS recruited components developmental programs. execution these is strongly influenced by epigenetic changes—DNA methylation histone post-translational modifications—that alter chromatin conformation modifying expression key genes. this review, we summarize recent advances highlight how DNA modifications, remodeling factors long noncoding RNAs, shape allow successful establishment both We anticipate analysis dynamic changes 3D structure single cells or tissue types will illuminate our understanding symbiotic orchestrated, opening exciting questions new perspectives modulate agronomical ecological traits linked

Язык: Английский

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A strategy for studying epigenetic diversity in natural populations: proof of concept in poplar and oak

Journal of Experimental Botany, Год журнала: 2024, Номер 75(18), С. 5568 - 5584

Опубликована: Июнь 18, 2024

Abstract In the last 20 years, several techniques have been developed for quantifying DNA methylation, most studied epigenetic marks in eukaryotes, including gold standard method, whole-genome bisulfite sequencing (WGBS). WGBS quantifies genome-wide methylation but has inconveniences rendering it less suitable population-scale studies. The high cost of deep and large amounts data generated prompted us to seek an alternative approach. Restricting studies parts genome would be a satisfactory had there not major limitation: need select upstream targets corresponding differentially methylated regions as targets. Given study numbers samples, we propose strategy investigating variation natural populations, taking into account structural complexity genomes, their size, content unique coding versus repeated transposable elements. We first identified highly variable subset genotypes representative biological diversity population by WGBS. then analysed variations these targeted at level capture (SeqCapBis). entire was validated applying another species. Our proof concept on populations two forest species: Populus nigra Quercus petraea.

Язык: Английский

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Enhancing Agricultural Sustainability Through Rhizomicrobiome: A Review

Journal of Basic Microbiology, Год журнала: 2024, Номер 64(11)

Опубликована: Июнь 20, 2024

Sustainable agriculture represents the responsible utilization of natural resources while safeguarding well-being environment. It encompasses objectives preserving environment, fostering economic growth, and promoting socioeconomic equality. To achieve sustainable development for humanity, it is imperative to prioritize agriculture. One significant approach achieving this transition extensive microbes, which play a crucial role due genetic reliance plants on beneficial functions provided by symbiotic microbes. This review focuses significance rhizospheric microbial communities, also known as rhizomicrobiome (RM). complex community microorganisms that live in rhizosphere influence plant's growth health. provides its host plant with various benefits related including biocontrol, biofertilization, phytostimulation, rhizoremediation, stress resistance, other advantageous properties. Yet, mechanisms RM contributes remain largely unknown. Investigating population presents opportunity advance toward Hence, study aims provide an overview diversity applications practices. Lately, there has been growing momentum areas rhizobiome research application includes engineering, synthetic microbiome application, agent-based modeling rhizobiome, metagenomic studies. So, developing bioformulations these support could serve promising solution future strategies aimed at new green revolution.

Язык: Английский

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