Plant–microbiome interactions: from community assembly to plant health

Nature Reviews Microbiology, Journal Year: 2020, Volume and Issue: 18(11), P. 607 - 621

Published: Aug. 12, 2020

Language: Английский

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MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health

Proceedings of the National Academy of Sciences, Journal Year: 2018, Volume and Issue: 115(22)

Published: April 23, 2018

Plant roots nurture a tremendous diversity of microbes via exudation photosynthetically fixed carbon sources. In turn, probiotic members the root microbiome promote plant growth and protect host against pathogens pests. Arabidopsis thaliana-Pseudomonas simiae WCS417 model system root-specific transcription factor MYB72 MYB72-controlled β-glucosidase BGLU42 emerged as important regulators beneficial rhizobacteria-induced systemic resistance (ISR) iron-uptake responses. regulates biosynthesis iron-mobilizing fluorescent phenolic compounds, after which activity is required for their excretion into rhizosphere. Metabolite fingerprinting revealed antimicrobial coumarin scopoletin dominant metabolite that produced in excreted rhizosphere MYB72- BGLU42-dependent manner. Shotgun-metagenome sequencing root-associated microbiota Col-0, myb72, mutant f6'h1 showed selectively impacts assembly microbial community We show inhibits soil-borne fungal Fusarium oxysporum Verticillium dahliae, while growth-promoting ISR-inducing rhizobacteria P. Pseudomonas capeferrum WCS358 are highly tolerant effect scopoletin. Collectively, our results demonstrate role coumarins point to scenario plants join forces trigger MYB72/BGLU42-dependent scopolin production excretion, resulting improved niche establishment partner immunity benefits plant.

Language: Английский

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Host selection shapes crop microbiome assembly and network complexity

New Phytologist, Journal Year: 2020, Volume and Issue: 229(2), P. 1091 - 1104

Published: Aug. 27, 2020

Plant microbiomes are essential to host health and productivity but the ecological processes that govern crop microbiome assembly not fully known. Here we examined bacterial communities across 684 samples from soils (rhizosphere bulk soil) multiple compartment niches (rhizoplane, root endosphere, phylloplane, leaf endosphere) in maize (Zea mays)-wheat (Triticum aestivum)/barley (Hordeum vulgare) rotation system under different fertilization practices at two contrasting sites. Our results demonstrate along soil-plant continuum is shaped predominantly by niche species rather than site or practice. From epiphytes endophytes, selection pressure sequentially increased diversity network complexity consequently reduced, with strongest effect endosphere. Source tracking indicates mainly derived gradually enriched filtered plant niches. Moreover, were dominated a few dominant taxa (c. 0.5% of phylotypes), bacilli identified as important biomarker for wheat barley Methylobacteriaceae maize. work provides comprehensive empirical evidence on selection, potential sources enrichment assembly, has implications future management manipulation sustainable agriculture.

Language: Английский

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Modulation of the Root Microbiome by Plant Molecules: The Basis for Targeted Disease Suppression and Plant Growth Promotion

Frontiers in Plant Science, Journal Year: 2020, Volume and Issue: 10

Published: Jan. 24, 2020

Plants host a mesmerizing diversity of microbes inside and around their roots, known as the microbiome. The microbiome is composed mostly fungi, bacteria, oomycetes, archaea that can be either pathogenic or beneficial for plant health fitness. To grow healthy, plants need to surveil soil niches roots detection microbes, in parallel maximize services nutrients uptake growth promotion. employ palette mechanisms modulate including structural modifications, exudation secondary metabolites coordinated action different defence responses. Here, we review current understanding on composition activity root how molecules shape structure root-associated microbial communities. Examples are given interactions occur rhizosphere between soilborne fungi. We also present some well-established examples harnessing highlight fitness by selecting Understanding manipulate aid design next-generation inoculants targeted disease suppression enhanced growth.

Language: Английский

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Linking Plant Secondary Metabolites and Plant Microbiomes: A Review

Frontiers in Plant Science, Journal Year: 2021, Volume and Issue: 12

Published: March 2, 2021

Plant secondary metabolites (PSMs) play many roles including defense against pathogens, pests, and herbivores; response to environmental stresses, mediating organismal interactions. Similarly, plant microbiomes participate in of the above-mentioned processes directly or indirectly by regulating metabolism. Studies have shown that plants can influence their microbiome secreting various and, turn, may also impact metabolome host plant. However, not much is known about communications between interacting partners phenotypic changes. In this article, we review patterns potential underlying mechanisms interactions PSMs microbiomes. We describe recent developments analytical approaches methods field. The applications these new increased our understanding relationships Though current studies primarily focused on model organisms, results obtained so far should help future agriculturally important facilitate development manipulate PSMs–microbiome with predictive outcomes for sustainable crop productions.

Language: Английский

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The structure and function of the global citrus rhizosphere microbiome

Nature Communications, Journal Year: 2018, Volume and Issue: 9(1)

Published: Nov. 14, 2018

Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome thought to play an important role in promoting citrus growth and health. Here, we report comprehensive analysis of the structural functional composition microbiome. We use both amplicon deep shotgun metagenomic sequencing bulk soil samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria Bacteroidetes. The core comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax Paraburkholderia, some which are potential plant beneficial microbes. also identify over-represented microbial traits mediating plant-microbe microbe-microbe interactions, nutrition acquisition promotion rhizosphere. results provide valuable information guide isolation culturing and, potentially, harness power improve production

Language: Английский

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Enabling sustainable agriculture through understanding and enhancement of microbiomes

New Phytologist, Journal Year: 2021, Volume and Issue: 230(6), P. 2129 - 2147

Published: March 4, 2021

Summary Harnessing plant‐associated microbiomes offers an invaluable strategy to help agricultural production become more sustainable while also meeting growing demands for food, feed and fiber. A plethora of interconnected interactions among the host, environment microbes, occurring both above below ground, drive recognition, recruitment colonization resulting in activation downstream host responses functionality. Dissecting these complex by integrating multiomic approaches, high‐throughput culturing, computational synthetic biology advances is providing deeper understanding structure function native microbial communities. Such insights are paving way towards development products as well engineered with communities capable delivering agronomic solutions. While there a market microbial‐based solutions improve crop productivity, challenges commercialization remain. The continued translation microbiome knowledge into real‐world scenarios will require concerted transdisciplinary research, cross‐training next generation scientists, targeted educational efforts prime growers general public successful adoption innovative technologies.

Language: Английский

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The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome

Microbiome, Journal Year: 2019, Volume and Issue: 7(1)

Published: Feb. 1, 2019

Soil microorganisms can mediate the occurrence of plant diseases. Potato common scab (CS) is a refractory disease caused by pathogenic Streptomyces that occurs worldwide, but little known about interactions between CS and soil microbiome. In this study, four soil-root system compartments (geocaulosphere (GS), rhizosphere (RS), root-zone (ZS), furrow (FS)) were analyzed for potato plants with naturally high (H) low (L) severity levels. We aimed to determine composition putative function microbiome associated CS.

Language: Английский

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Beneficial microbes going underground of root immunity

Plant Cell & Environment, Journal Year: 2019, Volume and Issue: 42(10), P. 2860 - 2870

Published: July 29, 2019

Plant roots interact with an enormous diversity of commensal, mutualistic, and pathogenic microbes, which poses a big challenge to distinguish beneficial microbes from harmful ones. Plants can effectively ward off pathogens following immune recognition conserved microbe-associated molecular patterns (MAMPs). However, such elicitors are essentially not different those neutral that abundantly present in the root microbiome. Recent studies indicate plant system plays active role influencing rhizosphere microbiome composition. Moreover, it has become increasingly clear root-invading including rhizobia arbuscular mycorrhiza, evade or suppress host immunity establish mutualistic relationship their host. Evidence is accumulating many free-living microbiota members responses, highlighting suppression as important function Thus, gate keeping functions restricted warding but also extend microbiota, likely promote colonization by prevent growth-defense tradeoffs triggered MAMP-rich environment.

Language: Английский

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Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root

Environmental Microbiology, Journal Year: 2021, Volume and Issue: 23(4), P. 2199 - 2214

Published: Jan. 15, 2021

While the environment is considered primary origin of plant microbiome, potential role seeds as a source transmitting microorganisms has not received much attention. Here we tested hypothesis that microbiome partially inherited through vertical transmission. An experimental culturing device was constructed to grow oak seedlings in microbe-free while keeping belowground and aboveground tissues separated. The microbial communities associated with acorn's embryo pericarp developing seeding's phyllosphere root systems were analysed using amplicon sequencing fungal ITS bacterial 16S rDNA. Results showed seed diverse non-randomly distributed within an acorn. composition strongly resembled found embryo, whereas roots each had less distinct community. Our findings demonstrate high level diversity spatial partitioning community both seedling, indicating inheritance, niche differentiation divergent transmission routes for establishment communities.

Language: Английский

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