NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice

Nature Biotechnology, Journal Year: 2019, Volume and Issue: 37(6), P. 676 - 684

Published: April 29, 2019

Language: Английский

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Rhizosphere microbiome structure alters to enable wilt resistance in tomato

Nature Biotechnology, Journal Year: 2018, Volume and Issue: 36(11), P. 1100 - 1109

Published: Oct. 8, 2018

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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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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Plant flavones enrich rhizosphere Oxalobacteraceae to improve maize performance under nitrogen deprivation

Nature Plants, Journal Year: 2021, Volume and Issue: 7(4), P. 481 - 499

Published: April 8, 2021

Language: Английский

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Systems Biology of Plant-Microbiome Interactions

Molecular Plant, Journal Year: 2019, Volume and Issue: 12(6), P. 804 - 821

Published: May 23, 2019

In natural environments, plants are exposed to diverse microbiota that they interact with in complex ways. While plant–pathogen interactions have been intensely studied understand defense mechanisms plants, many microbes and microbial communities can substantial beneficial effects on their plant host. Such include improved acquisition of nutrients, accelerated growth, resilience against pathogens, resistance abiotic stress conditions such as heat, drought, salinity. However, the bacterial strains or consortia host often cultivar species specific, posing an obstacle general application. Remarkably, signals trigger immune responses molecularly highly similar identical pathogenic microbes. Thus, it is unclear what determines outcome a particular microbe–host interaction which factors enable distinguish beneficials from pathogens. To unravel network genetic, microbial, metabolic interactions, including signaling events mediating comprehensive quantitative systems biology approaches will be needed.

Language: Английский

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Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome

Proceedings of the National Academy of Sciences, Journal Year: 2019, Volume and Issue: 116(25), P. 12558 - 12565

Published: May 31, 2019

Significance The root microbiome composition is largely determined by the soil inoculum, with a distinct contribution from host. molecular mechanisms which host influences its rhizobiome are only beginning to be discovered. Using hydroponics-based synthetic community approach, we probe how root-exuded specialized metabolites sculpt microbiome. We uncover role for coumarins in structuring rhizobiome, particularly limiting growth of Pseudomonas strain, propose mechanism action involving reactive oxygen species. Our findings support possibility that form part plant’s adaptive response iron deficiency goes beyond mobilization modulate and highlight avenues toward engineering rhizosphere plant health.

Language: Английский

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Rhizosphere Microbiome Assembly and Its Impact on Plant Growth

Journal of Agricultural and Food Chemistry, Journal Year: 2020, Volume and Issue: 68(18), P. 5024 - 5038

Published: April 7, 2020

Microorganisms colonizing the plant rhizosphere provide a number of beneficial functions for their host. Although an increasing investigations clarified great functional capabilities microbial communities, understanding precise mechanisms underlying impact microbiome assemblies is still limited. Also, not much known about various microbiome. In this review, we summarize current knowledge biotic and abiotic factors that shape as well traits are to plants growth disease-resistance. We give particular emphasis on root metabolites how contributes growth, yield, Finally, introduce new perspective novel method showing synthetic community construction provides effective approach unravel plant–microbes microbes–microbes interplays.

Language: Английский

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The Plant Microbiome: From Ecology to Reductionism and Beyond

Annual Review of Microbiology, Journal Year: 2020, Volume and Issue: 74(1), P. 81 - 100

Published: June 12, 2020

Methodological advances over the past two decades have propelled plant microbiome research, allowing field to comprehensively test ideas proposed a century ago and generate many new hypotheses. Studying distribution of microbial taxa genes across habitats has revealed importance various ecological evolutionary forces shaping microbiota. In particular, selection imposed by strongly shapes diversity composition microbiota leads adaptation associated with navigating immune system utilizing plant-derived resources. Reductionist approaches demonstrated that interaction between immunity is, in fact, bidirectional plants, microbiota, environment shape complex chemical dialogue collectively orchestrates plantmicrobiome. The next stage research will require integration reductionist establish general understanding assembly function both natural managed environments.

Language: Английский

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Plant developmental stage drives the differentiation in ecological role of the maize microbiome

Microbiome, Journal Year: 2021, Volume and Issue: 9(1)

Published: Aug. 13, 2021

Abstract Background Plants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how development impacts the assembly, functions interactions crop microbiomes are poorly understood. Here we examined both bacterial fungal across soils, epiphytic endophytic niches leaf root, plastic fake plant (representing environment-originating microbes) at three developmental stages maize two contrasting sites, further explored potential function phylloplane based on metagenomics. Results Our results suggested that stage had a much stronger influence diversity, composition interkingdom networks in compartments than strongest effect phylloplane. Phylloplane were co-shaped by growth seasonal environmental factors, air (represented plants) as its important source. Further, found more strongly driven deterministic processes early similar pattern was for late stage. Moreover, taxa played role network yield prediction stage, while did so Metagenomic analyses indicated possessed higher functional diversity genes related to nutrient provision enriched N assimilation C degradation Coincidently, abundant beneficial like Actinobacteria, Burkholderiaceae Rhizobiaceae observed saprophytic fungi Conclusions suggest influences microbiome assembly functions, take differentiated ecological different development. This study provides empirical evidence exerting strong selection during These findings have implications future tools manipulate sustainable increase primary productivity.

Language: Английский

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