Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival

Cell, Journal Year: 2018, Volume and Issue: 175(4), P. 973 - 983.e14

Published: Nov. 1, 2018

Language: Английский

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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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Core microbiomes for sustainable agroecosystems

Nature Plants, Journal Year: 2018, Volume and Issue: 4(5), P. 247 - 257

Published: April 24, 2018

Language: Английский

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Environmental DNA

Oxford University Press eBooks, Journal Year: 2018, Volume and Issue: unknown

Published: Feb. 15, 2018

Abstract Environmental DNA (eDNA), i.e. released in the environment by any living form, represents a formidable opportunity to gather high-throughput and standard information on distribution or feeding habits of species. It has therefore great potential for applications ecology biodiversity management. However, this research field is fast-moving, involves different areas expertise currently lacks approaches, which calls an up-to-date comprehensive synthesis. monitoring covers current methods based eDNA, with particular focus “eDNA metabarcoding”. Intended scientists managers, it provides background allow design sound experiments. revisits all steps necessary produce high-quality metabarcoding data such as sampling, metabarcode design, optimization PCR sequencing protocols, well analysis large datasets. All these are presented discussing challenges eDNA-based approaches infer parameters ecological processes. The last chapters book review how been used so far unravel novel patterns diversity space time, detect species, answer new questions various ecosystems organisms. constitutes essential reading graduate students, researchers practitioners who do not have strong molecular genetics willing use eDNA biomonitoring.

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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Research priorities for harnessing plant microbiomes in sustainable agriculture

PLoS Biology, Journal Year: 2017, Volume and Issue: 15(3), P. e2001793 - e2001793

Published: March 28, 2017

Feeding a growing world population amidst climate change requires optimizing the reliability, resource use, and environmental impacts of food production. One way to assist in achieving these goals is integrate beneficial plant microbiomes—i.e., those enhancing growth, nutrient use efficiency, abiotic stress tolerance, disease resistance—into agricultural This integration will require large-scale effort among academic researchers, industry farmers understand manage plant-microbiome interactions context modern systems. Here, we identify priorities for research this area: (1) develop model host–microbiome systems crop plants non-crop with associated microbial culture collections reference genomes, (2) define core microbiomes metagenomes systems, (3) elucidate rules synthetic, functionally programmable microbiome assembly, (4) determine functional mechanisms interactions, (5) characterize refine genotype-by-environment-by-microbiome-by-management interactions. Meeting should accelerate our ability design implement effective manipulations management strategies, which, turn, pay dividends both consumers producers supply.

Language: Английский

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The Plant Microbiota: Systems-Level Insights and Perspectives

Annual Review of Genetics, Journal Year: 2016, Volume and Issue: 50(1), P. 211 - 234

Published: Sept. 20, 2016

Plants do not grow as axenic organisms in nature, but host a diverse community of microorganisms, termed the plant microbiota. There is an increasing awareness that microbiota plays role growth and can provide protection from invading pathogens. Apart intense research on crop plants, Arabidopsis emerging valuable model system to investigate drivers shaping stable bacterial communities leaves roots tool decipher intricate relationship among its colonizing microorganisms. Gnotobiotic experimental systems help establish causal relationships between genotypes phenotypes test hypotheses biotic abiotic perturbations systematic way. We highlight major recent findings using comparative profiling omics analyses, discuss these approaches light establishment beneficial traits like nutrient acquisition health.

Language: Английский

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Microbiota and Host Nutrition across Plant and Animal Kingdoms

Cell Host & Microbe, Journal Year: 2015, Volume and Issue: 17(5), P. 603 - 616

Published: May 1, 2015

Language: Английский

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Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species

New Phytologist, Journal Year: 2015, Volume and Issue: 209(2), P. 798 - 811

Published: Oct. 15, 2015

Desert plants are hypothesized to survive the environmental stress inherent these regions in part thanks symbioses with microorganisms, and yet microbial species, communities they form, forces that influence them poorly understood. Here we report first comprehensive investigation of associated species Agave, which native semiarid arid Central North America emerging as biofuel feedstocks. We examined prokaryotic fungal rhizosphere, phyllosphere, leaf root endosphere, well proximal distal soil samples from cultivated agaves, through Illumina amplicon sequencing. Phylogenetic profiling revealed composition was primarily determined by plant compartment, whereas mainly influenced biogeography host species. Cultivated A. tequilana exhibited lower levels diversity compared although no differences were found endosphere. Agaves shared core taxa known promote growth confer tolerance abiotic stress, suggests common principles underpinning Agave-microbe interactions.

Language: Английский

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A practical guide to amplicon and metagenomic analysis of microbiome data

Protein & Cell, Journal Year: 2020, Volume and Issue: 12(5), P. 315 - 330

Published: May 11, 2020

Abstract Advances in high-throughput sequencing (HTS) have fostered rapid developments the field of microbiome research, and massive datasets are now being generated. However, diversity software tools complexity analysis pipelines make it difficult to access this field. Here, we systematically summarize advantages limitations methods. Then, recommend specific for amplicon metagenomic analyses, describe commonly-used databases, help researchers select appropriate tools. Furthermore, introduce statistical visualization methods suitable analysis, including alpha- beta-diversity, taxonomic composition, difference comparisons, correlation, networks, machine learning, evolution, source tracing, common styles informed choices. Finally, a step-by-step reproducible guide is introduced. We hope review will allow carry out data more effectively quickly order efficiently mine biological significance behind data.

Language: Английский

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