Microbiome definition re-visited: old concepts and new challenges

Microbiome, Год журнала: 2020, Номер 8(1)

Опубликована: Июнь 30, 2020

The field of microbiome research has evolved rapidly over the past few decades and become a topic great scientific public interest. As result this rapid growth in interest covering different fields, we are lacking clear commonly agreed definition term "microbiome." Moreover, consensus on best practices is missing. Recently, panel international experts discussed current gaps frame European-funded MicrobiomeSupport project. meeting brought together about 40 leaders from diverse areas, while more than hundred all world took part an online survey accompanying workshop. This article excerpts outcomes workshop corresponding embedded short historical introduction future outlook. We propose based compact, clear, comprehensive description provided by Whipps et al. 1988, amended with set novel recommendations considering latest technological developments findings. clearly separate terms microbiota provide discussion composition microbiota, heterogeneity dynamics microbiomes time space, stability resilience microbial networks, core microbiomes, functionally relevant keystone species as well co-evolutionary principles microbe-host inter-species interactions within microbiome. These broad definitions suggested unifying concepts will help to improve standardization studies future, could be starting point for integrated assessment data resulting transfer knowledge basic science into practice. Furthermore, standards important solving new challenges associated anthropogenic-driven changes planetary health, which understanding might play key role. Video Abstract.

Язык: Английский

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A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application

Journal of Advanced Research, Год журнала: 2019, Номер 19, С. 29 - 37

Опубликована: Март 20, 2019

Plants have evolved with a plethora of microorganisms having important roles for plant growth and health. A considerable amount information is now available on the structure dynamics microbiota as well functional capacities isolated community members. Due to interesting potential due current challenges in crop production there an urgent need bring microbial innovations into practice. Different approaches microbiome improvement exist. On one hand strains or strain combinations can be applied, however, field success often variable urgently required. Smart, knowledge-driven selection needed use suitable delivery formulations. other hand, farming practices genotype influence thus functioning. Therefore, appropriate breeding leading improved plant-microbiome interactions are avenues increase benefit microbiota. In conclusion, different making new generation inoculants application microbiome-based agro-management lines could lead better microbiome. This paper reviews importance functionalities bacterial discusses concepts regard plant-associated bacteria.

Язык: Английский

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Rhizosphere bacteriome structure and functions

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Фев. 11, 2022

Abstract Microbial composition and functions in the rhizosphere—an important microbial hotspot—are among most fascinating yet elusive topics ecology. We used 557 pairs of published 16S rDNA amplicon sequences from bulk soils rhizosphere different ecosystems around world to generalize bacterial characteristics with respect community diversity, composition, functions. The selects microorganisms soil function as a seed bank, reducing diversity. is enriched Bacteroidetes, Proteobacteria, other copiotrophs. Highly modular but unstable networks (common for r -strategists) reflect interactions adaptations dynamic conditions. Dormancy strategies are dominated by toxin–antitoxin systems, while sporulation common soils. Functional predictions showed that genes involved organic compound conversion, nitrogen fixation, denitrification were strongly (11–182%), nitrification depleted.

Язык: Английский

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Plant root-microbe communication in shaping root microbiomes

Plant Molecular Biology, Год журнала: 2016, Номер 90(6), С. 575 - 587

Опубликована: Янв. 4, 2016

A growing body of research is highlighting the impacts root-associated microbial communities can have on plant health and development. These include changes in yield quantity quality, timing key developmental stages tolerance biotic abiotic stresses. With such a range effects it clear that understanding factors contribute to plant-beneficial root microbiome may prove advantageous. Increasing demands for food by human population increases importance urgency how microbiomes be exploited increase crop yields reduce losses caused disease. In addition, climate change require novel approaches overcoming stresses as drought salinity well new emerging diseases. This review discusses current knowledge formation maintenance plant-microbe interactions with particular emphasis effect microbe-microbe shape at surface. Further, we discuss potential modification benefit agriculture production.

Язык: Английский

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Metabolomics in the Rhizosphere: Tapping into Belowground Chemical Communication

Trends in Plant Science, Год журнала: 2016, Номер 21(3), С. 256 - 265

Опубликована: Янв. 30, 2016

Язык: Английский

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Ecology and Evolution of Plant Microbiomes

Annual Review of Microbiology, Год журнала: 2019, Номер 73(1), С. 69 - 88

Опубликована: Май 15, 2019

Microorganisms colonizing plant surfaces and internal tissues provide a number of life-support functions for their host. Despite increasing recognition the vast functional capabilities microbiome, our understanding ecology evolution taxonomically hyperdiverse microbial communities is limited. Here, we review current knowledge genotypic phenotypic traits as well allogenic autogenic factors that shape microbiome composition functions. We give specific emphasis to impact domestication on assembly how insights into microbiomes wild relatives native habitats can contribute reinstate or enrich microorganisms with beneficial effects growth, development, health. Finally, introduce new concepts perspectives in research, particular community theory mechanistic framework unravel interplay distinct ecological processes-i.e., selection, dispersal, drift, diversification-that structure microbiome.

Язык: 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, Год журнала: 2020, Номер 10

Опубликована: Янв. 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.

Язык: Английский

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Let the Core Microbiota Be Functional

Trends in Plant Science, Год журнала: 2017, Номер 22(7), С. 583 - 595

Опубликована: Май 23, 2017

Язык: Английский

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Systems Biology of Plant-Microbiome Interactions

Molecular Plant, Год журнала: 2019, Номер 12(6), С. 804 - 821

Опубликована: Май 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.

Язык: Английский

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Influence of resistance breeding in common bean on rhizosphere microbiome composition and function

The ISME Journal, Год журнала: 2017, Номер 12(1), С. 212 - 224

Опубликована: Окт. 13, 2017

Язык: Английский

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