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

New Phytologist, Год журнала: 2015, Номер 209(2), С. 798 - 811

Опубликована: Окт. 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.

Язык: Английский

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Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

Microbiome, Год журнала: 2018, Номер 6(1)

Опубликована: Янв. 16, 2018

Harnessing beneficial microbes presents a promising strategy to optimize plant growth and agricultural sustainability. Little is known which extent how specifically soil microbiomes can be manipulated through different cropping practices. Here, we investigated wheat root microbial communities in system experiment consisting of conventional organic managements, both with tillage intensities. While richness was marginally affected, found pronounced effects on community composition, were specific for the respective microbiomes. Soil bacterial primarily structured by tillage, whereas fungal responded mainly management type additional tillage. In roots, also driving factor bacteria but not fungi, generally determined changes intensity. To quantify an "effect size" microbiota manipulation, that about 10% variation explained tested Cropping sensitive taxonomically diverse, they guilds taxa These included frequent members or co-occurring many other community, suggesting practices may allow manipulation influential members. Understanding abundance patterns basis towards developing strategies smart farming. For future targeted management—e.g., foster certain practices—a next step will identify functional traits microbes.

Язык: Английский

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Impact of plant domestication on rhizosphere microbiome assembly and functions

Plant Molecular Biology, Год журнала: 2015, Номер 90(6), С. 635 - 644

Опубликована: Июнь 17, 2015

The rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests diseases, facilitating nutrient acquisition helping plants to withstand abiotic stresses. Plants can actively recruit members of the soil microbial community positive feedbacks, but underlying mechanisms traits that drive assembly functions are largely unknown. Domestication species has substantially contributed human civilization, also caused a strong decrease in genetic diversity modern crop cultivars may have affected ability establish beneficial associations with microbes. Here, we review how shape domestication impacted via habitat expansion changes management practices, root exudation, architecture, litter quality. We propose "back roots" framework comprises exploration indigenous their native habitats identification ultimate goal reinstate been undermined during domestication.

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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Drought Stress and Root-Associated Bacterial Communities

Frontiers in Plant Science, Год журнала: 2018, Номер 8

Опубликована: Янв. 9, 2018

Root-associated bacterial communities play a vital role in maintaining health of the plant host. These exist complex relationships, where composition and abundance community members is dependent on number factors such as local soil chemistry, genotype phenotype, perturbations surrounding abiotic environment. One common perturbation, drought, has been shown to have drastic effects communities, yet little understood about underlying causes behind observed shifts microbial abundance. As drought may affect root both directly by modulating moisture availability, well indirectly altering chemistry phenotypes, we provide synthesis trends recent studies discuss possible directions for future research that hope will more knowledgeable predictions responses events.

Язык: Английский

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Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems

Microbiome, Год журнала: 2018, Номер 6(1)

Опубликована: Авг. 21, 2018

Soil microbiomes play an important role in the services and functioning of terrestrial ecosystems. However, little is known their vertical responses to restoration process contributions soil nutrient cycling subsurface profiles. Here, we investigated community assembly bacteria, archaea, fungi along (i.e., depths 0–300 cm) horizontal distance from trees 30–90 profiles a chronosequence reforestation sites that represent over 30 years restoration. In superficial layers (0–80 cm), bacterial fungal diversity decreased, whereas archaeal increased with increasing depth. As proceeded time, spatial variation communities while increased. Vertical distributions were more related properties, may be driven by gradient effect roots extending tree. Bacterial beta-diversity strongly multi-nutrient soil, respectively, playing major roles deep layers. Taken together, these results reveal new perspective on at fine scale single trees. Distinct response patterns underpinned as function during ex-arable land.

Язык: Английский

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Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria

Proceedings of the National Academy of Sciences, Год журнала: 2018, Номер 115(18)

Опубликована: Апрель 16, 2018

Significance Drought remains a critical obstacle to meeting the food demands of coming century. Understanding interplay between drought stress, plant development, and microbiome is central this challenge. Here, we demonstrate that causes enrichment distinct set microbes in roots, composed almost entirely monoderms, which lack outer membranes have thick cell walls. We under drought, roots increase production many metabolites, monoderms inhabiting drought-treated rhizosphere exhibit increased activity transporters connected with some these same compounds. The discovery drought-induced associated shifts metabolite exchange microbe reveal potential blueprint for manipulating microbiomes improved crop fitness.

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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Root exudates drive the soil-borne legacy of aboveground pathogen infection

Microbiome, Год журнала: 2018, Номер 6(1)

Опубликована: Сен. 12, 2018

Plants are capable of building up beneficial rhizosphere communities as is evidenced by disease-suppressive soils. However, it not known how and why soil bacterial impacted plant exposure to foliar pathogens if such responses might improve performance in the presence pathogen. Here, we conditioned growing multiple generations (five) Arabidopsis thaliana inoculated aboveground with Pseudomonas syringae pv tomato (Pst) same soil. We then examined a subsequent generation (sixth) grown pathogen-conditioned versus control-conditioned Moreover, assessed role altered root exudation profiles shaping microbiome infected plants.Plants showed increased levels jasmonic acid improved disease resistance. Illumina Miseq 16S rRNA gene tag sequencing revealed that both bulk were Pst infection. Infected plants exhibited significantly higher amino acids, nucleotides, long-chain organic acids (LCOAs) (C > 6) lower for sugars, alcohols, short-chain (SCOAs) ≤ 6). Interestingly, addition exogenous LCOA also elicited response.Collectively, our data suggest can recruit via modification patterns response benefit generations.

Язык: Английский

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Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health

Nature Communications, Год журнала: 2015, Номер 6(1)

Опубликована: Сен. 24, 2015

Abstract Host-associated bacterial communities can function as an important line of defence against pathogens in animals and plants. Empirical evidence theoretical predictions suggest that species-rich are more resistant to pathogen invasions. Yet, the underlying mechanisms unclear. Here, we experimentally test how resource competition networks resident affect invasion resistance plant Ralstonia solanacearum microcosms tomato rhizosphere. We find bipartite better predictors compared with community diversity. Specifically, a combination stabilizing configurations (low nestedness high connectance), clear niche overlap pathogen, reduce success, constrain growth within invaded have lower levels diseased plants greenhouse experiments. Bacterial network characteristics thus be explaining positive diversity–invasion relationships rhizosphere communities.

Язык: Английский

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