Plant–microbiome interactions: from community assembly to plant health

Nature Reviews Microbiology, Год журнала: 2020, Номер 18(11), С. 607 - 621

Опубликована: Авг. 12, 2020

Язык: Английский

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Feed Your Friends: Do Plant Exudates Shape the Root Microbiome?

Trends in Plant Science, Год журнала: 2017, Номер 23(1), С. 25 - 41

Опубликована: Окт. 17, 2017

Язык: Английский

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Plant Growth-Promoting Rhizobacteria: Context, Mechanisms of Action, and Roadmap to Commercialization of Biostimulants for Sustainable Agriculture

Frontiers in Plant Science, Год журнала: 2018, Номер 9

Опубликована: Окт. 23, 2018

Microbes of the phytomicrobiome are associated with every plant tissue and, in combination form holobiont. Plants regulate composition and activity their bacterial community carefully. These microbes provide a wide range services benefits to plant; return, provides microbial reduced carbon other metabolites. Soils generally moist environment, rich which supports extensive soil communities. The rhizomicrobiome is great importance agriculture owing diversity root exudates cell debris that attract diverse unique patterns colonization. play key roles nutrient acquisition assimilation, improved texture, secreting modulating extracellular molecules such as hormones, secondary metabolites, antibiotics various signal compounds, all leading enhancement growth. compounds they secrete constitute valuable biostimulants pivotal stress responses. Research has demonstrated inoculating plants plant-growth promoting rhizobacteria (PGPR) or treating microbe-to-plant can be an effective strategy stimulate crop Furthermore, these strategies improve tolerance for abiotic stresses (egs. drought, heat, salinity) likely become more frequent climate change conditions continue develop. This discovery resulted multifunctional PGPR-based formulations commercial agriculture, minimize use synthetic fertilizers agrochemicals. review update about role PGPR from collection commercialization low-cost agricultural inputs. First, we introduce concept context underlying food security 21st century. Next, mechanisms growth promotion by discussed, including exchange between roots how relationships modulate responses via induced systemic resistance. On application side, discussed rhizosphere colonization inoculants. final sections paper describe applications century roadmap technology.

Язык: Английский

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Microbial interactions within the plant holobiont

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

Опубликована: Март 27, 2018

Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage species that is often referred to as a "holobiont." Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities selected for host-adapted microorganisms impact fitness. However, high densities detected tissues, together fast generation time more ancient origin compared host, suggest microbe-microbe interactions are also important selective forces sculpting complex assemblages in phyllosphere, rhizosphere, endosphere compartments. Reductionist approaches conducted under laboratory conditions critical decipher strategies used specific cooperate compete within or outside tissues. Nonetheless, our understanding these shaping communities, along relevance host health natural context, remains sparse. Using examples obtained from reductionist community-level approaches, we discuss fundamental role (prokaryotes micro-eukaryotes) community structure health. We provide conceptual framework illustrating among microbiota members establishment maintenance host-microbial homeostasis.

Язык: Английский

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Host genotype and age shape the leaf and root microbiomes of a wild perennial plant

Nature Communications, Год журнала: 2016, Номер 7(1)

Опубликована: Июль 12, 2016

Bacteria living on and in leaves roots influence many aspects of plant health, so the extent a plant's genetic control over its microbiota is great interest to crop breeders evolutionary biologists. Laboratory-based studies, because they poorly simulate true environmental heterogeneity, may misestimate or totally miss certain host genes microbiome. Here we report large-scale field experiment disentangle effects genotype, environment, age year harvest bacterial communities associated with Boechera stricta (Brassicaceae), perennial wild mustard. Host microbiome evident but not roots, varies substantially among sites. Microbiome composition also shifts as plants age. Furthermore, large proportion leaf groups are shared suggesting inoculation from soil. Our results demonstrate how genotype-by-environment interactions contribute complexity assembly natural environments.

Язык: Английский

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Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival

Cell, Год журнала: 2018, Номер 175(4), С. 973 - 983.e14

Опубликована: Ноя. 1, 2018

Язык: Английский

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Metacoder: An R package for visualization and manipulation of community taxonomic diversity data

PLoS Computational Biology, Год журнала: 2017, Номер 13(2), С. e1005404 - e1005404

Опубликована: Фев. 21, 2017

Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa. These graph types do not convey hierarchical structure taxonomic classifications and are limited for categories. As alternative, we developed metacoder, R package easily parsing, manipulating, graphing publication-ready plots data. Metacoder includes a dynamic flexible function can parse most text-based formats contain classifications, taxon names, identifiers, sequence identifiers. then subset, sample, order this parsed data using set intuitive functions take into account nature Finally, extremely plotting enables quantitative representation up 4 arbitrary statistics simultaneously in tree format mapping size nodes edges. also allows exploration barcode primer bias integrating run digital PCR. Although it has been designed from research, metacoder be applied any component such gene ontology geographic location Our complements currently available tools community analysis provided open source with extensive online user manual.

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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Root Endophyte Colletotrichum tofieldiae Confers Plant Fitness Benefits that Are Phosphate Status Dependent

Cell, Год журнала: 2016, Номер 165(2), С. 464 - 474

Опубликована: Март 17, 2016

Highlights•Colletotrichum tofieldiae (Ct) is a fungal root endophyte of Arabidopsis•Ct transfers the macronutrient phosphorus to Arabidopsis shoots•Ct-mediated plant growth promotion needs an intact phosphate starvation response•A branch innate immune system essential for beneficial Ct activitiesSummaryA staggering diversity endophytic fungi associate with healthy plants in nature, but it usually unclear whether these represent stochastic encounters or provide host fitness benefits. Although most characterized species genus Colletotrichum are destructive pathogens, we show here that C. endemic natural thaliana populations central Spain. Colonization by initiates roots can also spread systemically into shoots. shoots, promotes growth, and increases fertility only under phosphorus-deficient conditions, nutrient status might have facilitated transition from pathogenic lifestyles. The host's response (PSR) controls colonization needed (PGP). PGP requires PEN2-dependent indole glucosinolate metabolism, component responses, indicating functional link between immunity PSR during interactions Ct.Graphical abstract

Язык: Английский

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Drought and host selection influence bacterial community dynamics in the grass root microbiome

The ISME Journal, Год журнала: 2017, Номер 11(12), С. 2691 - 2704

Опубликована: Июль 28, 2017

Abstract Root endophytes have been shown to important roles in determining host fitness under periods of drought stress, and yet the effect on broader root endosphere bacterial community remains largely uncharacterized. In this study, we present phylogenetic profiles communities associated with drought-treated rhizosphere tissues 18 species plants varying degrees tolerance belonging Poaceae family, including crop plants. Through 16S rRNA gene profiling across two distinct watering regimes developmental time points, demonstrate that there is a strong correlation between distance microbiome dissimilarity within tissues, weakens by inducing conserved shifts composition. We identify significant enrichment wide variety Actinobacteria during roots all hosts, higher than it surrounding environments. Furthermore, show observed result an absolute increase Actinobacterial abundance previously hypothesized mechanisms for enrichments soils are unlikely fully account phenomena here plant root.

Язык: Английский

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