Establishing Causality: Opportunities of Synthetic Communities for Plant Microbiome Research

Cell Host & Microbe, Год журнала: 2017, Номер 22(2), С. 142 - 155

Опубликована: Авг. 1, 2017

Язык: Английский

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From hairballs to hypotheses–biological insights from microbial networks

FEMS Microbiology Reviews, Год журнала: 2018, Номер 42(6), С. 761 - 780

Опубликована: Июль 25, 2018

Microbial networks are an increasingly popular tool to investigate microbial community structure, as they integrate multiple types of information and may represent systems-level behaviour. Interpreting these is not straightforward, the biological implications network properties unclear. Analysis allows researchers predict hub species interactions. Additionally, such analyses can help identify alternative states niches. Here, we review factors that result in spurious predictions address emergent be meaningful context microbiome. We also give overview studies analyse new hypotheses. Moreover, show a simulation how affected by choice environmental factors. For example, consistent across tools, heterogeneity induces modularity. highlight need for robust inference suggest strategies infer more reliably.

Язык: Английский

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Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria

Science, Год журнала: 2017, Номер 356(6340)

Опубликована: Май 25, 2017

Within the plant microbiota, mutualistic fungal and bacterial symbionts are striking examples of microorganisms playing crucial roles in nutrient acquisition. They have coevolved with their hosts since initial adaptation to land. Despite evolutionary distances that separate mycorrhizal nitrogen-fixing symbioses, these associations share a number highly conserved features, including specific symbiotic signaling pathways, root colonization strategies circumvent immune responses, functional host-microbe interface formation, central role phytohormones symbiosis-associated developmental pathways. We highlight recent emerging areas investigation relating evolutionarily mechanisms, an emphasis on more ancestral associations, consider what extent this knowledge can contribute understanding plant-microbiota as whole.

Язык: Английский

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The structure and function of the global citrus rhizosphere microbiome

Nature Communications, Год журнала: 2018, Номер 9(1)

Опубликована: Ноя. 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

Язык: Английский

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Drought Stress Results in a Compartment-Specific Restructuring of the Rice Root-Associated Microbiomes

mBio, Год журнала: 2017, Номер 8(4)

Опубликована: Июль 19, 2017

ABSTRACT Plant roots support complex microbial communities that can influence plant growth, nutrition, and health. While extensive characterizations of the composition spatial compartmentalization these have been performed in different species, there is relatively little known about impact abiotic stresses on root microbiota. Here, we used rice as a model to explore responses microbiomes drought stress. Using four distinct genotypes, grown soils from three fields, tracked drought-induced changes rhizosphere (the soil immediately surrounding root), endosphere interior), unplanted soils. Drought significantly altered overall bacterial fungal compositions all communities, with compartments showing greatest divergence well-watered controls. The response microbiota stress was taxonomically consistent across cultivars primarily driven by an enrichment multiple Actinobacteria Chloroflexi , well depletion several Acidobacteria Deltaproteobacteria . some overlap observed drought-responsive taxa were compartment specific, pattern likely arising preexisting compositional differences, plant-mediated processes affecting individual compartments. These results reveal stress, addition its well-characterized effects physiology, also restructuring suggest possibility constituents might contribute survival under extreme environmental conditions. IMPORTANCE With likelihood global climate will adversely affect crop yields, potential role enhancing performance makes it important elucidate variation. By detailed characterization effect root-associated rice, show undergo major involve shifts relative abundances diverse set bacteria drought. microbes, particular those enriched water deficit conditions, could potentially benefit they tolerance other stresses, provide protection opportunistic infection pathogenic microbes. identification future isolation microbes promote be mitigate losses adverse climate.

Язык: Английский

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Transmission of Bacterial Endophytes

Microorganisms, Год журнала: 2017, Номер 5(4), С. 70 - 70

Опубликована: Ноя. 10, 2017

Plants are hosts to complex communities of endophytic bacteria that colonize the interior both below- and aboveground tissues. Bacteria living inside plant tissues as endophytes can be horizontally acquired from environment with each new generation, or vertically transmitted generation via seed. A better understanding bacterial endophyte transmission routes modes will benefit studies plant–endophyte interactions in agricultural natural ecosystems. In this review, we provide an overview take plants, including seeds pollen, soil, atmosphere, insects. We discuss well-documented understudied routes, identify gaps our knowledge on how reach plants. Where little is available endophytes, draw pathogens potential routes. Colonization roots soil best studied route, probably most important, although more aerial parts stomatal colonization needed, conclusively confirm vertical transfer. While transfer likely occurs, obligate strictly transferred symbioses unusual Instead, plants appear ability respond a changing by acquiring its microbiome anew over lifetime individuals.

Язык: Английский

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Biofertilizers: An ecofriendly technology for nutrient recycling and environmental sustainability

Current Research in Microbial Sciences, Год журнала: 2021, Номер 3, С. 100094 - 100094

Опубликована: Дек. 20, 2021

Modern intensive agricultural practices face numerous challenges that pose major threats to global food security. In order address the nutritional requirements of ever-increasing world population, chemical fertilizers and pesticides are applied on large scale increase crop production. However, injudicious use agrochemicals has resulted in environmental pollution leading public health hazards. Moreover, agriculture soils continuously losing their quality physical properties as well (imbalance nutrients) biological health. Plant-associated microbes with plant growth- promoting traits have enormous potential solve these play a crucial role enhancing biomass yield. The beneficial mechanisms growth improvement include enhanced nutrient availability, phytohormone modulation, biocontrol phytopathogens amelioration biotic abiotic stresses. Solid-based or liquid bioinoculant formulation comprises inoculum preparation, addition cell protectants such glycerol, lactose, starch, good carrier material, proper packaging best delivery methods. Recent developments entrapment/microencapsulation, nano-immobilization microbial bioinoculants biofilm-based biofertilizers. This review critically examines current state-of-art strains biofertilizers important roles performed by maintaining soil fertility productivity.

Язык: Английский

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Field study reveals core plant microbiota and relative importance of their drivers

Environmental Microbiology, Год журнала: 2017, Номер 20(1), С. 124 - 140

Опубликована: Дек. 21, 2017

Harnessing plant microbiota can assist in sustainably increasing primary productivity to meet growing global demands for food and biofuel. However, development of rational microbiome-based approaches improving crop yield is currently hindered by a lack understanding the major biotic abiotic factors shaping microbiome under relevant field conditions. We examined bacterial fungal communities associated with both aerial (leaves, stalks) belowground (roots, soil) compartments four commercial sugarcane varieties (Saccharum spp.) grown several regions Australia. identified drivers conditions evaluated whether plants shared core microbiome. Sugarcane-associated microbial assemblages were primarily determined compartment, followed region, age, variety Yellow Canopy Syndrome (YCS). detected set members that influenced YCS incidence. Our study revealed key hub microorganisms networks leaves, stalks, roots rhizosphere soil despite location time-associated shifts community assemblages. Elucidating their functional roles identification keystone sustain health could provide technological breakthrough sustainable increase productivity.

Язык: Английский

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Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere

Nature Ecology & Evolution, Год журнала: 2019, Номер 3(10), С. 1445 - 1454

Опубликована: Сен. 26, 2019

Язык: Английский

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Soil microbiome: a key player for conservation of soil health under changing climate

Biodiversity and Conservation, Год журнала: 2019, Номер 28(8-9), С. 2405 - 2429

Опубликована: Апрель 4, 2019

Язык: Английский

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