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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Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

Nature Communications, Год журнала: 2021, Номер 12(1)

Опубликована: Март 31, 2021

Abstract Microorganisms play crucial roles in water recycling, pollution removal and resource recovery the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential absence high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read short-read recover 1083 MAGs, including 57 closed circular genomes, from 23 Danish full-scale treatment plants. MAGs account ~30% community relative abundance, meet stringent MIMAG draft requirements full-length genes. We information provided by combination with >13 years data, as well Raman microspectroscopy fluorescence situ hybridisation, uncover abundant undescribed lineages belonging important groups.

Язык: Английский

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Rethinking Crop Nutrition in Times of Modern Microbiology: Innovative Biofertilizer Technologies

Frontiers in Sustainable Food Systems, Год журнала: 2021, Номер 5

Опубликована: Фев. 19, 2021

Global population growth poses a threat to food security in an era of increased ecosystem degradation, climate change, soil erosion, and biodiversity loss. In this context, harnessing naturally-occurring processes such as those provided by plant-associated microorganisms presents promising strategy reduce dependency on agrochemicals. Biofertilizers are living microbes that enhance plant nutrition either mobilizing or increasing nutrient availability soils. Various microbial taxa including beneficial bacteria fungi currently used biofertilizers, they successfully colonize the rhizosphere, rhizoplane root interior. Despite their great potential improve fertility, biofertilizers have yet replace conventional chemical fertilizers commercial agriculture. last 10 years, multi-omics studies made significant step forward understanding drivers, roles, processes, mechanisms microbiome. However, translating knowledge microbiome functions order capitalize agroecosystems still remains challenge. Here, we address key factors limiting successful field applications suggest solutions based emerging strategies for product development. Finally, discuss importance biosafety guidelines propose new avenues research biofertilizer

Язык: Английский

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Synthetic biology 2020–2030: six commercially-available products that are changing our world

Nature Communications, Год журнала: 2020, Номер 11(1)

Опубликована: Дек. 11, 2020

Synthetic biology will transform how we grow food, what eat, and where source materials medicines. Here I have selected six products that are now on the market, highlighting underlying technologies projecting forward to future can be expected over next ten years.

Язык: Английский

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Polarization of microbial communities between competitive and cooperative metabolism

Nature Ecology & Evolution, Год журнала: 2021, Номер 5(2), С. 195 - 203

Опубликована: Янв. 4, 2021

Язык: Английский

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Machine learning for metabolic engineering: A review

Metabolic Engineering, Год журнала: 2020, Номер 63, С. 34 - 60

Опубликована: Ноя. 20, 2020

Machine learning provides researchers a unique opportunity to make metabolic engineering more predictable. In this review, we offer an introduction discipline in terms that are relatable engineers, as well providing in-depth illustrative examples leveraging omics data and improving production. We also include practical advice for the practitioner of management, algorithm libraries, computational resources, important non-technical issues. A variety applications ranging from pathway construction optimization, genetic editing cell factory testing, production scale-up discussed. Moreover, promising relationship between machine mechanistic models is thoroughly reviewed. Finally, future perspectives most directions combination disciplines examined.

Язык: Английский

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Can we control microbiota in spontaneous food fermentation? – Chinese liquor as a case example

Trends in Food Science & Technology, Год журнала: 2021, Номер 110, С. 321 - 331

Опубликована: Фев. 16, 2021

Fermented foods, with a history as long the human civilization, form an indispensable constituent in our daily life. However, most fermented foods are produced by spontaneous fermentation, and fermentation processes still uncontrolled. To ensure consistent food quality, it is of paramount importance to understand control fermentations. In fermentations, metabolic activity succession complex microbiota results desired flavour that key criterion decide consumers' preference. Therefore, compound formation microbial metabolism can be used target relatively little known about complexity associated formation. this review using Chinese liquor model system, we present biotechnological aspects crucial for including driving forces succession, formation, regulation Core microbiota, identified eventually construct synthetic (i.e. designed) microbiota. Meanwhile, environmental factors, affecting core also controlled regulate Furthermore, modelling predict, optimize so such fermentations become controllable, ultimate goal monitor, control, improve productivity safety foods.

Язык: Английский

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Design of synthetic human gut microbiome assembly and butyrate production

Nature Communications, Год журнала: 2021, Номер 12(1)

Опубликована: Май 31, 2021

The capability to design microbiomes with predictable functions would enable new technologies for applications in health, agriculture, and bioprocessing. Towards this goal, we develop a model-guided approach synthetic human gut production of the health-relevant metabolite butyrate. Our data-driven model quantifies microbial interactions impacting growth butyrate separately, providing key insights into ecological mechanisms driving production. We use our explore vast community space using design-test-learn cycle identify high butyrate-producing communities. can accurately predict assembly across wide range species richness. Guided by model, constraints on richness molecular factors production, including hydrogen sulfide, environmental pH, resource competition. In sum, provides flexible generalizable framework understanding predicting metabolic functions.

Язык: Английский

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Bacteria-driven phthalic acid ester biodegradation: Current status and emerging opportunities

Environment International, Год журнала: 2021, Номер 154, С. 106560 - 106560

Опубликована: Апрель 16, 2021

The extensive use of phthalic acid esters (PAEs) has led to their widespread distribution across various environments. As PAEs pose significant threats human health, it is urgent develop efficient strategies eliminate them from Bacteria-driven PAE biodegradation been considered as an inexpensive yet effective strategy restore the contaminated Despite great advances in bacterial culturing and sequencing, inherent complexity indigenous microbial community hinders us mechanistically understand situ efficiently harness degrading power bacteria. synthetic ecology provides a simple controllable model system address this problem. In review, we focus on current progress mediated by isolates communities, discuss prospective PAE-degrading communities research. It anticipated that theories approaches will revolutionize study bacteria-driven provide novel insights for developing bioremediation solutions.

Язык: Английский

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Solutions in microbiome engineering: prioritizing barriers to organism establishment

The ISME Journal, Год журнала: 2021, Номер 16(2), С. 331 - 338

Опубликована: Авг. 21, 2021

Abstract Microbiome engineering is increasingly being employed as a solution to challenges in health, agriculture, and climate. Often manipulation involves inoculation of new microbes designed improve function into preexisting microbial community. Despite, increased efforts microbiome inoculants frequently fail establish and/or confer long-lasting modifications on ecosystem function. We posit that one underlying cause these shortfalls the failure consider barriers organism establishment. This key challenge focus macroecology research, specifically invasion biology restoration ecology. adopt framework from summarizes establishment three categories: (1) propagule pressure, (2) environmental filtering, (3) biotic interactions factors. suggest most neglected factor we recommend number actions accelerate solutions.

Язык: Английский

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