Plant–microbiome interactions: from community assembly to plant health

Nature Reviews Microbiology, Journal Year: 2020, Volume and Issue: 18(11), P. 607 - 621

Published: Aug. 12, 2020

Language: Английский

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A practical guide to amplicon and metagenomic analysis of microbiome data

Protein & Cell, Journal Year: 2020, Volume and Issue: 12(5), P. 315 - 330

Published: May 11, 2020

Abstract Advances in high-throughput sequencing (HTS) have fostered rapid developments the field of microbiome research, and massive datasets are now being generated. However, diversity software tools complexity analysis pipelines make it difficult to access this field. Here, we systematically summarize advantages limitations methods. Then, recommend specific for amplicon metagenomic analyses, describe commonly-used databases, help researchers select appropriate tools. Furthermore, introduce statistical visualization methods suitable analysis, including alpha- beta-diversity, taxonomic composition, difference comparisons, correlation, networks, machine learning, evolution, source tracing, common styles informed choices. Finally, a step-by-step reproducible guide is introduced. We hope review will allow carry out data more effectively quickly order efficiently mine biological significance behind data.

Language: Английский

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Rhizosphere bacteriome structure and functions

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Feb. 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.

Language: Английский

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Biofertilizers: An ecofriendly technology for nutrient recycling and environmental sustainability

Current Research in Microbial Sciences, Journal Year: 2021, Volume and Issue: 3, P. 100094 - 100094

Published: Dec. 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.

Language: Английский

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Defining and quantifying the core microbiome: Challenges and prospects

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(51)

Published: Dec. 3, 2021

The term "core microbiome" has become widely used in microbial ecology over the last decade. Broadly, core microbiome refers to any set of taxa, or genomic and functional attributes associated with those that are characteristic a host environment interest. Most commonly, microbiomes measured as taxa shared among two more samples from particular environment. Despite popularity this its growing use, there is little consensus about how should be quantified practice. Here, we present brief history concept use representative sample literature review different metrics commonly for quantifying core. Empirical analyses have wide range microbiome, including arbitrary occurrence abundance cutoff values, focal taxonomic level ranging phyla amplicon sequence variants. However, many these susceptible sampling other biases. Developing standardized accounts such biases necessary testing specific hypotheses ecological roles microbiomes.

Language: Английский

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Abundance of kinless hubs within soil microbial networks are associated with high functional potential in agricultural ecosystems

Environment International, Journal Year: 2020, Volume and Issue: 142, P. 105869 - 105869

Published: June 25, 2020

Microbial taxa within complex ecological networks can be classified by their universal roles based on level of connectivity with other taxa. Highly connected an network (kinless hubs) are theoretically expected to support higher levels ecosystem functions than less (peripherals). Empirical evidence the role kinless hubs in regulating functional potential soil microbial communities, however, is largely unexplored and poorly understood agricultural ecosystems. Here, we built a correlation fungal bacterial using large-scale survey consisting 243 samples across functionally economically important ecosystems (wheat maize); found that relative abundance as positively significantly correlated genes including for C fixation, degradation, methanol, N cycling, P cycling S cycling. Structural equation modeling multiple properties further indicated hubs, but not provincial, connector or peripheral taxa, had direct significant positive relationships genes. Our findings provide novel associated high potential, implications understanding managing (through manipulating key species) at large spatial scale.

Language: Английский

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The root microbiome: Community assembly and its contributions to plant fitness

Journal of Integrative Plant Biology, Journal Year: 2022, Volume and Issue: 64(2), P. 230 - 243

Published: Jan. 14, 2022

The root microbiome refers to the community of microbes living in association with a plant's roots, and includes mutualists, pathogens, commensals. Here we focus on recent advances study commensal which is major research object microbiome-related researches. With rapid development new technologies, plant-commensal interactions can be explored unprecedented breadth depth. Both soil environment host plant drive assembly. bulk seed bank potential commensals, plants use exudates immune responses build healthy microbial communities from available microbes. extends functional system by participating variety processes, including nutrient absorption, growth promotion, resistance biotic abiotic stresses. Plants their microbiomes have evolved adaptation strategies over time. However, there still huge gap our understanding regulatory mechanisms interactions. In this review, summarize assembly effects these development, look at prospects for promoting sustainable agricultural through microbiome.

Language: Английский

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Enabling sustainable agriculture through understanding and enhancement of microbiomes

New Phytologist, Journal Year: 2021, Volume and Issue: 230(6), P. 2129 - 2147

Published: March 4, 2021

Summary Harnessing plant‐associated microbiomes offers an invaluable strategy to help agricultural production become more sustainable while also meeting growing demands for food, feed and fiber. A plethora of interconnected interactions among the host, environment microbes, occurring both above below ground, drive recognition, recruitment colonization resulting in activation downstream host responses functionality. Dissecting these complex by integrating multiomic approaches, high‐throughput culturing, computational synthetic biology advances is providing deeper understanding structure function native microbial communities. Such insights are paving way towards development products as well engineered with communities capable delivering agronomic solutions. While there a market microbial‐based solutions improve crop productivity, challenges commercialization remain. The continued translation microbiome knowledge into real‐world scenarios will require concerted transdisciplinary research, cross‐training next generation scientists, targeted educational efforts prime growers general public successful adoption innovative technologies.

Language: Английский

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Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogenXanthomonas

FEMS Microbiology Reviews, Journal Year: 2019, Volume and Issue: 44(1), P. 1 - 32

Published: Oct. 1, 2019

ABSTRACT Xanthomonas is a well-studied genus of bacterial plant pathogens whose members cause variety diseases in economically important crops worldwide. Genomic and functional studies these phytopathogens have provided significant understanding microbial-host interactions, virulence host adaptation mechanisms including microbial ecology epidemiology. In addition, several strains are as producers the extracellular polysaccharide, xanthan, used food pharmaceutical industries. This polymer has also been implicated phases disease cycle. this review, we summarise current knowledge on infection strategies regulatory networks controlling from species discuss novel opportunities that body work for control health.

Language: Английский

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From Microbiome to Traits: Designing Synthetic Microbial Communities for Improved Crop Resiliency

Frontiers in Plant Science, Journal Year: 2020, Volume and Issue: 11

Published: Aug. 27, 2020

Plants teem with microorganisms, whose tremendous diversity and role in plant-microbe interactions are being increasingly explored. Microbial communities create a functional bond their hosts express beneficial traits capable of enhancing plant performance. Therefore, significant task microbiome research has been identifying novel microbial that can contribute to crop productivity, particularly under adverse environmental conditions. However, although knowledge exponentially accumulated recent years, few methods regarding the process designing inoculants for agriculture have presented. A recently introduced approach is use synthetic (SynComs), which involves applying concepts from both ecology genetics design inoculants. Here, we discuss how translate this rationale delivering stable effective by tailoring SynComs microorganisms possessing robust colonization, prevalence throughout development specific functions plants. Computational methods, including machine learning artificial intelligence, will leverage approaches screening microbes while improving determining best combination desired phenotype. We focus on advances deepen our critically prospect using resiliency against stressful

Language: Английский

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