Microbiome definition re-visited: old concepts and new challenges

Microbiome, Journal Year: 2020, Volume and Issue: 8(1)

Published: June 30, 2020

The field of microbiome research has evolved rapidly over the past few decades and become a topic great scientific public interest. As result this rapid growth in interest covering different fields, we are lacking clear commonly agreed definition term "microbiome." Moreover, consensus on best practices is missing. Recently, panel international experts discussed current gaps frame European-funded MicrobiomeSupport project. meeting brought together about 40 leaders from diverse areas, while more than hundred all world took part an online survey accompanying workshop. This article excerpts outcomes workshop corresponding embedded short historical introduction future outlook. We propose based compact, clear, comprehensive description provided by Whipps et al. 1988, amended with set novel recommendations considering latest technological developments findings. clearly separate terms microbiota provide discussion composition microbiota, heterogeneity dynamics microbiomes time space, stability resilience microbial networks, core microbiomes, functionally relevant keystone species as well co-evolutionary principles microbe-host inter-species interactions within microbiome. These broad definitions suggested unifying concepts will help to improve standardization studies future, could be starting point for integrated assessment data resulting transfer knowledge basic science into practice. Furthermore, standards important solving new challenges associated anthropogenic-driven changes planetary health, which understanding might play key role. Video Abstract.

Language: 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, Journal Year: 2018, Volume and Issue: 9

Published: Oct. 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.

Language: Английский

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Research priorities for harnessing plant microbiomes in sustainable agriculture

PLoS Biology, Journal Year: 2017, Volume and Issue: 15(3), P. e2001793 - e2001793

Published: March 28, 2017

Feeding a growing world population amidst climate change requires optimizing the reliability, resource use, and environmental impacts of food production. One way to assist in achieving these goals is integrate beneficial plant microbiomes—i.e., those enhancing growth, nutrient use efficiency, abiotic stress tolerance, disease resistance—into agricultural This integration will require large-scale effort among academic researchers, industry farmers understand manage plant-microbiome interactions context modern systems. Here, we identify priorities for research this area: (1) develop model host–microbiome systems crop plants non-crop with associated microbial culture collections reference genomes, (2) define core microbiomes metagenomes systems, (3) elucidate rules synthetic, functionally programmable microbiome assembly, (4) determine functional mechanisms interactions, (5) characterize refine genotype-by-environment-by-microbiome-by-management interactions. Meeting should accelerate our ability design implement effective manipulations management strategies, which, turn, pay dividends both consumers producers supply.

Language: Английский

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Rhizosphere microbiome structure alters to enable wilt resistance in tomato

Nature Biotechnology, Journal Year: 2018, Volume and Issue: 36(11), P. 1100 - 1109

Published: Oct. 8, 2018

Language: Английский

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

The ISME Journal, Journal Year: 2017, Volume and Issue: 11(12), P. 2691 - 2704

Published: July 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.

Language: Английский

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Plant microbial diversity is suggested as the key to future biocontrol and health trends

FEMS Microbiology Ecology, Journal Year: 2017, Volume and Issue: 93(5)

Published: April 19, 2017

The microbiome of plants plays a crucial role in both plant and ecosystem health. Rapid advances multi-omics tools are dramatically increasing access to the consequently identification its links with diseases control those diseases. Recent insights reveal close, often symbiotic relationship between microorganisms plants. Microorganisms can stimulate germination growth, prevent diseases, promote stress resistance general fitness. Plants their associated form holobiont have be considered as co-evolved species assemblages consisting bacterial, archaeal diverse eukaryotic species. beneficial interplay host is responsible for maintaining health holobiont, while correlated microbial dysbioses. Microbial diversity was identified key factor preventing implemented biomarker protection strategies. Targeted predictive biocontrol approaches possible by developing microbiome-based solutions. Moreover, combined breeding strategies required. analysis data has brought about paradigm shift our understanding disease substantial consequences issues.

Language: Английский

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Biostimulant Action of Protein Hydrolysates: Unraveling Their Effects on Plant Physiology and Microbiome

Frontiers in Plant Science, Journal Year: 2017, Volume and Issue: 8

Published: Dec. 22, 2017

Plant-derived protein hydrolysates (PHs) have gained prominence as plant biostimulants because of their potential to increase the germination, productivity and quality a wide range horticultural agronomic crops. Application PHs can also alleviate negative effects abiotic stress due salinity, drought heavy metals. Recent studies aimed at uncovering mechanisms regulating these beneficial indicate that could be directly affecting plants by stimulating carbon nitrogen metabolism, interfering with hormonal activity. Indirect play role enhance nutrient availability in growth substrates, uptake nutrient-use efficiency plants. Moreover, stimulation microbiomes. Plants are colonized an abundant diverse assortment microbial taxa help acquire nutrients water withstand biotic stress. The substrates provided PHs, such amino acids, provide ideal food source for plant-associated microbes. Indeed, recent evidence microbiomes modified application supporting hypothesis might acting, least part, via changes composition activity communities. has great meet twin challenges feeding growing population while minimizing agriculture's impact on human health environment. However, fully realize further required shed light conferring products, well identify product formulations methods optimize benefits under agro-ecological conditions.

Language: Английский

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The seed microbiome: Origins, interactions, and impacts

Plant and Soil, Journal Year: 2017, Volume and Issue: 422(1-2), P. 7 - 34

Published: May 24, 2017

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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Plant microbiome–an account of the factors that shape community composition and diversity

Current Plant Biology, Journal Year: 2020, Volume and Issue: 23, P. 100161 - 100161

Published: July 1, 2020

Plants live in association with diverse microorganisms, collectively called the microbiome. These microbes either inside (endosphere) or outside (episphere) of plant tissues. Microbes play important roles ecology and physiology plants. Significant progress has been made revealing structure dynamics microbiome last few years. Various factors related to host, as well environment influence community composition diversity This review aimed provide a general account (host, microbe environment) that drive microbial plant. First, we gave an overview aboveground belowground microbiomes. Next, discussed which host are involved variation plants followed by importance microbe-microbe interactions elements structuring

Language: Английский

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