Microbiome definition re-visited: old concepts and new challenges

Microbiome, Год журнала: 2020, Номер 8(1)

Опубликована: Июнь 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.

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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A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application

Journal of Advanced Research, Год журнала: 2019, Номер 19, С. 29 - 37

Опубликована: Март 20, 2019

Plants have evolved with a plethora of microorganisms having important roles for plant growth and health. A considerable amount information is now available on the structure dynamics microbiota as well functional capacities isolated community members. Due to interesting potential due current challenges in crop production there an urgent need bring microbial innovations into practice. Different approaches microbiome improvement exist. On one hand strains or strain combinations can be applied, however, field success often variable urgently required. Smart, knowledge-driven selection needed use suitable delivery formulations. other hand, farming practices genotype influence thus functioning. Therefore, appropriate breeding leading improved plant-microbiome interactions are avenues increase benefit microbiota. In conclusion, different making new generation inoculants application microbiome-based agro-management lines could lead better microbiome. This paper reviews importance functionalities bacterial discusses concepts regard plant-associated bacteria.

Язык: Английский

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Environmental stress destabilizes microbial networks

The ISME Journal, Год журнала: 2021, Номер 15(6), С. 1722 - 1734

Опубликована: Янв. 15, 2021

Язык: Английский

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A specialized metabolic network selectively modulates Arabidopsis root microbiota

Science, Год журнала: 2019, Номер 364(6440)

Опубликована: Май 9, 2019

Mix of metabolites tunes root microbiota Uncharacterized biosynthetic genes in plant genomes suggest that plants make a plethora specialized metabolites. Huang et al. reconstructed three networks from the small mustard Arabidopsis thaliana . Promiscuous acyltransferases and dehydrogenases contributed to metabolite diversification. The may use these modulate surrounding its roots. Disruption pathways intervention with purified compounds caused changes microbiota. Science , this issue p. eaau6389

Язык: Английский

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Host selection shapes crop microbiome assembly and network complexity

New Phytologist, Год журнала: 2020, Номер 229(2), С. 1091 - 1104

Опубликована: Авг. 27, 2020

Plant microbiomes are essential to host health and productivity but the ecological processes that govern crop microbiome assembly not fully known. Here we examined bacterial communities across 684 samples from soils (rhizosphere bulk soil) multiple compartment niches (rhizoplane, root endosphere, phylloplane, leaf endosphere) in maize (Zea mays)-wheat (Triticum aestivum)/barley (Hordeum vulgare) rotation system under different fertilization practices at two contrasting sites. Our results demonstrate along soil-plant continuum is shaped predominantly by niche species rather than site or practice. From epiphytes endophytes, selection pressure sequentially increased diversity network complexity consequently reduced, with strongest effect endosphere. Source tracking indicates mainly derived gradually enriched filtered plant niches. Moreover, were dominated a few dominant taxa (c. 0.5% of phylotypes), bacilli identified as important biomarker for wheat barley Methylobacteriaceae maize. work provides comprehensive empirical evidence on selection, potential sources enrichment assembly, has implications future management manipulation sustainable agriculture.

Язык: Английский

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Initial soil microbiome composition and functioning predetermine future plant health

Science Advances, Год журнала: 2019, Номер 5(9)

Опубликована: Сен. 6, 2019

Soil microbiome composition and functioning determine the outcome of plant-pathogen interactions under natural field conditions.

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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Bacterial seed endophyte shapes disease resistance in rice

Nature Plants, Год журнала: 2021, Номер 7(1), С. 60 - 72

Опубликована: Янв. 4, 2021

Язык: Английский

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Disease-induced changes in plant microbiome assembly and functional adaptation

Microbiome, Год журнала: 2021, Номер 9(1)

Опубликована: Сен. 15, 2021

The plant microbiome is an integral part of the host and increasingly recognized as playing fundamental roles in growth health. Increasing evidence indicates that rhizosphere recruits beneficial microbes to suppress soil-borne pathogens. However, ecological processes govern assembly functions below- aboveground compartments under pathogen invasion are not fully understood. Here, we studied bacterial fungal communities associated with 12 (e.g., soils, roots, stems, fruits) chili pepper (Capsicum annuum L.) using amplicons (16S ITS) metagenomics approaches at main production sites China investigated how Fusarium wilt disease (FWD) affects assembly, co-occurrence patterns, plant-associated microbiomes.The amplicon data analyses revealed FWD affected less on reproductive organs (fruit) than vegetative (root stem), strongest impact upper stem epidermis. Fungal intra-kingdom networks were stable their more sensitive communities. analysis microbial interkingdom network further indicated destabilized induced importance taxa. Although diseased plants susceptible colonization by other pathogenic fungi, can also recruit potential bacteria. Some taxa enriched identified core for microbiomes hub networks. On hand, metagenomic significant enrichment several functional genes involved detoxification, biofilm formation, plant-microbiome signaling pathways (i.e., chemotaxis) plants.Together, demonstrate a could bacteria mitigate changes organ facilitate or its offspring survival. may attract through modulation pathways. These findings significantly advance our understanding interactions provide important harnessing sustainable agriculture. Video abstract.

Язык: Английский

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