Influence of plant genotype and soil on the wheat rhizosphere microbiome: evidences for a core microbiome across eight African and European soils DOI Open Access
Marie Simonin,

Cindy Dasilva,

Valeria Terzi

и другие.

FEMS Microbiology Ecology, Год журнала: 2020, Номер 96(6)

Опубликована: Апрель 7, 2020

ABSTRACT Here, we assessed the relative influence of wheat genotype, agricultural practices (conventional vs organic) and soil type on rhizosphere microbiome. We characterized prokaryotic (archaea bacteria) eukaryotic (fungi protists) communities in soils from four different countries (Cameroon, France, Italy, Senegal) determined if a core microbiome existed across these countries. The genotype had limited effect (2% variance) as majority microbial taxa were consistently associated to multiple genotypes grown same soil. Large differences richness community structure observed between eight studied (57% two (10% variance). Despite soils, that 177 (2 archaea, 103 bacteria, 41 fungi 31 detected rhizosphere, constituting In addition being prevalent, highly abundant collectively represented 50% reads our data set. Based results, identify list key future targets culturomics, metagenomics synthetic microbiomes. Additionally, show protists are an integral part holobiont is currently overlooked.

Язык: Английский

Plant–microbiome interactions: from community assembly to plant health DOI
Pankaj Trivedi, Jan E. Leach, Susannah G. Tringe

и другие.

Nature Reviews Microbiology, Год журнала: 2020, Номер 18(11), С. 607 - 621

Опубликована: Авг. 12, 2020

Язык: Английский

Процитировано

2416
Keystone taxa as drivers of microbiome structure and functioning DOI
Samiran Banerjee, Klaus Schlaeppi, Marcel G. A. van der Heijden

и другие.

Nature Reviews Microbiology, Год журнала: 2018, Номер 16(9), С. 567 - 576

Опубликована: Май 22, 2018

Язык: Английский

Процитировано

2152
A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application DOI Creative Commons
Stéphane Compant, Abdul Samad, Hanna Faist

и другие.

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

Процитировано

1141
Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots DOI Creative Commons
Samiran Banerjee, Florian Walder, Lucie Büchi

и другие.

The ISME Journal, Год журнала: 2019, Номер 13(7), С. 1722 - 1736

Опубликована: Март 8, 2019

Root-associated microbes play a key role in plant performance and productivity, making them important players agroecosystems. So far, very few studies have assessed the impact of different farming systems on root microbiota it is still unclear whether agricultural intensification influences structure complexity microbial communities. We investigated conventional, no-till, organic wheat fungal communities using PacBio SMRT sequencing samples collected from 60 farmlands Switzerland. Organic harbored much more complex network with significantly higher connectivity than conventional no-till systems. The abundance keystone taxa was highest under where lowest. also found strong negative association (R2 = 0.366; P < 0.0001) between connectivity. occurrence best explained by soil phosphorus levels, bulk density, pH, mycorrhizal colonization. majority are known to form arbuscular associations plants belong orders Glomerales, Paraglomerales, Diversisporales. Supporting this, fungi roots soils farming. To our knowledge, this first study report for agroecosystems, we demonstrate that reduces microbiome.

Язык: Английский

Процитировано

974
Core microbiomes for sustainable agroecosystems DOI
Hirokazu Toju, Kabir Peay, Masato Yamamichi

и другие.

Nature Plants, Год журнала: 2018, Номер 4(5), С. 247 - 257

Опубликована: Апрель 24, 2018

Язык: Английский

Процитировано

807
Host selection shapes crop microbiome assembly and network complexity DOI Creative Commons
Chao Xiong, Yong‐Guan Zhu, Juntao Wang

и другие.

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

Процитировано

514
Crying out for help with root exudates: adaptive mechanisms by which stressed plants assemble health-promoting soil microbiomes DOI
Stephen A. Rolfe,

Joseph Griffiths,

Jurriaan Ton

и другие.

Current Opinion in Microbiology, Год журнала: 2019, Номер 49, С. 73 - 82

Опубликована: Июнь 1, 2019

Язык: Английский

Процитировано

377
Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation DOI Creative Commons

Phillipe M. Rosado,

Deborah Catharine de Assis Leite, Gustavo Duarte

и другие.

The ISME Journal, Год журнала: 2018, Номер 13(4), С. 921 - 936

Опубликована: Дек. 5, 2018

Abstract Although the early coral reef-bleaching warning system (NOAA/USA) is established, there no feasible treatment that can minimize temperature bleaching and/or disease impacts on corals in field. Here, we present first attempts to extrapolate widespread and well-established use of bacterial consortia protect or improve health other organisms (e.g., humans plants) corals. Manipulation coral-associated microbiome was facilitated through addition a consortium native (isolated from Pocillopora damicornis surrounding seawater) putatively beneficial microorganisms for (pBMCs), including five Pseudoalteromonas sp., Halomonas taeanensis Cobetia marina-related species strains. The results controlled aquarium experiment two regimes (26 °C 30 °C) four treatments (pBMC; pBMC with pathogen challenge – Vibrio coralliilyticus, VC; challenge, control) revealed ability partially mitigate bleaching. Significantly reduced coral-bleaching metrics were observed pBMC-inoculated corals, contrast controls without addition, especially challenged which displayed strong signs as indicated by significantly lower photopigment contents Fv/Fm ratios. structure community also differed between specific bioindicators correlated inoculated sp.) VC Ruegeria sp.). Our indicate be manipulated lessen effect bleaching, thus helping alleviate stresses, BMCs representing promising novel approach minimizing mortality face increasing environmental impacts.

Язык: Английский

Процитировано

371
Plant Microbiome Engineering: Expected Benefits for Improved Crop Growth and Resilience DOI

Inessa Arif,

Maria Batool, Peer M. Schenk

и другие.

Trends in biotechnology, Год журнала: 2020, Номер 38(12), С. 1385 - 1396

Опубликована: Май 22, 2020

Язык: Английский

Процитировано

342
Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment DOI Creative Commons
Muneer Ahmad Malla, Anamika Dubey, Ashwani Kumar

и другие.

Frontiers in Immunology, Год журнала: 2019, Номер 9

Опубликована: Янв. 6, 2019

The interaction between the human microbiome and immune system has an effect on several metabolic functions impacts our well-being. Additionally, humans microbes can also play a key role in determining wellness or disease status of body. Dysbiosis is related to plethora diseases, including skin, inflammatory, metabolic, neurological disorders. A better understanding host-microbe essential for diagnosis appropriate treatment these ailments. significance host health led emergence new therapeutic approaches focused prescribed manipulation microbiome, either by removing harmful taxa reinstating missing beneficial functional roles they perform. Culturing large numbers microbial laboratory problematic at best, if not impossible. Consequently, this makes it very difficult comprehensively catalogue individual members comprising specific as well how communities function influence host-pathogen interactions. Recent advances sequencing technologies computational tools have allowed increasing number metagenomic studies be performed. These provided insights into other environments. In present review, agent its discussed. Advances high-throughput surveying interactions are correlation composition infectious diseases described previously reported covered well. Lastly, recent state-of-the-art bioinformatics software, workflows, applications analysing data summarized.

Язык: Английский

Процитировано

296