Let the Core Microbiota Be Functional

Lemanceau, Philippe; Blouin, Manuel; Müller, Daniel; Moënne‐Loccoz, Yvan

doi:10.1016/j.tplants.2017.04.008

Cited by 350 publications

(269 citation statements)

References 88 publications

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“…The core microbiome is considered to be a key component of the basic function of the holobionts, which is enriched, selected, and inherited through evolutionary processes (Lemanceau, Blouin, Muller, & Moënne-Loccoz, 2017). The core microbiomes are commonly used to reveal microbial species that are closely related to the health, growth, and physiology of the host plant and are currently widely used to describe the key species in human, soil, plant, lake, and wastewater treatment system (Chen, Wu, et al, 2018;Chen, Li, et al, 2018;Ji, Parks, Edwards, & Pruden, 2015;Turnbaugh et al, 2007;Zarraonaindia et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Characterization of the core microbiome in tobacco leaves during aging

Zhou

Zhang

et al. 2020

MicrobiologyOpen

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Microbiome plays an important role during the tobacco aging process which was an indispensable link in the production and processing of cigarettes. However, the structure and functions of microbiome have not been clarified during the tobacco aging process. In this study, 16S rDNA and ITS amplicon sequencing techniques were used to analyze the core microbiome of 15 tobacco samples from five different aging stages. The whole bacterial microbiome was classified into 29 microbial phyla and 132 orders. Enterobacteriales (63%), Pseudomonadales (16%), Sphingomonadales (8%), Xanthomonadales (4%), Burkholderiales (4%), Rhizobiales (3%), and Bacillales (2%) comprised the core bacterial microbiome. The whole fungal microbiome was classified into five microbial phyla and 52 orders. Incertae_sedis_Eurotiomycetes (27%), Wallemiales (25%), Sporidiobolales (17%), Capnodiales (5%), Eurotiales (2%), an unclassified Ascomycota (12%), and an unidentified Eurotiomycetes (4%) comprised the core fungal microbiome. FAPROTAX function prediction suggested that the core microbiome has a substantial potential for the carbon cycle, nitrate metabolism, aromatic compound degradation, chitinolysis, cellulolysis, and xylanolysis, but simultaneously, the core microbiome is also a source of human pathogens. The dynamics of the bacterial community were primarily determined by the total nitrogen in tobacco leaves during the aging process, while those of the fungal microbiome were primarily determined by total organic carbon. This study indicated that the core microbiome activities may play an important role in regulating the loss of carbon organic compounds and enhancing the secondary metabolites during tobacco leaves aging process.

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Section: Introductionmentioning

confidence: 99%

Characterization of the core microbiome in tobacco leaves during aging

Zhou

Zhang

et al. 2020

MicrobiologyOpen

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“…Exploring ways to manage entire microbial communities with beneficial functions on plant nutrition and health (i.e. functional microbiomes) is a recognized research priority (Lemanceau et al, 2017;Toju et al, 2018). Under field conditions, microbial community assembly from the plant's surrounding environment defines which taxa and potential functions will assist plant health and growth.…”

Section: Introductionmentioning

confidence: 99%

Different ecological processes drive the assembly of dominant and rare root-associated bacteria in a promiscuous legume

Ramoneda

Roux

Frossard

et al. 2020

Preprint

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Understanding how plant-associated microbial communities assemble and the roles they play in plant performance are major goals in microbial ecology. For nitrogen-fixing rhizobia, assemblages are mostly determined by filtering by the host as well as abiotic soil conditions. However, for legumes adapted to highly variable environments and nutrient-poor soils, filtering out rhizobial partners may not be an effective strategy to ensure symbiotic benefits. As a consequence, this can lead to net increases in rhizobial diversity driven by stochastic (neutral) assembly processes. Here, we addressed whether symbiotic promiscuity of rooibos (Aspalathus linearis Burm. Dahlgren), reflects increases in rhizobial diversity that are independent of the environmental conditions, following a neutral assembly. We performed a common garden experiment to assess whether root system size and location-and habitat-specific rhizobial propagule pools of rooibos affected rhizobial community diversity and composition. We found a dominance of drift in driving taxonomic turnover in the root nodule communities, but operating at different scales in the dominant Mesorhizobium symbionts and the rest of bacterial taxa. Specifically, drift triggered differentiation between the core rhizobial symbionts of rooibos due to dispersal limitation on a regional scale, whereas it dominated the assembly of non-dominant rhizobial taxa at the root level. This suggests the existence of a significant neutral component in rhizobial community assembly when selectivity by the host plant is low. We conclude that in this promiscuous legume neutral processes govern bacterial community root nodule community assembly, but that these operate at different scales in dominant and rare rhizobial symbionts of the plant.

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“…Nevertheless, we show that the core microbiota resulting from macroorganism interaction can be highlighted on a phylogenetic basis, with a taxa-specific phylogenetic signal. A perspective based on an adaptive rational would be to investigate these multiple-macroorganisms core microbiota and core network on a functional basis 19…”

Section: Resultsmentioning

confidence: 99%