Shared and host‐specific microbiome diversity and functioning of grapevine and accompanying weed plants

Samad, Abdul; Trognitz, Friederike; Compant, Stéphane; Antonielli, Livio; Sessitsch, Angela

doi:10.1111/1462-2920.13618

Cited by 108 publications

(70 citation statements)

References 96 publications

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“…In addition, the bacterial community structures were markedly different (p < 0.05) in the BS, RZS, RS, and TS samples between non-stony and stony soils, but there was no signi cant difference (p > 0.05) within the same soil type, based on the ANOSIM analysis (Table 2), further indicating that the soil microbiota induced by stony soils largely changed the microbiota of RS and TS in T. hemsleyanum. This was consistent with the observation that soil type was a major driver of microbiota in the root environment [34].…”

Section: Discussionsupporting

confidence: 92%

Soil bacterial communities associated with stony soils influence the tuber size of Tetrastigma hemsleyanum

Guo¹,

Hong²,

Zhang³

et al. 2020

Preprint

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Background Plants grown in stony soils have better-developed root systems and higher crop yields than those grown in non-stony soils. The roles of various physical and chemical effects of stony soils on plant growth have been published, but the roles of soil microbiota and rhizosphere microbiota have not been investigated. Methods Tetrastigma hemsleyanum plants were cultivated for two years in stony soils and in the same soil from which rock-fragments had been removed. The microbiome and the tuber transcriptome were analyzed, using multiple bioinformatics methods. Results The soil microbiota of these two soils were markedly different, and the stony soils contained high abundances of bacterial taxa belonging to the Actinobacteria, Rokubacteria, Rhizobiales, Desulfarculaceae, and Chthoniobacteraceae. These discriminatory taxa in soils may promote the tuber growth of T. hemsleyanum, through releasing nutrients from rocks and colonizing the rhizosphere and tuber surface of T. hemsleyanum. In addition, stony soils induced a dramatic change in the tuber’s transcriptome, particularly with respect to the pathways of phytohormone biosynthesis, photosynthesis, and biotic stress resistance, expression levels of which showed strong correlations with the aforementioned bacterial taxa. Conclusions These results indicated that beneficial effects of stony soils on plant growth may be closely correlated with their specific microbiota, which can, in turn, influence multiple biological processes of host. This is the first study to reveal the role of stony soils-driven microbiota in tuber growth, and stony soils can represent a microbial repository for the screening of microbial isolates to increase plant yield.

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Section: Discussionsupporting

confidence: 92%

Soil bacterial communities associated with stony soils influence the tuber size of Tetrastigma hemsleyanum

Guo¹,

Hong²,

Zhang³

et al. 2020

Preprint

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“…Our results demonstrated that the soil and rhizosphere associated with Dioon coralloid roots are highly diverse. As with other plants [25,66,67], the soil (bulk soil and rhizosphere) is more diverse in the number of OTUs and genera than the root endosphere, although these differences are not significant in our study (alpha diversity metrics). When we compared the rhizosphere and endosphere from the six Dioon samples (set 3 comparison), we found significant differences in the alpha diversity, with higher diversity on the outside than the inside of coralloid root, a common pattern reported previously in 30 species of angiosperms [68].…”

Section: A Taxonomically Diverse Bacterial Community Inside Dioon Corcontrasting

confidence: 56%

Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genusDioon

Suárez-Moo

Vovides

Griffith

et al. 2018

Preprint

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Cycads are among the few plants that have developed specialized roots to host nitrogenfixing bacteria. We describe the bacterial diversity of the coralloid roots from seven Dioon species and their surrounding rhizosphere and soil. Using 16S rRNA gene amplicon sequencing, we found that all coralloid roots are inhabited by a broad diversity of bacterial groups, including cyanobacteria and Rhizobiales among the most abundant groups. The diversity and composition of the endophytes are similar in the six Mexican species of Dioon that we evaluated, suggesting a recent divergence of Dioon populations and/or similar plantdriven restrictions in maintaining the coralloid root microbiome. Botanical garden samples and natural populations have a similar taxonomic composition, although the beta diversity differed between these populations. The rhizosphere surrounding the coralloid root serves as a reservoir and source of mostly diazotroph and plant growth-promoting groups that colonize the coralloid endosphere. In the case of cyanobacteria, the endosphere is enriched with Nostoc spp and Calothrix spp that are closely related to previously reported symbiont genera in cycads and other early divergent plants. The data reported here provide an in-depth taxonomic characterization of the bacterial community associated with coralloid root microbiome. The functional aspects of the endophytes, their biological interactions, and their evolutionary history are the next research step in this recently discovered diversity within the cycad coralloid root microbiome.

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“…NGS-based metagenomics is now contributing to deeper insights into the plant microbiome associations and interactions (Lebeis 2015, Samad et al 2017). Tissue culture system provided a good tool to study the microbial endophytes protected from environmental organisms.…”

Section: Discussionmentioning

confidence: 99%

Diverse cellular colonizing endophytic bacteria in field shoots and in vitro cultured papaya with physiological and functional implications

Thomas

Agrawal

Bharathkumar

2018

Physiologia Plantarum

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The study was envisaged to assess the extent of normally uncultivable endophytic bacteria in field papaya plants and in vitro established cultures adopting cultivation vs molecular analysis and microscopy. Surface-sterilized axillary shoot-buds of papaya 'Arka Surya' revealed high bacterial diversity as per 16S rRNA metagene amplicon sequencing (6 phyla, 10 classes, 21 families) with an abundance of Pseudomonas (Gammaproteobacteria), which also formed a common contaminant for in vitro cultured field explants. Molecular analysis of seedling shoot-tip-derived healthy proliferating cultures of three genotypes ('Arka Surya', 'Arka Prabhath', 'Red Lady') with regular monthly subculturing also displayed high bacterial diversity (11-16 phyla, >25 classes, >50 families, >200 genera) about 12-18 months after initial establishment. 'Arka Surya' and 'Red Lady' cultures bore predominantly Actinobacteria (75-78%) while 'Arka Prabhath' showed largely Alphaproteobacteria corroborating the slowly activated Methylobacterium sp. Bright-field direct microscopy on tissue sections and tissue homogenate and epi-fluorescence microscopy employing bacterial DNA probe SYTO-9 revealed abundant intracellular bacteria embracing the next-generation sequencing elucidated high taxonomic diversity. Phylogenetic investigation of communities by reconstruction of unobserved states- PICRUSt- functional annotation suggested significant operational roles for the bacterial-biome. Metabolism, environmental information processing, and genetic information processing constituted major Kyoto Encyclopedia of Genes and Genomes KEGG attributes. Papaya stocks occasionally displayed bacterial growth on culture medium arising from the activation of originally uncultivable organisms to cultivation. The organisms included Bacillus (35%), Methylobacterium (15%), Pseudomonas (10%) and seven other genera (40%). This study reveals a hidden world of diverse and abundant conventionally uncultivable cellular-colonizing endophytic bacteria in field shoots and micropropagating papaya stocks with high genotypic similarity and silent participation in various plant processes/pathways.

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Shared and host‐specific microbiome diversity and functioning of grapevine and accompanying weed plants

Cited by 108 publications

References 96 publications

Soil bacterial communities associated with stony soils influence the tuber size of Tetrastigma hemsleyanum

Soil bacterial communities associated with stony soils influence the tuber size of Tetrastigma hemsleyanum

Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genusDioon

Diverse cellular colonizing endophytic bacteria in field shoots and in vitro cultured papaya with physiological and functional implications

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