Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants

Turner, Thomas R.; Karunakaran, Ramakrishnan; Walshaw, John; Heavens, Darren; Alston, Mark; Swarbreck, David; Osbourn, Anne; Grant, Alastair; Poole, Philip S.

doi:10.1038/ismej.2013.119

Cited by 475 publications

(350 citation statements)

References 63 publications

(69 reference statements)

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“…A drawback of the GeoChip is the fact that novel functions and transcripts cannot be identified, and one is biased to the probes present in the chip (Dugat-Bony et al, 2012). Recently, metatranscriptomics in soil has been attempted on the rRNA to identify the active members of the microbial community in the rhizosphere of various crop species (Turner et al, 2013); Urich et al (2008) described the isolation and sequencing of mRNA from a sandy lawn as a means of describing the microbial transcriptome in the soil. The rhizosphere microbiome plays an essential role in plant health and productivity and it is often referred as the plant's second genome (Berendsen et al, 2012;Chaparro et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

Rhizosphere microbiome assemblage is affected by plant development

2013

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There is a concerted understanding of the ability of root exudates to influence the structure of rhizosphere microbial communities. However, our knowledge of the connection between plant development, root exudation and microbiome assemblage is limited. Here, we analyzed the structure of the rhizospheric bacterial community associated with Arabidopsis at four time points corresponding to distinct stages of plant development: seedling, vegetative, bolting and flowering. Overall, there were no significant differences in bacterial community structure, but we observed that the microbial community at the seedling stage was distinct from the other developmental time points. At a closer level, phylum such as Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and specific genera within those phyla followed distinct patterns associated with plant development and root exudation. These results suggested that the plant can select a subset of microbes at different stages of development, presumably for specific functions. Accordingly, metatranscriptomics analysis of the rhizosphere microbiome revealed that 81 unique transcripts were significantly (Po0.05) expressed at different stages of plant development. For instance, genes involved in streptomycin synthesis were significantly induced at bolting and flowering stages, presumably for disease suppression. We surmise that plants secrete blends of compounds and specific phytochemicals in the root exudates that are differentially produced at distinct stages of development to help orchestrate rhizosphere microbiome assemblage.

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Section: Discussionmentioning

confidence: 99%

Rhizosphere microbiome assemblage is affected by plant development

2013

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“…According to the UK Soil Observatory, the soil can be classified as Luvisol (WRB classification) and the soil texture was loamy with bits of chalk in the layer below the top layer. This soil was chosen as the history of its plant coverage is well documented and the microbial communities have been characterised in a previous study (Turner et al, 2013b).…”

Section: Methodsmentioning

confidence: 99%

“…However, interaction between plants and microbes is more general with plants shown to shape the rhizosphere microbiota in legumes, potatoes and suppressive soils (Sharma et al, 2005;Lebreton et al, 2007;Manter et al, 2010;Kinkel et al, 2011;Mendes et al, 2011;Turner et al, 2013b). Some microbial root colonists are saprophytes, which also colonise splinters of wood inserted into soil (Bulgarelli et al, 2012), but others are selected by exudation of nutrient sources and phytoalexins, such as glucosinolates and avenacins (Sonderby et al, 2007;Bressan et al, 2009;Turner et al, 2013b).…”

Section: Introductionmentioning

confidence: 99%

“…Some microbial root colonists are saprophytes, which also colonise splinters of wood inserted into soil (Bulgarelli et al, 2012), but others are selected by exudation of nutrient sources and phytoalexins, such as glucosinolates and avenacins (Sonderby et al, 2007;Bressan et al, 2009;Turner et al, 2013b). Furthermore, by altering the rhizosphere microbiota, plants induce formation of suppressive soil where growth of plant pathogens is inhibited (Lebreton et al, 2007;Kinkel et al, 2011;Mendes et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

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Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition

et al. 2015

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We examined succession of the rhizosphere microbiota of three model plants (Arabidopsis, Medicago and Brachypodium) in compost and sand and three crops (Brassica, Pisum and Triticum) in compost alone. We used serial inoculation of 24 independent replicate microcosms over three plant generations for each plant/soil combination. Stochastic variation between replicates was surprisingly weak and by the third generation, replicate microcosms for each plant had communities that were very similar to each other but different to those of other plants or unplanted soil. Microbiota diversity remained high in compost, but declined drastically in sand, with bacterial opportunists and putative autotrophs becoming dominant. These dramatic differences indicate that many microbes cannot thrive on plant exudates alone and presumably also require carbon sources and/or nutrients from soil. Arabidopsis had the weakest influence on its microbiota and in compost replicate microcosms converged on three alternative community compositions rather than a single distinctive community. Organisms selected in rhizospheres can have positive or negative effects. Two abundant bacteria are shown to promote plant growth, but in Brassica the pathogen Olpidium brassicae came to dominate the fungal community. So plants exert strong selection on the rhizosphere microbiota but soil composition is critical to its stability. microbial succession/ plant-microbe interactions/rhizosphere microbiota/selection.

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“…Previous studies showed that aerated forest, rice field, grassland soil and rhizosphere soil can harbor diverse methylotrophic communities (Lueders et al 2004;Radajewski et al 2002;Turner et al 2013;Stacheter et al 2013;Eyice et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Culture-dependent and culture-independent methods reveal diverse methylotrophic communities in terrestrial environments

Eyice

Schäfer

2015

Arch Microbiol

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Original citation:Eyice, Özge and Schäfer, Hendrik. (2015) Culture-dependent and culture-independent methods reveal diverse methylotrophic communities in terrestrial environments. Archives of Microbiology. Permanent WRAP url:http://wrap.warwick.ac.uk/73935 Copyright and reuse:The Warwick Research Archive Portal (WRAP) makes this work by researchers of the University of Warwick available open access under the following conditions. Copyright © and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. To the extent reasonable and practicable the material made available in WRAP has been checked for eligibility before being made available.Copies of full items can be used for personal research or study, educational, or not-for profit purposes without prior permission or charge. Provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way. Publisher's statement:The final publication is available at Springer via http://dx.doi.org/10.1007/s00203-015-1160-x A note on versions: The version presented here may differ from the published version or, version of record, if you wish to cite this item you are advised to consult the publisher's version. Please see the 'permanent WRAP url' above for details on accessing the published version and note that access may require a subscription. They are suggested to affect atmospheric chemistry and global climate. Methylotrophic microorganisms are considered as a significant sink for these compounds, therefore we analysed the diversity of terrestrial bacteria that utilise methanol, DMS and DMSO as carbon and energy source using culture-dependent and -independent methods. The effect of habitat type on the methylotrophic community structure was also investigated in rhizosphere and bulk soil. While thirteen strains affiliated to the genera

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Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants

Cited by 475 publications

References 63 publications

Rhizosphere microbiome assemblage is affected by plant development

Rhizosphere microbiome assemblage is affected by plant development

Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition

Culture-dependent and culture-independent methods reveal diverse methylotrophic communities in terrestrial environments

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