Journal ArticleDOI
Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota
Davide Bulgarelli,Matthias Rott,Klaus Schlaeppi,Emiel Ver Loren van Themaat,Nahal Ahmadinejad,Federica Assenza,Philipp Rauf,Bruno Huettel,Richard Reinhardt,Elmon Schmelzer,Joerg Peplies,Frank Oliver Gloeckner,Rudolf Amann,Thilo Eickhorst,Paul Schulze-Lefert +14 more
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TLDR
Methodology is described to characterize and compare soil- and root-inhabiting bacterial communities, which reveals not only a function for metabolically active plant cells but also for inert cell-wall features in the selection of soil bacteria for host colonization.Abstract:
The plant root defines the interface between a multicellular eukaryote and soil, one of the richest microbial ecosystems on Earth. Notably, soil bacteria are able to multiply inside roots as benign endophytes and modulate plant growth and development, with implications ranging from enhanced crop productivity to phytoremediation. Endophytic colonization represents an apparent paradox of plant innate immunity because plant cells can detect an array of microbe-associated molecular patterns (also known as MAMPs) to initiate immune responses to terminate microbial multiplication. Several studies attempted to describe the structure of bacterial root endophytes; however, different sampling protocols and low-resolution profiling methods make it difficult to infer general principles. Here we describe methodology to characterize and compare soil- and root-inhabiting bacterial communities, which reveals not only a function for metabolically active plant cells but also for inert cell-wall features in the selection of soil bacteria for host colonization. We show that the roots of Arabidopsis thaliana, grown in different natural soils under controlled environmental conditions, are preferentially colonized by Proteobacteria, Bacteroidetes and Actinobacteria, and each bacterial phylum is represented by a dominating class or family. Soil type defines the composition of root-inhabiting bacterial communities and host genotype determines their ribotype profiles to a limited extent. The identification of soil-type-specific members within the root-inhabiting assemblies supports our conclusion that these represent soil-derived root endophytes. Surprisingly, plant cell-wall features of other tested plant species seem to provide a sufficient cue for the assembly of approximately 40% of the Arabidopsis bacterial root-inhabiting microbiota, with a bias for Betaproteobacteria. Thus, this root sub-community may not be Arabidopsis-specific but saprophytic bacteria that would naturally be found on any plant root or plant debris in the tested soils. By contrast, colonization of Arabidopsis roots by members of the Actinobacteria depends on other cues from metabolically active host cells.read more
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Journal ArticleDOI
Going back to the roots: the microbial ecology of the rhizosphere.
TL;DR: Recent developments in rhizosphere research are discussed in relation to assessing the contribution of the micro- and macroflora to sustainable agriculture, nature conservation, the development of bio-energy crops and the mitigation of climate change.
Journal ArticleDOI
Structure and functions of the bacterial microbiota of plants
Davide Bulgarelli,Klaus Schlaeppi,Stijn Spaepen,Stijn Spaepen,Emiel Ver Loren van Themaat,Paul Schulze-Lefert +5 more
TL;DR: The plant microbiota emerges as a fundamental trait that includes mutualism enabled through diverse biochemical mechanisms, as revealed by studies on plant growth- Promoting and plant health-promoting bacteria.
Journal ArticleDOI
Defining the core Arabidopsis thaliana root microbiome
Derek S. Lundberg,Sarah L. Lebeis,Sur Herrera Paredes,Scott Yourstone,Jase Gehring,Stephanie Malfatti,Julien Tremblay,Anna Engelbrektson,Anna Engelbrektson,Victor Kunin,Victor Kunin,Tijana Glavina del Rio,Robert C. Edgar,Thilo Eickhorst,Ruth E. Ley,Philip Hugenholtz,Philip Hugenholtz,Susannah G. Tringe,Jeffery L. Dangl +18 more
TL;DR: The pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants is reported to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages.
Journal ArticleDOI
Induced systemic resistance by beneficial microbes
Corné M. J. Pieterse,Christos Zamioudis,Roeland L. Berendsen,David M. Weller,Saskia C. M. Van Wees,Peter A. H. M. Bakker +5 more
TL;DR: This review focuses on molecular processes at the interface between plant roots and ISR-eliciting mutualists, and on the progress in the understanding of ISR signaling and systemic defense priming.
Journal ArticleDOI
The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms
TL;DR: The main functions of rhizosphere microorganisms and how they impact on health and disease are reviewed and several strategies to redirect or reshape the rhizospheric microbiome in favor of microorganisms that are beneficial to plant growth and health are highlighted.
References
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Journal ArticleDOI
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
Elmar Pruesse,Christian Quast,Katrin Knittel,Bernhard M. Fuchs,Wolfgang Ludwig,Jörg Peplies,Frank Oliver Glöckner +6 more
TL;DR: SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains.
Journal ArticleDOI
Toward an ecological classification of soil bacteria.
TL;DR: Survey, experimental, and meta-analytical results suggest that certain bacterial phyla can be differentiated into copiotrophic and oligotrophic categories that correspond to the r- and K-selected categories used to describe the ecological attributes of plants and animals.
Journal ArticleDOI
A Renaissance of Elicitors: Perception of Microbe-Associated Molecular Patterns and Danger Signals by Pattern-Recognition Receptors
Thomas Boller,Georg Felix +1 more
TL;DR: Current evidence indicates that MAMPs, DAMPs, and effectors are all perceived as danger signals and induce a stereotypic defense response, and the importance of MAMP/PRR signaling for plant immunity is highlighted.
Journal ArticleDOI
Defining the core Arabidopsis thaliana root microbiome
Derek S. Lundberg,Sarah L. Lebeis,Sur Herrera Paredes,Scott Yourstone,Jase Gehring,Stephanie Malfatti,Julien Tremblay,Anna Engelbrektson,Anna Engelbrektson,Victor Kunin,Victor Kunin,Tijana Glavina del Rio,Robert C. Edgar,Thilo Eickhorst,Ruth E. Ley,Philip Hugenholtz,Philip Hugenholtz,Susannah G. Tringe,Jeffery L. Dangl +18 more
TL;DR: The pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants is reported to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages.
Journal ArticleDOI
Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere
Gabriele Berg,Kornelia Smalla +1 more
TL;DR: Physiological and molecular data on the factors that drive selection processes in the rhizosphere are presented and implications for agriculture, nature conservation and biotechnology will also be discussed.
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