Beneficial interactions between plant roots and rhizosphere microorganisms are pivotal for plant fitness. Nevertheless, the molecular mechanisms controlling the feedback between root architecture and microbial community structure remain elusive in maize. Here, we demonstrate that transcriptomic gradients along the longitudinal root axis associate with specific shifts in rhizosphere microbial diversity. Moreover, we have established that root-derived flavones predominantly promote the enrichment of bacteria of the taxa Oxalobacteraceae in the rhizosphere, which in turn promote maize growth and nitrogen acquisition. Genetic experiments demonstrate that LRT1-mediated lateral root development coordinates the interactions of the root system with flavone-dependent Oxalobacteraceae under nitrogen deprivation. In summary, these experiments reveal the genetic basis of the reciprocal interactions between root architecture and the composition and diversity of specific microbial taxa in the rhizosphere resulting in improved plant performance. These findings may open new avenues towards the breeding of high-yielding and nutrient-efficient crops by exploiting their interaction with beneficial soil microorganisms.

https://biblio.ugent.be/publication/8703757/file/8703766.pdf

Plant flavones enrich rhizosphere Oxalobacteraceae to improve maize performance under nitrogen deprivation

Methodological advances over the past two decades have propelled plant microbiome research, allowing the field to comprehensively test ideas proposed over a century ago and generate many new hypotheses. Studying the distribution of microbial taxa and genes across plant habitats has revealed the importance of various ecological and evolutionary forces shaping plant microbiota. In particular, selection imposed by plant habitats strongly shapes the diversity and composition of microbiota and leads to microbial adaptation associated with navigating the plant immune system and utilizing plant-derived resources. Reductionist approaches have demonstrated that the interaction between plant immunity and the plant microbiome is, in fact, bidirectional and that plants, microbiota, and the environment shape a complex chemical dialogue that collectively orchestrates the plantmicrobiome. The next stage in plant microbiome research will require the integration of ecological and reductionist approaches to establish a general understanding of the assembly and function in both natural and managed environments.

The Plant Microbiome: From Ecology to Reductionism and Beyond.

The diversity of secondary compounds in the plant kingdom is huge. About 200,000 compounds are known, which are grouped into amines, non-protein amino acids, peptides, alkaloids, glucosinolates, cyanogenic glucosides, organic acids, terpenoids, quinones, polyacetylenes, and phenolics. The group of phenolic compounds consists of polyphenols, oligophenols and monophenols or simple phenolic compounds such as benzoic and cinnamic acids and their hydroxylated derivatives. Among the thousands of compounds present in ecological interactions, simple phenolic acids are the most abundant in soils, and many are described as allelochemicals. Given the physiological and biochemical importance of these compounds, we review their biosynthesis and metabolic actions in plants.

Biosynthesis and metabolic actions of simple phenolic acids in plants

Contents Summary 35 I. Introduction 36 II. Tree CH4 fluxes 36 III. Tree emissions of soil-produced CH4 40 IV. Tree-produced CH4 42 V. Trees in forest CH4 budgets 44 VI. Conclusions 46 Acknowledgements 48 Author contributions 48 References 48 SUMMARY: Forest ecosystem methane (CH4 ) research has focused on soils, but trees are also important sources and sinks in forest CH4 budgets. Living and dead trees transport and emit CH4 produced in soils; living trees and dead wood emit CH4 produced inside trees by microorganisms; and trees produce CH4 through an abiotic photochemical process. Here, we review the state of the science on the production, consumption, transport, and emission of CH4 by living and dead trees, and the spatial and temporal dynamics of these processes across hydrologic gradients inclusive of wetland and upland ecosystems. Emerging research demonstrates that tree CH4 emissions can significantly increase the source strength of wetland forests, and modestly decrease the sink strength of upland forests. Scaling from stem or leaf measurements to trees or forests is limited by knowledge of the mechanisms by which trees transport soil-produced CH4 , microbial processes produce and oxidize CH4 inside trees, a lack of mechanistic models, the diffuse nature of forest CH4 fluxes, complex overlap between sources and sinks, and extreme variation across individuals. Understanding the complex processes that regulate CH4 source-sink dynamics in trees and forests requires cross-disciplinary research and new conceptual models that transcend the traditional binary classification of wetland vs upland forest.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15624

Methane production and emissions in trees and forests.

Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. Legumes, which form root nodule symbioses with nitrogen-fixing rhizobia, have served as model plants for understanding the genetics and evolution of beneficial plant-microbe interactions for decades, and thus have added value as models of plant-microbiome interactions. Here we use a common garden experiment with 16S rRNA gene amplicon and shotgun metagenomic sequencing to study the drivers of microbiome diversity and composition in three genotypes of the model legume Medicago truncatula grown in two native soil communities. Bacterial diversity decreased between external (rhizosphere) and internal plant compartments (root endosphere, nodule endosphere, and leaf endosphere). Community composition was shaped by strong compartment × soil origin and compartment × plant genotype interactions, driven by significant soil origin effects in the rhizosphere and significant plant genotype effects in the root endosphere. Nevertheless, all compartments were dominated by Ensifer, the genus of rhizobia that forms root nodule symbiosis with M. truncatula, and additional shotgun metagenomic sequencing suggests that the nodulating Ensifer were not genetically distinguishable from those elsewhere in the plant. We also identify a handful of OTUs that are common in nodule tissues, which are likely colonized from the root endosphere. Our results demonstrate strong host filtering effects, with rhizospheres driven by soil origin and internal plant compartments driven by host genetics, and identify several key nodule-inhabiting taxa that coexist with rhizobia in the native range. Our results set the stage for future functional genetic experiments aimed at expanding our pairwise understanding of legume-rhizobium symbiosis toward a more mechanistic understanding of plant microbiomes.

/pdf/soil-origin-and-plant-genotype-structure-distinct-microbiome-1fsimtk7lg.pdf

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula.

Plants have developed defense strategies for phytopathogen and herbivore protection via coordinated metabolic mechanisms. Low-molecular weight metabolites produced within plant tissues, such as salicylic acid, represent one such mechanism which likely mediates plant – microbe interactions above and below ground. Salicylic acid is a ubiquitous phytohormone at low levels in most plants, yet are concentrated defense compounds in Populus, likely acting as a selective filter for rhizosphere microbiomes. We propagated twelve Populus trichocarpa genotypes which varied an order of magnitude in salicylic acid (SA)-related secondary metabolites, in contrasting soils from two different origins. After four months of growth, plant properties (leaf growth, chlorophyll content, and net photosynthetic rate) and plant root metabolomics specifically targeting SA metabolites were measured via GC-MS. In addition, rhizosphere microbiome composition was measured via Illumina MiSeq sequencing of 16S and ITS2 rRNA-genes. Soil origin was the primary filter causing divergence in bacterial/archaeal and fungal communities with plant genotype secondarily influential. Both bacterial/archaeal and fungal evenness varied between soil origins and bacterial/archaeal diversity and evenness correlated with at least one SA metabolite (diversity: populin; evenness: total phenolics). The production of individual salicylic acid derivatives that varied by host genotype resulted in compositional differences for bacteria /archaea (tremuloidin) and fungi (salicylic acid) within one soil origin (Clatskanie) whereas soils from Corvallis did not illicit microbial compositional changes due to salicylic acid derivatives. Several dominant bacterial (e.g., Betaproteobacteria, Acidobacteria, Verrucomicrobia, Chloroflexi, Gemmatimonadete, Firmicutes) and one fungal phyla (Mortierellomycota) also correlated with specific SA secondary metabolites; bacterial phyla exhibited more negative interactions (declining abundance with increasing metabolite concentration) than positive interactions. These results indicate microbial communities diverge most among soil origin. However, within a soil origin, bacterial/archaeal communities are responsive to plant SA production within greenhouse-based rhizosphere microbiomes. Fungal microbiomes are impacted by root SA-metabolites, but overall to a lesser degree within this experimental context. These results suggest plant defense strategies, such as SA and its secondary metabolites, may partially drive patterns of both bacterial/archaeal and fungal taxa-specific colonization and assembly.

/pdf/rhizosphere-microbiomes-diverge-among-populus-trichocarpa-37gm2z9flr.pdf

Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin

While recent reports demonstrate that the direct emission of methane from living tree trunks may be a significant terrestrial emission source, there has been debate whether tree emissions are due to transport from soils or produced in the wood environment itself Reports of methanogens from wood of trees were prominent in the literature 40 years ago but have not been revisited with molecular ecology approaches We examined communities associated with Populus deltoides using rRNA gene sequence analyses and how these vary with tree and wood properties Our data indicate that wood environments are dominated by anaerobic microbiomes Methanogens are prominent in heartwood (mean 34% relative abundance) compared to sapwood environments (13%), and dominant operational taxonomic units (OTUs) were classified as the Methanobacterium sp Members of the Firmicutes phylum comprised 39% of total sequences and were in 42% greater abundance in sapwood over heartwood niches Tree diameter was the strongest predictor of methanogen abundance, but wood moisture content and pH were also significant predictors of taxon abundance and overall community composition Unlike microbiomes of the soil, rhizosphere and phyllosphere, wood associated communities are shaped by unique environmental conditions and may be prominent and overlooked sources of methane emissions in temperate forest systems

https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/nph.15346

Methanogenic Archaea dominate mature heartwood habitats of Eastern Cottonwood (Populus deltoides)

/pdf/correction-to-rhizosphere-microbiomes-diverge-among-populus-1rxa7cr66g.pdf

Correction to: Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin

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Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin

Methanogenic Archaea dominate mature heartwood habitats of Eastern Cottonwood (Populus deltoides)

Correction to: Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin