Analysis of leaf microbiome composition of near‐isogenic maize lines differing in broad‐spectrum disease resistance

Wagner, Maggie R.; Busby, Posy E.; Balint‐Kurti, Peter

doi:10.1111/nph.16284

Cited by 50 publications

(47 citation statements)

References 76 publications

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“…These patterns generally mirror studies in other systems (e.g., [33,62,79,80]). The mechanisms by which plant genotype in uences the microbiome are still being elucidated, but genetic studies to date suggest that plant genes related to disease resistance, cell walls, and root hair structure may contribute [81][82][83][84].…”

Section: Discussionmentioning

confidence: 99%

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

Brown

Grillo

Podowski

et al. 2020

Preprint

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Background 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. Results 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. Conclusions 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 towards a more mechanistic understanding of plant microbiomes.

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Section: Discussionmentioning

confidence: 99%

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

Brown

Grillo

Podowski

et al. 2020

Preprint

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“…As in previous work (Wagner et al , 2019) , we characterized bacterial and fungal communities by sequencing the V4 region of the 16S rDNA gene and the ITS1 region of the fungal rDNA gene, respectively. We amplified these barcoding genes using the standard primer pairs 515f/806r and ITS1f/ITS2, modified to include 3 to 6 random nucleotides upstream of the gene primers to increase library complexity (Lundberg et al 2013).…”

Section: Amplicon Library Preparation and Sequencingmentioning

confidence: 99%

“…As a result, we have limited ability to predict microbiome similarity between two host genotypes that are directly related ( e.g., within a known pedigree). Very recently, the introgression of quantitative trait loci was shown to alter leaf microbiomes across five generations of a breeding experiment for improved disease resistance in maize (Wagner et al , 2019) ; however, additional studies of this type are needed before we will be able to anticipate what microbiome changes might follow genetic improvement in crops or evolution in natural populations.…”

Section: Introductionmentioning

confidence: 99%

Heterosis of leaf and rhizosphere microbiomes in field-grown maize

Wagner

Roberts

Balint‐Kurti

et al. 2020

Preprint

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Word count (Total): 6693 Word count (Introduction): 818 Word count (Methods): 3241 Word count (Results): 1859 Word count (Discussion): 783 Number of figures: 6 (all in color) Number of tables: 1 Supporting Information: 4 tables + 7 figures (all in color) Word count (Acknowledgements): 105 Summary:• Macroorganisms' genotypes shape their phenotypes, which in turn shape the habitat available to potential microbial symbionts. This influence of host genotype on microbiome composition has been demonstrated in many systems; however, most previous studies have either compared unrelated genotypes or delved into molecular mechanisms. As a result, it is currently unclear whether the heritability of host-associated microbiomes follows similar patterns to the heritability of other complex traits. • We take a new approach to this question by comparing the microbiomes of diverse maize inbred lines and their F1 hybrid offspring, which we quantified in both rhizosphere and leaves of field-grown plants using 16S-v4 and ITS1 amplicon sequencing. • We show that inbred lines and hybrids differ consistently in composition of bacterial and fungal rhizosphere communities, as well as leaf-associated fungal communities. A wide range of microbiome features display heterosis within individual crosses, consistent with patterns for non-microbial maize phenotypes. For leaf microbiomes, these results were supported by the observation that broad-sense heritability in hybrids was substantially higher than narrow-sense heritability. • Our results support our hypothesis that at least some heterotic host traits affect microbiome composition in maize.

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“…These patterns generally mirror studies in other systems (e.g., [33,62,79,80]). The mechanisms by which plant genotype influences the microbiome are still being elucidated, but genetic studies to date suggest that plant genes related to disease resistance, cell walls, and root hair structure may contribute [81][82][83][84].…”

Section: Discussionmentioning

confidence: 99%

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

Brown

Grillo

Podowski

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: 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.Results: Bacterial diversity decreased between external (rhizosphere) and internal plant compartments (root endosphere, nodule endosphere, and leaf endosphere). Community composition was shaped by strong compartment x soil origin and compartment x 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.Conclusions: 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 towards a more mechanistic understanding of plant microbiomes.

show abstract

Analysis of leaf microbiome composition of near‐isogenic maize lines differing in broad‐spectrum disease resistance

Cited by 50 publications

References 76 publications

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

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

Heterosis of leaf and rhizosphere microbiomes in field-grown maize

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

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