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

Abstract 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.

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

Microbiome ◽

10.1186/s40168-020-00915-9 ◽

2020 ◽

Vol 8 (1) ◽

Author(s):

Shawn P. Brown ◽

Michael A. Grillo ◽

Justin C. Podowski ◽

Katy D. Heath

Keyword(s):

Medicago Truncatula ◽

Root Nodule ◽

Common Garden ◽

Added Value ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Plant Genotype ◽

Model Legume ◽

Shotgun Metagenomic Sequencing ◽

Soil Origin

Abstract 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 toward a more mechanistic understanding of plant microbiomes.

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

10.21203/rs.3.rs-44152/v1 ◽

2020 ◽

Author(s):

Shawn P. Brown ◽

Michael A. Grillo ◽

Justin C. Podowski ◽

Katy Denise Heath

Keyword(s):

Medicago Truncatula ◽

Root Nodule ◽

Common Garden ◽

Added Value ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Plant Genotype ◽

Model Legume ◽

Shotgun Metagenomic Sequencing ◽

Soil Origin

Abstract 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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An improved genome release (version Mt4.0) for the model legume Medicago truncatula

BMC Genomics ◽

10.1186/1471-2164-15-312 ◽

2014 ◽

Vol 15 (1) ◽

pp. 312 ◽

Cited By ~ 191

Author(s):

Haibao Tang ◽

Vivek Krishnakumar ◽

Shelby Bidwell ◽

Benjamin Rosen ◽

Agnes Chan ◽

...

Keyword(s):

Medicago Truncatula ◽

Model Legume

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Guidelines for Genetic Nomenclature and Community Governance for the Model Legume Medicago truncatula

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2001.14.12.1364 ◽

2001 ◽

Vol 14 (12) ◽

pp. 1364-1367 ◽

Cited By ~ 14

Author(s):

Kathryn A. VandenBosch ◽

Julia Frugoli

Keyword(s):

Medicago Truncatula ◽

Rapid Growth ◽

Model System ◽

Gene Nomenclature ◽

Community Governance ◽

Model Legume ◽

The Past ◽

Genetic Nomenclature ◽

International Collaborations

At the 2nd Medicago meeting (a satellite of the 1999 IS-MPMI meeting in Amsterdam), investigators perceived a need for standardization of genetic nomenclature in Medicago truncatula, due to the rapid growth of research on this species in the past few years. Establishment of such standards grew out of discussions begun at this meeting and continued electronically throughout the M. truncatula community. The proposed standards presented here are the consensus results of those discussions. In addition to standards for gene nomenclature, a method for community governance and a website for cataloging gene names and submitting new ones are presented. The purpose of implementing these guidelines is to help maintain consistency in the literature, to avoid redundancy, to contribute to the accuracy of databases, and, in general, to aid the international collaborations that have made M. truncatula a model system for legume biology.

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Structure and antimicrobial activity of NCR169, a nodule-specific cysteine-rich peptide of Medicago truncatula

Scientific Reports ◽

10.1038/s41598-021-89485-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Noriyoshi Isozumi ◽

Yuya Masubuchi ◽

Tomohiro Imamura ◽

Masashi Mori ◽

Hironori Koga ◽

...

Keyword(s):

Antimicrobial Activity ◽

Medicago Truncatula ◽

Mechanism Of Action ◽

Disulfide Bonds ◽

Sinorhizobium Meliloti ◽

Bound State ◽

Disulfide Linkage ◽

Model Legume ◽

Nmr Structures ◽

And Function

AbstractA model legume, Medicago truncatula, has over 600 nodule-specific cysteine-rich (NCR) peptides required for symbiosis with rhizobia. Among them, NCR169, an essential factor for establishing symbiosis, has four cysteine residues that are indispensable for its function. However, knowledge of NCR169 structure and mechanism of action is still lacking. In this study, we solved two NMR structures of NCR169 caused by different disulfide linkage patterns. We show that both structures have a consensus C-terminal β-sheet attached to an extended N-terminal region with dissimilar features; one moves widely, whereas the other is relatively stapled. We further revealed that the disulfide bonds of NCR169 contribute to its structural stability and solubility. Regarding the function, one of the NCR169 oxidized forms could bind to negatively charged bacterial phospholipids. Furthermore, the positively charged lysine-rich region of NCR169 may be responsible for its antimicrobial activity against Escherichia coli and Sinorhizobium meliloti. This active region was disordered even in the phospholipid bound state, suggesting that the disordered conformation of this region is key to its function. Morphological observations suggested the mechanism of action of NCR169 on bacteria. The present study on NCR169 provides new insights into the structure and function of NCR peptides.

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A method for the isolation of root hairs from the model legume Medicago truncatula

Journal of Experimental Botany ◽

10.1093/jxb/erg245 ◽

2003 ◽

Vol 54 (391) ◽

pp. 2245-2250 ◽

Cited By ~ 12

Author(s):

J. Ramos

Keyword(s):

Medicago Truncatula ◽

Root Hairs ◽

Model Legume

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Functional specialization of Arf paralogs in nodules of model legume, Medicago truncatula

Plant Growth Regulation ◽

10.1007/s10725-016-0227-2 ◽

2016 ◽

Vol 81 (3) ◽

pp. 501-510 ◽

Cited By ~ 1

Author(s):

Elif Yüzbaşıoğlu ◽

Eda Dalyan ◽

Abdülrezzak Memon ◽

Gül Öz ◽

Bayram Yüksel

Keyword(s):

Medicago Truncatula ◽

Functional Specialization ◽

Model Legume

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Comparison of nodule endophyte composition, diversity, and gene content between Medicago truncatula genotypes

Phytobiomes Journal ◽

10.1094/pbiomes-10-20-0077-r ◽

2021 ◽

Author(s):

Mannix Burns ◽

Brendan Epstein ◽

Liana Burghardt

Keyword(s):

Functional Groups ◽

Medicago Truncatula ◽

Root Nodules ◽

Bacterial Endophytes ◽

Host Genotype ◽

Model Legume ◽

Symbiotic Relationships ◽

Functional Assays ◽

Altered Gene ◽

Significant Direct Effect

Leguminous plants form symbiotic relationships with rhizobia. These nitrogen-fixing bacteria live in specialized root organs called nodules. While rhizobia form the most notable host relationship within root nodules, other bacterial endophytes also inhabit these root nodules and can influence host-rhizobia interactions as well as exert effects of their own, whether beneficial or detrimental. In this study, we investigate differences in nodule communities between genotypes (A17 and R108) of a single plant species, the model legume Medicago truncatula. While diversity of endophytes in nodules was similar across hosts, both nodule endophyte composition and gene functional groups differed. In contrast to the significant direct effect of host genotype, neither the presence nor identity of a host in the previous generation (either A17 or R108) had a significant effect on the nodule endophyte diversity or composition. However, whether or not a host was present altered gene functional groups. We conclude that genetic variation within a legume host species can play an important role in the establishment of nodule microbiomes. Further studies, including GWAS and functional assays, can open the door for engineering and optimizing nodule endophyte communities that promote growth or have other beneficial qualities.

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