Genome‐wide association studies on the phyllosphere microbiome: Embracing complexity in host–microbe interactions

Beilsmith, Kathleen; Thoen, Manus P. M.; Brachi, Benjamin; Gloss, Andrew D.; Khan, Mohammad Haneef; Bergelson, Joy

doi:10.1111/tpj.14170

Cited by 86 publications

(59 citation statements)

References 140 publications

(162 reference statements)

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“…A rapidly growing body of literature has documented the in uence that the microbiome can have on critical plant traits including disease resistance [2][3][4][5], nutrient acquisition and growth [6][7][8][9], abiotic stress tolerance [10,11], and owering phenology [12,13]. Thus, the microbiome can be viewed as an extended phenotype of the plant genome that can enhance the ability of plants to cope with environmental stressors [1,10,[14][15][16]. A fuller understanding of plant microbiomes is critical for improvements in environmental sustainability [17], agriculture [18], and conservation [19].…”

Section: Introductionmentioning

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: Introductionmentioning

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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“…Beilsmith et al . () discuss how microbiome GWAS can be used to phenotype microbial taxa or microbial functions, and how these studies provide a view of the plant–microbe interactions that occur in natural environments. They also highlight how future studies will use GWAS to identify plant genes or microorganisms for use in breeding or engineering properties such as yield or pathogen resistance.…”

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confidence: 99%

From genome to phenome: genome‐wide association studies and other approaches that bridge the genotype to phenotype gap

Fernie

Gutierrez-Marcos

2019

The Plant Journal

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“…Using this strategy, many studies revealed the microbial association in the phyllosphere of different plants such as mountain shrubs (Ruiz-Pérez et al 2016), seagrass (Fahimipour et al 2017), subarctic grass (Uroz et al 2016), and equatorial forest canopies (Lambais et al 2006). The studies revealed that plant leaves are colonized by a huge and diverse group of microorganisms, including bacteria, fungi, and viruses (Rastogi et al 2013;Morella et al 2018;Sapp et al 2018;Beilsmith et al 2019). High-throughput molecular methods or culture-independent molecular techniques have interpreted the phyllosphere microbial community today (Table 5.5).…”

Section: How To Study Phyllosphere Microbiome?mentioning

confidence: 99%

Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications

Sivakumar

Sathishkumar

Selvakumar

et al. 2020

Sustainable Development and Biodiversity

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The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.

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Genome‐wide association studies on the phyllosphere microbiome: Embracing complexity in host–microbe interactions

Cited by 86 publications

References 140 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

From genome to phenome: genome‐wide association studies and other approaches that bridge the genotype to phenotype gap

Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications

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