Amino Acid Availability Determines Plant Immune Homeostasis in the Rhizosphere Microbiome
ABSTRACT Microbes possess conserved microbe-associated molecular patterns (MAMPs) that are recognized by plant receptors to induce pattern-triggered immunity (PTI). Despite containing the same MAMPs as pathogens, commensals thrive in the plant rhizosphere microbiome, indicating they must suppress or...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2023-04-01
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| Series: | mBio |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/mbio.03424-22 |
| _version_ | 1797839618095185920 |
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| author | Yang Liu Andrew J. Wilson Jiatong Han Alisa Hui Lucy O’Sullivan Tao Huan Cara H. Haney |
| author_facet | Yang Liu Andrew J. Wilson Jiatong Han Alisa Hui Lucy O’Sullivan Tao Huan Cara H. Haney |
| author_sort | Yang Liu |
| collection | DOAJ |
| description | ABSTRACT Microbes possess conserved microbe-associated molecular patterns (MAMPs) that are recognized by plant receptors to induce pattern-triggered immunity (PTI). Despite containing the same MAMPs as pathogens, commensals thrive in the plant rhizosphere microbiome, indicating they must suppress or evade host immunity. Previous work found that bacterial-secreted gluconic acid is sufficient to suppress PTI. Here, we show that gluconic acid biosynthesis is not necessary for immunity suppression by the beneficial bacterial strain Pseudomonas simiae WCS417. We performed a forward genetic screen with EMS-mutagenized P. simiae WCS417 and a flagellin-inducible CYP71A12pro:GUS reporter as a PTI readout. We identified a loss of function mutant in ornithine carbamoyltransferase argF, which is required for ornithine conversion to arginine, that cannot suppress PTI or acidify the rhizosphere. Fungal pathogens use alkalization through production of ammonia and glutamate, and arginine biosynthetic precursors, to promote their own growth and virulence. While a ΔargF mutant has a growth defect in the rhizosphere, we found that restoring growth with exogenous arginine resulted in rhizosphere alkalization in a mutant that cannot make gluconic acid, indicating that arginine biosynthesis is required for both growth and acidification. Furthermore, blocking bacterial arginine, glutamine, or proline biosynthesis through genetic mutations or feedback inhibition by adding corresponding amino acids, resulted in rhizosphere alkalization. Untargeted metabolomics determined that ornithine, an alkaline molecule, accumulates under conditions associated with rhizosphere alkalization. Our findings show that bacterial amino acid biosynthesis contributes to acidification by preventing accumulation of ornithine and the resulting alkalization. IMPORTANCE Understanding how microbiota evade and suppress host immunity is critical to our knowledge of how beneficial microbes persist in association with a host. Prior work has shown that secretion of organic acids by beneficial microbes is sufficient to suppress plant immunity. This work shows that microbial amino acid metabolism is not only critical for growth in the plant rhizosphere microbiome, but also for regulation of plant rhizosphere pH, and, consequentially, regulation of plant immunity. We found that, in the absence of microbial glutamate and arginine metabolism, rhizosphere alkalization and microbial overgrowth occurs. Collectively, our findings suggest that, by regulating nutrient availability, plants have the potential to regulate their immune homeostasis in the rhizosphere microbiome. |
| first_indexed | 2024-04-09T15:59:46Z |
| format | Article |
| id | doaj.art-921829a0870c485589407919c4816b4b |
| institution | Directory Open Access Journal |
| issn | 2150-7511 |
| language | English |
| last_indexed | 2024-04-09T15:59:46Z |
| publishDate | 2023-04-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mBio |
| spelling | doaj.art-921829a0870c485589407919c4816b4b2023-04-25T13:04:57ZengAmerican Society for MicrobiologymBio2150-75112023-04-0114210.1128/mbio.03424-22Amino Acid Availability Determines Plant Immune Homeostasis in the Rhizosphere MicrobiomeYang Liu0Andrew J. Wilson1Jiatong Han2Alisa Hui3Lucy O’Sullivan4Tao Huan5Cara H. Haney6Department of Microbiology and Immunology, The University of British Columbia, Vancouver, CanadaDepartment of Microbiology and Immunology, The University of British Columbia, Vancouver, CanadaDepartment of Microbiology and Immunology, The University of British Columbia, Vancouver, CanadaDepartment of Chemistry, The University of British Columbia, Vancouver, CanadaDepartment of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USADepartment of Chemistry, The University of British Columbia, Vancouver, CanadaDepartment of Microbiology and Immunology, The University of British Columbia, Vancouver, CanadaABSTRACT Microbes possess conserved microbe-associated molecular patterns (MAMPs) that are recognized by plant receptors to induce pattern-triggered immunity (PTI). Despite containing the same MAMPs as pathogens, commensals thrive in the plant rhizosphere microbiome, indicating they must suppress or evade host immunity. Previous work found that bacterial-secreted gluconic acid is sufficient to suppress PTI. Here, we show that gluconic acid biosynthesis is not necessary for immunity suppression by the beneficial bacterial strain Pseudomonas simiae WCS417. We performed a forward genetic screen with EMS-mutagenized P. simiae WCS417 and a flagellin-inducible CYP71A12pro:GUS reporter as a PTI readout. We identified a loss of function mutant in ornithine carbamoyltransferase argF, which is required for ornithine conversion to arginine, that cannot suppress PTI or acidify the rhizosphere. Fungal pathogens use alkalization through production of ammonia and glutamate, and arginine biosynthetic precursors, to promote their own growth and virulence. While a ΔargF mutant has a growth defect in the rhizosphere, we found that restoring growth with exogenous arginine resulted in rhizosphere alkalization in a mutant that cannot make gluconic acid, indicating that arginine biosynthesis is required for both growth and acidification. Furthermore, blocking bacterial arginine, glutamine, or proline biosynthesis through genetic mutations or feedback inhibition by adding corresponding amino acids, resulted in rhizosphere alkalization. Untargeted metabolomics determined that ornithine, an alkaline molecule, accumulates under conditions associated with rhizosphere alkalization. Our findings show that bacterial amino acid biosynthesis contributes to acidification by preventing accumulation of ornithine and the resulting alkalization. IMPORTANCE Understanding how microbiota evade and suppress host immunity is critical to our knowledge of how beneficial microbes persist in association with a host. Prior work has shown that secretion of organic acids by beneficial microbes is sufficient to suppress plant immunity. This work shows that microbial amino acid metabolism is not only critical for growth in the plant rhizosphere microbiome, but also for regulation of plant rhizosphere pH, and, consequentially, regulation of plant immunity. We found that, in the absence of microbial glutamate and arginine metabolism, rhizosphere alkalization and microbial overgrowth occurs. Collectively, our findings suggest that, by regulating nutrient availability, plants have the potential to regulate their immune homeostasis in the rhizosphere microbiome.https://journals.asm.org/doi/10.1128/mbio.03424-22PTIamino acid biosynthesisinnate immunitypHplant-microbe interactionsrhizosphere-inhabiting microbes |
| spellingShingle | Yang Liu Andrew J. Wilson Jiatong Han Alisa Hui Lucy O’Sullivan Tao Huan Cara H. Haney Amino Acid Availability Determines Plant Immune Homeostasis in the Rhizosphere Microbiome mBio PTI amino acid biosynthesis innate immunity pH plant-microbe interactions rhizosphere-inhabiting microbes |
| title | Amino Acid Availability Determines Plant Immune Homeostasis in the Rhizosphere Microbiome |
| title_full | Amino Acid Availability Determines Plant Immune Homeostasis in the Rhizosphere Microbiome |
| title_fullStr | Amino Acid Availability Determines Plant Immune Homeostasis in the Rhizosphere Microbiome |
| title_full_unstemmed | Amino Acid Availability Determines Plant Immune Homeostasis in the Rhizosphere Microbiome |
| title_short | Amino Acid Availability Determines Plant Immune Homeostasis in the Rhizosphere Microbiome |
| title_sort | amino acid availability determines plant immune homeostasis in the rhizosphere microbiome |
| topic | PTI amino acid biosynthesis innate immunity pH plant-microbe interactions rhizosphere-inhabiting microbes |
| url | https://journals.asm.org/doi/10.1128/mbio.03424-22 |
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